chore(deps): update anchore dependencies (#5479)

Signed-off-by: anchore-oss-update-bot <anchore-oss-update-bot@users.noreply.github.com>
Co-authored-by: anchore-oss-update-bot <anchore-oss-update-bot@users.noreply.github.com>

.binny.yaml

@@ -16,7 +16,7 @@ tools:
   # used to upload test fixture cache
   - name: oras
     version:
-      want: v1.3.4
+      want: v1.3.6
     method: github-release
     with:
       repo: oras-project/oras

.github/actions/bootstrap/action.yaml

@@ -6,10 +6,6 @@ description: "Bootstrap all syft tools and dependencies on top of go-make's setu
 # We add the syft-specific extras here: apt packages and the test fixture cache.
 
 inputs:
-  go-version:
-    description: "Go version to install (passed to go-make/setup)"
-    required: true
-    default: "1.26.2"
   cache-key-prefix:
     description: "Prefix all cache keys with this value (passed to go-make/setup)"
     required: true
@@ -30,9 +26,8 @@ runs:
   using: "composite"
   steps:
     - name: Setup go + go-make tooling
-      uses: anchore/go-make/.github/actions/setup@abf41688f36f2cbec13105747abbe8e60f5c56ca # v0.9.3
+      uses: anchore/go-make/.github/actions/setup@cf465259f4c9f0b0b0bcb35164ede11f7dc6d9f6 # v0.9.6
       with:
-        go-version: ${{ inputs.go-version }}
         cache-key-prefix: ${{ inputs.cache-key-prefix }}
         cache-enabled: ${{ inputs.cache-enabled }}
 

.github/workflows/release.yaml

@@ -89,13 +89,13 @@ jobs:
         uses: docker/setup-buildx-action@f87e5991a6d7451dcb8d9637bfbc97413f497069 # v4.4.1
 
       - name: Login to Docker Hub
-        uses: docker/login-action@dbcb813823bdd20940b903addbd779551569679f #v4.6.0
+        uses: docker/login-action@81c6f93d4bc991e510b342a00b419b3bb4efc5c6 #v4.7.0
         with:
           username: ${{ secrets.ANCHOREOSSWRITE_DH_USERNAME }}
           password: ${{ secrets.ANCHOREOSSWRITE_DH_PAT }}
 
       - name: Login to GitHub Container Registry
-        uses: docker/login-action@dbcb813823bdd20940b903addbd779551569679f #v4.6.0
+        uses: docker/login-action@81c6f93d4bc991e510b342a00b419b3bb4efc5c6 #v4.7.0
         with:
           registry: ghcr.io
           username: ${{ github.actor }}

.github/workflows/validate-github-actions.yaml

@@ -25,7 +25,7 @@ jobs:
           persist-credentials: false
 
       - name: "Run zizmor"
-        uses: zizmorcore/zizmor-action@cc914d7f3750a2d13d75c7f184a1060aa0e9d482 # v0.6.4
+        uses: zizmorcore/zizmor-action@53290badfa369cb0bf7ad16342cb62c2fa47ac7b # v0.8.0
         with:
           # there is a pass/fail gate as a repo ruleset (if there is no ruleset configured then the action will pass by default)
           advanced-security: true

.github/workflows/validations.yaml

@@ -99,10 +99,7 @@ jobs:
       # go-make's setup only (not ./.github/actions/bootstrap): binny ships no windows release, so binny tools
       # are unavailable here (`make unit` skips the fixture refresh on windows)
       - name: Setup go + go-make tooling
-        uses: anchore/go-make/.github/actions/setup@abf41688f36f2cbec13105747abbe8e60f5c56ca # v0.9.3
-        with:
-          # keep in sync with the go-version default in ./.github/actions/bootstrap
-          go-version: "1.26.2"
+        uses: anchore/go-make/.github/actions/setup@cf465259f4c9f0b0b0bcb35164ede11f7dc6d9f6 # v0.9.6
 
       # the binny-free version of `make download-test-fixture-cache` (keep the oras version in sync with .binny.yaml)
       - name: Download test fixture cache
@@ -195,10 +192,7 @@ jobs:
 
       # go-make's setup only (not ./.github/actions/bootstrap): the test only needs make + the snapshot binary
       - name: Setup go + go-make tooling
-        uses: anchore/go-make/.github/actions/setup@abf41688f36f2cbec13105747abbe8e60f5c56ca # v0.9.3
-        with:
-          # keep in sync with the go-version default in ./.github/actions/bootstrap
-          go-version: "1.26.2"
+        uses: anchore/go-make/.github/actions/setup@cf465259f4c9f0b0b0bcb35164ede11f7dc6d9f6 # v0.9.6
 
       - name: Install Podman
         run: |
@@ -228,10 +222,7 @@ jobs:
 
       # go-make's setup only (not ./.github/actions/bootstrap): the test only needs make + the snapshot binary
       - name: Setup go + go-make tooling
-        uses: anchore/go-make/.github/actions/setup@abf41688f36f2cbec13105747abbe8e60f5c56ca # v0.9.3
-        with:
-          # keep in sync with the go-version default in ./.github/actions/bootstrap
-          go-version: "1.26.2"
+        uses: anchore/go-make/.github/actions/setup@cf465259f4c9f0b0b0bcb35164ede11f7dc6d9f6 # v0.9.6
 
       - name: Install Buildah
         run: |

.make/go.mod

@@ -2,11 +2,11 @@ module github.com/anchore/syft/.make
 
 go 1.26.0
 
-require github.com/anchore/go-make v0.9.3
+require github.com/anchore/go-make v0.9.6
 
 require (
-	github.com/bmatcuk/doublestar/v4 v4.10.2 // indirect
+	github.com/bmatcuk/doublestar/v4 v4.10.3 // indirect
 	github.com/goccy/go-yaml v1.19.2 // indirect
-	golang.org/x/mod v0.41.0 // indirect
-	golang.org/x/sys v0.48.0 // indirect
+	golang.org/x/mod v0.42.0 // indirect
+	golang.org/x/sys v0.49.0 // indirect
 )

.make/go.sum

@@ -1,10 +1,10 @@
-github.com/anchore/go-make v0.9.3 h1:D+MkpvEJsOGwkOqKN0rd2zYi9jEzwKtZreNysH0DenI=
-github.com/anchore/go-make v0.9.3/go.mod h1:4HuELygGhxex2SaCEgfCbZ0geJ3xFkqtWpmt1NrYwPg=
-github.com/bmatcuk/doublestar/v4 v4.10.2 h1:eF7W7HWKg3z9NrWV9pTLnNeoXaqq3Tq9DNKXVMfoCnw=
-github.com/bmatcuk/doublestar/v4 v4.10.2/go.mod h1:xBQ8jztBU6kakFMg+8WGxn0c6z1fTSPVIjEY1Wr7jzc=
+github.com/anchore/go-make v0.9.6 h1:HjO7H/M/WZ4v3B73/EuShuQHHblQJGwHDrl/MqCavWs=
+github.com/anchore/go-make v0.9.6/go.mod h1:zE6KeB+nY+sMSWHYx2uaiOznLAq3CD9JvFlzWDDpKw4=
+github.com/bmatcuk/doublestar/v4 v4.10.3 h1:1UIv1+fqH3++ViVkpnaPTB+Pi1UHycnPFAq14zgK+gI=
+github.com/bmatcuk/doublestar/v4 v4.10.3/go.mod h1:xBQ8jztBU6kakFMg+8WGxn0c6z1fTSPVIjEY1Wr7jzc=
 github.com/goccy/go-yaml v1.19.2 h1:PmFC1S6h8ljIz6gMRBopkjP1TVT7xuwrButHID66PoM=
 github.com/goccy/go-yaml v1.19.2/go.mod h1:XBurs7gK8ATbW4ZPGKgcbrY1Br56PdM69F7LkFRi1kA=
-golang.org/x/mod v0.41.0 h1:qJmnOUb4YB+FsEuM3HcWucdZASCPGhsX6uljO6pog0c=
-golang.org/x/mod v0.41.0/go.mod h1:Ek9pY8RKWXwsWvd3rQiHYtMqkjSUV+s1Rj7j4H5Ur6o=
-golang.org/x/sys v0.48.0 h1:bbX/i/6MgT9BVLM9RT1thmxL04yeTAhbEz4SyadbXoo=
-golang.org/x/sys v0.48.0/go.mod h1:hNLxWAXmnKAxqDtdwIYC4bM9oQPEecfsnNMuSxOs3og=
+golang.org/x/mod v0.42.0 h1:ICeL3t2L30ljSPHHxDnR4fqVcBt/zR2zJAb9juavmQg=
+golang.org/x/mod v0.42.0/go.mod h1:u5fzIrRInkL8MaO1cbRkUHT64v303YIT5KEqpNr7jRs=
+golang.org/x/sys v0.49.0 h1:XbzkgYJHdqh/8m2Uu0W/dQv8nktxx4BFHp1M0gROTXA=
+golang.org/x/sys v0.49.0/go.mod h1:hNLxWAXmnKAxqDtdwIYC4bM9oQPEecfsnNMuSxOs3og=

cmd/syft/internal/options/catalog.go

@@ -102,6 +102,7 @@ func (cfg Catalog) ToSBOMConfig(id clio.Identification) *syft.CreateSBOMConfig {
 		WithComplianceConfig(cfg.ToComplianceConfig()).
 		WithUnknownsConfig(cfg.ToUnknownsConfig()).
 		WithSearchConfig(cfg.ToSearchConfig()).
+		WithArchiveConfig(cfg.ToArchiveConfig()).
 		WithPackagesConfig(cfg.ToPackagesConfig()).
 		WithLicenseConfig(cfg.ToLicenseConfig()).
 		WithFilesConfig(cfg.ToFilesConfig()).
@@ -118,6 +119,15 @@ func (cfg Catalog) ToSearchConfig() cataloging.SearchConfig {
 	}
 }
 
+func (cfg Catalog) ToArchiveConfig() cataloging.ArchiveSearchConfig {
+	return cataloging.DefaultArchiveSearchConfig().
+		WithIncludeIndexedArchives(cfg.Package.SearchIndexedArchives).
+		WithIncludeUnindexedArchives(cfg.Package.SearchUnindexedArchives).
+		WithMaxDepth(cfg.Package.NestedArchiveMaxDepth).
+		WithMaxMemoryBytes(cfg.Package.NestedArchiveMaxMemoryBytes).
+		WithMaxDiskBytes(cfg.Package.NestedArchiveMaxDiskBytes)
+}
+
 func (cfg Catalog) ToRelationshipsConfig() cataloging.RelationshipsConfig {
 	return cataloging.RelationshipsConfig{
 		PackageFileOwnership:        cfg.Relationships.PackageFileOwnership,
@@ -136,6 +146,7 @@ func (cfg Catalog) ToComplianceConfig() cataloging.ComplianceConfig {
 
 func (cfg Catalog) ToUnknownsConfig() cataloging.UnknownsConfig {
 	return cataloging.UnknownsConfig{
+		RemoveWhenPackagesDefined:         cfg.Unknowns.RemoveWhenPackagesDefined,
 		IncludeExecutablesWithoutPackages: cfg.Unknowns.ExecutablesWithoutPackages,
 		IncludeUnexpandedArchives:         cfg.Unknowns.UnexpandedArchives,
 	}
@@ -169,10 +180,6 @@ func (cfg Catalog) ToLicenseConfig() cataloging.LicenseConfig {
 }
 
 func (cfg Catalog) ToPackagesConfig() pkgcataloging.Config {
-	archiveSearch := cataloging.ArchiveSearchConfig{
-		IncludeIndexedArchives:   cfg.Package.SearchIndexedArchives,
-		IncludeUnindexedArchives: cfg.Package.SearchUnindexedArchives,
-	}
 	return pkgcataloging.Config{
 		Binary: binary.DefaultClassifierCatalogerConfig(),
 		Cpp: cpp.DefaultCatalogerConfig().
@@ -219,7 +226,7 @@ func (cfg Catalog) ToPackagesConfig() pkgcataloging.Config {
 			WithMavenLocalRepositoryDir(cfg.Java.MavenLocalRepositoryDir).
 			WithUseNetwork(*multiLevelOption(false, enrichmentEnabled(cfg.Enrich, task.Java, task.Maven), cfg.Java.UseNetwork)).
 			WithMavenBaseURL(cfg.Java.MavenURL).
-			WithArchiveTraversal(archiveSearch, cfg.Java.MaxParentRecursiveDepth).
+			WithMaxParentRecursiveDepth(cfg.Java.MaxParentRecursiveDepth).
 			WithResolveTransitiveDependencies(cfg.Java.ResolveTransitiveDependencies),
 	}
 }

cmd/syft/internal/options/pkg.go

@@ -6,9 +6,12 @@ import (
 )
 
 type packageConfig struct {
-	SearchUnindexedArchives         bool `yaml:"search-unindexed-archives" json:"search-unindexed-archives" mapstructure:"search-unindexed-archives"`
-	SearchIndexedArchives           bool `yaml:"search-indexed-archives" json:"search-indexed-archives" mapstructure:"search-indexed-archives"`
-	ExcludeBinaryOverlapByOwnership bool `yaml:"exclude-binary-overlap-by-ownership" json:"exclude-binary-overlap-by-ownership" mapstructure:"exclude-binary-overlap-by-ownership"` // exclude synthetic binary packages owned by os package files
+	SearchUnindexedArchives         bool  `yaml:"search-unindexed-archives" json:"search-unindexed-archives" mapstructure:"search-unindexed-archives"`
+	SearchIndexedArchives           bool  `yaml:"search-indexed-archives" json:"search-indexed-archives" mapstructure:"search-indexed-archives"`
+	ExcludeBinaryOverlapByOwnership bool  `yaml:"exclude-binary-overlap-by-ownership" json:"exclude-binary-overlap-by-ownership" mapstructure:"exclude-binary-overlap-by-ownership"` // exclude synthetic binary packages owned by os package files
+	NestedArchiveMaxDepth           int   `yaml:"nested-archive-max-depth" json:"nested-archive-max-depth" mapstructure:"nested-archive-max-depth"`
+	NestedArchiveMaxMemoryBytes     int64 `yaml:"nested-archive-max-memory-bytes" json:"nested-archive-max-memory-bytes" mapstructure:"nested-archive-max-memory-bytes"`
+	NestedArchiveMaxDiskBytes       int64 `yaml:"nested-archive-max-disk-bytes" json:"nested-archive-max-disk-bytes" mapstructure:"nested-archive-max-disk-bytes"`
 }
 
 var _ interface {
@@ -17,12 +20,17 @@ var _ interface {
 
 func (o *packageConfig) DescribeFields(descriptions clio.FieldDescriptionSet) {
 	descriptions.Add(&o.SearchIndexedArchives, `search within archives that do contain a file index to search against (zip)
-note: for now this only applies to the java package cataloger`)
+note: this only applies to the java package cataloger, and is ignored when nested-archive-max-depth is not 0 (every archive is searched)`)
 	descriptions.Add(&o.SearchUnindexedArchives, `search within archives that do not contain a file index to search against (tar, tar.gz, tar.bz2, etc)
 note: enabling this may result in a performance impact since all discovered compressed tars will be decompressed
-note: for now this only applies to the java package cataloger`)
+note: this only applies to the java package cataloger, and is ignored when nested-archive-max-depth is not 0 (every archive is searched)`)
 	descriptions.Add(&o.ExcludeBinaryOverlapByOwnership, `allows users to exclude synthetic binary packages from the sbom
 these packages are removed if an overlap with a non-synthetic package is found`)
+	descriptions.Add(&o.NestedArchiveMaxDepth, `maximum depth to recursively catalog nested archives (0 = disabled, -1 = as deep as 16 levels, the most allowed)
+note: when enabled this replaces the java cataloger's own unbounded jar-in-jar recursion, so archives deeper than this are reported as unknowns rather than cataloged`)
+	descriptions.Add(&o.NestedArchiveMaxMemoryBytes, `maximum bytes of nested archive content held in memory at once (0 = none, -1 = unbounded)`)
+	descriptions.Add(&o.NestedArchiveMaxDiskBytes, `maximum bytes of nested archive content on disk at once (0 = none, -1 = unbounded)
+note: this and nested-archive-max-memory-bytes cannot both be 0 when nested-archive-max-depth is not 0`)
 }
 
 func defaultPackageConfig() packageConfig {
@@ -31,5 +39,8 @@ func defaultPackageConfig() packageConfig {
 		SearchIndexedArchives:           c.IncludeIndexedArchives,
 		SearchUnindexedArchives:         c.IncludeUnindexedArchives,
 		ExcludeBinaryOverlapByOwnership: true,
+		NestedArchiveMaxDepth:           c.MaxDepth,
+		NestedArchiveMaxMemoryBytes:     c.MaxMemoryBytes,
+		NestedArchiveMaxDiskBytes:       c.MaxDiskBytes,
 	}
 }

cmd/syft/internal/options/pkg_test.go

@@ -0,0 +1,53 @@
+package options
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/anchore/syft/syft/cataloging"
+)
+
+func Test_packageConfigDefaultsMatchArchiveSearchConfig(t *testing.T) {
+	want := cataloging.DefaultArchiveSearchConfig()
+	got := defaultPackageConfig()
+
+	assert.Equal(t, want.MaxDepth, got.NestedArchiveMaxDepth)
+	assert.Equal(t, want.MaxMemoryBytes, got.NestedArchiveMaxMemoryBytes)
+	assert.Equal(t, want.MaxDiskBytes, got.NestedArchiveMaxDiskBytes)
+
+	require.Zero(t, got.NestedArchiveMaxDepth, "nested archive cataloging must be off by default")
+}
+
+func Test_ToArchiveConfig(t *testing.T) {
+	defaults := cataloging.DefaultArchiveSearchConfig()
+
+	t.Run("defaults round trip unchanged", func(t *testing.T) {
+		cfg := Catalog{Package: defaultPackageConfig()}
+		got := cfg.ToArchiveConfig()
+
+		assert.Equal(t, defaults.MaxDepth, got.MaxDepth)
+		assert.Equal(t, defaults.MaxMemoryBytes, got.MaxMemoryBytes)
+		assert.Equal(t, defaults.MaxDiskBytes, got.MaxDiskBytes)
+	})
+
+	t.Run("every setting is threaded through", func(t *testing.T) {
+		// a key that parses but is not carried into the archive config is invisible in a config
+		// dump, so assert each one arrives
+		cfg := Catalog{Package: packageConfig{
+			NestedArchiveMaxDepth:       3,
+			NestedArchiveMaxMemoryBytes: 111,
+			NestedArchiveMaxDiskBytes:   3333,
+			SearchIndexedArchives:       true,
+			SearchUnindexedArchives:     true,
+		}}
+		got := cfg.ToArchiveConfig()
+
+		assert.Equal(t, 3, got.MaxDepth)
+		assert.Equal(t, int64(111), got.MaxMemoryBytes)
+		assert.Equal(t, int64(3333), got.MaxDiskBytes)
+		assert.True(t, got.IncludeIndexedArchives)
+		assert.True(t, got.IncludeUnindexedArchives)
+	})
+}

cmd/syft/internal/ui/ui.go

@@ -5,6 +5,7 @@ import (
 	"fmt"
 	"io"
 	"os"
+	"strings"
 	"sync"
 	"time"
 
@@ -186,7 +187,12 @@ func (m *UI) Update(msg tea.Msg) (tea.Model, tea.Cmd) {
 }
 
 func (m UI) View() string {
-	return m.frame.View()
+	v := m.frame.View()
+	// bubbletea erases the line the cursor rests on at exit, which would drop the frame's last line
+	if !strings.HasSuffix(v, "\n") {
+		return v + "\n"
+	}
+	return v
 }
 
 var (

cmd/syft/internal/ui/ui_test.go

@@ -0,0 +1,31 @@
+package ui
+
+import (
+	"io"
+	"testing"
+
+	tea "github.com/charmbracelet/bubbletea"
+	"github.com/stretchr/testify/require"
+
+	"github.com/anchore/bubbly/bubbles/frame"
+)
+
+var _ tea.Model = (*staticModel)(nil)
+
+type staticModel string
+
+func Test_UI_viewEndsOnAnEmptyLine(t *testing.T) {
+	// bubbletea erases the line the cursor rests on when the program stops, so a view whose last line
+	// carries content loses it. Unless a log line happened to be in the footer, that dropped the last row
+	// of the cataloging tree on any source that logs nothing.
+	subject := New(io.Discard, false)
+	subject.frame.(*frame.Frame).AppendModel(staticModel("first row\nlast row"))
+
+	require.Equal(t, "first row\nlast row\n", subject.View())
+}
+
+func (m staticModel) Init() tea.Cmd { return nil }
+
+func (m staticModel) Update(tea.Msg) (tea.Model, tea.Cmd) { return m, nil }
+
+func (m staticModel) View() string { return string(m) }

go.mod

@@ -12,7 +12,7 @@ require (
 	github.com/acobaugh/osrelease v0.1.0
 	github.com/adrg/xdg v0.5.3
 	github.com/anchore/bubbly v0.2.2
-	github.com/anchore/clio v0.1.1
+	github.com/anchore/clio v0.1.2
 	github.com/anchore/fangs v0.1.1
 	github.com/anchore/go-collections v0.1.1
 	github.com/anchore/go-homedir v0.1.1
@@ -22,28 +22,28 @@ require (
 	github.com/anchore/go-sync v0.1.2
 	github.com/anchore/go-version v1.2.2-0.20200701162849-18adb9c92b9b
 	github.com/anchore/packageurl-go v0.2.0
-	github.com/anchore/stereoscope v0.3.4
+	github.com/anchore/stereoscope v0.4.0
 	github.com/anmitsu/go-shlex v0.0.0-20200514113438-38f4b401e2be
 	github.com/aquasecurity/go-pep440-version v0.0.1
 	github.com/bitnami/go-version v0.0.0-20250131085805-b1f57a8634ef
 	github.com/blakesmith/ar v0.0.0-20190502131153-809d4375e1fb
-	github.com/bmatcuk/doublestar/v4 v4.10.2
+	github.com/bmatcuk/doublestar/v4 v4.10.3
 	github.com/cespare/xxhash/v2 v2.3.0
 	github.com/charmbracelet/bubbles v1.0.0
 	github.com/charmbracelet/bubbletea v1.3.10
 	github.com/charmbracelet/lipgloss v1.1.0
 	github.com/dave/jennifer v1.7.1
-	github.com/deitch/magic v0.0.0-20230404182410-1ff89d7342da
+	github.com/deitch/magic v1.0.0
 	github.com/diskfs/go-diskfs v1.9.4
 	github.com/distribution/reference v0.6.0
 	github.com/dustin/go-humanize v1.1.0
 	github.com/elliotchance/phpserialize v1.4.0
 	github.com/facebookincubator/nvdtools v0.1.5
-	github.com/github/go-spdx/v2 v2.7.1
-	github.com/gkampitakis/go-snaps v0.5.23
+	github.com/github/go-spdx/v2 v2.8.0
+	github.com/gkampitakis/go-snaps v0.5.24
 	github.com/go-git/go-billy/v5 v5.9.2
 	github.com/go-git/go-git/v5 v5.19.3
-	github.com/go-test/deep v1.1.1
+	github.com/go-test/deep v1.1.2
 	github.com/go-viper/mapstructure/v2 v2.5.0
 	github.com/goccy/go-yaml v1.19.2
 	github.com/gohugoio/hashstructure v0.6.0
@@ -51,8 +51,8 @@ require (
 	github.com/google/go-containerregistry v0.22.1
 	github.com/google/licensecheck v0.3.1
 	github.com/google/uuid v1.6.0
-	github.com/gookit/color v1.6.2
-	github.com/gpustack/gguf-parser-go v0.26.4
+	github.com/gookit/color v1.6.3
+	github.com/gpustack/gguf-parser-go v0.27.0
 	github.com/hashicorp/go-cleanhttp v0.5.2
 	github.com/hashicorp/go-getter v1.8.10
 	github.com/hashicorp/go-multierror v1.1.1
@@ -62,7 +62,7 @@ require (
 	github.com/jedib0t/go-pretty/v6 v6.8.3
 	github.com/jinzhu/copier v0.4.0
 	github.com/kastenhq/goversion v0.0.0-20230811215019-93b2f8823953
-	github.com/klauspost/compress v1.20.1
+	github.com/klauspost/compress v1.20.3
 	github.com/magiconair/properties v1.18.12
 	github.com/mholt/archives v0.1.5
 	github.com/moby/sys/mountinfo v0.7.2
@@ -93,11 +93,11 @@ require (
 	go.uber.org/goleak v1.3.0
 	go.yaml.in/yaml/v3 v3.0.5
 	golang.org/x/exp v0.0.0-20260410095643-746e56fc9e2f
-	golang.org/x/mod v0.41.0
+	golang.org/x/mod v0.42.0
 	golang.org/x/net v0.61.0
 	golang.org/x/time v0.16.0
-	golang.org/x/tools v0.51.0
-	modernc.org/sqlite v1.60.1
+	golang.org/x/tools v0.52.0
+	modernc.org/sqlite v1.61.0
 )
 
 require (
@@ -123,9 +123,9 @@ require (
 	github.com/GoogleCloudPlatform/opentelemetry-operations-go/exporter/metric v0.57.0 // indirect
 	github.com/GoogleCloudPlatform/opentelemetry-operations-go/internal/resourcemapping v0.57.0 // indirect
 	github.com/Masterminds/goutils v1.1.1 // indirect
-	github.com/Microsoft/go-winio v0.6.3-0.20251027160822-ad3df93bed29 // indirect
+	github.com/Microsoft/go-winio v0.6.3-0.20260930231756-f19d9717deb0 // indirect
 	github.com/Microsoft/hcsshim v0.15.0-rc.4 // indirect
-	github.com/ProtonMail/go-crypto v1.4.1 // indirect
+	github.com/ProtonMail/go-crypto v1.5.2 // indirect
 	github.com/STARRY-S/zip v0.2.3 // indirect
 	github.com/VividCortex/ewma v1.2.0 // indirect
 	github.com/agext/levenshtein v1.2.1 // indirect
@@ -156,7 +156,6 @@ require (
 	github.com/aws/smithy-go v1.28.1 // indirect
 	github.com/aymanbagabas/go-osc52/v2 v2.0.1 // indirect
 	github.com/bahlo/generic-list-go v0.2.0 // indirect
-	github.com/becheran/wildmatch-go v1.0.0 // indirect
 	github.com/bgentry/go-netrc v0.0.0-20140422174119-9fd32a8b3d3d // indirect
 	github.com/bodgit/plumbing v1.3.0 // indirect
 	github.com/bodgit/sevenzip v1.6.1 // indirect
@@ -173,7 +172,7 @@ require (
 	github.com/cncf/xds/go v0.0.0-20260202195803-dba9d589def2 // indirect
 	github.com/containerd/cgroups/v3 v3.1.3 // indirect
 	github.com/containerd/containerd/api v1.12.0 // indirect
-	github.com/containerd/containerd/v2 v2.4.1 // indirect
+	github.com/containerd/containerd/v2 v2.4.2 // indirect
 	github.com/containerd/continuity v0.5.0 // indirect
 	github.com/containerd/errdefs v1.0.0 // indirect
 	github.com/containerd/errdefs/pkg v0.3.0 // indirect
@@ -182,16 +181,16 @@ require (
 	github.com/containerd/log/otel v0.1.0 // indirect
 	github.com/containerd/platforms v1.0.0-rc.5 // indirect
 	github.com/containerd/plugin v1.1.0 // indirect
-	github.com/containerd/stargz-snapshotter/estargz v0.18.2 // indirect
+	github.com/containerd/stargz-snapshotter/estargz v0.19.0 // indirect
 	github.com/containerd/ttrpc v1.2.9 // indirect
 	github.com/containerd/typeurl/v2 v2.3.0 // indirect
 	github.com/containers/libtrust v0.0.0-20230121012942-c1716e8a8d01 // indirect
 	github.com/containers/ocicrypt v1.3.2 // indirect
 	github.com/cyberphone/json-canonicalization v0.0.0-20241213102144-19d51d7fe467 // indirect
 	github.com/cyphar/filepath-securejoin v0.7.0 // indirect
-	github.com/docker/cli v29.8.2+incompatible // indirect
-	github.com/docker/docker-credential-helpers v0.9.8 // indirect
-	github.com/docker/go-connections v0.8.1 // indirect
+	github.com/docker/cli v29.9.2+incompatible // indirect
+	github.com/docker/docker-credential-helpers v0.9.10 // indirect
+	github.com/docker/go-connections v0.8.2 // indirect
 	github.com/docker/go-units v0.5.0 // indirect
 	github.com/dsnet/compress v0.0.2-0.20230904184137-39efe44ab707 // indirect
 	github.com/emirpasic/gods v1.18.1 // indirect
@@ -202,16 +201,16 @@ require (
 	github.com/felixge/fgprof v0.9.5 // indirect
 	github.com/felixge/httpsnoop v1.1.0 // indirect
 	github.com/fsnotify/fsnotify v1.10.1 // indirect
-	github.com/gabriel-vasile/mimetype v1.4.15 // indirect
+	github.com/gabriel-vasile/mimetype v1.4.16 // indirect
 	github.com/gkampitakis/ciinfo v0.3.4 // indirect
 	github.com/go-git/gcfg v1.5.1-0.20230307220236-3a3c6141e376 // indirect
-	github.com/go-jose/go-jose/v4 v4.1.5 // indirect
+	github.com/go-jose/go-jose/v4 v4.1.6 // indirect
 	github.com/go-logr/logr v1.4.4 // indirect
 	github.com/go-logr/stdr v1.2.2 // indirect
 	github.com/go-restruct/restruct v1.2.0-alpha // indirect
 	github.com/golang/groupcache v0.0.0-20241129210726-2c02b8208cf8 // indirect
 	github.com/google/go-intervals v0.0.2 // indirect
-	github.com/google/pprof v0.0.0-20260802141513-ef3492d7dac3 // indirect
+	github.com/google/pprof v0.0.0-20261016150608-1facf8f91b50 // indirect
 	github.com/google/s2a-go v0.1.10 // indirect
 	github.com/googleapis/enterprise-certificate-proxy v0.3.22 // indirect
 	github.com/googleapis/gax-go/v2 v2.24.1 // indirect
@@ -225,7 +224,7 @@ require (
 	github.com/jbenet/go-context v0.0.0-20150711004518-d14ea06fba99 // indirect
 	github.com/json-iterator/go v1.1.12 // indirect
 	github.com/kevinburke/ssh_config v1.2.0 // indirect
-	github.com/klauspost/pgzip v1.2.6 // indirect
+	github.com/klauspost/pgzip v1.2.7 // indirect
 	github.com/kr/pretty v0.3.1 // indirect
 	github.com/kr/text v0.2.0 // indirect
 	github.com/lucasb-eyer/go-colorful v1.3.0 // indirect
@@ -233,8 +232,8 @@ require (
 	github.com/mattn/go-colorable v0.1.14 // indirect
 	github.com/mattn/go-isatty v0.0.24 // indirect
 	github.com/mattn/go-localereader v0.0.2-0.20220822084749-2491eb6c1c75 // indirect
-	github.com/mattn/go-runewidth v0.0.27 // indirect
-	github.com/mattn/go-sqlite3 v1.14.48 // indirect
+	github.com/mattn/go-runewidth v0.0.31 // indirect
+	github.com/mattn/go-sqlite3 v1.14.52 // indirect
 	github.com/mgutz/ansi v0.0.0-20200706080929-d51e80ef957d // indirect
 	github.com/miekg/pkcs11 v1.1.2 // indirect
 	github.com/mikelolasagasti/xz v1.0.1 // indirect
@@ -246,8 +245,8 @@ require (
 	github.com/mitchellh/reflectwalk v1.0.2 // indirect
 	github.com/moby/docker-image-spec v1.3.1 // indirect
 	github.com/moby/locker v1.0.1 // indirect
-	github.com/moby/moby/api v1.56.0 // indirect
-	github.com/moby/moby/client v0.6.0 // indirect
+	github.com/moby/moby/api v1.56.1 // indirect
+	github.com/moby/moby/client v0.6.2 // indirect
 	github.com/moby/sys/capability v0.4.0 // indirect
 	github.com/moby/sys/signal v0.7.1 // indirect
 	github.com/moby/sys/user v0.4.1 // indirect
@@ -257,7 +256,7 @@ require (
 	github.com/muesli/ansi v0.0.0-20230316100256-276c6243b2f6 // indirect
 	github.com/muesli/cancelreader v0.2.2 // indirect
 	github.com/muesli/termenv v0.16.0 // indirect
-	github.com/ncruces/go-strftime v1.0.0 // indirect
+	github.com/ncruces/go-strftime v1.1.0 // indirect
 	github.com/nwaples/rardecode/v2 v2.4.1 // indirect
 	github.com/olekukonko/cat v0.0.0-20250911104152-50322a0618f6 // indirect
 	github.com/olekukonko/errors v1.2.0 // indirect
@@ -284,7 +283,7 @@ require (
 	github.com/sahilm/fuzzy v0.1.1 // indirect
 	github.com/secure-systems-lab/go-securesystemslib v0.11.1 // indirect
 	github.com/shopspring/decimal v1.4.0 // indirect
-	github.com/sigstore/fulcio v1.8.7 // indirect
+	github.com/sigstore/fulcio v1.8.8 // indirect
 	github.com/sigstore/protobuf-specs v0.5.2 // indirect
 	github.com/sigstore/sigstore v1.10.11 // indirect
 	github.com/sirupsen/logrus v1.10.2 // indirect
@@ -308,9 +307,10 @@ require (
 	github.com/tidwall/match v1.1.1 // indirect
 	github.com/tidwall/pretty v1.2.1 // indirect
 	github.com/tidwall/sjson v1.2.5 // indirect
+	github.com/varlink/go v0.4.1-0.20261015173642-c935be0c53f7 // indirect
 	github.com/vbatts/tar-split v0.12.3 // indirect
-	github.com/vbauerster/cupwriter v0.0.4 // indirect
-	github.com/vbauerster/mpb/v8 v8.14.0 // indirect
+	github.com/vbauerster/cupwriter v0.0.5 // indirect
+	github.com/vbauerster/mpb/v8 v8.16.2 // indirect
 	github.com/xanzy/ssh-agent v0.3.3 // indirect
 	github.com/xeipuuv/gojsonpointer v0.0.0-20190905194746-02993c407bfb // indirect
 	github.com/xeipuuv/gojsonreference v0.0.0-20180127040603-bd5ef7bd5415 // indirect
@@ -327,8 +327,8 @@ require (
 	go.opentelemetry.io/otel/sdk v1.46.0 // indirect
 	go.opentelemetry.io/otel/sdk/metric v1.46.0 // indirect
 	go.opentelemetry.io/otel/trace v1.46.0 // indirect
-	go.podman.io/image/v5 v5.41.2 // indirect
-	go.podman.io/storage v1.64.1 // indirect
+	go.podman.io/image/v5 v5.42.0 // indirect
+	go.podman.io/storage v1.65.0 // indirect
 	go4.org v0.0.0-20230225012048-214862532bf5 // indirect
 	golang.org/x/crypto v0.58.0 // indirect
 	golang.org/x/oauth2 v0.37.0 // indirect
@@ -344,7 +344,7 @@ require (
 	google.golang.org/grpc v1.84.0 // indirect
 	google.golang.org/protobuf v1.36.12 // indirect
 	gopkg.in/warnings.v0 v0.1.2 // indirect
-	modernc.org/libc v1.77.1 // indirect
+	modernc.org/libc v1.79.0 // indirect
 	modernc.org/mathutil v1.7.1 // indirect
 	modernc.org/memory v1.12.1 // indirect
 )

go.sum

@@ -99,15 +99,15 @@ github.com/Masterminds/semver/v3 v3.5.0/go.mod h1:4V+yj/TJE1HU9XfppCwVMZq3I84lpr
 github.com/Masterminds/sprig/v3 v3.3.0 h1:mQh0Yrg1XPo6vjYXgtf5OtijNAKJRNcTdOOGZe3tPhs=
 github.com/Masterminds/sprig/v3 v3.3.0/go.mod h1:Zy1iXRYNqNLUolqCpL4uhk6SHUMAOSCzdgBfDb35Lz0=
 github.com/Microsoft/go-winio v0.5.2/go.mod h1:WpS1mjBmmwHBEWmogvA2mj8546UReBk4v8QkMxJ6pZY=
-github.com/Microsoft/go-winio v0.6.3-0.20251027160822-ad3df93bed29 h1:0kQAzHq8vLs7Pptv+7TxjdETLf/nIqJpIB4oC6Ba4vY=
-github.com/Microsoft/go-winio v0.6.3-0.20251027160822-ad3df93bed29/go.mod h1:ZWa7ssZJT30CCDGJ7fk/2SBTq9BIQrrVjrcss0UW2s0=
+github.com/Microsoft/go-winio v0.6.3-0.20260930231756-f19d9717deb0 h1:71VU8kW/LCxJkx41+YYys1EgQO+AUnPa1TrxTSyYUCU=
+github.com/Microsoft/go-winio v0.6.3-0.20260930231756-f19d9717deb0/go.mod h1:ma0QpxizD4fyyzJ1C7MIblymTD2Nxz5Mho/3CepwIZg=
 github.com/Microsoft/hcsshim v0.15.0-rc.4 h1:aZFX4LH0S20Lgjq0wG61StIClj7im4yzrxIClkaR8Z8=
 github.com/Microsoft/hcsshim v0.15.0-rc.4/go.mod h1:BA9CBztgu4h/6Jsvo1O1M4qjWw09PoYpaEYgexPE578=
 github.com/OneOfOne/xxhash v1.2.2/go.mod h1:HSdplMjZKSmBqAxg5vPj2TmRDmfkzw+cTzAElWljhcU=
 github.com/OneOfOne/xxhash v1.2.8 h1:31czK/TI9sNkxIKfaUfGlU47BAxQ0ztGgd9vPyqimf8=
 github.com/OneOfOne/xxhash v1.2.8/go.mod h1:eZbhyaAYD41SGSSsnmcpxVoRiQ/MPUTjUdIIOT9Um7Q=
-github.com/ProtonMail/go-crypto v1.4.1 h1:9RfcZHqEQUvP8RzecWEUafnZVtEvrBVL9BiF67IQOfM=
-github.com/ProtonMail/go-crypto v1.4.1/go.mod h1:e1OaTyu5SYVrO9gKOEhTc+5UcXtTUa+P3uLudwcgPqo=
+github.com/ProtonMail/go-crypto v1.5.2 h1:cucYnvqcY7UOXVD//mSyjeaPY0SSN3v5cDkYPxumINk=
+github.com/ProtonMail/go-crypto v1.5.2/go.mod h1:/RaSu30DaKO4RY+XdV/ACcCcZkGr7AhUIduq5sjzzCo=
 github.com/STARRY-S/zip v0.2.3 h1:luE4dMvRPDOWQdeDdUxUoZkzUIpTccdKdhHHsQJ1fm4=
 github.com/STARRY-S/zip v0.2.3/go.mod h1:lqJ9JdeRipyOQJrYSOtpNAiaesFO6zVDsE8GIGFaoSk=
 github.com/VividCortex/ewma v1.2.0 h1:f58SaIzcDXrSy3kWaHNvuJgJ3Nmz59Zji6XoJR/q1ow=
@@ -126,8 +126,8 @@ github.com/alecthomas/units v0.0.0-20151022065526-2efee857e7cf/go.mod h1:ybxpYRF
 github.com/alecthomas/units v0.0.0-20190717042225-c3de453c63f4/go.mod h1:ybxpYRFXyAe+OPACYpWeL0wqObRcbAqCMya13uyzqw0=
 github.com/anchore/bubbly v0.2.2 h1:53JHRlpaNZjMcUYdz7n1U7+kOhy0zsJv9gpGEXvTcz8=
 github.com/anchore/bubbly v0.2.2/go.mod h1:M4twoFkczlfuNdU8QV7oQjVJwPbxdUWRMfKydcLba0U=
-github.com/anchore/clio v0.1.1 h1:9bkYnaFbpT0J3G0qSHyQqa/lpK5zV0C9Gtgh82H/jj0=
-github.com/anchore/clio v0.1.1/go.mod h1:CFPIopJlakJbBpKtAL/EPpj4W9hgBO7PfFc8N2FAtlE=
+github.com/anchore/clio v0.1.2 h1:kCWNUkJsRJ5A103fFSLG+CSqIP9bOIFX2X5GEnup0HM=
+github.com/anchore/clio v0.1.2/go.mod h1:LqoM9TUMDolUMaPV4hslLvuooqIjpTN8J7V/rBqk/Zc=
 github.com/anchore/fangs v0.1.1 h1:NBTHocmWM2/0gNhebpoE/wEB0Z0nxh2lESww2o/Uf5M=
 github.com/anchore/fangs v0.1.1/go.mod h1:82oZuk4+RynOvAoxnXKmI1zO5xk/kbOw+5t4fAAPSsk=
 github.com/anchore/go-collections v0.1.1 h1:kGlmSehs+ctTBZr+98F2+taHeolHy+XDx1Nczl8GZc8=
@@ -150,8 +150,8 @@ github.com/anchore/go-version v1.2.2-0.20200701162849-18adb9c92b9b h1:e1bmaoJfZV
 github.com/anchore/go-version v1.2.2-0.20200701162849-18adb9c92b9b/go.mod h1:Bkc+JYWjMCF8OyZ340IMSIi2Ebf3uwByOk6ho4wne1E=
 github.com/anchore/packageurl-go v0.2.0 h1:CkrM4RMUwrEGAiE1OVlxaZNzWj0TuHRey7o4T/EAErk=
 github.com/anchore/packageurl-go v0.2.0/go.mod h1:2JCgOQMIsqZ7TmliXG4PnUthPJAKE3mWQbsW2XHjAOE=
-github.com/anchore/stereoscope v0.3.4 h1:dT5AfjCTXUJowMiRIc+VBQVwvwnIEwnxxwA1GwAkMxw=
-github.com/anchore/stereoscope v0.3.4/go.mod h1:+HxqHTt7dvH8mea0mf3ulqkf084VvHiT1grpAQf5uEs=
+github.com/anchore/stereoscope v0.4.0 h1:MDL7YFRDaGzhCdjm/s+em1D/X9HwnZMYupfgg+mvqPI=
+github.com/anchore/stereoscope v0.4.0/go.mod h1:hYJsi3M8a8N1O66u+rMQSgv5TREGM7QIjKBjPPnwiD8=
 github.com/andreyvit/diff v0.0.0-20170406064948-c7f18ee00883/go.mod h1:rCTlJbsFo29Kk6CurOXKm700vrz8f0KW0JNfpkRJY/8=
 github.com/andybalholm/brotli v1.2.0 h1:ukwgCxwYrmACq68yiUqwIWnGY0cTPox/M94sVwToPjQ=
 github.com/andybalholm/brotli v1.2.0/go.mod h1:rzTDkvFWvIrjDXZHkuS16NPggd91W3kUSvPlQ1pLaKY=
@@ -217,8 +217,6 @@ github.com/aymanbagabas/go-udiff v0.3.1 h1:LV+qyBQ2pqe0u42ZsUEtPiCaUoqgA9gYRDs3v
 github.com/aymanbagabas/go-udiff v0.3.1/go.mod h1:G0fsKmG+P6ylD0r6N/KgQD/nWzgfnl8ZBcNLgcbrw8E=
 github.com/bahlo/generic-list-go v0.2.0 h1:5sz/EEAK+ls5wF+NeqDpk5+iNdMDXrh3z3nPnH1Wvgk=
 github.com/bahlo/generic-list-go v0.2.0/go.mod h1:2KvAjgMlE5NNynlg/5iLrrCCZ2+5xWbdbCW3pNTGyYg=
-github.com/becheran/wildmatch-go v1.0.0 h1:mE3dGGkTmpKtT4Z+88t8RStG40yN9T+kFEGj2PZFSzA=
-github.com/becheran/wildmatch-go v1.0.0/go.mod h1:gbMvj0NtVdJ15Mg/mH9uxk2R1QCistMyU7d9KFzroX4=
 github.com/beorn7/perks v0.0.0-20180321164747-3a771d992973/go.mod h1:Dwedo/Wpr24TaqPxmxbtue+5NUziq4I4S80YR8gNf3Q=
 github.com/beorn7/perks v1.0.0/go.mod h1:KWe93zE9D1o94FZ5RNwFwVgaQK1VOXiVxmqh+CedLV8=
 github.com/beorn7/perks v1.0.1/go.mod h1:G2ZrVWU2WbWT9wwq4/hrbKbnv/1ERSJQ0ibhJ6rlkpw=
@@ -229,8 +227,8 @@ github.com/bitnami/go-version v0.0.0-20250131085805-b1f57a8634ef h1:TSFnfbbu2oAO
 github.com/bitnami/go-version v0.0.0-20250131085805-b1f57a8634ef/go.mod h1:9iglf1GG4oNRJ39bZ5AZrjgAFD2RwQbXw6Qf7Cs47wo=
 github.com/blakesmith/ar v0.0.0-20190502131153-809d4375e1fb h1:m935MPodAbYS46DG4pJSv7WO+VECIWUQ7OJYSoTrMh4=
 github.com/blakesmith/ar v0.0.0-20190502131153-809d4375e1fb/go.mod h1:PkYb9DJNAwrSvRx5DYA+gUcOIgTGVMNkfSCbZM8cWpI=
-github.com/bmatcuk/doublestar/v4 v4.10.2 h1:eF7W7HWKg3z9NrWV9pTLnNeoXaqq3Tq9DNKXVMfoCnw=
-github.com/bmatcuk/doublestar/v4 v4.10.2/go.mod h1:xBQ8jztBU6kakFMg+8WGxn0c6z1fTSPVIjEY1Wr7jzc=
+github.com/bmatcuk/doublestar/v4 v4.10.3 h1:1UIv1+fqH3++ViVkpnaPTB+Pi1UHycnPFAq14zgK+gI=
+github.com/bmatcuk/doublestar/v4 v4.10.3/go.mod h1:xBQ8jztBU6kakFMg+8WGxn0c6z1fTSPVIjEY1Wr7jzc=
 github.com/bodgit/plumbing v1.3.0 h1:pf9Itz1JOQgn7vEOE7v7nlEfBykYqvUYioC61TwWCFU=
 github.com/bodgit/plumbing v1.3.0/go.mod h1:JOTb4XiRu5xfnmdnDJo6GmSbSbtSyufrsyZFByMtKEs=
 github.com/bodgit/sevenzip v1.6.1 h1:kikg2pUMYC9ljU7W9SaqHXhym5HyKm8/M/jd31fYan4=
@@ -300,8 +298,8 @@ github.com/containerd/cgroups/v3 v3.1.3 h1:eUNflyMddm18+yrDmZPn3jI7C5hJ9ahABE5q6
 github.com/containerd/cgroups/v3 v3.1.3/go.mod h1:PKZ2AcWmSBsY/tJUVhtS/rluX0b1uq1GmPO1ElCmbOw=
 github.com/containerd/containerd/api v1.12.0 h1:kuQm82SbDrCuO4n7hf2L8zsBtZLuympyq5X/VotfX2A=
 github.com/containerd/containerd/api v1.12.0/go.mod h1:EBcSzoi9Vl18cdODaXUCskf3D2NT8lsSXeZJnU5jIUc=
-github.com/containerd/containerd/v2 v2.4.1 h1:DUx/ZJN7cEu0WuzHClDB+68H/bqMEH5pWoEjf0ae4hc=
-github.com/containerd/containerd/v2 v2.4.1/go.mod h1:vgLdtvl3prFk1d3ZVqQcsDD5Q9IKM+vAIdU54U85w+I=
+github.com/containerd/containerd/v2 v2.4.2 h1:p6Qg+xbEz8lvwdhHDx0U469xENvp4LgGBx+E7djXkGw=
+github.com/containerd/containerd/v2 v2.4.2/go.mod h1:vgLdtvl3prFk1d3ZVqQcsDD5Q9IKM+vAIdU54U85w+I=
 github.com/containerd/continuity v0.5.0 h1:7a85HZpCSs+1Zps0Ee3DPSuAWY+0SJM1JNM51nlEVDg=
 github.com/containerd/continuity v0.5.0/go.mod h1:/lNJvtJKUQStBzpVQ1+rasXO1LAWtUQssk28EZvJ3nE=
 github.com/containerd/errdefs v1.0.0 h1:tg5yIfIlQIrxYtu9ajqY42W3lpS19XqdxRQeEwYG8PI=
@@ -318,8 +316,8 @@ github.com/containerd/platforms v1.0.0-rc.5 h1:vXd569rDrz8LeMXzAnBsy6LADV5YtsD8o
 github.com/containerd/platforms v1.0.0-rc.5/go.mod h1:lKlMXyLybmBedS/JJm11uDofzI8L2v0J2ZbYvNsbq1A=
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@@ -344,8 +342,8 @@ github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSs
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@@ -353,14 +351,14 @@ github.com/distribution/reference v0.6.0 h1:0IXCQ5g4/QMHHkarYzh5l+u8T3t73zM5Qvfr
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@@ -419,15 +417,15 @@ github.com/frankban/quicktest v1.14.6/go.mod h1:4ptaffx2x8+WTWXmUCuVU6aPUX1/Mz7z
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@@ -443,8 +441,8 @@ github.com/go-git/go-git/v5 v5.19.3/go.mod h1:Ye4C8dVigkqrv9UsB4NMdSLV4yAIkLiIhW
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@@ -458,8 +456,8 @@ github.com/go-restruct/restruct v1.2.0-alpha h1:2Lp474S/9660+SJjpVxoKuWX09JsXHSr
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@@ -555,8 +553,8 @@ github.com/google/pprof v0.0.0-20210609004039-a478d1d731e9/go.mod h1:kpwsk12EmLe
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@@ -575,12 +573,12 @@ github.com/googleapis/gax-go/v2 v2.24.1/go.mod h1:bWeBei0NVwaNZKb2y1HUBS7gLXIF3/
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@@ -666,11 +664,11 @@ github.com/kevinburke/ssh_config v1.2.0/go.mod h1:CT57kijsi8u/K/BOFA39wgDQJ9CxiF
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@@ -711,10 +709,10 @@ github.com/mattn/go-isatty v0.0.24 h1:tGZZoVgT/KiqK1c8ocVLeDS8BSWMRd47J3Lbz7vsRe
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@@ -748,10 +746,10 @@ github.com/moby/docker-image-spec v1.3.1 h1:jMKff3w6PgbfSa69GfNg+zN/XLhfXJGnEx3N
 github.com/moby/docker-image-spec v1.3.1/go.mod h1:eKmb5VW8vQEh/BAr2yvVNvuiJuY6UIocYsFu/DxxRpo=
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@@ -777,8 +775,8 @@ github.com/muesli/cancelreader v0.2.2/go.mod h1:3XuTXfFS2VjM+HTLZY9Ak0l6eUKfijIf
 github.com/muesli/termenv v0.16.0 h1:S5AlUN9dENB57rsbnkPyfdGuWIlkmzJjbFf0Tf5FWUc=
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@@ -884,8 +882,8 @@ github.com/saintfish/chardet v0.0.0-20230101081208-5e3ef4b5456d h1:hrujxIzL1woJ7
 github.com/saintfish/chardet v0.0.0-20230101081208-5e3ef4b5456d/go.mod h1:uugorj2VCxiV1x+LzaIdVa9b4S4qGAcH6cbhh4qVxOU=
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@@ -901,8 +899,8 @@ github.com/sergi/go-diff v1.4.0 h1:n/SP9D5ad1fORl+llWyN+D6qoUETXNZARKjyY2/KVCw=
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@@ -996,14 +994,16 @@ github.com/tv42/httpunix v0.0.0-20150427012821-b75d8614f926/go.mod h1:9ESjWnEqri
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@@ -1072,10 +1072,10 @@ go.opentelemetry.io/otel/sdk/metric v1.46.0/go.mod h1:I1PbKrdVc8Qu8HYVDNtqVIwLwj
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@@ -1147,8 +1147,8 @@ golang.org/x/mod v0.8.0/go.mod h1:iBbtSCu2XBx23ZKBPSOrRkjjQPZFPuis4dIYUhu/chs=
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@@ -1410,8 +1410,8 @@ golang.org/x/tools v0.1.12/go.mod h1:hNGJHUnrk76NpqgfD5Aqm5Crs+Hm0VOH/i9J2+nxYbc
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-golang.org/x/tools v0.51.0 h1:k4Xc/1Om9jwkBJBo4NVLMSARBoWtK10mx+W5BnXCeAI=
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@@ -1608,20 +1608,20 @@ honnef.co/go/tools v0.0.1-2020.1.3/go.mod h1:X/FiERA/W4tHapMX5mGpAtMSVEeEUOyHaw9
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-modernc.org/ccgo/v4 v4.36.1 h1:ZNIUZAryN0UgnJwtyxrdEzcFc3yD4Cu4AzjfPXsLsIE=
-modernc.org/ccgo/v4 v4.36.1/go.mod h1:rrtGc2QkS239nYb/mQNuBMyjq3/y3ZXWbBjPoV3wqzA=
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-modernc.org/gc/v3 v3.1.5 h1:21ldfPfRYE31Tb7B3mwAK8gy1AxP4+dKjrOQPfqakoc=
-modernc.org/gc/v3 v3.1.5/go.mod h1:HFK/6AGESC7Ex+EZJhJ2Gni6cTaYpSMmU/cT9RmlfYY=
+modernc.org/gc/v3 v3.2.0 h1:/Y3LGDMQaoYf55PebP1qsZ5FDGgAZyG1RYKEHeQzh1o=
+modernc.org/gc/v3 v3.2.0/go.mod h1:HFK/6AGESC7Ex+EZJhJ2Gni6cTaYpSMmU/cT9RmlfYY=
 modernc.org/goabi0 v0.2.0 h1:HvEowk7LxcPd0eq6mVOAEMai46V+i7Jrj13t4AzuNks=
 modernc.org/goabi0 v0.2.0/go.mod h1:CEFRnnJhKvWT1c1JTI3Avm+tgOWbkOu5oPA8eH8LnMI=
-modernc.org/libc v1.77.1 h1:Ct8j47QtiZ1Enj2DtFXQtUqrPCAjdCmPjtCuvrYQ0Hs=
-modernc.org/libc v1.77.1/go.mod h1:87/pZ4L6nD1zqW4nItuS12YO7hN1igAah34xjnQo/W0=
+modernc.org/libc v1.79.0 h1:9Dvvv++bAMSkSuBzuOFAatbTV5OIoq6Y6FohmD3e7q8=
+modernc.org/libc v1.79.0/go.mod h1:uT3kR61NsbeKJSLqq83GJwSnZMVLlSjyAz4DfTaBy1M=
 modernc.org/mathutil v1.7.1 h1:GCZVGXdaN8gTqB1Mf/usp1Y/hSqgI2vAGGP4jZMCxOU=
 modernc.org/mathutil v1.7.1/go.mod h1:4p5IwJITfppl0G4sUEDtCr4DthTaT47/N3aT6MhfgJg=
 modernc.org/memory v1.12.1 h1:nFMiWrpStgZczNl6XI9GnIk/rWhYIyHGUaR04pGbp9g=
@@ -1630,8 +1630,8 @@ modernc.org/opt v0.2.0 h1:tGyef5ApycA7FSEOMraay9SaTk5zmbx7Tu+cJs4QKZg=
 modernc.org/opt v0.2.0/go.mod h1:03fq9lsNfvkYSfxrfUhZCWPk1lm4cq4N+Bh//bEtgns=
 modernc.org/sortutil v1.2.1 h1:+xyoGf15mM3NMlPDnFqrteY07klSFxLElE2PVuWIJ7w=
 modernc.org/sortutil v1.2.1/go.mod h1:7ZI3a3REbai7gzCLcotuw9AC4VZVpYMjDzETGsSMqJE=
-modernc.org/sqlite v1.60.1 h1:/blz53O951KWFOso4QQvEs/Fq6cDBKLtMVrYNSeJVKw=
-modernc.org/sqlite v1.60.1/go.mod h1:1dIoEagfDE72QytD5scH1lxARtaUgKgHC/NuApA27r0=
+modernc.org/sqlite v1.61.0 h1:sQi63oLQ9uquAUA4CzOisH35Q3pEszkPBuHM0tFL8CY=
+modernc.org/sqlite v1.61.0/go.mod h1:f4gr5tbpx2umklaT/QVtbi/50hNdM+4ng+2zMo8KXJ0=
 modernc.org/strutil v1.2.1 h1:UneZBkQA+DX2Rp35KcM69cSsNES9ly8mQWD71HKlOA0=
 modernc.org/strutil v1.2.1/go.mod h1:EHkiggD70koQxjVdSBM3JKM7k6L0FbGE5eymy9i3B9A=
 modernc.org/token v1.1.0 h1:Xl7Ap9dKaEs5kLoOQeQmPWevfnk/DM5qcLcYlA8ys6Y=

internal/archive/README.md

@@ -0,0 +1,106 @@
+# internal/archive
+
+Opens one archive as its own filesystem so the ordinary catalogers can run against its contents.
+The archive cataloger task (`internal/task/archive_tasks.go`) drives the recursion; this package
+does everything for a single archive.
+
+## Flow
+
+```
+Extract(ctx, reader, archiveCoordinates, limiter, exclusions) -> *Resolver
+  acquire          read in place if the reader is already seekable, else hold in memory / spill to disk
+  identifyFormat   internal/file.IdentifyArchive first, end-of-central-directory fallback for stub-prefixed zips
+  Resolver.extract every entry -> entryHeader -> Resolver.add (excluded entries are never stored)
+  digestsOf        SHA-1 of the archive itself
+```
+
+`Extract` returns `nil` for content that is not an archive (a bare compression format such as a
+gzipped file that is not a tar counts as not an archive), `ErrDiskLimitReached` when the archive's
+own bytes cannot be placed, and otherwise a `Resolver` whose `Cleanup` releases everything.
+
+## Resolver
+
+One type does the work: `Resolver` is fed entries by `Extract`, holds their content, indexes them,
+and implements `file.Resolver` over the result. Each entry is a `node` carrying its header and a
+`blob`; the archive's own bytes, when they have to be held at all, are one more blob.
+
+Every location it returns extends the archive's coordinates: `RealPath` and `FileSystemID` stay
+those of the outermost archive on the scanned filesystem, and `FullPath` is the `!/`-delimited
+chain down to the entry (`/app.war!/WEB-INF/lib/dep.jar!/META-INF/MANIFEST.MF`). `LocalPath` is the
+entry's path within this archive.
+
+## Where bytes live
+
+Blobs are held in memory while the memory limit admits them and in one spill file per archive
+(`archive-spill-*`) once it does not; when a chunk is refused, everything held in memory moves to
+the file first. The file is created on first use, so most archives never touch the filesystem, and
+blobs are located in it by offset with no framing of their own. It goes under the scan's temp root
+when the context carries one (`internal/tmpdir`), otherwise the system temp directory.
+
+Anything already random-access (an `*os.File`, or a nested archive read out of its parent's
+resolver) is used in place and costs nothing, so only a top-level stream is ever copied. Its memory
+is refunded once it is extracted and digested; bytes it spilled wait for `Cleanup` with the entries.
+
+## Limits
+
+`Limits` bound what one scan holds *at once*; each falls as archives are released. For both limits,
+positive is the bound, zero forbids the resource, negative is unbounded.
+
+- `Limiter` is scan-wide; a `charge` is one archive's draw on it. Bytes are charged as they land,
+  never from declared sizes.
+- Memory refused → content moves to disk. Disk refused → the archive's own bytes cannot be placed
+  (`ErrDiskLimitReached`, archive skipped) or an entry cannot be stored (`Resolver.Truncated`, the
+  entries stored so far are still cataloged).
+- Index bookkeeping is approximated as `approxIndexBytesPerEntry` (2 KiB) per node, listed or
+  implied by an entry's path, plus name length. It lives in memory, so it is charged to the memory
+  limit, spilling held content to make room; only a zero memory limit lets it fall back to the disk
+  budget so that configuration still indexes. An entry whose index cost is refused is dropped like
+  one whose content is, and marks the resolver `Truncated`.
+- `Budget` bounds the bytes decompressed under one top-level archive, summed over everything nested
+  in it. Unlike `Limits` it never refills, so a recursive bomb whose every level fits the limits
+  still ends (`errBudgetSpent`, the resolver is `Truncated`).
+- `Limiter.Peak` reports the most held at once over the scan, for reporting.
+
+## Hostile archives
+
+Nothing an archive declares is trusted. Content is charged chunk by chunk as it decompresses, so a
+deflate or gzip bomb stops at the disk limit with the entry dropped whole. Every node is charged
+against the memory limit, including directories implied by deep paths, so an archive of millions of
+tiny entries or of a few entries with 4 KiB names stops at the memory limit. A recursive bomb stops
+at the `Budget`. Names longer than PATH_MAX are refused, and nesting stops at the task's `MaxDepth`.
+See the bomb tests in `extract_test.go`.
+
+## Lookup
+
+Entries are indexed in a stereoscope `filetree.FileTree` + `filetree.Index` and searched with
+`filetree.SearchContext`, the same index the directory and image resolvers use. A query may name an
+entry by its full path or by its `LocalPath` (leading slash optional); a full path into another
+archive in the scan names nothing. Directories implied by entry paths exist for `HasPath` but are
+never files. The last entry at a path wins over earlier
+duplicates, as it does on extraction; a file and a directory at one path keep the first.
+
+Links resolve inside the archive only, as the file tree resolves them: a hard link names its target
+from the archive root. A lookup matching a link and its target returns one location, with
+`AccessPath` the full path matched and `FullPath` that of the file read. Dangling and cyclic links are not
+files. `AllLocations` enumerates every non-directory path, links included. Answers are sorted by path.
+
+## Other pieces
+
+- `Exclusions`: the scan's exclusion patterns, of which only the `**/` shape means the same thing
+  re-rooted at an archive. Matched against each entry path and its parent directories at extraction
+  time. `syft.CreateSBOM` passes the source's patterns to the task, which builds one `Exclusions`
+  for the scan.
+- `Traversal`: put on the context by the task so a cataloger (java) knows which archive it is inside,
+  what its digests are, and which packages describe its parent. `VirtualPath(location)` converts a
+  location's `FullPath` to the java cataloger's colon-delimited `app.war:WEB-INF/lib/inner.jar`
+  form, escaping `%` and `:` in entry names. `Container` and `EntryCoordinates` split and build the
+  coordinates of files within archives (the SPDX and CycloneDX formats use them too); `OwnerContainers` and
+  `OwnedCoordinates` map package-owned file paths to coordinates in the right archive.
+- `WithNestedCataloging` / `NestedCatalogingEnabled`: `syft.CreateSBOM` marks the context when the
+  archive task is running, so the java cataloger leaves nested archives to the task instead of
+  opening them itself.
+- `entryHeader`: keeps regular files, directories and links only (no devices or fifos), cleans entry names to
+  archive-relative paths, refuses names longer than PATH_MAX or containing control characters, line
+  separators or the `!/` archive path separator (marking the resolver truncated), and drops header
+  fields nothing reads (PAX records, user and group names, sub-second and access times) since the
+  header is held for the life of the archive.

internal/archive/exclusions.go

@@ -0,0 +1,38 @@
+package archive
+
+import (
+	"strings"
+
+	"github.com/bmatcuk/doublestar/v4"
+)
+
+// Exclusions are the scan's exclusion patterns that apply inside archives.
+//
+// A scan accepts three pattern shapes: `./x` anchored at the scan root, `*/x` exactly one level below
+// it, and `**/x` at any depth. Only the last means the same thing when re-rooted at an archive, so
+// only it reaches inside one.
+type Exclusions []string
+
+func NewExclusions(scanPatterns []string) Exclusions {
+	var out Exclusions
+	for _, pattern := range scanPatterns {
+		if strings.HasPrefix(pattern, "**/") {
+			// a trailing slash reads as "a directory" but makes doublestar match nothing (issue #4839)
+			out = append(out, strings.TrimSuffix(pattern, "/"))
+		}
+	}
+	return out
+}
+
+// Excludes reports whether an archive-relative path, or any directory above it, matches a pattern.
+// Directories are checked because an archive need not list a directory before the files in it.
+func (e Exclusions) Excludes(entryPath string) bool {
+	for _, pattern := range e {
+		for end := len(entryPath); end > 0; end = strings.LastIndexByte(entryPath[:end], '/') {
+			if matched, _ := doublestar.Match(pattern, entryPath[:end]); matched {
+				return true
+			}
+		}
+	}
+	return false
+}

internal/archive/exclusions_test.go

@@ -0,0 +1,56 @@
+package archive
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestNewExclusions(t *testing.T) {
+	tests := []struct {
+		name  string
+		given []string
+		want  Exclusions
+	}{
+		{name: "nothing configured"},
+		{name: "root-anchored does not reach inside", given: []string{"./nested/marker.txt"}},
+		{name: "one level down is anchored too", given: []string{"*/vendor"}},
+		{name: "any depth reaches inside", given: []string{"**/*.rpm"}, want: Exclusions{"**/*.rpm"}},
+		{name: "mixed keeps only the any-depth patterns", given: []string{"./a", "**/b", "*/c", "**/d"}, want: Exclusions{"**/b", "**/d"}},
+		// a trailing slash makes doublestar match nothing (issue #4839)
+		{name: "a trailing slash is trimmed", given: []string{"**/vendor/"}, want: Exclusions{"**/vendor"}},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			assert.Equal(t, tt.want, NewExclusions(tt.given))
+		})
+	}
+}
+
+func TestExclusions_Excludes(t *testing.T) {
+	exclusions := NewExclusions([]string{"**/vendor", "**/*.rpm"})
+
+	tests := []struct {
+		path string
+		want bool
+	}{
+		{"vendor", true},
+		{"a/vendor", true},
+		{"vendor/x/y.go", true},
+		{"a/vendor/y.go", true},
+		{"pkg.rpm", true},
+		{"deep/down/pkg.rpm", true},
+		{"keep/vendored.txt", false},
+		{"vendor-ish", false},
+		{"keep.txt", false},
+		{"PKG.RPM", false},
+	}
+	for _, tt := range tests {
+		t.Run(tt.path, func(t *testing.T) {
+			assert.Equal(t, tt.want, exclusions.Excludes(tt.path))
+		})
+	}
+
+	assert.False(t, NewExclusions(nil).Excludes("anything"))
+	assert.False(t, Exclusions{"["}.Excludes("keep.txt"), "a malformed pattern excludes nothing")
+}

internal/archive/extract.go

@@ -0,0 +1,263 @@
+package archive
+
+import (
+	"bytes"
+	"context"
+	"crypto"
+	"errors"
+	"fmt"
+	"io"
+	"path"
+
+	"github.com/mholt/archives"
+
+	"github.com/anchore/syft/internal"
+	intFile "github.com/anchore/syft/internal/file"
+	"github.com/anchore/syft/internal/log"
+	"github.com/anchore/syft/syft/file"
+)
+
+// ErrUnsupportedFormat is returned for an archive in a format that is not extracted (see supportedExtractor).
+var ErrUnsupportedFormat = errors.New("archive format is not supported")
+
+// Extract opens the archive read from r as its own filesystem, holding its bytes and entries within
+// the limiter's bounds. It returns nil when the content is not an archive, ErrUnsupportedFormat when it
+// is one that is not extracted, and ErrDiskLimitReached when the archive's own bytes cannot be placed
+// within the disk limit. The caller must Cleanup the result.
+//
+// archiveCoordinates are those of the archive file itself; every location the resolver returns
+// extends them with its entry path (see file.Coordinates).
+func Extract(ctx context.Context, r io.Reader, archiveCoordinates file.Coordinates, limiter *Limiter, exclusions Exclusions) (*Resolver, error) {
+	charge := limiter.charge()
+	resolver := newResolver(ctx, archiveCoordinates, charge)
+	archivePath := archiveCoordinates.FullNestedPath()
+
+	// deferred so that a panic in a decoder still gives back the charge and removes any spill file
+	succeeded := false
+	defer func() {
+		if !succeeded {
+			resolver.Cleanup()
+		}
+	}()
+
+	content, release, err := resolver.acquire(r)
+	if err != nil {
+		return nil, err
+	}
+	// the archive's own bytes are needed only until they are extracted and digested
+	defer release()
+
+	format, err := identifyFormat(ctx, path.Base(archiveCoordinates.LocalPath()), content)
+	if format == nil || err != nil {
+		return nil, err
+	}
+
+	if err := resolver.extract(ctx, format, content, exclusions); err != nil {
+		return nil, fmt.Errorf("unable to extract archive %q: %w", archivePath, err)
+	}
+	resolver.Digests = digestsOf(ctx, content, archivePath)
+	succeeded = true
+	return resolver, nil
+}
+
+// acquire makes the archive's own bytes random-access, which identifying, extracting and digesting
+// them needs. Bytes that already are, such as a file on disk or an entry of a parent archive, are
+// read in place and cost nothing. Anything else is held within the limits like an entry, and the
+// returned release gives back what memory it takes; bytes spilled to disk stay until Cleanup.
+// Reaching the disk limit yields ErrDiskLimitReached.
+func (r *Resolver) acquire(content io.Reader) (ReaderAtSeeker, func(), error) {
+	if ras, ok := content.(ReaderAtSeeker); ok {
+		return ras, func() {}, nil
+	}
+	var b blob
+	if err := r.put(&b, content); err != nil {
+		if errors.Is(err, ErrDiskLimitReached) {
+			return nil, nil, err
+		}
+		return nil, nil, fmt.Errorf("unable to read archive content: %w", err)
+	}
+	return r.open(&b), func() { r.discard(&b) }, nil
+}
+
+// identifyFormat returns the format able to extract this content, or nil when it is not an archive.
+//
+// Identification from the head of the stream wins: a tar holding one jar ends in that jar's central
+// directory, and reading the tar as a zip would lose the rest. The end of the stream is consulted
+// only when the head identifies nothing supported, which is how a zip appended to a launcher script (a
+// Spring Boot executable jar) is found, and how a java resource adapter (a zip named .rar) is read.
+func identifyFormat(ctx context.Context, name string, content ReaderAtSeeker) (archives.Extractor, error) {
+	if _, err := content.Seek(0, io.SeekStart); err != nil {
+		return nil, nil
+	}
+	format, _, err := intFile.IdentifyArchive(ctx, name, content)
+	if err == nil {
+		if extractor := supportedExtractor(format); extractor != nil {
+			return extractor, nil
+		}
+	}
+	if HasZipEndOfCentralDirectory(content) {
+		return archives.Zip{}, nil
+	}
+	if err == nil && holdsFiles(format) {
+		return nil, fmt.Errorf("%w: %s", ErrUnsupportedFormat, format.MediaType())
+	}
+	return nil, nil
+}
+
+// holdsFiles reports whether the format is an archive of files rather than a bare compression format,
+// such as a gzipped man page, which holds one stream and is not cataloged as an archive.
+func holdsFiles(format archives.Format) bool {
+	switch f := format.(type) {
+	case archives.CompressedArchive:
+		return f.Extraction != nil
+	case archives.Extractor:
+		return true
+	}
+	return false
+}
+
+// supportedExtractor admits only the zip and tar families, the tar family optionally compressed. Other
+// formats mholt identifies, such as 7z and rar, pull in decoders that have not been exercised against
+// untrusted input here, so they are not opened until they are deliberately supported. A bare
+// compression format, such as a gzipped file that is not a tar, is not extractable either.
+func supportedExtractor(format archives.Format) archives.Extractor {
+	switch f := format.(type) {
+	case archives.Zip:
+		return f
+	case archives.Tar:
+		return f
+	case archives.CompressedArchive:
+		if _, ok := f.Extraction.(archives.Tar); ok {
+			return f
+		}
+	}
+	return nil
+}
+
+// extract adds every entry of the archive. Reaching the disk limit stops the walk and marks the
+// resolver truncated rather than failing.
+func (r *Resolver) extract(ctx context.Context, format archives.Extractor, content ReaderAtSeeker, exclusions Exclusions) error {
+	if _, err := content.Seek(0, io.SeekStart); err != nil {
+		return err
+	}
+	var source io.Reader = content
+	if ca, ok := format.(archives.CompressedArchive); ok && ca.Compression != nil {
+		// a compressed tar decompresses everything to reach each header, including entries skipped whole
+		// and whatever an entry leaves unread, so the budget is charged for every byte the decoder
+		// produces rather than for what is kept. A zip or a plain tar seeks past what it skips
+		rc, err := ca.OpenReader(content)
+		if err != nil {
+			return err
+		}
+		defer internal.CloseAndLogError(rc, "decompressor")
+		source, format, r.metered = &meteredReader{ctx: ctx, reader: rc, budget: r.budget}, ca.Extraction, true
+	}
+	err := format.Extract(ctx, source, func(_ context.Context, f archives.FileInfo) error {
+		hdr, ok := r.entryHeader(f)
+		if !ok || exclusions.Excludes(hdr.Name) {
+			return nil
+		}
+		if !f.Mode().IsRegular() {
+			return r.add(hdr, nil)
+		}
+		entry, err := f.Open()
+		if err != nil {
+			log.WithFields("entry", hdr.Name, "error", err).Trace("unable to open archive entry, skipping it")
+			return nil
+		}
+		defer func() {
+			if err := entry.Close(); err != nil {
+				log.WithFields("entry", hdr.Name, "error", err).Trace("unable to close archive entry")
+			}
+		}()
+		return r.add(hdr, entry)
+	})
+	r.finish()
+	if errors.Is(err, ErrDiskLimitReached) {
+		r.truncate(fmt.Errorf("extraction stopped: %w", err))
+		return nil
+	}
+	if errors.Is(err, errBudgetSpent) {
+		r.truncate(fmt.Errorf("extraction stopped, possible decompression bomb: %w", err))
+		return nil
+	}
+	if err != nil && ctx.Err() == nil && r.entries > 0 {
+		// the stream broke partway (a truncated .tar.gz); what was read before that is still good
+		r.truncate(fmt.Errorf("extraction stopped early: %w", err))
+		return nil
+	}
+	return err
+}
+
+// archiveDigestHashes are the digests taken of an archive as a whole: SHA-1, matching what the java
+// cataloger reports for a jar.
+var archiveDigestHashes = []crypto.Hash{crypto.SHA1}
+
+// digestsOf digests the archive's own bytes while they are in hand. A failure is logged and returns
+// nothing rather than discarding an archive that extracted fine.
+func digestsOf(ctx context.Context, content ReaderAtSeeker, archivePath string) []file.Digest {
+	if _, err := content.Seek(0, io.SeekStart); err != nil {
+		log.WithFields("archive", archivePath, "error", err).Trace("unable to rewind archive content for digests")
+		return nil
+	}
+	digests, err := intFile.NewDigestsFromFile(ctx, io.NopCloser(content), archiveDigestHashes)
+	if err != nil {
+		log.WithFields("archive", archivePath, "error", err).Trace("unable to digest archive")
+		return nil
+	}
+	return digests
+}
+
+var (
+	// zipLocalFileHeaderSignature starts every entry in a zip.
+	zipLocalFileHeaderSignature = []byte{'P', 'K', 0x03, 0x04}
+
+	// zipEOCDSignature starts the end-of-central-directory record that closes every zip. Readers
+	// locate the central directory from it, which is why a zip with data prepended still opens.
+	zipEOCDSignature = []byte{'P', 'K', 0x05, 0x06}
+)
+
+const (
+	// maxAppendedArchiveStubBytes is how far into a file an appended zip's first entry is looked for. A
+	// Spring Boot launcher stub is about 9 KB.
+	maxAppendedArchiveStubBytes = 64 * 1024
+
+	// maxZipEOCDSearch is how far from the end the end-of-central-directory record can start: the 22
+	// byte record plus a comment of up to 65535 bytes.
+	maxZipEOCDSearch = 22 + 65535
+)
+
+// MayHideAnAppendedArchive reports whether a zip entry signature appears in the head of the stream,
+// which a zip appended to a launcher stub does and a file that merely has an archive's extension
+// almost never does. The returned reader replays what was consumed.
+func MayHideAnAppendedArchive(r io.Reader) (io.Reader, bool) {
+	head := make([]byte, maxAppendedArchiveStubBytes)
+	n, err := io.ReadFull(r, head)
+	if err != nil && !errors.Is(err, io.EOF) && !errors.Is(err, io.ErrUnexpectedEOF) {
+		return r, false
+	}
+	head = head[:n]
+	found := bytes.Contains(head, zipLocalFileHeaderSignature)
+
+	if seeker, ok := r.(io.Seeker); ok {
+		if _, err := seeker.Seek(0, io.SeekStart); err == nil {
+			return r, found
+		}
+	}
+	return io.MultiReader(bytes.NewReader(head), r), found
+}
+
+// HasZipEndOfCentralDirectory reports whether the content ends in a zip end-of-central-directory
+// record, the one part of a zip whose position is known without parsing it.
+func HasZipEndOfCentralDirectory(r ReaderAtSeeker) bool {
+	size, err := r.Seek(0, io.SeekEnd)
+	if err != nil || size < int64(len(zipEOCDSignature)) {
+		return false
+	}
+	window := min(size, int64(maxZipEOCDSearch))
+	buf := make([]byte, window)
+	if _, err := r.ReadAt(buf, size-window); err != nil && !errors.Is(err, io.EOF) {
+		return false
+	}
+	return bytes.Contains(buf, zipEOCDSignature)
+}

internal/archive/extract_test.go

@@ -0,0 +1,706 @@
+package archive
+
+import (
+	"archive/tar"
+	"archive/zip"
+	"bytes"
+	"compress/gzip"
+	"context"
+	"fmt"
+	"io"
+	"io/fs"
+	"math/rand"
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"github.com/mholt/archives"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	stereoscopeFile "github.com/anchore/stereoscope/pkg/file"
+	"github.com/anchore/syft/syft/file"
+)
+
+var sampleFiles = map[string]string{
+	"file1.txt":     "content1",
+	"dir/file2.txt": "content2",
+}
+
+func Test_identifyFormat(t *testing.T) {
+	ctx := context.Background()
+	launcher := append([]byte("#!/bin/bash\nexec java -jar \"$0\" \"$@\"\nexit 0\n"), zipBytes(t, sampleFiles)...)
+
+	tests := []struct {
+		name        string
+		data        []byte
+		want        archives.Extractor
+		unsupported bool
+	}{
+		{"test.zip", zipBytes(t, sampleFiles), archives.Zip{}, false},
+		{"test.tar.gz", tarGzBytes(t, sampleFiles), archives.CompressedArchive{}, false},
+		{"plain.txt", []byte("just text"), nil, false},
+		// identified by mholt, but not opened until their decoders are deliberately supported
+		{"test.7z", []byte("7z\xbc\xaf\x27\x1c\x00\x04"), nil, true},
+		{"test.rar", []byte("Rar!\x1a\x07\x01\x00"), nil, true},
+		// a bare compression format holds one stream, not files
+		{"page.1.gz", gzBytes(t, "a man page"), nil, false},
+		// a java resource adapter archive is a zip that shares rar's extension
+		{"adapter.rar", zipBytes(t, sampleFiles), archives.Zip{}, false},
+		// the name can be claimed by identification, so the probe alone must not admit prose
+		{"app.jar", []byte("plain text, no central directory anywhere in it"), nil, false},
+		{"bundle", []byte("plain text, no central directory anywhere in it"), nil, false},
+		// content sniffing types this as a shell script; only its tail says zip
+		{"app.jar", launcher, archives.Zip{}, false},
+	}
+	for _, tt := range tests {
+		t.Run(fmt.Sprintf("%s/%d bytes", tt.name, len(tt.data)), func(t *testing.T) {
+			got, err := identifyFormat(ctx, tt.name, bytes.NewReader(tt.data))
+			if tt.unsupported {
+				assert.ErrorIs(t, err, ErrUnsupportedFormat)
+			} else {
+				assert.NoError(t, err)
+			}
+			if tt.want == nil {
+				assert.Nil(t, got)
+				return
+			}
+			assert.IsType(t, tt.want, got)
+		})
+	}
+}
+
+func TestResolver_extract_storesEveryEntryInMemoryWhenUnbounded(t *testing.T) {
+	for name, data := range map[string][]byte{
+		"test.zip":    zipBytes(t, sampleFiles),
+		"test.tar.gz": tarGzBytes(t, sampleFiles),
+	} {
+		t.Run(name, func(t *testing.T) {
+			r, root := extractBytes(t, data, name, nil)
+			assert.NoError(t, r.Truncated)
+			assert.Zero(t, r.written)
+			assert.Empty(t, filesIn(t, root))
+
+			entries := readStore(t, r)
+			assert.Equal(t, "content1", entries["file1.txt"].body)
+			assert.Equal(t, "content2", entries["dir/file2.txt"].body)
+		})
+	}
+}
+
+func TestResolver_extract_diskLimitTruncatesAtTheEntryThatDoesNotFit(t *testing.T) {
+	// each entry costs its index estimate plus its content on disk
+	record := approxIndexBytes(tar.Header{Name: "file1.txt"})
+	data := zipBytes(t, map[string]string{"file1.txt": "a", "file2.txt": "b", "file3.txt": "c"})
+
+	r, _ := extractBytes(t, data, "test.zip", diskCharge(2*(record+1)+record))
+
+	assert.Error(t, r.Truncated)
+	assert.Equal(t, []string{"file1.txt", "file2.txt"}, storedNames(t, r), "the refused entry is not stored")
+	entries := readStore(t, r)
+	assert.Equal(t, "a", entries["file1.txt"].body)
+	assert.Equal(t, "b", entries["file2.txt"].body)
+}
+
+func TestResolver_extract_diskLimitBitesMidEntry(t *testing.T) {
+	// a tar is walked entry by entry, so the limit can bite part way through an entry
+	data := tarGzBytes(t, map[string]string{
+		"a/first.txt":  strings.Repeat("a", 40*1024),
+		"b/second.txt": strings.Repeat("b", 40*1024),
+	})
+	const budget = 80 * 1024
+	charge := diskCharge(budget)
+
+	r, root := extractBytes(t, data, "test.tar.gz", charge)
+
+	assert.Error(t, r.Truncated)
+	assert.Equal(t, []string{"a", "a/first.txt", "b"}, storedNames(t, r), "the directory a refused entry implied stays")
+	assert.Greater(t, r.written, int64(40*1024), "the first entry landed whole and the second part way")
+	_, disk := charge.held()
+	assert.LessOrEqual(t, disk, int64(budget))
+	assert.Greater(t, disk, r.written, "the index estimate is charged to disk too")
+
+	info, err := os.Stat(filepath.Join(root, spillFile(t, root)))
+	require.NoError(t, err)
+	assert.Equal(t, r.written, info.Size())
+}
+
+func TestResolver_extract_directoryOnlyArchivesAreBoundedByTheIndexEstimate(t *testing.T) {
+	var entries []testEntry
+	for i := range 50 {
+		entries = append(entries, testEntry{name: fmt.Sprintf("d%04d/", i), dir: true})
+	}
+	room := approxIndexBytes(tar.Header{Name: "d0000"}) * 10
+
+	for name, data := range map[string][]byte{
+		"dirs.zip":    zipFromEntries(t, entries),
+		"dirs.tar.gz": tarGzFromEntries(t, entries),
+	} {
+		t.Run(name, func(t *testing.T) {
+			r, _ := extractBytes(t, data, name, diskCharge(room))
+			assert.Error(t, r.Truncated)
+			assert.Len(t, storedNames(t, r), 10)
+		})
+	}
+}
+
+func TestResolver_extract_entryNamesAreCleanedAndNothingIsWrittenUnderThem(t *testing.T) {
+	entries := []testEntry{
+		{name: "../../etc/passwd", body: "evil"},
+		{name: "/etc/hosts", body: "pwned"},
+		{name: "META-INF/", dir: true, mode: 0o555},
+		{name: "META-INF/MANIFEST.MF", body: "Manifest-Version: 1.0"},
+		{name: "passwd", link: "../../../../etc/passwd"},
+		{name: "shadow", link: "/etc/shadow"},
+		{name: "bin/link.txt", link: "../lib/real.txt"},
+	}
+
+	for name, data := range map[string][]byte{
+		"evil.zip":    zipFromEntries(t, entries),
+		"evil.tar.gz": tarGzFromEntries(t, entries),
+	} {
+		t.Run(name, func(t *testing.T) {
+			r, root := extractBytes(t, data, name, nil)
+			require.NoError(t, r.Truncated)
+
+			assert.Equal(t, []string{"META-INF", "META-INF/MANIFEST.MF", "bin", "bin/link.txt", "etc", "etc/hosts", "etc/passwd", "passwd", "shadow"},
+				storedNames(t, r))
+			assert.Empty(t, filesIn(t, root), "entries live in the store, never under their own names")
+			assert.NoFileExists(t, filepath.Join(t.TempDir(), "..", "etc", "passwd"))
+
+			got := readStore(t, r)
+			assert.Equal(t, "evil", got["etc/passwd"].body)
+			assert.Equal(t, "pwned", got["etc/hosts"].body)
+			assert.Equal(t, stereoscopeFile.TypeDirectory, got["META-INF"].kind)
+			assert.Equal(t, fs.FileMode(0o555), got["META-INF"].mode.Perm())
+			assert.Equal(t, "Manifest-Version: 1.0", got["META-INF/MANIFEST.MF"].body)
+
+			// links are headers carrying their target verbatim; the index resolves them inside the archive
+			for _, link := range []string{"passwd", "shadow", "bin/link.txt"} {
+				assert.Equal(t, stereoscopeFile.TypeSymLink, got[link].kind)
+				assert.Empty(t, got[link].body)
+			}
+			assert.Equal(t, "../../../../etc/passwd", got["passwd"].linkTarget)
+			assert.Equal(t, "/etc/shadow", got["shadow"].linkTarget)
+			assert.Equal(t, "../lib/real.txt", got["bin/link.txt"].linkTarget)
+		})
+	}
+}
+
+func TestResolver_extract_dataEdgeCases(t *testing.T) {
+	t.Run("an empty archive is not an error", func(t *testing.T) {
+		r, _ := extractBytes(t, zipBytes(t, map[string]string{}), "test.zip", nil)
+		assert.Zero(t, r.entries)
+		assert.NoError(t, r.Truncated)
+	})
+
+	t.Run("a zero-byte entry costs no disk", func(t *testing.T) {
+		r, _ := extractBytes(t, zipBytes(t, map[string]string{"empty.txt": ""}), "test.zip", memCharge(0))
+		assert.Equal(t, []string{"empty.txt"}, storedNames(t, r))
+		assert.Zero(t, r.written)
+		assert.Empty(t, readStore(t, r)["empty.txt"].body)
+	})
+
+	t.Run("unicode entry names survive", func(t *testing.T) {
+		names := map[string]string{
+			"café/naïve.txt": "accents",
+			"日本語/ファイル.txt":   "japanese",
+			"emoji-🎉.txt":    "emoji",
+		}
+		r, _ := extractBytes(t, zipBytes(t, names), "test.zip", nil)
+		entries := readStore(t, r)
+		for name, want := range names {
+			assert.Equal(t, want, entries[name].body, name)
+		}
+	})
+
+	t.Run("an entry name with too many path components is skipped and reported", func(t *testing.T) {
+		atCap := strings.Repeat("a/", maxEntryNameDepth-1) + "f"
+		data := zipBytes(t, map[string]string{
+			atCap: "at the cap",
+			strings.Repeat("b/", maxEntryNameDepth) + "f": "over the cap",
+		})
+		r, _ := extractBytes(t, data, "test.zip", nil)
+		names := storedNames(t, r)
+		assert.Contains(t, names, atCap)
+		assert.Len(t, names, maxEntryNameDepth, "only the entry at the cap and its implied directories")
+		assert.ErrorContains(t, r.Truncated, "path components")
+	})
+
+	t.Run("an entry whose chain is longer than a path is skipped and reported", func(t *testing.T) {
+		// the chain is the archive's own path, the separator, then the name
+		fits := strings.Repeat("a", MaxPathBytes-len("test-archive!/"))
+		data := zipBytes(t, map[string]string{
+			fits:       "at the cap",
+			fits + "b": "over the cap",
+		})
+		r, _ := extractBytes(t, data, "test.zip", nil)
+		assert.Equal(t, []string{fits}, storedNames(t, r))
+		assert.ErrorContains(t, r.Truncated, "archive chain")
+	})
+
+	t.Run("an over-long entry name is skipped", func(t *testing.T) {
+		data := zipBytes(t, map[string]string{
+			strings.Repeat("a/", maxEntryNameBytes) + "f": "deep",
+			"ok.txt": "fine",
+		})
+		r, _ := extractBytes(t, data, "test.zip", nil)
+		assert.Equal(t, []string{"ok.txt"}, storedNames(t, r))
+	})
+}
+
+func TestResolver_extract_unsafeEntryNamesAreRefusedAndReported(t *testing.T) {
+	jar := string(zipBytes(t, map[string]string{"META-INF/MANIFEST.MF": "real"}))
+	tests := []struct {
+		name   string
+		forged string
+	}{
+		{name: "archive path separator", forged: "a.jar!/META-INF/MANIFEST.MF"},
+		{name: "line break", forged: "x\nlayerID: sha256:forged"},
+		{name: "unicode line separator", forged: "x\u2028y"},
+		{name: "C1 control", forged: "x\u0085y"},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			data := zipBytes(t, map[string]string{"a.jar": jar, tt.forged: "forged"})
+			r, _ := extractBytes(t, data, "outer.zip", nil)
+			assert.Equal(t, []string{"a.jar"}, storedNames(t, r))
+			require.Error(t, r.Truncated)
+			assert.Contains(t, r.Truncated.Error(), fmt.Sprintf("%q", tt.forged))
+		})
+	}
+}
+
+func TestResolver_extract_excludedEntriesAreNeverStored(t *testing.T) {
+	data := zipBytes(t, map[string]string{
+		"keep.txt":          "kept",
+		"vendor/lib.go":     "excluded by directory",
+		"deep/down/pkg.rpm": "excluded by name",
+	})
+	limiter := NewLimiter(Limits{MaxMemoryBytes: 1 << 20, MaxDiskBytes: -1})
+	r, _ := resolverIn(t, limiter.charge())
+	content := bytes.NewReader(data)
+
+	format, err := identifyFormat(context.Background(), "test.zip", content)
+	require.NoError(t, err)
+	err = r.extract(context.Background(), format, content,
+		NewExclusions([]string{"**/vendor", "**/*.rpm"}))
+	require.NoError(t, err)
+	require.NoError(t, r.Truncated)
+
+	assert.Equal(t, []string{"keep.txt"}, storedNames(t, r))
+	mem, _ := limiter.InUse()
+	assert.Equal(t, approxIndexBytes(tar.Header{Name: "keep.txt"})+4, mem, "an excluded entry costs nothing")
+}
+
+// a compressed tar reader decompresses a skipped entry to reach the next header, so skipping must still
+// spend the budget or an excluded or oversized entry would decompress without bound
+func TestResolver_extract_skippedCompressedTarBytesSpendTheBudget(t *testing.T) {
+	big := strings.Repeat("\x00", 4<<20)
+	tests := []struct {
+		name       string
+		exclusions []string
+		entryCap   int64
+	}{
+		{name: "excluded entry", exclusions: []string{"**/*.bin"}, entryCap: maxEntryBytes},
+		{name: "entry over the size cap", entryCap: 1 << 10},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			defer func(prev int64) { maxEntryBytes = prev }(maxEntryBytes)
+			maxEntryBytes = tt.entryCap
+
+			data := tarGzFromEntries(t, []testEntry{{name: "bomb.bin", body: big}, {name: "after.txt", body: "after"}})
+			r, _ := resolverIn(t, memCharge(1<<30))
+			r.budget = NewBudget(1 << 20)
+			content := bytes.NewReader(data)
+			format, err := identifyFormat(context.Background(), "test.tar.gz", content)
+			require.NoError(t, err)
+
+			require.NoError(t, r.extract(context.Background(), format, content, NewExclusions(tt.exclusions)))
+			require.Error(t, r.Truncated)
+			assert.Empty(t, storedNames(t, r), "the walk stopped at the entry that spent the budget")
+			assert.Zero(t, r.budget.remaining)
+		})
+	}
+}
+
+// a body behind a header that doesn't read as a regular file (here a socket per its mode bits) is never
+// opened, but the tar reader still decompresses it to reach the next header
+func TestResolver_extract_bodiesOfNonRegularTarEntriesSpendTheBudget(t *testing.T) {
+	var buf bytes.Buffer
+	gw := gzip.NewWriter(&buf)
+	tw := tar.NewWriter(gw)
+	body := strings.Repeat("\x00", 4<<20)
+	require.NoError(t, tw.WriteHeader(&tar.Header{Name: "sock", Typeflag: tar.TypeReg, Mode: 0o140644, Size: int64(len(body))}))
+	_, err := tw.Write([]byte(body))
+	require.NoError(t, err)
+	require.NoError(t, tw.WriteHeader(&tar.Header{Name: "after.txt", Typeflag: tar.TypeReg, Mode: 0o644, Size: 5}))
+	_, err = tw.Write([]byte("after"))
+	require.NoError(t, err)
+	require.NoError(t, tw.Close())
+	require.NoError(t, gw.Close())
+
+	r, _ := resolverIn(t, memCharge(1<<30))
+	r.budget = NewBudget(1 << 20)
+	content := bytes.NewReader(buf.Bytes())
+	format, err := identifyFormat(context.Background(), "test.tar.gz", content)
+	require.NoError(t, err)
+
+	require.NoError(t, r.extract(context.Background(), format, content, nil))
+	assert.ErrorIs(t, r.Truncated, errBudgetSpent)
+	assert.Empty(t, storedNames(t, r))
+	assert.Zero(t, r.budget.remaining)
+}
+
+// a zip or a plain tar seeks past what it skips, so an excluded entry there costs nothing
+func TestResolver_extract_skippedSeekableBytesAreFree(t *testing.T) {
+	entries := []testEntry{{name: "bomb.bin", body: strings.Repeat("\x00", 4<<20)}, {name: "after.txt", body: "after"}}
+	var plainTar bytes.Buffer
+	tw := tar.NewWriter(&plainTar)
+	for _, e := range entries {
+		hdr := e.header()
+		require.NoError(t, tw.WriteHeader(&hdr))
+		_, err := tw.Write([]byte(e.body))
+		require.NoError(t, err)
+	}
+	require.NoError(t, tw.Close())
+
+	for name, data := range map[string][]byte{"test.zip": zipFromEntries(t, entries), "test.tar": plainTar.Bytes()} {
+		t.Run(name, func(t *testing.T) {
+			r, _ := resolverIn(t, memCharge(1<<30))
+			r.budget = NewBudget(1 << 20)
+			content := bytes.NewReader(data)
+			format, err := identifyFormat(context.Background(), name, content)
+			require.NoError(t, err)
+
+			require.NoError(t, r.extract(context.Background(), format, content, NewExclusions([]string{"**/*.bin"})))
+			require.NoError(t, r.Truncated)
+			assert.Equal(t, []string{"after.txt"}, storedNames(t, r))
+		})
+	}
+}
+
+func TestExtract_readsEntriesAndDigestsTheArchive(t *testing.T) {
+	data := zipBytes(t, map[string]string{"dir/hello.txt": "hello world"})
+
+	extracted, err := Extract(context.Background(), bytes.NewReader(data), file.Coordinates{RealPath: "app.war", FileSystemID: "parentFS", FullPath: "app.war!/some/path/app.zip"}, nil, nil)
+	require.NoError(t, err)
+	require.NotNil(t, extracted)
+	t.Cleanup(extracted.Cleanup)
+
+	assert.NoError(t, extracted.Truncated)
+	require.Len(t, extracted.Digests, 1)
+	assert.Equal(t, "sha1", extracted.Digests[0].Algorithm)
+
+	locations, err := extracted.FilesByGlob("**/*.txt")
+	require.NoError(t, err)
+	require.Len(t, locations, 1)
+	assert.Equal(t, file.Coordinates{RealPath: "app.war", FileSystemID: "parentFS", FullPath: "app.war!/some/path/app.zip!/dir/hello.txt"},
+		locations[0].Coordinates)
+
+	reader, err := extracted.FileContentsByLocation(locations[0])
+	require.NoError(t, err)
+	body, err := io.ReadAll(reader)
+	require.NoError(t, err)
+	assert.Equal(t, "hello world", string(body))
+}
+
+func TestExtract_heldContentIsReleasedOnceExtracted(t *testing.T) {
+	// the archive's own bytes are only needed to extract and digest it; afterwards the limiter holds
+	// the entries and the index estimate alone
+	data := zipBytes(t, map[string]string{"hello.txt": "hi"})
+	limiter := NewLimiter(Limits{MaxMemoryBytes: -1, MaxDiskBytes: -1})
+
+	extracted, err := Extract(context.Background(), unseekable{bytes.NewReader(data)}, file.NewCoordinates("app.zip", ""), limiter, nil)
+	require.NoError(t, err)
+	t.Cleanup(extracted.Cleanup)
+
+	mem, disk := limiter.InUse()
+	assert.Equal(t, approxIndexBytes(tar.Header{Name: "hello.txt"})+2, mem)
+	assert.Zero(t, disk)
+}
+
+func TestExtract_heldContentWrittenToDiskStaysUntilCleanup(t *testing.T) {
+	// only a top-level stream is ever held; a nested archive is read out of its parent, which is held
+	// for the whole descent anyway, so spilled bytes wait for Cleanup with the entries
+	ctx, root := scanContext(t)
+	data := zipBytes(t, map[string]string{"hello.txt": "hi"})
+	limiter := NewLimiter(Limits{MaxMemoryBytes: 0, MaxDiskBytes: -1})
+
+	extracted, err := Extract(ctx, unseekable{bytes.NewReader(data)}, file.NewCoordinates("app.zip", ""), limiter, nil)
+	require.NoError(t, err)
+	t.Cleanup(extracted.Cleanup)
+
+	require.Len(t, filesIn(t, root), 1, "the archive's bytes and its entries share one file")
+	_, disk := limiter.InUse()
+	assert.Equal(t, approxIndexBytes(tar.Header{Name: "hello.txt"})+2+int64(len(data)), disk)
+
+	extracted.Cleanup()
+	assert.Empty(t, filesIn(t, root))
+	_, disk = limiter.InUse()
+	assert.Zero(t, disk)
+}
+
+func TestExtract_aTruncatedStreamKeepsWhatWasRead(t *testing.T) {
+	// a .tar.gz cut off partway breaks the stream for every entry after the cut; the ones before it are
+	// still good and must not be thrown away
+	noise := make([]byte, 64*1024)
+	rand.New(rand.NewSource(1)).Read(noise)
+	data := tarGzBytes(t, map[string]string{"a.txt": "first", "b.bin": string(noise)})
+	cut := data[:len(data)/2]
+
+	extracted, err := Extract(context.Background(), bytes.NewReader(cut), file.NewCoordinates("app.tar.gz", ""), NewLimiter(unboundedLimits), nil)
+	require.NoError(t, err)
+	require.NotNil(t, extracted)
+	t.Cleanup(extracted.Cleanup)
+
+	assert.Error(t, extracted.Truncated)
+	locations, err := extracted.FilesByGlob("**")
+	require.NoError(t, err)
+	assert.Equal(t, []string{"/a.txt"}, localPaths(locations))
+}
+
+func TestExtract_aPanicStillReleasesEverything(t *testing.T) {
+	// a decoder panicking on hostile bytes must not leak the charge or the spill file
+	ctx, root := scanContext(t)
+	limiter := NewLimiter(Limits{MaxMemoryBytes: 0, MaxDiskBytes: -1})
+
+	require.Panics(t, func() {
+		_, _ = Extract(ctx, &panicsAfter{n: 4096}, file.NewCoordinates("app.zip", ""), limiter, nil)
+	})
+
+	mem, disk := limiter.InUse()
+	assert.Zero(t, mem)
+	assert.Zero(t, disk)
+	assert.Empty(t, filesIn(t, root))
+}
+
+// panicsAfter hands out n zero bytes, then panics.
+type panicsAfter struct{ n int }
+
+func (p *panicsAfter) Read(b []byte) (int, error) {
+	if p.n <= 0 {
+		panic("decoder blew up")
+	}
+	n := min(len(b), p.n)
+	clear(b[:n])
+	p.n -= n
+	return n, nil
+}
+
+func TestExtract_archiveBytesThatCannotBePlacedAreSkipped(t *testing.T) {
+	data := zipBytes(t, sampleFiles)
+	limiter := NewLimiter(Limits{MaxMemoryBytes: 0, MaxDiskBytes: 0})
+
+	_, err := Extract(context.Background(), unseekable{bytes.NewReader(data)}, file.NewCoordinates("app.zip", ""), limiter, nil)
+	assert.ErrorIs(t, err, ErrDiskLimitReached)
+
+	// read in place, the same bytes cost nothing; only the entries are refused
+	extracted, err := Extract(context.Background(), bytes.NewReader(data), file.NewCoordinates("app.zip", ""), limiter, nil)
+	require.NoError(t, err)
+	require.NotNil(t, extracted)
+	t.Cleanup(extracted.Cleanup)
+	assert.Error(t, extracted.Truncated)
+	locations, err := extracted.FilesByGlob("**/*")
+	require.NoError(t, err)
+	assert.Empty(t, locations)
+}
+
+func Test_HasZipEndOfCentralDirectory(t *testing.T) {
+	tests := []struct {
+		name string
+		data []byte
+		want bool
+	}{
+		{"a plain zip", zipBytes(t, sampleFiles), true},
+		{"a zip behind a launcher script", append([]byte("#!/bin/bash\nexit 0\n"), zipBytes(t, sampleFiles)...), true},
+		{"prose", []byte("this is not an archive, it is a sentence"), false},
+		{"a tar.gz", tarGzBytes(t, sampleFiles), false},
+		{"empty", nil, false},
+		{"shorter than the signature", []byte("PK"), false},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			assert.Equal(t, tt.want, HasZipEndOfCentralDirectory(bytes.NewReader(tt.data)))
+		})
+	}
+}
+
+func Test_MayHideAnAppendedArchive(t *testing.T) {
+	launcher := append([]byte("#!/bin/bash\nexit 0\n"), zipBytes(t, sampleFiles)...)
+	prose := []byte("plain text, whatever the extension claims")
+
+	t.Run("a seekable reader is rewound and returned as is", func(t *testing.T) {
+		reader := bytes.NewReader(launcher)
+		got, found := MayHideAnAppendedArchive(reader)
+		assert.True(t, found)
+		assert.Same(t, reader, got)
+		rest, err := io.ReadAll(got)
+		require.NoError(t, err)
+		assert.Equal(t, launcher, rest)
+	})
+
+	t.Run("an unseekable reader replays what was consumed", func(t *testing.T) {
+		got, found := MayHideAnAppendedArchive(unseekable{bytes.NewReader(launcher)})
+		assert.True(t, found)
+		rest, err := io.ReadAll(got)
+		require.NoError(t, err)
+		assert.Equal(t, launcher, rest)
+	})
+
+	t.Run("prose hides nothing", func(t *testing.T) {
+		got, found := MayHideAnAppendedArchive(unseekable{bytes.NewReader(prose)})
+		assert.False(t, found)
+		rest, err := io.ReadAll(got)
+		require.NoError(t, err)
+		assert.Equal(t, prose, rest)
+	})
+}
+
+// zeros is a reader of n zero bytes: the most compressible content there is.
+func zeros(n int64) io.Reader {
+	return io.LimitReader(zeroSource{}, n)
+}
+
+type zeroSource struct{}
+
+func (zeroSource) Read(p []byte) (int, error) {
+	clear(p)
+	return len(p), nil
+}
+
+func TestExtract_decompressionBombIsBoundedByTheLimits(t *testing.T) {
+	// 64 MiB of zeros compresses to a few hundred KiB. The declared size is never trusted: bytes are
+	// charged as they land, so the limits hold whatever the archive claims
+	const inflated = 64 << 20
+	limits := Limits{MaxMemoryBytes: 1 << 20, MaxDiskBytes: 4 << 20}
+
+	var zipBomb bytes.Buffer
+	zw := zip.NewWriter(&zipBomb)
+	w, err := zw.Create("bomb.bin")
+	require.NoError(t, err)
+	_, err = io.Copy(w, zeros(inflated))
+	require.NoError(t, err)
+	require.NoError(t, zw.Close())
+
+	var tarBomb bytes.Buffer
+	gw := gzip.NewWriter(&tarBomb)
+	tw := tar.NewWriter(gw)
+	require.NoError(t, tw.WriteHeader(&tar.Header{Name: "bomb.bin", Mode: 0o644, Size: inflated, Typeflag: tar.TypeReg}))
+	_, err = io.Copy(tw, zeros(inflated))
+	require.NoError(t, err)
+	require.NoError(t, tw.Close())
+	require.NoError(t, gw.Close())
+
+	for name, data := range map[string][]byte{"bomb.zip": zipBomb.Bytes(), "bomb.tar.gz": tarBomb.Bytes()} {
+		t.Run(name, func(t *testing.T) {
+			require.Less(t, len(data), 1<<20, "the fixture must be a bomb: small on disk, huge inflated")
+			ctx, root := scanContext(t)
+			limiter := NewLimiter(limits)
+
+			r, err := Extract(ctx, bytes.NewReader(data), file.NewCoordinates(name, ""), limiter, nil)
+			require.NoError(t, err)
+			require.NotNil(t, r)
+			t.Cleanup(r.Cleanup)
+
+			assert.Error(t, r.Truncated)
+			locations, err := r.FilesByGlob("**/*")
+			require.NoError(t, err)
+			assert.Empty(t, locations, "the entry that did not fit is not cataloged in part")
+
+			peakMemory, peakDisk := limiter.Peak()
+			assert.LessOrEqual(t, peakMemory, limits.MaxMemoryBytes)
+			assert.LessOrEqual(t, peakDisk, limits.MaxDiskBytes)
+
+			r.Cleanup()
+			assert.Empty(t, filesIn(t, root))
+		})
+	}
+}
+
+func TestExtract_entryCountBombIsBoundedByTheMemoryLimit(t *testing.T) {
+	// every entry is a node in memory whatever the disk limit says, so a tiny archive of many entries
+	// is bounded by the memory limit alone
+	limits := Limits{MaxMemoryBytes: 1 << 20, MaxDiskBytes: -1}
+	limiter := NewLimiter(limits)
+
+	r, err := Extract(context.Background(), bytes.NewReader(manyEntryZip(t, 20_000)), file.NewCoordinates("many.zip", ""), limiter, nil)
+	require.NoError(t, err)
+	t.Cleanup(r.Cleanup)
+
+	assert.Error(t, r.Truncated)
+	assert.Less(t, r.entries, 20_000)
+	assert.LessOrEqual(t, int64(nodeCount(r))*approxIndexBytesPerEntry, limits.MaxMemoryBytes+approxIndexBytesPerEntry,
+		"nodes held must not exceed what the memory limit paid for")
+	peakMemory, _ := limiter.Peak()
+	assert.LessOrEqual(t, peakMemory, limits.MaxMemoryBytes)
+}
+
+func TestExtract_deepPathBombIsBoundedByTheMemoryLimit(t *testing.T) {
+	// 100 entries whose names each imply 250 distinct directories would be 25,000 nodes; the implied
+	// directories are charged as nodes, so the memory limit bounds them too
+	files := map[string]string{}
+	for i := range 100 {
+		var b strings.Builder
+		for j := range maxEntryNameDepth - 6 {
+			fmt.Fprintf(&b, "%03d-%03d/", i, j)
+		}
+		b.WriteString("f")
+		require.LessOrEqual(t, b.Len(), maxEntryNameBytes)
+		files[b.String()] = "x"
+	}
+	limits := Limits{MaxMemoryBytes: 8 << 20, MaxDiskBytes: -1}
+	limiter := NewLimiter(limits)
+
+	r, err := Extract(context.Background(), bytes.NewReader(zipBytes(t, files)), file.NewCoordinates("deep.zip", ""), limiter, nil)
+	require.NoError(t, err)
+	t.Cleanup(r.Cleanup)
+
+	assert.Error(t, r.Truncated)
+	assert.LessOrEqual(t, int64(nodeCount(r))*approxIndexBytesPerEntry, limits.MaxMemoryBytes+approxIndexBytesPerEntry)
+	peakMemory, _ := limiter.Peak()
+	assert.LessOrEqual(t, peakMemory, limits.MaxMemoryBytes)
+}
+
+func TestExtract_locationsKeepTheTopLevelRealPath(t *testing.T) {
+	data := zipBytes(t, map[string]string{"dir/hello.txt": "hello world"})
+
+	// a top-level archive's coordinates, with FullPath unset or set to RealPath, name entries alike
+	for _, archive := range []file.Coordinates{
+		{RealPath: "/app.zip"},
+		{RealPath: "/app.zip", FullPath: "/app.zip"},
+	} {
+		extracted, err := Extract(context.Background(), bytes.NewReader(data), archive, nil, nil)
+		require.NoError(t, err)
+		require.NotNil(t, extracted)
+		t.Cleanup(extracted.Cleanup)
+
+		locations, err := extracted.FilesByPath("dir/hello.txt")
+		require.NoError(t, err)
+		require.Len(t, locations, 1)
+		assert.Equal(t, file.Coordinates{RealPath: "/app.zip", FullPath: "/app.zip!/dir/hello.txt"}, locations[0].Coordinates)
+		assert.Equal(t, "/dir/hello.txt", locations[0].LocalPath())
+
+		for _, loc := range []file.Location{
+			locations[0],
+			file.NewLocation("dir/hello.txt"),
+			file.NewLocation("/dir/hello.txt"),
+			file.NewLocationFromCoordinates(file.Coordinates{RealPath: "/app.zip", FullPath: "/app.zip!/dir/hello.txt"}),
+		} {
+			reader, err := extracted.FileContentsByLocation(loc)
+			require.NoError(t, err, "location %s", loc)
+			body, err := io.ReadAll(reader)
+			require.NoError(t, err)
+			assert.Equal(t, "hello world", string(body))
+
+			metadata, err := extracted.FileMetadataByLocation(loc)
+			require.NoError(t, err, "location %s", loc)
+			assert.Equal(t, "/app.zip!/dir/hello.txt", metadata.Path)
+		}
+
+		_, err = extracted.FileContentsByLocation(file.NewLocationFromCoordinates(file.Coordinates{RealPath: "/other.zip", FullPath: "/other.zip!/dir/hello.txt"}))
+		assert.Error(t, err, "an entry of another archive is not read from this one")
+	}
+}

internal/archive/helpers_test.go

@@ -0,0 +1,344 @@
+package archive
+
+import (
+	"archive/tar"
+	"archive/zip"
+	"bytes"
+	"compress/gzip"
+	"context"
+	"fmt"
+	"io"
+	"io/fs"
+	"os"
+	"sort"
+	"testing"
+
+	"github.com/stretchr/testify/require"
+
+	stereoscopeFile "github.com/anchore/stereoscope/pkg/file"
+	"github.com/anchore/syft/internal/tmpdir"
+	"github.com/anchore/syft/syft/file"
+)
+
+// held reports what this charge is currently holding, in memory and on disk.
+func (c *charge) held() (memory, disk int64) {
+	if c == nil {
+		return 0, 0
+	}
+	c.limiter.mu.Lock()
+	defer c.limiter.mu.Unlock()
+	return c.inMemory, c.onDisk
+}
+
+// heldInMemory reports the content the resolver is still holding in memory.
+func (r *Resolver) heldInMemory() int64 {
+	var total int64
+	for _, b := range r.held {
+		total += int64(len(b.mem))
+	}
+	return total
+}
+
+// unseekable hides a reader's Seek and ReadAt, forcing content through the held path.
+type unseekable struct{ io.Reader }
+
+// testEntry is one entry of a fixture archive: a directory when dir is set, a link when link is set
+// (hard when hard is set, otherwise symbolic), otherwise a regular file.
+type testEntry struct {
+	name string
+	body string
+	link string
+	hard bool
+	dir  bool
+	mode fs.FileMode
+}
+
+// header is the tar header this entry would carry.
+func (e testEntry) header() tar.Header {
+	switch {
+	case e.dir:
+		return tar.Header{Name: e.name, Mode: int64(e.modeOr(0o755)), Typeflag: tar.TypeDir}
+	case e.link != "" && e.hard:
+		return tar.Header{Name: e.name, Mode: 0o644, Typeflag: tar.TypeLink, Linkname: e.link}
+	case e.link != "":
+		return tar.Header{Name: e.name, Mode: 0o777, Typeflag: tar.TypeSymlink, Linkname: e.link}
+	}
+	return tar.Header{Name: e.name, Mode: int64(e.modeOr(0o644)), Size: int64(len(e.body)), Typeflag: tar.TypeReg}
+}
+
+func fileEntries(files map[string]string) []testEntry {
+	names := make([]string, 0, len(files))
+	for name := range files {
+		names = append(names, name)
+	}
+	// limits bite as the walk proceeds, so entry order decides what lands before a truncation
+	sort.Strings(names)
+	entries := make([]testEntry, 0, len(names))
+	for _, name := range names {
+		entries = append(entries, testEntry{name: name, body: files[name]})
+	}
+	return entries
+}
+
+func zipBytes(t testing.TB, files map[string]string) []byte {
+	return zipFromEntries(t, fileEntries(files))
+}
+
+func zipFromEntries(t testing.TB, entries []testEntry) []byte {
+	t.Helper()
+	var buf bytes.Buffer
+	w := zip.NewWriter(&buf)
+	for _, e := range entries {
+		hdr := &zip.FileHeader{Name: e.name}
+		body := e.body
+		switch {
+		case e.dir:
+			hdr.SetMode(fs.ModeDir | e.modeOr(0o755))
+		case e.link != "":
+			hdr.SetMode(fs.ModeSymlink | 0o777)
+			body = e.link
+		default:
+			hdr.SetMode(e.modeOr(0o644))
+		}
+		fw, err := w.CreateHeader(hdr)
+		require.NoError(t, err)
+		_, err = fw.Write([]byte(body))
+		require.NoError(t, err)
+	}
+	require.NoError(t, w.Close())
+	return buf.Bytes()
+}
+
+func gzBytes(t testing.TB, body string) []byte {
+	t.Helper()
+	var buf bytes.Buffer
+	gw := gzip.NewWriter(&buf)
+	_, err := gw.Write([]byte(body))
+	require.NoError(t, err)
+	require.NoError(t, gw.Close())
+	return buf.Bytes()
+}
+
+func tarGzBytes(t testing.TB, files map[string]string) []byte {
+	return tarGzFromEntries(t, fileEntries(files))
+}
+
+func tarGzFromEntries(t testing.TB, entries []testEntry) []byte {
+	t.Helper()
+	var buf bytes.Buffer
+	gw := gzip.NewWriter(&buf)
+	tw := tar.NewWriter(gw)
+	for _, e := range entries {
+		hdr := e.header()
+		require.NoError(t, tw.WriteHeader(&hdr))
+		_, err := tw.Write([]byte(e.body))
+		require.NoError(t, err)
+	}
+	require.NoError(t, tw.Close())
+	require.NoError(t, gw.Close())
+	return buf.Bytes()
+}
+
+func (e testEntry) modeOr(fallback fs.FileMode) fs.FileMode {
+	if e.mode != 0 {
+		return e.mode
+	}
+	return fallback
+}
+
+func regularHeader(name string, size int64) tar.Header {
+	return tar.Header{Name: name, Size: size, Mode: 0o600, Typeflag: tar.TypeReg}
+}
+
+// scanContext returns a context whose temp root is a fresh directory, and that directory.
+func scanContext(t testing.TB) (context.Context, string) {
+	t.Helper()
+	root := t.TempDir()
+	return tmpdir.WithValue(context.Background(), tmpdir.FromPath(root)), root
+}
+
+// filesIn lists the regular files directly in dir.
+func filesIn(t testing.TB, dir string) []string {
+	t.Helper()
+	entries, err := os.ReadDir(dir)
+	require.NoError(t, err)
+	var names []string
+	for _, e := range entries {
+		if !e.IsDir() {
+			names = append(names, e.Name())
+		}
+	}
+	return names
+}
+
+// spillFile is the one file a resolver has written, or "" when it has not.
+func spillFile(t testing.TB, dir string) string {
+	t.Helper()
+	files := filesIn(t, dir)
+	require.LessOrEqual(t, len(files), 1)
+	if len(files) == 0 {
+		return ""
+	}
+	return files[0]
+}
+
+// resolverIn makes an empty resolver over the given charge that spills into dir, along with that
+// directory. Its entries are added by the test.
+func resolverIn(t testing.TB, charge *charge) (*Resolver, string) {
+	t.Helper()
+	root := t.TempDir()
+	ctx := tmpdir.WithValue(context.Background(), tmpdir.FromPath(root))
+	r := newResolver(ctx, file.NewCoordinates("test-archive", ""), charge)
+	t.Cleanup(r.Cleanup)
+	return r, root
+}
+
+// addAll adds entries in the order given and finishes the resolver.
+func addAll(t testing.TB, r *Resolver, entries []testEntry) {
+	t.Helper()
+	for _, e := range entries {
+		require.NoError(t, r.add(e.header(), bytes.NewReader([]byte(e.body))))
+	}
+	r.finish()
+}
+
+// resolverOver builds a resolver holding the given files within a memory bound.
+func resolverOver(t testing.TB, maxInMemory int64, files map[string]string) *Resolver {
+	t.Helper()
+	r, _ := resolverIn(t, memCharge(maxInMemory))
+	r.archiveCoordinates = file.NewCoordinates("outer.jar", "")
+	addAll(t, r, fileEntries(files))
+	return r
+}
+
+// resolverFrom builds a resolver holding the given entries, links and directories included, with
+// ample memory.
+func resolverFrom(t testing.TB, entries ...testEntry) *Resolver {
+	t.Helper()
+	r, _ := resolverIn(t, memCharge(1<<20))
+	r.archiveCoordinates = file.NewCoordinates("outer.jar", "")
+	addAll(t, r, entries)
+	return r
+}
+
+// extractBytes extracts an archive into a resolver built over the given charge.
+func extractBytes(t testing.TB, data []byte, name string, charge *charge) (*Resolver, string) {
+	t.Helper()
+	r, root := resolverIn(t, charge)
+	content := bytes.NewReader(data)
+	format, err := identifyFormat(context.Background(), name, content)
+	require.NoError(t, err)
+	require.NotNil(t, format, "fixture must identify as an archive")
+	require.NoError(t, r.extract(context.Background(), format, content, nil))
+	return r, root
+}
+
+func readEntry(t testing.TB, r ReaderAtSeeker) string {
+	t.Helper()
+	_, err := r.Seek(0, io.SeekStart)
+	require.NoError(t, err)
+	b, err := io.ReadAll(r)
+	require.NoError(t, err)
+	return string(b)
+}
+
+// storedEntry is one entry read back out of a resolver.
+type storedEntry struct {
+	body       string
+	linkTarget string
+	mode       fs.FileMode
+	kind       stereoscopeFile.Type
+}
+
+// readStore reads every stored entry by name: files, links, and directories listed or implied.
+func readStore(t testing.TB, r *Resolver) map[string]storedEntry {
+	t.Helper()
+	out := map[string]storedEntry{}
+	for _, ref := range r.tree.AllFiles(stereoscopeFile.AllTypes()...) {
+		entry, err := r.index.Get(ref)
+		require.NoError(t, err)
+		out[entry.Metadata.Path] = storedEntry{
+			body:       readEntry(t, r.open(r.content[ref.ID()])),
+			linkTarget: entry.Metadata.LinkDestination,
+			mode:       entry.Metadata.FileInfo.Mode(),
+			kind:       entry.Metadata.Type,
+		}
+	}
+	return out
+}
+
+// storedNames lists every listed entry's name, files and directories alike.
+func storedNames(t testing.TB, r *Resolver) []string {
+	t.Helper()
+	var names []string
+	for name := range readStore(t, r) {
+		names = append(names, name)
+	}
+	sort.Strings(names)
+	return names
+}
+
+// nodeCount is every path the tree holds, including directories the archive never listed.
+func nodeCount(r *Resolver) int {
+	return len(r.tree.AllRealPaths())
+}
+
+// contentAt is the blob held for the entry at a rooted path.
+func contentAt(t testing.TB, r *Resolver, p string) *blob {
+	t.Helper()
+	_, res, err := r.tree.File(stereoscopeFile.Path(p))
+	require.NoError(t, err)
+	require.NotNil(t, res)
+	return r.content[res.Reference.ID()]
+}
+
+// memCharge is a charge against a memory bound with disk unbounded.
+func memCharge(maxMemory int64) *charge {
+	return NewLimiter(Limits{MaxMemoryBytes: maxMemory, MaxDiskBytes: -1}).charge()
+}
+
+// diskCharge is a charge against a disk bound with memory refusing everything.
+func diskCharge(maxDisk int64) *charge {
+	return NewLimiter(Limits{MaxDiskBytes: maxDisk}).charge()
+}
+
+// localPaths lists the local entry path of every location (rather than full nested archive path), sorted.
+func localPaths(locations []file.Location) []string {
+	var out []string
+	for _, loc := range locations {
+		out = append(out, loc.LocalPath())
+	}
+	sort.Strings(out)
+	return out
+}
+
+// manyEntryZip is a zip of count one-byte files.
+func manyEntryZip(t testing.TB, count int) []byte {
+	t.Helper()
+	files := make(map[string]string, count)
+	for i := range count {
+		files[fmt.Sprintf("e%06d.txt", i)] = "x"
+	}
+	return zipBytes(t, files)
+}
+
+// extractedResolver extracts one archive through Extract and returns the resolver, along with the scan
+// temp root its spill file would appear under.
+func extractedResolver(t testing.TB, data []byte, limits Limits) (*Resolver, string) {
+	t.Helper()
+	ctx, root := scanContext(t)
+
+	r, err := Extract(ctx, bytes.NewReader(data), file.NewCoordinates("app.zip", ""), NewLimiter(limits), nil)
+	require.NoError(t, err)
+	require.NotNil(t, r)
+	t.Cleanup(r.Cleanup)
+
+	return r, root
+}
+
+var (
+	unboundedLimits = Limits{MaxMemoryBytes: -1, MaxDiskBytes: -1}
+
+	// spillingLimits hold nothing in memory, so every entry lands in the spill file
+	spillingLimits = Limits{MaxMemoryBytes: 0, MaxDiskBytes: -1}
+)

internal/archive/limits.go

@@ -0,0 +1,202 @@
+package archive
+
+import (
+	"errors"
+	"sync"
+)
+
+// Budget bounds the bytes decompressed under one top-level archive, summed over every archive nested in
+// it. Unlike Limits it never refills as archives are released: it bounds work, not what is held at once,
+// which is what stops a recursive bomb (42.zip) whose every level fits the limits on its own. A nil
+// *Budget admits everything.
+//
+// ponytail: no lock, since the archive walk is sequential; guard it if the walk ever runs concurrently.
+type Budget struct {
+	remaining int64
+}
+
+func NewBudget(bytes int64) *Budget {
+	return &Budget{remaining: bytes}
+}
+
+// take spends n bytes, or reports false (and spends the rest) when fewer than n remain.
+func (b *Budget) take(n int64) bool {
+	if b == nil {
+		return true
+	}
+	if n > b.remaining {
+		b.remaining = 0
+		return false
+	}
+	b.remaining -= n
+	return true
+}
+
+var errBudgetSpent = errors.New("archive tree decompression budget spent")
+
+// ErrDiskLimitReached reports that placing an archive's content would exceed the disk limit.
+var ErrDiskLimitReached = errors.New("archive content would exceed the disk limit")
+
+// Limits bound how much archive content one scan holds at once. Each limit falls as archives are
+// released, so it bounds peak usage rather than the total ever written.
+//
+// For both limits: positive is the bound, zero forbids the resource, negative is unbounded.
+type Limits struct {
+	// MaxMemoryBytes bounds archive content held in memory. Content that does not fit is written to
+	// disk instead.
+	MaxMemoryBytes int64
+
+	// MaxDiskBytes bounds archive content written to disk. Content that does not fit is dropped and
+	// the archive is skipped or truncated.
+	MaxDiskBytes int64
+}
+
+// Limiter tracks how much archive content a scan holds right now against its Limits. A nil *Limiter
+// enforces nothing.
+type Limiter struct {
+	limits Limits
+
+	mu     sync.Mutex
+	memory int64
+	disk   int64
+
+	peakMemory int64
+	peakDisk   int64
+}
+
+func NewLimiter(limits Limits) *Limiter {
+	return &Limiter{limits: limits}
+}
+
+// Peak reports the most memory and disk held at any one moment.
+func (l *Limiter) Peak() (memory, disk int64) {
+	if l == nil {
+		return 0, 0
+	}
+	l.mu.Lock()
+	defer l.mu.Unlock()
+	return l.peakMemory, l.peakDisk
+}
+
+// InUse reports the memory and disk held right now.
+func (l *Limiter) InUse() (memory, disk int64) {
+	if l == nil {
+		return 0, 0
+	}
+	l.mu.Lock()
+	defer l.mu.Unlock()
+	return l.memory, l.disk
+}
+
+// charge starts accounting for one archive. Releasing the charge gives back everything it took.
+func (l *Limiter) charge() *charge {
+	if l == nil {
+		return nil
+	}
+	return &charge{limiter: l}
+}
+
+// charge is one archive's draw on a Limiter. A nil *charge admits everything.
+//
+// Bytes are charged as they land, never from the sizes an archive declares, since those can lie.
+type charge struct {
+	limiter  *Limiter
+	inMemory int64
+	onDisk   int64
+}
+
+func admits(limit, held, n int64) bool {
+	switch {
+	case limit < 0:
+		return true
+	case limit == 0:
+		return false
+	default:
+		return held+n <= limit
+	}
+}
+
+// memory charges n bytes held in memory, or reports false (charging nothing) when the memory limit
+// does not admit them.
+func (c *charge) memory(n int64) bool {
+	if c == nil || n <= 0 {
+		return true
+	}
+	l := c.limiter
+	l.mu.Lock()
+	defer l.mu.Unlock()
+	if !admits(l.limits.MaxMemoryBytes, l.memory, n) {
+		return false
+	}
+	l.memory += n
+	c.inMemory += n
+	l.peakMemory = max(l.peakMemory, l.memory)
+	return true
+}
+
+// disk charges n bytes written to disk, or reports false (charging nothing) when the disk limit does
+// not admit them.
+func (c *charge) disk(n int64) bool {
+	if c == nil || n <= 0 {
+		return true
+	}
+	l := c.limiter
+	l.mu.Lock()
+	defer l.mu.Unlock()
+	if !admits(l.limits.MaxDiskBytes, l.disk, n) {
+		return false
+	}
+	l.disk += n
+	c.onDisk += n
+	l.peakDisk = max(l.peakDisk, l.disk)
+	return true
+}
+
+// index charges n bytes of index bookkeeping, which lives in memory whatever the limits say. A zero
+// memory limit is a valid configuration that must still index archives, so only then does the cost
+// fall back to the disk budget; a bounded memory limit bounds the index too.
+func (c *charge) index(n int64) bool {
+	if c.memory(n) {
+		return true
+	}
+	return c != nil && c.limiter.limits.MaxMemoryBytes == 0 && c.disk(n)
+}
+
+// refundMemory gives back n bytes no longer held in memory.
+func (c *charge) refundMemory(n int64) {
+	if c == nil || n <= 0 {
+		return
+	}
+	l := c.limiter
+	l.mu.Lock()
+	defer l.mu.Unlock()
+	n = min(n, c.inMemory)
+	l.memory -= n
+	c.inMemory -= n
+}
+
+// refundDisk gives back n bytes no longer on disk.
+func (c *charge) refundDisk(n int64) {
+	if c == nil || n <= 0 {
+		return
+	}
+	l := c.limiter
+	l.mu.Lock()
+	defer l.mu.Unlock()
+	n = min(n, c.onDisk)
+	l.disk -= n
+	c.onDisk -= n
+}
+
+// release gives back everything this charge took. Safe to call more than once.
+func (c *charge) release() {
+	if c == nil {
+		return
+	}
+	l := c.limiter
+	l.mu.Lock()
+	defer l.mu.Unlock()
+	l.memory -= c.inMemory
+	l.disk -= c.onDisk
+	c.inMemory, c.onDisk = 0, 0
+}

internal/archive/limits_test.go

@@ -0,0 +1,178 @@
+package archive
+
+import (
+	"sync"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+func TestLimiter_chargeAndRelease(t *testing.T) {
+	limiter := NewLimiter(Limits{MaxMemoryBytes: 100, MaxDiskBytes: 200})
+
+	first := limiter.charge()
+	require.True(t, first.memory(60))
+	require.True(t, first.disk(150))
+
+	mem, disk := limiter.InUse()
+	assert.Equal(t, int64(60), mem)
+	assert.Equal(t, int64(150), disk)
+
+	second := limiter.charge()
+	assert.False(t, second.memory(50), "60 + 50 is over the memory limit")
+	assert.False(t, second.disk(60), "150 + 60 is over the disk limit")
+	assert.True(t, second.memory(40), "and exactly at the limit is admitted")
+
+	mem, _ = limiter.InUse()
+	assert.Equal(t, int64(100), mem, "a refused charge takes nothing")
+
+	first.release()
+	mem, disk = limiter.InUse()
+	assert.Equal(t, int64(40), mem, "release gives back exactly what that charge took")
+	assert.Zero(t, disk)
+
+	first.release()
+	mem, _ = limiter.InUse()
+	assert.Equal(t, int64(40), mem, "releasing twice must not give back what was never taken")
+}
+
+func TestLimiter_refund(t *testing.T) {
+	limiter := NewLimiter(Limits{MaxDiskBytes: 100})
+	charge := limiter.charge()
+
+	require.True(t, charge.disk(80))
+	charge.refundDisk(80)
+
+	_, disk := limiter.InUse()
+	assert.Zero(t, disk)
+	assert.True(t, charge.disk(100), "the refunded room is available again")
+
+	charge.refundDisk(500)
+	_, disk = limiter.InUse()
+	assert.Zero(t, disk, "a refund larger than what was charged cannot drive the limiter negative")
+}
+
+func TestLimiter_threeStateReadingIsUniform(t *testing.T) {
+	t.Run("positive is the limit", func(t *testing.T) {
+		c := NewLimiter(Limits{MaxMemoryBytes: 100, MaxDiskBytes: 100}).charge()
+		assert.True(t, c.memory(100))
+		assert.False(t, c.memory(1))
+		assert.True(t, c.disk(100))
+		assert.False(t, c.disk(1))
+	})
+
+	t.Run("zero refuses unconditionally on both", func(t *testing.T) {
+		c := NewLimiter(Limits{MaxMemoryBytes: 0, MaxDiskBytes: 0}).charge()
+		assert.False(t, c.memory(1))
+		assert.False(t, c.disk(1))
+	})
+
+	t.Run("negative admits unconditionally on both", func(t *testing.T) {
+		c := NewLimiter(Limits{MaxMemoryBytes: -1, MaxDiskBytes: -1}).charge()
+		assert.True(t, c.memory(1_000_000_000))
+		assert.True(t, c.disk(1_000_000_000))
+	})
+}
+
+func TestLimiter_nilIsUnbounded(t *testing.T) {
+	var limiter *Limiter
+	charge := limiter.charge()
+	assert.Nil(t, charge)
+
+	assert.True(t, charge.memory(1_000_000))
+	assert.True(t, charge.disk(1_000_000))
+	charge.refundDisk(10)
+	charge.release()
+
+	mem, disk := charge.held()
+	assert.Zero(t, mem)
+	assert.Zero(t, disk)
+
+	mem, disk = limiter.InUse()
+	assert.Zero(t, mem)
+	assert.Zero(t, disk)
+
+	mem, disk = limiter.Peak()
+	assert.Zero(t, mem)
+	assert.Zero(t, disk)
+}
+
+func TestLimiter_concurrentChargesAgree(t *testing.T) {
+	limiter := NewLimiter(Limits{MaxMemoryBytes: 1_000_000, MaxDiskBytes: -1})
+
+	var wg sync.WaitGroup
+	charges := make([]*charge, 50)
+	for i := range charges {
+		charges[i] = limiter.charge()
+		wg.Add(1)
+		go func(c *charge) {
+			defer wg.Done()
+			for range 100 {
+				c.memory(1)
+				c.disk(2)
+			}
+		}(charges[i])
+	}
+	wg.Wait()
+
+	mem, disk := limiter.InUse()
+	assert.Equal(t, int64(50*100), mem)
+	assert.Equal(t, int64(50*100*2), disk)
+
+	for _, c := range charges {
+		c.release()
+	}
+	mem, disk = limiter.InUse()
+	assert.Zero(t, mem)
+	assert.Zero(t, disk)
+}
+
+func TestLimiter_peak(t *testing.T) {
+	t.Run("is a high-water mark", func(t *testing.T) {
+		l := NewLimiter(Limits{MaxMemoryBytes: -1, MaxDiskBytes: -1})
+
+		first := l.charge()
+		require.True(t, first.memory(100))
+		require.True(t, first.disk(300))
+		first.release()
+
+		second := l.charge()
+		require.True(t, second.memory(40))
+		require.True(t, second.disk(50))
+
+		memory, disk := l.InUse()
+		assert.Equal(t, int64(40), memory)
+		assert.Equal(t, int64(50), disk)
+
+		peakMemory, peakDisk := l.Peak()
+		assert.Equal(t, int64(100), peakMemory, "the peak is the most held at once, not the most recently held")
+		assert.Equal(t, int64(300), peakDisk)
+	})
+
+	t.Run("counts concurrent holders together", func(t *testing.T) {
+		l := NewLimiter(Limits{MaxMemoryBytes: -1, MaxDiskBytes: -1})
+
+		outer := l.charge()
+		require.True(t, outer.memory(100))
+		inner := l.charge()
+		require.True(t, inner.memory(60))
+		inner.release()
+		outer.release()
+
+		peakMemory, _ := l.Peak()
+		assert.Equal(t, int64(160), peakMemory)
+	})
+
+	t.Run("a refused charge does not move it", func(t *testing.T) {
+		l := NewLimiter(Limits{MaxMemoryBytes: 50, MaxDiskBytes: 50})
+
+		c := l.charge()
+		assert.False(t, c.memory(500))
+		assert.False(t, c.disk(500))
+
+		peakMemory, peakDisk := l.Peak()
+		assert.Zero(t, peakMemory)
+		assert.Zero(t, peakDisk)
+	})
+}

internal/archive/resolver.go

@@ -0,0 +1,575 @@
+package archive
+
+import (
+	"archive/tar"
+	"context"
+	"errors"
+	"fmt"
+	"io"
+	"io/fs"
+	"os"
+	"path"
+	"slices"
+	"sort"
+	"strings"
+	"time"
+	"unicode"
+
+	"github.com/dustin/go-humanize"
+	"github.com/mholt/archives"
+
+	stereoscopeFile "github.com/anchore/stereoscope/pkg/file"
+	"github.com/anchore/stereoscope/pkg/filetree"
+	intFile "github.com/anchore/syft/internal/file"
+	"github.com/anchore/syft/internal/log"
+	"github.com/anchore/syft/internal/tmpdir"
+	"github.com/anchore/syft/syft/file"
+)
+
+// Resolver is one archive opened as its own filesystem: a file.Resolver over the entries Extract fed
+// into it, holding their content within the scan's limits. Entries are indexed in a stereoscope file
+// tree, the same index the directory and image resolvers search.
+//
+// Locations it returns keep the outermost archive's RealPath and carry the entry's FullPath. Queries
+// may name an entry either by its full path or by its path within the archive (see rootedPath).
+type Resolver struct {
+	// Digests are of the archive file itself.
+	Digests []file.Digest
+
+	// Truncated is non-nil when the resolver covers only part of the archive, and says why: the disk limit
+	// or the decompression budget stopped extraction early, or an entry was too large or unreadable.
+	Truncated error
+
+	archiveCoordinates file.Coordinates
+	charge             *charge
+	budget             *Budget
+	metered            bool // the budget is charged as the archive is decoded (see meteredReader), not in put
+
+	// content is held in memory while the memory limit admits it and in one spill file once it does
+	// not. The file is created on first use, so an archive that stays in memory never touches the
+	// filesystem, and blobs are located in it by offset with no framing of their own.
+	tempDir *tmpdir.TempDir
+	held    []*blob // blobs in memory, in the order they were added
+	file    *os.File
+	remove  func()
+	written int64
+	chunk   []byte
+
+	tree    *filetree.FileTree
+	index   filetree.Index
+	search  filetree.Searcher // built by finish, once every entry is in the tree
+	content map[stereoscopeFile.ID]*blob
+	entries int // non-directory entries added
+}
+
+var _ file.Resolver = (*Resolver)(nil)
+
+// newResolver returns an empty resolver whose locations extend the archive's coordinates, spilling into
+// the scan's temp root when ctx carries one (see internal/tmpdir).
+func newResolver(ctx context.Context, archiveCoordinates file.Coordinates, charge *charge) *Resolver {
+	return &Resolver{
+		archiveCoordinates: archiveCoordinates,
+		charge:             charge,
+		budget:             budgetFromContext(ctx),
+		tempDir:            tmpdir.FromContext(ctx),
+		tree:               filetree.New(),
+		index:              filetree.NewIndex(),
+		content:            map[stereoscopeFile.ID]*blob{},
+	}
+}
+
+// Cleanup removes everything the archive holds on disk and releases its charge against the limiter.
+// Readers handed out before are no longer valid. Safe to call more than once.
+func (r *Resolver) Cleanup() {
+	if r == nil {
+		return
+	}
+	r.releaseStorage()
+	r.charge.release()
+}
+
+// approxIndexBytesPerEntry estimates what holding one tree node costs beyond its content: the node, its
+// header and metadata, and its index slots. It is charged for every node an entry creates, including
+// the directories its path implies, so an archive of many tiny entries or of a few entries with very
+// deep paths is still bounded by the limits.
+const approxIndexBytesPerEntry = 2 * 1024
+
+func approxIndexBytes(hdr tar.Header) int64 {
+	return approxIndexBytesPerEntry + int64(len(hdr.Name)+len(hdr.Linkname))
+}
+
+// add stores and indexes one entry, reading its content in full now since archive readers are
+// sequential. Reaching a limit stores nothing for this entry and returns ErrDiskLimitReached; entries
+// added before it remain usable. The last entry at a path wins, as it does when the archive is
+// extracted (tar appends updates, an OCI layer applies in order, and java's legacy zip reading
+// overwrites too), so a stale earlier copy, such as an older pom.properties, can't stand in for what is
+// really there.
+func (r *Resolver) add(hdr tar.Header, content io.Reader) error {
+	entryPath := path.Clean("/" + hdr.Name)
+	if entryPath == "/" {
+		return nil
+	}
+	replacing, ok := r.replace(entryPath, hdr)
+	if !ok {
+		return nil
+	}
+
+	// directories the path implies that do not exist yet are nodes this entry pays for. Walking from the
+	// deepest parent up stops at the first that exists, since its ancestors exist too
+	var newDirs []string
+	for i := strings.LastIndexByte(entryPath, '/'); i > 0; i = strings.LastIndexByte(entryPath[:i], '/') {
+		if r.tree.HasPath(stereoscopeFile.Path(entryPath[:i])) {
+			break
+		}
+		newDirs = append(newDirs, entryPath[:i])
+	}
+	slices.Reverse(newDirs)
+	if !r.chargeIndex(approxIndexBytes(hdr) + int64(len(newDirs))*approxIndexBytesPerEntry) {
+		return ErrDiskLimitReached
+	}
+	// indexed as if listed, since a search for a directory's children looks the directory up by name
+	for _, dir := range newDirs {
+		if err := r.store(dir, tar.Header{Name: dir, Typeflag: tar.TypeDir, Mode: 0o755}, &blob{}); err != nil {
+			log.WithFields("entry", hdr.Name, "error", err).Trace("skipping archive entry")
+			return nil
+		}
+	}
+
+	b := &blob{}
+	if hdr.Typeflag == tar.TypeReg && content != nil {
+		// reading one byte past the cap is how an entry over it is told apart from one exactly at it
+		err := r.put(b, io.LimitReader(content, maxEntryBytes+1))
+		if err == nil && b.size > maxEntryBytes {
+			err = errEntryTooLarge
+		}
+		if err != nil {
+			r.discard(b)
+			if errors.Is(err, errEntryTooLarge) {
+				r.truncate(fmt.Errorf("an entry was skipped: %w of %s", err, humanize.IBytes(uint64(maxEntryBytes))))
+				return nil
+			}
+			if errors.Is(err, ErrDiskLimitReached) || errors.Is(err, errBudgetSpent) {
+				return err
+			}
+			// a damaged entry (a CRC mismatch, a corrupt deflate stream) costs only that entry
+			r.truncate(fmt.Errorf("entry %q could not be read: %w", hdr.Name, err))
+			return nil
+		}
+	}
+
+	if err := r.store(entryPath, hdr, b); err != nil {
+		// a path the tree cannot hold, such as a file beneath another file's name
+		r.discard(b)
+		log.WithFields("entry", hdr.Name, "error", err).Trace("skipping archive entry")
+		return nil
+	}
+	if hdr.Typeflag != tar.TypeDir && !replacing {
+		r.entries++
+	}
+	return nil
+}
+
+// replace clears the way for an entry at a path that is already held, reporting whether it did and
+// false when the entry should be dropped. A later non-directory entry replaces an earlier one, refunding
+// what it held. A file and a directory at one path keep the first, since swapping kinds would mean
+// re-parenting what is already beneath it.
+func (r *Resolver) replace(entryPath string, hdr tar.Header) (replacing, ok bool) {
+	exists, res, _ := r.tree.File(stereoscopeFile.Path(entryPath))
+	if !exists || !res.HasReference() {
+		return false, true
+	}
+	earlier, err := r.index.Get(*res.Reference)
+	if err != nil || earlier.IsDir() || hdr.Typeflag == tar.TypeDir {
+		return false, false
+	}
+	// a removed node's index entry is left behind, but searches only answer with references in the tree
+	if err := r.tree.RemovePath(stereoscopeFile.Path(entryPath)); err != nil {
+		log.WithFields("entry", hdr.Name, "error", err).Trace("unable to replace archive entry")
+		return false, false
+	}
+	if b := r.content[res.ID()]; b != nil {
+		r.discard(b)
+	}
+	delete(r.content, res.ID())
+	return true, true
+}
+
+func (r *Resolver) store(rooted string, hdr tar.Header, b *blob) error {
+	ref, err := r.addToTree(rooted, hdr)
+	if err != nil {
+		return err
+	}
+	metadata := stereoscopeFile.NewMetadata(hdr, r.open(b))
+	metadata.Path = entryPath(rooted)
+	r.index.Add(*ref, metadata)
+	r.content[ref.ID()] = b
+	return nil
+}
+
+func (r *Resolver) addToTree(entryPath string, hdr tar.Header) (*stereoscopeFile.Reference, error) {
+	p := stereoscopeFile.Path(entryPath)
+	switch hdr.Typeflag {
+	case tar.TypeDir:
+		return r.tree.AddDir(p)
+	case tar.TypeSymlink:
+		return r.tree.AddSymLink(p, stereoscopeFile.Path(hdr.Linkname))
+	case tar.TypeLink:
+		// a hard link names its target from the archive root
+		return r.tree.AddHardLink(p, stereoscopeFile.Path(path.Join("/", hdr.Linkname)))
+	default:
+		return r.tree.AddFile(p)
+	}
+}
+
+// maxEntryBytes caps any one entry, as the legacy java extraction did (see intFile.SafeCopy): without it
+// a single entry of an overlapping-entry zip bomb can decompress up to the disk limit.
+var maxEntryBytes int64 = intFile.PerFileReadLimit
+
+var errEntryTooLarge = errors.New("archive entry exceeds the per-entry size cap")
+
+// truncate marks the resolver as covering part of the archive, keeping the first reason given.
+func (r *Resolver) truncate(err error) {
+	if r.Truncated == nil {
+		r.Truncated = err
+	}
+}
+
+// chargeIndex charges index bookkeeping, which lives in memory. Content held in memory can move to
+// disk to make room for it; the index cannot, so when it is refused the entries are.
+func (r *Resolver) chargeIndex(n int64) bool {
+	if r.charge.index(n) {
+		return true
+	}
+	if len(r.held) == 0 || r.spill() != nil {
+		return false
+	}
+	return r.charge.index(n)
+}
+
+// finish builds the search context once every entry is added.
+func (r *Resolver) finish() {
+	r.search = filetree.NewSearchContext(r.tree, r.index)
+}
+
+// linkDestination is the rooted path a link points at inside the archive. A hard link names its
+// target from the archive root, as does an absolute symlink, so "/etc/passwd" is an entry of this
+// archive and never the host's. A relative symlink is joined onto the link's own directory, and
+// cleaning against the root keeps "../../x" inside the archive.
+func linkDestination(linkPath, linkname string, hard bool) string {
+	if hard || path.IsAbs(linkname) {
+		return path.Join("/", linkname)
+	}
+	return path.Join(path.Dir(linkPath), linkname)
+}
+
+// entryPath is a node's path within the archive: archive-relative with no leading slash.
+func entryPath(rooted string) string {
+	return strings.TrimPrefix(rooted, "/")
+}
+
+// fullPath is how paths leave the resolver: the archive's own full path, then the entry path.
+func (r *Resolver) fullPath(rooted string) string {
+	return r.archiveCoordinates.FullNestedPath() + file.ArchivePathSeparator + entryPath(rooted)
+}
+
+// rootedPath is the tree path a query names, which is either form a path takes: a full path is trimmed to
+// the entry path within this archive, and anything else (a LocalPath, with or without its leading slash)
+// is taken as archive-relative already, since the tree looks a relative path up from its root. The archive's full path with a trailing "!" (what path.Dir gives for an entry at the root)
+// names the root. A full path into another archive in the scan names nothing here and reports false.
+func (r *Resolver) rootedPath(userPath string) (string, bool) {
+	if rest, ok := strings.CutPrefix(userPath, r.archiveCoordinates.FullNestedPath()); ok {
+		if rest == file.ArchivePathSeparator[:1] {
+			return "/", true
+		}
+		if strings.HasPrefix(rest, file.ArchivePathSeparator) {
+			// keep the separator's slash as the rooted path's
+			return path.Clean(rest[len(file.ArchivePathSeparator)-1:]), true
+		}
+	}
+	if r.outside(userPath) {
+		return "", false
+	}
+	return path.Clean(userPath), true
+}
+
+// outside reports whether a path not under this archive's full path is a full path from the scan
+// nonetheless: every full path in this archive tree starts with the outermost archive's real path and a
+// separator. The real path alone is taken as an entry path, so an entry named like the outermost archive
+// is found by its LocalPath.
+func (r *Resolver) outside(userPath string) bool {
+	rest, ok := strings.CutPrefix(userPath, r.archiveCoordinates.RealPath)
+	return ok && strings.HasPrefix(rest, file.ArchivePathSeparator)
+}
+
+// coordinates name an entry by the outermost archive's real path, which never includes a path inside an
+// archive, and its full path through every archive.
+func (r *Resolver) coordinates(rooted string) file.Coordinates {
+	return file.Coordinates{
+		RealPath:     r.archiveCoordinates.RealPath,
+		FileSystemID: r.archiveCoordinates.FileSystemID,
+		FullPath:     r.fullPath(rooted),
+	}
+}
+
+// location names a resolution: a link is reported at its target's path with the link's own full path
+// as the access path.
+func (r *Resolver) location(res stereoscopeFile.Resolution) file.Location {
+	coordinates := r.coordinates(string(res.RealPath))
+	if res.RequestPath == "" || res.RequestPath == res.RealPath {
+		return file.NewLocationFromCoordinates(coordinates)
+	}
+	return file.NewVirtualLocationFromCoordinates(coordinates, r.fullPath(string(res.RequestPath)))
+}
+
+// resolve finds the file a path names, following links, and reports false for directories and
+// paths the archive never listed.
+func (r *Resolver) resolve(userPath string) (*stereoscopeFile.Resolution, bool) {
+	rooted, ok := r.rootedPath(userPath)
+	if !ok {
+		return nil, false
+	}
+	res, err := r.search.SearchByPath(rooted, filetree.FollowBasenameLinks)
+	if err != nil || res == nil || !res.HasReference() {
+		return nil, false
+	}
+	entry, err := r.index.Get(*res.Reference)
+	if err != nil || entry.IsDir() {
+		return nil, false
+	}
+	return res, true
+}
+
+func (r *Resolver) FileContentsByLocation(location file.Location) (io.ReadCloser, error) {
+	res, ok := r.resolve(location.FullNestedPath())
+	if !ok {
+		return nil, fmt.Errorf("no archive entry for path=%q", location.FullNestedPath())
+	}
+	return entryReader{r.open(r.content[res.ID()])}, nil
+}
+
+func (r *Resolver) FileMetadataByLocation(location file.Location) (file.Metadata, error) {
+	rooted, ok := r.rootedPath(location.FullNestedPath())
+	if !ok {
+		return file.Metadata{}, fmt.Errorf("no archive entry for path=%q", location.FullNestedPath())
+	}
+	exists, res, err := r.tree.File(stereoscopeFile.Path(rooted))
+	if err != nil || !exists || !res.HasReference() {
+		return file.Metadata{}, fmt.Errorf("no archive entry for path=%q", location.FullNestedPath())
+	}
+	entry, err := r.index.Get(*res.Reference)
+	if err != nil {
+		return file.Metadata{}, err
+	}
+	// the index holds entry paths; callers get full paths, as with locations
+	metadata := entry.Metadata
+	metadata.Path = r.fullPath(rooted)
+	if metadata.LinkDestination != "" {
+		metadata.LinkDestination = r.fullPath(linkDestination(rooted, metadata.LinkDestination, metadata.Type == stereoscopeFile.TypeHardLink))
+	}
+	return metadata, nil
+}
+
+func (r *Resolver) HasPath(userPath string) bool {
+	rooted, ok := r.rootedPath(userPath)
+	return ok && r.tree.HasPath(stereoscopeFile.Path(rooted))
+}
+
+func (r *Resolver) FilesByPath(paths ...string) ([]file.Location, error) {
+	var out []file.Location
+	var seen []stereoscopeFile.ID // few paths are asked for at once
+	for _, userPath := range paths {
+		res, ok := r.resolve(userPath)
+		if !ok || slices.Contains(seen, res.ID()) {
+			continue
+		}
+		seen = append(seen, res.ID())
+		out = append(out, r.location(*res))
+	}
+	return out, nil
+}
+
+func (r *Resolver) FilesByGlob(patterns ...string) ([]file.Location, error) {
+	var out []file.Location
+	seen := stereoscopeFile.NewFileReferenceSet()
+	for _, pattern := range patterns {
+		rooted, ok := r.rootedPath(pattern)
+		if !ok {
+			continue
+		}
+		results, err := r.searchByGlob(rooted)
+		if err != nil {
+			return nil, fmt.Errorf("invalid glob %q: %w", pattern, err)
+		}
+		for _, res := range results {
+			if !res.HasReference() || seen.Contains(*res.Reference) {
+				continue
+			}
+			entry, err := r.index.Get(*res.Reference)
+			if err != nil || entry.IsDir() {
+				continue
+			}
+			seen.Add(*res.Reference)
+			out = append(out, r.location(res))
+		}
+	}
+	sortLocations(out)
+	return out, nil
+}
+
+// searchByGlob is the index search, except that stereoscope answers "<dir>/*" by looking the directory
+// up by name and the root has none, so "/*" (or "*") walks the tree instead.
+func (r *Resolver) searchByGlob(pattern string) ([]stereoscopeFile.Resolution, error) {
+	if strings.TrimPrefix(pattern, "/") == "*" {
+		return r.tree.FilesByGlob("/*", filetree.FollowBasenameLinks)
+	}
+	return r.search.SearchByGlob(pattern, filetree.FollowBasenameLinks)
+}
+
+// sortLocations orders answers by path, which decides how locations group into packages when results
+// merge into the SBOM.
+func sortLocations(locations []file.Location) {
+	sort.Slice(locations, func(i, j int) bool {
+		if a, b := locations[i].FullNestedPath(), locations[j].FullNestedPath(); a != b {
+			return a < b
+		}
+		return locations[i].AccessPath < locations[j].AccessPath
+	})
+}
+
+func (r *Resolver) FilesByMIMEType(types ...string) ([]file.Location, error) {
+	results, err := r.search.SearchByMIMEType(types...)
+	if err != nil {
+		return nil, err
+	}
+	var out []file.Location
+	for _, res := range results {
+		if res.HasReference() {
+			out = append(out, r.location(res))
+		}
+	}
+	sortLocations(out)
+	return out, nil
+}
+
+// RelativeFileByPath resolves against the archive root: an archive has no layers to be relative to.
+func (r *Resolver) RelativeFileByPath(_ file.Location, userPath string) *file.Location {
+	locations, _ := r.FilesByPath(userPath)
+	if len(locations) == 0 {
+		return nil
+	}
+	return &locations[0]
+}
+
+func (r *Resolver) AllLocations(ctx context.Context) <-chan file.Location {
+	out := make(chan file.Location)
+	go func() {
+		defer close(out)
+		refs := r.tree.AllFiles(stereoscopeFile.TypeRegular, stereoscopeFile.TypeSymLink, stereoscopeFile.TypeHardLink)
+		sort.Slice(refs, func(i, j int) bool { return refs[i].RealPath < refs[j].RealPath })
+		for _, ref := range refs {
+			select {
+			case out <- r.location(stereoscopeFile.Resolution{RequestPath: ref.RealPath, Reference: &ref}):
+			case <-ctx.Done():
+				return
+			}
+		}
+	}()
+	return out
+}
+
+// entryReader gives an entry's reader the Close the resolver interface requires. The resolver owns
+// the bytes, so there is nothing to close.
+type entryReader struct {
+	ReaderAtSeeker
+}
+
+func (entryReader) Close() error { return nil }
+
+// maxEntryNameBytes is the longest entry name stored: PATH_MAX. Every path component becomes a node,
+// so a longer name is a cheap way to inflate the index and no filesystem could hold it anyway.
+const maxEntryNameBytes = MaxPathBytes
+
+// MaxPathBytes is PATH_MAX, the longest whole archive chain a scan stores or a decoded document may build.
+// Each nested file copies its container's chain, so without it a long name shared by many small entries
+// costs memory quadratic in the document.
+const MaxPathBytes = 4096
+
+// MaxDepth is the deepest archives nest: a scan stops there whatever depth is configured, and a decoded
+// document is held to it. No real nesting comes close, and a hostile archive (a zip quine, a recursive bomb)
+// must still end.
+const MaxDepth = 16
+
+// maxEntryNameDepth is the most path components an entry name may have. Adding an entry costs work per
+// component, and no real archive nests anywhere near this deep.
+const maxEntryNameDepth = 256
+
+// entryHeader builds the header stored for one archive entry, or reports false for an entry not worth
+// carrying: device nodes, fifos and sockets, which no cataloger reads, and names that cannot be a path
+// inside the archive. A name refused as unsafe marks the resolver truncated.
+//
+// The name is cleaned to an archive-relative path with no leading slash, so "../x" names x at the
+// archive root rather than anything outside it. Symlinks are stored as headers, never followed on the
+// host; the resolver resolves their targets inside the archive.
+func (r *Resolver) entryHeader(f archives.FileInfo) (tar.Header, bool) {
+	mode := f.Mode()
+	if !mode.IsRegular() && !mode.IsDir() && mode.Type()&fs.ModeSymlink == 0 {
+		log.WithFields("entry", f.NameInArchive, "mode", mode).Debug("skipping non-regular archive entry")
+		return tar.Header{}, false
+	}
+
+	name, err := EntryName(f.NameInArchive)
+	if err != nil {
+		r.truncate(fmt.Errorf("an entry was skipped: %w", err))
+		return tar.Header{}, false
+	}
+	if name == "" {
+		return tar.Header{}, false
+	}
+	// held to the chain length a decoder accepts back, so the SBOM round-trips
+	if chain := len(r.archiveCoordinates.FullNestedPath()) + len(file.ArchivePathSeparator) + len(name); chain > MaxPathBytes {
+		r.truncate(fmt.Errorf("an entry was skipped: its path of %d bytes within the archive chain exceeds the %d byte cap", chain, MaxPathBytes))
+		return tar.Header{}, false
+	}
+
+	hdr, err := tar.FileInfoHeader(f.FileInfo, f.LinkTarget)
+	if err != nil {
+		log.WithFields("entry", f.NameInArchive, "error", err).Debug("skipping archive entry with an unusable header")
+		return tar.Header{}, false
+	}
+	hdr.Name = name
+	hdr.Linkname = f.LinkTarget
+
+	// nothing reads these, and the header is held for the life of the archive
+	hdr.PAXRecords = nil
+	hdr.Uname, hdr.Gname = "", ""
+	hdr.AccessTime, hdr.ChangeTime = time.Time{}, time.Time{}
+	hdr.ModTime = hdr.ModTime.Truncate(time.Second)
+
+	return *hdr, true
+}
+
+// EntryName cleans an archive entry's name to a path relative to the archive root, returning "" when it
+// names nothing inside the archive. This is the trust boundary for names: every one ends up in FullPath
+// and the encoders, so a name that could forge an archive boundary ("!/") or a line in a line-oriented
+// format (control characters, unicode line separators) is refused. Decoders building nested coordinates
+// from a document hold its names to the same rules.
+func EntryName(name string) (string, error) {
+	if len(name) > maxEntryNameBytes {
+		return "", fmt.Errorf("entry name of %d bytes exceeds the %d byte cap", len(name), maxEntryNameBytes)
+	}
+	if strings.IndexFunc(name, isUnsafeNameRune) >= 0 {
+		return "", fmt.Errorf("entry name %q contains a control character", name)
+	}
+	cleaned := strings.TrimPrefix(path.Clean("/"+name), "/")
+	if depth := strings.Count(cleaned, "/") + 1; depth > maxEntryNameDepth {
+		return "", fmt.Errorf("entry name of %d path components exceeds the %d component cap", depth, maxEntryNameDepth)
+	}
+	if strings.Contains(cleaned, file.ArchivePathSeparator) {
+		return "", fmt.Errorf("entry name %q contains the archive path separator %q", name, file.ArchivePathSeparator)
+	}
+	return cleaned, nil
+}
+
+func isUnsafeNameRune(c rune) bool {
+	return unicode.IsControl(c) || c == '\u2028' || c == '\u2029'
+}

internal/archive/resolver_test.go

@@ -0,0 +1,506 @@
+package archive
+
+import (
+	"archive/tar"
+	"bytes"
+	"context"
+	"io"
+	"path"
+	"sort"
+	"strings"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	stereoscopeFile "github.com/anchore/stereoscope/pkg/file"
+	"github.com/anchore/syft/syft/file"
+)
+
+var jarEntriesFixture = map[string]string{
+	"META-INF/MANIFEST.MF":                          "Manifest-Version: 1.0\n",
+	"META-INF/maven/com.example/lib/pom.properties": "groupId=com.example\n",
+	"META-INF/maven/com.example/lib/pom.xml":        "<project/>",
+	"LICENSE":                                       "Apache License 2.0",
+	"BOOT-INF/lib/inner.jar":                        "PK\x03\x04 not really",
+	"com/example/Thing.class":                       "bytecode",
+}
+
+func TestResolver_add_refusedEntryIsNotStored(t *testing.T) {
+	// a half-stored pom a cataloger parses is worse than an absent one
+	r, _ := resolverIn(t, NewLimiter(Limits{MaxMemoryBytes: 0, MaxDiskBytes: 0}).charge())
+
+	err := r.add(regularHeader("a.txt", 3), bytes.NewReader([]byte("abc")))
+	assert.ErrorIs(t, err, ErrDiskLimitReached)
+	assert.Empty(t, storedNames(t, r))
+	assert.False(t, r.HasPath("a.txt"))
+}
+
+func TestResolver_add_refusedContentLeavesNoNodeBehind(t *testing.T) {
+	// the index estimate is admitted, then the content is refused
+	record := approxIndexBytes(regularHeader("dir/a.txt", 0)) + approxIndexBytesPerEntry // the entry and the directory it implies
+	r, _ := resolverIn(t, diskCharge(record+2))
+
+	err := r.add(regularHeader("dir/a.txt", 3), bytes.NewReader([]byte("abc")))
+	assert.ErrorIs(t, err, ErrDiskLimitReached)
+	assert.False(t, r.HasPath("dir/a.txt"))
+	assert.True(t, r.HasPath("dir"), "the directories it implied stay")
+}
+
+func TestResolver_add_directoryEntriesHoldNoContent(t *testing.T) {
+	r, _ := resolverIn(t, memCharge(1<<20))
+
+	require.NoError(t, r.add(tar.Header{Name: "lib", Typeflag: tar.TypeDir, Mode: 0o755}, nil))
+
+	assert.Zero(t, r.heldInMemory())
+	assert.Empty(t, readStore(t, r)["lib"].body)
+}
+
+func TestResolver_add_indexDoesNotFallBackToDiskWhenMemoryIsBounded(t *testing.T) {
+	// the index lives in memory, so a bounded memory limit bounds it; only a zero limit defers to disk
+	limiter := NewLimiter(Limits{MaxMemoryBytes: 1024, MaxDiskBytes: -1})
+	r, _ := resolverIn(t, limiter.charge())
+
+	err := r.add(regularHeader("a.txt", 0), bytes.NewReader(nil))
+	assert.ErrorIs(t, err, ErrDiskLimitReached)
+	_, disk := limiter.InUse()
+	assert.Zero(t, disk)
+}
+
+func TestResolver_add_indexMakesRoomBySpillingHeldContent(t *testing.T) {
+	record := approxIndexBytes(regularHeader("a.txt", 0))
+	r, dir := resolverIn(t, memCharge(2*record+50))
+
+	require.NoError(t, r.add(regularHeader("a.txt", 100), bytes.NewReader(bytes.Repeat([]byte("a"), 100))))
+	require.Equal(t, int64(100), r.heldInMemory())
+
+	// b's index does not fit beside a's content, so a's content moves to disk and b is indexed
+	require.NoError(t, r.add(regularHeader("b.txt", 3), bytes.NewReader([]byte("bbb"))))
+	r.finish()
+
+	assert.Equal(t, int64(3), r.heldInMemory())
+	assert.NotEmpty(t, spillFile(t, dir))
+	assert.Equal(t, []string{"a.txt", "b.txt"}, storedNames(t, r))
+	assert.Equal(t, strings.Repeat("a", 100), readStore(t, r)["a.txt"].body)
+}
+
+func TestResolver_add_lastEntryAtAPathWins(t *testing.T) {
+	r, _ := resolverIn(t, memCharge(1<<20))
+
+	require.NoError(t, r.add(regularHeader("a.txt", 5), bytes.NewReader([]byte("first"))))
+	require.NoError(t, r.add(regularHeader("a.txt", 6), bytes.NewReader([]byte("second"))))
+	require.NoError(t, r.add(regularHeader("b.txt", 1), bytes.NewReader([]byte("b"))))
+	require.NoError(t, r.add(tar.Header{Name: "b.txt", Typeflag: tar.TypeSymlink, Linkname: "a.txt"}, nil))
+	r.finish()
+
+	assert.Equal(t, "second", readStore(t, r)["a.txt"].body)
+	assert.Equal(t, "a.txt", readStore(t, r)["b.txt"].linkTarget, "a later entry may change kind")
+	assert.Equal(t, 2, r.entries)
+	assert.Equal(t, int64(len("second")), r.heldInMemory(), "the earlier copy is refunded")
+
+	locations, err := r.FilesByGlob("**/a.txt")
+	require.NoError(t, err)
+	require.Len(t, locations, 1)
+	reader, err := r.FileContentsByLocation(locations[0])
+	require.NoError(t, err)
+	assert.Equal(t, "second", readEntry(t, reader.(entryReader).ReaderAtSeeker))
+}
+
+func TestResolver_add_fileAndDirectoryAtOnePathKeepsTheFirst(t *testing.T) {
+	r, _ := resolverIn(t, memCharge(1<<20))
+
+	require.NoError(t, r.add(regularHeader("a/b", 1), bytes.NewReader([]byte("x"))))
+	require.NoError(t, r.add(regularHeader("a", 4), bytes.NewReader([]byte("file"))))
+	require.NoError(t, r.add(regularHeader("c", 4), bytes.NewReader([]byte("file"))))
+	require.NoError(t, r.add(tar.Header{Name: "c", Typeflag: tar.TypeDir, Mode: 0o755}, nil))
+	r.finish()
+
+	got := readStore(t, r)
+	assert.Equal(t, stereoscopeFile.TypeDirectory, got["a"].kind)
+	assert.Equal(t, "file", got["c"].body)
+}
+
+func TestResolver_pathsAndContents(t *testing.T) {
+	r := resolverOver(t, 1<<20, jarEntriesFixture)
+
+	locations, err := r.FilesByPath("/META-INF/MANIFEST.MF")
+	require.NoError(t, err)
+	require.Len(t, locations, 1)
+
+	assert.True(t, r.HasPath("/META-INF/MANIFEST.MF"))
+	assert.True(t, r.HasPath("META-INF/MANIFEST.MF"), "a path may arrive with or without the leading slash")
+	assert.False(t, r.HasPath("/nope"))
+
+	reader, err := r.FileContentsByLocation(locations[0])
+	require.NoError(t, err)
+	body, err := io.ReadAll(reader)
+	require.NoError(t, err)
+	require.NoError(t, reader.Close())
+	assert.Equal(t, "Manifest-Version: 1.0\n", string(body))
+}
+
+func TestResolver_fullPathsOutsideTheArchiveNameNothing(t *testing.T) {
+	r, _ := resolverIn(t, memCharge(1<<20))
+	r.archiveCoordinates = file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/dep.jar"}
+	addAll(t, r, fileEntries(map[string]string{"/app.war": "same name", "/META-INF/MANIFEST.MF": "m"}))
+
+	locations, err := r.FilesByPath("/app.war!/WEB-INF/lib/dep.jar!/META-INF/MANIFEST.MF")
+	require.NoError(t, err)
+	assert.Len(t, locations, 1, "a full path in this archive")
+
+	for _, p := range []string{"/app.war!/WEB-INF/lib/dep.jar", "/app.war!/WEB-INF/lib/other.jar!/META-INF/MANIFEST.MF"} {
+		locations, err = r.FilesByPath(p)
+		require.NoError(t, err)
+		assert.Empty(t, locations, "%s is outside the archive", p)
+		assert.False(t, r.HasPath(p), p)
+	}
+
+	for _, p := range []string{"app.war", "/app.war"} {
+		locations, err = r.FilesByPath(p)
+		require.NoError(t, err)
+		require.Len(t, locations, 1, "%s is an entry path named like the outermost archive", p)
+		assert.Equal(t, "/app.war!/WEB-INF/lib/dep.jar!/app.war", locations[0].FullPath, p)
+	}
+
+	again, err := r.FilesByPath(locations[0].LocalPath())
+	require.NoError(t, err)
+	assert.Equal(t, locations, again, "a LocalPath finds its own entry")
+}
+
+func TestResolver_mimeTypesAreSniffedFromContent(t *testing.T) {
+	r := resolverOver(t, 1<<20, map[string]string{
+		"notes.txt": "just some text",
+		"run.sh":    "#!/bin/bash\necho hello\n",
+	})
+
+	locations, err := r.FilesByMIMEType("text/x-shellscript")
+	require.NoError(t, err)
+	assert.Equal(t, []string{"/run.sh"}, localPaths(locations))
+}
+
+func TestResolver_answersAreOrdered(t *testing.T) {
+	// order decides which locations group into which package when results merge into the SBOM
+	entries := map[string]string{}
+	for _, name := range []string{
+		"b/z.jar", "a/y.jar", "c/x.jar", "a/b/c/w.jar", "z.jar", "a.jar",
+	} {
+		entries[name] = "PK\x03\x04 not really"
+	}
+	r := resolverOver(t, 1<<20, entries)
+
+	first, err := r.FilesByGlob("**/*.jar")
+	require.NoError(t, err)
+	require.Len(t, first, len(entries))
+
+	byMIME, err := r.FilesByMIMEType("application/octet-stream")
+	require.NoError(t, err)
+
+	for range 8 {
+		again, err := r.FilesByGlob("**/*.jar")
+		require.NoError(t, err)
+		assert.Equal(t, first, again)
+
+		mimeAgain, err := r.FilesByMIMEType("application/octet-stream")
+		require.NoError(t, err)
+		assert.Equal(t, byMIME, mimeAgain)
+
+		var all []string
+		for loc := range r.AllLocations(context.Background()) {
+			all = append(all, loc.LocalPath())
+		}
+		assert.True(t, sort.StringsAreSorted(all))
+	}
+
+	var paths []string
+	for _, loc := range first {
+		paths = append(paths, loc.LocalPath())
+	}
+	assert.True(t, sort.StringsAreSorted(paths), "ordered by path, not merely stable")
+}
+
+func TestResolver_impliedDirectoriesArePathsButNotFiles(t *testing.T) {
+	r := resolverOver(t, 1<<20, jarEntriesFixture)
+
+	assert.True(t, r.HasPath("META-INF"))
+	assert.True(t, r.HasPath("/META-INF/maven"))
+
+	locations, err := r.FilesByPath("META-INF")
+	require.NoError(t, err)
+	assert.Empty(t, locations)
+	locations, err = r.FilesByGlob("**/maven")
+	require.NoError(t, err)
+	assert.Empty(t, locations)
+}
+
+// stereoscope finds a directory's children by looking the directory up by name: directories the archive
+// never listed must be indexed, and the root, which has no name, answered another way
+func TestResolver_globsForADirectorysChildren(t *testing.T) {
+	r := resolverOver(t, 1<<20, map[string]string{
+		"LICENSE":                    "root",
+		"META-INF/LICENSE.txt":       "nested",
+		"META-INF/maven/g/a/pom.xml": "deeper",
+	})
+
+	assert.Equal(t, []string{"/LICENSE"}, globPaths(t, r, "/*"))
+	assert.Equal(t, []string{"/LICENSE"}, globPaths(t, r, "*"))
+	assert.Equal(t, []string{"/META-INF/LICENSE.txt"}, globPaths(t, r, "/META-INF/*"))
+	assert.Equal(t, []string{"/META-INF/LICENSE.txt"}, globPaths(t, r, "META-INF/*"))
+	assert.Equal(t, []string{"/META-INF/maven/g/a/pom.xml"}, globPaths(t, r, "**/a/*"))
+}
+
+func TestResolver_invalidGlobIsAnError(t *testing.T) {
+	r := resolverOver(t, 1<<20, jarEntriesFixture)
+	_, err := r.FilesByGlob("**/[")
+	assert.Error(t, err)
+}
+
+func globPaths(t *testing.T, r *Resolver, pattern string) []string {
+	t.Helper()
+	locations, err := r.FilesByGlob(pattern)
+	require.NoError(t, err)
+	return localPaths(locations)
+}
+
+// several paths to one file answer as one location: the file's own path when it matched, otherwise
+// the lowest-sorting link
+func TestResolver_linksCollapseToOnePath(t *testing.T) {
+	tests := []struct {
+		name    string
+		entries []testEntry
+		pattern string
+		want    []string
+		reason  string
+	}{
+		{
+			name: "the file itself beats every link to it",
+			entries: []testEntry{
+				{name: "opt/real.jar", body: "PK\x03\x04"},
+				{name: "opt/a-sym.jar", link: "real.jar"},
+				{name: "opt/z-sym.jar", link: "real.jar"},
+				{name: "opt/hard.jar", link: "opt/real.jar", hard: true},
+			},
+			pattern: "**/*.jar",
+			want:    []string{"/opt/real.jar"},
+			reason:  "one file, so one location - and it is named by the path that holds it",
+		},
+		{
+			name: "with no candidate naming the file, the lowest-sorting link wins",
+			entries: []testEntry{
+				{name: "opt/real.bin", body: "PK\x03\x04"},
+				{name: "opt/z-sym.jar", link: "real.bin"},
+				{name: "opt/a-sym.jar", link: "real.bin"},
+				{name: "opt/m-sym.jar", link: "real.bin"},
+			},
+			pattern: "**/*.jar",
+			want:    []string{"/opt/real.bin"},
+			reason:  "the content is the target's, so that is the real path the answer carries",
+		},
+		{
+			name: "distinct files stay distinct",
+			entries: []testEntry{
+				{name: "opt/one.jar", body: "one"},
+				{name: "opt/two.jar", body: "two"},
+				{name: "opt/one-sym.jar", link: "one.jar"},
+			},
+			pattern: "**/*.jar",
+			want:    []string{"/opt/one.jar", "/opt/two.jar"},
+			reason:  "collapsing is per file, not per pattern",
+		},
+		{
+			name: "a dangling link is not a file",
+			entries: []testEntry{
+				{name: "opt/real.jar", body: "PK\x03\x04"},
+				{name: "opt/gone.jar", link: "missing.jar"},
+			},
+			pattern: "**/*.jar",
+			want:    []string{"/opt/real.jar"},
+			reason:  "it names no content",
+		},
+		{
+			name: "two dangling links are two paths, not one",
+			entries: []testEntry{
+				{name: "opt/a.jar", link: "missing.jar"},
+				{name: "opt/b.jar", link: "missing.jar"},
+			},
+			pattern: "**/*.jar",
+			want:    nil,
+			reason:  "a link to nothing is not a file",
+		},
+		{
+			name: "a chain of links collapses onto the file at its end",
+			entries: []testEntry{
+				{name: "opt/real.jar", body: "PK\x03\x04"},
+				{name: "opt/mid.jar", link: "real.jar"},
+				{name: "opt/outer.jar", link: "mid.jar"},
+			},
+			pattern: "**/*.jar",
+			want:    []string{"/opt/real.jar"},
+			reason:  "following one hop at a time reaches the same file from every path",
+		},
+		{
+			name: "a cycle resolves to nothing rather than looping",
+			entries: []testEntry{
+				{name: "opt/a.jar", link: "b.jar"},
+				{name: "opt/b.jar", link: "a.jar"},
+			},
+			pattern: "**/*.jar",
+			want:    nil,
+			reason:  "neither reaches a file",
+		},
+		{
+			name: "a hard link resolves from the archive root, not from its own directory",
+			entries: []testEntry{
+				{name: "opt/real.jar", body: "PK\x03\x04"},
+				{name: "opt/nested/hard.jar", link: "opt/real.jar", hard: true},
+			},
+			pattern: "**/*.jar",
+			want:    []string{"/opt/real.jar"},
+			reason:  "read as relative it would resolve to opt/nested/opt/real.jar and dangle",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			r := resolverFrom(t, tt.entries...)
+			assert.Equal(t, tt.want, globPaths(t, r, tt.pattern), tt.reason)
+		})
+	}
+}
+
+func TestResolver_collapsedLocationReadsTheTarget(t *testing.T) {
+	r := resolverFrom(t,
+		testEntry{name: "opt/real.bin", body: "PK\x03\x04 real contents"},
+		testEntry{name: "opt/a-sym.jar", link: "real.bin"},
+		testEntry{name: "opt/z-sym.jar", link: "real.bin"},
+	)
+
+	locations, err := r.FilesByGlob("**/*.jar")
+	require.NoError(t, err)
+	require.Len(t, locations, 1)
+
+	assert.Equal(t, "/opt/real.bin", locations[0].LocalPath(), "content comes from the file")
+	assert.Equal(t, "outer.jar!/opt/a-sym.jar", locations[0].AccessPath, "the path searched by is the one matched")
+
+	reader, err := r.FileContentsByLocation(locations[0])
+	require.NoError(t, err)
+	t.Cleanup(func() { require.NoError(t, reader.Close()) })
+
+	body, err := io.ReadAll(reader)
+	require.NoError(t, err)
+	assert.Equal(t, "PK\x03\x04 real contents", string(body),
+		"a location standing for a link must still read the file's bytes, not the link's none")
+}
+
+func TestResolver_fullPathsAreTrimmedToEntryPaths(t *testing.T) {
+	// catalogers build queries from the full paths the resolver hands out, e.g. path.Dir plus a sibling
+	r := resolverOver(t, 1<<20, map[string]string{"pom.xml": "a", "lib/dep.jar": "b"})
+
+	locations, err := r.FilesByPath("outer.jar!/lib/dep.jar")
+	require.NoError(t, err)
+	require.Len(t, locations, 1)
+	assert.Equal(t, "outer.jar!/lib/dep.jar", locations[0].AccessPath)
+
+	locations, err = r.FilesByPath(path.Join(path.Dir(locations[0].AccessPath), "../pom.xml"))
+	require.NoError(t, err)
+	require.Len(t, locations, 1, "a sibling at the archive root is reached through the full path")
+	assert.Equal(t, "outer.jar!/pom.xml", locations[0].FullNestedPath())
+
+	assert.True(t, r.HasPath(path.Dir("outer.jar!/pom.xml")), "the directory of a root entry is the root")
+	assert.True(t, r.HasPath("lib/dep.jar"), "an entry path is still accepted")
+
+	locations, err = r.FilesByGlob("outer.jar!/**/*.jar")
+	require.NoError(t, err)
+	require.Len(t, locations, 1)
+}
+
+func TestResolver_danglingLinkHasNoContent(t *testing.T) {
+	r := resolverFrom(t, testEntry{name: "opt/gone.jar", link: "missing.jar"})
+
+	var locations []file.Location
+	for l := range r.AllLocations(context.Background()) {
+		locations = append(locations, l)
+	}
+	require.Len(t, locations, 1)
+	assert.Equal(t, "/opt/gone.jar", locations[0].LocalPath())
+
+	_, err := r.FileContentsByLocation(locations[0])
+	assert.Error(t, err, "a link to nothing has no content to read")
+
+	metadata, err := r.FileMetadataByLocation(locations[0])
+	require.NoError(t, err)
+	assert.Equal(t, "outer.jar!/opt/missing.jar", metadata.LinkDestination,
+		"where it pointed is still reported, resolved against the link's own directory")
+}
+
+func TestResolver_mimeTypeAnswersOnlyWithFiles(t *testing.T) {
+	r := resolverFrom(t,
+		testEntry{name: "opt/real.jar", body: "PK\x03\x04 zip contents here"},
+		testEntry{name: "opt/sym.jar", link: "real.jar"},
+		testEntry{name: "opt/hard.jar", link: "opt/real.jar", hard: true},
+		testEntry{name: "opt/gone.jar", link: "missing.jar"},
+		testEntry{name: "opt/notes.txt", body: "hello world"},
+	)
+
+	byMIME := func(types ...string) []string {
+		t.Helper()
+		locations, err := r.FilesByMIMEType(types...)
+		require.NoError(t, err)
+		return localPaths(locations)
+	}
+
+	assert.Equal(t, []string{"/opt/real.jar"}, byMIME("application/zip"),
+		"the file answers, not the two links to it")
+	assert.Equal(t, []string{"/opt/notes.txt"}, byMIME("text/plain"))
+	assert.Empty(t, byMIME(""),
+		"a link sniffs to no type, and must not be reachable by asking for that")
+	assert.Equal(t, []string{"/opt/notes.txt", "/opt/real.jar"}, byMIME("application/zip", "text/plain"))
+}
+
+// AllLocations enumerates what the archive holds rather than searching for files: the file metadata
+// cataloger records a row per path, links included
+func TestResolver_allLocationsKeepsEveryPath(t *testing.T) {
+	r := resolverFrom(t,
+		testEntry{name: "opt/real.jar", body: "PK\x03\x04"},
+		testEntry{name: "opt/sym.jar", link: "real.jar"},
+		testEntry{name: "opt/gone.jar", link: "missing.jar"},
+	)
+
+	var got []string
+	for l := range r.AllLocations(context.Background()) {
+		got = append(got, l.LocalPath())
+	}
+	assert.Equal(t, []string{"/opt/gone.jar", "/opt/real.jar", "/opt/sym.jar"}, got,
+		"every path the archive names, links included")
+}
+
+func TestResolver_add_anEntryOverTheCapIsSkippedAndReadNoFurther(t *testing.T) {
+	// one entry of an overlapping-entry bomb can inflate without bound; it must stop at the cap, cost
+	// the archive only that entry, and say so
+	orig := maxEntryBytes
+	maxEntryBytes = 1024
+	t.Cleanup(func() { maxEntryBytes = orig })
+
+	r, _ := resolverIn(t, memCharge(-1))
+	endless := &countingReader{r: zeroSource{}}
+	require.NoError(t, r.add(tar.Header{Name: "bomb.bin", Typeflag: tar.TypeReg, Mode: 0o644}, endless))
+	require.NoError(t, r.add(tar.Header{Name: "ok.txt", Typeflag: tar.TypeReg, Mode: 0o644}, strings.NewReader("ok")))
+	r.finish()
+
+	assert.LessOrEqual(t, endless.n, 1024+copyChunkSize, "reading stops just past the cap")
+	assert.ErrorIs(t, r.Truncated, errEntryTooLarge)
+	assert.ErrorContains(t, r.Truncated, "per-entry size cap of 1.0 KiB")
+	locations, err := r.FilesByGlob("**")
+	require.NoError(t, err)
+	assert.Equal(t, []string{"/ok.txt"}, localPaths(locations))
+}
+
+type countingReader struct {
+	r io.Reader
+	n int
+}
+
+func (c *countingReader) Read(p []byte) (int, error) {
+	n, err := c.r.Read(p)
+	c.n += n
+	return n, err
+}

internal/archive/storage.go

@@ -0,0 +1,217 @@
+package archive
+
+import (
+	"bytes"
+	"context"
+	"errors"
+	"fmt"
+	"io"
+	"os"
+
+	"github.com/anchore/syft/internal/log"
+)
+
+// copyChunkSize is how many bytes are read and charged at a time, bounding how far a charge runs
+// ahead of what is actually held.
+const copyChunkSize = 32 * 1024
+
+// spillFilePattern names the one file an archive's content spills into, as in os.CreateTemp.
+const spillFilePattern = "archive-spill-*"
+
+// ReaderAtSeeker is the random access an archive format needs: a zip is read from its central
+// directory at the end of the stream.
+type ReaderAtSeeker interface {
+	io.Reader
+	io.ReaderAt
+	io.Seeker
+}
+
+// blob is one piece of content the resolver holds: in memory, or at an offset in its spill file once
+// memory refused it. Moving changes nothing that points at the blob.
+type blob struct {
+	mem  []byte // content while held in memory
+	off  int64  // where content starts in the spill file once written there
+	size int64
+}
+
+// put reads content in full into b, since archive readers are sequential. Each chunk is charged before it
+// is held, so a stream larger than the memory limit is never held in full. Reaching the disk limit
+// returns ErrDiskLimitReached; what landed in the file before that stays there and stays charged.
+func (r *Resolver) put(b *blob, content io.Reader) error {
+	if r.chunk == nil {
+		r.chunk = make([]byte, copyChunkSize)
+	}
+	for {
+		n, readErr := content.Read(r.chunk)
+		if n > 0 {
+			// content read through a meteredReader was charged as it was decoded
+			if !r.metered && !r.budget.take(int64(n)) {
+				return errBudgetSpent
+			}
+			if err := r.write(b, r.chunk[:n]); err != nil {
+				return err
+			}
+		}
+		if readErr == nil {
+			continue
+		}
+		if errors.Is(readErr, io.EOF) {
+			break
+		}
+		return readErr
+	}
+	return nil
+}
+
+// meteredReader charges the decompression budget for every byte read through it and stops once ctx is
+// done, so nothing a decoder produces gets around the budget.
+type meteredReader struct {
+	ctx    context.Context
+	reader io.Reader
+	budget *Budget
+}
+
+func (m *meteredReader) Read(p []byte) (int, error) {
+	if err := m.ctx.Err(); err != nil {
+		return 0, err
+	}
+	n, err := m.reader.Read(p)
+	if n > 0 && !m.budget.take(int64(n)) {
+		return 0, errBudgetSpent
+	}
+	return n, err
+}
+
+// write appends p to b: into memory while the memory limit admits it, otherwise into the spill file
+// after everything held in memory is moved there first.
+func (r *Resolver) write(b *blob, p []byte) error {
+	n := int64(len(p))
+	onDisk := b.mem == nil && b.size > 0
+	if !onDisk {
+		if r.charge.memory(n) {
+			if b.mem == nil {
+				r.held = append(r.held, b)
+			}
+			b.mem = append(b.mem, p...)
+			b.size += n
+			return nil
+		}
+		if err := r.spill(); err != nil {
+			return err
+		}
+	}
+
+	if err := r.openFile(); err != nil {
+		return err
+	}
+	if !r.charge.disk(n) {
+		return ErrDiskLimitReached
+	}
+	if b.size == 0 {
+		b.off = r.written
+	}
+	// b is always the blob most recently written, so it ends where the file does
+	w, err := r.file.WriteAt(p, r.written)
+	r.written += int64(w)
+	b.size += int64(w)
+	r.charge.refundDisk(n - int64(w))
+	if err != nil {
+		return fmt.Errorf("unable to write archive content to disk: %w", err)
+	}
+	return nil
+}
+
+// spill moves every blob held in memory into the spill file, charging the disk limit as bytes land
+// and refunding the memory they leave.
+func (r *Resolver) spill() error {
+	if len(r.held) == 0 {
+		return nil
+	}
+	if err := r.openFile(); err != nil {
+		return err
+	}
+	log.WithFields("archive", r.archiveCoordinates.FullNestedPath(), "held", len(r.held), "bytes", r.written).
+		Debug("archive content does not fit in memory; writing it to disk")
+
+	for len(r.held) > 0 {
+		b := r.held[0]
+		n := int64(len(b.mem))
+		if !r.charge.disk(n) {
+			return ErrDiskLimitReached
+		}
+		if _, err := r.file.WriteAt(b.mem, r.written); err != nil {
+			return fmt.Errorf("unable to write archive content to disk: %w", err)
+		}
+		b.off, b.mem = r.written, nil
+		r.written += n
+		r.charge.refundMemory(n)
+		r.held = r.held[1:]
+	}
+	return nil
+}
+
+func (r *Resolver) openFile() error {
+	if r.file != nil {
+		return nil
+	}
+	var err error
+	if r.tempDir != nil {
+		r.file, r.remove, err = r.tempDir.NewFile(spillFilePattern)
+	} else {
+		r.file, err = os.CreateTemp("", spillFilePattern)
+		r.remove = func() {
+			if err := os.Remove(r.file.Name()); err != nil {
+				log.WithFields("path", r.file.Name(), "error", err).Trace("unable to remove archive temp file")
+			}
+		}
+	}
+	if err != nil {
+		return fmt.Errorf("unable to create archive temp file: %w", err)
+	}
+	return nil
+}
+
+// discard drops a blob's bytes held in memory and refunds them. Bytes it holds on disk stay until
+// Cleanup.
+func (r *Resolver) discard(b *blob) {
+	for i, held := range r.held {
+		if held == b {
+			r.held = append(r.held[:i], r.held[i+1:]...)
+			break
+		}
+	}
+	r.charge.refundMemory(int64(len(b.mem)))
+	b.mem, b.size = nil, 0
+}
+
+// open returns a reader over a blob's content, wherever it is. The reader supports Read, Seek and
+// ReadAt, so a nested archive can be read where it lies.
+func (r *Resolver) open(b *blob) ReaderAtSeeker {
+	switch {
+	case b.mem != nil:
+		return bytes.NewReader(b.mem)
+	case b.size == 0:
+		return bytes.NewReader(nil)
+	default:
+		return io.NewSectionReader(r.file, b.off, b.size)
+	}
+}
+
+// releaseStorage refunds every blob held in memory and closes, removes and refunds the spill file.
+// Readers from open must not be used after this. Safe to call more than once.
+func (r *Resolver) releaseStorage() {
+	for _, b := range r.held {
+		r.charge.refundMemory(int64(len(b.mem)))
+		b.mem = nil
+	}
+	r.held = nil
+	if r.file == nil {
+		return
+	}
+	if err := r.file.Close(); err != nil {
+		log.WithFields("archive", r.archiveCoordinates.FullNestedPath(), "error", err).Trace("unable to close archive temp file")
+	}
+	r.remove()
+	r.charge.refundDisk(r.written)
+	r.file, r.remove, r.written = nil, nil, 0
+}

internal/archive/storage_test.go

@@ -0,0 +1,276 @@
+package archive
+
+import (
+	"archive/zip"
+	"bytes"
+	"fmt"
+	"io"
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+func TestResolver_put_holdsSmallContentInMemory(t *testing.T) {
+	s, dir := resolverIn(t, memCharge(1024))
+
+	var b blob
+	require.NoError(t, s.put(&b, bytes.NewReader([]byte("hello"))))
+
+	assert.Equal(t, int64(5), s.heldInMemory())
+	assert.Empty(t, filesIn(t, dir))
+	assert.Equal(t, "hello", readEntry(t, s.open(&b)))
+}
+
+func TestResolver_put_spillsToDiskAndKeepsTheSameBlobs(t *testing.T) {
+	// nodes pointing at a blob are not rebuilt when its content moves
+	s, dir := resolverIn(t, memCharge(8))
+
+	var first, second blob
+	require.NoError(t, s.put(&first, bytes.NewReader([]byte("aaaa"))))
+	require.Equal(t, int64(4), s.heldInMemory())
+
+	require.NoError(t, s.put(&second, bytes.NewReader([]byte("bbbbbb"))))
+
+	assert.Zero(t, s.heldInMemory(), "everything moves out, not just the blob that did not fit")
+	assert.NotEmpty(t, spillFile(t, dir))
+	assert.Equal(t, int64(10), s.written)
+	assert.Equal(t, "aaaa", readEntry(t, s.open(&first)))
+	assert.Equal(t, "bbbbbb", readEntry(t, s.open(&second)))
+}
+
+func TestResolver_put_threeStateLimits(t *testing.T) {
+	body := []byte(strings.Repeat("e", 500))
+
+	t.Run("a zero memory limit sends everything to disk", func(t *testing.T) {
+		charge := NewLimiter(Limits{MaxMemoryBytes: 0, MaxDiskBytes: 10_000}).charge()
+		s, dir := resolverIn(t, charge)
+
+		var b blob
+		require.NoError(t, s.put(&b, bytes.NewReader(body)))
+
+		assert.Zero(t, s.heldInMemory())
+		assert.NotEmpty(t, spillFile(t, dir))
+		assert.Equal(t, body, []byte(readEntry(t, s.open(&b))))
+		mem, disk := charge.held()
+		assert.Zero(t, mem)
+		assert.Equal(t, int64(500), disk)
+	})
+
+	t.Run("a negative memory limit holds content regardless of how much is already held", func(t *testing.T) {
+		charge := NewLimiter(Limits{MaxMemoryBytes: -1, MaxDiskBytes: 10_000}).charge()
+		require.True(t, charge.memory(1_000_000))
+		s, dir := resolverIn(t, charge)
+
+		var b blob
+		require.NoError(t, s.put(&b, bytes.NewReader(body)))
+
+		assert.Empty(t, filesIn(t, dir))
+		mem, disk := charge.held()
+		assert.Equal(t, int64(1_000_000+len(body)), mem)
+		assert.Zero(t, disk)
+	})
+
+	t.Run("a zero disk limit still holds what memory admits", func(t *testing.T) {
+		charge := NewLimiter(Limits{MaxMemoryBytes: 10_000, MaxDiskBytes: 0}).charge()
+		s, dir := resolverIn(t, charge)
+
+		var b blob
+		require.NoError(t, s.put(&b, bytes.NewReader(body)))
+
+		assert.Empty(t, filesIn(t, dir))
+		mem, disk := charge.held()
+		assert.Equal(t, int64(len(body)), mem)
+		assert.Zero(t, disk)
+	})
+
+	t.Run("a negative disk limit writes with no ceiling", func(t *testing.T) {
+		s, dir := resolverIn(t, NewLimiter(Limits{MaxMemoryBytes: 0, MaxDiskBytes: -1}).charge())
+
+		var b blob
+		require.NoError(t, s.put(&b, bytes.NewReader(body)))
+
+		assert.NotEmpty(t, spillFile(t, dir))
+		assert.Equal(t, body, []byte(readEntry(t, s.open(&b))))
+	})
+
+	t.Run("a nil charge holds everything in memory", func(t *testing.T) {
+		s, dir := resolverIn(t, nil)
+
+		var b blob
+		require.NoError(t, s.put(&b, bytes.NewReader(body)))
+
+		assert.Empty(t, filesIn(t, dir))
+		assert.Equal(t, body, []byte(readEntry(t, s.open(&b))))
+	})
+}
+
+func TestResolver_put_bytesReadBeforeTheLimitRefusedAreNotLost(t *testing.T) {
+	body := []byte(strings.Repeat("b", 250))
+	charge := NewLimiter(Limits{MaxMemoryBytes: 100, MaxDiskBytes: 10_000}).charge()
+	s, _ := resolverIn(t, charge)
+
+	var b blob
+	require.NoError(t, s.put(&b, bytes.NewReader(body)))
+
+	assert.Equal(t, body, []byte(readEntry(t, s.open(&b))))
+	mem, disk := charge.held()
+	assert.Zero(t, mem, "nothing stays charged to a limit that refused")
+	assert.Equal(t, int64(250), disk)
+}
+
+// peakTrackingReader records the highest memory charge observed while being read.
+type peakTrackingReader struct {
+	r      io.Reader
+	charge *charge
+	peak   int64
+}
+
+func (p *peakTrackingReader) Read(b []byte) (int, error) {
+	n, err := p.r.Read(b)
+	if mem, _ := p.charge.held(); mem > p.peak {
+		p.peak = mem
+	}
+	return n, err
+}
+
+func TestResolver_put_neverBuffersBeyondTheMemoryLimit(t *testing.T) {
+	const limit = int64(3 * copyChunkSize)
+	body := []byte(strings.Repeat("c", 10*copyChunkSize))
+	charge := NewLimiter(Limits{MaxMemoryBytes: limit, MaxDiskBytes: int64(len(body)) + 1}).charge()
+	tracked := &peakTrackingReader{r: bytes.NewReader(body), charge: charge}
+	s, _ := resolverIn(t, charge)
+
+	var b blob
+	require.NoError(t, s.put(&b, tracked))
+
+	assert.Equal(t, body, []byte(readEntry(t, s.open(&b))))
+	assert.LessOrEqual(t, tracked.peak, limit, "memory charged must never exceed the limit, even transiently")
+	mem, disk := charge.held()
+	assert.Zero(t, mem)
+	assert.Equal(t, int64(len(body)), disk)
+}
+
+func TestResolver_put_diskLimitIsTerminal(t *testing.T) {
+	tests := []struct {
+		name   string
+		limits Limits
+	}{
+		{"a disk limit that is exceeded", Limits{MaxDiskBytes: 100}},
+		{"a zero disk limit", Limits{MaxMemoryBytes: 10, MaxDiskBytes: 0}},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			charge := NewLimiter(tt.limits).charge()
+			s, dir := resolverIn(t, charge)
+
+			var b blob
+			err := s.put(&b, bytes.NewReader([]byte(strings.Repeat("d", 500))))
+			require.ErrorIs(t, err, ErrDiskLimitReached)
+
+			s.Cleanup()
+			assert.Empty(t, filesIn(t, dir), "cleanup removes the partial file")
+			mem, disk := charge.held()
+			assert.Zero(t, mem)
+			assert.Zero(t, disk, "and refunds it")
+		})
+	}
+}
+
+func TestResolver_cleanupRefundsEverythingAndIsIdempotent(t *testing.T) {
+	charge := NewLimiter(Limits{MaxMemoryBytes: 8, MaxDiskBytes: -1}).charge()
+	s, dir := resolverIn(t, charge)
+
+	var spilled, held blob
+	require.NoError(t, s.put(&spilled, bytes.NewReader([]byte("spilled to disk"))))
+	require.NoError(t, s.put(&held, bytes.NewReader([]byte("held"))))
+	mem, disk := charge.held()
+	require.Equal(t, int64(4), mem)
+	require.Equal(t, int64(15), disk)
+	require.Equal(t, "held", readEntry(t, s.open(&held)))
+
+	s.Cleanup()
+
+	assert.Empty(t, filesIn(t, dir))
+	mem, disk = charge.held()
+	assert.Zero(t, mem)
+	assert.Zero(t, disk)
+	_, err := io.ReadAll(s.open(&spilled))
+	assert.Error(t, err, "readers over the spill file are no longer valid")
+	s.Cleanup()
+	mem, disk = charge.held()
+	assert.Zero(t, mem, "a second cleanup refunds nothing twice")
+	assert.Zero(t, disk)
+}
+
+func TestResolver_put_discardRefundsWhatIsHeldInMemory(t *testing.T) {
+	charge := memCharge(1024)
+	s, _ := resolverIn(t, charge)
+
+	var keep, drop blob
+	require.NoError(t, s.put(&keep, bytes.NewReader([]byte("keep"))))
+	require.NoError(t, s.put(&drop, bytes.NewReader([]byte("dropped"))))
+
+	s.discard(&drop)
+
+	mem, _ := charge.held()
+	assert.Equal(t, int64(4), mem)
+	assert.Equal(t, int64(4), s.heldInMemory())
+	assert.Empty(t, readEntry(t, s.open(&drop)))
+	assert.Equal(t, "keep", readEntry(t, s.open(&keep)))
+}
+
+func TestResolver_filesystemCostDoesNotTrackEntryCount(t *testing.T) {
+	small, smallRoot := extractedResolver(t, manyEntryZip(t, 2), spillingLimits)
+	large, largeRoot := extractedResolver(t, manyEntryZip(t, 5000), spillingLimits)
+
+	assert.Len(t, filesIn(t, smallRoot), 1)
+	assert.Len(t, filesIn(t, largeRoot), 1, "5000 entries cost the same filesystem entries as 2")
+
+	assert.Equal(t, 2, small.entries)
+	assert.Equal(t, 5000, large.entries)
+
+	// entries cost their content and nothing else on disk: no headers, no padding
+	assert.Equal(t, int64(2), small.written)
+	assert.Equal(t, int64(5000), large.written)
+}
+
+func TestResolver_anEntryAtTheEndIsReadBySeeking(t *testing.T) {
+	// the reader over an entry is a bounded window at its offset, not a re-read of what precedes it
+	const filler = 64 * 1024
+
+	var buf bytes.Buffer
+	zw := zip.NewWriter(&buf)
+	for i := range 8 {
+		w, err := zw.Create(fmt.Sprintf("filler%d.bin", i))
+		require.NoError(t, err)
+		_, err = w.Write(bytes.Repeat([]byte{byte(i)}, filler))
+		require.NoError(t, err)
+	}
+	last, err := zw.Create("zz-last.txt")
+	require.NoError(t, err)
+	wanted := strings.Repeat("last", 64)
+	_, err = last.Write([]byte(wanted))
+	require.NoError(t, err)
+	require.NoError(t, zw.Close())
+
+	r, root := extractedResolver(t, buf.Bytes(), spillingLimits)
+
+	body, err := os.ReadFile(filepath.Join(root, spillFile(t, root)))
+	require.NoError(t, err)
+	offset := int64(bytes.Index(body, []byte(wanted)))
+	require.Greater(t, offset, int64(len(body))*9/10, "the last entry must really be at the end of the file")
+
+	reader := r.open(contentAt(t, r, "/zz-last.txt"))
+	end, err := reader.Seek(0, io.SeekEnd)
+	require.NoError(t, err)
+	assert.Equal(t, int64(len(wanted)), end)
+
+	head := make([]byte, 8)
+	_, err = reader.ReadAt(head, 0)
+	require.NoError(t, err)
+	assert.Equal(t, wanted[:8], string(head))
+}

internal/archive/traversal.go

@@ -0,0 +1,194 @@
+package archive
+
+import (
+	"context"
+	"path"
+	"slices"
+	"strings"
+
+	"github.com/anchore/syft/syft/file"
+	"github.com/anchore/syft/syft/pkg"
+)
+
+// Traversal describes the archive whose contents a cataloger is running against. The archive
+// cataloger task puts one on the context before running catalogers inside an archive, so a cataloger
+// such as java can describe the archive it is inside without owning the recursion.
+type Traversal struct {
+	// Location is the archive file's location within its parent filesystem, including the access path
+	// it was reached by, so VirtualPath(Location) is the chain from the scan root as seen through that
+	// access path. The files inside it extend its real coordinates instead (see ContainerPath).
+	Location file.Location
+
+	// Digests are of the archive file itself, taken during extraction; a cataloger running inside the
+	// archive cannot compute them since the archive is not inside itself.
+	Digests []file.Digest
+
+	// Parent is the traversal of the archive this one is nested in, nil for an archive at the scan root.
+	Parent *Traversal
+
+	// Packages are those the catalogers found describing this archive (located at it), filled in once
+	// they have run. Catalogers inside a nested archive read them through Parent, as java does to link a
+	// nested jar to the jar that holds it.
+	Packages []pkg.Package
+}
+
+// FullPathIn is the full path of the entry at entryPath inside the archive whose full path is
+// containerPath, or entryPath itself for a blank containerPath (the scan root).
+func FullPathIn(containerPath, entryPath string) string {
+	if containerPath == "" {
+		return entryPath
+	}
+	// cleaning an already clean path allocates nothing
+	return containerPath + file.ArchivePathSeparator + strings.TrimPrefix(path.Clean(entryPath), "/")
+}
+
+// OwnerContainers are the containers a package owns files within: the container of each of its
+// locations, each once, as coordinates whose FullPath is the container's full path (blank at the scan
+// root). A package without locations owns files at the scan root. See OwnedCoordinates.
+func OwnerContainers(p pkg.Package) []file.Coordinates {
+	var out []file.Coordinates
+	for _, l := range p.Locations.ToUnorderedSlice() {
+		c := file.Coordinates{FileSystemID: l.FileSystemID}
+		if container := ContainerPath(l.Coordinates); container != "" {
+			c.RealPath, c.FullPath = l.RealPath, container
+		}
+		if !slices.Contains(out, c) {
+			out = append(out, c)
+		}
+	}
+	if len(out) == 0 {
+		out = append(out, file.Coordinates{})
+	}
+	return out
+}
+
+// OwnedCoordinates are the coordinates of the file at ownedPath within container, one of
+// OwnerContainers. At the scan root the path may still need resolving (it may pass through links).
+func OwnedCoordinates(container file.Coordinates, ownedPath string) file.Coordinates {
+	if container.FullPath == "" {
+		return file.Coordinates{RealPath: ownedPath, FileSystemID: container.FileSystemID}
+	}
+	return file.Coordinates{
+		RealPath:     container.RealPath,
+		FileSystemID: container.FileSystemID,
+		FullPath:     FullPathIn(container.FullPath, ownedPath),
+	}
+}
+
+// FullTraversalArchivePath is the archive's own full path, which is the ContainerPath of every file inside it. Outside
+// any archive (a nil Traversal) it is blank, as for files on the scanned filesystem.
+func (t *Traversal) FullTraversalArchivePath() string {
+	if t == nil {
+		return ""
+	}
+	return t.Location.FullNestedPath()
+}
+
+// ContainerPath returns the full path of the archive directly holding the file at c, or blank for a
+// file on the scanned filesystem, whether or not its FullPath is set.
+func ContainerPath(c file.Coordinates) string {
+	entries, ok := archiveEntries(c)
+	if !ok {
+		return ""
+	}
+	if i := strings.LastIndex(entries, file.ArchivePathSeparator); i >= 0 {
+		return c.RealPath + file.ArchivePathSeparator + entries[:i]
+	}
+	return c.RealPath
+}
+
+// ContainingArchive returns the coordinates of the archive directly holding the file at c, reporting false
+// for a file on the scanned filesystem.
+func ContainingArchive(c file.Coordinates) (file.Coordinates, bool) {
+	containerPath := ContainerPath(c)
+	if containerPath == "" {
+		return file.Coordinates{}, false
+	}
+	container := file.Coordinates{RealPath: c.RealPath, FileSystemID: c.FileSystemID}
+	if containerPath != c.RealPath {
+		container.FullPath = containerPath
+	}
+	return container, true
+}
+
+// archiveEntries is the "!/"-delimited chain of entry paths after RealPath, reporting false for a file
+// not inside an archive. RealPath is split off first, so a "!/" in it is not taken for a boundary.
+func archiveEntries(c file.Coordinates) (string, bool) {
+	remain, ok := strings.CutPrefix(c.FullNestedPath(), c.RealPath)
+	if !ok {
+		return "", false
+	}
+	return strings.CutPrefix(remain, file.ArchivePathSeparator)
+}
+
+// VirtualPath returns the colon-delimited chain of archives from the scan root to loc, ending in loc
+// itself as accessed: "app.war:WEB-INF/lib/dep.jar". Outside any archive it is the location's path
+// unchanged. In an entry name '%' is escaped as "%25" and then ':' as "%3A", so splitting on ':'
+// recovers the archive boundaries and no two entry names share an escaped form. Leading slashes are
+// dropped to match the java cataloger, which joins slash-less zip entry names onto the containing
+// archive's path.
+func VirtualPath(loc file.Location) string {
+	accessPath := loc.Path()
+	entries, ok := archiveEntries(loc.Coordinates)
+	if !ok {
+		return accessPath
+	}
+	segments := strings.Split(entries, file.ArchivePathSeparator)
+	if rest, ok := strings.CutPrefix(accessPath, ContainerPath(loc.Coordinates)); ok && strings.HasPrefix(rest, file.ArchivePathSeparator) {
+		accessPath = rest[len(file.ArchivePathSeparator):]
+	}
+	segments[len(segments)-1] = accessPath
+	for i, s := range segments {
+		segments[i] = strings.TrimPrefix(escapeEntryPath(s), "/")
+	}
+	return loc.RealPath + ":" + strings.Join(segments, ":")
+}
+
+var entryPathEscaper = strings.NewReplacer("%", "%25", ":", "%3A")
+
+func escapeEntryPath(p string) string {
+	if !strings.ContainsAny(p, "%:") {
+		return p
+	}
+	return entryPathEscaper.Replace(p)
+}
+
+type traversalCtxKey struct{}
+
+func WithTraversal(ctx context.Context, t *Traversal) context.Context {
+	return context.WithValue(ctx, traversalCtxKey{}, t)
+}
+
+// TraversalFromContext returns the archive traversal on the context, or nil outside an archive.
+func TraversalFromContext(ctx context.Context) *Traversal {
+	t, _ := ctx.Value(traversalCtxKey{}).(*Traversal)
+	return t
+}
+
+type budgetCtxKey struct{}
+
+// WithBudget sets the decompression budget that Extract spends from, for this archive and every archive
+// extracted beneath it.
+func WithBudget(ctx context.Context, b *Budget) context.Context {
+	return context.WithValue(ctx, budgetCtxKey{}, b)
+}
+
+func budgetFromContext(ctx context.Context) *Budget {
+	b, _ := ctx.Value(budgetCtxKey{}).(*Budget)
+	return b
+}
+
+type nestedCatalogingCtxKey struct{}
+
+// WithNestedCataloging marks the context of a scan whose archive cataloger task will extract every
+// archive and run the catalogers inside it. syft.CreateSBOM sets it before any task runs, so a
+// cataloger that would otherwise open archives itself can leave them to the task instead.
+func WithNestedCataloging(ctx context.Context) context.Context {
+	return context.WithValue(ctx, nestedCatalogingCtxKey{}, true)
+}
+
+// NestedCatalogingEnabled reports whether the archive cataloger task is extracting archives in this scan.
+func NestedCatalogingEnabled(ctx context.Context) bool {
+	enabled, _ := ctx.Value(nestedCatalogingCtxKey{}).(bool)
+	return enabled
+}

internal/archive/traversal_test.go

@@ -0,0 +1,113 @@
+package archive
+
+import (
+	"context"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/anchore/syft/syft/file"
+)
+
+func TestTraversalContextRoundTrip(t *testing.T) {
+	assert.Nil(t, TraversalFromContext(context.Background()))
+
+	trav := &Traversal{Location: file.NewLocation("app.war")}
+	ctx := WithTraversal(context.Background(), trav)
+	require.Same(t, trav, TraversalFromContext(ctx))
+
+	child := &Traversal{Location: locationIn("app.war", "WEB-INF/lib/dep.jar")}
+	ctx = WithTraversal(ctx, child)
+	require.Same(t, child, TraversalFromContext(ctx))
+}
+
+// locationIn is a location as the Resolver returns it: the outermost archive's real path, and the chain
+// of entry paths within it.
+func locationIn(realPath, archivePath string) file.Location {
+	return file.NewLocationFromCoordinates(file.Coordinates{RealPath: realPath, FullPath: realPath + file.ArchivePathSeparator + archivePath})
+}
+
+func TestContainerPath(t *testing.T) {
+	assert.Equal(t, "", ContainerPath(file.NewCoordinates("/app.war", "")))
+	assert.Equal(t, "", ContainerPath(file.Coordinates{RealPath: "/app.war", FullPath: "/app.war"}), "a top-level file whose FullPath is set")
+	assert.Equal(t, "", ContainerPath(file.Coordinates{RealPath: "/odd!/name"}), "a separator in a top-level real path is not an archive boundary")
+	assert.Equal(t, "", ContainerPath(file.Coordinates{RealPath: "/odd!/name", FullPath: "/odd!/name"}), "nor when FullPath is set")
+	assert.Equal(t, "/odd!/name.zip", ContainerPath(locationIn("/odd!/name.zip", "a.txt").Coordinates))
+	assert.Equal(t, "/odd!/name.zip!/b.jar", ContainerPath(locationIn("/odd!/name.zip", "b.jar!/a.txt").Coordinates))
+	assert.Equal(t, "/app.war", ContainerPath(locationIn("/app.war", "WEB-INF/lib/dep.jar").Coordinates))
+	assert.Equal(t, "/app.war!/WEB-INF/lib/dep.jar",
+		ContainerPath(locationIn("/app.war", "WEB-INF/lib/dep.jar!/META-INF/MANIFEST.MF").Coordinates))
+}
+
+func TestVirtualPath(t *testing.T) {
+	tests := []struct {
+		name     string
+		location file.Location
+		expected string
+	}{
+		{
+			name:     "outside an archive returns the path unchanged",
+			location: file.NewLocation("/WEB-INF/lib/dep.jar"),
+			expected: "/WEB-INF/lib/dep.jar",
+		},
+		{
+			name:     "outside an archive preserves a relative path",
+			location: file.NewLocation("some/dir/example.jar"),
+			expected: "some/dir/example.jar",
+		},
+		{
+			name:     "outside an archive with FullPath set returns the path unchanged",
+			location: file.NewLocationFromCoordinates(file.Coordinates{RealPath: "/odd!/name.jar", FullPath: "/odd!/name.jar"}),
+			expected: "/odd!/name.jar",
+		},
+		{
+			name:     "single level trims leading slash",
+			location: locationIn("app.war", "/WEB-INF/lib/dep.jar"),
+			expected: "app.war:WEB-INF/lib/dep.jar",
+		},
+		{
+			name:     "single level with slash-less entry",
+			location: locationIn("app.war", "WEB-INF/lib/dep.jar"),
+			expected: "app.war:WEB-INF/lib/dep.jar",
+		},
+		{
+			name:     "multi-level chain",
+			location: locationIn("app.war", "WEB-INF/lib/dep.jar!/inner/most.jar"),
+			expected: "app.war:WEB-INF/lib/dep.jar:inner/most.jar",
+		},
+		{
+			// a colon in the entry name must not be mistaken for a chain delimiter
+			name:     "colon in entry path is escaped",
+			location: locationIn("app.war", "WEB-INF/lib/dep:special.jar"),
+			expected: "app.war:WEB-INF/lib/dep%3Aspecial.jar",
+		},
+		{
+			name:     "every colon in the entry path is escaped",
+			location: locationIn("app.war", "lib/a:b:c.jar"),
+			expected: "app.war:lib/a%3Ab%3Ac.jar",
+		},
+		{
+			// or the literal text %3A would collide with an escaped colon
+			name:     "the escape character is itself escaped",
+			location: locationIn("outer.zip", "a%3Ab.jar"),
+			expected: "outer.zip:a%253Ab.jar",
+		},
+		{
+			name:     "access path is preferred over real path",
+			location: file.NewVirtualLocation("/real/dep.jar", "/link/dep.jar"),
+			expected: "/link/dep.jar",
+		},
+		{
+			name: "access path within an archive replaces the last entry",
+			location: file.NewVirtualLocationFromCoordinates(
+				file.Coordinates{RealPath: "app.war", FullPath: "app.war!/WEB-INF/lib/real.jar"}, "app.war!/WEB-INF/lib/link.jar"),
+			expected: "app.war:WEB-INF/lib/link.jar",
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			assert.Equal(t, tt.expected, VirtualPath(tt.location))
+		})
+	}
+}

internal/bus/helpers.go

@@ -1,6 +1,9 @@
 package bus
 
 import (
+	"context"
+	"sync"
+
 	"github.com/wagoodman/go-partybus"
 	"github.com/wagoodman/go-progress"
 
@@ -36,7 +39,82 @@ func Notify(message string) {
 	})
 }
 
-func StartCatalogerTask(info monitor.GenericTask, size int64, initialStage string) *monitor.TaskProgress {
+type catalogerTaskRegistryKey struct{}
+
+// catalogerTaskRegistry remembers the progress row each cataloger publishes. A cataloger runs once
+// over the scan root and again inside every archive the archive cataloger walks; a re-run reports
+// into the row it already owns rather than publishing another, and republishing an ID would replace
+// the live row with one the UI never sees completed.
+type catalogerTaskRegistry struct {
+	mu   sync.Mutex
+	rows map[string]*monitor.TaskProgress
+}
+
+// WithCatalogerTaskRegistry returns a context under which each cataloger publishes one progress row
+// however many times it runs. A context that already carries a registry is returned unchanged.
+func WithCatalogerTaskRegistry(ctx context.Context) context.Context {
+	if catalogerTaskRegistryFromContext(ctx) != nil {
+		return ctx
+	}
+	return context.WithValue(ctx, catalogerTaskRegistryKey{}, &catalogerTaskRegistry{
+		rows: make(map[string]*monitor.TaskProgress),
+	})
+}
+
+func catalogerTaskRegistryFromContext(ctx context.Context) *catalogerTaskRegistry {
+	reg, _ := ctx.Value(catalogerTaskRegistryKey{}).(*catalogerTaskRegistry)
+	return reg
+}
+
+// catalogerTaskKey identifies the row a task owns: its ID when it has one, otherwise its parent and
+// title (file catalogers publish no ID).
+func catalogerTaskKey(info monitor.GenericTask) string {
+	if info.ID != "" {
+		return "id:" + info.ID
+	}
+	return "title:" + info.ParentID + "/" + info.Title.Default
+}
+
+func StartCatalogerTask(ctx context.Context, info monitor.GenericTask, size int64, initialStage string) *monitor.TaskProgress {
+	reg := catalogerTaskRegistryFromContext(ctx)
+	if reg == nil {
+		return publishCatalogerTask(info, size, initialStage)
+	}
+
+	reg.mu.Lock()
+	defer reg.mu.Unlock()
+
+	key := catalogerTaskKey(info)
+	if row, ok := reg.rows[key]; ok {
+		resumeCatalogerTask(row, size, initialStage)
+		return row
+	}
+
+	t := publishCatalogerTask(info, size, initialStage)
+	reg.rows[key] = t
+
+	return t
+}
+
+// resumeCatalogerTask reopens a row an earlier run completed and grows its total by what this run
+// adds, so the row does not read as finished mid-walk. A row carrying a real failure keeps it.
+func resumeCatalogerTask(row *monitor.TaskProgress, size int64, initialStage string) {
+	if size < 0 || row.Size() < 0 {
+		row.SetTotal(-1)
+	} else {
+		row.SetTotal(row.Size() + size)
+	}
+
+	if progress.IsErrCompleted(row.Error()) {
+		row.SetError(nil)
+	}
+
+	if initialStage != "" {
+		row.AtomicStage.Set(initialStage)
+	}
+}
+
+func publishCatalogerTask(info monitor.GenericTask, size int64, initialStage string) *monitor.TaskProgress {
 	t := &monitor.TaskProgress{
 		AtomicStage: progress.NewAtomicStage(initialStage),
 		Manual:      progress.NewManual(size),

internal/bus/helpers_test.go

@@ -0,0 +1,152 @@
+package bus
+
+import (
+	"context"
+	"errors"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"github.com/wagoodman/go-progress"
+
+	"github.com/anchore/syft/syft/event/monitor"
+)
+
+func digestsTask() monitor.GenericTask {
+	return monitor.GenericTask{
+		Title:    monitor.Title{Default: "File digests"},
+		ParentID: monitor.TopLevelCatalogingTaskID,
+	}
+}
+
+func TestStartCatalogerTask_withoutARegistryEveryRunPublishes(t *testing.T) {
+	// the right answer for a caller driving a single pass: nothing re-runs, so nothing should be reused
+	ctx := context.Background()
+
+	first := StartCatalogerTask(ctx, digestsTask(), 2, "")
+	second := StartCatalogerTask(ctx, digestsTask(), 3, "")
+
+	assert.NotSame(t, first, second)
+	assert.Equal(t, int64(2), first.Size())
+	assert.Equal(t, int64(3), second.Size())
+}
+
+func TestStartCatalogerTask_reRunReportsIntoTheRowItAlreadyOwns(t *testing.T) {
+	ctx := WithCatalogerTaskRegistry(context.Background())
+
+	first := StartCatalogerTask(ctx, digestsTask(), 2, "")
+	first.Increment()
+	first.Increment()
+	first.SetCompleted()
+
+	// the archive walk reaches the same cataloger again, over an archive's contents this time
+	second := StartCatalogerTask(ctx, digestsTask(), 3, "")
+	require.Same(t, first, second, "a re-run must find the row it already published")
+
+	assert.Equal(t, int64(5), second.Size(), "the total must cover both runs, not just the first")
+	assert.False(t, progress.IsCompleted(second), "a row with work still to do must not read as complete")
+
+	for i := 0; i < 3; i++ {
+		second.Increment()
+	}
+	second.SetCompleted()
+
+	assert.Equal(t, int64(5), second.Current())
+	assert.Equal(t, int64(5), second.Size(), "the count must not run past the total")
+	assert.True(t, progress.IsCompleted(second))
+}
+
+func TestStartCatalogerTask_aTotalResolvedOnCompletionIsAddable(t *testing.T) {
+	// a run that could not say how much it would do says so when it signs off (Manual.SetCompleted
+	// backfills the total from the count), so by the time a re-run arrives there is a real number to
+	// add to. This is the file metadata cataloger's shape: it publishes -1 every run.
+	ctx := WithCatalogerTaskRegistry(context.Background())
+
+	row := StartCatalogerTask(ctx, digestsTask(), -1, "")
+	row.Increment()
+	row.SetCompleted()
+	require.Equal(t, int64(1), row.Size(), "signing off must resolve the total to what the run did")
+
+	require.Same(t, row, StartCatalogerTask(ctx, digestsTask(), -1, ""))
+	assert.Equal(t, int64(-1), row.Size(), "a re-run that cannot say its own size makes the row indeterminate again")
+
+	row.Increment()
+	row.SetCompleted()
+	assert.Equal(t, int64(2), row.Current())
+	assert.Equal(t, int64(2), row.Size(), "and signing off resolves it again, over both runs")
+}
+
+func TestStartCatalogerTask_indeterminateTotalsStayIndeterminate(t *testing.T) {
+	// a run whose size is unknown cannot be added to one that is known
+	tests := []struct {
+		name        string
+		first, next int64
+		complete    func(row *monitor.TaskProgress)
+	}{
+		{
+			name:  "the re-run cannot say its own size",
+			first: 2, next: -1,
+			complete: func(row *monitor.TaskProgress) { row.Increment(); row.SetCompleted() },
+		},
+		{
+			name:  "the first run did nothing, so completing resolved nothing",
+			first: -1, next: 3,
+			complete: func(row *monitor.TaskProgress) { row.SetCompleted() },
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			ctx := WithCatalogerTaskRegistry(context.Background())
+
+			row := StartCatalogerTask(ctx, digestsTask(), tt.first, "")
+			tt.complete(row)
+
+			require.Same(t, row, StartCatalogerTask(ctx, digestsTask(), tt.next, ""))
+			assert.Equal(t, int64(-1), row.Size())
+			assert.False(t, progress.IsCompleted(row), "an indeterminate row is not complete until it says so")
+		})
+	}
+}
+
+func TestStartCatalogerTask_aFailedRowKeepsItsFailure(t *testing.T) {
+	// a later run finding nothing wrong does not mean the earlier one succeeded
+	ctx := WithCatalogerTaskRegistry(context.Background())
+	failure := errors.New("unable to read the thing")
+
+	row := StartCatalogerTask(ctx, digestsTask(), 2, "")
+	row.SetError(failure)
+
+	require.Same(t, row, StartCatalogerTask(ctx, digestsTask(), 3, ""))
+	assert.ErrorIs(t, row.Error(), failure)
+}
+
+func TestStartCatalogerTask_rowsAreKeyedByTaskIdentity(t *testing.T) {
+	ctx := WithCatalogerTaskRegistry(context.Background())
+
+	byID := func(id string) monitor.GenericTask {
+		return monitor.GenericTask{ID: id, Title: monitor.Title{Default: "shared title"}}
+	}
+
+	assert.Same(t, StartCatalogerTask(ctx, byID("a"), -1, ""), StartCatalogerTask(ctx, byID("a"), -1, ""))
+	assert.NotSame(t, StartCatalogerTask(ctx, byID("a"), -1, ""), StartCatalogerTask(ctx, byID("b"), -1, ""),
+		"an ID is the identity where there is one, even when two tasks share a title")
+
+	// a task publishing without an ID, as every file cataloger does, is keyed by where it sits and what
+	// it is called
+	underCataloging := monitor.GenericTask{Title: monitor.Title{Default: "Files"}, ParentID: "cataloging"}
+	underSomethingElse := monitor.GenericTask{Title: monitor.Title{Default: "Files"}, ParentID: "other"}
+
+	assert.Same(t, StartCatalogerTask(ctx, underCataloging, -1, ""), StartCatalogerTask(ctx, underCataloging, -1, ""))
+	assert.NotSame(t, StartCatalogerTask(ctx, underCataloging, -1, ""), StartCatalogerTask(ctx, underSomethingElse, -1, ""))
+}
+
+func TestWithCatalogerTaskRegistry_isIdempotent(t *testing.T) {
+	// anything that re-runs catalogers may ask for a registry; a second one would hold none of the rows
+	// already published and every re-run would publish again
+	ctx := WithCatalogerTaskRegistry(context.Background())
+	row := StartCatalogerTask(ctx, digestsTask(), 2, "")
+
+	nested := WithCatalogerTaskRegistry(ctx)
+	assert.Same(t, row, StartCatalogerTask(nested, digestsTask(), 2, ""))
+}

internal/capabilities/generate/discover_cataloger_configs.go

@@ -9,6 +9,7 @@ import (
 	"os"
 	"path/filepath"
 	"regexp"
+	"slices"
 	"strings"
 
 	"github.com/anchore/syft/internal/capabilities/internal"
@@ -31,6 +32,10 @@ type ConfigInfo struct {
 
 var appConfigAnnotationPattern = regexp.MustCompile(`^//\s*app-config:\s*(.+)$`)
 
+// embeddedFieldsAnnotationPattern matches "// capabilities-fields: A, B" on an embedded struct, which limits
+// the embedded fields listed to the ones named (for a shared type the cataloger reads only part of).
+var embeddedFieldsAnnotationPattern = regexp.MustCompile(`^//\s*capabilities-fields:\s*(.+)$`)
+
 // DiscoverConfigs walks the cataloger directory and discovers all configuration structs
 // Returns map where key is "packageName.StructName" (e.g., "golang.CatalogerConfig")
 func DiscoverConfigs(repoRoot string) (map[string]ConfigInfo, error) {
@@ -160,6 +165,9 @@ func extractCatalogerConfigFieldsRecursive(structType *ast.StructType, visitedTy
 		if len(field.Names) == 0 {
 			// this is an embedded field - resolve and extract its fields
 			embeddedFields := resolveEmbeddedStructFields(field.Type, visitedTypes)
+			if only := embeddedFieldAllowlist(field.Doc); only != nil {
+				embeddedFields = slices.DeleteFunc(embeddedFields, func(f ConfigField) bool { return !only[f.Name] })
+			}
 			fields = append(fields, embeddedFields...)
 			continue
 		}
@@ -195,6 +203,26 @@ func extractCatalogerConfigFieldsRecursive(structType *ast.StructType, visitedTy
 	return fields
 }
 
+// embeddedFieldAllowlist returns the field names from a "capabilities-fields:" annotation, or nil when there
+// is none (every exported embedded field is listed).
+func embeddedFieldAllowlist(commentGroup *ast.CommentGroup) map[string]bool {
+	if commentGroup == nil {
+		return nil
+	}
+	for _, comment := range commentGroup.List {
+		matches := embeddedFieldsAnnotationPattern.FindStringSubmatch(comment.Text)
+		if len(matches) < 2 {
+			continue
+		}
+		only := make(map[string]bool)
+		for _, name := range strings.Split(matches[1], ",") {
+			only[strings.TrimSpace(name)] = true
+		}
+		return only
+	}
+	return nil
+}
+
 // resolveEmbeddedStructFields resolves an embedded struct type and extracts its fields recursively
 func resolveEmbeddedStructFields(fieldType ast.Expr, visitedTypes map[string]bool) []ConfigField {
 	// extract the type name from the expression

internal/capabilities/generate/discover_cataloger_configs_test.go

@@ -457,3 +457,32 @@ func TestDiscoverAllowedConfigStructs(t *testing.T) {
 		t.Logf("  - %s", configType)
 	}
 }
+
+func TestEmbeddedFieldAllowlist(t *testing.T) {
+	comments := func(lines ...string) *ast.CommentGroup {
+		g := &ast.CommentGroup{}
+		for _, l := range lines {
+			g.List = append(g.List, &ast.Comment{Text: l})
+		}
+		return g
+	}
+
+	tests := []struct {
+		name string
+		doc  *ast.CommentGroup
+		want map[string]bool
+	}{
+		{name: "no doc lists every field", doc: nil, want: nil},
+		{name: "no annotation lists every field", doc: comments("// Deprecated: use something else."), want: nil},
+		{
+			name: "annotation limits to the named fields",
+			doc:  comments("// Deprecated: use something else.", "// capabilities-fields: IncludeIndexedArchives, IncludeUnindexedArchives"),
+			want: map[string]bool{"IncludeIndexedArchives": true, "IncludeUnindexedArchives": true},
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			require.Equal(t, tt.want, embeddedFieldAllowlist(tt.doc))
+		})
+	}
+}

internal/cmptest/common_options.go

@@ -69,5 +69,5 @@ func locationSorter(a, b file.Location) int {
 		return strings.Compare(a.AccessPath, b.AccessPath)
 	}
 
-	return strings.Compare(a.RealPath, b.RealPath)
+	return strings.Compare(a.FullNestedPath(), b.FullNestedPath())
 }

internal/cmptest/location.go

@@ -14,5 +14,5 @@ func DefaultLocationComparer(x, y file.Location) bool {
 }
 
 func LocationComparerWithoutLayer(x, y file.Location) bool {
-	return cmp.Equal(x.RealPath, y.RealPath) && cmp.Equal(x.AccessPath, y.AccessPath)
+	return cmp.Equal(x.FullNestedPath(), y.FullNestedPath()) && cmp.Equal(x.AccessPath, y.AccessPath)
 }

internal/constants.go

@@ -3,7 +3,7 @@ package internal
 const (
 	// JSONSchemaVersion is the current schema version output by the JSON encoder
 	// This is roughly following the "SchemaVer" guidelines for versioning the JSON schema. Please see schema/json/README.md for details on how to increment.
-	JSONSchemaVersion = "16.1.11"
+	JSONSchemaVersion = "16.1.12"
 
 	// Changelog
 	// 16.1.0 - reformulated the python pdm fields (added "URL" and removed the unused "path" field).
@@ -18,4 +18,5 @@ const (
 	// 16.1.9 - add Symbols (grouped by owning package import path) to GolangBinaryBuildinfoEntry metadata
 	// 16.1.10 - add SafeTensorsModelInfo metadata type for the safetensors AI model cataloger
 	// 16.1.11 - add CpanDistribution and CpanUnpackedRelease metadata types for the perl catalogers
+	// 16.1.12 - add fullPath to file coordinates, naming the nested archive chain a file was found in (blank for files not within an archive)
 )

internal/file/copy.go

@@ -6,13 +6,13 @@ import (
 	"io"
 )
 
-const perFileReadLimit = 2 * GB
+// PerFileReadLimit is the most read from any one archive entry, guarding against decompression bombs.
+const PerFileReadLimit = 2 * GB
 
-// safeCopy limits the copy from the reader. This is useful when extracting files from archives to
-// protect against decompression bomb attacks.
-func safeCopy(writer io.Writer, reader io.Reader) error {
-	numBytes, err := io.Copy(writer, io.LimitReader(reader, perFileReadLimit))
-	if numBytes >= perFileReadLimit {
+// SafeCopy bounds the copy to guard against decompression bombs when extracting from archives.
+func SafeCopy(writer io.Writer, reader io.Reader) error {
+	numBytes, err := io.Copy(writer, io.LimitReader(reader, PerFileReadLimit))
+	if numBytes >= PerFileReadLimit {
 		return fmt.Errorf("zip read limit hit (potential decompression bomb attack)")
 	}
 	// Propagate decompression / read errors up to the caller. io.Copy

internal/file/copy_test.go

@@ -29,7 +29,7 @@ func (r *errReader) Read(p []byte) (int, error) {
 func TestSafeCopy(t *testing.T) {
 	t.Run("clean copy returns nil", func(t *testing.T) {
 		var buf bytes.Buffer
-		if err := safeCopy(&buf, strings.NewReader("hello")); err != nil {
+		if err := SafeCopy(&buf, strings.NewReader("hello")); err != nil {
 			t.Fatalf("unexpected error: %v", err)
 		}
 		if got := buf.String(); got != "hello" {
@@ -38,12 +38,12 @@ func TestSafeCopy(t *testing.T) {
 	})
 
 	t.Run("propagates decompression error", func(t *testing.T) {
-		// #4806: safeCopy used to drop non-EOF errors, so the caller
+		// #4806: SafeCopy used to drop non-EOF errors, so the caller
 		// would persist a partial buffer as a successful extract and
 		// downstream catalogers silently read empty manifests.
 		sentinel := errors.New("flate: corrupt input before offset 42")
 		var buf bytes.Buffer
-		err := safeCopy(&buf, &errReader{data: []byte("partial"), err: sentinel})
+		err := SafeCopy(&buf, &errReader{data: []byte("partial"), err: sentinel})
 		if err == nil {
 			t.Fatalf("expected error to be returned, got nil")
 		}
@@ -56,7 +56,7 @@ func TestSafeCopy(t *testing.T) {
 		// The old code had a dead io.EOF branch that labelled clean
 		// reads as decompression bombs; keep the happy path clean.
 		var buf bytes.Buffer
-		err := safeCopy(&buf, io.LimitReader(strings.NewReader("abc"), 3))
+		err := SafeCopy(&buf, io.LimitReader(strings.NewReader("abc"), 3))
 		if err != nil {
 			t.Fatalf("unexpected error on clean copy: %v", err)
 		}

internal/file/tar_file_traversal.go

@@ -70,7 +70,7 @@ func ExtractGlobsFromTarToUniqueTempFile(ctx context.Context, archivePath, dir s
 		}
 		defer internal.CloseAndLogError(packedFile, archivePath)
 
-		if err := safeCopy(tempFile, packedFile); err != nil {
+		if err := SafeCopy(tempFile, packedFile); err != nil {
 			return fmt.Errorf("unable to copy source=%q for tar=%q: %w", file.Name(), archivePath, err)
 		}
 

internal/file/zip_file_traversal.go

@@ -101,7 +101,7 @@ func ExtractFromZipToUniqueTempFile(ctx context.Context, archivePath, dir string
 			return fmt.Errorf("unable to extract directories, only files: %s", file.NameInArchive)
 		}
 
-		if err := safeCopy(tempFile, zippedFile); err != nil {
+		if err := SafeCopy(tempFile, zippedFile); err != nil {
 			return fmt.Errorf("unable to copy source=%q for zip=%q: %w", file.NameInArchive, archivePath, err)
 		}
 
@@ -138,7 +138,7 @@ func ContentsFromZip(ctx context.Context, archivePath string, paths ...string) (
 		}
 
 		var buffer bytes.Buffer
-		if err := safeCopy(&buffer, zippedFile); err != nil {
+		if err := SafeCopy(&buffer, zippedFile); err != nil {
 			return fmt.Errorf("unable to copy source=%q for zip=%q: %w", file.NameInArchive, archivePath, err)
 		}
 
@@ -210,7 +210,7 @@ func extractSingleFile(file archives.FileInfo, expandedFilePath, archivePath str
 			}
 		}()
 
-		if err := safeCopy(outputFile, zippedFile); err != nil {
+		if err := SafeCopy(outputFile, zippedFile); err != nil {
 			return fmt.Errorf("unable to copy source=%q to dest=%q for zip=%q: %w", file.NameInArchive, outputFile.Name(), archivePath, err)
 		}
 	}

internal/os/feature_detection.go

@@ -49,7 +49,7 @@ func findRhelFeatures(resolver file.Resolver, release *linux.Release) error {
 	for _, contentManifestFile := range contentManifestFiles {
 		found, err := fileMatchesAny(resolver, contentManifestFile, rhelEUSPatterns...)
 		if err != nil {
-			return fmt.Errorf("unable to read content manifest from %s: %w", contentManifestFile.RealPath, err)
+			return fmt.Errorf("unable to read content manifest from %s: %w", contentManifestFile.FullNestedPath(), err)
 		}
 		if found {
 			release.ExtendedSupport = true
@@ -163,9 +163,9 @@ func hasActiveUbuntuESMService(resolver file.Resolver) (bool, error) {
 func hasEnabledESMServiceInStatus(resolver file.Resolver, location file.Location) (bool, error) {
 	contents, err := resolver.FileContentsByLocation(location)
 	if err != nil {
-		return false, fmt.Errorf("unable to read ubuntu-advantage status from %s: %w", location.RealPath, err)
+		return false, fmt.Errorf("unable to read ubuntu-advantage status from %s: %w", location.FullNestedPath(), err)
 	}
-	defer internal.CloseAndLogError(contents, location.RealPath)
+	defer internal.CloseAndLogError(contents, location.FullNestedPath())
 
 	var status struct {
 		Services []struct {
@@ -174,7 +174,7 @@ func hasEnabledESMServiceInStatus(resolver file.Resolver, location file.Location
 		} `json:"services"`
 	}
 	if err := json.NewDecoder(contents).Decode(&status); err != nil {
-		return false, fmt.Errorf("unable to parse ubuntu-advantage status from %s: %w", location.RealPath, err)
+		return false, fmt.Errorf("unable to parse ubuntu-advantage status from %s: %w", location.FullNestedPath(), err)
 	}
 
 	// pro status values are enabled/disabled/n-a/warning/—; only "enabled" proves the stream is active.
@@ -200,8 +200,8 @@ func hasInstalledESMPackage(packages *pkg.Collection) bool {
 func fileMatchesAny(resolver file.Resolver, location file.Location, patterns ...*regexp.Regexp) (bool, error) {
 	contents, err := resolver.FileContentsByLocation(location)
 	if err != nil {
-		return false, fmt.Errorf("unable to read %s: %w", location.RealPath, err)
+		return false, fmt.Errorf("unable to read %s: %w", location.FullNestedPath(), err)
 	}
-	defer internal.CloseAndLogError(contents, location.RealPath)
+	defer internal.CloseAndLogError(contents, location.FullNestedPath())
 	return internal.MatchAnyFromReader(contents, patterns...)
 }

internal/relationship/binary/binary_dependencies.go

@@ -71,7 +71,7 @@ func compareElfBinaryPackages(s *sbom.SBOM) []artifact.ID {
 	pkgsToDelete := make([]artifact.ID, 0)
 	for _, elfPkg := range allElfPackages(s) {
 		for _, loc := range onlyPrimaryEvidenceLocations(elfPkg) {
-			for _, otherPkg := range s.Artifacts.Packages.PackagesByPath(loc.RealPath) {
+			for _, otherPkg := range s.Artifacts.Packages.PackagesByPath(loc.FullNestedPath()) {
 				// we only care about comparing binary packages to each other (not other types)
 				if otherPkg.Type != pkg.BinaryPkg {
 					continue
@@ -130,7 +130,7 @@ func populateRelationships(exec file.Executable, parentPkg pkg.Package, resolver
 
 		for _, loc := range libLocations {
 			// are you in our index?
-			realBaseName := path.Base(loc.RealPath)
+			realBaseName := path.Base(loc.FullNestedPath())
 			pkgCollection := index.owningLibraryPackage(realBaseName)
 			if pkgCollection.PackageCount() < 1 {
 				addRelationship(

internal/relationship/binary/shared_library_index.go

@@ -3,6 +3,7 @@ package binary
 import (
 	"path"
 
+	"github.com/anchore/syft/internal/archive"
 	"github.com/anchore/syft/internal/log"
 	"github.com/anchore/syft/internal/sbomsync"
 	"github.com/anchore/syft/syft/file"
@@ -63,7 +64,7 @@ func locationsThatProvideLibraries(accessor sbomsync.Accessor) (map[string]file.
 				continue
 			}
 
-			basename := path.Base(coord.RealPath)
+			basename := path.Base(coord.FullNestedPath())
 			set := libLocationsByBasename[basename]
 			set.Add(coord)
 			allLibLocations.Add(coord)
@@ -82,6 +83,11 @@ func packagesWithLibraryOwnership(resolver file.Resolver, accessor sbomsync.Acce
 			var ownedFilePaths []string
 			if p.Type == pkg.BinaryPkg {
 				for _, loc := range p.Locations.ToSlice() {
+					if archive.ContainerPath(loc.Coordinates) != "" {
+						// a path within an archive cannot be resolved from the scan root; the location is the library
+						addLibraryOwner(packagesByLibraryPath, allLibLocations, loc.Coordinates, p)
+						continue
+					}
 					ownedFilePaths = append(ownedFilePaths, loc.Path())
 				}
 			} else {
@@ -114,18 +120,19 @@ func populatePackagesByLibraryPath(
 		}
 
 		for _, loc := range ownedLocation {
-			// if the location is a library, add the package to the set of packages that own the library
-			if !allLibLocations.Contains(loc.Coordinates) {
-				continue
-			}
-
-			if _, ok := packagesByLibraryPath[loc.Coordinates]; !ok {
-				packagesByLibraryPath[loc.Coordinates] = pkg.NewCollection()
-			}
-
-			// we have a library path, add the package to the set of packages that own the library
-			packagesByLibraryPath[loc.Coordinates].Add(p)
+			addLibraryOwner(packagesByLibraryPath, allLibLocations, loc.Coordinates, p)
 		}
 	}
 	return packagesByLibraryPath
 }
+
+// addLibraryOwner records p as an owner of the file at coordinates when that file is a library.
+func addLibraryOwner(packagesByLibraryPath map[file.Coordinates]*pkg.Collection, allLibLocations file.CoordinateSet, coordinates file.Coordinates, p pkg.Package) {
+	if !allLibLocations.Contains(coordinates) {
+		return
+	}
+	if _, ok := packagesByLibraryPath[coordinates]; !ok {
+		packagesByLibraryPath[coordinates] = pkg.NewCollection()
+	}
+	packagesByLibraryPath[coordinates].Add(p)
+}

internal/relationship/by_file_ownership.go

@@ -6,6 +6,7 @@ import (
 	"github.com/bmatcuk/doublestar/v4"
 	"github.com/scylladb/go-set/strset"
 
+	"github.com/anchore/syft/internal/archive"
 	"github.com/anchore/syft/internal/log"
 	"github.com/anchore/syft/internal/sbomsync"
 	"github.com/anchore/syft/syft/artifact"
@@ -100,7 +101,7 @@ func findOwnershipByFilesRelationships(resolver file.Resolver, catalog *pkg.Coll
 	// Now establish relationships, considering symlinks
 	for _, candidateOwnerPkg := range catalog.Sorted() {
 		id := candidateOwnerPkg.ID()
-		if candidateOwnerPkg.Metadata == nil {
+		if candidateOwnerPkg.Metadata == nil || withinArchive(candidateOwnerPkg) {
 			continue
 		}
 
@@ -164,7 +165,7 @@ func directOwnersByPath(catalog *pkg.Collection) map[pkg.Type]*strset.Set {
 
 	// First, identify direct ownership of all files
 	for _, p := range catalog.Sorted() {
-		if p.Metadata == nil {
+		if p.Metadata == nil || withinArchive(p) {
 			continue
 		}
 
@@ -192,6 +193,21 @@ func directOwnersByPath(catalog *pkg.Collection) map[pkg.Type]*strset.Set {
 	return directOwnership
 }
 
+// withinArchive reports whether every location of p is inside an archive. Such a package's owned files
+// are paths within its archive, not the scan root, so it is not treated as a file owner.
+func withinArchive(p pkg.Package) bool {
+	locations := p.Locations.ToSlice()
+	if len(locations) == 0 {
+		return false
+	}
+	for _, l := range locations {
+		if archive.ContainerPath(l.Coordinates) == "" {
+			return false
+		}
+	}
+	return true
+}
+
 func resolvePaths(ownedFilePath string, resolver file.Resolver) []string {
 	// though we have a string path, we need to resolve symlinks and other filesystem oddities since we cannot assume this is a real path
 	var locs []file.Location
@@ -206,6 +222,8 @@ func resolvePaths(ownedFilePath string, resolver file.Resolver) []string {
 
 	ownedFilePaths := strset.New(ownedFilePath)
 	for _, loc := range locs {
+		// Owned file paths are currently based on the top-level resolver, which is always the RealPath and includes
+		// all files found within archives at that location
 		ownedFilePaths.Add(loc.RealPath)
 	}
 	return ownedFilePaths.List()

internal/relationship/by_file_ownership_test.go

@@ -78,6 +78,56 @@ func TestOwnershipByFilesRelationship(t *testing.T) {
 				return []pkg.Package{parent, child}, []artifact.Relationship{relationship}
 			},
 		},
+		{
+			name: "package-within-archive-is-not-a-file-owner",
+			setup: func(t testing.TB) ([]pkg.Package, []artifact.Relationship) {
+				nestedOwner := pkg.Package{
+					Locations: file.NewLocationSet(file.NewLocationFromCoordinates(file.Coordinates{
+						RealPath: "/rootfs.tar",
+						FullPath: "/rootfs.tar!/var/lib/rpm/Packages",
+					})),
+					Type: pkg.RpmPkg,
+					Metadata: pkg.RpmDBEntry{
+						Files: []pkg.RpmFileRecord{{Path: "/d/path"}},
+					},
+				}
+				nestedOwner.SetID()
+
+				child := pkg.Package{
+					Locations: file.NewLocationSet(file.NewLocation("/d/path")),
+					Type:      pkg.BinaryPkg,
+				}
+				child.SetID()
+
+				return []pkg.Package{nestedOwner, child}, nil
+			},
+		},
+		{
+			// the archive's own package (when it has one) is found by its path; what is inside it is
+			// linked to that package by CONTAINS, not owned by whoever owns the archive file
+			name: "top-level-owner-of-an-archive-does-not-own-packages-within-it",
+			setup: func(t testing.TB) ([]pkg.Package, []artifact.Relationship) {
+				parent := pkg.Package{
+					Locations: file.NewLocationSet(file.NewLocation("/var/lib/rpm/Packages")),
+					Type:      pkg.RpmPkg,
+					Metadata: pkg.RpmDBEntry{
+						Files: []pkg.RpmFileRecord{{Path: "/opt/bundle.tar"}},
+					},
+				}
+				parent.SetID()
+
+				child := pkg.Package{
+					Locations: file.NewLocationSet(file.NewLocationFromCoordinates(file.Coordinates{
+						RealPath: "/opt/bundle.tar",
+						FullPath: "/opt/bundle.tar!/lib/thing.jar",
+					})),
+					Type: pkg.JavaPkg,
+				}
+				child.SetID()
+
+				return []pkg.Package{parent, child}, nil
+			},
+		},
 		{
 			name: "only-real-file-owner-gets-ownership-relationship-not-symlink-owner",
 			resolver: mockFR{

internal/relationship/evident_by_test.go

@@ -15,18 +15,9 @@ func TestRelationshipsEvidentBy(t *testing.T) {
 
 	c := pkg.NewCollection()
 
-	coordA := file.Coordinates{
-		RealPath:     "/somewhere/real",
-		FileSystemID: "abc",
-	}
-	coordC := file.Coordinates{
-		RealPath:     "/somewhere/real",
-		FileSystemID: "abc",
-	}
-	coordD := file.Coordinates{
-		RealPath:     "/somewhere/real",
-		FileSystemID: "abc",
-	}
+	coordA := file.NewCoordinates("/somewhere/real", "abc")
+	coordC := file.NewCoordinates("/somewhere/real", "abc")
+	coordD := file.NewCoordinates("/somewhere/real", "abc")
 	pkgA := pkg.Package{
 		Locations: file.NewLocationSet(
 			// added!
@@ -39,10 +30,7 @@ func TestRelationshipsEvidentBy(t *testing.T) {
 	pkgA.SetID()
 	c.Add(pkgA)
 
-	coordB := file.Coordinates{
-		RealPath:     "/somewhere-else/real",
-		FileSystemID: "def",
-	}
+	coordB := file.NewCoordinates("/somewhere-else/real", "def")
 	pkgB := pkg.Package{
 		Locations: file.NewLocationSet(
 			// added!

internal/relationship/index_test.go

@@ -21,12 +21,8 @@ func Test_Index(t *testing.T) {
 	p3 := pkg.Package{
 		Name: "pkg-3",
 	}
-	c1 := file.Coordinates{
-		RealPath: "/coords/1",
-	}
-	c2 := file.Coordinates{
-		RealPath: "/coords/2",
-	}
+	c1 := file.NewCoordinates("/coords/1", "")
+	c2 := file.NewCoordinates("/coords/2", "")
 
 	for _, p := range []*pkg.Package{&p1, &p2, &p3} {
 		p.SetID()
@@ -156,18 +152,10 @@ func Test_Coordinates(t *testing.T) {
 	p3 := pkg.Package{
 		Name: "pkg-3",
 	}
-	c1 := file.Coordinates{
-		RealPath: "/coords/1",
-	}
-	c2 := file.Coordinates{
-		RealPath: "/coords/2",
-	}
-	c3 := file.Coordinates{
-		RealPath: "/coords/3",
-	}
-	c4 := file.Coordinates{
-		RealPath: "/coords/4",
-	}
+	c1 := file.NewCoordinates("/coords/1", "")
+	c2 := file.NewCoordinates("/coords/2", "")
+	c3 := file.NewCoordinates("/coords/3", "")
+	c4 := file.NewCoordinates("/coords/4", "")
 
 	for _, p := range []*pkg.Package{&p1, &p2, &p3} {
 		p.SetID()
@@ -237,10 +225,10 @@ func TestRemove(t *testing.T) {
 	p1 := pkg.Package{Name: "pkg-1"}
 	p2 := pkg.Package{Name: "pkg-2"}
 	p3 := pkg.Package{Name: "pkg-3"}
-	c1 := file.Coordinates{RealPath: "/coords/1"}
-	c2 := file.Coordinates{RealPath: "/coords/2"}
-	c3 := file.Coordinates{RealPath: "/coords/3"}
-	c4 := file.Coordinates{RealPath: "/coords/4"}
+	c1 := file.NewCoordinates("/coords/1", "")
+	c2 := file.NewCoordinates("/coords/2", "")
+	c3 := file.NewCoordinates("/coords/3", "")
+	c4 := file.NewCoordinates("/coords/4", "")
 
 	for _, p := range []*pkg.Package{&p1, &p2, &p3} {
 		p.SetID()

internal/spdxlicense/license_list.go

@@ -2131,40 +2131,40 @@ var urlToLicense = map[string]string{
 	"raw.githubusercontent.com/NTIA/scos-sensor/refs/heads/master/LICENSE.md":                                        "NTIA-PD",
 	"raw.githubusercontent.com/OpenMDW/OpenMDW/refs/heads/main/1.0/LICENSE.openmdw":                                  "OpenMDW-1.0",
 	"raw.githubusercontent.com/blackhole89/notekit/master/data/fonts/Charter%20license.txt":                          "Bitstream-Charter",
-	"raw.githubusercontent.com/landtuna/open-mtools/6c04c2882eca7c4313ec267766ea53ac9bfe129b/mdump.c": "Informatica",
-	"raw.githubusercontent.com/landtuna/open-mtools/6c04c2882eca7c4313ec267766ea53ac9bfe129b/msend.c": "Informatica",
-	"rc.quest.com/topics/openssh/license.php#tcpwrappers":                                             "TCP-wrappers",
-	"research.cs.wisc.edu/condor/license.html#condor":                                                 "Condor-1.1",
-	"research.scea.com/scea_shared_source_license.html":                                               "SCEA",
-	"romanrm.net/mit-zero":                                                                                                                       "MIT-0",
-	"sam.zoy.org/wtfpl/COPYING":                                                                                                                  "WTFPL",
-	"scancode-licensedb.aboutcode.org/bsd-unchanged":                                                                                             "BSD-2-Clause-pos-unchanged",
-	"scripts.sil.org/cms/scripts/page.php?item_id=OFL10_web":                                                                                     "OFL-1.0-no-RFN",
-	"scripts.sil.org/cms/scripts/page.php?item_id=OFL_web":                                                                                       "OFL-1.1-no-RFN",
-	"slicer.org/LICENSE":                                                                                                                         "3D-Slicer-1.0",
-	"solderpad.org/licenses/SHL-0.5/":                                                                                                            "SHL-0.5",
-	"solderpad.org/licenses/SHL-0.51/":                                                                                                           "SHL-0.51",
-	"source.icu-project.org/repos/icu/icu/trunk/license.html":                                                                                    "ICU",
-	"sourceforge.net/p/buddy/gitcode/ci/master/tree/README":                                                                                      "Buddy",
-	"sourceforge.net/p/ctrio/git/ci/master/tree/README":                                                                                          "ISC-Veillard",
-	"sourceforge.net/p/mcj/xfig/ci/master/tree/src/Makefile.am":                                                                                  "Xfig",
-	"sourceforge.net/p/netpbm/code/HEAD/tree/super_stable/converter/other/pnmtorle.c":                                                            "URT-RLE",
-	"sourceforge.net/p/netpbm/code/HEAD/tree/super_stable/converter/other/rletopnm.c":                                                            "URT-RLE",
-	"sourceforge.net/p/netpbm/code/HEAD/tree/super_stable/converter/ppm/ppmtompeg/jrevdct.c#l1189":                                               "MPEG-SSG",
-	"sourceforge.net/p/netpbm/code/HEAD/tree/super_stable/editor/pnmstitch.c#l2":                                                                 "pnmstitch",
-	"sourceforge.net/p/netpbm/code/HEAD/tree/super_stable/netpbm.c#l8":                                                                           "HPND-Pbmplus",
-	"sourceforge.net/p/sbcl/sbcl/ci/master/tree/src/code/loop.lisp":                                                                              "LOOP",
-	"sourceforge.net/p/trustedqsl/tqsl/ci/master/tree/LICENSE.txt":                                                                               "TrustedQSL",
-	"sourceforge.net/p/xmedcon/code/ci/master/tree/libs/dicom/README":                                                                            "OFFIS",
-	"sourceforge.net/p/xmedcon/code/ci/master/tree/libs/ljpg/":                                                                                   "IJG-short",
-	"sourceforge.net/projects/sevenzip/files/LZMA%20SDK/":                                                                                        "LZMA-SDK-9.22",
-	"sources.debian.org/copyright/license/debianutils/4.11.2/":                                                                                   "SMAIL-GPL",
-	"sources.debian.org/src/openmpi/4.1.0-10/ompi/debuggers/msgq_interface.h/?hl=19#L19":                                                         "mpi-permissive",
-	"sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/licenses/BitTorrent?r1=1.1&r2=1.1.1.1&diff_format=s":                                       "BitTorrent-1.0",
-	"sourceware.org/bzip2/1.0.5/bzip2-manual-1.0.5.html":                                                                                         "bzip2-1.0.6",
-	"sourceware.org/cgit/binutils-gdb/tree/include/coff/sym.h#n11":                                                                               "MIPS",
-	"sourceware.org/cgit/binutils-gdb/tree/include/coff/symconst.h#n11":                                                                          "ThirdEye",
-	"sourceware.org/cgit/valgrind/tree/mpi/libmpiwrap.c":                                                                                         "bzip2-1.0.6",
+	"raw.githubusercontent.com/landtuna/open-mtools/6c04c2882eca7c4313ec267766ea53ac9bfe129b/mdump.c":                "Informatica",
+	"raw.githubusercontent.com/landtuna/open-mtools/6c04c2882eca7c4313ec267766ea53ac9bfe129b/msend.c":                "Informatica",
+	"rc.quest.com/topics/openssh/license.php#tcpwrappers":                                                            "TCP-wrappers",
+	"research.cs.wisc.edu/condor/license.html#condor":                                                                "Condor-1.1",
+	"research.scea.com/scea_shared_source_license.html":                                                              "SCEA",
+	"romanrm.net/mit-zero":                                                                                           "MIT-0",
+	"sam.zoy.org/wtfpl/COPYING":                                                                                      "WTFPL",
+	"scancode-licensedb.aboutcode.org/bsd-unchanged":                                                                 "BSD-2-Clause-pos-unchanged",
+	"scripts.sil.org/cms/scripts/page.php?item_id=OFL10_web":                                                         "OFL-1.0-no-RFN",
+	"scripts.sil.org/cms/scripts/page.php?item_id=OFL_web":                                                           "OFL-1.1-no-RFN",
+	"slicer.org/LICENSE":                                                                                             "3D-Slicer-1.0",
+	"solderpad.org/licenses/SHL-0.5/":                                                                                "SHL-0.5",
+	"solderpad.org/licenses/SHL-0.51/":                                                                               "SHL-0.51",
+	"source.icu-project.org/repos/icu/icu/trunk/license.html":                                                        "ICU",
+	"sourceforge.net/p/buddy/gitcode/ci/master/tree/README":                                                          "Buddy",
+	"sourceforge.net/p/ctrio/git/ci/master/tree/README":                                                              "ISC-Veillard",
+	"sourceforge.net/p/mcj/xfig/ci/master/tree/src/Makefile.am":                                                      "Xfig",
+	"sourceforge.net/p/netpbm/code/HEAD/tree/super_stable/converter/other/pnmtorle.c":                                "URT-RLE",
+	"sourceforge.net/p/netpbm/code/HEAD/tree/super_stable/converter/other/rletopnm.c":                                "URT-RLE",
+	"sourceforge.net/p/netpbm/code/HEAD/tree/super_stable/converter/ppm/ppmtompeg/jrevdct.c#l1189":                   "MPEG-SSG",
+	"sourceforge.net/p/netpbm/code/HEAD/tree/super_stable/editor/pnmstitch.c#l2":                                     "pnmstitch",
+	"sourceforge.net/p/netpbm/code/HEAD/tree/super_stable/netpbm.c#l8":                                               "HPND-Pbmplus",
+	"sourceforge.net/p/sbcl/sbcl/ci/master/tree/src/code/loop.lisp":                                                  "LOOP",
+	"sourceforge.net/p/trustedqsl/tqsl/ci/master/tree/LICENSE.txt":                                                   "TrustedQSL",
+	"sourceforge.net/p/xmedcon/code/ci/master/tree/libs/dicom/README":                                                "OFFIS",
+	"sourceforge.net/p/xmedcon/code/ci/master/tree/libs/ljpg/":                                                       "IJG-short",
+	"sourceforge.net/projects/sevenzip/files/LZMA%20SDK/":                                                            "LZMA-SDK-9.22",
+	"sources.debian.org/copyright/license/debianutils/4.11.2/":                                                       "SMAIL-GPL",
+	"sources.debian.org/src/openmpi/4.1.0-10/ompi/debuggers/msgq_interface.h/?hl=19#L19":                             "mpi-permissive",
+	"sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/licenses/BitTorrent?r1=1.1&r2=1.1.1.1&diff_format=s":           "BitTorrent-1.0",
+	"sourceware.org/bzip2/1.0.5/bzip2-manual-1.0.5.html":                                                             "bzip2-1.0.6",
+	"sourceware.org/cgit/binutils-gdb/tree/include/coff/sym.h#n11":                                                   "MIPS",
+	"sourceware.org/cgit/binutils-gdb/tree/include/coff/symconst.h#n11":                                              "ThirdEye",
+	"sourceware.org/cgit/valgrind/tree/mpi/libmpiwrap.c":                                                             "bzip2-1.0.6",
 	"sourceware.org/git/?p=binutils-gdb.git;a=blob;f=libiberty/strcasecmp.c;h=131d81c2ce7881fa48c363dc5bf5fb302c61ce0b;hb=HEAD":                  "BSD-4.3RENO",
 	"sourceware.org/git/?p=binutils-gdb.git;a=blob;f=readline/readline/support/wcwidth.c;h=0f5ec995796f4813abbcf4972aec0378ab74722a;hb=HEAD#l55": "HPND-Markus-Kuhn",
 	"sourceware.org/git/?p=bzip2.git;a=blob;f=LICENSE;hb=bzip2-1.0.6":                                                                            "bzip2-1.0.6",

internal/task/archive_nesting_test.go

@@ -0,0 +1,699 @@
+package task
+
+import (
+	"context"
+	"fmt"
+	"io/fs"
+	"os"
+	"path/filepath"
+	"sort"
+	"strings"
+	"sync"
+	"testing"
+	"time"
+
+	"github.com/scylladb/go-set/strset"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/anchore/syft/internal/archive"
+	"github.com/anchore/syft/internal/sbomsync"
+	"github.com/anchore/syft/internal/testutils"
+	"github.com/anchore/syft/syft/artifact"
+	"github.com/anchore/syft/syft/cataloging"
+	"github.com/anchore/syft/syft/file"
+	"github.com/anchore/syft/syft/pkg"
+	"github.com/anchore/syft/syft/pkg/cataloger/java"
+	"github.com/anchore/syft/syft/sbom"
+)
+
+// This file covers nesting across archive families. The other nested-archive fixtures are all zips,
+// so a zip-specific mechanism would pass them; the requirement here is that an archive of one family
+// inside another behaves as it would inside its own family - same packages, same container-path chain,
+// same CONTAINS edges, same depth accounting.
+//
+// Chains are built in the test rather than committed as binaries, so each case can vary which family
+// sits at which level.
+
+// archiveFamily is one archive format buildNestedArchive can produce.
+//
+// ".jar" is its own family rather than a flavour of zip: the java cataloger meets it as a jar wherever
+// it sits, while the archive task descends into it like any other zip. That differs mid-chain from at
+// the leaf, so the matrix below uses a jar as container and as payload.
+type archiveFamily string
+
+const (
+	familyZip   archiveFamily = ".zip"
+	familyJar   archiveFamily = ".jar"
+	familyTar   archiveFamily = ".tar"
+	familyTarGz archiveFamily = ".tar.gz"
+	familyTgz   archiveFamily = ".tgz"
+)
+
+// nestPlan describes one chain to build: a family per level (outermost first), the entries for the
+// innermost archive, and extras to add beside the nested archive at a given level. The extras grade
+// the levels' sizes or entry counts, which is how the limit cases place a bound between two levels.
+type nestPlan struct {
+	families []archiveFamily
+	leaf     map[string][]byte
+	extra    map[int]map[string][]byte
+}
+
+// nestedArchive is one built chain: the outermost archive's bytes, and the addresses that chain
+// composes to at each level.
+type nestedArchive struct {
+	// name is the outermost archive's file name, as written into the scanned directory.
+	name string
+	// bytes is the outermost archive.
+	bytes []byte
+	// sizes is each archive's size in bytes, outermost first. A container is never smaller than what it
+	// holds, so these decrease, and the limit cases place a bound between two of them.
+	sizes []int
+	// paths is each archive's path within its parent, outermost first; paths[0] is the outermost archive
+	// as the scan's resolver reports it.
+	paths []string
+	// containerPaths is each archive's full path, the container path its own contents carry, outermost first.
+	containerPaths []string
+	// virtualPaths is the same chain in java's colon-joined form, outermost first.
+	virtualPaths []string
+}
+
+// nestingRow is one line of the depth-3 matrix.
+type nestingRow struct {
+	name     string
+	families []archiveFamily
+	why      string
+}
+
+// nestingVisit is one filesystem the archive cataloger's sub-pipeline was run against.
+type nestingVisit struct {
+	virtualPath string
+	fullPath    string
+	depth       int
+	// heldFiles are the spill files live at this moment, sampled only when the probe was given a temp
+	// dir to look in. A nested archive's own bytes are read where they lie, so one appears per archive
+	// whose entries did not fit in memory.
+	heldFiles []string
+}
+
+// nestingProbe records one visit per filesystem the archive cataloger runs its sub-pipeline against,
+// reading the chain off the traversal on the context.
+type nestingProbe struct {
+	// tempDir, when set, is where extraction work directories live
+	tempDir string
+
+	mu     sync.Mutex
+	visits []nestingVisit
+}
+
+func Test_mixedFamilyNesting_leafIsCatalogedOnceWithTheFullChain(t *testing.T) {
+	// family order must not change the result: the same package, addressed by a chain naming its own
+	// containers in its own order
+	for _, row := range nestingRows() {
+		t.Run(row.name, func(t *testing.T) {
+			scanDir := t.TempDir()
+			nested := writeNestedArchive(t, scanDir, nestPlan{families: row.families, leaf: markerLeaf()})
+
+			probe := &nestingProbe{}
+			s := runNesting(t, scanDir, 3, defaultLimits(), markerTask(), probe.task())
+
+			assert.Equal(t, 1, packageCount(s, "marker-pkg"), "%s: the leaf package must be cataloged exactly once", row.why)
+
+			locs := leafLocations(s)
+			require.Len(t, locs, 1, "the leaf must be reached by exactly one path")
+			// exact, never a substring: a partially composed chain passes a substring check
+			assert.Equal(t, nested.leafContainerPath(), archive.ContainerPath(locs[0].Coordinates),
+				"the chain must name all three archives outer-to-inner")
+			assert.Equal(t, nested.leafContainerPath()+"!/nested/marker.txt", locs[0].FullNestedPath(),
+				"the path stays relative to the archive the file came from")
+
+			assert.Equal(t, nested.containerPaths, probe.containerPaths(),
+				"every level must be cataloged, outer to inner, whatever families they are")
+		})
+	}
+}
+
+func Test_mixedFamilyNesting_containsEdgesChainAtEveryLevel(t *testing.T) {
+	// the edges make the chain navigable in the SBOM. The archive-to-archive edges must not depend on
+	// the file catalogers having recorded the inner archives, since the default file selection does not
+	for _, row := range nestingRows() {
+		t.Run(row.name, func(t *testing.T) {
+			scanDir := t.TempDir()
+			nested := writeNestedArchive(t, scanDir, nestPlan{families: row.families, leaf: markerLeaf()})
+
+			s := withArchiveContains(t, runNesting(t, scanDir, 3, defaultLimits(), markerTask()))
+
+			// each archive's coordinates as seen in its parent; the outermost sits in the scanned
+			// directory, so it carries no filesystem id of its own
+			archiveCoords := make([]file.Coordinates, len(row.families))
+			for i := range row.families {
+				archiveCoords[i] = nested.coordinates(i)
+			}
+
+			fileEdges := strset.New()
+			pkgEdges := strset.New()
+			for _, rel := range s.Relationships {
+				if rel.Type != artifact.ContainsRelationship {
+					continue
+				}
+				from, ok := rel.From.(file.Coordinates)
+				if !ok {
+					continue
+				}
+				switch to := rel.To.(type) {
+				case file.Coordinates:
+					fileEdges.Add(coordKey(from) + " -> " + coordKey(to))
+				case pkg.Package:
+					pkgEdges.Add(coordKey(from) + " -> " + to.Name)
+				}
+			}
+
+			for i := 0; i < len(archiveCoords)-1; i++ {
+				assert.True(t, fileEdges.Has(coordKey(archiveCoords[i])+" -> "+coordKey(archiveCoords[i+1])),
+					"expected a CONTAINS edge from %s to %s", nested.paths[i], nested.paths[i+1])
+			}
+
+			innermost := archiveCoords[len(archiveCoords)-1]
+			assert.True(t, pkgEdges.Has(coordKey(innermost)+" -> marker-pkg"),
+				"expected a CONTAINS edge from %s to the leaf package", nested.paths[len(nested.paths)-1])
+
+			// with file cataloging on, files inside an archive get an edge from it too
+			s = withArchiveContains(t, runNesting(t, scanDir, 3, defaultLimits(), markerTask(), fileMetadataTask()))
+			var leafEdge bool
+			for _, rel := range s.Relationships {
+				from, _ := rel.From.(file.Coordinates)
+				to, _ := rel.To.(file.Coordinates)
+				leafEdge = leafEdge || (from == innermost && to == file.Coordinates{RealPath: innermost.RealPath, FullPath: innermost.FullNestedPath() + "!/nested/marker.txt"})
+			}
+			assert.True(t, leafEdge, "expected a CONTAINS edge from the innermost archive to the leaf file")
+		})
+	}
+}
+
+func Test_mixedFamilyNesting_everyJarIsCatalogedOnceUnderItsChain(t *testing.T) {
+	// two mechanisms meet a jar: the java cataloger catalogs it as a package, the archive task descends
+	// into it. A jar at any level must do both, exactly once each; the failure mode is a duplicate, not an
+	// error. The colon-joined virtual paths are in already-published SBOMs, so they must name the chain.
+	for _, row := range nestingRows() {
+		var jarLevels []int
+		for i, family := range row.families {
+			if family == familyJar {
+				jarLevels = append(jarLevels, i)
+			}
+		}
+		if len(jarLevels) == 0 {
+			continue
+		}
+
+		t.Run(row.name, func(t *testing.T) {
+			scanDir := t.TempDir()
+			nested := writeNestedArchive(t, scanDir, nestPlan{families: row.families, leaf: markerLeaf()})
+
+			probe := &nestingProbe{}
+			s := runNesting(t, scanDir, 3, defaultLimits(), markerTask(), javaTask(), probe.task())
+
+			for _, level := range jarLevels {
+				name := fmt.Sprintf("level%d", level)
+				assert.Equal(t, 1, packageCount(s, name), "the jar's own package must be cataloged exactly once")
+				assert.Equal(t, nested.virtualPaths[level], javaVirtualPaths(s)[name],
+					"the jar's virtual path must be its own place in the chain")
+			}
+
+			// and the archive task still descended through every level
+			assert.Equal(t, nested.containerPaths, probe.containerPaths())
+			locs := leafLocations(s)
+			require.Len(t, locs, 1)
+			assert.Equal(t, nested.leafContainerPath(), archive.ContainerPath(locs[0].Coordinates))
+		})
+	}
+}
+
+func Test_mixedFamilyNesting_depthCountsLevelsNotFamilies(t *testing.T) {
+	// two rows with different families at every level, so the bound is shown not to turn on which
+	// families are involved
+	for _, row := range nestingRows()[:2] {
+		t.Run(row.name, func(t *testing.T) {
+			scanDir := t.TempDir()
+			nested := writeNestedArchive(t, scanDir, nestPlan{families: row.families, leaf: markerLeaf()})
+
+			probe := &nestingProbe{}
+			s := runNesting(t, scanDir, 2, defaultLimits(), markerTask(), fileMetadataTask(), probe.task())
+
+			assert.Equal(t, nested.containerPaths[:2], probe.containerPaths(),
+				"at depth 2 the outer and middle archives are cataloged and the innermost is not")
+			assert.Zero(t, packageCount(s, "marker-pkg"),
+				"the leaf is one level past the bound, so its package must be absent")
+
+			// the innermost archive is still cataloged as a file, inside the middle archive
+			innermost := nested.coordinates(2)
+			_, ok := s.Artifacts.FileMetadata[innermost]
+			assert.True(t, ok, "the undescended archive must still be recorded as a file at %s", coordKey(innermost))
+
+			// and what was left unexplored is said out loud, not silently dropped
+			reasons := s.Artifacts.Unknowns[innermost]
+			require.Len(t, reasons, 1, "unknowns: %v", s.Artifacts.Unknowns)
+			assert.Contains(t, reasons[0], "depth limit was reached")
+		})
+	}
+}
+
+func Test_mixedFamilyNesting_aNestedArchiveIsReadWhereItLies(t *testing.T) {
+	// an archive's own bytes are read where they lie: a scanned file from disk, a nested archive from
+	// its parent's entries. Nothing copies them, so at most one spill file per level appears whatever
+	// the memory limit; only entries are held, and only they can be written out.
+	scanDir := t.TempDir()
+	tempDir := isolatedTempDir(t)
+	nested := writeNestedArchive(t, scanDir, gradedChain())
+
+	for _, tc := range []struct {
+		name          string
+		memoryBytes   int64
+		wantHeldFiles []string
+	}{
+		{
+			name:        "with room in memory for every level's entries",
+			memoryBytes: int64(2 * (nested.sizes[0] + nested.sizes[1] + nested.sizes[2])),
+		},
+		{
+			name:          "with a memory limit of zero, so every level's entries are written out",
+			memoryBytes:   0,
+			wantHeldFiles: []string{"archive-spill", "archive-spill", "archive-spill"},
+		},
+	} {
+		t.Run(tc.name, func(t *testing.T) {
+			probe := &nestingProbe{tempDir: tempDir}
+			bounds := archive.Limits{MaxMemoryBytes: tc.memoryBytes, MaxDiskBytes: -1}
+
+			s := runNesting(t, scanDir, 3, bounds, markerTask(), probe.task())
+
+			deepest := probe.deepestVisit()
+			require.Equal(t, 3, deepest.depth, "the sample must be taken with all three levels still held")
+			assert.Equal(t, tc.wantHeldFiles, deepest.heldFiles)
+
+			assert.Equal(t, nested.containerPaths, probe.containerPaths())
+			locs := leafLocations(s)
+			require.Len(t, locs, 1)
+			assert.Equal(t, nested.leafContainerPath(), archive.ContainerPath(locs[0].Coordinates))
+		})
+	}
+}
+
+func Test_mixedFamilyNesting_diskLimitTruncatesTheLevelItCannotAdmit(t *testing.T) {
+	// the walk descends before it unwinds, so the outer and middle archives still hold their entries
+	// when the innermost level's do not fit in memory. With nothing admitted on disk that level is
+	// cataloged from nothing, the shallower ones keep what they found, and the scan finishes. An
+	// implementation that waited for capacity would deadlock, hence the timeout.
+	scanDir := t.TempDir()
+	nested := writeNestedArchive(t, scanDir, deepChain())
+
+	// a sibling of a different family, processed once the chain has been released, so cataloged in full
+	require.NoError(t, os.WriteFile(
+		filepath.Join(scanDir, "sibling.tgz"),
+		testutils.TarGz(t, map[string][]byte{"nested/marker.txt": []byte("sibling")}),
+		0o644,
+	))
+
+	// room for the outer two levels' entries (each about the size of the archive it holds) but not the
+	// innermost's payload, which is half an archive larger than the slack
+	memoryLimit := int64(nested.sizes[0] + nested.sizes[1] + deepChainPayloadBytes/2)
+
+	probe := &nestingProbe{}
+	bounds := archive.Limits{MaxMemoryBytes: memoryLimit, MaxDiskBytes: 0}
+
+	s := runNesting(t, scanDir, 3, bounds, markerTask(), probe.task())
+
+	want := append(append([]string{}, nested.containerPaths...), "/sibling.tgz")
+	assert.ElementsMatch(t, want, probe.containerPaths(),
+		"every level is visited, the truncated one with nothing inside it")
+
+	containers := strset.New()
+	for _, loc := range leafLocations(s) {
+		containers.Add(archive.ContainerPath(loc.Coordinates))
+	}
+	assert.False(t, containers.Has(nested.leafContainerPath()), "the truncated level's contents must be absent")
+	assert.True(t, containers.Has("/sibling.tgz"), "the sibling of a different family must be cataloged fully")
+
+	var truncated []string
+	for coords, reasons := range s.Artifacts.Unknowns {
+		for _, reason := range reasons {
+			if strings.Contains(reason, "disk limit") {
+				truncated = append(truncated, coords.FullNestedPath())
+			}
+		}
+	}
+	assert.Equal(t, []string{nested.coordinates(2).FullNestedPath()}, truncated,
+		"the truncation is recorded against the archive that reached the limit")
+}
+
+func defaultLimits() archive.Limits {
+	return archiveLimits(cataloging.DefaultArchiveSearchConfig())
+}
+
+// runNesting runs the archive cataloger task over scanDir with the given sub-pipeline and returns the
+// SBOM it built. It runs on its own goroutine and fails if the task has not finished in time.
+//
+// The depth-3 limit cases need the timeout: the walk descends before it unwinds, so the outer and
+// middle archives still hold their content when the inner one is refused. An implementation that
+// waited for capacity would deadlock, and a test asserting only the result would hang rather than fail.
+func runNesting(t *testing.T, scanDir string, depth int, bounds archive.Limits, subPipeline ...Task) *sbom.SBOM {
+	t.Helper()
+	tsk := newLimitedTestTask(t, depth, bounds, subPipeline...)
+	s := &sbom.SBOM{Artifacts: sbom.Artifacts{
+		Packages:     pkg.NewCollection(),
+		FileMetadata: map[file.Coordinates]file.Metadata{},
+	}}
+
+	done := make(chan error, 1)
+	go func() {
+		done <- tsk.Execute(context.Background(), dirTestResolver{dir: scanDir}, sbomsync.NewBuilder(s))
+	}()
+
+	select {
+	case err := <-done:
+		require.NoError(t, err, "reaching a bound must not fail the scan")
+		return s
+	case <-time.After(60 * time.Second):
+		t.Fatal("the scan did not finish in time: reaching a limit must skip the archive that " +
+			"reached it, never wait for capacity that nothing in the chain will release")
+		return nil
+	}
+}
+
+// withArchiveContains runs the task that follows every scan with archive cataloging on.
+func withArchiveContains(t *testing.T, s *sbom.SBOM) *sbom.SBOM {
+	t.Helper()
+	require.NoError(t, NewArchiveContainsTask().Execute(context.Background(), nil, sbomsync.NewBuilder(s)))
+	return s
+}
+
+// markerTask emits one package per "marker.txt" found, so the matrix asserts behavior without
+// depending on any real cataloger's fixture format.
+func markerTask() Task {
+	return NewTask("marker-cataloger", func(_ context.Context, resolver file.Resolver, builder sbomsync.Builder) error {
+		locations, err := resolver.FilesByGlob("**/marker.txt")
+		if err != nil {
+			return err
+		}
+		for _, loc := range locations {
+			p := pkg.Package{
+				Name:      "marker-pkg",
+				Version:   "1.0.0",
+				Type:      pkg.BinaryPkg,
+				Locations: file.NewLocationSet(loc),
+			}
+			p.SetID()
+			builder.AddPackages(p)
+		}
+		return nil
+	})
+}
+
+// javaTask is the java archive cataloger as the cataloging factory builds it, so a jar is met as a jar
+// wherever it sits in a chain.
+func javaTask() Task {
+	return NewPackageTask(CatalogingFactoryConfig{}, java.NewArchiveCataloger(java.DefaultArchiveCatalogerConfig()))
+}
+
+// fileMetadataTask records every file, so each file inside an archive gets an archive-to-file edge.
+func fileMetadataTask() Task {
+	return newFileMetadataCatalogerTask(file.AllFilesSelection)
+}
+
+// pack builds one archive of this family holding the given entries.
+func (f archiveFamily) pack(t *testing.T, base string, entries map[string][]byte) []byte {
+	t.Helper()
+	switch f {
+	case familyZip:
+		return testutils.Zip(t, entries)
+	case familyJar:
+		// a manifest makes it a real jar to the java cataloger at any level; the package java reports is
+		// named after the file, not the manifest title
+		return testutils.Jar(t, base, "1.0", entries)
+	case familyTar:
+		return testutils.Tar(t, entries)
+	case familyTarGz, familyTgz:
+		return testutils.TarGz(t, entries)
+	}
+	t.Fatalf("unknown archive family %q", f)
+	return nil
+}
+
+// leafContainerPath is the container path the innermost archive's contents carry: every archive, outer to
+// inner. Assert it exactly, never as a substring: a partially composed chain passes a substring check.
+func (n nestedArchive) leafContainerPath() string {
+	return n.containerPaths[len(n.containerPaths)-1]
+}
+
+// coordinates are those of the archive at the given level: the outermost archive's path, and the chain
+// of entries within it.
+func (n nestedArchive) coordinates(level int) file.Coordinates {
+	return file.Coordinates{RealPath: n.paths[0], FullPath: strings.Join(n.paths[:level+1], "!/")}
+}
+
+// buildNestedArchive builds one archive per family given, each holding the next, with leaf inside
+// the innermost.
+func buildNestedArchive(t *testing.T, plan nestPlan) nestedArchive {
+	t.Helper()
+	require.NotEmpty(t, plan.families, "a chain needs at least one level")
+
+	out := nestedArchive{
+		sizes:          make([]int, len(plan.families)),
+		paths:          make([]string, len(plan.families)),
+		containerPaths: make([]string, len(plan.families)),
+		virtualPaths:   make([]string, len(plan.families)),
+	}
+
+	// the level index goes in every name and path segment, so no two levels share a path and a chain
+	// assertion cannot pass on a value composed from the wrong level
+	for i, family := range plan.families {
+		base := fmt.Sprintf("level%d", i)
+		if i == 0 {
+			// the outermost archive is a file in the scanned directory, which the resolver reports rooted
+			out.name = base + string(family)
+			out.paths[i] = "/" + out.name
+			continue
+		}
+		out.paths[i] = fmt.Sprintf("nest%d/%s%s", i, base, family)
+	}
+
+	for i := range plan.families {
+		if i == 0 {
+			out.containerPaths[i] = out.paths[0]
+			out.virtualPaths[i] = out.paths[0]
+			continue
+		}
+		out.containerPaths[i] = out.containerPaths[i-1] + "!/" + out.paths[i]
+		out.virtualPaths[i] = out.virtualPaths[i-1] + ":" + out.paths[i]
+	}
+
+	// built innermost first, because each level's bytes are an entry of the level above it
+	var packed []byte
+	for i := len(plan.families) - 1; i >= 0; i-- {
+		entries := map[string][]byte{}
+		if i == len(plan.families)-1 {
+			for name, body := range plan.leaf {
+				entries[name] = body
+			}
+		} else {
+			entries[out.paths[i+1]] = packed
+		}
+		for name, body := range plan.extra[i] {
+			entries[name] = body
+		}
+		packed = plan.families[i].pack(t, fmt.Sprintf("level%d", i), entries)
+		out.sizes[i] = len(packed)
+	}
+	out.bytes = packed
+
+	return out
+}
+
+// writeNestedArchive writes the chain's outermost archive into dir and returns the chain.
+func writeNestedArchive(t *testing.T, dir string, plan nestPlan) nestedArchive {
+	t.Helper()
+	nested := buildNestedArchive(t, plan)
+	require.NoError(t, os.WriteFile(filepath.Join(dir, nested.name), nested.bytes, 0o644))
+	return nested
+}
+
+// markerLeaf is the family-agnostic leaf payload: one file no archive format has an opinion about,
+// found by markerTask. It keeps the rows comparable - the same package must come out whichever
+// families the chain is made of.
+func markerLeaf() map[string][]byte {
+	return map[string][]byte{"nested/marker.txt": []byte("leaf")}
+}
+
+// nestingRows is the depth-3 matrix. Each row covers a case the others do not.
+func nestingRows() []nestingRow {
+	return []nestingRow{
+		{
+			name:     "tar.gz/zip/jar",
+			families: []archiveFamily{familyTarGz, familyZip, familyJar},
+			why:      "the headline case: compressed tar outermost, jar innermost",
+		},
+		{
+			name:     "zip/tar.gz/jar",
+			families: []archiveFamily{familyZip, familyTarGz, familyJar},
+			why:      "compressed tar in the middle, where the stream-only format is not the entry point",
+		},
+		{
+			name:     "jar/tar/zip",
+			families: []archiveFamily{familyJar, familyTar, familyZip},
+			why:      "jar as a container rather than a payload",
+		},
+		{
+			name:     "tgz/tar/jar",
+			families: []archiveFamily{familyTgz, familyTar, familyJar},
+			why:      "the .tgz alias resolving at a non-outermost boundary",
+		},
+		{
+			name:     "tar/jar/tar.gz",
+			families: []archiveFamily{familyTar, familyJar, familyTarGz},
+			why:      "compressed tar as the innermost, which nothing else covers",
+		},
+	}
+}
+
+func (p *nestingProbe) task() Task {
+	return NewTask("nesting-probe", func(ctx context.Context, _ file.Resolver, _ sbomsync.Builder) error {
+		trav := archive.TraversalFromContext(ctx)
+		visit := nestingVisit{}
+		if trav != nil {
+			visit.virtualPath = archive.VirtualPath(trav.Location)
+			visit.fullPath = trav.FullTraversalArchivePath()
+			visit.depth = strings.Count(archive.VirtualPath(trav.Location), ":") + 1
+		}
+		if p.tempDir != "" {
+			visit.heldFiles = heldFiles(p.tempDir)
+		}
+
+		p.mu.Lock()
+		defer p.mu.Unlock()
+		p.visits = append(p.visits, visit)
+		return nil
+	})
+}
+
+// containerPaths is the chain of every archive whose contents were cataloged, in visit order.
+func (p *nestingProbe) containerPaths() []string {
+	p.mu.Lock()
+	defer p.mu.Unlock()
+	var out []string
+	for _, v := range p.visits {
+		if v.fullPath == "" {
+			continue
+		}
+		out = append(out, v.fullPath)
+	}
+	return out
+}
+
+// deepestVisit is the visit at the innermost level reached, the only moment at which every level of a
+// chain is still held and its routing observable. It returns the whole visit so a case can also assert
+// it got as deep as it meant to: an empty overflow sample from a visit that never left the scan root
+// would otherwise read as "nothing overflowed".
+func (p *nestingProbe) deepestVisit() nestingVisit {
+	p.mu.Lock()
+	defer p.mu.Unlock()
+	var best nestingVisit
+	for _, v := range p.visits {
+		if v.depth > best.depth {
+			best = v
+		}
+	}
+	return best
+}
+
+// heldFiles names the spill files live under tempDir, one "archive-spill" per archive holding content
+// that did not fit in memory. Meaningful only while the archives are still held, so it is sampled from
+// inside the sub-pipeline rather than after the scan.
+func heldFiles(tempDir string) (names []string) {
+	_ = filepath.WalkDir(tempDir, func(_ string, d fs.DirEntry, err error) error {
+		if err != nil || d.IsDir() || !strings.HasPrefix(d.Name(), "archive-") {
+			return nil //nolint:nilerr // an unreadable directory holds nothing this probe can report
+		}
+		// the name is the pattern with os.CreateTemp's random suffix in place of the "*"
+		names = append(names, d.Name()[:strings.LastIndexByte(d.Name(), '-')])
+		return nil
+	})
+	sort.Strings(names)
+	return names
+}
+
+// isolatedTempDir points archive extraction at a directory of this test's own, so an overflow sample
+// sees only this scan's work directories.
+func isolatedTempDir(t *testing.T) string {
+	t.Helper()
+	dir := t.TempDir()
+	t.Setenv("TMPDIR", dir) // unix
+	t.Setenv("TMP", dir)    // windows
+	t.Setenv("TEMP", dir)   // windows fallback
+	require.Equal(t, dir, os.TempDir(), "extraction must be writing where the probe is looking")
+	return dir
+}
+
+func leafLocations(s *sbom.SBOM) []file.Location {
+	var out []file.Location
+	for _, p := range s.Artifacts.Packages.Sorted() {
+		if p.Name != "marker-pkg" {
+			continue
+		}
+		out = append(out, p.Locations.ToSlice()...)
+	}
+	return out
+}
+
+func javaVirtualPaths(s *sbom.SBOM) map[string]string {
+	out := map[string]string{}
+	for _, p := range s.Artifacts.Packages.Sorted() {
+		if metadata, ok := p.Metadata.(pkg.JavaArchive); ok {
+			out[p.Name] = metadata.VirtualPath
+		}
+	}
+	return out
+}
+
+func packageCount(s *sbom.SBOM, name string) int {
+	var n int
+	for _, p := range s.Artifacts.Packages.Sorted() {
+		if p.Name == name {
+			n++
+		}
+	}
+	return n
+}
+
+func coordKey(c file.Coordinates) string {
+	return c.FullNestedPath()
+}
+
+// gradedChain is the headline row with each level padded so the three archives have clearly different
+// sizes: a container is never smaller than what it holds, so a bound can only be placed between two
+// levels if they are graded on purpose.
+func gradedChain() nestPlan {
+	return nestPlan{
+		families: []archiveFamily{familyTarGz, familyZip, familyJar},
+		leaf:     markerLeaf(),
+		extra: map[int]map[string][]byte{
+			0: {"pad0.bin": incompressible(24 * 1024)},
+			1: {"pad1.bin": incompressible(24 * 1024)},
+			2: {"pad2.bin": incompressible(8 * 1024)},
+		},
+	}
+}
+
+// deepChainPayloadBytes is the size of deepChain's leaf payload.
+const deepChainPayloadBytes = 64 * 1024
+
+// deepChain is the headline row with one large, incompressible payload at the leaf and no other
+// padding. The payload dominates every level, so the three archives are about the same size. It sorts
+// before the marker so it is the first entry refused when the leaf archive's entries do not fit.
+func deepChain() nestPlan {
+	return nestPlan{
+		families: []archiveFamily{familyTarGz, familyZip, familyJar},
+		leaf: map[string][]byte{
+			"0-payload.bin":     incompressible(deepChainPayloadBytes),
+			"nested/marker.txt": []byte("leaf"),
+		},
+	}
+}

internal/task/archive_tasks.go

@@ -0,0 +1,501 @@
+package task
+
+import (
+	"context"
+	"errors"
+	"fmt"
+	"io"
+	"maps"
+	"runtime/debug"
+	"slices"
+	"time"
+
+	"github.com/dustin/go-humanize"
+
+	"github.com/anchore/syft/internal"
+	"github.com/anchore/syft/internal/archive"
+	"github.com/anchore/syft/internal/bus"
+	"github.com/anchore/syft/internal/log"
+	"github.com/anchore/syft/internal/mimetype"
+	"github.com/anchore/syft/internal/sbomsync"
+	"github.com/anchore/syft/internal/unknown"
+	"github.com/anchore/syft/syft/artifact"
+	"github.com/anchore/syft/syft/cataloging"
+	"github.com/anchore/syft/syft/cataloging/pkgcataloging"
+	"github.com/anchore/syft/syft/event/monitor"
+	"github.com/anchore/syft/syft/file"
+	"github.com/anchore/syft/syft/pkg"
+	"github.com/anchore/syft/syft/sbom"
+)
+
+const ArchiveCatalogerTaskName = "archive-cataloger"
+
+// NewArchiveCatalogerTask returns a task that extracts every archive it finds, runs the same tasks
+// against the archive's contents as a standalone filesystem, and records
+// CONTAINS relationships from the archive to the packages found directly inside it. It recurses into the archives
+// it extracts up to cfg.MaxDepth; the task drops itself from the tasks so that is the only recursion.
+//
+// Each archive is handled as the scan root is: pkgTasks, then the archives nested in it, then fileTasks,
+// which see the packages found in the nested archives (see Traversal.PackageFiles).
+//
+// The task is the authority on which archives were not cataloged and why; with
+// unknowns.IncludeUnexpandedArchives it also reports archives in formats it does not extract.
+//
+// exclusions are the scan's exclusion patterns, applied inside each archive. Returns nil when archive
+// cataloging is disabled (MaxDepth == 0; negative or beyond archive.MaxDepth means as deep as archive.MaxDepth).
+func NewArchiveCatalogerTask(cfg cataloging.ArchiveSearchConfig, unknowns cataloging.UnknownsConfig, pkgTasks, fileTasks []Task, exclusions []string) Task {
+	return newArchiveCatalogerTask(cfg.MaxDepth, archiveLimits(cfg), unknowns.IncludeUnexpandedArchives, pkgTasks, fileTasks, exclusions)
+}
+
+func archiveLimits(cfg cataloging.ArchiveSearchConfig) archive.Limits {
+	return archive.Limits{MaxMemoryBytes: cfg.MaxMemoryBytes, MaxDiskBytes: cfg.MaxDiskBytes}
+}
+
+func newArchiveCatalogerTask(maxDepth int, limits archive.Limits, reportUnsupportedUnknowns bool, pkgTasks, fileTasks []Task, exclusions []string) Task {
+	if maxDepth == 0 {
+		return nil
+	}
+	pkgTasks, fileTasks = withoutArchiveCataloger(pkgTasks), withoutArchiveCataloger(fileTasks)
+	if len(pkgTasks)+len(fileTasks) == 0 {
+		return nil
+	}
+
+	fn := func(ctx context.Context, resolver file.Resolver, builder sbomsync.Builder) error {
+		// catalogers run once per archive, and each must report into the one progress row it owns
+		ctx = bus.WithCatalogerTaskRegistry(ctx)
+
+		c := &archiveCataloger{
+			maxDepth:                  maxDepth,
+			reportUnsupportedUnknowns: reportUnsupportedUnknowns,
+			pkgTasks:                  pkgTasks,
+			fileTasks:                 fileTasks,
+			limiter:                   archive.NewLimiter(limits),
+			exclusions:                archive.NewExclusions(exclusions),
+			progress:                  bus.StartCatalogerTask(ctx, archiveCatalogerProgressInfo(), -1, ""),
+		}
+		err := c.catalog(ctx, resolver, 0, builder)
+		c.progress.AtomicStage.Set(fmt.Sprintf("%s archives", humanize.Comma(c.progress.Current())))
+		c.progress.SetCompleted()
+		c.logStats()
+		return err
+	}
+	return NewTask(ArchiveCatalogerTaskName, fn, pkgcataloging.PackageTag, "archive")
+}
+
+func archiveCatalogerProgressInfo() monitor.GenericTask {
+	return monitor.GenericTask{
+		Title: monitor.Title{
+			Default: "Archives",
+		},
+		ID:       ArchiveCatalogerTaskName,
+		ParentID: monitor.TopLevelCatalogingTaskID,
+	}
+}
+
+func withoutArchiveCataloger(tasks []Task) []Task {
+	var out []Task
+	for _, t := range tasks {
+		if t == nil || t.Name() == ArchiveCatalogerTaskName {
+			continue
+		}
+		out = append(out, t)
+	}
+	return out
+}
+
+type archiveCataloger struct {
+	maxDepth                  int
+	reportUnsupportedUnknowns bool
+	pkgTasks                  []Task
+	fileTasks                 []Task
+	limiter                   *archive.Limiter
+	exclusions                archive.Exclusions
+
+	// progress is the one row for the whole walk: its count is how many archives have been entered
+	progress *monitor.TaskProgress
+
+	// ancestors are the digests of the archives the walk is currently inside. The walk is depth-first
+	// and sequential, so this is a stack.
+	ancestors []file.Digest
+
+	// the archive that spent the longest on its own extraction and cataloging, excluding nested archives
+	slowest     time.Duration
+	slowestPath string
+}
+
+// logStats reports what the walk cost, once. The peaks are the most held against each limit at any
+// one moment, comparable to the configured bounds.
+func (c *archiveCataloger) logStats() {
+	peakMemory, peakDisk := c.limiter.Peak()
+	fields := []any{
+		"archives", c.progress.Current(),
+		"peak-memory", humanize.Bytes(uint64(peakMemory)),
+		"peak-disk", humanize.Bytes(uint64(peakDisk)),
+	}
+	if c.slowestPath != "" {
+		fields = append(fields, "slowest", c.slowestPath, "slowest-took", c.slowest.Round(time.Millisecond))
+	}
+	log.WithFields(fields...).Info("nested archive cataloging complete")
+}
+
+// catalog processes every archive in the resolver, recursing into each up to maxDepth.
+func (c *archiveCataloger) catalog(ctx context.Context, resolver file.Resolver, depth int, builder sbomsync.Builder) error {
+	return c.catalogCandidates(ctx, resolver, c.discoverArchives(resolver), depth, builder)
+}
+
+func (c *archiveCataloger) catalogCandidates(ctx context.Context, resolver file.Resolver, candidates []archiveCandidate, depth int, builder sbomsync.Builder) error {
+	maxDepth := c.maxDepth
+	// a deeper scan would write chains no decoder accepts back
+	if maxDepth < 0 || maxDepth > archive.MaxDepth {
+		maxDepth = archive.MaxDepth
+	}
+	if depth >= maxDepth {
+		// java's own recursion is off while this task runs, so an archive left here is otherwise lost
+		// without a trace
+		for _, candidate := range candidates {
+			if candidate.sniffedAsArchive {
+				recordArchiveUnknown(builder, candidate.location.Coordinates, "nested archive not cataloged: the nested archive depth limit was reached")
+			}
+		}
+		return nil
+	}
+	var errs error
+	for _, candidate := range candidates {
+		if err := ctx.Err(); err != nil {
+			return err
+		}
+		if err := c.processArchive(ctx, resolver, candidate, depth, builder); err != nil {
+			errs = unknown.Append(errs, candidate.location, err)
+		}
+	}
+	return errs
+}
+
+// processArchive processes the given candidate archive, catching panics
+//
+//nolint:funlen
+func (c *archiveCataloger) processArchive(ctx context.Context, parentResolver file.Resolver, candidate archiveCandidate, depth int, builder sbomsync.Builder) (err error) {
+	// the decoders run on untrusted bytes; a panic in one costs this archive, not the scan
+	defer func() {
+		if r := recover(); r != nil {
+			// the stack goes to the log, not the reason: the reason lands in the published SBOM's unknowns
+			log.WithFields("path", candidate.location.FullNestedPath()).Debugf("archive cataloging panic stack:\n%s", debug.Stack())
+			err = fmt.Errorf("panic while cataloging archive: %v", r)
+		}
+	}()
+
+	location := candidate.location
+	content, err := parentResolver.FileContentsByLocation(location)
+	if err != nil {
+		return err
+	}
+	defer internal.CloseAndLogError(content, location.FullNestedPath())
+
+	var archiveContent io.Reader = content
+	if !candidate.sniffedAsArchive {
+		var mayHide bool
+		if archiveContent, mayHide = archive.MayHideAnAppendedArchive(content); !mayHide {
+			return nil
+		}
+	}
+
+	started := time.Now()
+
+	if depth == 0 {
+		// one budget for this archive and everything nested in it, however deep
+		ctx = archive.WithBudget(ctx, archive.NewBudget(archiveTreeBudget(parentResolver, location)))
+	}
+
+	// extracted files keep the real path and filesystem ID of the outermost archive; the chain of entries
+	// to each is carried as its archive path. The chain names real paths, not the link the archive was
+	// reached by, so it is stable and joins to the archive's package location by prefix.
+	traversal := &archive.Traversal{Location: location, Parent: archive.TraversalFromContext(ctx)}
+	archivePath := location.FullNestedPath()
+	extracted, err := archive.Extract(ctx, archiveContent, location.Coordinates, c.limiter, c.exclusions)
+	if errors.Is(err, archive.ErrUnsupportedFormat) {
+		if c.reportUnsupportedUnknowns {
+			recordArchiveUnknown(builder, location.Coordinates, "archive not cataloged: "+err.Error())
+		}
+		return nil
+	}
+	if errors.Is(err, archive.ErrDiskLimitReached) {
+		// nothing is released while this archive waits, so skip it rather than block the scan
+		recordArchiveUnknown(builder, location.Coordinates, "archive skipped: its content would exceed the disk limit")
+		return nil
+	}
+	if err != nil {
+		return err
+	}
+	if extracted == nil {
+		// a format with no extractor, or a candidate whose head only looked like an appended archive.
+		// Logged rather than returned: an image can hold thousands of these
+		log.WithFields("archive", archivePath, "sniffed-as-archive", candidate.sniffedAsArchive).
+			Trace("no extractor could read this candidate; skipping")
+		return nil
+	}
+	defer extracted.Cleanup()
+
+	// an archive whose bytes match one it is nested in (a zip quine) would recurse forever
+	if c.isAncestor(extracted.Digests) {
+		recordArchiveUnknown(builder, location.Coordinates, "archive not cataloged: it is identical to an archive that contains it")
+		return nil
+	}
+	c.ancestors = append(c.ancestors, extracted.Digests...)
+	defer func() { c.ancestors = c.ancestors[:len(c.ancestors)-len(extracted.Digests)] }()
+
+	if extracted.Truncated != nil {
+		recordArchiveUnknown(builder, location.Coordinates, "archive cataloged from part of its contents: "+extracted.Truncated.Error())
+	}
+
+	traversal.Digests = extracted.Digests
+	ctx = archive.WithTraversal(ctx, traversal)
+
+	c.progress.Increment()
+
+	// everything found in this archive and the archives nested in it, merged into the parent's SBOM once complete
+	found := &sbom.SBOM{Artifacts: sbom.Artifacts{Packages: pkg.NewCollection()}}
+	foundBuilder := sbomsync.NewBuilder(found)
+	runArchiveTasks(ctx, c.pkgTasks, extracted, location.Coordinates, foundBuilder)
+	direct := found.Artifacts.Packages.Sorted()
+	traversal.Packages = packagesAt(direct, location.Coordinates)
+
+	// self time excludes descending, so a containing archive is not charged for what it contains
+	selfTime := time.Since(started)
+
+	// as at the scan root, nested archives are cataloged before this archive's files, so the packages
+	// describing them (located in this archive) select their files here
+	errs := c.catalogCandidates(ctx, extracted, c.discoverArchives(extracted), depth+1, foundBuilder)
+
+	started = time.Now()
+	runArchiveTasks(ctx, c.fileTasks, extracted, location.Coordinates, foundBuilder)
+	// the files within it are related once the scan has decided which it describes (see NewArchiveContainsTask)
+	for _, p := range direct {
+		found.Relationships = append(found.Relationships, artifact.Relationship{From: location.Coordinates, To: p, Type: artifact.ContainsRelationship})
+	}
+	mergeArchiveResults(found, builder)
+	c.progress.AtomicStage.Set(humanize.Comma(c.progress.Current()) + " archives (" + archivePath + ")")
+
+	if took := selfTime + time.Since(started); took > c.slowest {
+		c.slowest, c.slowestPath = took, archivePath
+	}
+
+	return errs
+}
+
+// a top-level archive and everything nested in it may decompress to archiveTreeRatio times its size, or
+// archiveTreeFloorBytes if that is more. Real trees (a war of jars, a layer of tarballs) expand a few
+// times over; a recursive bomb expands by orders of magnitude at every level.
+var (
+	archiveTreeRatio      int64 = 100
+	archiveTreeFloorBytes int64 = 1 << 30
+)
+
+func archiveTreeBudget(resolver file.Resolver, location file.Location) int64 {
+	var size int64
+	if m, err := resolver.FileMetadataByLocation(location); err == nil && m.FileInfo != nil {
+		size = m.Size()
+	}
+	return max(archiveTreeRatio*size, archiveTreeFloorBytes)
+}
+
+func (c *archiveCataloger) isAncestor(digests []file.Digest) bool {
+	for _, d := range digests {
+		if slices.Contains(c.ancestors, d) {
+			return true
+		}
+	}
+	return false
+}
+
+// packagesAt returns the packages located at the given coordinates, i.e. those describing the file there.
+func packagesAt(pkgs []pkg.Package, coordinates file.Coordinates) []pkg.Package {
+	var out []pkg.Package
+	for _, p := range pkgs {
+		if locatedAt(p, coordinates) {
+			out = append(out, p)
+		}
+	}
+	return out
+}
+
+// locatedAt reports whether one of p's locations is at the given coordinates.
+func locatedAt(p pkg.Package, coordinates file.Coordinates) bool {
+	for _, l := range p.Locations.ToUnorderedSlice() {
+		if l.Coordinates == coordinates {
+			return true
+		}
+	}
+	return false
+}
+
+func recordArchiveUnknown(builder sbomsync.Builder, coordinates file.Coordinates, reason string) {
+	appendUnknowns(builder, ArchiveCatalogerTaskName, []unknown.CoordinateError{{Coordinates: coordinates, Reason: errors.New(reason)}})
+}
+
+// runArchiveTasks runs each task against the archive's contents.
+//
+// Failures are recorded as RunTask records them at the top level: errors carrying coordinates keep
+// them, anything else is attributed to the archive. A failure never fails the archive or the scan.
+func runArchiveTasks(ctx context.Context, tasks []Task, resolver file.Resolver, archiveCoordinates file.Coordinates, builder sbomsync.Builder) {
+	for _, t := range tasks {
+		err := runSubTaskSafely(ctx, t, resolver, builder)
+		if err == nil {
+			continue
+		}
+		log.WithFields("task", t.Name(), "error", err).Trace("archive sub-cataloger task reported an error")
+
+		unknowns, remaining := unknown.ExtractCoordinateErrors(err)
+		if remaining != nil {
+			unknowns = append(unknowns, unknown.CoordinateError{Coordinates: archiveCoordinates, Reason: remaining})
+		}
+		appendUnknowns(builder, t.Name(), unknowns)
+	}
+}
+
+// runSubTaskSafely is runTaskSafely without the task name in a panic's error, since appendUnknowns
+// already prefixes it.
+func runSubTaskSafely(ctx context.Context, t Task, resolver file.Resolver, builder sbomsync.Builder) (err error) {
+	defer func() {
+		if r := recover(); r != nil {
+			log.WithFields("task", t.Name()).Debugf("archive sub-cataloger task panic stack:\n%s", debug.Stack())
+			err = fmt.Errorf("panic: %v", r)
+		}
+	}()
+	return t.Execute(ctx, resolver, builder)
+}
+
+// archiveCandidate is one file the walk will try to open.
+type archiveCandidate struct {
+	location file.Location
+
+	// sniffedAsArchive is true when the file's content types it as an archive. Such a file that cannot
+	// be extracted is a broken archive and is reported; a file that is a candidate only by name is
+	// passed over silently.
+	sniffedAsArchive bool
+}
+
+// zipArchiveGlobs find files named like zip archives whose content did not sniff as one, such as a
+// Spring Boot executable jar: a launcher script with a zip appended. The name only decides what gets
+// opened; the end-of-central-directory record decides whether it is an archive.
+//
+// Globs rather than a MIME lookup, because asking for every executable, script and unrecognized file
+// returned thousands of locations that were all discarded.
+var zipArchiveGlobs = []string{
+	"**/*.jar", "**/*.war", "**/*.ear", "**/*.par", "**/*.sar", "**/*.nar", "**/*.kar",
+	"**/*.hpi", "**/*.jpi", "**/*.far", "**/*.rar", "**/*.zip", "**/*.apk", "**/*.aar",
+	"**/*.egg", "**/*.whl", "**/*.lpkg", "**/*.zap", "**/*.exe",
+}
+
+var archiveMIMETypes = slices.Sorted(slices.Values(mimetype.ArchiveMIMETypeSet.List()))
+
+// discoverArchives returns every file worth opening: those whose content is an archive, plus those
+// named like a zip whose tail may still hold one.
+func (c *archiveCataloger) discoverArchives(resolver file.Resolver) []archiveCandidate {
+	archives, err := resolver.FilesByMIMEType(archiveMIMETypes...)
+	if err != nil {
+		log.WithFields("error", err).Debug("unable to list archive files for recursive cataloging")
+		return nil
+	}
+
+	var candidates []archiveCandidate
+	seen := map[file.Coordinates]int{}
+	for _, loc := range archives {
+		seen[loc.Coordinates] = len(candidates)
+		candidates = append(candidates, archiveCandidate{location: loc, sniffedAsArchive: true})
+	}
+
+	namedLikeZips, err := resolver.FilesByGlob(zipArchiveGlobs...)
+	if err != nil {
+		log.WithFields("error", err).Debug("unable to list files that may carry an appended archive")
+		return candidates
+	}
+	for _, loc := range namedLikeZips {
+		if i, dup := seen[loc.Coordinates]; dup {
+			// a MIME hit is the bare real path; the name it is reached by (a link such as
+			// lib/dep.jar -> ../store/3f9a1c) is what name-based catalogers like java key off
+			if prev := candidates[i].location; prev.AccessPath == "" || prev.AccessPath == prev.FullNestedPath() {
+				candidates[i].location = loc
+			}
+			continue
+		}
+		seen[loc.Coordinates] = len(candidates)
+		candidates = append(candidates, archiveCandidate{location: loc})
+	}
+	return candidates
+}
+
+// mergeArchiveResults copies everything found in an archive into its parent's SBOM.
+func mergeArchiveResults(found *sbom.SBOM, builder sbomsync.Builder) {
+	if pkgs := found.Artifacts.Packages.Sorted(); len(pkgs) > 0 {
+		builder.AddPackages(pkgs...)
+	}
+	if accessor, ok := builder.(sbomsync.Accessor); ok {
+		accessor.WriteToSBOM(func(s *sbom.SBOM) {
+			mergeFileArtifacts(&s.Artifacts, &found.Artifacts)
+		})
+	}
+	if len(found.Relationships) > 0 {
+		builder.AddRelationships(found.Relationships...)
+	}
+}
+
+// NewArchiveContainsTask relates each archive to every file the SBOM describes directly within it. It must
+// run after every other task, so the files within archives are those the scan root's configuration
+// selects (file selection, unknowns, package evidence) and no others.
+func NewArchiveContainsTask() Task {
+	fn := func(_ context.Context, _ file.Resolver, builder sbomsync.Builder) error {
+		var rels []artifact.Relationship
+		builder.(sbomsync.Accessor).ReadFromSBOM(func(s *sbom.SBOM) {
+			rels = archiveContains(s.AllCoordinates())
+		})
+		builder.AddRelationships(rels...)
+		return nil
+	}
+	return NewTask("archive-contains", fn)
+}
+
+// archiveContains relates the archive holding each file within one to that file, and each such archive to
+// the archive holding it, so an archive the SBOM does not otherwise describe still links what is within it.
+func archiveContains(coordinates []file.Coordinates) []artifact.Relationship {
+	related := file.NewCoordinateSet(coordinates...)
+	var rels []artifact.Relationship
+	for _, c := range coordinates {
+		for {
+			container, ok := archive.ContainingArchive(c)
+			if !ok {
+				break
+			}
+			rels = append(rels, artifact.Relationship{From: container, To: c, Type: artifact.ContainsRelationship})
+			if related.Contains(container) {
+				break
+			}
+			related.Add(container)
+			c = container
+		}
+	}
+	return rels
+}
+
+func mergeFileArtifacts(dst, src *sbom.Artifacts) {
+	mergeInto(&dst.FileMetadata, src.FileMetadata)
+	mergeInto(&dst.FileDigests, src.FileDigests)
+	mergeInto(&dst.FileContents, src.FileContents)
+	mergeInto(&dst.FileLicenses, src.FileLicenses)
+	mergeInto(&dst.Executables, src.Executables)
+	if len(src.Unknowns) > 0 && dst.Unknowns == nil {
+		dst.Unknowns = map[file.Coordinates][]string{}
+	}
+	for coordinates, reasons := range src.Unknowns {
+		dst.Unknowns[coordinates] = append(dst.Unknowns[coordinates], reasons...)
+	}
+}
+
+func mergeInto[K comparable, V any](dst *map[K]V, src map[K]V) {
+	if len(src) == 0 {
+		return
+	}
+	if *dst == nil {
+		*dst = make(map[K]V, len(src))
+	}
+	maps.Copy(*dst, src)
+}

internal/task/archive_tasks_test.go

@@ -0,0 +1,957 @@
+package task
+
+import (
+	"bytes"
+	"context"
+	"crypto/sha1"
+	"encoding/hex"
+	"errors"
+	"fmt"
+	"io"
+	"io/fs"
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+	"time"
+
+	"github.com/bmatcuk/doublestar/v4"
+	"github.com/scylladb/go-set/strset"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"github.com/wagoodman/go-partybus"
+	"github.com/wagoodman/go-progress"
+
+	stereoscopeFile "github.com/anchore/stereoscope/pkg/file"
+	"github.com/anchore/syft/internal/archive"
+	"github.com/anchore/syft/internal/bus"
+	"github.com/anchore/syft/internal/mimetype"
+	"github.com/anchore/syft/internal/sbomsync"
+	"github.com/anchore/syft/internal/testutils"
+	"github.com/anchore/syft/internal/unknown"
+	"github.com/anchore/syft/syft/artifact"
+	"github.com/anchore/syft/syft/cataloging"
+	"github.com/anchore/syft/syft/event"
+	"github.com/anchore/syft/syft/event/monitor"
+	"github.com/anchore/syft/syft/file"
+	"github.com/anchore/syft/syft/pkg"
+	"github.com/anchore/syft/syft/sbom"
+)
+
+// dirTestResolver is a minimal file.Resolver over a directory. FilesByMIMEType sniffs each file's
+// content as a real resolver does; FileContentsByLocation opens the file, which is random-access.
+type dirTestResolver struct {
+	file.Resolver
+	dir  string
+	fsid string
+}
+
+// streamingDirResolver is dirTestResolver handing out plain streams, so an archive's own bytes must be
+// held in memory or written to disk rather than read in place.
+type streamingDirResolver struct {
+	dirTestResolver
+}
+
+func (d streamingDirResolver) FileContentsByLocation(loc file.Location) (io.ReadCloser, error) {
+	f, err := d.dirTestResolver.FileContentsByLocation(loc)
+	if err != nil {
+		return nil, err
+	}
+	return struct {
+		io.Reader
+		io.Closer
+	}{f, f}, nil
+}
+
+// panickingDirResolver is dirTestResolver whose reads of one file panic, standing in for a decoder
+// that panics on hostile bytes.
+type panickingDirResolver struct {
+	dirTestResolver
+	path string
+}
+
+func (d panickingDirResolver) FileContentsByLocation(loc file.Location) (io.ReadCloser, error) {
+	if loc.RealPath == d.path {
+		return io.NopCloser(panicReader{}), nil
+	}
+	return d.dirTestResolver.FileContentsByLocation(loc)
+}
+
+type panicReader struct{}
+
+func (panicReader) Read([]byte) (int, error) { panic("decoder blew up") }
+
+func Test_archiveCataloger_aPanicCostsOnlyThatArchive(t *testing.T) {
+	rootDir := t.TempDir()
+	for _, name := range []string{"bad.zip", "good.zip"} {
+		require.NoError(t, os.WriteFile(filepath.Join(rootDir, name), testutils.Zip(t, map[string][]byte{"a.txt": []byte("a")}), 0o600))
+	}
+
+	var seen []string
+	tsk := newTestTask(t, cataloging.DefaultArchiveSearchConfig().WithMaxDepth(1), capturingTask(t, &seen, nil))
+
+	resolver := panickingDirResolver{dirTestResolver: dirTestResolver{dir: rootDir}, path: "/bad.zip"}
+	err := tsk.Execute(context.Background(), resolver, sbomsync.NewBuilder(newTestSBOM()))
+
+	// a coordinate error becomes an unknown; a plain error (or an escaped panic) would fail the scan
+	coordErrs, remaining := unknown.ExtractCoordinateErrors(err)
+	require.NoError(t, remaining)
+	require.Len(t, coordErrs, 1)
+	assert.Equal(t, "/bad.zip", coordErrs[0].Coordinates.RealPath)
+	assert.EqualError(t, coordErrs[0].Reason, "panic while cataloging archive: decoder blew up", "no stack trace in the SBOM-bound reason")
+	assert.Equal(t, []string{"/good.zip"}, seen, "the sibling is still cataloged")
+}
+
+func newTestTask(t *testing.T, cfg cataloging.ArchiveSearchConfig, subPipeline ...Task) Task {
+	t.Helper()
+	tsk := NewArchiveCatalogerTask(cfg, cataloging.UnknownsConfig{}, subPipeline, nil, nil)
+	require.NotNil(t, tsk)
+	return tsk
+}
+
+// newLimitedTestTask builds the task with the limiter's own limits, where zero forbids the resource.
+func newLimitedTestTask(t *testing.T, maxDepth int, limits archive.Limits, subPipeline ...Task) Task {
+	t.Helper()
+	tsk := newArchiveCatalogerTask(maxDepth, limits, false, subPipeline, nil, nil)
+	require.NotNil(t, tsk)
+	return tsk
+}
+
+func newTestSBOM() *sbom.SBOM {
+	return &sbom.SBOM{Artifacts: sbom.Artifacts{Packages: pkg.NewCollection()}}
+}
+
+func countingTask(ran *int) Task {
+	return NewTask("count-runs", func(_ context.Context, _ file.Resolver, _ sbomsync.Builder) error {
+		*ran++
+		return nil
+	})
+}
+
+// capturingTask records the virtual path of every archive the sub-pipeline is run against and how many
+// files its resolver holds.
+func capturingTask(t *testing.T, seen *[]string, fileCounts *map[string]int) Task {
+	return NewTask("capture", func(ctx context.Context, r file.Resolver, _ sbomsync.Builder) error {
+		trav := archive.TraversalFromContext(ctx)
+		require.NotNil(t, trav)
+		*seen = append(*seen, archive.VirtualPath(trav.Location))
+		if fileCounts != nil {
+			locs, err := r.FilesByGlob("**")
+			require.NoError(t, err)
+			(*fileCounts)[archive.VirtualPath(trav.Location)] = len(locs)
+		}
+		return nil
+	})
+}
+
+func Test_archiveCataloger_truncationStillCatalogs(t *testing.T) {
+	// reaching a limit is a truncation, not a failure: the sub-pipeline still runs over what was stored
+	big := bytes.Repeat([]byte("x"), 4096)
+	outerZip := testutils.Zip(t, map[string][]byte{
+		"a/small.txt": []byte("small"),
+		"b/big.txt":   big,
+	})
+
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "outer.zip"), outerZip, 0o600))
+
+	// nothing is held in memory, so each entry is charged to disk: small.txt lands, big.txt is refused
+	limits := archive.Limits{MaxMemoryBytes: 0, MaxDiskBytes: 6000}
+
+	var seen []string
+	fileCounts := map[string]int{}
+	tsk := newLimitedTestTask(t, 1, limits, capturingTask(t, &seen, &fileCounts))
+
+	s := newTestSBOM()
+	err := tsk.Execute(context.Background(), dirTestResolver{dir: rootDir}, sbomsync.NewBuilder(s))
+
+	require.NoError(t, err, "a truncated extraction must not fail the scan")
+	assert.Equal(t, []string{"/outer.zip"}, seen, "the sub-pipeline must run over the partial contents")
+	assert.Equal(t, 1, fileCounts["/outer.zip"], "only the entry stored before the limit is visible")
+
+	reasons, ok := s.Artifacts.Unknowns[file.NewCoordinates("/outer.zip", "")]
+	require.True(t, ok, "the truncation must be recorded against the archive; got %v", s.Artifacts.Unknowns)
+	require.Len(t, reasons, 1)
+	assert.Contains(t, reasons[0], "archive cataloged from part of its contents")
+	assert.Contains(t, reasons[0], ArchiveCatalogerTaskName, "the unknown names the task that recorded it")
+}
+
+func Test_archiveCataloger_aDamagedEntryCostsOnlyThatEntry(t *testing.T) {
+	rootDir := t.TempDir()
+	// entry data overwritten but headers and end-of-central-directory intact: detected as an archive,
+	// and data.bin fails when it is read. ok.txt comes after it and is intact.
+	corrupt := testutils.Zip(t, map[string][]byte{"data.bin": incompressible(4096), "ok.txt": []byte("ok")})
+	require.Greater(t, len(corrupt), 1024)
+	for i := 100; i < 600; i++ {
+		corrupt[i] ^= 0xff
+	}
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "corrupt.zip"), corrupt, 0o600))
+
+	var seen []string
+	fileCounts := map[string]int{}
+	tsk := newTestTask(t, cataloging.DefaultArchiveSearchConfig().WithMaxDepth(1), capturingTask(t, &seen, &fileCounts))
+
+	s := newTestSBOM()
+	require.NoError(t, tsk.Execute(context.Background(), dirTestResolver{dir: rootDir}, sbomsync.NewBuilder(s)))
+
+	assert.Equal(t, []string{"/corrupt.zip"}, seen, "the archive is still cataloged")
+	assert.Equal(t, 1, fileCounts["/corrupt.zip"], "from the entries that could be read")
+	reasons := s.Artifacts.Unknowns[file.NewCoordinates("/corrupt.zip", "")]
+	require.Len(t, reasons, 1)
+	assert.Contains(t, reasons[0], `entry "data.bin" could not be read`)
+}
+
+func Test_NewArchiveCatalogerTask_gating(t *testing.T) {
+	someTask := NewTask("noop", func(_ context.Context, _ file.Resolver, _ sbomsync.Builder) error { return nil })
+
+	tests := []struct {
+		name        string
+		cfg         cataloging.ArchiveSearchConfig
+		subPipeline []Task
+		wantTask    bool
+	}{
+		{
+			name:        "disabled at depth 0",
+			cfg:         cataloging.DefaultArchiveSearchConfig(),
+			subPipeline: []Task{someTask},
+		},
+		{
+			name:        "no sub-pipeline",
+			cfg:         cataloging.DefaultArchiveSearchConfig().WithMaxDepth(2),
+			subPipeline: nil,
+		},
+		{
+			name:        "enabled",
+			cfg:         cataloging.DefaultArchiveSearchConfig().WithMaxDepth(2),
+			subPipeline: []Task{someTask},
+			wantTask:    true,
+		},
+		{
+			name:        "enabled at negative depth",
+			cfg:         cataloging.DefaultArchiveSearchConfig().WithMaxDepth(-1),
+			subPipeline: []Task{someTask},
+			wantTask:    true,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			got := NewArchiveCatalogerTask(tt.cfg, cataloging.UnknownsConfig{}, tt.subPipeline, nil, nil)
+			if tt.wantTask {
+				require.NotNil(t, got)
+				assert.Equal(t, ArchiveCatalogerTaskName, got.Name())
+				return
+			}
+			assert.Nil(t, got)
+		})
+	}
+}
+
+func Test_archiveCataloger_depthStopsAtTheCeiling(t *testing.T) {
+	// "unbounded" must still end, or a zip quine or recursive bomb runs forever, and a configured depth
+	// past the ceiling must too, or the SBOM holds chains no decoder accepts back
+	chain := testutils.Zip(t, map[string][]byte{"deep.txt": []byte("deep")})
+	for range archive.MaxDepth + 4 {
+		chain = testutils.Zip(t, map[string][]byte{"n.zip": chain})
+	}
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "outer.zip"), chain, 0o600))
+
+	for _, depth := range []int{-1, archive.MaxDepth + 2} {
+		t.Run(fmt.Sprint(depth), func(t *testing.T) {
+			var seen []string
+			tsk := newTestTask(t, cataloging.DefaultArchiveSearchConfig().WithMaxDepth(depth), capturingTask(t, &seen, nil))
+			_ = tsk.Execute(context.Background(), dirTestResolver{dir: rootDir}, sbomsync.NewBuilder(newTestSBOM()))
+
+			assert.Len(t, seen, archive.MaxDepth)
+		})
+	}
+}
+
+func Test_archiveCataloger_anArchiveIdenticalToAnAncestorIsNotEntered(t *testing.T) {
+	// a zip quine contains itself. Building one is impractical, so the walk is started as if it were
+	// already inside an archive with these exact bytes, which is the state a quine reaches one level down
+	outerZip := testutils.Zip(t, map[string][]byte{"a.txt": []byte("a")})
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "outer.zip"), outerZip, 0o600))
+
+	var ran int
+	c := newTestCataloger(-1, archive.NewLimiter(archive.Limits{MaxMemoryBytes: -1, MaxDiskBytes: -1}), countingTask(&ran))
+	sum := sha1.Sum(outerZip)
+	c.ancestors = []file.Digest{{Algorithm: "sha1", Value: hex.EncodeToString(sum[:])}}
+
+	s := newTestSBOM()
+	require.NoError(t, c.catalog(context.Background(), dirTestResolver{dir: rootDir}, 0, sbomsync.NewBuilder(s)))
+
+	assert.Zero(t, ran, "the sub-pipeline must not run inside a repeat of an ancestor")
+	reasons := s.Artifacts.Unknowns[file.NewCoordinates("/outer.zip", "")]
+	require.Len(t, reasons, 1)
+	assert.Contains(t, reasons[0], "identical to an archive that contains it")
+	assert.Len(t, c.ancestors, 1, "the walk leaves the ancestor stack as it found it")
+}
+
+func Test_archiveCataloger_stopsWhenTheContextIsCancelled(t *testing.T) {
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "outer.zip"), testutils.Zip(t, map[string][]byte{"a.txt": []byte("a")}), 0o600))
+
+	ctx, cancel := context.WithCancel(context.Background())
+	cancel()
+
+	var ran int
+	tsk := newTestTask(t, cataloging.DefaultArchiveSearchConfig().WithMaxDepth(1), countingTask(&ran))
+	err := tsk.Execute(ctx, dirTestResolver{dir: rootDir}, sbomsync.NewBuilder(newTestSBOM()))
+
+	require.ErrorIs(t, err, context.Canceled)
+	assert.Zero(t, ran)
+}
+
+func Test_archiveCataloger_decompressionBudgetIsSharedByATreeAndFreshPerTopLevelArchive(t *testing.T) {
+	// a recursive bomb fits the limits one level at a time, so what bounds it is the total decompressed
+	// under one top-level archive
+	origRatio, origFloor := archiveTreeRatio, archiveTreeFloorBytes
+	archiveTreeRatio, archiveTreeFloorBytes = 0, 100_000
+	t.Cleanup(func() { archiveTreeRatio, archiveTreeFloorBytes = origRatio, origFloor })
+
+	zeros := make([]byte, 60_000)
+	nested := testutils.Zip(t, map[string][]byte{"zeros.bin": zeros})
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "bomb.zip"), testutils.Zip(t, map[string][]byte{"a.zip": nested, "b.zip": nested}), 0o600))
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "sibling.zip"), testutils.Zip(t, map[string][]byte{"zeros.bin": zeros}), 0o600))
+
+	var seen []string
+	fileCounts := map[string]int{}
+	tsk := newTestTask(t, cataloging.DefaultArchiveSearchConfig().WithMaxDepth(2), capturingTask(t, &seen, &fileCounts))
+	s := newTestSBOM()
+	require.NoError(t, tsk.Execute(context.Background(), dirTestResolver{dir: rootDir}, sbomsync.NewBuilder(s)))
+
+	assert.Equal(t, 1, fileCounts["/bomb.zip:a.zip"], "the first nested archive fits the tree's budget")
+	assert.Equal(t, 0, fileCounts["/bomb.zip:b.zip"], "the second does not: the budget is shared, not per archive")
+	reasons := s.Artifacts.Unknowns[file.Coordinates{RealPath: "/bomb.zip", FullPath: "/bomb.zip!/b.zip"}]
+	require.Len(t, reasons, 1)
+	assert.Contains(t, reasons[0], "possible decompression bomb")
+	assert.Equal(t, 1, fileCounts["/sibling.zip"], "another top-level archive starts with a fresh budget")
+}
+
+func Test_archiveCataloger_noSelfContainsEdge(t *testing.T) {
+	// a jar java cannot identify records an unknown at its own coordinates; that must not turn into
+	// "x.jar CONTAINS x.jar", which a graph walker would loop on
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "x.jar"), testutils.Zip(t, map[string][]byte{"readme.txt": []byte("no manifest")}), 0o600))
+
+	tsk := newTestTask(t, cataloging.DefaultArchiveSearchConfig().WithMaxDepth(1), javaTask(), fileMetadataTask())
+	s := newTestSBOM()
+	s.Artifacts.FileMetadata = map[file.Coordinates]file.Metadata{}
+	_ = tsk.Execute(context.Background(), dirTestResolver{dir: rootDir}, sbomsync.NewBuilder(s))
+	withArchiveContains(t, s)
+
+	require.Contains(t, s.Artifacts.Unknowns, file.NewCoordinates("/x.jar", ""), "the fixture must reproduce the unknown")
+	var contains int
+	for _, rel := range s.Relationships {
+		if rel.Type != artifact.ContainsRelationship {
+			continue
+		}
+		contains++
+		assert.NotEqual(t, rel.From.ID(), rel.To.ID(), "self-referential CONTAINS edge: %+v", rel)
+	}
+	assert.Positive(t, contains, "the archive still contains its files")
+}
+
+func Test_NewArchiveContainsTask(t *testing.T) {
+	// a file within an archive is contained only when the SBOM describes it, as a file at the scan root is
+	// listed only then; an executable no package owns is recorded whatever the file selection
+	in := func(fullPath string) file.Coordinates {
+		return file.Coordinates{RealPath: "/outer.tar", FileSystemID: "layer", FullPath: fullPath}
+	}
+	outer := file.NewCoordinates("/outer.tar", "layer")
+	jar := in("/outer.tar!/lib/app.jar")
+	manifest := in("/outer.tar!/lib/app.jar!/META-INF/MANIFEST.MF")
+	unknownExe := in("/outer.tar!/bin/setup.exe")
+
+	s := newTestSBOM()
+	s.Artifacts.FileMetadata = map[file.Coordinates]file.Metadata{manifest: {}, file.NewCoordinates("/loose.txt", "layer"): {}}
+	s.Artifacts.Executables = map[file.Coordinates]file.Executable{in("/outer.tar!/bin/tool"): {}}
+	s.Artifacts.Unknowns = map[file.Coordinates][]string{unknownExe: {"no package identified in executable file"}}
+
+	withArchiveContains(t, s)
+
+	type edge struct{ from, to file.Coordinates }
+	var edges []edge
+	for _, r := range s.Relationships {
+		assert.Equal(t, artifact.ContainsRelationship, r.Type)
+		edges = append(edges, edge{r.From.(file.Coordinates), r.To.(file.Coordinates)})
+	}
+	assert.ElementsMatch(t, []edge{
+		{jar, manifest},
+		{outer, jar}, // the jar is not described itself, but is on the way to what is
+		{outer, unknownExe},
+	}, edges)
+}
+
+func Test_NewArchiveCatalogerTask_dropsItselfFromSubPipeline(t *testing.T) {
+	// a copy of itself in the sub-pipeline would process every nesting level twice
+	cfg := cataloging.DefaultArchiveSearchConfig().WithMaxDepth(2)
+
+	innerZip := testutils.Zip(t, map[string][]byte{"leaf.txt": []byte("leaf")})
+	outerZip := testutils.Zip(t, map[string][]byte{"nested/inner.zip": innerZip})
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "outer.zip"), outerZip, 0o600))
+
+	var ran int
+	countTask := countingTask(&ran)
+
+	poisoned := []Task{countTask, NewArchiveCatalogerTask(cfg, cataloging.UnknownsConfig{}, []Task{countTask}, nil, nil)}
+	require.NotNil(t, poisoned[1])
+
+	tsk := newTestTask(t, cfg, poisoned...)
+	require.NoError(t, tsk.Execute(context.Background(), dirTestResolver{dir: rootDir}, sbomsync.NewBuilder(newTestSBOM())))
+
+	assert.Equal(t, 2, ran, "two archives, one sub-pipeline task each")
+
+	t.Run("a sub-pipeline of nothing but itself yields no task", func(t *testing.T) {
+		only := []Task{NewArchiveCatalogerTask(cfg, cataloging.UnknownsConfig{}, []Task{countTask}, nil, nil)}
+		assert.Nil(t, NewArchiveCatalogerTask(cfg, cataloging.UnknownsConfig{}, only, nil, nil))
+	})
+}
+
+func Test_archiveCataloger_nestedArchivesKeepTheLayerFileSystemID(t *testing.T) {
+	// extracted files keep the layer digest as their FileSystemID at every level; the nesting chain
+	// rides on the traversal's VirtualPath and the coordinate's FullPath
+	innerZip := testutils.Zip(t, map[string][]byte{"leaf.txt": []byte("leaf")})
+	outerZip := testutils.Zip(t, map[string][]byte{"nested/inner.zip": innerZip})
+
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "outer.zip"), outerZip, 0o600))
+
+	const layerDigest = "sha256:1111111111111111111111111111111111111111111111111111111111111111"
+
+	var chains, fsids []string
+	captureTask := NewTask("capture-fsid", func(ctx context.Context, _ file.Resolver, _ sbomsync.Builder) error {
+		trav := archive.TraversalFromContext(ctx)
+		require.NotNil(t, trav)
+		chains = append(chains, archive.VirtualPath(trav.Location))
+		fsids = append(fsids, trav.Location.FileSystemID)
+		return nil
+	})
+
+	tsk := newTestTask(t, cataloging.DefaultArchiveSearchConfig().WithMaxDepth(2), captureTask)
+	require.NoError(t, tsk.Execute(context.Background(), dirTestResolver{dir: rootDir, fsid: layerDigest}, sbomsync.NewBuilder(newTestSBOM())))
+
+	assert.Equal(t, []string{layerDigest, layerDigest}, fsids)
+	assert.ElementsMatch(t, []string{"/outer.zip", "/outer.zip:nested/inner.zip"}, chains)
+}
+
+// twoLayerResolver reports the same archive path under two filesystem ids with different content, as an
+// all-layers image scan does for an archive rewritten in a later layer.
+type twoLayerResolver struct {
+	file.Resolver
+	path      string
+	contentBy map[string][]byte
+}
+
+func Test_archiveCataloger_sameArchivePathInTwoLayersDoesNotCollide(t *testing.T) {
+	resolver := twoLayerResolver{
+		path: "/app/bundle.zip",
+		contentBy: map[string][]byte{
+			"layer-one": testutils.Zip(t, map[string][]byte{"lib/config.json": []byte(`{"v":1}`)}),
+			"layer-two": testutils.Zip(t, map[string][]byte{"lib/config.json": []byte(`{"v":2}`)}),
+		},
+	}
+
+	var chains []string
+	fileTask := NewTask("record-files", func(ctx context.Context, r file.Resolver, builder sbomsync.Builder) error {
+		trav := archive.TraversalFromContext(ctx)
+		require.NotNil(t, trav)
+		chains = append(chains, trav.Location.FileSystemID)
+
+		locs, err := r.FilesByGlob("**")
+		require.NoError(t, err)
+		metadata := map[file.Coordinates]file.Metadata{}
+		for _, loc := range locs {
+			metadata[loc.Coordinates] = file.Metadata{Path: loc.RealPath}
+		}
+		builder.(sbomsync.Accessor).WriteToSBOM(func(s *sbom.SBOM) {
+			s.Artifacts.FileMetadata = metadata
+		})
+		return nil
+	})
+
+	tsk := newTestTask(t, cataloging.DefaultArchiveSearchConfig().WithMaxDepth(1), fileTask)
+
+	s := &sbom.SBOM{Artifacts: sbom.Artifacts{
+		Packages:     pkg.NewCollection(),
+		FileMetadata: map[file.Coordinates]file.Metadata{},
+	}}
+	require.NoError(t, tsk.Execute(context.Background(), resolver, sbomsync.NewBuilder(s)))
+
+	assert.ElementsMatch(t, []string{"layer-one", "layer-two"}, chains)
+	// the tables are keyed by Coordinates, so a collision is a silently missing entry
+	assert.Len(t, s.Artifacts.FileMetadata, 2)
+}
+
+func Test_archiveCataloger_subPipelineFailureIsRecordedAsAnUnknown(t *testing.T) {
+	// runSubPipeline bypasses RunTask, where the coordinate-error to unknown conversion lives
+	outerZip := testutils.Zip(t, map[string][]byte{"lib/broken.json": []byte("{")})
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "outer.zip"), outerZip, 0o600))
+
+	cfg := cataloging.DefaultArchiveSearchConfig().WithMaxDepth(1)
+
+	t.Run("a coordinate error keeps the coordinates the cataloger named", func(t *testing.T) {
+		failing := NewTask("failing-cataloger", func(_ context.Context, r file.Resolver, _ sbomsync.Builder) error {
+			locs, err := r.FilesByGlob("**")
+			require.NoError(t, err)
+			require.NotEmpty(t, locs)
+			var errs error
+			for _, loc := range locs {
+				errs = unknown.Append(errs, loc, errors.New("unable to parse"))
+			}
+			return errs
+		})
+
+		tsk := newTestTask(t, cfg, failing)
+		s := newTestSBOM()
+		require.NoError(t, tsk.Execute(context.Background(), dirTestResolver{dir: rootDir}, sbomsync.NewBuilder(s)),
+			"a cataloger failing inside an archive must not fail the archive or the scan")
+
+		require.Len(t, s.Artifacts.Unknowns, 1)
+		for coords, reasons := range s.Artifacts.Unknowns {
+			assert.Equal(t, "/outer.zip!/lib/broken.json", coords.FullNestedPath(), "the inner coordinates must survive the merge")
+			assert.Equal(t, "/outer.zip", coords.RealPath, "and must be addressable per archive")
+			assert.Equal(t, []string{"failing-cataloger: unable to parse"}, reasons)
+		}
+	})
+
+	t.Run("an error with no coordinates is attributed to the archive", func(t *testing.T) {
+		failing := NewTask("bare-error-cataloger", func(_ context.Context, _ file.Resolver, _ sbomsync.Builder) error {
+			return errors.New("cataloger blew up")
+		})
+
+		tsk := newTestTask(t, cfg, failing)
+		s := newTestSBOM()
+		require.NoError(t, tsk.Execute(context.Background(), dirTestResolver{dir: rootDir}, sbomsync.NewBuilder(s)))
+
+		require.Len(t, s.Artifacts.Unknowns, 1)
+		reasons, ok := s.Artifacts.Unknowns[file.NewCoordinates("/outer.zip", "")]
+		require.True(t, ok, "an error with no location of its own belongs to the containing archive")
+		assert.Equal(t, []string{"bare-error-cataloger: cataloger blew up"}, reasons)
+	})
+
+	t.Run("a panicking cataloger is recovered and recorded", func(t *testing.T) {
+		panicking := NewTask("panicking-cataloger", func(_ context.Context, _ file.Resolver, _ sbomsync.Builder) error {
+			panic("nope")
+		})
+
+		tsk := newTestTask(t, cfg, panicking)
+		s := newTestSBOM()
+		require.NoError(t, tsk.Execute(context.Background(), dirTestResolver{dir: rootDir}, sbomsync.NewBuilder(s)),
+			"a panic inside an archive must not fail the scan")
+
+		reasons, ok := s.Artifacts.Unknowns[file.NewCoordinates("/outer.zip", "")]
+		require.True(t, ok)
+		require.Len(t, reasons, 1)
+		assert.Equal(t, "panicking-cataloger: panic: nope", reasons[0])
+	})
+}
+
+func Test_archiveCataloger_subPipelineUnknownsAreAddedNotReplaced(t *testing.T) {
+	outerZip := testutils.Zip(t, map[string][]byte{"lib/thing.json": []byte("{}")})
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "outer.zip"), outerZip, 0o600))
+
+	preexisting := file.Coordinates{RealPath: "/outer.zip", FullPath: "/outer.zip!/lib/thing.json"}
+	writer := NewTask("scratch-writer", func(_ context.Context, _ file.Resolver, builder sbomsync.Builder) error {
+		builder.(sbomsync.Accessor).WriteToSBOM(func(s *sbom.SBOM) {
+			if s.Artifacts.Unknowns == nil {
+				s.Artifacts.Unknowns = map[file.Coordinates][]string{}
+			}
+			s.Artifacts.Unknowns[preexisting] = append(s.Artifacts.Unknowns[preexisting], "recorded by the cataloger itself")
+		})
+		return nil
+	})
+	failing := NewTask("failing-cataloger", func(_ context.Context, _ file.Resolver, _ sbomsync.Builder) error {
+		return errors.New("boom")
+	})
+
+	tsk := newTestTask(t, cataloging.DefaultArchiveSearchConfig().WithMaxDepth(1), writer, failing)
+	s := newTestSBOM()
+	require.NoError(t, tsk.Execute(context.Background(), dirTestResolver{dir: rootDir}, sbomsync.NewBuilder(s)))
+
+	assert.Equal(t, []string{"recorded by the cataloger itself"}, s.Artifacts.Unknowns[preexisting])
+	assert.Equal(t, []string{"failing-cataloger: boom"}, s.Artifacts.Unknowns[file.NewCoordinates("/outer.zip", "")])
+}
+
+func Test_archiveCataloger_limitsFallWhenAnArchiveIsReleased(t *testing.T) {
+	entry := bytes.Repeat([]byte("z"), 400)
+	entries := map[string][]byte{}
+	for i := range 5 {
+		entries[fmt.Sprintf("e%d.bin", i)] = entry
+	}
+
+	rootDir := t.TempDir()
+	for _, name := range []string{"one.zip", "two.zip"} {
+		require.NoError(t, os.WriteFile(filepath.Join(rootDir, name), testutils.Zip(t, entries), 0o600))
+	}
+
+	// room in memory for one archive's entries and their index cost, not for two at once
+	limiter := archive.NewLimiter(archive.Limits{MaxMemoryBytes: 20000, MaxDiskBytes: 0})
+
+	// sampled while the archive is still held
+	var extracted []int
+	var peakMemory int64
+	sample := NewTask("sample", func(_ context.Context, r file.Resolver, _ sbomsync.Builder) error {
+		locs, err := r.FilesByGlob("**")
+		require.NoError(t, err)
+		extracted = append(extracted, len(locs))
+		if mem, _ := limiter.InUse(); mem > peakMemory {
+			peakMemory = mem
+		}
+		return nil
+	})
+
+	c := newTestCataloger(1, limiter, sample)
+	require.NoError(t, c.catalog(context.Background(), dirTestResolver{dir: rootDir}, 0, sbomsync.NewBuilder(newTestSBOM())))
+
+	assert.Equal(t, []int{5, 5}, extracted,
+		"both archives must extract in full: the first is released before the second is admitted")
+	assert.Positive(t, peakMemory, "entries within the memory limit are held in memory")
+
+	mem, disk := limiter.InUse()
+	assert.Zero(t, mem, "the memory limit must fall back to nothing once the walk unwinds")
+	assert.Zero(t, disk, "and so must the disk limit")
+}
+
+func newTestCataloger(maxDepth int, limiter *archive.Limiter, subPipeline ...Task) *archiveCataloger {
+	return &archiveCataloger{
+		maxDepth: maxDepth,
+		pkgTasks: subPipeline,
+		limiter:  limiter,
+		progress: bus.StartCatalogerTask(context.Background(), archiveCatalogerProgressInfo(), -1, ""),
+	}
+}
+
+func Test_archiveCataloger_archiveWhoseOwnBytesExceedTheDiskLimitIsSkipped(t *testing.T) {
+	// a streamed archive's own bytes must be placed before it can be opened; when they do not fit on
+	// disk the archive is skipped rather than waited for, and a sibling that fits is cataloged in full
+	oversized := testutils.Zip(t, map[string][]byte{"payload.bin": incompressible(8000)})
+	small := testutils.Zip(t, map[string][]byte{"ok.txt": []byte("ok")})
+
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "oversized.zip"), oversized, 0o600))
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "small.zip"), small, 0o600))
+
+	// room for the small archive's bytes, its one entry and that entry's index cost
+	diskLimit := int64(len(small)) + 3000
+	require.Greater(t, int64(len(oversized)), diskLimit, "the fixture must actually exceed the limit")
+
+	limits := archive.Limits{MaxMemoryBytes: 0, MaxDiskBytes: diskLimit}
+
+	var seen []string
+	fileCounts := map[string]int{}
+	tsk := newLimitedTestTask(t, 1, limits, capturingTask(t, &seen, &fileCounts))
+
+	s := newTestSBOM()
+	require.NoError(t, tsk.Execute(context.Background(), streamingDirResolver{dirTestResolver{dir: rootDir}}, sbomsync.NewBuilder(s)),
+		"reaching a limit must not fail the scan")
+
+	assert.Equal(t, []string{"/small.zip"}, seen, "the oversized archive is skipped and the sibling is still cataloged")
+	assert.Equal(t, 1, fileCounts["/small.zip"])
+
+	reasons := s.Artifacts.Unknowns[file.NewCoordinates("/oversized.zip", "")]
+	require.Len(t, reasons, 1, "the skip must be recorded against the archive; got %v", s.Artifacts.Unknowns)
+	assert.Contains(t, reasons[0], "archive skipped")
+}
+
+func Test_archiveCataloger_discoverArchivesSelectsTarFamily(t *testing.T) {
+	marker := map[string][]byte{"nested/marker.txt": []byte("hello")}
+
+	scanDir := t.TempDir()
+	for name, body := range map[string][]byte{
+		"bundle.tar.gz": testutils.TarGz(t, marker),
+		"bundle.tgz":    testutils.TarGz(t, marker),
+		"bundle.tar":    testutils.Tar(t, marker),
+		"bundle.zip":    testutils.Zip(t, marker),
+		"notes.txt":     []byte("not an archive at all"),
+	} {
+		require.NoError(t, os.WriteFile(filepath.Join(scanDir, name), body, 0o600))
+	}
+
+	var seen []string
+	fileCounts := map[string]int{}
+	tsk := newTestTask(t, cataloging.DefaultArchiveSearchConfig().WithMaxDepth(1), capturingTask(t, &seen, &fileCounts))
+	require.NoError(t, tsk.Execute(context.Background(), dirTestResolver{dir: scanDir}, sbomsync.NewBuilder(newTestSBOM())))
+
+	assert.ElementsMatch(t, []string{"/bundle.tar.gz", "/bundle.tgz", "/bundle.tar", "/bundle.zip"}, seen,
+		"every tar-family archive must be reached, and the plain text file must not be")
+	for _, archivePath := range seen {
+		assert.Equal(t, 1, fileCounts[archivePath], "%s must have been extracted", archivePath)
+	}
+
+	t.Run("the MIME types the tar family is sniffed as are in the set discovery asks for", func(t *testing.T) {
+		for _, mt := range []string{"application/x-tar", "application/gzip", "application/x-gtar", "application/zip"} {
+			assert.True(t, mimetype.ArchiveMIMETypeSet.Has(mt), "%s must be a candidate archive type", mt)
+		}
+	})
+}
+
+type recordingPublisher struct {
+	events []partybus.Event
+}
+
+func Test_archiveCatalogerTask_publishesOneProgressRowPerCataloger(t *testing.T) {
+	// a consumer keying rows by ID (as the syft CLI does) replaces a republished row and never sees it
+	// complete, so each cataloger keeps to the one row it already owns
+	inner := testutils.Zip(t, map[string][]byte{"inner/file.txt": []byte("hello")})
+	scanDir := t.TempDir()
+	for _, name := range []string{"one.zip", "two.zip"} {
+		require.NoError(t, os.WriteFile(filepath.Join(scanDir, name), inner, 0o600))
+	}
+
+	publisher := &recordingPublisher{}
+	bus.Set(publisher)
+	t.Cleanup(func() { bus.Set(nil) })
+
+	// the archive row's stage as each archive's sub-pipeline starts: the previous archive is done by then,
+	// so the row must read the walk's own count rather than anything a nested cataloger left behind
+	var rows []*monitor.TaskProgress
+	var stageAtEntry []string
+	noisy := NewTask("noisy", func(ctx context.Context, _ file.Resolver, _ sbomsync.Builder) error {
+		stageAtEntry = append(stageAtEntry, publisher.events[0].Value.(progress.StagedProgressable).Stage())
+		p := bus.StartCatalogerTask(ctx, monitor.GenericTask{ID: "noisy"}, 3, "")
+		rows = append(rows, p)
+		p.AtomicStage.Set("working on something")
+		p.Add(3)
+		p.SetCompleted()
+		return nil
+	})
+
+	tsk := newTestTask(t, cataloging.DefaultArchiveSearchConfig().WithMaxDepth(1), noisy)
+	require.NoError(t, tsk.Execute(context.Background(), dirTestResolver{dir: scanDir}, sbomsync.NewBuilder(newTestSBOM())))
+
+	var started []string
+	for _, e := range publisher.events {
+		if e.Type != event.CatalogerTaskStarted {
+			continue
+		}
+		info, ok := e.Source.(monitor.GenericTask)
+		require.True(t, ok, "expected a generic task as the event source")
+		started = append(started, info.ID)
+	}
+
+	assert.Equal(t, []string{ArchiveCatalogerTaskName, "noisy"}, started,
+		"each cataloger publishes one row, however many archives the walk enters")
+
+	require.Len(t, rows, 2, "the sub-pipeline ran once per archive")
+	assert.Same(t, rows[0], rows[1], "both runs must report into the one row that cataloger owns")
+	assert.Equal(t, int64(6), rows[0].Current(), "what every run found is counted onto that row")
+
+	require.Len(t, publisher.events, 2)
+	prog, ok := publisher.events[0].Value.(progress.StagedProgressable)
+	require.True(t, ok)
+	assert.ErrorIs(t, prog.Error(), progress.ErrCompleted, "the row must be completed, or a waiting consumer never finishes")
+	assert.Equal(t, int64(2), prog.Current(), "the archive row counts every archive the walk entered")
+	assert.Equal(t, "2 archives", prog.Stage(), "and says so once the walk is done")
+
+	// one.zip sorts before two.zip, and the resolver walks the scan directory in lexical order
+	assert.Equal(t, []string{"", "1 archives (/one.zip)"}, stageAtEntry,
+		"the row must take its stage back from the sub-pipeline once an archive is done")
+}
+
+func Test_archiveCataloger_reportsPeakUsageAndTheSlowestArchive(t *testing.T) {
+	// self time excludes nested archives, or the outer archive would be named every scan
+	innerJar := testutils.Zip(t, map[string][]byte{"README.txt": []byte("inner")})
+	outerZip := testutils.Zip(t, map[string][]byte{"lib/inner.jar": innerJar})
+
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "outer.zip"), outerZip, 0o600))
+
+	const innerWork = 40 * time.Millisecond
+	slow := NewTask("slow-inside-the-inner-archive", func(ctx context.Context, _ file.Resolver, _ sbomsync.Builder) error {
+		if trav := archive.TraversalFromContext(ctx); trav != nil && strings.HasSuffix(archive.VirtualPath(trav.Location), "inner.jar") {
+			time.Sleep(innerWork)
+		}
+		return nil
+	})
+
+	limiter := archive.NewLimiter(archive.Limits{MaxMemoryBytes: -1, MaxDiskBytes: -1})
+	c := newTestCataloger(3, limiter, slow)
+	require.NoError(t, c.catalog(context.Background(), dirTestResolver{dir: rootDir}, 0, sbomsync.NewBuilder(newTestSBOM())))
+
+	assert.Equal(t, "/outer.zip!/lib/inner.jar", c.slowestPath, "the slowest archive is named by its full chain")
+	assert.GreaterOrEqual(t, c.slowest, innerWork)
+	assert.Equal(t, int64(2), c.progress.Current())
+
+	// the peaks outlive the walk that set them
+	peakMemory, _ := limiter.Peak()
+	assert.Positive(t, peakMemory, "entries held in memory must show on the peak")
+	memory, disk := limiter.InUse()
+	assert.Zero(t, memory)
+	assert.Zero(t, disk)
+}
+
+func Test_archiveCataloger_slowestIsUnsetWhenNoArchiveIsCataloged(t *testing.T) {
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "notes.txt"), []byte("not an archive"), 0o600))
+
+	noop := NewTask("noop", func(context.Context, file.Resolver, sbomsync.Builder) error { return nil })
+	c := newTestCataloger(2, archive.NewLimiter(archive.Limits{MaxMemoryBytes: -1, MaxDiskBytes: -1}), noop)
+	require.NoError(t, c.catalog(context.Background(), dirTestResolver{dir: rootDir}, 0, sbomsync.NewBuilder(newTestSBOM())))
+
+	assert.Empty(t, c.slowestPath)
+	assert.Zero(t, c.progress.Current())
+	c.logStats() // must not panic with nothing to report
+}
+
+func Test_archiveCataloger_aMisnamedNonArchiveIsNotAnError(t *testing.T) {
+	// the name says archive, the content does not: it is never opened
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "notes.zip"),
+		[]byte("this is prose, not an archive, whatever the extension claims\n"), 0o600))
+
+	var ran int
+	tsk := newTestTask(t, cataloging.DefaultArchiveSearchConfig().WithMaxDepth(1), countingTask(&ran))
+
+	err := tsk.Execute(context.Background(), dirTestResolver{dir: rootDir}, sbomsync.NewBuilder(newTestSBOM()))
+
+	assert.NoError(t, err, "a file that is not an archive is not a failure to report")
+	assert.Zero(t, ran, "and nothing is cataloged inside it")
+}
+
+func Test_archiveCataloger_catalogsAZipBehindALauncherScript(t *testing.T) {
+	// the Spring Boot executable jar shape: content sniffing types it as a shell script, so it reaches
+	// the walk only by name and qualifies only by its end-of-central-directory record
+	inner := testutils.Zip(t, map[string][]byte{"nested/marker.txt": []byte("found me")})
+	prefixed := append([]byte("#!/bin/bash\nexec java -jar \"$0\" \"$@\"\nexit 0\n"),
+		testutils.Zip(t, map[string][]byte{"BOOT-INF/lib/inner.jar": inner})...)
+
+	rootDir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(rootDir, "app.jar"), prefixed, 0o600))
+
+	var seen []string
+	tsk := newTestTask(t, cataloging.DefaultArchiveSearchConfig().WithMaxDepth(3), capturingTask(t, &seen, nil))
+	require.NoError(t, tsk.Execute(context.Background(), dirTestResolver{dir: rootDir}, sbomsync.NewBuilder(newTestSBOM())))
+
+	assert.Equal(t, []string{"/app.jar", "/app.jar:BOOT-INF/lib/inner.jar"}, seen,
+		"the stub must not hide the archive, and the walk must carry on into what it holds")
+}
+
+func (d dirTestResolver) FilesByMIMEType(types ...string) ([]file.Location, error) {
+	return filesByMIMEType(d.dir, d.fsid, types...)
+}
+
+func filesByMIMEType(dir, fsid string, types ...string) ([]file.Location, error) {
+	wanted := strset.New(types...)
+	var locs []file.Location
+	err := filepath.WalkDir(dir, func(path string, entry fs.DirEntry, err error) error {
+		if err != nil || entry.IsDir() {
+			return err
+		}
+		f, err := os.Open(path)
+		if err != nil {
+			return err
+		}
+		mimeType := stereoscopeFile.MIMEType(f)
+		if closeErr := f.Close(); closeErr != nil {
+			return closeErr
+		}
+		if !wanted.Has(mimeType) {
+			return nil
+		}
+		rel, err := filepath.Rel(dir, path)
+		if err != nil {
+			return err
+		}
+		coords := file.Coordinates{RealPath: "/" + filepath.ToSlash(rel), FileSystemID: fsid}
+		locs = append(locs, file.NewLocationFromCoordinates(coords))
+		return nil
+	})
+	return locs, err
+}
+
+func (d dirTestResolver) FileContentsByLocation(loc file.Location) (io.ReadCloser, error) {
+	return os.Open(filepath.Join(d.dir, filepath.FromSlash(loc.RealPath)))
+}
+
+func (d dirTestResolver) FileMetadataByLocation(loc file.Location) (file.Metadata, error) {
+	info, err := os.Stat(filepath.Join(d.dir, filepath.FromSlash(loc.RealPath)))
+	return file.Metadata{FileInfo: info}, err
+}
+
+// matchesAnyGlob matches the resolver-relative path with a leading slash, the form a real resolver
+// globs over. No patterns matches everything.
+func matchesAnyGlob(root, path string, patterns []string) bool {
+	if len(patterns) == 0 {
+		return true
+	}
+	rel, err := filepath.Rel(root, path)
+	if err != nil {
+		return false
+	}
+	rel = "/" + filepath.ToSlash(rel)
+	for _, pattern := range patterns {
+		if ok, err := doublestar.Match(pattern, rel); err == nil && ok {
+			return true
+		}
+	}
+	return false
+}
+
+func (r twoLayerResolver) FilesByGlob(_ ...string) ([]file.Location, error) {
+	return nil, nil
+}
+
+func (d dirTestResolver) FilesByGlob(patterns ...string) ([]file.Location, error) {
+	var locs []file.Location
+	err := filepath.WalkDir(d.dir, func(path string, entry fs.DirEntry, err error) error {
+		if err != nil || entry.IsDir() {
+			return err
+		}
+		if !matchesAnyGlob(d.dir, path, patterns) {
+			return nil
+		}
+		rel, err := filepath.Rel(d.dir, path)
+		if err != nil {
+			return err
+		}
+		coords := file.Coordinates{RealPath: "/" + filepath.ToSlash(rel), FileSystemID: d.fsid}
+		locs = append(locs, file.NewLocationFromCoordinates(coords))
+		return nil
+	})
+	return locs, err
+}
+
+func (r twoLayerResolver) FilesByMIMEType(_ ...string) ([]file.Location, error) {
+	var locs []file.Location
+	for _, fsid := range []string{"layer-one", "layer-two"} {
+		locs = append(locs, file.NewLocationFromCoordinates(file.NewCoordinates(r.path, fsid)))
+	}
+	return locs, nil
+}
+
+func (r twoLayerResolver) FileContentsByLocation(loc file.Location) (io.ReadCloser, error) {
+	body, ok := r.contentBy[loc.FileSystemID]
+	if !ok {
+		return nil, os.ErrNotExist
+	}
+	return io.NopCloser(bytes.NewReader(body)), nil
+}
+
+// FileMetadataByLocation reports no metadata, so the archive falls back to the minimum budget.
+func (r twoLayerResolver) FileMetadataByLocation(file.Location) (file.Metadata, error) {
+	return file.Metadata{}, os.ErrNotExist
+}
+
+// incompressible returns n bytes deflate cannot shrink, so an archive built from them has a
+// predictable size to set a limit against.
+func incompressible(n int) []byte {
+	b := make([]byte, n)
+	x := uint32(12345)
+	for i := range b {
+		x = x*1664525 + 1013904223
+		b[i] = byte(x >> 24)
+	}
+	return b
+}
+
+func (p *recordingPublisher) Publish(e partybus.Event) {
+	p.events = append(p.events, e)
+}

internal/task/file_tasks.go

@@ -47,7 +47,7 @@ func newFileDigestCatalogerTask(selection file.Selection, hashers []crypto.Hash,
 		result, err := filedigest.NewCataloger(hashers).Catalog(ctx, resolver, coordinates...)
 
 		accessor.WriteToSBOM(func(sbom *sbom.SBOM) {
-			sbom.Artifacts.FileDigests = result
+			mergeInto(&sbom.Artifacts.FileDigests, result)
 		})
 
 		return err
@@ -78,7 +78,7 @@ func newFileMetadataCatalogerTask(selection file.Selection, tags ...string) Task
 		result, err := filemetadata.NewCataloger().Catalog(ctx, resolver, coordinates...)
 
 		accessor.WriteToSBOM(func(sbom *sbom.SBOM) {
-			sbom.Artifacts.FileMetadata = result
+			mergeInto(&sbom.Artifacts.FileMetadata, result)
 		})
 
 		return err
@@ -104,7 +104,7 @@ func newFileContentCatalogerTask(cfg filecontent.Config, tags ...string) Task {
 		result, err := filecontent.NewCataloger(cfg).Catalog(ctx, resolver)
 
 		accessor.WriteToSBOM(func(sbom *sbom.SBOM) {
-			sbom.Artifacts.FileContents = result
+			mergeInto(&sbom.Artifacts.FileContents, result)
 		})
 
 		return err
@@ -130,7 +130,7 @@ func newExecutableCatalogerTask(selection file.Selection, cfg executable.Config,
 		result, err := executable.NewCataloger(cfg).CatalogCtx(ctx, resolver)
 
 		accessor.WriteToSBOM(func(sbom *sbom.SBOM) {
-			sbom.Artifacts.Executables = result
+			mergeInto(&sbom.Artifacts.Executables, result)
 		})
 
 		return err

internal/task/file_tasks_test.go

@@ -40,19 +40,13 @@ func Test_coordinatesForSelection(t *testing.T) {
 				Relationships: []artifact.Relationship{
 					{
 						From: pkg.Package{},
-						To: file.Coordinates{
-							RealPath:     "path",
-							FileSystemID: "fs",
-						},
+						To:   file.NewCoordinates("path", "fs"),
 						Type: artifact.ContainsRelationship,
 					},
 				},
 			},
 			files: []file.Coordinates{
-				{
-					RealPath:     "path",
-					FileSystemID: "fs",
-				},
+				file.NewCoordinates("path", "fs"),
 			},
 			ok: true,
 		},
@@ -63,10 +57,7 @@ func Test_coordinatesForSelection(t *testing.T) {
 				Relationships: []artifact.Relationship{
 					{
 						From: pkg.Package{},
-						To: file.Coordinates{
-							RealPath:     "path",
-							FileSystemID: "fs",
-						},
+						To:   file.NewCoordinates("path", "fs"),
 						// wrong type
 						Type: artifact.DependencyOfRelationship,
 					},
@@ -82,10 +73,7 @@ func Test_coordinatesForSelection(t *testing.T) {
 				Relationships: []artifact.Relationship{
 					{
 						From: file.Coordinates{}, // wrong type
-						To: file.Coordinates{
-							RealPath:     "path",
-							FileSystemID: "fs",
-						},
+						To:   file.NewCoordinates("path", "fs"),
 						Type: artifact.ContainsRelationship,
 					},
 				},

internal/task/package_task_factory.go

@@ -3,9 +3,11 @@ package task
 import (
 	"context"
 	"fmt"
+	"path"
 	"strings"
 	"unicode"
 
+	"github.com/anchore/syft/internal/archive"
 	"github.com/anchore/syft/internal/bus"
 	"github.com/anchore/syft/internal/log"
 	"github.com/anchore/syft/internal/relationship"
@@ -48,7 +50,7 @@ func NewPackageTask(cfg CatalogingFactoryConfig, c pkg.Cataloger, tags ...string
 			HideOnSuccess: true,
 		}
 
-		t := bus.StartCatalogerTask(info, -1, "")
+		t := bus.StartCatalogerTask(ctx, info, -1, "")
 
 		pkgs, relationships, err := c.Catalog(ctx, resolver)
 
@@ -167,7 +169,7 @@ func applyComplianceRules(p *pkg.Package, cfg cataloging.ComplianceConfig) (bool
 		loc := "unknown"
 		locs := p.Locations.ToSlice()
 		if len(locs) > 0 {
-			loc = locs[0].Path()
+			loc = locs[0].FullNestedPath()
 		}
 		switch action {
 		case cataloging.ComplianceActionDrop:
@@ -236,10 +238,10 @@ func packageFileOwnershipRelationships(p pkg.Package, resolver file.PathResolver
 
 	locations := map[artifact.ID]file.Location{}
 
-	for _, path := range fileOwner.OwnedFiles() {
-		pathRefs, err := resolver.FilesByPath(path)
+	for _, ownedPath := range fileOwner.OwnedFiles() {
+		pathRefs, err := resolver.FilesByPath(ownedPath)
 		if err != nil {
-			return nil, fmt.Errorf("unable to find path for path=%q: %w", path, err)
+			return nil, fmt.Errorf("unable to find path for path=%q: %w", ownedPath, err)
 		}
 
 		if len(pathRefs) == 0 {
@@ -250,8 +252,13 @@ func packageFileOwnershipRelationships(p pkg.Package, resolver file.PathResolver
 		}
 
 		for _, ref := range pathRefs {
+			// an archive looks a relative path up from its root, but an owned path may be relative to
+			// anything (a python RECORD is relative to site-packages), so only an absolute one owns a file in one
+			if archive.ContainerPath(ref.Coordinates) != "" && !path.IsAbs(ownedPath) {
+				continue
+			}
 			if oldRef, ok := locations[ref.ID()]; ok {
-				log.Debugf("found path duplicate of %s", oldRef.RealPath)
+				log.Debugf("found path duplicate of %s", oldRef.FullNestedPath())
 			}
 			locations[ref.ID()] = ref
 		}

internal/task/package_task_factory_test.go

@@ -1,11 +1,15 @@
 package task
 
 import (
+	"bytes"
+	"context"
 	"testing"
 
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 
+	"github.com/anchore/syft/internal/archive"
+	"github.com/anchore/syft/internal/testutils"
 	"github.com/anchore/syft/syft/artifact"
 	"github.com/anchore/syft/syft/cataloging"
 	"github.com/anchore/syft/syft/cpe"
@@ -64,8 +68,8 @@ func TestApplyCompliance(t *testing.T) {
 	p2 := pkg.Package{Name: "", Version: "1.0"}   // missing name
 	p3 := pkg.Package{Name: "pkg-3", Version: ""} // missing version
 	p4 := pkg.Package{Name: "pkg-4", Version: ""} // missing version
-	c1 := file.Coordinates{RealPath: "/coords/1"}
-	c2 := file.Coordinates{RealPath: "/coords/2"}
+	c1 := file.NewCoordinates("/coords/1", "")
+	c2 := file.NewCoordinates("/coords/2", "")
 
 	for _, p := range []*pkg.Package{&p1, &p2, &p3, &p4} {
 		p.SetID()
@@ -281,3 +285,28 @@ func TestApplyComplianceRules_DropAndStub(t *testing.T) {
 	assert.False(t, isCompliant)
 	assert.Equal(t, cataloging.UnknownStubValue, p.Version)
 }
+
+func Test_packageFileOwnershipRelationships_exactPathsWithinAnArchive(t *testing.T) {
+	// a wheel's RECORD is relative to site-packages: looked up from the wheel's root it finds the file, but
+	// only an exact path owns one, as at the scan root
+	data := testutils.Zip(t, map[string]string{"pip/__init__.py": "", "bin/tool": ""})
+	whl, err := archive.Extract(context.Background(), bytes.NewReader(data), file.NewCoordinates("/pip.whl", ""),
+		archive.NewLimiter(archive.Limits{MaxMemoryBytes: 1 << 20}), archive.NewExclusions(nil))
+	require.NoError(t, err)
+	t.Cleanup(whl.Cleanup)
+
+	found, err := whl.FilesByPath("pip/__init__.py")
+	require.NoError(t, err)
+	require.Len(t, found, 1, "a relative path still finds the file")
+
+	p := pkg.Package{Name: "pip", Metadata: pkg.PythonPackage{Files: []pkg.PythonFileRecord{{Path: "pip/__init__.py"}, {Path: "/bin/tool"}}}}
+	p.SetID()
+	rels, err := packageFileOwnershipRelationships(p, whl)
+	require.NoError(t, err)
+
+	var owned []string
+	for _, r := range rels {
+		owned = append(owned, r.To.(file.Coordinates).FullNestedPath())
+	}
+	assert.Equal(t, []string{"/pip.whl!/bin/tool"}, owned)
+}

internal/task/scope_tasks.go

@@ -40,10 +40,11 @@ func packagesToRemove(accessor sbomsync.Accessor) []artifact.ID {
 					}
 				case "":
 					if isPrimaryEvidence {
-						if exists := filterDuplicates[getKey(p, l)]; exists {
+						k := getKey(p, l)
+						if exists := filterDuplicates[k]; exists {
 							break
 						}
-						filterDuplicates[getKey(p, l)] = true
+						filterDuplicates[k] = true
 						noPrimary = false
 						break
 					}
@@ -59,5 +60,5 @@ func packagesToRemove(accessor sbomsync.Accessor) []artifact.ID {
 }
 
 func getKey(pkg pkg.Package, loc file.Location) string {
-	return fmt.Sprintf("%s-%s-%s-%s", pkg.Name, pkg.Version, loc.RealPath, loc.AccessPath)
+	return fmt.Sprintf("%s-%s-%s-%s", pkg.Name, pkg.Version, loc.FullNestedPath(), loc.AccessPath)
 }

internal/task/unknowns_tasks.go

@@ -2,8 +2,11 @@ package task
 
 import (
 	"context"
+	"path"
+	"slices"
 	"strings"
 
+	"github.com/anchore/syft/internal/archive"
 	intFile "github.com/anchore/syft/internal/file"
 	"github.com/anchore/syft/internal/log"
 	"github.com/anchore/syft/internal/sbomsync"
@@ -36,11 +39,20 @@ func (c unknownsLabelerTask) finalize(resolver file.Resolver, s *sbom.SBOM) {
 	hasPackageReference := coordinateReferenceLookup(resolver, s)
 
 	if c.RemoveWhenPackagesDefined {
-		for coords := range s.Artifacts.Unknowns {
+		for coords, reasons := range s.Artifacts.Unknowns {
 			if !hasPackageReference(coords) {
 				continue
 			}
-			delete(s.Artifacts.Unknowns, coords)
+			// what the archive cataloger reports is about the archive's contents (left out, cut short),
+			// which a package describing the archive does not account for
+			kept := slices.DeleteFunc(reasons, func(r string) bool {
+				return !strings.HasPrefix(r, formatUnknown("", ArchiveCatalogerTaskName))
+			})
+			if len(kept) == 0 {
+				delete(s.Artifacts.Unknowns, coords)
+				continue
+			}
+			s.Artifacts.Unknowns[coords] = kept
 		}
 	}
 
@@ -59,7 +71,7 @@ func (c unknownsLabelerTask) finalize(resolver file.Resolver, s *sbom.SBOM) {
 	if c.IncludeUnexpandedArchives {
 		ctx := context.Background()
 		for coords := range s.Artifacts.FileMetadata {
-			format, _, notArchiveErr := intFile.IdentifyArchive(ctx, coords.RealPath, nil)
+			format, _, notArchiveErr := intFile.IdentifyArchive(ctx, coords.FullNestedPath(), nil)
 			if format != nil && notArchiveErr == nil && !hasPackageReference(coords) {
 				s.Artifacts.Unknowns[coords] = append(s.Artifacts.Unknowns[coords], "archive not cataloged")
 			}
@@ -71,6 +83,7 @@ func formatUnknown(err string, task ...string) string {
 	return strings.Join(task, "/") + ": " + err
 }
 
+//nolint:gocognit
 func coordinateReferenceLookup(resolver file.Resolver, s *sbom.SBOM) func(coords file.Coordinates) bool {
 	allPackageCoords := file.NewCoordinateSet()
 
@@ -83,7 +96,28 @@ func coordinateReferenceLookup(resolver file.Resolver, s *sbom.SBOM) func(coords
 	// relationships for these owned files may be disabled, but we always want to include them
 	for p := range s.Artifacts.Packages.Enumerate() {
 		if f, ok := p.Metadata.(pkg.FileOwner); ok {
+			// owned paths are within the containers the package was found in
+			var archives []file.Coordinates
+			atRoot := false
+			for _, container := range archive.OwnerContainers(p) {
+				if container.FullPath == "" {
+					atRoot = true
+				} else {
+					archives = append(archives, container)
+				}
+			}
 			for _, ownedFilePath := range f.OwnedFiles() {
+				// an archive's contents are not in this resolver to follow links in, and only an absolute owned
+				// path names a file in one (see packageFileOwnershipRelationships)
+				if path.IsAbs(ownedFilePath) {
+					for _, container := range archives {
+						allPackageCoords.Add(archive.OwnedCoordinates(container, ownedFilePath))
+					}
+				}
+				if !atRoot {
+					continue
+				}
+
 				// resolve these owned files, as they may have symlinks
 				// but coordinates we will test against are always absolute paths
 				locations, err := resolver.FilesByPath(ownedFilePath)

internal/task/unknowns_tasks_test.go

@@ -0,0 +1,120 @@
+package task
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+
+	"github.com/anchore/syft/syft/artifact"
+	"github.com/anchore/syft/syft/cataloging"
+	"github.com/anchore/syft/syft/file"
+	"github.com/anchore/syft/syft/pkg"
+	"github.com/anchore/syft/syft/sbom"
+)
+
+func Test_unknownsLabeler_archiveReasonsSurvivePackages(t *testing.T) {
+	jar := file.NewCoordinates("/app.jar", "")
+	p := pkg.Package{Name: "app", Locations: file.NewLocationSet(file.NewLocationFromCoordinates(jar))}
+	p.SetID()
+	s := &sbom.SBOM{Artifacts: sbom.Artifacts{
+		Packages: pkg.NewCollection(p),
+		Unknowns: map[file.Coordinates][]string{jar: {
+			formatUnknown("archive cataloged from part of its contents: too big", ArchiveCatalogerTaskName),
+			formatUnknown("unable to read manifest", "java-archive-cataloger"),
+		}},
+	}}
+
+	unknownsLabelerTask{cataloging.UnknownsConfig{RemoveWhenPackagesDefined: true}}.finalize(file.NewMockResolverForPaths(), s)
+
+	assert.Equal(t, []string{formatUnknown("archive cataloged from part of its contents: too big", ArchiveCatalogerTaskName)}, s.Artifacts.Unknowns[jar],
+		"a package describing the archive explains a parse failure, not contents left out")
+}
+
+func Test_unknownsLabeler_archiveContentsAreReportedByFullPath(t *testing.T) {
+	// a package describing an archive does not account for the files within it
+	war := file.NewCoordinates("/app.war", "layer")
+	in := func(fullPath string) file.Coordinates {
+		return file.Coordinates{RealPath: "/app.war", FileSystemID: "layer", FullPath: fullPath}
+	}
+	nativeLib := in("/app.war!/WEB-INF/lib/jna.jar!/linux-x86-64/libjnidispatch.so")
+	unidentifiedJar := in("/app.war!/WEB-INF/lib/javax.inject-1.jar")
+	p := pkg.Package{Name: "app", Locations: file.NewLocationSet(file.NewLocationFromCoordinates(war))}
+	p.SetID()
+	noPackage := formatUnknown("no package identified in archive", "java-archive-cataloger")
+
+	s := &sbom.SBOM{
+		Artifacts: sbom.Artifacts{
+			Packages:    pkg.NewCollection(p),
+			Executables: map[file.Coordinates]file.Executable{nativeLib: {}},
+			Unknowns:    map[file.Coordinates][]string{unidentifiedJar: {noPackage}},
+		},
+		Relationships: []artifact.Relationship{{From: war, To: unidentifiedJar, Type: artifact.ContainsRelationship}},
+	}
+
+	unknownsLabelerTask{cataloging.UnknownsConfig{RemoveWhenPackagesDefined: true, IncludeExecutablesWithoutPackages: true}}.finalize(file.NewMockResolverForPaths(), s)
+
+	assert.Equal(t, map[file.Coordinates][]string{
+		nativeLib:       {formatUnknown("no package identified in executable file", unknownsLabelerTaskName)},
+		unidentifiedJar: {noPackage},
+	}, s.Artifacts.Unknowns)
+}
+
+func Test_unknownsLabeler_relativeOwnedPathsNameNothingInAnArchive(t *testing.T) {
+	// a python RECORD lists paths relative to site-packages, which resolve nowhere at the scan root either
+	whl := func(fullPath string) file.Coordinates {
+		return file.Coordinates{RealPath: "/pip.whl", FullPath: fullPath}
+	}
+	tool := whl("/pip.whl!/pip/tool")
+	p := pkg.Package{
+		Name:      "pip",
+		Locations: file.NewLocationSet(file.NewLocationFromCoordinates(whl("/pip.whl!/pip.dist-info/METADATA"))),
+		Metadata:  pkg.PythonPackage{Files: []pkg.PythonFileRecord{{Path: "pip/tool"}}},
+	}
+	p.SetID()
+	s := &sbom.SBOM{Artifacts: sbom.Artifacts{
+		Packages:    pkg.NewCollection(p),
+		Executables: map[file.Coordinates]file.Executable{tool: {}},
+	}}
+
+	unknownsLabelerTask{cataloging.UnknownsConfig{IncludeExecutablesWithoutPackages: true}}.finalize(file.NewMockResolverForPaths(), s)
+
+	assert.NotEmpty(t, s.Artifacts.Unknowns[tool])
+}
+
+func Test_unknownsLabeler_ownedFilesAreWithinTheOwnersContainer(t *testing.T) {
+	atRoot := file.NewCoordinates("/usr/bin/foo", "")
+	inArchive := file.Coordinates{RealPath: "/rootfs.tar", FullPath: "/rootfs.tar!/usr/bin/foo"}
+	owner := func(at file.Coordinates) pkg.Package {
+		p := pkg.Package{
+			Name:      "owner",
+			Type:      pkg.RpmPkg,
+			Locations: file.NewLocationSet(file.NewLocationFromCoordinates(at)),
+			Metadata:  pkg.RpmDBEntry{Files: []pkg.RpmFileRecord{{Path: "/usr/bin/foo"}}},
+		}
+		p.SetID()
+		return p
+	}
+
+	tests := []struct {
+		name       string
+		owner      file.Coordinates
+		referenced file.Coordinates
+	}{
+		{name: "an owner at the scan root", owner: file.NewCoordinates("/var/lib/rpm/Packages", ""), referenced: atRoot},
+		{name: "an owner inside an archive", owner: file.Coordinates{RealPath: "/rootfs.tar", FullPath: "/rootfs.tar!/var/lib/rpm/Packages"}, referenced: inArchive},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			s := &sbom.SBOM{Artifacts: sbom.Artifacts{
+				Packages:    pkg.NewCollection(owner(tt.owner)),
+				Executables: map[file.Coordinates]file.Executable{atRoot: {}, inArchive: {}},
+			}}
+
+			unknownsLabelerTask{cataloging.UnknownsConfig{IncludeExecutablesWithoutPackages: true}}.finalize(file.NewMockResolverForPaths("/usr/bin/foo"), s)
+
+			for _, exe := range []file.Coordinates{atRoot, inArchive} {
+				assert.Equal(t, exe != tt.referenced, len(s.Artifacts.Unknowns[exe]) > 0, exe.FullNestedPath())
+			}
+		})
+	}
+}

internal/testutils/archives.go

@@ -0,0 +1,84 @@
+package testutils
+
+import (
+	"archive/tar"
+	"archive/zip"
+	"bytes"
+	"compress/gzip"
+	"fmt"
+	"io"
+	"sort"
+	"testing"
+
+	"github.com/stretchr/testify/require"
+)
+
+// Zip builds a zip of the entries in sorted name order: archive limits bite as entries are read, so
+// order decides which land before a truncation.
+func Zip[T ~string | ~[]byte](t testing.TB, entries map[string]T) []byte {
+	t.Helper()
+	var buf bytes.Buffer
+	zw := zip.NewWriter(&buf)
+	for _, name := range sortedNames(entries) {
+		w, err := zw.Create(name)
+		require.NoError(t, err)
+		_, err = w.Write([]byte(entries[name]))
+		require.NoError(t, err)
+	}
+	require.NoError(t, zw.Close())
+	return buf.Bytes()
+}
+
+// Tar builds a tar of the entries in sorted name order.
+func Tar[T ~string | ~[]byte](t testing.TB, entries map[string]T) []byte {
+	t.Helper()
+	var buf bytes.Buffer
+	writeTar(t, &buf, entries)
+	return buf.Bytes()
+}
+
+// TarGz builds a gzipped tar of the entries in sorted name order.
+func TarGz[T ~string | ~[]byte](t testing.TB, entries map[string]T) []byte {
+	t.Helper()
+	var buf bytes.Buffer
+	gw := gzip.NewWriter(&buf)
+	writeTar(t, gw, entries)
+	require.NoError(t, gw.Close())
+	return buf.Bytes()
+}
+
+// Jar is the smallest jar the java cataloger identifies, a manifest naming the artifact, plus extra.
+func Jar(t testing.TB, title, version string, extra map[string][]byte) []byte {
+	t.Helper()
+	entries := map[string][]byte{"META-INF/MANIFEST.MF": Manifest(title, version)}
+	for name, body := range extra {
+		entries[name] = body
+	}
+	return Zip(t, entries)
+}
+
+// Manifest is a jar manifest naming the artifact.
+func Manifest(title, version string) []byte {
+	return fmt.Appendf(nil, "Manifest-Version: 1.0\nImplementation-Title: %s\nImplementation-Version: %s\n", title, version)
+}
+
+func writeTar[T ~string | ~[]byte](t testing.TB, w io.Writer, entries map[string]T) {
+	t.Helper()
+	tw := tar.NewWriter(w)
+	for _, name := range sortedNames(entries) {
+		body := []byte(entries[name])
+		require.NoError(t, tw.WriteHeader(&tar.Header{Name: name, Mode: 0o644, Size: int64(len(body)), Typeflag: tar.TypeReg}))
+		_, err := tw.Write(body)
+		require.NoError(t, err)
+	}
+	require.NoError(t, tw.Close())
+}
+
+func sortedNames[T any](entries map[string]T) []string {
+	names := make([]string, 0, len(entries))
+	for name := range entries {
+		names = append(names, name)
+	}
+	sort.Strings(names)
+	return names
+}

internal/unknown/coordinate_error.go

@@ -23,9 +23,9 @@ var _ error = (*CoordinateError)(nil)
 
 func (u *CoordinateError) Error() string {
 	if u.Coordinates.FileSystemID == "" {
-		return fmt.Sprintf("%s: %v", u.Coordinates.RealPath, u.Reason)
+		return fmt.Sprintf("%s: %v", u.Coordinates.FullNestedPath(), u.Reason)
 	}
-	return fmt.Sprintf("%s (%s): %v", u.Coordinates.RealPath, u.Coordinates.FileSystemID, u.Reason)
+	return fmt.Sprintf("%s (%s): %v", u.Coordinates.FullNestedPath(), u.Coordinates.FileSystemID, u.Reason)
 }
 
 // New returns a new CoordinateError unless the reason is a CoordinateError itself, in which case

internal/unknown/coordinate_error_test.go

@@ -169,9 +169,7 @@ func Test_Join(t *testing.T) {
 }
 
 func Test_flatten(t *testing.T) {
-	coords := file.Coordinates{
-		RealPath: "real/path",
-	}
+	coords := file.NewCoordinates("real/path", "")
 	e1 := fmt.Errorf("e1")
 	e2 := fmt.Errorf("e2")
 	c1 := New(coords, fmt.Errorf("c1"))

internal/unknown/path_error.go

@@ -19,6 +19,8 @@ func ProcessPathErrors(err error) error {
 	if pathErrorRegex.MatchString(errText) {
 		foundPath := pathErrorRegex.ReplaceAllString(err.Error(), "$1")
 		if foundPath != "" {
+			// a path in an error text is taken as is: nesting is never inferred from "!/" in it, since a real
+			// path can hold one too. A caller with the location in hand should use New instead
 			return New(file.NewLocation(foundPath), err)
 		}
 	}

internal/unknown/path_error_test.go

@@ -17,28 +17,29 @@ func Test_ProcessPathErrors(t *testing.T) {
 		{
 			errorText: `prefix path="/var/lib/thing" suffix`,
 			expected: &CoordinateError{
-				Coordinates: file.Coordinates{
-					RealPath: "/var/lib/thing",
-				},
-				Reason: fmt.Errorf(`prefix path="/var/lib/thing" suffix`),
+				Coordinates: file.NewCoordinates("/var/lib/thing", ""),
+				Reason:      fmt.Errorf(`prefix path="/var/lib/thing" suffix`),
 			},
 		},
 		{
 			errorText: `prefix path="/var/lib/thing"`,
 			expected: &CoordinateError{
-				Coordinates: file.Coordinates{
-					RealPath: "/var/lib/thing",
-				},
-				Reason: fmt.Errorf(`prefix path="/var/lib/thing"`),
+				Coordinates: file.NewCoordinates("/var/lib/thing", ""),
+				Reason:      fmt.Errorf(`prefix path="/var/lib/thing"`),
 			},
 		},
 		{
 			errorText: `path="/var/lib/thing" suffix`,
 			expected: &CoordinateError{
-				Coordinates: file.Coordinates{
-					RealPath: "/var/lib/thing",
-				},
-				Reason: fmt.Errorf(`path="/var/lib/thing" suffix`),
+				Coordinates: file.NewCoordinates("/var/lib/thing", ""),
+				Reason:      fmt.Errorf(`path="/var/lib/thing" suffix`),
+			},
+		},
+		{
+			errorText: `path="/data/Hello!/world.txt"`,
+			expected: &CoordinateError{
+				Coordinates: file.NewCoordinates("/data/Hello!/world.txt", ""),
+				Reason:      fmt.Errorf(`path="/data/Hello!/world.txt"`),
 			},
 		},
 		{

schema/json/schema-latest.json

@@ -1,6 +1,6 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "anchore.io/schema/syft/json/16.1.11/document",
+  "$id": "anchore.io/schema/syft/json/16.1.12/document",
   "$ref": "#/$defs/Document",
   "$defs": {
     "AlpmDbEntry": {
@@ -716,11 +716,15 @@
       "properties": {
         "path": {
           "type": "string",
-          "description": "RealPath is the canonical absolute form of the path accessed (all symbolic links have been followed and relative path components like '.' and '..' have been removed)."
+          "description": "RealPath is the canonical absolute form of the path accessed (all symbolic links have been followed and relative path components like '.' and '..' have been removed). For a file found within an archive, it is the real path of the outermost archive on the scanned filesystem."
         },
         "layerID": {
           "type": "string",
-          "description": "FileSystemID is an ID representing and entire filesystem. For container images, this is a layer digest. For directories or a root filesystem, this is blank."
+          "description": "FileSystemID is an ID representing an entire filesystem. For container images, this is a layer digest. For directories or a root filesystem, this is blank. A file inside an archive carries the FileSystemID of the filesystem the archive was found in."
+        },
+        "fullPath": {
+          "type": "string",
+          "description": "FullPath is the full path to the file: RealPath, then for a file within an archive a \"!/\"-delimited chain of entry paths through any nested archives, ending with the file's own entry path (e.g. \"/app.war!/WEB-INF/lib/dep.jar!/META-INF/MANIFEST.MF\"). Each segment is a real path (links resolved) relative to the archive before it. For a file not within an archive it is blank, so coordinates outside archives are unchanged by the field (in JSON, equality and ID)."
         }
       },
       "type": "object",
@@ -2544,15 +2548,19 @@
       "properties": {
         "path": {
           "type": "string",
-          "description": "RealPath is the canonical absolute form of the path accessed (all symbolic links have been followed and relative path components like '.' and '..' have been removed)."
+          "description": "RealPath is the canonical absolute form of the path accessed (all symbolic links have been followed and relative path components like '.' and '..' have been removed). For a file found within an archive, it is the real path of the outermost archive on the scanned filesystem."
         },
         "layerID": {
           "type": "string",
-          "description": "FileSystemID is an ID representing and entire filesystem. For container images, this is a layer digest. For directories or a root filesystem, this is blank."
+          "description": "FileSystemID is an ID representing an entire filesystem. For container images, this is a layer digest. For directories or a root filesystem, this is blank. A file inside an archive carries the FileSystemID of the filesystem the archive was found in."
+        },
+        "fullPath": {
+          "type": "string",
+          "description": "FullPath is the full path to the file: RealPath, then for a file within an archive a \"!/\"-delimited chain of entry paths through any nested archives, ending with the file's own entry path (e.g. \"/app.war!/WEB-INF/lib/dep.jar!/META-INF/MANIFEST.MF\"). Each segment is a real path (links resolved) relative to the archive before it. For a file not within an archive it is blank, so coordinates outside archives are unchanged by the field (in JSON, equality and ID)."
         },
         "accessPath": {
           "type": "string",
-          "description": "AccessPath is the path used to retrieve file contents (which may or may not have hardlinks / symlinks in the path)"
+          "description": "AccessPath is the path used to retrieve file contents (which may or may not have hardlinks / symlinks in the path). For a file within an archive, it is a full path (see Coordinates.FullPath)."
         },
         "annotations": {
           "additionalProperties": {

syft/archive_cataloger_test.go

@@ -0,0 +1,678 @@
+package syft
+
+import (
+	"archive/tar"
+	"bytes"
+	"compress/gzip"
+	"context"
+	"os"
+	"path/filepath"
+	"sort"
+	"sync"
+	"testing"
+	"unicode/utf8"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"github.com/wagoodman/go-partybus"
+	"github.com/wagoodman/go-progress"
+
+	"github.com/anchore/syft/internal/archive"
+	"github.com/anchore/syft/internal/bus"
+	"github.com/anchore/syft/internal/task"
+	"github.com/anchore/syft/internal/testutils"
+	"github.com/anchore/syft/syft/artifact"
+	"github.com/anchore/syft/syft/cataloging"
+	"github.com/anchore/syft/syft/cataloging/filecataloging"
+	"github.com/anchore/syft/syft/cataloging/pkgcataloging"
+	"github.com/anchore/syft/syft/event"
+	"github.com/anchore/syft/syft/event/monitor"
+	"github.com/anchore/syft/syft/file"
+	"github.com/anchore/syft/syft/pkg"
+	"github.com/anchore/syft/syft/pkg/cataloger/java"
+	"github.com/anchore/syft/syft/sbom"
+	"github.com/anchore/syft/syft/source"
+	"github.com/anchore/syft/syft/source/directorysource"
+)
+
+// Every CreateSBOM call pays to compile the license scanner, so the end-to-end behavior is asserted
+// over one scan of one fixture directory rather than a scan per claim. The fixture holds every shape
+// the claims need; the subtests read the one SBOM.
+//
+// scan root
+//
+//	loose.txt                          an ordinary file, counted by the file catalogers
+//	nested/marker.txt                  excluded by the root-anchored pattern ./nested/marker.txt
+//	app.zip                            nested/marker.txt, nested/keep.txt, nested/excluded.txt (**/excluded.txt)
+//	app/data.zip                       nested/marker.txt, under a directory
+//	outer.zip                          outer/marker.txt
+//	  deeper/inner.zip                 nested/marker.txt, two levels down
+//	  skip/inner-excluded.zip          nested/marker.txt, excluded by **/inner-excluded.zip
+//	  日本語/café-🎉/unicode.zip          nested/marker.txt, under a non-ASCII path
+//	pkg.rpm                            a zip holding a marker, excluded by **/*.rpm
+//	KEPT.RPM                           the same zip, kept: the pattern is lower-case (a distinct base
+//	                                   name, so the two coexist on a case-insensitive filesystem)
+//	app.war                            WEB-INF/lib/war-lib-2.0.jar
+//	bundle.zip                         lib/zip-lib-1.2.jar
+//	bundle.tar.gz                      lib/tgz-lib-1.2.jar
+var fixtureExclusions = []string{"./nested/marker.txt", "**/excluded.txt", "**/inner-excluded.zip", "**/*.rpm"}
+
+func writeFixture(t *testing.T) string {
+	t.Helper()
+	dir := t.TempDir()
+	write := func(name string, data []byte) {
+		require.NoError(t, os.MkdirAll(filepath.Dir(filepath.Join(dir, name)), 0o755))
+		require.NoError(t, os.WriteFile(filepath.Join(dir, name), data, 0o644))
+	}
+	markerZip := testutils.Zip(t, map[string]string{"nested/marker.txt": "hello"})
+
+	write("loose.txt", []byte("outside"))
+	write("nested/marker.txt", []byte("at the root"))
+	write("app.zip", testutils.Zip(t, map[string]string{
+		"nested/marker.txt":   "hello",
+		"nested/keep.txt":     "hello",
+		"nested/excluded.txt": "hello",
+	}))
+	write("app/data.zip", markerZip)
+	write("outer.zip", testutils.Zip(t, map[string][]byte{
+		"outer/marker.txt":        []byte("hello"),
+		"deeper/inner.zip":        markerZip,
+		"skip/inner-excluded.zip": markerZip,
+		"日本語/café-🎉/unicode.zip":  markerZip,
+	}))
+	write("pkg.rpm", markerZip)
+	write("KEPT.RPM", markerZip)
+	write("app.war", testutils.Zip(t, map[string][]byte{
+		"WEB-INF/lib/war-lib-2.0.jar": testutils.Jar(t, "war-lib", "2.0", nil),
+	}))
+	write("bundle.zip", testutils.Zip(t, map[string][]byte{
+		"lib/zip-lib-1.2.jar": testutils.Jar(t, "zip-lib", "1.2", nil),
+	}))
+	write("bundle.tar.gz", testutils.TarGz(t, map[string][]byte{
+		"lib/tgz-lib-1.2.jar": testutils.Jar(t, "tgz-lib", "1.2", nil),
+	}))
+	return dir
+}
+
+func TestArchiveCataloger(t *testing.T) {
+	scanDir := writeFixture(t)
+	resolvedScanDir, err := filepath.EvalSymlinks(scanDir)
+	require.NoError(t, err)
+
+	resolvedScanDir = filepath.ToSlash(resolvedScanDir)
+
+	recorder := &recordingBus{}
+	bus.Set(recorder)
+	t.Cleanup(func() { bus.Set(nil) })
+
+	var (
+		probeMu sync.Mutex
+		seen    []string // every .txt and .zip path any resolver handed a cataloger could see
+	)
+	probe := resolverProbeCataloger{globs: []string{"**/*.txt", "**/*.zip"}, record: func(paths []string) {
+		probeMu.Lock()
+		defer probeMu.Unlock()
+		seen = append(seen, paths...)
+	}}
+
+	// the java catalogers come from the factory, as the CLI builds them: the flag handing recursion
+	// to the archive task is derived onto the factory's config. Both legacy search settings are off,
+	// the cell of the matrix that looks like a bug: with the feature on they no longer gate anything
+	packages := pkgcataloging.DefaultConfig()
+	packages.JavaArchive.IncludeIndexedArchives = false
+	packages.JavaArchive.IncludeUnindexedArchives = false
+	cfg := DefaultCreateSBOMConfig().
+		WithCatalogerSelection(cataloging.NewSelectionRequest().WithDefaults("java")).
+		WithCatalogers(
+			pkgcataloging.NewAlwaysEnabledCatalogerReference(markerCataloger{}),
+			pkgcataloging.NewAlwaysEnabledCatalogerReference(probe),
+		).
+		WithPackagesConfig(packages).
+		WithFilesConfig(filecataloging.DefaultConfig().WithSelection(file.AllFilesSelection)).
+		WithArchiveConfig(cataloging.DefaultArchiveSearchConfig().WithMaxDepth(3))
+
+	s := scanDirWithExclusions(t, scanDir, cfg, fixtureExclusions...)
+
+	t.Run("markers are found at every depth under archive-relative paths", func(t *testing.T) {
+		// the location's RealPath is the outermost archive; FullPath adds the chain of entries within it
+		assert.Equal(t, []string{
+			"KEPT.RPM!/nested/marker.txt",
+			"app.zip!/nested/marker.txt",
+			"app/data.zip!/nested/marker.txt",
+			"outer.zip!/deeper/inner.zip!/nested/marker.txt",
+			"outer.zip!/outer/marker.txt",
+			"outer.zip!/日本語/café-🎉/unicode.zip!/nested/marker.txt",
+		}, packageLocations(s, "marker-pkg"))
+	})
+
+	t.Run("archive contents do not leak into the parent tree", func(t *testing.T) {
+		for _, loc := range packageLocations(s, "marker-pkg") {
+			assert.NotContains(t, loc, ".zip/", "a joined path smears the archive's contents into the parent's tree")
+			assert.NotContains(t, loc, "!//", "a nested path must not be rooted")
+		}
+	})
+
+	t.Run("unicode entry names survive to output", func(t *testing.T) {
+		for _, loc := range packageLocations(s, "marker-pkg") {
+			assert.True(t, utf8.ValidString(loc))
+		}
+	})
+
+	t.Run("a CONTAINS relationship links each archive to what was found inside", func(t *testing.T) {
+		var containers []string
+		for _, p := range s.Artifacts.Packages.Sorted() {
+			if p.Name != "marker-pkg" {
+				continue
+			}
+			for _, rel := range s.Relationships {
+				if rel.Type != artifact.ContainsRelationship || rel.To.ID() != p.ID() {
+					continue
+				}
+				if coords, ok := rel.From.(file.Coordinates); ok {
+					containers = append(containers, coords.FullNestedPath())
+				}
+			}
+		}
+		sort.Strings(containers)
+		assert.Equal(t, []string{
+			"KEPT.RPM",
+			"app.zip",
+			"app/data.zip",
+			"outer.zip",
+			"outer.zip!/deeper/inner.zip",
+			"outer.zip!/日本語/café-🎉/unicode.zip",
+		}, containers, "the archive file, named in its own parent, contains the package")
+	})
+
+	t.Run("each file within an archive is contained by that archive", func(t *testing.T) {
+		containers := fileContainers(s)
+		assert.Equal(t, "app.zip", containers["app.zip!/nested/keep.txt"])
+		assert.Equal(t, "outer.zip!/deeper/inner.zip", containers["outer.zip!/deeper/inner.zip!/nested/marker.txt"])
+		assert.Equal(t, "outer.zip", containers["outer.zip!/deeper/inner.zip"])
+	})
+
+	t.Run("exclusions are the scan's own", func(t *testing.T) {
+		// there is no archive-specific exclusion setting: a scan pattern's shape decides whether it
+		// reaches inside an archive, and an excluded entry is absent from the archive's filesystem
+		// rather than present and skipped
+		markers := packageLocations(s, "marker-pkg")
+		assert.NotContains(t, markers, "nested/marker.txt", "a root-anchored pattern excludes the file at the scan root")
+		assert.Contains(t, markers, "app.zip!/nested/marker.txt", "and says nothing about the same path inside an archive")
+		assert.NotContains(t, markers, "pkg.rpm!/nested/marker.txt", "an archive whose own path is excluded is not extracted")
+		assert.Contains(t, markers, "KEPT.RPM!/nested/marker.txt", "a lower-case pattern does not match an upper-case name")
+		assert.NotContains(t, markers, "outer.zip!/skip/inner-excluded.zip!/nested/marker.txt", "a nested archive is excluded at its own level")
+
+		assert.Contains(t, seen, "app.zip!/nested/keep.txt")
+		assert.NotContains(t, seen, "app.zip!/nested/excluded.txt", "a **/ pattern excludes inside an archive, from the index itself")
+		assert.Contains(t, seen, "outer.zip!/deeper/inner.zip", "the probe ran inside outer.zip")
+		assert.NotContains(t, seen, "outer.zip!/skip/inner-excluded.zip", "the excluded inner archive is absent from outer's filesystem")
+	})
+
+	t.Run("a jar inside an archive is cataloged exactly once, under the virtual path java gives it", func(t *testing.T) {
+		// the failure mode is a duplicate: a jar inside a zip can be reached by the task's walk and by
+		// the java cataloger's own unarchiving. The colon-delimited virtual path appears in published
+		// SBOMs, so it must not change with the mechanism; for a directory source the archive's path
+		// is relative, so the chain has no leading separator
+		assert.Equal(t, map[string][]string{
+			"war-lib": {"app.war:WEB-INF/lib/war-lib-2.0.jar"},
+			"zip-lib": {"bundle.zip:lib/zip-lib-1.2.jar"},
+			"tgz-lib": {"bundle.tar.gz:lib/tgz-lib-1.2.jar"},
+		}, javaVirtualPaths(s), "with both legacy search settings off, every container is still descended")
+	})
+
+	t.Run("no extraction path reaches the SBOM", func(t *testing.T) {
+		// covers syft/archive-content-identity#nested-paths-are-archive-relative: file cataloging is
+		// the one path that enumerates every location rather than searching for them, so a resolver
+		// root that leaked would land in FileMetadata and gain a CONTAINS edge
+		var paths []string
+		for coords := range s.Artifacts.FileMetadata {
+			paths = append(paths, coords.RealPath)
+		}
+		for _, p := range s.Artifacts.Packages.Sorted() {
+			for _, loc := range p.Locations.ToSlice() {
+				paths = append(paths, loc.RealPath, loc.AccessPath)
+			}
+		}
+		for _, rel := range s.Relationships {
+			for _, end := range []artifact.Identifiable{rel.From, rel.To} {
+				if coords, ok := end.(file.Coordinates); ok {
+					paths = append(paths, coords.RealPath)
+				}
+			}
+		}
+		require.NotEmpty(t, paths)
+		for _, p := range paths {
+			assert.NotContains(t, p, "archive-spill-", "the spill file reached the SBOM at %q", p)
+			if filepath.IsAbs(p) {
+				// the directory resolver has always reported the scan root absolute: it is the path the
+				// user asked for. Anything else absolute is a filesystem this feature invented
+				assert.Equal(t, resolvedScanDir, p, "only the scanned directory itself may be reported absolute")
+			}
+		}
+	})
+
+	t.Run("file metadata covers every entry of every archive, and nothing else", func(t *testing.T) {
+		// an exact set is also the reproducibility check: anything of a per-run temp directory reaching
+		// output would fail it
+		var got []string
+		for coords := range s.Artifacts.FileMetadata {
+			if archive.ContainerPath(coords) == "" {
+				continue
+			}
+			got = append(got, coords.FullNestedPath())
+		}
+		sort.Strings(got)
+		assert.Equal(t, []string{
+			"KEPT.RPM!/nested/marker.txt",
+			"app.war!/WEB-INF/lib/war-lib-2.0.jar",
+			"app.war!/WEB-INF/lib/war-lib-2.0.jar!/META-INF/MANIFEST.MF",
+			"app.zip!/nested/keep.txt",
+			"app.zip!/nested/marker.txt",
+			"app/data.zip!/nested/marker.txt",
+			"bundle.tar.gz!/lib/tgz-lib-1.2.jar",
+			"bundle.tar.gz!/lib/tgz-lib-1.2.jar!/META-INF/MANIFEST.MF",
+			"bundle.zip!/lib/zip-lib-1.2.jar",
+			"bundle.zip!/lib/zip-lib-1.2.jar!/META-INF/MANIFEST.MF",
+			"outer.zip!/deeper/inner.zip",
+			"outer.zip!/deeper/inner.zip!/nested/marker.txt",
+			"outer.zip!/outer/marker.txt",
+			"outer.zip!/日本語/café-🎉/unicode.zip",
+			"outer.zip!/日本語/café-🎉/unicode.zip!/nested/marker.txt",
+		}, got)
+	})
+
+	t.Run("file catalogers publish one progress row counting archive contents", func(t *testing.T) {
+		// the file catalogers run once over the scan root and again over every archive; each must
+		// report into one row carrying the total of every run, or the count runs past the total and
+		// renders as an overshot bar that reads as complete mid-walk
+		rows := map[string][]*progress.Manual{}
+		for _, e := range recorder.events {
+			if e.Type != event.CatalogerTaskStarted {
+				continue
+			}
+			info, ok := e.Source.(monitor.GenericTask)
+			require.True(t, ok)
+			tp, ok := e.Value.(*monitor.TaskProgress)
+			require.True(t, ok)
+			rows[info.Title.Default] = append(rows[info.Title.Default], tp.Manual)
+		}
+		for _, title := range []string{"File digests", "File metadata"} {
+			published := rows[title]
+			require.Len(t, published, 1, "%s must publish exactly one row for the whole scan", title)
+			row := published[0]
+			assert.Greater(t, row.Current(), int64(len(s.Artifacts.FileMetadata))/2,
+				"%s must count the files inside the archives, got %d", title, row.Current())
+			if row.Size() >= 0 {
+				assert.Equal(t, row.Current(), row.Size(), "%s total must cover every run that reported into it", title)
+			}
+		}
+	})
+}
+
+// TestArchiveCataloger_featureOff is the one comparison that needs a second scan: with the task
+// disabled, java's own unarchiving reaches the jars its legacy settings admit, under the same virtual
+// path the task gives them.
+func TestArchiveCataloger_featureOff(t *testing.T) {
+	scanDir := writeFixture(t)
+
+	cfg := DefaultCreateSBOMConfig().
+		WithCatalogerSelection(cataloging.NewSelectionRequest().WithDefaults("java"))
+
+	s := scanDirWithExclusions(t, scanDir, cfg, fixtureExclusions...)
+
+	// indexed archives (zip, war) are searched by default and unindexed ones (tar.gz) are not, so
+	// what a user gets without the feature depends on settings the feature makes irrelevant
+	assert.Equal(t, map[string][]string{
+		"war-lib": {"app.war:WEB-INF/lib/war-lib-2.0.jar"},
+		"zip-lib": {"bundle.zip:lib/zip-lib-1.2.jar"},
+	}, javaVirtualPaths(s), "java's own recursion finds each once, under the virtual path the task also reports")
+
+	t.Run("the top-level archive search booleans reach java", func(t *testing.T) {
+		cfg := DefaultCreateSBOMConfig().
+			WithCatalogerSelection(cataloging.NewSelectionRequest().WithDefaults("java")).
+			WithArchiveConfig(cataloging.DefaultArchiveSearchConfig().WithIncludeUnindexedArchives(true))
+
+		s := scanDirWithExclusions(t, scanDir, cfg, fixtureExclusions...)
+
+		assert.Contains(t, javaVirtualPaths(s), "tgz-lib")
+		assert.False(t, cfg.Packages.JavaArchive.IncludeUnindexedArchives, "the caller's config is not written to")
+	})
+}
+
+func TestArchiveCataloger_jarReachedThroughALinkIsIdentified(t *testing.T) {
+	// a content-addressed layout (pnpm, nix, bazel): the jar is stored under a hash and only the link
+	// to it is named like a jar
+	var buf bytes.Buffer
+	gw := gzip.NewWriter(&buf)
+	tw := tar.NewWriter(gw)
+	jar := testutils.Jar(t, "json-simple", "1.1.1", nil)
+	require.NoError(t, tw.WriteHeader(&tar.Header{Name: "store/3f9a1c", Mode: 0o644, Size: int64(len(jar))}))
+	_, err := tw.Write(jar)
+	require.NoError(t, err)
+	require.NoError(t, tw.WriteHeader(&tar.Header{Name: "app/lib/json-simple-1.1.1.jar", Typeflag: tar.TypeSymlink, Linkname: "../../store/3f9a1c"}))
+	require.NoError(t, tw.Close())
+	require.NoError(t, gw.Close())
+
+	dir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "bundle.tar.gz"), buf.Bytes(), 0o644))
+
+	cfg := DefaultCreateSBOMConfig().
+		WithCatalogerSelection(cataloging.NewSelectionRequest().WithDefaults("java")).
+		WithFilesConfig(filecataloging.DefaultConfig().WithSelection(file.AllFilesSelection)).
+		WithArchiveConfig(cataloging.DefaultArchiveSearchConfig().WithMaxDepth(2))
+	s := scanDirWithExclusions(t, dir, cfg)
+
+	assert.Equal(t, []string{"bundle.tar.gz!/store/3f9a1c"}, packageLocations(s, "json-simple"))
+
+	// the jar's own files are addressed by its real path, the same one its package location names
+	manifest := file.Coordinates{RealPath: "bundle.tar.gz", FullPath: "bundle.tar.gz!/store/3f9a1c!/META-INF/MANIFEST.MF"}
+	assert.Contains(t, s.Artifacts.FileMetadata, manifest)
+}
+
+func TestArchiveCataloger_defaultFileSelectionCoversRootJars(t *testing.T) {
+	// with the default owned-by-package selection, a jar at the root is described by the archive task,
+	// so the root file catalogers must run after it or the jar gets no file entries at all
+	dir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "app.jar"), testutils.Jar(t, "app", "1.0", nil), 0o644))
+
+	for name, depth := range map[string]int{"feature off": 0, "feature on": 1} {
+		t.Run(name, func(t *testing.T) {
+			cfg := DefaultCreateSBOMConfig().
+				WithCatalogerSelection(cataloging.NewSelectionRequest().WithDefaults("java")).
+				WithArchiveConfig(cataloging.DefaultArchiveSearchConfig().WithMaxDepth(depth))
+			s := scanDirWithExclusions(t, dir, cfg)
+
+			require.Equal(t, []string{"app.jar"}, packageLocations(s, "app"))
+			jar := file.NewCoordinates("app.jar", "")
+			assert.Contains(t, s.Artifacts.FileMetadata, jar)
+			assert.Contains(t, s.Artifacts.FileDigests, jar)
+		})
+	}
+}
+
+func TestArchiveCataloger_defaultFileSelectionCoversNestedJars(t *testing.T) {
+	// a nested jar's package is found inside the jar but located in the archive holding it, so that
+	// archive's file catalogers must run after it, as the root's do
+	dir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "outer.zip"), testutils.Zip(t, map[string][]byte{
+		"lib/inner.jar": testutils.Jar(t, "inner", "1.0", nil),
+		"readme.txt":    []byte("hello"),
+		"empty.zip":     testutils.Zip(t, map[string]string{"a.txt": "hello"}),
+	}), 0o644))
+
+	cfg := DefaultCreateSBOMConfig().
+		WithCatalogerSelection(cataloging.NewSelectionRequest().WithDefaults("java")).
+		WithArchiveConfig(cataloging.DefaultArchiveSearchConfig().WithMaxDepth(2))
+	s := scanDirWithExclusions(t, dir, cfg)
+
+	require.Equal(t, []string{"outer.zip!/lib/inner.jar"}, packageLocations(s, "inner"))
+	jar := file.Coordinates{RealPath: "outer.zip", FullPath: "outer.zip!/lib/inner.jar"}
+	assert.Contains(t, s.Artifacts.FileMetadata, jar)
+	assert.Contains(t, s.Artifacts.FileDigests, jar)
+	assert.Equal(t, "outer.zip", fileContainers(s)["outer.zip!/lib/inner.jar"])
+
+	// as at the root, a file no package owns is not described, nor is an archive in which nothing was found
+	var described []string
+	for _, c := range s.AllCoordinates() {
+		described = append(described, c.FullNestedPath())
+	}
+	assert.NotContains(t, described, "outer.zip!/readme.txt")
+	assert.NotContains(t, described, "outer.zip!/empty.zip")
+	assert.NotContains(t, described, "outer.zip!/empty.zip!/a.txt")
+}
+
+func TestArchiveCataloger_archiveUnknowns(t *testing.T) {
+	dir := t.TempDir()
+	plain := testutils.Zip(t, map[string]string{"readme.txt": "hi"})
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "outer.zip"), testutils.Zip(t, map[string][]byte{
+		"lib/inner.jar": testutils.Jar(t, "inner", "1.0", nil),
+		"lib/plain.zip": plain,
+	}), 0o644))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "plain.zip"), plain, 0o644))
+
+	scan := func(depth int) map[string][]string {
+		cfg := DefaultCreateSBOMConfig().
+			WithCatalogerSelection(cataloging.NewSelectionRequest().WithDefaults("java")).
+			WithUnknownsConfig(cataloging.DefaultUnknownsConfig()).
+			WithFilesConfig(filecataloging.DefaultConfig().WithSelection(file.AllFilesSelection)).
+			WithArchiveConfig(cataloging.DefaultArchiveSearchConfig().WithMaxDepth(depth))
+		out := map[string][]string{}
+		for c, reasons := range scanDirWithExclusions(t, dir, cfg).Artifacts.Unknowns {
+			out[c.FullNestedPath()] = reasons
+		}
+		return out
+	}
+
+	t.Run("an expanded archive is not reported as not cataloged", func(t *testing.T) {
+		assert.Empty(t, scan(3))
+	})
+
+	t.Run("an archive past the depth limit is reported once, by the archive cataloger", func(t *testing.T) {
+		unknowns := scan(1)
+		assert.NotContains(t, unknowns, "outer.zip")
+		for _, nested := range []string{"outer.zip!/lib/inner.jar", "outer.zip!/lib/plain.zip"} {
+			require.Len(t, unknowns[nested], 1, nested)
+			assert.Contains(t, unknowns[nested][0], "depth limit was reached")
+		}
+	})
+
+	t.Run("an archive is reported as not cataloged when nesting is off", func(t *testing.T) {
+		assert.Equal(t, []string{"archive not cataloged"}, scan(0)["plain.zip"])
+	})
+}
+
+func TestArchiveCataloger_unsupportedArchiveFormatsAreReported(t *testing.T) {
+	dir := t.TempDir()
+	var page bytes.Buffer
+	gw := gzip.NewWriter(&page)
+	_, err := gw.Write([]byte("a man page"))
+	require.NoError(t, err)
+	require.NoError(t, gw.Close())
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "outer.zip"), testutils.Zip(t, map[string][]byte{
+		"legacy.7z": []byte("7z\xbc\xaf\x27\x1c\x00\x04"),
+		"page.1.gz": page.Bytes(),
+	}), 0o644))
+
+	cfg := DefaultCreateSBOMConfig().
+		WithCatalogerSelection(cataloging.NewSelectionRequest().WithDefaults("java")).
+		WithUnknownsConfig(cataloging.DefaultUnknownsConfig()).
+		WithFilesConfig(filecataloging.DefaultConfig().WithSelection(file.AllFilesSelection)).
+		WithArchiveConfig(cataloging.DefaultArchiveSearchConfig().WithMaxDepth(3))
+	unknowns := map[string][]string{}
+	for c, reasons := range scanDirWithExclusions(t, dir, cfg).Artifacts.Unknowns {
+		unknowns[c.FullNestedPath()] = reasons
+	}
+
+	assert.Equal(t, map[string][]string{
+		"outer.zip!/legacy.7z": {"archive-cataloger: archive not cataloged: archive format is not supported: application/x-7z-compressed"},
+	}, unknowns, "a bare compressed file holds no files, so it is not an archive left uncataloged")
+}
+
+func TestArchiveCataloger_javaParentLinkageMatchesTheLegacyPath(t *testing.T) {
+	// a consumer walking java DEPENDENCY_OF edges (the only structure SPDX and CycloneDX keep) must see
+	// the same war-to-jar linkage whether or not the archive task does the recursion
+	dir := t.TempDir()
+	war := testutils.Jar(t, "app", "1.0", map[string][]byte{
+		"WEB-INF/lib/lib-2.0.jar": testutils.Jar(t, "lib", "2.0", nil),
+	})
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "app.war"), war, 0o644))
+
+	for name, depth := range map[string]int{"feature off": 0, "feature on": 2} {
+		t.Run(name, func(t *testing.T) {
+			cfg := DefaultCreateSBOMConfig().
+				WithCatalogerSelection(cataloging.NewSelectionRequest().WithDefaults("java")).
+				WithArchiveConfig(cataloging.DefaultArchiveSearchConfig().WithMaxDepth(depth))
+			s := scanDirWithExclusions(t, dir, cfg)
+
+			var edges []string
+			for _, rel := range s.Relationships {
+				from, fromOK := rel.From.(pkg.Package)
+				to, toOK := rel.To.(pkg.Package)
+				if fromOK && toOK && rel.Type == artifact.DependencyOfRelationship {
+					edges = append(edges, from.Name+" -> "+to.Name)
+				}
+			}
+			assert.Equal(t, []string{"lib -> app"}, edges)
+
+			var parent string
+			for _, p := range s.Artifacts.Packages.Sorted() {
+				if m, ok := p.Metadata.(pkg.JavaArchive); ok && p.Name == "lib" && m.Parent != nil {
+					parent = m.Parent.Name
+				}
+			}
+			assert.Equal(t, "app", parent)
+		})
+	}
+}
+
+func TestArchiveCataloger_descriptorRecordsArchiveConfig(t *testing.T) {
+	// a consumer must be able to tell from the SBOM alone how deep archive contents were searched
+	cfg := DefaultCreateSBOMConfig().
+		WithCatalogerSelection(cataloging.NewSelectionRequest().WithDefaults("java")).
+		WithArchiveConfig(cataloging.DefaultArchiveSearchConfig().WithMaxDepth(3))
+	s := scanDirWithExclusions(t, t.TempDir(), cfg)
+
+	trail, ok := s.Descriptor.Configuration.(configurationAuditTrail)
+	require.True(t, ok)
+	assert.Equal(t, 3, trail.Archive.MaxDepth)
+	assert.Contains(t, trail.Catalogers.Used, task.ArchiveCatalogerTaskName)
+}
+
+func TestArchiveCataloger_javaArchiveDepthIsAConfigError(t *testing.T) {
+	// depth and limits are not java settings; setting them on java's deprecated copy must fail fast
+	// rather than be silently ignored
+	for name, set := range map[string]func(*cataloging.ArchiveSearchConfig){
+		"max depth":        func(c *cataloging.ArchiveSearchConfig) { c.MaxDepth = 3 },
+		"max memory bytes": func(c *cataloging.ArchiveSearchConfig) { c.MaxMemoryBytes = 1 },
+		"max disk bytes":   func(c *cataloging.ArchiveSearchConfig) { c.MaxDiskBytes = 1 },
+	} {
+		t.Run(name, func(t *testing.T) {
+			supplied := java.DefaultArchiveCatalogerConfig()
+			supplied.ArchiveSearchConfig = cataloging.ArchiveSearchConfig{}
+			set(&supplied.ArchiveSearchConfig)
+			cfg := DefaultCreateSBOMConfig().WithPackagesConfig(pkgcataloging.Config{JavaArchive: supplied})
+
+			src, err := directorysource.New(directorysource.Config{Path: t.TempDir()})
+			require.NoError(t, err)
+			t.Cleanup(func() { _ = src.Close() })
+
+			_, err = cfg.Create(context.Background(), src)
+			require.ErrorContains(t, err, "set them with CreateSBOMConfig.Archive")
+		})
+	}
+}
+
+// packageLocations lists the full path of every location of every package with the name.
+func packageLocations(s *sbom.SBOM, name string) []string {
+	var out []string
+	for _, p := range s.Artifacts.Packages.Sorted() {
+		if p.Name != name {
+			continue
+		}
+		for _, loc := range p.Locations.ToSlice() {
+			out = append(out, loc.FullNestedPath())
+		}
+	}
+	sort.Strings(out)
+	return out
+}
+
+// javaVirtualPaths maps each java package name to the virtual paths it was reported under; a name
+// with two entries was cataloged twice.
+func javaVirtualPaths(s *sbom.SBOM) map[string][]string {
+	out := map[string][]string{}
+	for _, p := range s.Artifacts.Packages.Sorted() {
+		if metadata, ok := p.Metadata.(pkg.JavaArchive); ok {
+			out[p.Name] = append(out[p.Name], metadata.VirtualPath)
+		}
+	}
+	return out
+}
+
+// markerCataloger is a stub package cataloger emitting one package per "marker.txt" it finds, so the
+// end-to-end tests assert behavior without depending on any real cataloger's fixture format.
+type markerCataloger struct{}
+
+func (markerCataloger) Name() string { return "marker-cataloger" }
+
+func (markerCataloger) Catalog(_ context.Context, resolver file.Resolver) ([]pkg.Package, []artifact.Relationship, error) {
+	locations, err := resolver.FilesByGlob("**/marker.txt")
+	if err != nil {
+		return nil, nil, err
+	}
+	var pkgs []pkg.Package
+	for _, loc := range locations {
+		p := pkg.Package{
+			Name:      "marker-pkg",
+			Version:   "1.0.0",
+			Type:      pkg.BinaryPkg,
+			Locations: file.NewLocationSet(loc),
+		}
+		p.SetID()
+		pkgs = append(pkgs, p)
+	}
+	return pkgs, nil, nil
+}
+
+// resolverProbeCataloger reports what the resolver it was handed can see, which is how "absent from
+// the index" is told from "present and skipped" within a scan.
+type resolverProbeCataloger struct {
+	globs  []string
+	record func([]string)
+}
+
+func (resolverProbeCataloger) Name() string { return "resolver-probe-cataloger" }
+
+func (c resolverProbeCataloger) Catalog(_ context.Context, resolver file.Resolver) ([]pkg.Package, []artifact.Relationship, error) {
+	locations, err := resolver.FilesByGlob(c.globs...)
+	if err != nil {
+		return nil, nil, err
+	}
+	var paths []string
+	for _, loc := range locations {
+		paths = append(paths, loc.FullNestedPath())
+	}
+	c.record(paths)
+	return nil, nil, nil
+}
+
+// recordingBus captures the progress rows a scan publishes.
+type recordingBus struct {
+	mu     sync.Mutex
+	events []partybus.Event
+}
+
+func (p *recordingBus) Publish(e partybus.Event) {
+	p.mu.Lock()
+	defer p.mu.Unlock()
+	p.events = append(p.events, e)
+}
+
+// fileContainers maps the full path of each file an archive CONTAINS to the archive's full path.
+func fileContainers(s *sbom.SBOM) map[string]string {
+	out := map[string]string{}
+	for _, r := range s.Relationships {
+		from, fromFile := r.From.(file.Coordinates)
+		to, toFile := r.To.(file.Coordinates)
+		if r.Type == artifact.ContainsRelationship && fromFile && toFile {
+			out[to.FullNestedPath()] = from.FullNestedPath()
+		}
+	}
+	return out
+}
+
+// scanDirWithExclusions scans with the given exclusion patterns configured on the source, where
+// exclusions live; archive cataloging has no exclusion setting of its own.
+func scanDirWithExclusions(t *testing.T, dir string, cfg *CreateSBOMConfig, exclude ...string) *sbom.SBOM {
+	t.Helper()
+	src, err := directorysource.New(directorysource.Config{
+		Path:    dir,
+		Exclude: source.ExcludeConfig{Paths: exclude},
+	})
+	require.NoError(t, err)
+	t.Cleanup(func() { _ = src.Close() })
+
+	s, err := cfg.Create(context.Background(), src)
+	require.NoError(t, err)
+	return s
+}

syft/cataloging/archive_search.go

@@ -1,17 +1,49 @@
 package cataloging
 
+import "github.com/anchore/stereoscope/pkg/file"
+
+const (
+	// DefaultArchiveMaxDepth is 0: nested archives are not cataloged unless asked for.
+	DefaultArchiveMaxDepth = 0
+
+	// DefaultArchiveMaxMemoryBytes bounds the archive content held in memory at once. It decides only
+	// whether an archive costs a write: content that does not fit goes to disk and is cataloged anyway.
+	DefaultArchiveMaxMemoryBytes = 2 * file.GB
+
+	// DefaultArchiveMaxDiskBytes bounds the archive content on disk at once. Content that does not fit
+	// has nowhere to go, so the archive holding it is skipped or truncated. Set high as a backstop
+	// against a pathological archive filling the disk.
+	DefaultArchiveMaxDiskBytes = 100 * file.GB
+)
+
 type ArchiveSearchConfig struct {
 	// IncludeIndexedArchives indicates whether to search within indexed archive files (e.g., .zip).
 	IncludeIndexedArchives bool `yaml:"include-indexed-archives" json:"include-indexed-archives" mapstructure:"include-indexed-archives"`
 
 	// IncludeUnindexedArchives indicates whether to search within unindexed archive files (e.g., .tar*).
 	IncludeUnindexedArchives bool `yaml:"include-unindexed-archives" json:"include-unindexed-archives" mapstructure:"include-unindexed-archives"`
+
+	// MaxDepth is how many levels of nested archives to catalog: 0 disables it, and no setting goes deeper than 16 levels
+	// (negative goes that deep).
+	MaxDepth int `yaml:"max-depth" json:"max-depth" mapstructure:"max-depth"`
+
+	// MaxMemoryBytes bounds the archive content held in memory at once; content that does not fit is
+	// written to disk. Zero holds nothing in memory, negative is unbounded.
+	MaxMemoryBytes int64 `yaml:"max-memory-bytes" json:"max-memory-bytes" mapstructure:"max-memory-bytes"`
+
+	// MaxDiskBytes bounds the archive content written to disk at once; an archive whose content does
+	// not fit is skipped or truncated. Zero writes nothing to disk, negative is unbounded. MaxMemoryBytes
+	// and MaxDiskBytes cannot both be zero while MaxDepth is not.
+	MaxDiskBytes int64 `yaml:"max-disk-bytes" json:"max-disk-bytes" mapstructure:"max-disk-bytes"`
 }
 
 func DefaultArchiveSearchConfig() ArchiveSearchConfig {
 	return ArchiveSearchConfig{
 		IncludeIndexedArchives:   true,
 		IncludeUnindexedArchives: false,
+		MaxDepth:                 DefaultArchiveMaxDepth,
+		MaxMemoryBytes:           DefaultArchiveMaxMemoryBytes,
+		MaxDiskBytes:             DefaultArchiveMaxDiskBytes,
 	}
 }
 
@@ -24,3 +56,18 @@ func (c ArchiveSearchConfig) WithIncludeUnindexedArchives(include bool) ArchiveS
 	c.IncludeUnindexedArchives = include
 	return c
 }
+
+func (c ArchiveSearchConfig) WithMaxDepth(depth int) ArchiveSearchConfig {
+	c.MaxDepth = depth
+	return c
+}
+
+func (c ArchiveSearchConfig) WithMaxMemoryBytes(size int64) ArchiveSearchConfig {
+	c.MaxMemoryBytes = size
+	return c
+}
+
+func (c ArchiveSearchConfig) WithMaxDiskBytes(size int64) ArchiveSearchConfig {
+	c.MaxDiskBytes = size
+	return c
+}

syft/cataloging/archive_search_test.go

@@ -0,0 +1,36 @@
+package cataloging
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestDefaultArchiveSearchConfig(t *testing.T) {
+	cfg := DefaultArchiveSearchConfig()
+
+	assert.True(t, cfg.IncludeIndexedArchives)
+	assert.False(t, cfg.IncludeUnindexedArchives)
+	assert.Equal(t, DefaultArchiveMaxDepth, cfg.MaxDepth)
+	assert.Equal(t, int64(DefaultArchiveMaxMemoryBytes), cfg.MaxMemoryBytes)
+	assert.Equal(t, int64(DefaultArchiveMaxDiskBytes), cfg.MaxDiskBytes)
+}
+
+func TestArchiveSearchConfig_WithMethods(t *testing.T) {
+	cfg := DefaultArchiveSearchConfig()
+
+	cfg = cfg.WithMaxDepth(5)
+	assert.Equal(t, 5, cfg.MaxDepth)
+
+	cfg = cfg.WithMaxMemoryBytes(1024)
+	assert.Equal(t, int64(1024), cfg.MaxMemoryBytes)
+
+	cfg = cfg.WithMaxDiskBytes(2048)
+	assert.Equal(t, int64(2048), cfg.MaxDiskBytes)
+
+	cfg = cfg.WithIncludeIndexedArchives(false)
+	assert.False(t, cfg.IncludeIndexedArchives)
+
+	cfg = cfg.WithIncludeUnindexedArchives(true)
+	assert.True(t, cfg.IncludeUnindexedArchives)
+}

syft/configuration_audit_trail.go

@@ -16,6 +16,7 @@ type configurationAuditTrail struct {
 	DataGeneration cataloging.DataGenerationConfig `json:"data-generation" yaml:"data-generation" mapstructure:"data-generation"`
 	Packages       pkgcataloging.Config            `json:"packages" yaml:"packages" mapstructure:"packages"`
 	Files          filecataloging.Config           `json:"files" yaml:"files" mapstructure:"files"`
+	Archive        cataloging.ArchiveSearchConfig  `json:"archive" yaml:"archive" mapstructure:"archive"`
 	Licenses       cataloging.LicenseConfig        `json:"licenses" yaml:"licenses" mapstructure:"licenses"`
 	Catalogers     catalogerManifest               `json:"catalogers" yaml:"catalogers" mapstructure:"catalogers"`
 	ExtraConfigs   any                             `json:"extra,omitempty" yaml:"extra" mapstructure:"extra"`

syft/create_sbom.go

@@ -10,6 +10,7 @@ import (
 	"github.com/scylladb/go-set/strset"
 
 	"github.com/anchore/go-sync"
+	"github.com/anchore/syft/internal/archive"
 	"github.com/anchore/syft/internal/bus"
 	"github.com/anchore/syft/internal/licenses"
 	"github.com/anchore/syft/internal/log"
@@ -38,7 +39,7 @@ func CreateSBOM(ctx context.Context, src source.Source, cfg *CreateSBOMConfig) (
 
 	srcMetadata := src.Describe()
 
-	taskGroups, audit, err := cfg.makeTaskGroups(srcMetadata)
+	taskGroups, audit, err := cfg.makeTaskGroups(srcMetadata, sourceExclusions(src))
 	if err != nil {
 		return nil, err
 	}
@@ -57,8 +58,9 @@ func CreateSBOM(ctx context.Context, src source.Source, cfg *CreateSBOMConfig) (
 				Search:         cfg.Search,
 				Relationships:  cfg.Relationships,
 				DataGeneration: cfg.DataGeneration,
-				Packages:       cfg.Packages,
+				Packages:       cfg.packagesWithArchiveSearch(),
 				Files:          cfg.Files,
+				Archive:        cfg.Archive,
 				Licenses:       cfg.Licenses,
 				Catalogers:     *audit,
 				ExtraConfigs:   cfg.ToolConfiguration,
@@ -88,8 +90,8 @@ func CreateSBOM(ctx context.Context, src source.Source, cfg *CreateSBOMConfig) (
 		}
 	}
 
-	catalogingProgress := monitorCatalogingTask(src.ID(), taskGroups)
-	packageCatalogingProgress := monitorPackageCatalogingTask()
+	catalogingProgress := monitorCatalogingTask(ctx, src.ID(), taskGroups)
+	packageCatalogingProgress := monitorPackageCatalogingTask(ctx)
 
 	builder := sbomsync.NewBuilder(&s, monitorPackageCount(packageCatalogingProgress))
 	for i := range taskGroups {
@@ -112,6 +114,14 @@ func setupContext(ctx context.Context, cfg *CreateSBOMConfig) (context.Context,
 	// configure parallel executors
 	ctx = setContextExecutors(ctx, cfg)
 
+	// one progress row per cataloger for the whole scan, however many archives it is run against
+	ctx = bus.WithCatalogerTaskRegistry(ctx)
+
+	// the archive cataloger task recurses into jars too, so the java cataloger must not unarchive them itself
+	if cfg.Archive.MaxDepth != 0 {
+		ctx = archive.WithNestedCataloging(ctx)
+	}
+
 	// configure temp dir factory for catalogers (if not already set)
 	if tmpdir.FromContext(ctx) == nil {
 		ctx, _ = tmpdir.Root(ctx, "syft-cataloger")
@@ -173,7 +183,7 @@ func monitorPackageCount(prog *monitor.TaskProgress) func(s *sbom.SBOM) {
 	}
 }
 
-func monitorPackageCatalogingTask() *monitor.TaskProgress {
+func monitorPackageCatalogingTask(ctx context.Context) *monitor.TaskProgress {
 	info := monitor.GenericTask{
 		Title: monitor.Title{
 			Default: "Packages",
@@ -183,10 +193,10 @@ func monitorPackageCatalogingTask() *monitor.TaskProgress {
 		ParentID:      monitor.TopLevelCatalogingTaskID,
 	}
 
-	return bus.StartCatalogerTask(info, -1, "")
+	return bus.StartCatalogerTask(ctx, info, -1, "")
 }
 
-func monitorCatalogingTask(srcID artifact.ID, tasks [][]task.Task) *monitor.TaskProgress {
+func monitorCatalogingTask(ctx context.Context, srcID artifact.ID, tasks [][]task.Task) *monitor.TaskProgress {
 	info := monitor.GenericTask{
 		Title: monitor.Title{
 			Default:      "Catalog contents",
@@ -203,7 +213,7 @@ func monitorCatalogingTask(srcID artifact.ID, tasks [][]task.Task) *monitor.Task
 		length += int64(len(tg))
 	}
 
-	return bus.StartCatalogerTask(info, length, "")
+	return bus.StartCatalogerTask(ctx, info, length, "")
 }
 
 func formatTaskNames(tasks []task.Task) []string {
@@ -218,3 +228,12 @@ func formatTaskNames(tasks []task.Task) []string {
 	sort.Strings(list)
 	return list
 }
+
+// sourceExclusions returns the exclusion patterns the source was configured with, so the same
+// exclusions apply inside the archives found in it.
+func sourceExclusions(src source.Source) []string {
+	if excluder, ok := src.(source.PathExcluder); ok {
+		return excluder.ExcludedPaths()
+	}
+	return nil
+}

syft/create_sbom_config.go

@@ -28,6 +28,7 @@ type CreateSBOMConfig struct {
 	Packages           pkgcataloging.Config
 	Licenses           cataloging.LicenseConfig
 	Files              filecataloging.Config
+	Archive            cataloging.ArchiveSearchConfig
 	Parallelism        int
 	CatalogerSelection cataloging.SelectionRequest
 
@@ -49,6 +50,7 @@ func DefaultCreateSBOMConfig() *CreateSBOMConfig {
 		Packages:             pkgcataloging.DefaultConfig(),
 		Licenses:             cataloging.DefaultLicenseConfig(),
 		Files:                filecataloging.DefaultConfig(),
+		Archive:              cataloging.DefaultArchiveSearchConfig(),
 		Parallelism:          0, // use default: run in parallel based on number of CPUs
 		packageTaskFactories: task.DefaultPackageTaskFactories(),
 
@@ -144,6 +146,13 @@ func (c *CreateSBOMConfig) WithFilesConfig(cfg filecataloging.Config) *CreateSBO
 	return c
 }
 
+// WithArchiveConfig sets how archives are cataloged: how deep to recurse into nested archives (MaxDepth
+// 0, the default, does not recurse) and how much extracted content the scan may hold at once.
+func (c *CreateSBOMConfig) WithArchiveConfig(cfg cataloging.ArchiveSearchConfig) *CreateSBOMConfig {
+	c.Archive = cfg
+	return c
+}
+
 // WithoutFiles allows for disabling file cataloging altogether.
 func (c *CreateSBOMConfig) WithoutFiles() *CreateSBOMConfig {
 	c.Files = filecataloging.Config{
@@ -183,14 +192,15 @@ func (c *CreateSBOMConfig) WithCatalogers(catalogerRefs ...pkgcataloging.Catalog
 // groups, where each task in a group can be run concurrently, while tasks in different groups must be run serially.
 // The final set of task groups is returned along with a cataloger manifest that describes the catalogers that were
 // selected and the tokens that were sensitive to this selection (both for adding and removing from the final set).
-func (c *CreateSBOMConfig) makeTaskGroups(src source.Description) ([][]task.Task, *catalogerManifest, error) {
+//
+// exclusions are the source's exclusion patterns, which the archive cataloger applies inside each archive.
+func (c *CreateSBOMConfig) makeTaskGroups(src source.Description, exclusions []string) ([][]task.Task, *catalogerManifest, error) {
 	var taskGroups [][]task.Task
 
 	// generate package and file tasks based on the configuration
 	environmentTasks := c.environmentTasks()
 	scopeTasks := c.scopeTasks()
 	relationshipsTasks := c.relationshipTasks(src)
-	unknownTasks := c.unknownsTasks()
 	osFeatureDetectionTasks := c.osFeatureDetectionTasks()
 
 	pkgTasks, fileTasks, selectionEvidence, err := c.selectTasks(src)
@@ -198,11 +208,29 @@ func (c *CreateSBOMConfig) makeTaskGroups(src source.Description) ([][]task.Task
 		return nil, nil, err
 	}
 
+	// the same package and file catalogers run against the contents of every archive, after the scan
+	// root and before relationship and unknowns post-processing
+	archiveTask := task.NewArchiveCatalogerTask(c.Archive, c.Unknowns, pkgTasks, fileTasks, exclusions)
+
+	// the archive cataloger reports the archives it does not expand, which the labeler can only guess at
+	unknowns := c.Unknowns
+	if archiveTask != nil {
+		unknowns.IncludeUnexpandedArchives = false
+	}
+	unknownTasks := unknownsTasks(unknowns)
+
 	// combine the user-provided and configured tasks
-	if c.Files.Selection == file.FilesOwnedByPackageSelection {
+	switch {
+	case c.Files.Selection == file.FilesOwnedByPackageSelection && archiveTask != nil:
+		// the archive task describes archives at the root too (java leaves them to it), so the root file
+		// catalogers must run after it to see those packages
+		taskGroups = append(taskGroups, pkgTasks, []task.Task{archiveTask}, fileTasks)
+	case c.Files.Selection == file.FilesOwnedByPackageSelection:
 		// special case: we need the package info when we are cataloging files owned by packages
 		taskGroups = append(taskGroups, pkgTasks, fileTasks)
-	} else {
+	case archiveTask != nil:
+		taskGroups = append(taskGroups, append(pkgTasks, fileTasks...), []task.Task{archiveTask})
+	default:
 		taskGroups = append(taskGroups, append(pkgTasks, fileTasks...))
 	}
 
@@ -226,6 +254,11 @@ func (c *CreateSBOMConfig) makeTaskGroups(src source.Description) ([][]task.Task
 		taskGroups = append(taskGroups, osFeatureDetectionTasks)
 	}
 
+	// archives are related to the files within them only once every task has decided which files are described
+	if archiveTask != nil {
+		taskGroups = append(taskGroups, []task.Task{task.NewArchiveContainsTask()})
+	}
+
 	// identifying the environment (i.e. the linux release) must be done first as this is required for package cataloging
 	taskGroups = append(
 		[][]task.Task{
@@ -237,6 +270,9 @@ func (c *CreateSBOMConfig) makeTaskGroups(src source.Description) ([][]task.Task
 	var allTasks []task.Task
 	allTasks = append(allTasks, pkgTasks...)
 	allTasks = append(allTasks, fileTasks...)
+	if archiveTask != nil {
+		allTasks = append(allTasks, archiveTask)
+	}
 
 	return taskGroups, &catalogerManifest{
 		Requested: selectionEvidence.Request,
@@ -260,7 +296,7 @@ func (c *CreateSBOMConfig) selectTasks(src source.Description) ([]task.Task, []t
 		SearchConfig:         c.Search,
 		RelationshipsConfig:  c.Relationships,
 		DataGenerationConfig: c.DataGeneration,
-		PackagesConfig:       c.Packages,
+		PackagesConfig:       c.packagesWithArchiveSearch(),
 		LicenseConfig:        c.Licenses,
 		ComplianceConfig:     c.Compliance,
 		FilesConfig:          c.Files,
@@ -440,10 +476,10 @@ func (c *CreateSBOMConfig) environmentTasks() []task.Task {
 
 // unknownsTasks returns a set of tasks that perform any necessary post-processing
 // to identify SBOM elements as unknowns
-func (c *CreateSBOMConfig) unknownsTasks() []task.Task {
+func unknownsTasks(cfg cataloging.UnknownsConfig) []task.Task {
 	var tasks []task.Task
 
-	if t := task.NewUnknownsLabelerTask(c.Unknowns); t != nil {
+	if t := task.NewUnknownsLabelerTask(cfg); t != nil {
 		tasks = append(tasks, t)
 	}
 
@@ -461,12 +497,36 @@ func (c *CreateSBOMConfig) osFeatureDetectionTasks() []task.Task {
 	return tasks
 }
 
+// packagesWithArchiveSearch returns a copy of the packages config with the top-level archive search
+// booleans applied to java, which is still the only cataloger that reads them.
+//
+// ponytail: a top-level boolean wins only when it differs from the default, so callers who set just
+// java's deprecated copy see no change. Delete this along with that field.
+func (c *CreateSBOMConfig) packagesWithArchiveSearch() pkgcataloging.Config {
+	pkgs := c.Packages
+	def := cataloging.DefaultArchiveSearchConfig()
+	java := &pkgs.JavaArchive.ArchiveSearchConfig
+	if c.Archive.IncludeIndexedArchives != def.IncludeIndexedArchives {
+		java.IncludeIndexedArchives = c.Archive.IncludeIndexedArchives
+	}
+	if c.Archive.IncludeUnindexedArchives != def.IncludeUnindexedArchives {
+		java.IncludeUnindexedArchives = c.Archive.IncludeUnindexedArchives
+	}
+	return pkgs
+}
+
 func (c *CreateSBOMConfig) validate() error {
 	if c.Relationships.ExcludeBinaryPackagesWithFileOwnershipOverlap {
 		if !c.Relationships.PackageFileOwnershipOverlap {
 			return fmt.Errorf("invalid configuration: to exclude binary packages based on file ownership overlap relationships, cataloging file ownership overlap relationships must be enabled")
 		}
 	}
+	if j := c.Packages.JavaArchive.ArchiveSearchConfig; j.MaxDepth != 0 || j.MaxMemoryBytes != 0 || j.MaxDiskBytes != 0 {
+		return fmt.Errorf("invalid configuration: nested archive depth and limits are not java cataloger settings, set them with CreateSBOMConfig.Archive")
+	}
+	if a := c.Archive; a.MaxDepth != 0 && a.MaxMemoryBytes == 0 && a.MaxDiskBytes == 0 {
+		return fmt.Errorf("invalid configuration: nested archive cataloging is enabled but its memory and disk limits are both 0, leaving nowhere to extract archives")
+	}
 	return nil
 }
 

syft/create_sbom_config_test.go

@@ -18,6 +18,7 @@ import (
 	"github.com/anchore/syft/syft/cataloging/pkgcataloging"
 	"github.com/anchore/syft/syft/file"
 	"github.com/anchore/syft/syft/pkg"
+	"github.com/anchore/syft/syft/pkg/cataloger/java"
 	"github.com/anchore/syft/syft/source"
 )
 
@@ -329,7 +330,7 @@ func TestCreateSBOMConfig_makeTaskGroups(t *testing.T) {
 			require.NotEmpty(t, tt.wantTaskNames)
 
 			// test the subject
-			gotTasks, gotManifest, err := tt.cfg.makeTaskGroups(tt.src)
+			gotTasks, gotManifest, err := tt.cfg.makeTaskGroups(tt.src, nil)
 			tt.wantErr(t, err)
 			if err != nil {
 				return
@@ -554,6 +555,31 @@ func TestCreateSBOMConfig_validate(t *testing.T) {
 				),
 			wantErr: assert.Error,
 		},
+		{
+			name: "nested archives enabled with no memory or disk",
+			cfg: DefaultCreateSBOMConfig().WithArchiveConfig(
+				cataloging.DefaultArchiveSearchConfig().WithMaxDepth(1).WithMaxMemoryBytes(0).WithMaxDiskBytes(0),
+			),
+			wantErr: assert.Error,
+		},
+		{
+			name: "nested archives enabled with memory only",
+			cfg: DefaultCreateSBOMConfig().WithArchiveConfig(
+				cataloging.DefaultArchiveSearchConfig().WithMaxDepth(1).WithMaxDiskBytes(0),
+			),
+		},
+		{
+			name: "nested archives enabled with disk only",
+			cfg: DefaultCreateSBOMConfig().WithArchiveConfig(
+				cataloging.DefaultArchiveSearchConfig().WithMaxDepth(1).WithMaxMemoryBytes(0),
+			),
+		},
+		{
+			name: "nested archives disabled with no memory or disk",
+			cfg: DefaultCreateSBOMConfig().WithArchiveConfig(
+				cataloging.DefaultArchiveSearchConfig().WithMaxMemoryBytes(0).WithMaxDiskBytes(0),
+			),
+		},
 	}
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
@@ -564,3 +590,64 @@ func TestCreateSBOMConfig_validate(t *testing.T) {
 		})
 	}
 }
+
+func TestCreateSBOMConfig_archiveTaskGroup(t *testing.T) {
+	src := source.Description{Metadata: source.DirectoryMetadata{}}
+
+	archiveTaskIn := func(groups [][]task.Task) bool {
+		for _, group := range groups {
+			for _, tsk := range group {
+				if tsk.Name() == task.ArchiveCatalogerTaskName {
+					return true
+				}
+			}
+		}
+		return false
+	}
+
+	t.Run("no archive task by default", func(t *testing.T) {
+		// the feature is off by default, and off must mean no task at all rather than a registered
+		// task that does nothing: a registered task is reported as a selected cataloger
+		groups, manifest, err := DefaultCreateSBOMConfig().makeTaskGroups(src, nil)
+		require.NoError(t, err)
+		assert.False(t, archiveTaskIn(groups))
+		assert.NotContains(t, manifest.Used, task.ArchiveCatalogerTaskName)
+	})
+
+	t.Run("archive task is present at negative depth", func(t *testing.T) {
+		cfg := DefaultCreateSBOMConfig().
+			WithArchiveConfig(cataloging.DefaultArchiveSearchConfig().WithMaxDepth(-1))
+		groups, _, err := cfg.makeTaskGroups(src, nil)
+		require.NoError(t, err)
+		assert.True(t, archiveTaskIn(groups))
+	})
+
+	t.Run("archive task is present when enabled", func(t *testing.T) {
+		cfg := DefaultCreateSBOMConfig().
+			WithArchiveConfig(cataloging.DefaultArchiveSearchConfig().WithMaxDepth(2))
+		groups, manifest, err := cfg.makeTaskGroups(src, nil)
+		require.NoError(t, err)
+		assert.True(t, archiveTaskIn(groups))
+		assert.Contains(t, manifest.Used, task.ArchiveCatalogerTaskName, "the manifest must say archive contents were searched")
+	})
+
+	t.Run("enabling the feature does not mutate the caller's package config", func(t *testing.T) {
+		// the java side learns the archive task is running from the context, not from its config: a
+		// consumer who handed us a package config gets it back exactly as supplied.
+		supplied := java.DefaultArchiveCatalogerConfig().WithUseNetwork(true)
+
+		cfg := DefaultCreateSBOMConfig().
+			WithArchiveConfig(cataloging.DefaultArchiveSearchConfig().WithMaxDepth(2)).
+			WithPackagesConfig(pkgcataloging.Config{JavaArchive: supplied})
+
+		_, _, err := cfg.makeTaskGroups(src, nil)
+		require.NoError(t, err)
+
+		assert.Equal(t, supplied, cfg.Packages.JavaArchive,
+			"the caller's java config must come back byte-identical")
+		assert.True(t, cfg.Packages.JavaArchive.UseNetwork,
+			"a caller-supplied field must survive untouched")
+		assert.Zero(t, cfg.Packages.JavaArchive.MaxDepth,
+			"java's own squash-inlined depth must not be written to either")
+	})
+}

syft/file/cataloger/executable/cataloger.go

@@ -64,11 +64,11 @@ func (i *Cataloger) CatalogCtx(ctx context.Context, resolver file.Resolver) (map
 		return nil, err
 	}
 
-	prog := catalogingProgress(int64(len(locs)))
+	prog := catalogingProgress(ctx, int64(len(locs)))
 
 	results := make(map[file.Coordinates]file.Executable)
 	errs := sync.Collect(&ctx, cataloging.ExecutorFile, sync.ToSeq(locs), func(loc file.Location) (*file.Executable, error) {
-		prog.AtomicStage.Set(loc.Path())
+		prog.AtomicStage.Set(loc.FullNestedPath())
 
 		exec, err := processExecutableLocation(loc, resolver)
 		if err != nil {
@@ -93,15 +93,15 @@ func (i *Cataloger) CatalogCtx(ctx context.Context, resolver file.Resolver) (map
 func processExecutableLocation(loc file.Location, resolver file.Resolver) (exec *file.Executable, err error) {
 	reader, err := resolver.FileContentsByLocation(loc)
 	if err != nil {
-		log.WithFields("error", err, "path", loc.RealPath).Debug("unable to get file contents")
+		log.WithFields("error", err, "path", loc.FullNestedPath()).Debug("unable to get file contents")
 		return nil, fmt.Errorf("unable to get file contents: %w", err)
 	}
-	defer internal.CloseAndLogError(reader, loc.RealPath)
+	defer internal.CloseAndLogError(reader, loc.FullNestedPath())
 
 	defer func() {
 		if r := recover(); r != nil {
 			// a malformed binary must not take down the whole SBOM; the caller records this as an unknown
-			log.WithFields("path", loc.RealPath, "panic", r).Debug("recovered from panic while reading executable")
+			log.WithFields("path", loc.FullNestedPath(), "panic", r).Debug("recovered from panic while reading executable")
 			log.Tracef("executable panic stack:\n%s", debug.Stack())
 			exec, err = nil, fmt.Errorf("recovered from panic while reading executable: %v", r)
 		}
@@ -109,14 +109,14 @@ func processExecutableLocation(loc file.Location, resolver file.Resolver) (exec
 
 	uReader, err := unionreader.GetUnionReader(reader)
 	if err != nil {
-		log.WithFields("error", err, "path", loc.RealPath).Debug("unable to get union reader")
+		log.WithFields("error", err, "path", loc.FullNestedPath()).Debug("unable to get union reader")
 		return nil, fmt.Errorf("unable to get union reader: %w", err)
 	}
 
 	return processExecutable(loc, uReader)
 }
 
-func catalogingProgress(locations int64) *monitor.TaskProgress {
+func catalogingProgress(ctx context.Context, locations int64) *monitor.TaskProgress {
 	info := monitor.GenericTask{
 		Title: monitor.Title{
 			Default: "Executables",
@@ -124,7 +124,7 @@ func catalogingProgress(locations int64) *monitor.TaskProgress {
 		ParentID: monitor.TopLevelCatalogingTaskID,
 	}
 
-	return bus.StartCatalogerTask(info, locations, "")
+	return bus.StartCatalogerTask(ctx, info, locations, "")
 }
 
 func filterByGlobs(locs []file.Location, globs []string) ([]file.Location, error) {
@@ -146,7 +146,7 @@ func filterByGlobs(locs []file.Location, globs []string) ([]file.Location, error
 
 func locationMatchesGlob(loc file.Location, globs []string) (bool, error) {
 	for _, glob := range globs {
-		for _, path := range []string{loc.RealPath, loc.AccessPath} {
+		for _, path := range []string{loc.LocalPath(), loc.AccessPath} {
 			if path == "" {
 				continue
 			}
@@ -169,13 +169,13 @@ func processExecutable(loc file.Location, reader unionreader.UnionReader) (*file
 
 	format, err := findExecutableFormat(reader)
 	if err != nil {
-		log.Debugf("unable to determine executable kind for %v: %v", loc.RealPath, err)
+		log.Debugf("unable to determine executable kind for %v: %v", loc.FullNestedPath(), err)
 		return nil, fmt.Errorf("unable to determine executable kind: %w", err)
 	}
 
 	if format == "" {
 		// this is not an "unknown", so just log -- this binary does not have parseable data in it
-		log.Debugf("unable to determine executable format for %q", loc.RealPath)
+		log.Debugf("unable to determine executable format for %q", loc.FullNestedPath())
 		return nil, nil
 	}
 
@@ -184,17 +184,17 @@ func processExecutable(loc file.Location, reader unionreader.UnionReader) (*file
 	switch format {
 	case file.ELF:
 		if err = findELFFeatures(&data, reader); err != nil {
-			log.WithFields("error", err, "path", loc.RealPath).Trace("unable to determine ELF features")
+			log.WithFields("error", err, "path", loc.FullNestedPath()).Trace("unable to determine ELF features")
 			err = fmt.Errorf("unable to determine ELF features: %w", err)
 		}
 	case file.PE:
 		if err = findPEFeatures(&data, reader); err != nil {
-			log.WithFields("error", err, "path", loc.RealPath).Trace("unable to determine PE features")
+			log.WithFields("error", err, "path", loc.FullNestedPath()).Trace("unable to determine PE features")
 			err = fmt.Errorf("unable to determine PE features: %w", err)
 		}
 	case file.MachO:
 		if err = findMachoFeatures(&data, reader); err != nil {
-			log.WithFields("error", err, "path", loc.RealPath).Trace("unable to determine Macho features")
+			log.WithFields("error", err, "path", loc.FullNestedPath()).Trace("unable to determine Macho features")
 			err = fmt.Errorf("unable to determine Macho features: %w", err)
 		}
 	}

syft/file/cataloger/filecontent/cataloger.go

@@ -44,7 +44,7 @@ func NewCataloger(cfg Config) *Cataloger {
 	}
 }
 
-func (i *Cataloger) Catalog(_ context.Context, resolver file.Resolver) (map[file.Coordinates]string, error) {
+func (i *Cataloger) Catalog(ctx context.Context, resolver file.Resolver) (map[file.Coordinates]string, error) {
 	results := make(map[file.Coordinates]string)
 	var locations []file.Location
 	var errs error
@@ -54,10 +54,10 @@ func (i *Cataloger) Catalog(_ context.Context, resolver file.Resolver) (map[file
 		return nil, err
 	}
 
-	prog := catalogingProgress(int64(len(locations)))
+	prog := catalogingProgress(ctx, int64(len(locations)))
 
 	for _, location := range locations {
-		prog.AtomicStage.Set(location.Path())
+		prog.AtomicStage.Set(location.FullNestedPath())
 
 		metadata, err := resolver.FileMetadataByLocation(location)
 		if err != nil {
@@ -98,12 +98,12 @@ func (i *Cataloger) catalogLocation(resolver file.Resolver, location file.Locati
 	if err != nil {
 		return "", err
 	}
-	defer internal.CloseAndLogError(contentReader, location.AccessPath)
+	defer internal.CloseAndLogError(contentReader, location.FullNestedPath())
 
 	buf := &bytes.Buffer{}
 	encoder := base64.NewEncoder(base64.StdEncoding, buf)
 	if _, err = io.Copy(encoder, contentReader); err != nil {
-		return "", internal.ErrPath{Context: "content-cataloger", Path: location.RealPath, Err: err}
+		return "", internal.ErrPath{Context: "content-cataloger", Path: location.FullNestedPath(), Err: err}
 	}
 	// note: it's important to close the reader before reading from the buffer since closing will flush the remaining bytes
 	if err := encoder.Close(); err != nil {
@@ -113,7 +113,7 @@ func (i *Cataloger) catalogLocation(resolver file.Resolver, location file.Locati
 	return buf.String(), nil
 }
 
-func catalogingProgress(locations int64) *monitor.TaskProgress {
+func catalogingProgress(ctx context.Context, locations int64) *monitor.TaskProgress {
 	info := monitor.GenericTask{
 		Title: monitor.Title{
 			Default: "File contents",
@@ -121,5 +121,5 @@ func catalogingProgress(locations int64) *monitor.TaskProgress {
 		ParentID: monitor.TopLevelCatalogingTaskID,
 	}
 
-	return bus.StartCatalogerTask(info, locations, "")
+	return bus.StartCatalogerTask(ctx, info, locations, "")
 }

syft/file/cataloger/filedigest/cataloger.go

@@ -42,15 +42,27 @@ func (i *Cataloger) Catalog(ctx context.Context, resolver file.Resolver, coordin
 		locations = intCataloger.AllRegularFiles(ctx, resolver)
 	} else {
 		for _, c := range coordinates {
-			locs, err := resolver.FilesByPath(c.RealPath)
+			locs, err := resolver.FilesByPath(c.FullNestedPath())
 			if err != nil {
-				return nil, fmt.Errorf("unable to get file locations for path %q: %w", c.RealPath, err)
+				return nil, fmt.Errorf("unable to get file locations for path %q: %w", c.FullNestedPath(), err)
 			}
 			locations = append(locations, locs...)
 		}
 	}
 
-	prog := catalogingProgress(int64(len(locations)))
+	// symlinks resolve to the same file, so drop repeated coordinates to avoid hashing the same contents more than once
+	seen := make(map[file.Coordinates]struct{}, len(locations))
+	unique := locations[:0]
+	for _, l := range locations {
+		if _, ok := seen[l.Coordinates]; ok {
+			continue
+		}
+		seen[l.Coordinates] = struct{}{}
+		unique = append(unique, l)
+	}
+	locations = unique
+
+	prog := catalogingProgress(ctx, int64(len(locations)))
 
 	err := sync.Collect(&ctx, cataloging.ExecutorFile, sync.ToSeq(locations), func(location file.Location) ([]file.Digest, error) {
 		result, err := i.catalogLocation(ctx, resolver, location)
@@ -59,10 +71,10 @@ func (i *Cataloger) Catalog(ctx context.Context, resolver file.Resolver, coordin
 			return nil, nil
 		}
 
-		prog.AtomicStage.Set(location.Path())
+		prog.AtomicStage.Set(location.FullNestedPath())
 
 		if internal.IsErrPathPermission(err) {
-			log.Debugf("file digests cataloger skipping %q: %+v", location.RealPath, err)
+			log.Debugf("file digests cataloger skipping %q: %+v", location.FullNestedPath(), err)
 			return nil, unknown.New(location, err)
 		}
 
@@ -103,12 +115,12 @@ func (i *Cataloger) catalogLocation(ctx context.Context, resolver file.Resolver,
 	if err != nil {
 		return nil, err
 	}
-	defer internal.CloseAndLogError(contentReader, location.AccessPath)
+	defer internal.CloseAndLogError(contentReader, location.FullNestedPath())
 
 	defer func() {
 		if r := recover(); r != nil {
 			// the caller records this as an unknown for the location instead of failing the whole SBOM
-			log.WithFields("path", location.RealPath, "panic", r).Debug("recovered from panic while digesting file")
+			log.WithFields("path", location.FullNestedPath(), "panic", r).Debug("recovered from panic while digesting file")
 			log.Tracef("file digest panic stack:\n%s", debug.Stack())
 			digests, err = nil, fmt.Errorf("recovered from panic while digesting file: %v", r)
 		}
@@ -116,13 +128,13 @@ func (i *Cataloger) catalogLocation(ctx context.Context, resolver file.Resolver,
 
 	digests, err = intFile.NewDigestsFromFile(ctx, contentReader, i.hashes)
 	if err != nil {
-		return nil, internal.ErrPath{Context: "digests-cataloger", Path: location.RealPath, Err: err}
+		return nil, internal.ErrPath{Context: "digests-cataloger", Path: location.FullNestedPath(), Err: err}
 	}
 
 	return digests, nil
 }
 
-func catalogingProgress(locations int64) *monitor.TaskProgress {
+func catalogingProgress(ctx context.Context, locations int64) *monitor.TaskProgress {
 	info := monitor.GenericTask{
 		Title: monitor.Title{
 			Default: "File digests",
@@ -130,5 +142,5 @@ func catalogingProgress(locations int64) *monitor.TaskProgress {
 		ParentID: monitor.TopLevelCatalogingTaskID,
 	}
 
-	return bus.StartCatalogerTask(info, locations, "")
+	return bus.StartCatalogerTask(ctx, info, locations, "")
 }

syft/file/cataloger/filedigest/cataloger_test.go

@@ -7,6 +7,7 @@ import (
 	"io"
 	"os"
 	"path/filepath"
+	"sync"
 	"testing"
 
 	"github.com/stretchr/testify/assert"
@@ -207,6 +208,45 @@ func TestFileDigestCataloger_GivenCoordinates(t *testing.T) {
 
 }
 
+// countingResolver records how many times each coordinate's contents are opened
+type countingResolver struct {
+	file.Resolver
+	lock   sync.Mutex
+	counts map[file.Coordinates]int
+}
+
+func (r *countingResolver) FileContentsByLocation(l file.Location) (io.ReadCloser, error) {
+	r.lock.Lock()
+	r.counts[l.Coordinates]++
+	r.lock.Unlock()
+	return r.Resolver.FileContentsByLocation(l)
+}
+
+func TestDigestsCataloger_hashesEachCoordinateOnce(t *testing.T) {
+	testImage := "image-file-type-mix"
+
+	testutils.SkipWithoutLinuxContainers(t)
+	img := imagetest.GetFixtureImage(t, "docker-archive", testImage)
+
+	src := stereoscopesource.New(img, stereoscopesource.ImageConfig{
+		Reference: testImage,
+	})
+
+	resolver, err := src.FileResolver(source.SquashedScope)
+	require.NoError(t, err)
+
+	// /symlink-1 and /file-1.txt both resolve to the same coordinates
+	counter := &countingResolver{Resolver: resolver, counts: make(map[file.Coordinates]int)}
+
+	actual, err := NewCataloger([]crypto.Hash{crypto.MD5}).Catalog(context.Background(), counter)
+	require.NoError(t, err)
+	require.NotEmpty(t, actual)
+
+	for c, n := range counter.counts {
+		assert.Equal(t, 1, n, "contents of %+v opened %d times", c, n)
+	}
+}
+
 type panicReader struct{}
 
 func (panicReader) Read([]byte) (int, error) { panic("boom") }

syft/file/cataloger/filemetadata/cataloger.go

@@ -34,7 +34,7 @@ func (i *Cataloger) Catalog(ctx context.Context, resolver file.Resolver, coordin
 			go func() {
 				defer close(ch)
 				for _, c := range coordinates {
-					locs, err := resolver.FilesByPath(c.RealPath)
+					locs, err := resolver.FilesByPath(c.FullNestedPath())
 					if err != nil {
 						errs = unknown.Append(errs, c, err)
 						continue
@@ -53,9 +53,9 @@ func (i *Cataloger) Catalog(ctx context.Context, resolver file.Resolver, coordin
 		}()
 	}
 
-	prog := catalogingProgress(-1)
+	prog := catalogingProgress(ctx, -1)
 	for location := range locations {
-		prog.AtomicStage.Set(location.Path())
+		prog.AtomicStage.Set(location.FullNestedPath())
 
 		metadata, err := resolver.FileMetadataByLocation(location)
 		if err != nil {
@@ -76,7 +76,7 @@ func (i *Cataloger) Catalog(ctx context.Context, resolver file.Resolver, coordin
 	return results, errs
 }
 
-func catalogingProgress(locations int64) *monitor.TaskProgress {
+func catalogingProgress(ctx context.Context, locations int64) *monitor.TaskProgress {
 	info := monitor.GenericTask{
 		Title: monitor.Title{
 			Default: "File metadata",
@@ -84,5 +84,5 @@ func catalogingProgress(locations int64) *monitor.TaskProgress {
 		ParentID: monitor.TopLevelCatalogingTaskID,
 	}
 
-	return bus.StartCatalogerTask(info, locations, "")
+	return bus.StartCatalogerTask(ctx, info, locations, "")
 }

syft/file/cataloger/internal/all_regular_files.go

@@ -12,16 +12,16 @@ func AllRegularFiles(ctx context.Context, resolver file.Resolver) (locations []f
 	ctx, cancel := context.WithCancel(ctx)
 	defer cancel()
 	for location := range resolver.AllLocations(ctx) {
-		resolvedLocations, err := resolver.FilesByPath(location.RealPath)
+		resolvedLocations, err := resolver.FilesByPath(location.LocalPath())
 		if err != nil {
-			log.Debugf("unable to resolve %+v: %+v", location, err)
+			log.Debugf("unable to resolve %q: %+v", location.FullNestedPath(), err)
 			continue
 		}
 
 		for _, resolvedLocation := range resolvedLocations {
 			metadata, err := resolver.FileMetadataByLocation(resolvedLocation)
 			if err != nil {
-				log.Debugf("unable to get metadata for %+v: %+v", location, err)
+				log.Debugf("unable to get metadata for %q: %+v", resolvedLocation.FullNestedPath(), err)
 				continue
 			}
 

syft/file/coordinate_set.go

@@ -78,6 +78,9 @@ func (s CoordinateSet) ToSlice(sorters ...func(a, b Coordinates) int) []Coordina
 	if !sorted {
 		sort.SliceStable(coordinates, func(i, j int) bool {
 			if coordinates[i].FileSystemID == coordinates[j].FileSystemID {
+				if coordinates[i].RealPath == coordinates[j].RealPath {
+					return coordinates[i].FullNestedPath() < coordinates[j].FullNestedPath()
+				}
 				return coordinates[i].RealPath < coordinates[j].RealPath
 			}
 			return coordinates[i].FileSystemID < coordinates[j].FileSystemID

syft/file/coordinates.go

@@ -2,18 +2,46 @@ package file
 
 import (
 	"fmt"
+	"strings"
 
 	"github.com/anchore/syft/internal/log"
 	"github.com/anchore/syft/syft/artifact"
 )
 
+const ArchivePathSeparator = "!/"
+
 // Coordinates contains the minimal information needed to describe how to find a file within any possible source object (e.g. image and directory sources)
 type Coordinates struct {
-	// RealPath is the canonical absolute form of the path accessed (all symbolic links have been followed and relative path components like '.' and '..' have been removed).
+	// RealPath is the canonical absolute form of the path accessed (all symbolic links have been followed and relative path components like '.' and '..' have been removed). For a file found within an archive, it is the real path of the outermost archive on the scanned filesystem.
 	RealPath string `json:"path" cyclonedx:"path"`
 
-	// FileSystemID is an ID representing and entire filesystem. For container images, this is a layer digest. For directories or a root filesystem, this is blank.
+	// FileSystemID is an ID representing an entire filesystem. For container images, this is a layer digest. For directories or a root filesystem, this is blank. A file inside an archive carries the FileSystemID of the filesystem the archive was found in.
 	FileSystemID string `json:"layerID,omitempty" cyclonedx:"layerID"`
+
+	// FullPath is the full path to the file: RealPath, then for a file within an archive a "!/"-delimited chain of entry paths through any nested archives, ending with the file's own entry path (e.g. "/app.war!/WEB-INF/lib/dep.jar!/META-INF/MANIFEST.MF"). Each segment is a real path (links resolved) relative to the archive before it. For a file not within an archive it is blank, so coordinates outside archives are unchanged by the field (in JSON, equality and ID).
+	FullPath string `json:"fullPath,omitempty" cyclonedx:"fullPath"`
+}
+
+// FullNestedPath is FullPath, or RealPath where FullPath is blank.
+func (c Coordinates) FullNestedPath() string {
+	if c.FullPath == "" {
+		return c.RealPath
+	}
+	return c.FullPath
+}
+
+// LocalPath is the rooted path within the resolver holding the file: the last entry path in FullPath, or
+// RealPath for a file not within an archive. RealPath is cut off before looking for a separator, so a
+// "!/" in a real path is never taken for an archive boundary.
+func (c Coordinates) LocalPath() string {
+	entries, ok := strings.CutPrefix(c.FullPath, c.RealPath+ArchivePathSeparator)
+	if !ok {
+		return c.RealPath
+	}
+	if i := strings.LastIndex(entries, ArchivePathSeparator); i >= 0 {
+		entries = entries[i+len(ArchivePathSeparator):]
+	}
+	return "/" + entries
 }
 
 func NewCoordinates(realPath, fsID string) Coordinates {
@@ -40,9 +68,22 @@ func (c Coordinates) String() string {
 	if c.FileSystemID != "" {
 		str += fmt.Sprintf(" Layer=%q", c.FileSystemID)
 	}
+
+	if c.FullNestedPath() != c.RealPath {
+		str += fmt.Sprintf(" FullPath=%q", c.FullNestedPath())
+	}
 	return fmt.Sprintf("Location<%s>", str)
 }
 
 func (c Coordinates) GetCoordinates() Coordinates {
 	return c
 }
+
+// HashInclude keeps a FullPath that adds nothing to RealPath out of the artifact ID hash (see
+// artifact.IDByHash), so coordinates outside archives keep the IDs they had before the field existed.
+func (c Coordinates) HashInclude(field string, _ any) (bool, error) {
+	if field == "FullPath" && c.FullNestedPath() == c.RealPath {
+		return false, nil
+	}
+	return true, nil
+}

syft/file/location.go

@@ -33,7 +33,7 @@ type LocationData struct {
 	// note: it is IMPORTANT to ignore anything but the coordinates for a Location when considering the ID (hash value)
 	// since the coordinates are the minimally correct ID for a location (symlinks should not come into play)
 
-	// AccessPath is the path used to retrieve file contents (which may or may not have hardlinks / symlinks in the path)
+	// AccessPath is the path used to retrieve file contents (which may or may not have hardlinks / symlinks in the path). For a file within an archive, it is a full path (see Coordinates.FullPath).
 	AccessPath string `hash:"ignore" json:"accessPath"`
 
 	// ref is the stereoscope file reference relative to the stereoscope.FileCatalog that has more information about this location.
@@ -110,12 +110,12 @@ func NewVirtualLocation(realPath, accessPath string) Location {
 		}}
 }
 
-// NewLocationFromCoordinates creates a new location for the given Coordinates.
+// NewLocationFromCoordinates creates a new location for the given Coordinates, accessed by their full path.
 func NewLocationFromCoordinates(coordinates Coordinates) Location {
 	return Location{
 		LocationData: LocationData{
 			Coordinates: coordinates,
-			AccessPath:  coordinates.RealPath,
+			AccessPath:  coordinates.FullNestedPath(),
 		},
 		LocationMetadata: LocationMetadata{
 			Annotations: map[string]string{},
@@ -205,11 +205,13 @@ func NewVirtualLocationFromDirectory(responsePath, responseAccessPath string, re
 	}
 }
 
+// Path is the path this location was accessed by, or its full path (see Coordinates.FullNestedPath). For a
+// file within an archive both are full paths, so use LocalPath for path arithmetic against the resolver.
 func (l Location) Path() string {
 	if l.AccessPath != "" {
 		return l.AccessPath
 	}
-	return l.RealPath
+	return l.FullNestedPath()
 }
 
 func (l Location) String() string {
@@ -220,10 +222,14 @@ func (l Location) String() string {
 
 	str += fmt.Sprintf("RealPath=%q", l.RealPath)
 
-	if l.AccessPath != "" && l.AccessPath != l.RealPath {
+	if l.AccessPath != "" {
 		str += fmt.Sprintf(" AccessPath=%q", l.AccessPath)
 	}
 
+	if l.FullNestedPath() != l.RealPath {
+		str += fmt.Sprintf(" FullPath=%q", l.FullNestedPath())
+	}
+
 	if l.FileSystemID != "" {
 		str += fmt.Sprintf(" Layer=%q", l.FileSystemID)
 	}
@@ -231,7 +237,7 @@ func (l Location) String() string {
 }
 
 func (l Location) Equals(other Location) bool {
-	return l.RealPath == other.RealPath &&
+	return l.FullNestedPath() == other.FullNestedPath() &&
 		l.AccessPath == other.AccessPath &&
 		l.FileSystemID == other.FileSystemID
 }

syft/file/location_set.go

@@ -5,6 +5,7 @@ import (
 	"sort"
 
 	"github.com/gohugoio/hashstructure"
+	"github.com/scylladb/go-set/strset"
 
 	"github.com/anchore/syft/internal/log"
 )
@@ -112,8 +113,13 @@ func (s *LocationSet) Empty() bool {
 }
 
 func (s LocationSet) Hash() (uint64, error) {
-	// access paths and filesystem IDs are not considered when hashing a location set, only the real paths
-	return hashstructure.Hash(s.CoordinateSet().Paths(), &hashstructure.HashOptions{
+	// access paths and filesystem IDs are not considered when hashing a location set, only the full paths
+	// (unlike CoordinateSet.Paths, which ownership-by-overlap needs as real paths only)
+	paths := strset.New()
+	for _, c := range s.CoordinateSet().ToUnorderedSlice() {
+		paths.Add(c.FullNestedPath())
+	}
+	return hashstructure.Hash(paths.List(), &hashstructure.HashOptions{
 		ZeroNil:      true,
 		SlicesAsSets: true,
 	})

syft/file/location_set_test.go

@@ -4,6 +4,7 @@ import (
 	"sort"
 	"testing"
 
+	"github.com/gohugoio/hashstructure"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 
@@ -255,6 +256,10 @@ func TestLocationSet_Hash(t *testing.T) {
 		},
 	}
 
+	inA := NewLocationFromCoordinates(Coordinates{RealPath: "/app.war", FullPath: "/app.war!/a.jar!/package.json"})
+	inB := NewLocationFromCoordinates(Coordinates{RealPath: "/app.war", FullPath: "/app.war!/b.jar!/package.json"})
+	etcFull := Location{LocationData: LocationData{Coordinates: Coordinates{RealPath: "/etc/hosts", FileSystemID: "a", FullPath: "/etc/hosts"}}}
+
 	tests := []struct {
 		name string
 		setA LocationSet
@@ -297,6 +302,18 @@ func TestLocationSet_Hash(t *testing.T) {
 			setB: NewLocationSet(binB, etcB),
 			want: assert.Equal,
 		},
+		{
+			name: "same outer archive but different nested entries have different hashes",
+			setA: NewLocationSet(inA),
+			setB: NewLocationSet(inB),
+			want: assert.NotEqual,
+		},
+		{
+			name: "a full path equal to the real path has the same hash as a blank one",
+			setA: NewLocationSet(etcA),
+			setB: NewLocationSet(etcFull),
+			want: assert.Equal,
+		},
 	}
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
@@ -308,3 +325,13 @@ func TestLocationSet_Hash(t *testing.T) {
 		})
 	}
 }
+
+// IDs outside archives must not change from when only real paths were hashed
+func TestLocationSet_Hash_unchangedOutsideArchives(t *testing.T) {
+	want, err := hashstructure.Hash([]string{"/etc/hosts", "/bin"}, &hashstructure.HashOptions{ZeroNil: true, SlicesAsSets: true})
+	require.NoError(t, err)
+
+	got, err := NewLocationSet(NewLocation("/etc/hosts"), NewVirtualLocation("/bin", "/usr/bin")).Hash()
+	require.NoError(t, err)
+	assert.Equal(t, want, got)
+}

syft/file/location_test.go

@@ -1,9 +1,11 @@
 package file
 
 import (
+	"encoding/json"
 	"testing"
 
 	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
 
 	"github.com/anchore/stereoscope/pkg/file"
 )
@@ -48,3 +50,73 @@ func TestLocation_ID(t *testing.T) {
 	}
 
 }
+
+func TestLocation_fullPathIsIdentity(t *testing.T) {
+	a := NewLocationFromCoordinates(Coordinates{RealPath: "/a.jar", FullPath: "/a.jar!/META-INF/MANIFEST.MF"})
+	b := NewLocationFromCoordinates(Coordinates{RealPath: "/b.jar", FullPath: "/b.jar!/META-INF/MANIFEST.MF"})
+
+	assert.False(t, a.Equals(b))
+	assert.NotEqual(t, a.String(), b.String())
+	assert.Contains(t, a.String(), `RealPath="/a.jar"`)
+}
+
+func TestLocation_JSON(t *testing.T) {
+	tests := []struct {
+		name     string
+		location Location
+		expected string
+	}{
+		{
+			name:     "a file outside an archive writes no fullPath",
+			location: NewVirtualLocationFromDirectory("/etc/os-release", "/etc/link", file.Reference{}).WithAnnotation("k", "v"),
+			expected: `{"path":"/etc/os-release","accessPath":"/etc/link","annotations":{"k":"v"}}`,
+		},
+		{
+			name:     "a file within an archive writes its full path",
+			location: NewLocationFromCoordinates(Coordinates{RealPath: "/app.war", FileSystemID: "layer", FullPath: "/app.war!/META-INF/MANIFEST.MF"}),
+			expected: `{"path":"/app.war","layerID":"layer","fullPath":"/app.war!/META-INF/MANIFEST.MF","accessPath":"/app.war!/META-INF/MANIFEST.MF"}`,
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			data, err := json.Marshal(tt.location)
+			require.NoError(t, err)
+			assert.JSONEq(t, tt.expected, string(data))
+
+			var decoded Location
+			require.NoError(t, json.Unmarshal(data, &decoded))
+			assert.Equal(t, tt.location.Coordinates, decoded.Coordinates, "decoding fills FullPath back in")
+			assert.Equal(t, tt.location.AccessPath, decoded.AccessPath)
+
+			data, err = json.Marshal(tt.location.Coordinates)
+			require.NoError(t, err)
+			var coordinates Coordinates
+			require.NoError(t, json.Unmarshal(data, &coordinates))
+			assert.Equal(t, tt.location.Coordinates, coordinates)
+		})
+	}
+}
+
+func TestCoordinates_ID_unchangedByTopLevelFullRealPath(t *testing.T) {
+	assert.Equal(t, Coordinates{RealPath: "/a"}.ID(), NewCoordinates("/a", "").ID())
+	assert.NotEqual(t, NewCoordinates("/a", "").ID(), Coordinates{RealPath: "/a", FullPath: "/a!/b"}.ID())
+}
+
+func TestCoordinates_LocalPath(t *testing.T) {
+	assert.Equal(t, "/a.jar", NewCoordinates("/a.jar", "").LocalPath())
+	assert.Equal(t, "/a.jar", Coordinates{RealPath: "/a.jar"}.LocalPath())
+	assert.Equal(t, "/META-INF/MANIFEST.MF", Coordinates{RealPath: "/a.war", FullPath: "/a.war!/lib/b.jar!/META-INF/MANIFEST.MF"}.LocalPath())
+	assert.Equal(t, "/data/Hello!/world.txt", NewCoordinates("/data/Hello!/world.txt", "").LocalPath(), "a separator in a real path is not an archive boundary")
+	assert.Equal(t, "/data/Hello!/world.txt", Coordinates{RealPath: "/data/Hello!/world.txt", FullPath: "/data/Hello!/world.txt"}.LocalPath())
+	assert.Equal(t, "/x.txt", Coordinates{RealPath: "/data/Hello!/a.zip", FullPath: "/data/Hello!/a.zip!/x.txt"}.LocalPath())
+	assert.Equal(t, "/x.txt", Coordinates{RealPath: "/data/Hello!/a.zip", FullPath: "/data/Hello!/a.zip!/b.jar!/x.txt"}.LocalPath())
+}
+
+func TestLocation_Path(t *testing.T) {
+	nested := Coordinates{RealPath: "/a.war", FullPath: "/a.war!/lib/b.jar!/META-INF/MANIFEST.MF"}
+	assert.Equal(t, "/a.jar", NewLocation("/a.jar").Path())
+	assert.Equal(t, "/link", NewVirtualLocation("/a.jar", "/link").Path())
+	assert.Equal(t, nested.FullPath, NewLocationFromCoordinates(nested).Path())
+	assert.Equal(t, nested.FullPath, Location{LocationData: LocationData{Coordinates: nested}}.Path(), "a nested location without an access path is still full")
+	assert.Equal(t, nested.FullPath, NewVirtualLocationFromCoordinates(nested, nested.FullPath).Path())
+}

syft/file/locations.go

@@ -83,7 +83,12 @@ func LocationSorter(layers []string) func(a, b Location) int { //nolint:gocognit
 			return strings.Compare(a.AccessPath, b.AccessPath)
 		}
 
-		return strings.Compare(a.RealPath, b.RealPath)
+		if a.RealPath != b.RealPath {
+			return strings.Compare(a.RealPath, b.RealPath)
+		}
+
+		// the same path in different archives is a different file
+		return strings.Compare(a.FullNestedPath(), b.FullNestedPath())
 	}
 }
 
@@ -118,6 +123,11 @@ func CoordinatesSorter(layers []string) func(a, b Coordinates) int {
 			}
 		}
 
-		return strings.Compare(a.RealPath, b.RealPath)
+		if a.RealPath != b.RealPath {
+			return strings.Compare(a.RealPath, b.RealPath)
+		}
+
+		// the same path in different archives is a different file
+		return strings.Compare(a.FullNestedPath(), b.FullNestedPath())
 	}
 }

syft/file/locations_test.go

@@ -6,6 +6,7 @@ import (
 	"testing"
 
 	"github.com/google/go-cmp/cmp"
+	"github.com/stretchr/testify/assert"
 
 	"github.com/anchore/syft/internal/evidence"
 )
@@ -555,3 +556,24 @@ func TestLocationAndCoordinatesSorters(t *testing.T) {
 		})
 	}
 }
+
+func TestSorters_fullPathBreaksTies(t *testing.T) {
+	// the same path in two archives must sort the same way whatever order the inputs arrive in, or
+	// output built from map iteration is not reproducible
+	a := Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/a.jar!/META-INF/MANIFEST.MF"}
+	b := Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/b.jar!/META-INF/MANIFEST.MF"}
+	want := []string{a.FullNestedPath(), b.FullNestedPath()}
+
+	for _, in := range [][]Coordinates{{a, b}, {b, a}} {
+		coords := slices.Clone(in)
+		slices.SortFunc(coords, CoordinatesSorter(nil))
+		assert.Equal(t, want, []string{coords[0].FullNestedPath(), coords[1].FullNestedPath()}, "CoordinatesSorter")
+
+		locs := []Location{NewLocationFromCoordinates(in[0]), NewLocationFromCoordinates(in[1])}
+		slices.SortFunc(locs, LocationSorter(nil))
+		assert.Equal(t, want, []string{locs[0].FullNestedPath(), locs[1].FullNestedPath()}, "LocationSorter")
+
+		got := NewCoordinateSet(in...).ToSlice()
+		assert.Equal(t, want, []string{got[0].FullNestedPath(), got[1].FullNestedPath()}, "CoordinateSet.ToSlice")
+	}
+}

syft/file/mock_resolver.go

@@ -60,9 +60,9 @@ func NewMockResolverForPathsWithMetadata(metadata map[Coordinates]Metadata) *Moc
 		l := NewLocationFromCoordinates(c)
 		locations = append(locations, l)
 		mimeTypeIndex[m.MIMEType] = append(mimeTypeIndex[m.MIMEType], l)
-		ext := path.Ext(l.RealPath)
+		ext := path.Ext(l.FullNestedPath())
 		extension[ext] = append(extension[ext], l)
-		bn := path.Base(l.RealPath)
+		bn := path.Base(l.FullNestedPath())
 		basename[bn] = append(basename[bn], l)
 	}
 
@@ -97,9 +97,9 @@ func NewMockResolverForMediaTypes(mediaTypes map[string][]Location) *MockResolve
 		mediaTypeIndex[mediaType] = append(mediaTypeIndex[mediaType], locs...)
 		for _, l := range locs {
 			locations = append(locations, l)
-			ext := path.Ext(l.RealPath)
+			ext := path.Ext(l.FullNestedPath())
 			extension[ext] = append(extension[ext], l)
-			bn := path.Base(l.RealPath)
+			bn := path.Base(l.FullNestedPath())
 			basename[bn] = append(basename[bn], l)
 		}
 	}
@@ -121,7 +121,7 @@ func (r MockResolver) ImageReference() string {
 // HasPath indicates if the given path exists in the underlying source.
 func (r MockResolver) HasPath(path string) bool {
 	for _, l := range r.locations {
-		if l.RealPath == path {
+		if l.FullNestedPath() == path {
 			return true
 		}
 	}
@@ -142,7 +142,7 @@ func (r MockResolver) FileContentsByLocation(location Location) (io.ReadCloser,
 		}
 	}
 
-	return nil, fmt.Errorf("no file for location: %v", location)
+	return nil, fmt.Errorf("no file for location: %q", location.FullNestedPath())
 }
 
 // FilesByPath returns all Locations that match the given paths.
@@ -150,7 +150,7 @@ func (r MockResolver) FilesByPath(paths ...string) ([]Location, error) {
 	var results []Location
 	for _, p := range paths {
 		for _, location := range r.locations {
-			if p == location.RealPath {
+			if p == location.LocalPath() {
 				results = append(results, NewLocation(p))
 			}
 		}
@@ -164,7 +164,7 @@ func (r MockResolver) FilesByGlob(patterns ...string) ([]Location, error) {
 	var results []Location
 	for _, pattern := range patterns {
 		for _, location := range r.locations {
-			matches, err := doublestar.Match(pattern, location.RealPath)
+			matches, err := doublestar.Match(pattern, location.LocalPath())
 			if err != nil {
 				return nil, err
 			}

syft/format/common/cyclonedxhelpers/to_format_model.go

@@ -14,6 +14,7 @@ import (
 	"github.com/anchore/syft/syft/artifact"
 	"github.com/anchore/syft/syft/cpe"
 	"github.com/anchore/syft/syft/file"
+	formatInternal "github.com/anchore/syft/syft/format/internal"
 	"github.com/anchore/syft/syft/format/internal/cyclonedxutil/helpers"
 	"github.com/anchore/syft/syft/linux"
 	"github.com/anchore/syft/syft/pkg"
@@ -42,7 +43,8 @@ func ToFormatModel(s sbom.SBOM) *cyclonedx.BOM {
 	cdxBOM.SerialNumber = uuid.New().URN()
 	cdxBOM.Metadata = toBomDescriptor(s.Descriptor.Name, s.Descriptor.Version, s.Source)
 
-	coordinates, locationSorter := getCoordinates(s)
+	locationSorter, coordinateSorter := formatInternal.GetLocationSorters(s)
+	top, entries := formatInternal.ArchiveEntries(s.AllCoordinates(), coordinateSorter)
 
 	// Packages
 	packages := s.Artifacts.Packages.Sorted()
@@ -52,40 +54,7 @@ func ToFormatModel(s sbom.SBOM) *cyclonedx.BOM {
 	}
 	components = append(components, toOSComponent(s.Artifacts.LinuxDistribution)...)
 
-	artifacts := s.Artifacts
-
-	for _, coordinate := range coordinates {
-		var metadata *file.Metadata
-		// File Info
-		fileMetadata, exists := artifacts.FileMetadata[coordinate]
-		// no file metadata then don't include in SBOM
-		// the syft config allows for sometimes only capturing files owned by packages
-		// so there can be a map miss here where we have less metadata than all coordinates
-		if !exists {
-			continue
-		}
-		if fileMetadata.Type == stfile.TypeDirectory ||
-			fileMetadata.Type == stfile.TypeSocket ||
-			fileMetadata.Type == stfile.TypeSymLink {
-			// skip dir, symlinks and sockets for the final bom
-			continue
-		}
-		metadata = &fileMetadata
-
-		// Digests
-		var digests []file.Digest
-		if digestsForLocation, exists := artifacts.FileDigests[coordinate]; exists {
-			digests = digestsForLocation
-		}
-
-		cdxHashes := digestsToHashes(digests)
-		components = append(components, cyclonedx.Component{
-			BOMRef: string(coordinate.ID()),
-			Type:   cyclonedx.ComponentTypeFile,
-			Name:   metadata.Path,
-			Hashes: &cdxHashes,
-		})
-	}
+	components = append(components, toFileComponents(s.Artifacts, entries, top)...)
 	cdxBOM.Components = &components
 
 	dependencies := toDependencies(s.Relationships)
@@ -96,19 +65,41 @@ func ToFormatModel(s sbom.SBOM) *cyclonedx.BOM {
 	return cdxBOM
 }
 
-func getCoordinates(s sbom.SBOM) ([]file.Coordinates, func(a, b file.Location) int) {
-	var layers []string
-	if m, ok := s.Source.Metadata.(source.ImageMetadata); ok {
-		for _, l := range m.Layers {
-			layers = append(layers, l.Digest)
+// toFileComponents describes each of coordinates that is a regular file with metadata, named by its path
+// (within its archive, for a file within one), with the files within it nested in its component.
+func toFileComponents(artifacts sbom.Artifacts, entries map[file.Coordinates][]file.Coordinates, coordinates []file.Coordinates) []cyclonedx.Component {
+	var components []cyclonedx.Component
+	for _, coordinate := range coordinates {
+		nested := toFileComponents(artifacts, entries, entries[coordinate])
+		// no file metadata then don't include in SBOM
+		// the syft config allows for sometimes only capturing files owned by packages
+		// so there can be a map miss here where we have less metadata than all coordinates
+		metadata, exists := artifacts.FileMetadata[coordinate]
+		if !isFileComponent(metadata, exists) && len(nested) == 0 {
+			continue
 		}
+
+		cdxHashes := digestsToHashes(artifacts.FileDigests[coordinate])
+		component := cyclonedx.Component{
+			BOMRef: string(coordinate.ID()),
+			Type:   cyclonedx.ComponentTypeFile,
+			Name:   coordinate.LocalPath(),
+			Hashes: &cdxHashes,
+		}
+		if len(nested) > 0 {
+			component.Components = &nested
+		}
+		components = append(components, component)
 	}
+	return components
+}
 
-	coordSorter := file.CoordinatesSorter(layers)
-	coordinates := s.AllCoordinates()
-
-	slices.SortFunc(coordinates, coordSorter)
-	return coordinates, file.LocationSorter(layers)
+// isFileComponent skips dirs, symlinks and sockets for the final bom
+func isFileComponent(metadata file.Metadata, exists bool) bool {
+	return exists &&
+		metadata.Type != stfile.TypeDirectory &&
+		metadata.Type != stfile.TypeSocket &&
+		metadata.Type != stfile.TypeSymLink
 }
 
 func digestsToHashes(digests []file.Digest) []cyclonedx.Hash {

syft/format/common/cyclonedxhelpers/to_format_model_test.go

@@ -608,3 +608,65 @@ func Test_toOSBomRef(t *testing.T) {
 		})
 	}
 }
+
+func Test_nestedArchiveFiles(t *testing.T) {
+	top := file.NewCoordinates("/etc/os-release", "")
+	inA := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/a.jar!/META-INF/MANIFEST.MF"}
+	inB := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/b.jar!/odd:na%me.txt"}
+	inWar := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/index.html"}
+	dir := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/c.jar!/META-INF"}
+	sha := []file.Digest{{Algorithm: "sha256", Value: "abc"}}
+	s := sbom.SBOM{Artifacts: sbom.Artifacts{
+		FileMetadata: map[file.Coordinates]file.Metadata{
+			// a directory resolver's metadata path is the path on the host, not the one scanned
+			top:   {Path: "/host/scan/etc/os-release"},
+			inA:   {},
+			inB:   {},
+			inWar: {},
+			dir:   {Type: stfile.TypeDirectory},
+		},
+		FileDigests: map[file.Coordinates][]file.Digest{inA: sha},
+	}}
+
+	bom := ToFormatModel(s)
+
+	type node struct {
+		Name     string
+		Children []node
+	}
+	var tree func(cs *[]cyclonedx.Component) []node
+	tree = func(cs *[]cyclonedx.Component) []node {
+		if cs == nil {
+			return nil
+		}
+		var out []node
+		for _, c := range *cs {
+			require.Equal(t, cyclonedx.ComponentTypeFile, c.Type)
+			out = append(out, node{Name: c.Name, Children: tree(c.Components)})
+		}
+		return out
+	}
+	// each archive holding a file is a component, synthesized when not otherwise described; an archive
+	// holding only skipped files is left out
+	assert.Equal(t, []node{
+		{Name: "/app.war", Children: []node{
+			{Name: "/WEB-INF/lib/a.jar", Children: []node{{Name: "/META-INF/MANIFEST.MF"}}},
+			{Name: "/WEB-INF/lib/b.jar", Children: []node{{Name: "/odd:na%me.txt"}}},
+			{Name: "/index.html"},
+		}},
+		{Name: "/etc/os-release"},
+	}, tree(bom.Components))
+
+	decoded, err := helpers.ToSyftModel(bom)
+	require.NoError(t, err)
+
+	war := file.NewCoordinates("/app.war", "")
+	a := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/a.jar"}
+	b := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/b.jar"}
+	var got []file.Coordinates
+	for c := range decoded.Artifacts.FileMetadata {
+		got = append(got, c)
+	}
+	assert.ElementsMatch(t, []file.Coordinates{top, war, a, b, inA, inB, inWar}, got)
+	assert.Equal(t, map[file.Coordinates][]file.Digest{inA: sha}, decoded.Artifacts.FileDigests)
+}

syft/format/common/spdxhelpers/to_format_model.go

@@ -6,6 +6,7 @@ import (
 	"crypto/sha1"
 	"fmt"
 	"path"
+	"path/filepath"
 	"slices"
 	"sort"
 	"strings"
@@ -53,7 +54,9 @@ func ToFormatModel(s sbom.SBOM) *spdx.Document {
 	rels := relationship.NewIndex(s.Relationships...)
 	packages, otherLicenses := toPackages(rels, s.Artifacts.Packages, s)
 
-	allRelationships := toRelationships(rels.All())
+	sourceFile := toSourceFile(s)
+	files, archiveRelationships := toFiles(s, sourceFile)
+	allRelationships := append(toRelationships(rels.All()), archiveRelationships...)
 
 	// for valid SPDX we need a document describes relationship
 	describesID := spdx.ElementID("DOCUMENT")
@@ -62,8 +65,7 @@ func ToFormatModel(s sbom.SBOM) *spdx.Document {
 	if rootPackage != nil {
 		describesID = rootPackage.PackageSPDXIdentifier
 
-		// add all relationships from the document root to all other packages
-		allRelationships = append(allRelationships, toRootRelationships(rootPackage, packages)...)
+		allRelationships = append(allRelationships, toRootRelationships(rootPackage, sourceFile, packages, files, allRelationships)...)
 
 		// append the root package
 		packages = append(packages, rootPackage)
@@ -155,25 +157,64 @@ func ToFormatModel(s sbom.SBOM) *spdx.Document {
 			CreatorComment: "",
 		},
 		Packages:      packages,
-		Files:         toFiles(s),
+		Files:         files,
 		Relationships: allRelationships,
 		OtherLicenses: convertOtherLicense(otherLicenses),
 	}
 }
 
-func toRootRelationships(rootPackage *spdx.Package, packages []*spdx.Package) (out []*spdx.Relationship) {
-	for _, p := range packages {
+// toRootRelationships relates the root package to every package, and to each file nothing else CONTAINS: what is
+// within an archive is reached only through the archive's file, and an owned file through its package. When the
+// source is itself a file, the root package DESCRIBES it, and a scanned directory CONTAINS those files instead. A
+// package containing files must have analyzed them, so the root package then gets a verification code over them.
+func toRootRelationships(rootPackage *spdx.Package, sourceFile *file.Coordinates, packages []*spdx.Package, files []*spdx.File, relationships []*spdx.Relationship) (out []*spdx.Relationship) {
+	contained := map[spdx.ElementID]struct{}{}
+	for _, r := range relationships {
+		if r.Relationship == string(helpers.ContainsRelationship) {
+			contained[r.RefB.ElementRefID] = struct{}{}
+		}
+	}
+	relate := func(a spdx.ElementID, typ helpers.RelationshipType, b spdx.ElementID) {
 		out = append(out, &spdx.Relationship{
-			RefA: spdx.DocElementID{
-				ElementRefID: rootPackage.PackageSPDXIdentifier,
-			},
-			Relationship: string(helpers.ContainsRelationship),
-			RefB: spdx.DocElementID{
-				ElementRefID: p.PackageSPDXIdentifier,
-			},
+			RefA:         spdx.DocElementID{ElementRefID: a},
+			Relationship: string(typ),
+			RefB:         spdx.DocElementID{ElementRefID: b},
 		})
 	}
-	return
+
+	fileContainer := rootPackage.PackageSPDXIdentifier
+	if sourceFile != nil {
+		id := toSPDXID(*sourceFile)
+		relate(rootPackage.PackageSPDXIdentifier, helpers.DescribesRelationship, id)
+		contained[id] = struct{}{}
+		if isScanRoot(*sourceFile) {
+			fileContainer = id
+		}
+	}
+
+	for _, p := range packages {
+		relate(rootPackage.PackageSPDXIdentifier, helpers.ContainsRelationship, p.PackageSPDXIdentifier)
+	}
+	var sha1s []string
+	for _, f := range files {
+		if _, has := contained[f.FileSPDXIdentifier]; has {
+			continue
+		}
+		relate(fileContainer, helpers.ContainsRelationship, f.FileSPDXIdentifier)
+		if fileContainer != rootPackage.PackageSPDXIdentifier {
+			continue
+		}
+		for _, c := range f.Checksums {
+			if c.Algorithm == spdx.SHA1 {
+				sha1s = append(sha1s, c.Value)
+				break
+			}
+		}
+	}
+
+	rootPackage.PackageVerificationCode = toVerificationCode(sha1s)
+	rootPackage.FilesAnalyzed = rootPackage.PackageVerificationCode != nil
+	return out
 }
 
 //nolint:funlen
@@ -355,7 +396,7 @@ func toSPDXID(identifiable artifact.Identifiable) spdx.ElementID {
 			return spdx.ElementID(helpers.SanitizeElementID(id))
 		}
 		p := ""
-		parts := strings.Split(it.RealPath, "/")
+		parts := strings.Split(it.FullNestedPath(), "/")
 		for i := len(parts); i > 0; i-- {
 			part := parts[i-1]
 			if len(part) == 0 {
@@ -663,8 +704,11 @@ func toRelationships(relationships []artifact.Relationship) (result []*spdx.Rela
 			continue
 		}
 
-		// FIXME: we are only currently including Package -> * relationships
-		if _, ok := r.From.(pkg.Package); !ok {
+		// FIXME: we are only currently including Package -> * relationships, plus an archive containing a
+		// package found inside it, which is the only structure nested archive cataloging records for
+		// non-java packages. Every file-side From is in the document: toFiles covers every coordinate a
+		// relationship names, and itself relates each archive to the files within it.
+		if _, ok := r.From.(pkg.Package); !ok && !isFileContainsPackage(r) {
 			log.Debugf("skipping non-package relationship: %+v", r)
 			continue
 		}
@@ -683,6 +727,12 @@ func toRelationships(relationships []artifact.Relationship) (result []*spdx.Rela
 	return result
 }
 
+func isFileContainsPackage(r artifact.Relationship) bool {
+	_, fromFile := r.From.(file.Coordinates)
+	_, toPkg := r.To.(pkg.Package)
+	return fromFile && toPkg && r.Type == artifact.ContainsRelationship
+}
+
 func lookupRelationship(ty artifact.RelationshipType) (bool, helpers.RelationshipType, string) {
 	switch ty {
 	case artifact.ContainsRelationship:
@@ -697,60 +747,60 @@ func lookupRelationship(ty artifact.RelationshipType) (bool, helpers.Relationshi
 	return false, "", ""
 }
 
-func toFiles(s sbom.SBOM) (results []*spdx.File) {
-	artifacts := s.Artifacts
+const layerIDCommentPrefix = "layerID: "
 
+// toFiles describes every file, including each archive holding one. A file within an archive is named by
+// its path in that archive, and the archive CONTAINS it.
+func toFiles(s sbom.SBOM, sourceFile *file.Coordinates) (results []*spdx.File, archiveRelationships []*spdx.Relationship) {
 	_, coordinateSorter := formatInternal.GetLocationSorters(s)
+	top, entries := formatInternal.ArchiveEntries(s.AllCoordinates(), coordinateSorter)
 
-	coordinates := s.AllCoordinates()
-	slices.SortFunc(coordinates, coordinateSorter)
-
-	for _, c := range coordinates {
-		var metadata *file.Metadata
-		if metadataForLocation, exists := artifacts.FileMetadata[c]; exists {
-			metadata = &metadataForLocation
+	// a file holding entries is an archive, whatever its content starts with (such as a launch script)
+	describe := func(c file.Coordinates, name string) *spdx.File {
+		f := toFile(s.Artifacts, c, name)
+		if len(entries[c]) > 0 {
+			f.FileTypes = withArchiveType(f.FileTypes)
 		}
+		return f
+	}
 
-		var digests []file.Digest
-		if digestsForLocation, exists := artifacts.FileDigests[c]; exists {
-			digests = digestsForLocation
+	var addEntries func(archive file.Coordinates)
+	addEntries = func(archive file.Coordinates) {
+		for _, c := range entries[archive] {
+			archiveRelationships = append(archiveRelationships, &spdx.Relationship{
+				RefA:         spdx.DocElementID{ElementRefID: toSPDXID(archive)},
+				Relationship: string(helpers.ContainsRelationship),
+				RefB:         spdx.DocElementID{ElementRefID: toSPDXID(c)},
+			})
+			results = append(results, describe(c, strings.TrimPrefix(c.LocalPath(), "/")))
+			addEntries(c)
 		}
-
-		// if we don't have any metadata or digests for this location
-		// then the file is most likely a symlink or non-regular file
-		// for now we include a 0 sha1 digest as requested by the spdx spec
-		// TODO: update location code in core SBOM so that we can map complex links
-		// back to their real file digest location.
-		if len(digests) == 0 {
-			digests = append(digests, file.Digest{Algorithm: "sha1", Value: "0000000000000000000000000000000000000000"})
-		}
-
-		// TODO: add file classifications (?) and content as a snippet
-
-		var comment string
-		if c.FileSystemID != "" {
-			comment = fmt.Sprintf("layerID: %s", c.FileSystemID)
-		}
-
-		relativePath, err := convertAbsoluteToRelative(c.RealPath)
+	}
+	for _, c := range top {
+		name, err := convertAbsoluteToRelative(c.RealPath)
 		if err != nil {
 			log.Debugf("unable to convert relative path '%s' to absolute path: %s", c.RealPath, err)
-			relativePath = c.RealPath
+			name = c.RealPath
 		}
-
-		results = append(results, &spdx.File{
-			FileSPDXIdentifier: toSPDXID(c),
-			FileComment:        comment,
-			// required, no attempt made to determine license information
-			LicenseConcluded:  noAssertion,
-			FileCopyrightText: noAssertion,
-			Checksums:         toFileChecksums(digests),
-			FileName:          relativePath,
-			FileTypes:         toFileTypes(metadata),
-			LicenseInfoInFiles: []string{ // required in SPDX 2.2
-				helpers.NOASSERTION,
-			},
-		})
+		var archive *source.FileMetadata
+		if isScanRoot(c) {
+			// the scanned root is the root package, unless it is the file the source is
+			if sourceFile == nil || c != *sourceFile {
+				continue
+			}
+			name = "."
+			if m, ok := s.Source.Metadata.(source.FileMetadata); ok {
+				archive = &m
+				name = filepath.Base(m.Path)
+			}
+		}
+		f := describe(c, name)
+		if archive != nil {
+			// an extracted archive is the archive file, not the directory it was extracted to
+			f.FileTypes = withArchiveType(toFileTypes(&file.Metadata{MIMEType: archive.MIMEType}))
+		}
+		results = append(results, f)
+		addEntries(c)
 	}
 
 	// sort by real path then virtual path to ensure the result is stable across multiple runs
@@ -760,7 +810,90 @@ func toFiles(s sbom.SBOM) (results []*spdx.File) {
 		}
 		return results[i].FileName < results[j].FileName
 	})
-	return results
+	return results, archiveRelationships
+}
+
+// toSourceFile finds the file the scanned source is: a directory, or an extracted archive, is the scanned root,
+// while a single file is indexed beside its parent directory, which was not scanned.
+func toSourceFile(s sbom.SBOM) *file.Coordinates {
+	var top []file.Coordinates
+	for _, c := range s.AllCoordinates() {
+		if c.FullNestedPath() == c.RealPath {
+			top = append(top, c)
+		}
+	}
+	match := isScanRoot
+	switch m := s.Source.Metadata.(type) {
+	case source.DirectoryMetadata:
+	case source.FileMetadata:
+		name := filepath.Base(m.Path)
+		single := func(c file.Coordinates) bool { return strings.TrimPrefix(c.RealPath, "/") == name }
+		if slices.ContainsFunc(top, single) {
+			match = single
+		}
+	default:
+		return nil
+	}
+	i := slices.IndexFunc(top, match)
+	if i < 0 {
+		return nil
+	}
+	return &top[i]
+}
+
+// withArchiveType adds the archive file type, in place of other
+func withArchiveType(types []string) []string {
+	if slices.Contains(types, string(helpers.ArchiveFileType)) {
+		return types
+	}
+	types = slices.DeleteFunc(types, func(t string) bool { return t == string(helpers.OtherFileType) })
+	return append(types, string(helpers.ArchiveFileType))
+}
+
+func isScanRoot(c file.Coordinates) bool {
+	return c.RealPath == "" || c.RealPath == "/"
+}
+
+func toFile(artifacts sbom.Artifacts, c file.Coordinates, name string) *spdx.File {
+	var metadata *file.Metadata
+	if metadataForLocation, exists := artifacts.FileMetadata[c]; exists {
+		metadata = &metadataForLocation
+	}
+
+	var digests []file.Digest
+	if digestsForLocation, exists := artifacts.FileDigests[c]; exists {
+		digests = digestsForLocation
+	}
+
+	// if we don't have any metadata or digests for this location
+	// then the file is most likely a symlink or non-regular file
+	// for now we include a 0 sha1 digest as requested by the spdx spec
+	// TODO: update location code in core SBOM so that we can map complex links
+	// back to their real file digest location.
+	if len(digests) == 0 {
+		digests = append(digests, file.Digest{Algorithm: "sha1", Value: "0000000000000000000000000000000000000000"})
+	}
+
+	// TODO: add file classifications (?) and content as a snippet
+
+	var comment string
+	if c.FileSystemID != "" {
+		comment = layerIDCommentPrefix + c.FileSystemID
+	}
+
+	return &spdx.File{
+		FileSPDXIdentifier: toSPDXID(c),
+		FileComment:        comment,
+		// required, no attempt made to determine license information
+		LicenseConcluded:  noAssertion,
+		FileCopyrightText: noAssertion,
+		Checksums:         toFileChecksums(digests),
+		FileName:          name,
+		FileTypes:         toFileTypes(metadata),
+		LicenseInfoInFiles: []string{ // required in SPDX 2.2
+			helpers.NOASSERTION,
+		},
+	}
 }
 
 func toFileChecksums(digests []file.Digest) (checksums []spdx.Checksum) {
@@ -836,7 +969,7 @@ func newPackageVerificationCode(rels *relationship.Index, p pkg.Package, sbom sb
 	// if a sha1 for a file is provided, then the validator will fail if the package does not have
 	// a package verification code
 	coordinates := rels.Coordinates(p, artifact.ContainsRelationship)
-	var digests []file.Digest
+	var sha1s []string
 	for _, c := range coordinates {
 		digest := sbom.Artifacts.FileDigests[c]
 		if len(digest) == 0 {
@@ -850,27 +983,23 @@ func newPackageVerificationCode(rels *relationship.Index, p pkg.Package, sbom sb
 				break
 			}
 		}
-		digests = append(digests, d)
+		sha1s = append(sha1s, d.Value)
 	}
+	return toVerificationCode(sha1s)
+}
 
-	if len(digests) == 0 {
+func toVerificationCode(sha1s []string) *spdx.PackageVerificationCode {
+	if len(sha1s) == 0 {
 		return nil
 	}
 
 	// sort templist in ascending order by SHA1 value
-	sort.SliceStable(digests, func(i, j int) bool {
-		return digests[i].Value < digests[j].Value
-	})
+	sort.Strings(sha1s)
 
 	// filelist = templist with "/n"s removed. /* ordered sequence of SHA1 values with no separators
-	var b strings.Builder
-	for _, digest := range digests {
-		b.WriteString(digest.Value)
-	}
-
 	//nolint:gosec
 	hasher := sha1.New()
-	_, _ = hasher.Write([]byte(b.String()))
+	_, _ = hasher.Write([]byte(strings.Join(sha1s, "")))
 	return &spdx.PackageVerificationCode{
 		// 7.9.1: Package Verification Code Value
 		// Cardinality: mandatory, one

syft/format/common/spdxhelpers/to_format_model_test.go

@@ -4,6 +4,7 @@ import (
 	"context"
 	"fmt"
 	"regexp"
+	"slices"
 	"strings"
 	"testing"
 
@@ -14,6 +15,7 @@ import (
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 
+	stfile "github.com/anchore/stereoscope/pkg/file"
 	"github.com/anchore/syft/internal/relationship"
 	"github.com/anchore/syft/internal/sourcemetadata"
 	"github.com/anchore/syft/syft/artifact"
@@ -556,7 +558,7 @@ func Test_toFiles(t *testing.T) {
 	tests := []struct {
 		name string
 		in   sbom.SBOM
-		want spdx.File
+		want []string
 	}{
 		{
 			name: "File paths are converted to relative in final SPDX collection",
@@ -584,16 +586,57 @@ func Test_toFiles(t *testing.T) {
 					},
 				},
 			},
-			want: spdx.File{
-				FileName: "some/path",
+			want: []string{"some/path"},
+		},
+		{
+			name: "the scanned root is the root package, not a file",
+			in: sbom.SBOM{Artifacts: sbom.Artifacts{FileMetadata: map[file.Coordinates]file.Metadata{
+				{RealPath: ""}:     {Type: stfile.TypeDirectory},
+				{RealPath: "/etc"}: {Type: stfile.TypeDirectory},
+			}}},
+			want: []string{"etc"},
+		},
+		{
+			name: "a scanned directory is a file",
+			in: sbom.SBOM{
+				Source: source.Description{Metadata: source.DirectoryMetadata{Path: "/dir"}},
+				Artifacts: sbom.Artifacts{FileMetadata: map[file.Coordinates]file.Metadata{
+					{RealPath: ""}:     {Type: stfile.TypeDirectory},
+					{RealPath: "/etc"}: {Type: stfile.TypeDirectory},
+				}},
 			},
+			want: []string{".", "etc"},
+		},
+		{
+			name: "a scanned file is indexed beside its parent directory, which was not scanned",
+			in: sbom.SBOM{
+				Source: source.Description{Metadata: source.FileMetadata{Path: "/dir/go.mod"}},
+				Artifacts: sbom.Artifacts{FileMetadata: map[file.Coordinates]file.Metadata{
+					{RealPath: ""}:        {Type: stfile.TypeDirectory},
+					{RealPath: "/go.mod"}: {Type: stfile.TypeRegular},
+				}},
+			},
+			want: []string{"go.mod"},
+		},
+		{
+			name: "the absolute root is the root package, not a file",
+			in: sbom.SBOM{Artifacts: sbom.Artifacts{FileMetadata: map[file.Coordinates]file.Metadata{
+				{RealPath: "/"}:    {Type: stfile.TypeDirectory},
+				{RealPath: "/etc"}: {Type: stfile.TypeDirectory},
+			}}},
+			want: []string{"etc"},
 		},
 	}
 
 	for _, test := range tests {
-		files := toFiles(test.in)
-		got := files[0]
-		assert.Equal(t, test.want.FileName, got.FileName)
+		t.Run(test.name, func(t *testing.T) {
+			files, _ := toFiles(test.in, toSourceFile(test.in))
+			var names []string
+			for _, f := range files {
+				names = append(names, f.FileName)
+			}
+			assert.Equal(t, test.want, names)
+		})
 	}
 }
 
@@ -762,10 +805,7 @@ func Test_fileIDsForPackage(t *testing.T) {
 		Name: "bogus",
 	}
 
-	c := file.Coordinates{
-		RealPath:     "/path",
-		FileSystemID: "nowhere",
-	}
+	c := file.NewCoordinates("/path", "nowhere")
 
 	docElementId := func(identifiable artifact.Identifiable) spdx.DocElementID {
 		return spdx.DocElementID{
@@ -824,7 +864,7 @@ func Test_fileIDsForPackage(t *testing.T) {
 			expected: nil,
 		},
 		{
-			name: "ignore file-to-package",
+			name: "include an archive file containing a package",
 			relationships: []artifact.Relationship{
 				{
 					From: c,
@@ -832,6 +872,23 @@ func Test_fileIDsForPackage(t *testing.T) {
 					Type: artifact.ContainsRelationship,
 				},
 			},
+			expected: []*spdx.Relationship{
+				{
+					Relationship: "CONTAINS",
+					RefA:         docElementId(c),
+					RefB:         docElementId(p),
+				},
+			},
+		},
+		{
+			name: "ignore other file-to-package",
+			relationships: []artifact.Relationship{
+				{
+					From: c,
+					To:   p,
+					Type: artifact.DependencyOfRelationship,
+				},
+			},
 			expected: nil,
 		},
 		{
@@ -1010,17 +1067,13 @@ func Test_toSPDXID(t *testing.T) {
 		expected string
 	}{
 		{
-			name: "short filename",
-			it: file.Coordinates{
-				RealPath: "/short/path/file.txt",
-			},
+			name:     "short filename",
+			it:       file.NewCoordinates("/short/path/file.txt", ""),
 			expected: "File-short-path-file.txt",
 		},
 		{
-			name: "long filename",
-			it: file.Coordinates{
-				RealPath: "/some/long/path/with/a/lot/of-text/that-contains-a/file.txt",
-			},
+			name:     "long filename",
+			it:       file.NewCoordinates("/some/long/path/with/a/lot/of-text/that-contains-a/file.txt", ""),
 			expected: "File-...a-lot-of-text-that-contains-a-file.txt",
 		},
 		{
@@ -1146,6 +1199,287 @@ func Test_otherLicenses(t *testing.T) {
 	}
 }
 
+func Test_nestedArchiveFiles(t *testing.T) {
+	top := file.NewCoordinates("/etc/os-release", "sha256:layer")
+	inA := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/a.jar!/META-INF/MANIFEST.MF", FileSystemID: "sha256:layer"}
+	inB := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/b.jar!/odd:na%me.txt", FileSystemID: "sha256:layer"}
+	owned := file.NewCoordinates("/usr/bin/tool", "sha256:layer")
+	a := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/a.jar", FileSystemID: "sha256:layer"}
+	war := file.NewCoordinates("/app.war", "sha256:layer")
+	b := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/b.jar", FileSystemID: "sha256:layer"}
+	topPkg := pkg.Package{Name: "top"}
+	topPkg.SetID()
+	nestedPkg := pkg.Package{Name: "nested"}
+	nestedPkg.SetID()
+
+	sources := []source.Description{
+		{Name: "img", Metadata: source.ImageMetadata{UserInput: "img:latest", ManifestDigest: "sha256:abc"}},
+		{Name: "dir", Metadata: source.DirectoryMetadata{Path: "/dir"}},
+	}
+	for _, src := range sources {
+		t.Run(src.Name, func(t *testing.T) {
+			s := sbom.SBOM{
+				Source: src,
+				Artifacts: sbom.Artifacts{
+					Packages:     pkg.NewCollection(topPkg, nestedPkg),
+					FileMetadata: map[file.Coordinates]file.Metadata{top: {}, inA: {}, inB: {}, owned: {}},
+				},
+				Relationships: []artifact.Relationship{
+					{From: topPkg, To: owned, Type: artifact.ContainsRelationship},
+					{From: a, To: nestedPkg, Type: artifact.ContainsRelationship},
+				},
+			}
+
+			doc := ToFormatModel(s)
+
+			// each archive holding a described file is described too, named by its path in its own container
+			names := map[spdx.ElementID]string{}
+			for _, f := range doc.Files {
+				names[f.FileSPDXIdentifier] = f.FileName
+				assert.Equal(t, "layerID: sha256:layer", f.FileComment)
+			}
+			assert.Equal(t, map[spdx.ElementID]string{
+				toSPDXID(top):   "etc/os-release",
+				toSPDXID(owned): "usr/bin/tool",
+				toSPDXID(war):   "app.war",
+				toSPDXID(a):     "WEB-INF/lib/a.jar",
+				toSPDXID(b):     "WEB-INF/lib/b.jar",
+				toSPDXID(inA):   "META-INF/MANIFEST.MF",
+				toSPDXID(inB):   "odd:na%me.txt",
+			}, names)
+
+			var described []spdx.ElementID
+			var contains [][2]spdx.ElementID
+			for _, r := range doc.Relationships {
+				switch r.Relationship {
+				case string(helpers.DescribesRelationship):
+					described = append(described, r.RefB.ElementRefID)
+				case string(helpers.ContainsRelationship):
+					contains = append(contains, [2]spdx.ElementID{r.RefA.ElementRefID, r.RefB.ElementRefID})
+				}
+			}
+			rootPkg := doc.Packages[len(doc.Packages)-1]
+			root := rootPkg.PackageSPDXIdentifier
+			assert.Equal(t, []spdx.ElementID{root}, described)
+
+			// the root contains every package, but only the files nothing else does: not what is within an archive,
+			// nor an owned file
+			assert.ElementsMatch(t, [][2]spdx.ElementID{
+				{root, toSPDXID(topPkg)},
+				{root, toSPDXID(nestedPkg)},
+				{root, toSPDXID(top)},
+				{root, toSPDXID(war)},
+				{toSPDXID(topPkg), toSPDXID(owned)},
+				{toSPDXID(a), toSPDXID(nestedPkg)},
+				{toSPDXID(war), toSPDXID(a)},
+				{toSPDXID(war), toSPDXID(b)},
+				{toSPDXID(a), toSPDXID(inA)},
+				{toSPDXID(b), toSPDXID(inB)},
+			}, contains)
+
+			// a package containing files must have analyzed them
+			assert.True(t, rootPkg.FilesAnalyzed)
+			assert.NotNil(t, rootPkg.PackageVerificationCode)
+
+			// other tools may instead have the document describe the top-level files directly
+			describesFiles := ToFormatModel(s)
+			for _, r := range describesFiles.Relationships {
+				if r.RefA.ElementRefID == root && (r.RefB.ElementRefID == toSPDXID(top) || r.RefB.ElementRefID == toSPDXID(war)) {
+					r.RefA.ElementRefID = "DOCUMENT"
+					r.Relationship = string(helpers.DescribesRelationship)
+				}
+			}
+
+			for _, d := range []struct {
+				name string
+				doc  *spdx.Document
+			}{
+				{name: "root contains files", doc: doc},
+				{name: "document describes files", doc: describesFiles},
+			} {
+				t.Run(d.name, func(t *testing.T) {
+					decoded, err := ToSyftModel(d.doc)
+					require.NoError(t, err)
+
+					assert.Equal(t, src.Name, decoded.Source.Name)
+					assert.IsType(t, src.Metadata, decoded.Source.Metadata)
+
+					// decoded paths are relative, as SPDX names are
+					relative := func(c file.Coordinates) file.Coordinates {
+						c.RealPath = strings.TrimPrefix(c.RealPath, "/")
+						c.FullPath = strings.TrimPrefix(c.FullPath, "/")
+						return c
+					}
+					var got []file.Coordinates
+					for c := range decoded.Artifacts.FileMetadata {
+						got = append(got, c)
+					}
+					assert.ElementsMatch(t, []file.Coordinates{relative(top), relative(owned), relative(war), relative(a), relative(b), relative(inA), relative(inB)}, got)
+
+					var gotContains []artifact.Relationship
+					for _, r := range decoded.Relationships {
+						_, fromFile := r.From.(file.Coordinates)
+						_, toFile := r.To.(file.Coordinates)
+						if fromFile && toFile {
+							gotContains = append(gotContains, r)
+						}
+					}
+					assert.ElementsMatch(t, []artifact.Relationship{
+						{From: relative(war), To: relative(a), Type: artifact.ContainsRelationship},
+						{From: relative(war), To: relative(b), Type: artifact.ContainsRelationship},
+						{From: relative(a), To: relative(inA), Type: artifact.ContainsRelationship},
+						{From: relative(b), To: relative(inB), Type: artifact.ContainsRelationship},
+					}, gotContains)
+				})
+			}
+		})
+	}
+}
+
+func Test_sourceFile(t *testing.T) {
+	root := file.NewCoordinates("", "")
+	war := file.NewCoordinates("/app.war", "")
+	jar := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/a.jar"}
+	etc := file.NewCoordinates("/etc/os-release", "")
+	p := pkg.Package{Name: "p"}
+	p.SetID()
+
+	tests := []struct {
+		name   string
+		source source.Description
+		files  []file.Coordinates
+		// relationships as "from type to", with the root package as "root"
+		want         []string
+		wantAnalyzed bool
+		// the file types of the file the root package describes
+		wantTypes []string
+		// decoded files, and the file relationships among them, as "from type to"
+		wantFiles    []string
+		wantContains []string
+	}{
+		{
+			name:   "a scanned directory is described, and contains what is at its root",
+			source: source.Description{Name: "dir", Metadata: source.DirectoryMetadata{Path: "/dir"}},
+			files:  []file.Coordinates{root, etc, war, jar},
+			want: []string{
+				"root DESCRIBES .",
+				"root CONTAINS p",
+				". CONTAINS etc/os-release",
+				". CONTAINS app.war",
+				"app.war CONTAINS a.jar",
+			},
+			// the scanned root decodes back to the scanned root, and holds nothing as an archive would
+			wantFiles:    []string{"", "etc/os-release", "app.war", "app.war!/a.jar"},
+			wantContains: []string{"app.war contains app.war!/a.jar"},
+		},
+		{
+			name:   "an extracted archive is described, and contains what is at its root",
+			source: source.Description{Name: "t.tar", Metadata: source.FileMetadata{Path: "/dir/t.tar"}},
+			files:  []file.Coordinates{root, etc},
+			want: []string{
+				"root DESCRIBES t.tar",
+				"root CONTAINS p",
+				"t.tar CONTAINS etc/os-release",
+			},
+			// the scanned root is the directory the archive was extracted to, but describes the archive
+			wantTypes: []string{"ARCHIVE"},
+			// the described archive is the scanned root, holding what is at the root
+			wantFiles: []string{"", "etc/os-release"},
+		},
+		{
+			name:   "an extracted archive takes its file types from its MIME type",
+			source: source.Description{Name: "t.zip", Metadata: source.FileMetadata{Path: "/dir/t.zip", MIMEType: "application/zip"}},
+			files:  []file.Coordinates{root, etc},
+			want: []string{
+				"root DESCRIBES t.zip",
+				"root CONTAINS p",
+				"t.zip CONTAINS etc/os-release",
+			},
+			wantTypes: []string{"APPLICATION", "ARCHIVE"},
+			wantFiles: []string{"", "etc/os-release"},
+		},
+		{
+			name:   "a scanned file is described, but not its parent directory",
+			source: source.Description{Name: "app.war", Metadata: source.FileMetadata{Path: "/dir/app.war"}},
+			files:  []file.Coordinates{root, war, jar},
+			want: []string{
+				"root DESCRIBES app.war",
+				"root CONTAINS p",
+				"app.war CONTAINS a.jar",
+			},
+			// an archive read in place is the scanned root too, so decodes as if it had been extracted
+			wantFiles: []string{"", "a.jar"},
+		},
+		{
+			name:   "without the scanned root, the root package contains what is at its root",
+			source: source.Description{Name: "dir", Metadata: source.DirectoryMetadata{Path: "/dir"}},
+			files:  []file.Coordinates{etc},
+			want: []string{
+				"root CONTAINS p",
+				"root CONTAINS etc/os-release",
+			},
+			wantAnalyzed: true,
+			wantFiles:    []string{"etc/os-release"},
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			metadata := map[file.Coordinates]file.Metadata{}
+			for _, c := range tt.files {
+				metadata[c] = file.Metadata{}
+			}
+			s := sbom.SBOM{
+				Source:    tt.source,
+				Artifacts: sbom.Artifacts{Packages: pkg.NewCollection(p), FileMetadata: metadata},
+			}
+
+			doc := ToFormatModel(s)
+
+			rootPkg := doc.Packages[len(doc.Packages)-1]
+			names := map[spdx.ElementID]string{rootPkg.PackageSPDXIdentifier: "root", toSPDXID(p): "p"}
+			for _, f := range doc.Files {
+				names[f.FileSPDXIdentifier] = f.FileName
+			}
+			var got []string
+			for _, r := range doc.Relationships {
+				if r.RefA.ElementRefID == "DOCUMENT" {
+					continue
+				}
+				got = append(got, names[r.RefA.ElementRefID]+" "+r.Relationship+" "+names[r.RefB.ElementRefID])
+			}
+			assert.ElementsMatch(t, tt.want, got)
+			assert.Equal(t, tt.wantAnalyzed, rootPkg.FilesAnalyzed)
+			if tt.wantTypes != nil {
+				for _, r := range doc.Relationships {
+					if r.RefA.ElementRefID == rootPkg.PackageSPDXIdentifier && r.Relationship == string(helpers.DescribesRelationship) {
+						i := slices.IndexFunc(doc.Files, func(f *spdx.File) bool { return f.FileSPDXIdentifier == r.RefB.ElementRefID })
+						require.GreaterOrEqual(t, i, 0)
+						assert.Equal(t, tt.wantTypes, doc.Files[i].FileTypes)
+					}
+				}
+			}
+
+			decoded, err := ToSyftModel(doc)
+			require.NoError(t, err)
+
+			var gotFiles []string
+			for c := range decoded.Artifacts.FileMetadata {
+				gotFiles = append(gotFiles, c.FullNestedPath())
+			}
+			assert.ElementsMatch(t, tt.wantFiles, gotFiles)
+
+			var gotContains []string
+			for _, r := range decoded.Relationships {
+				if from, ok := r.From.(file.Coordinates); ok {
+					to, _ := r.To.(file.Coordinates)
+					gotContains = append(gotContains, from.FullNestedPath()+" "+string(r.Type)+" "+to.FullNestedPath())
+				}
+			}
+			assert.ElementsMatch(t, tt.wantContains, gotContains)
+		})
+	}
+}
+
 func Test_toRootPackage_name(t *testing.T) {
 	tests := []struct {
 		name     string
@@ -1191,3 +1525,27 @@ func Test_toRootPackage_name(t *testing.T) {
 		})
 	}
 }
+
+func Test_toFiles_archiveType(t *testing.T) {
+	// a file holding entries is an archive, even when its content starts like something else, such as a Spring Boot
+	// executable jar's launch script
+	jar := file.NewCoordinates("/app.jar", "")
+	s := sbom.SBOM{Artifacts: sbom.Artifacts{FileMetadata: map[file.Coordinates]file.Metadata{
+		jar:                                   {MIMEType: "text/x-shellscript"},
+		file.NewCoordinates("/plain.zip", ""): {MIMEType: "application/zip"},
+		{RealPath: "/app.jar", FullPath: "/app.jar!/lib/b.jar!/c.txt"}: {MIMEType: "text/plain"},
+	}}}
+
+	files, _ := toFiles(s, nil)
+	got := map[string][]string{}
+	for _, f := range files {
+		got[f.FileName] = f.FileTypes
+	}
+	assert.Equal(t, map[string][]string{
+		"app.jar":   {"TEXT", "ARCHIVE"},
+		"plain.zip": {"APPLICATION", "ARCHIVE"},
+		// added only to hold its entry, with no metadata of its own
+		"lib/b.jar": {"ARCHIVE"},
+		"c.txt":     {"TEXT"},
+	}, got)
+}

syft/format/common/spdxhelpers/to_syft_model.go

@@ -38,6 +38,9 @@ func ToSyftModel(doc *spdx.Document) (*sbom.SBOM, error) {
 
 	spdxIDMap := make(map[string]any)
 
+	// found before the root package and its relationships are removed
+	sourceFile := findSourceFile(doc)
+
 	s := &sbom.SBOM{
 		Source: extractSource(spdxIDMap, doc),
 		Artifacts: sbom.Artifacts{
@@ -50,7 +53,7 @@ func ToSyftModel(doc *spdx.Document) (*sbom.SBOM, error) {
 
 	collectSyftPackages(s, spdxIDMap, doc)
 
-	collectSyftFiles(s, spdxIDMap, doc)
+	collectSyftFiles(s, spdxIDMap, doc, sourceFile)
 
 	s.Relationships = toSyftRelationships(spdxIDMap, doc)
 
@@ -379,26 +382,122 @@ func collectSyftPackages(s *sbom.SBOM, spdxIDMap map[string]any, doc *spdx.Docum
 	}
 }
 
-func collectSyftFiles(s *sbom.SBOM, spdxIDMap map[string]any, doc *spdx.Document) {
+// findSourceFile returns the file the root package DESCRIBES when it CONTAINS files: an archive scanned as the source
+// is the scanned root, so what it contains is at the root rather than within an archive.
+func findSourceFile(doc *spdx.Document) spdx.ElementID {
+	roots := findRootPackages(doc)
+	if len(roots) != 1 {
+		return ""
+	}
+	var described spdx.ElementID
+	containers := map[spdx.ElementID]bool{}
+	for _, r := range doc.Relationships {
+		switch helpers.RelationshipType(r.Relationship) {
+		case helpers.DescribesRelationship:
+			if r.RefA.ElementRefID == roots[0].PackageSPDXIdentifier {
+				described = r.RefB.ElementRefID
+			}
+		case helpers.ContainsRelationship:
+			containers[r.RefA.ElementRefID] = true
+		}
+	}
+	if !containers[described] {
+		return ""
+	}
+	return described
+}
+
+func collectSyftFiles(s *sbom.SBOM, spdxIDMap map[string]any, doc *spdx.Document, sourceFile spdx.ElementID) {
+	files := map[spdx.ElementID]*spdx.File{}
 	for _, p := range doc.Packages {
 		for _, f := range p.Files {
-			l := toSyftLocation(f)
-			spdxIDMap[string(f.FileSPDXIdentifier)] = l
+			files[f.FileSPDXIdentifier] = f
+		}
+	}
+	for _, f := range doc.Files {
+		files[f.FileSPDXIdentifier] = f
+	}
 
-			s.Artifacts.FileMetadata[l.Coordinates] = toFileMetadata(f)
-			s.Artifacts.FileDigests[l.Coordinates] = toFileDigests(f)
+	nested := newNestedFiles[spdx.ElementID]()
+	for id, f := range files {
+		nested.own[id] = toSyftCoordinates(f)
+	}
+	if c, ok := nested.own[sourceFile]; ok {
+		// the scanned root
+		c.RealPath = ""
+		nested.own[sourceFile] = c
+	}
+	for _, r := range doc.Relationships {
+		container, entry := r.RefA.ElementRefID, r.RefB.ElementRefID
+		switch helpers.RelationshipType(r.Relationship) {
+		case helpers.ContainsRelationship:
+		case helpers.ContainedByRelationship:
+			container, entry = entry, container
+		default:
+			continue
+		}
+		// the scanned root holds what is at the root, not within an archive
+		if files[container] != nil && files[entry] != nil && !isScanRoot(nested.own[container]) {
+			nested.container[entry] = container
 		}
 	}
 
-	for _, f := range doc.Files {
-		l := toSyftLocation(f)
-		spdxIDMap[string(f.FileSPDXIdentifier)] = l
+	for id, f := range files {
+		c, ok := nested.coordinates(id)
+		if !ok {
+			continue
+		}
+		l := file.NewLocationFromCoordinates(c)
+		spdxIDMap[string(id)] = l
 
 		s.Artifacts.FileMetadata[l.Coordinates] = toFileMetadata(f)
 		s.Artifacts.FileDigests[l.Coordinates] = toFileDigests(f)
 	}
 }
 
+// nestedFiles resolves the coordinates of files within archives, where an archive file CONTAINS a file
+// named by its path within the archive.
+type nestedFiles[K comparable] struct {
+	own       map[K]file.Coordinates
+	container map[K]K
+	resolved  map[K]file.Coordinates
+	refused   map[K]bool
+}
+
+func newNestedFiles[K comparable]() nestedFiles[K] {
+	return nestedFiles[K]{own: map[K]file.Coordinates{}, container: map[K]K{}, resolved: map[K]file.Coordinates{}, refused: map[K]bool{}}
+}
+
+// coordinates reports false for a file within a chain a scan would refuse (a bad name, too deep, too long), and
+// for everything within it. Such a file is dropped rather than moved, since no scan put it anywhere else.
+func (n nestedFiles[K]) coordinates(id K) (file.Coordinates, bool) {
+	// walk up to a resolved or outermost file, then resolve back down, so a long chain costs no stack
+	chain := []K{id}
+	for {
+		next, ok := n.container[chain[len(chain)-1]]
+		if _, resolved := n.resolved[chain[len(chain)-1]]; resolved || !ok {
+			break
+		}
+		// a containment cycle ends where it started
+		delete(n.container, chain[len(chain)-1])
+		chain = append(chain, next)
+	}
+	for i := len(chain) - 1; i >= 0; i-- {
+		if _, ok := n.resolved[chain[i]]; ok {
+			continue
+		}
+		c := n.own[chain[i]]
+		if i+1 < len(chain) {
+			container := chain[i+1]
+			nested, ok := internal.NestedCoordinates(n.resolved[container], c.RealPath)
+			n.refused[chain[i]] = !ok || n.refused[container]
+			c = nested
+		}
+		n.resolved[chain[i]] = c
+	}
+	return n.resolved[id], !n.refused[id]
+}
+
 func toFileDigests(f *spdx.File) (digests []file.Digest) {
 	for _, digest := range f.Checksums {
 		digests = append(digests, file.Digest{
@@ -452,6 +551,10 @@ func collectDocRelationships(spdxIDMap map[string]any, doc *spdx.Document) (out
 		}
 		a := spdxIDMap[string(r.RefA.ElementRefID)]
 		b := spdxIDMap[string(r.RefB.ElementRefID)]
+		if rel, ok := fileContainsRelationship(helpers.RelationshipType(r.Relationship), a, b); ok {
+			out = append(out, rel)
+			continue
+		}
 		from, fromOk := a.(pkg.Package)
 		toPackage, toPackageOk := b.(pkg.Package)
 		toLocation, toLocationOk := b.(file.Location)
@@ -505,6 +608,31 @@ func collectDocRelationships(spdxIDMap map[string]any, doc *spdx.Document) (out
 	return out
 }
 
+// fileContainsRelationship decodes an archive file containing a file or package within it.
+func fileContainsRelationship(typ helpers.RelationshipType, a, b any) (artifact.Relationship, bool) {
+	switch typ {
+	case helpers.ContainsRelationship:
+	case helpers.ContainedByRelationship:
+		a, b = b, a
+	default:
+		return artifact.Relationship{}, false
+	}
+	container, ok := a.(file.Location)
+	if !ok || isScanRoot(container.Coordinates) {
+		return artifact.Relationship{}, false
+	}
+	var entry artifact.Identifiable
+	switch to := b.(type) {
+	case file.Location:
+		entry = to.Coordinates
+	case pkg.Package:
+		entry = to
+	default:
+		return artifact.Relationship{}, false
+	}
+	return artifact.Relationship{From: container.Coordinates, To: entry, Type: artifact.ContainsRelationship}, true
+}
+
 // collectPackageFileRelationships add relationships for direct files
 func collectPackageFileRelationships(spdxIDMap map[string]any, doc *spdx.Document) (out []artifact.Relationship) {
 	for _, p := range doc.Packages {
@@ -530,23 +658,22 @@ func collectPackageFileRelationships(spdxIDMap map[string]any, doc *spdx.Documen
 }
 
 func toSyftCoordinates(f *spdx.File) file.Coordinates {
-	const layerIDPrefix = "layerID: "
-	var fileSystemID string
-	if strings.HasPrefix(f.FileComment, layerIDPrefix) {
-		fileSystemID = strings.TrimPrefix(f.FileComment, layerIDPrefix)
-	}
-	if strings.HasPrefix(string(f.FileSPDXIdentifier), layerIDPrefix) {
-		fileSystemID = strings.TrimPrefix(string(f.FileSPDXIdentifier), layerIDPrefix)
-	}
-	return file.Coordinates{
-		RealPath:     f.FileName,
-		FileSystemID: fileSystemID,
-	}
+	return coordinatesFromFile(f.FileName, f.FileComment, string(f.FileSPDXIdentifier))
 }
 
-func toSyftLocation(f *spdx.File) file.Location {
-	l := file.NewVirtualLocationFromCoordinates(toSyftCoordinates(f), f.FileName)
-	return l
+func coordinatesFromFile(name, comment, id string) file.Coordinates {
+	// the scanned root
+	if name == "." {
+		name = ""
+	}
+	c := file.NewCoordinates(name, "")
+	if v, ok := strings.CutPrefix(comment, layerIDCommentPrefix); ok {
+		c.FileSystemID = v
+	}
+	if v, ok := strings.CutPrefix(id, layerIDCommentPrefix); ok {
+		c.FileSystemID = v
+	}
+	return c
 }
 
 func requireAndTrimPrefix(val any, prefix string) string {

syft/format/common/spdxhelpers/to_syft_model_test.go

@@ -2,6 +2,7 @@ package spdxhelpers
 
 import (
 	"reflect"
+	"strings"
 	"testing"
 
 	"github.com/google/go-cmp/cmp"
@@ -12,6 +13,7 @@ import (
 	"github.com/stretchr/testify/require"
 
 	"github.com/anchore/packageurl-go"
+	"github.com/anchore/syft/internal/archive"
 	"github.com/anchore/syft/syft/artifact"
 	"github.com/anchore/syft/syft/file"
 	"github.com/anchore/syft/syft/pkg"
@@ -795,3 +797,24 @@ func Test_skipsPackagesWithGeneratedFromRelationship(t *testing.T) {
 	assert.NotNil(t, s.Artifacts.Packages.Package("1"))
 	assert.Nil(t, s.Artifacts.Packages.Package("1-src"))
 }
+
+func Test_nestedFiles_longChainIsCapped(t *testing.T) {
+	// a document can claim any chain; it decodes no deeper than a scan goes, without recursing per level, and
+	// what is past that is dropped
+	n := newNestedFiles[int]()
+	const length = 100_000
+	for i := range length {
+		n.own[i] = file.NewCoordinates("/a.jar", "")
+		if i > 0 {
+			n.container[i] = i - 1
+		}
+	}
+
+	for i := length - 1; i >= 0; i-- {
+		c, ok := n.coordinates(i)
+		assert.Equal(t, i <= archive.MaxDepth, ok, "%d", i)
+		if ok {
+			assert.Equal(t, "/a.jar"+strings.Repeat("!/a.jar", i), c.FullNestedPath())
+		}
+	}
+}

syft/format/common/spdxhelpers/to_syft_model_v3.go

@@ -31,6 +31,9 @@ func ToSyftModelV3(doc *spdx.Document) (*sbom.SBOM, error) {
 
 	spdxMap := ptrMap[any]{}
 
+	// found before the root package and its relationships are removed
+	sourceFile := v3findSourceFile(doc)
+
 	s := &sbom.SBOM{
 		Source: v3extractSource(spdxMap, doc),
 		Artifacts: sbom.Artifacts{
@@ -45,7 +48,7 @@ func ToSyftModelV3(doc *spdx.Document) (*sbom.SBOM, error) {
 
 	v3collectSyftPackages(s, spdxMap, relationships, doc)
 
-	v3collectSyftFiles(s, spdxMap, doc)
+	v3collectSyftFiles(s, spdxMap, doc, sourceFile)
 
 	s.Relationships = v3toSyftRelationships(spdxMap, doc)
 
@@ -282,21 +285,87 @@ func v3collectSyftPackages(s *sbom.SBOM, spdxMap ptrMap[any], relationships ptrM
 	}
 }
 
-func v3collectSyftFiles(s *sbom.SBOM, spdxMap ptrMap[any], doc *spdx.Document) {
-	found := ptrMap[struct{}]{}
+// v3findSourceFile returns the file the root package DESCRIBES when it CONTAINS files: an archive scanned as the
+// source is the scanned root, so what it contains is at the root rather than within an archive.
+func v3findSourceFile(doc *spdx.Document) spdx.AnyFile {
+	roots := v3findRootPackages(doc)
+	if len(roots) != 1 {
+		return nil
+	}
+	var described spdx.AnyFile
+	containers := ptrMap[bool]{}
+	for _, r := range doc.Elements.Relationships() {
+		from := r.GetFrom()
+		if from == nil {
+			continue
+		}
+		switch r.GetType() {
+		case spdx.RelationshipType_Describes:
+			if from == spdx.AnyElement(roots[0]) {
+				for _, to := range r.GetTo() {
+					if f, ok := to.(spdx.AnyFile); ok {
+						described = f
+					}
+				}
+			}
+		case spdx.RelationshipType_Contains:
+			containers.Set(from, true)
+		}
+	}
+	if described == nil || !containers.Get(described) {
+		return nil
+	}
+	return described
+}
+
+func v3collectSyftFiles(s *sbom.SBOM, spdxMap ptrMap[any], doc *spdx.Document, sourceFile spdx.AnyFile) {
+	nested := newNestedFiles[reflect.Value]()
+	var files []spdx.AnyFile
 	for _, elementList := range []spdx.ElementList{doc.Elements, doc.RootElements} {
 		for _, f := range elementList.Files() {
-			if found.Has(f) {
+			if _, found := nested.own[ptrTo(f)]; found {
 				continue
 			}
-			found.Set(f, struct{}{})
-			l := v3toSyftLocation(f)
-			spdxMap.Set(f, l)
-
-			s.Artifacts.FileMetadata[l.Coordinates] = v3toFileMetadata(f)
-			s.Artifacts.FileDigests[l.Coordinates] = v3toFileDigests(f)
+			nested.own[ptrTo(f)] = v3toSyftCoordinates(f)
+			files = append(files, f)
 		}
 	}
+	if sourceFile != nil {
+		if c, ok := nested.own[ptrTo(sourceFile)]; ok {
+			// the scanned root
+			c.RealPath = ""
+			nested.own[ptrTo(sourceFile)] = c
+		}
+	}
+	for _, r := range doc.Elements.Relationships() {
+		container, ok := r.GetFrom().(spdx.AnyFile)
+		if !ok || r.GetType() != spdx.RelationshipType_Contains {
+			continue
+		}
+		for _, to := range r.GetTo() {
+			entry, ok := to.(spdx.AnyFile)
+			if !ok {
+				continue
+			}
+			_, knownContainer := nested.own[ptrTo(container)]
+			_, knownEntry := nested.own[ptrTo(entry)]
+			if knownContainer && knownEntry && !isScanRoot(nested.own[ptrTo(container)]) {
+				nested.container[ptrTo(entry)] = ptrTo(container)
+			}
+		}
+	}
+
+	for _, f := range files {
+		c, ok := nested.coordinates(ptrTo(f))
+		if !ok {
+			continue
+		}
+		l := file.NewLocationFromCoordinates(c)
+		spdxMap.Set(f, l)
+
+		s.Artifacts.FileMetadata[l.Coordinates] = v3toFileMetadata(f)
+		s.Artifacts.FileDigests[l.Coordinates] = v3toFileDigests(f)
+	}
 }
 
 func v3toFileDigests(f spdx.AnyFile) (digests []file.Digest) {
@@ -341,6 +410,12 @@ func v3collectDocRelationships(spdxMap ptrMap[any], doc *spdx.Document) (out []a
 
 		for _, to := range r.GetTo() {
 			b := spdxMap.Get(to)
+			if r.GetType() == spdx.RelationshipType_Contains {
+				if rel, ok := fileContainsRelationship(helpers.ContainsRelationship, a, b); ok {
+					out = append(out, rel)
+					continue
+				}
+			}
 			from, fromOk := a.(pkg.Package)
 			toPackage, toPackageOk := b.(pkg.Package)
 			toLocation, toLocationOk := b.(file.Location)
@@ -393,23 +468,7 @@ func v3collectDocRelationships(spdxMap ptrMap[any], doc *spdx.Document) (out []a
 }
 
 func v3toSyftCoordinates(f spdx.AnyFile) file.Coordinates {
-	const layerIDPrefix = "layerID: "
-	var fileSystemID string
-	if strings.HasPrefix(f.GetComment(), layerIDPrefix) {
-		fileSystemID = strings.TrimPrefix(f.GetComment(), layerIDPrefix)
-	}
-	if strings.HasPrefix(f.GetID(), layerIDPrefix) {
-		fileSystemID = strings.TrimPrefix(f.GetID(), layerIDPrefix)
-	}
-	return file.Coordinates{
-		RealPath:     f.GetName(),
-		FileSystemID: fileSystemID,
-	}
-}
-
-func v3toSyftLocation(f spdx.AnyFile) file.Location {
-	l := file.NewVirtualLocationFromCoordinates(v3toSyftCoordinates(f), f.GetName())
-	return l
+	return coordinatesFromFile(f.GetName(), f.GetComment(), f.GetID())
 }
 
 func v3findQualifierValue(purl packageurl.PackageURL, qualifier string) string {

syft/format/common/spdxhelpers/to_syft_model_v3_test.go

@@ -193,14 +193,14 @@ func TestToSyftModelV3_documentConversion(t *testing.T) {
 	assert.Equal(t, "BSD-3-Clause AND GPL-2.0+", pkg2Concluded[0].Value)
 
 	// Verify files
-	coords1 := file.Coordinates{RealPath: "/src/main.go"}
+	coords1 := file.NewCoordinates("/src/main.go", "")
 	digests, ok := result.Artifacts.FileDigests[coords1]
 	require.True(t, ok, "file1 digests not found")
 	require.Len(t, digests, 1)
 	assert.Equal(t, "sha256", digests[0].Algorithm)
 	assert.Equal(t, "abc123", digests[0].Value)
 
-	coords2 := file.Coordinates{RealPath: "/src/util.go"}
+	coords2 := file.NewCoordinates("/src/util.go", "")
 	_, ok = result.Artifacts.FileMetadata[coords2]
 	assert.True(t, ok, "file2 metadata not found")
 
@@ -434,3 +434,44 @@ func Test_v3parseSPDXLicenses(t *testing.T) {
 	require.Len(t, declared, 1)
 	assert.Equal(t, "Apache-2.0 AND BSD-3-Clause", declared[0].Value)
 }
+
+func TestToSyftModelV3_nestedArchiveFiles(t *testing.T) {
+	war := &spdx.File{ID: "war", Name: "/app.war", Comment: "layerID: sha256:layer"}
+	jar := &spdx.File{ID: "jar", Name: "WEB-INF/lib/a.jar"}
+	manifest := &spdx.File{ID: "manifest", Name: "META-INF/MANIFEST.MF"}
+	p := &spdx.Package{ID: "pkg", Name: "a"}
+	warContainsJar := &spdx.Relationship{From: war, To: spdx.ElementList{jar}, Type: spdx.RelationshipType_Contains}
+	jarContains := &spdx.Relationship{From: jar, To: spdx.ElementList{manifest, p}, Type: spdx.RelationshipType_Contains}
+
+	doc := &spdx.Document{SpdxDocument: spdx.SpdxDocument{
+		Elements: spdx.ElementList{war, jar, manifest, p, warContainsJar, jarContains},
+	}}
+
+	s, err := ToSyftModelV3(doc)
+	require.NoError(t, err)
+
+	wantWar := file.NewCoordinates("/app.war", "sha256:layer")
+	wantJar := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/a.jar", FileSystemID: "sha256:layer"}
+	wantManifest := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/a.jar!/META-INF/MANIFEST.MF", FileSystemID: "sha256:layer"}
+	var got []file.Coordinates
+	for c := range s.Artifacts.FileMetadata {
+		got = append(got, c)
+	}
+	assert.ElementsMatch(t, []file.Coordinates{wantWar, wantJar, wantManifest}, got)
+
+	var fileRels []string
+	for _, r := range s.Relationships {
+		if from, ok := r.From.(file.Coordinates); ok {
+			to := "package"
+			if c, ok := r.To.(file.Coordinates); ok {
+				to = c.FullNestedPath()
+			}
+			fileRels = append(fileRels, from.FullNestedPath()+" "+string(r.Type)+" "+to)
+		}
+	}
+	assert.ElementsMatch(t, []string{
+		"/app.war contains /app.war!/WEB-INF/lib/a.jar",
+		"/app.war!/WEB-INF/lib/a.jar contains /app.war!/WEB-INF/lib/a.jar!/META-INF/MANIFEST.MF",
+		"/app.war!/WEB-INF/lib/a.jar contains package",
+	}, fileRels)
+}

syft/format/cyclonedxjson/encoder_test.go

@@ -114,6 +114,45 @@ func TestCycloneDxImageEncoder(t *testing.T) {
 	)
 }
 
+func TestCycloneDxSourcePackageEncoder(t *testing.T) {
+	dir := t.TempDir()
+	testutil.AssertEncoderAgainstGoldenSnapshot(t,
+		testutil.EncoderSnapshotTestConfig{
+			Subject:                     testutil.SourcePackagesInput(t, dir),
+			Format:                      getEncoder(t),
+			UpdateSnapshot:              *updateSnapshot,
+			PersistRedactionsInSnapshot: true,
+			IsJSON:                      true,
+			Redactor:                    redactor(dir),
+		},
+	)
+}
+
+func TestCycloneDxSourcePackageEncoder_SpecVersions(t *testing.T) {
+	s := testutil.SourcePackagesInput(t, t.TempDir())
+	tests := []struct {
+		version string
+		want    bool
+	}{
+		{version: "1.4", want: false},
+		{version: "1.5", want: false},
+		{version: "1.6", want: true},
+		{version: cyclonedxutil.DefaultVersion, want: true},
+	}
+	for _, tt := range tests {
+		t.Run(tt.version, func(t *testing.T) {
+			enc, err := NewFormatEncoderWithConfig(EncoderConfig{Version: tt.version})
+			require.NoError(t, err)
+
+			var buf bytes.Buffer
+			require.NoError(t, enc.Encode(&buf, s))
+
+			// the source-distribution reference type only exists from spec 1.6
+			assert.Equal(t, tt.want, strings.Contains(buf.String(), `"source-distribution"`))
+		})
+	}
+}
+
 func redactor(values ...string) testutil.Redactor {
 	return testutil.NewRedactions().
 		WithValuesRedacted(values...).

syft/format/cyclonedxjson/testdata/snapshot/TestCycloneDxSourcePackageEncoder.golden

@@ -0,0 +1,275 @@
+{
+  "$schema": "http://cyclonedx.org/schema/bom-1.7.schema.json",
+  "bomFormat": "CycloneDX",
+  "specVersion": "1.7",
+  "serialNumber": "urn:uuid:redacted",
+  "version": 1,
+  "metadata": {
+    "timestamp": "timestamp:redacted",
+    "tools": {
+      "components": [
+        {
+          "type": "application",
+          "author": "anchore",
+          "name": "syft",
+          "version": "v0.42.0-bogus"
+        }
+      ]
+    },
+    "component": {
+      "bom-ref": "redacted",
+      "type": "file",
+      "name": "some/path"
+    }
+  },
+  "components": [
+    {
+      "bom-ref": "pkg:deb/debian/attr@1%3A2.4.47-2%2Bb1?arch=amd64&distro=debian-12&package-id=5cc0e8979d7f5115&upstream=attr%401%3A2.4.47-2",
+      "type": "library",
+      "name": "attr",
+      "version": "1:2.4.47-2+b1",
+      "purl": "pkg:deb/debian/attr@1%3A2.4.47-2%2Bb1?arch=amd64&distro=debian-12&upstream=attr%401%3A2.4.47-2",
+      "externalReferences": [
+        {
+          "url": "pkg:deb/debian/attr@1%3A2.4.47-2?arch=source&distro=debian-12",
+          "type": "source-distribution"
+        }
+      ],
+      "properties": [
+        {
+          "name": "syft:package:foundBy",
+          "value": "dpkg-db-cataloger"
+        },
+        {
+          "name": "syft:package:type",
+          "value": "deb"
+        },
+        {
+          "name": "syft:package:metadataType",
+          "value": "dpkg-db-entry"
+        },
+        {
+          "name": "syft:location:0:path",
+          "value": "/var/lib/dpkg/status"
+        },
+        {
+          "name": "syft:metadata:installedSize",
+          "value": "0"
+        },
+        {
+          "name": "syft:metadata:source",
+          "value": "attr"
+        },
+        {
+          "name": "syft:metadata:sourceVersion",
+          "value": "1:2.4.47-2"
+        }
+      ]
+    },
+    {
+      "bom-ref": "pkg:rpm/centos/bind-export-libs@9.11.13-3.el8?arch=x86_64&distro=centos-8&epoch=32&package-id=6008fca05ca7b418&upstream=bind-9.11.13-3.el8.src.rpm",
+      "type": "library",
+      "name": "bind-export-libs",
+      "version": "32:9.11.13-3.el8",
+      "purl": "pkg:rpm/centos/bind-export-libs@9.11.13-3.el8?arch=x86_64&distro=centos-8&epoch=32&upstream=bind-9.11.13-3.el8.src.rpm",
+      "externalReferences": [
+        {
+          "url": "pkg:rpm/centos/bind@9.11.13-3.el8?arch=src&distro=centos-8&epoch=32",
+          "type": "source-distribution"
+        }
+      ],
+      "properties": [
+        {
+          "name": "syft:package:foundBy",
+          "value": "rpm-db-cataloger"
+        },
+        {
+          "name": "syft:package:type",
+          "value": "rpm"
+        },
+        {
+          "name": "syft:package:metadataType",
+          "value": "rpm-db-entry"
+        },
+        {
+          "name": "syft:location:0:path",
+          "value": "/var/lib/rpm/Packages"
+        },
+        {
+          "name": "syft:metadata:epoch",
+          "value": "32"
+        },
+        {
+          "name": "syft:metadata:release",
+          "value": "3.el8"
+        },
+        {
+          "name": "syft:metadata:size",
+          "value": "0"
+        },
+        {
+          "name": "syft:metadata:sourceRpm",
+          "value": "bind-9.11.13-3.el8.src.rpm"
+        }
+      ]
+    },
+    {
+      "bom-ref": "pkg:apk/alpine/busybox@1.35.0-r17?arch=x86_64&distro=alpine-3.16.3&package-id=aa74af1190de1c40",
+      "type": "library",
+      "name": "busybox",
+      "version": "1.35.0-r17",
+      "purl": "pkg:apk/alpine/busybox@1.35.0-r17?arch=x86_64&distro=alpine-3.16.3",
+      "properties": [
+        {
+          "name": "syft:package:foundBy",
+          "value": "apk-db-cataloger"
+        },
+        {
+          "name": "syft:package:type",
+          "value": "apk"
+        },
+        {
+          "name": "syft:package:metadataType",
+          "value": "apk-db-entry"
+        },
+        {
+          "name": "syft:location:0:path",
+          "value": "/lib/apk/db/installed"
+        },
+        {
+          "name": "syft:metadata:installedSize",
+          "value": "0"
+        },
+        {
+          "name": "syft:metadata:originPackage",
+          "value": "busybox"
+        },
+        {
+          "name": "syft:metadata:size",
+          "value": "0"
+        }
+      ]
+    },
+    {
+      "bom-ref": "pkg:alpm/arch/gcc-libs@13.2.1-3?arch=x86_64&distro=arch-rolling&package-id=58a2fcf749a9a3cc&upstream=gcc",
+      "type": "library",
+      "name": "gcc-libs",
+      "version": "13.2.1-3",
+      "purl": "pkg:alpm/arch/gcc-libs@13.2.1-3?arch=x86_64&distro=arch-rolling&upstream=gcc",
+      "properties": [
+        {
+          "name": "syft:package:foundBy",
+          "value": "alpm-db-cataloger"
+        },
+        {
+          "name": "syft:package:type",
+          "value": "alpm"
+        },
+        {
+          "name": "syft:package:metadataType",
+          "value": "alpm-db-entry"
+        },
+        {
+          "name": "syft:location:0:path",
+          "value": "/var/lib/pacman/local/gcc-libs-13.2.1-3/desc"
+        },
+        {
+          "name": "syft:metadata:architecture",
+          "value": "x86_64"
+        },
+        {
+          "name": "syft:metadata:basepackage",
+          "value": "gcc"
+        },
+        {
+          "name": "syft:metadata:package",
+          "value": "gcc-libs"
+        },
+        {
+          "name": "syft:metadata:size",
+          "value": "0"
+        },
+        {
+          "name": "syft:metadata:version",
+          "value": "13.2.1-3"
+        }
+      ]
+    },
+    {
+      "bom-ref": "pkg:apk/alpine/libc-utils@0.7.2-r3?arch=x86_64&distro=alpine-3.16.3&package-id=16a8c7b19fde6f4f&upstream=libc-dev",
+      "type": "library",
+      "name": "libc-utils",
+      "version": "0.7.2-r3",
+      "purl": "pkg:apk/alpine/libc-utils@0.7.2-r3?arch=x86_64&distro=alpine-3.16.3&upstream=libc-dev",
+      "properties": [
+        {
+          "name": "syft:package:foundBy",
+          "value": "apk-db-cataloger"
+        },
+        {
+          "name": "syft:package:type",
+          "value": "apk"
+        },
+        {
+          "name": "syft:package:metadataType",
+          "value": "apk-db-entry"
+        },
+        {
+          "name": "syft:location:0:path",
+          "value": "/lib/apk/db/installed"
+        },
+        {
+          "name": "syft:metadata:installedSize",
+          "value": "0"
+        },
+        {
+          "name": "syft:metadata:originPackage",
+          "value": "libc-dev"
+        },
+        {
+          "name": "syft:metadata:size",
+          "value": "0"
+        }
+      ]
+    },
+    {
+      "bom-ref": "pkg:deb/debian/libpam-runtime@1.5.2-6%2Bdeb12u1?arch=all&distro=debian-12&package-id=7b4ddc97df57aec4&upstream=pam",
+      "type": "library",
+      "name": "libpam-runtime",
+      "version": "1.5.2-6+deb12u1",
+      "purl": "pkg:deb/debian/libpam-runtime@1.5.2-6%2Bdeb12u1?arch=all&distro=debian-12&upstream=pam",
+      "externalReferences": [
+        {
+          "url": "pkg:deb/debian/pam@1.5.2-6%2Bdeb12u1?arch=source&distro=debian-12",
+          "type": "source-distribution"
+        }
+      ],
+      "properties": [
+        {
+          "name": "syft:package:foundBy",
+          "value": "dpkg-db-cataloger"
+        },
+        {
+          "name": "syft:package:type",
+          "value": "deb"
+        },
+        {
+          "name": "syft:package:metadataType",
+          "value": "dpkg-db-entry"
+        },
+        {
+          "name": "syft:location:0:path",
+          "value": "/var/lib/dpkg/status"
+        },
+        {
+          "name": "syft:metadata:installedSize",
+          "value": "0"
+        },
+        {
+          "name": "syft:metadata:source",
+          "value": "pam"
+        }
+      ]
+    }
+  ]
+}

syft/format/cyclonedxxml/encoder_test.go

@@ -87,6 +87,20 @@ func TestCycloneDxImageEncoder(t *testing.T) {
 	)
 }
 
+func TestCycloneDxSourcePackageEncoder(t *testing.T) {
+	dir := t.TempDir()
+	testutil.AssertEncoderAgainstGoldenSnapshot(t,
+		testutil.EncoderSnapshotTestConfig{
+			Subject:                     testutil.SourcePackagesInput(t, dir),
+			Format:                      getEncoder(t),
+			UpdateSnapshot:              *updateSnapshot,
+			PersistRedactionsInSnapshot: true,
+			IsJSON:                      false,
+			Redactor:                    redactor(dir),
+		},
+	)
+}
+
 func redactor(values ...string) testutil.Redactor {
 	return testutil.NewRedactions().
 		WithValuesRedacted(values...).

syft/format/cyclonedxxml/testdata/snapshot/TestCycloneDxSourcePackageEncoder.golden

@@ -0,0 +1,121 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<bom xmlns="http://cyclonedx.org/schema/bom/1.7" serialNumber="redacted" version="1">
+  <metadata>
+    <timestamp>redacted</timestamp>
+    <tools>
+      <components>
+        <component type="application">
+          <author>anchore</author>
+          <name>syft</name>
+          <version>v0.42.0-bogus</version>
+        </component>
+      </components>
+    </tools>
+    <component bom-ref="redacted" type="file">
+      <name>some/path</name>
+    </component>
+  </metadata>
+  <components>
+    <component bom-ref="pkg:deb/debian/attr@1%3A2.4.47-2%2Bb1?arch=amd64&amp;distro=debian-12&amp;package-id=5cc0e8979d7f5115&amp;upstream=attr%401%3A2.4.47-2" type="library">
+      <name>attr</name>
+      <version>1:2.4.47-2+b1</version>
+      <purl>pkg:deb/debian/attr@1%3A2.4.47-2%2Bb1?arch=amd64&amp;distro=debian-12&amp;upstream=attr%401%3A2.4.47-2</purl>
+      <externalReferences>
+        <reference type="source-distribution">
+          <url>pkg:deb/debian/attr@1%3A2.4.47-2?arch=source&amp;distro=debian-12</url>
+        </reference>
+      </externalReferences>
+      <properties>
+        <property name="syft:package:foundBy">dpkg-db-cataloger</property>
+        <property name="syft:package:type">deb</property>
+        <property name="syft:package:metadataType">dpkg-db-entry</property>
+        <property name="syft:location:0:path">/var/lib/dpkg/status</property>
+        <property name="syft:metadata:installedSize">0</property>
+        <property name="syft:metadata:source">attr</property>
+        <property name="syft:metadata:sourceVersion">1:2.4.47-2</property>
+      </properties>
+    </component>
+    <component bom-ref="pkg:rpm/centos/bind-export-libs@9.11.13-3.el8?arch=x86_64&amp;distro=centos-8&amp;epoch=32&amp;package-id=6008fca05ca7b418&amp;upstream=bind-9.11.13-3.el8.src.rpm" type="library">
+      <name>bind-export-libs</name>
+      <version>32:9.11.13-3.el8</version>
+      <purl>pkg:rpm/centos/bind-export-libs@9.11.13-3.el8?arch=x86_64&amp;distro=centos-8&amp;epoch=32&amp;upstream=bind-9.11.13-3.el8.src.rpm</purl>
+      <externalReferences>
+        <reference type="source-distribution">
+          <url>pkg:rpm/centos/bind@9.11.13-3.el8?arch=src&amp;distro=centos-8&amp;epoch=32</url>
+        </reference>
+      </externalReferences>
+      <properties>
+        <property name="syft:package:foundBy">rpm-db-cataloger</property>
+        <property name="syft:package:type">rpm</property>
+        <property name="syft:package:metadataType">rpm-db-entry</property>
+        <property name="syft:location:0:path">/var/lib/rpm/Packages</property>
+        <property name="syft:metadata:epoch">32</property>
+        <property name="syft:metadata:release">3.el8</property>
+        <property name="syft:metadata:size">0</property>
+        <property name="syft:metadata:sourceRpm">bind-9.11.13-3.el8.src.rpm</property>
+      </properties>
+    </component>
+    <component bom-ref="pkg:apk/alpine/busybox@1.35.0-r17?arch=x86_64&amp;distro=alpine-3.16.3&amp;package-id=aa74af1190de1c40" type="library">
+      <name>busybox</name>
+      <version>1.35.0-r17</version>
+      <purl>pkg:apk/alpine/busybox@1.35.0-r17?arch=x86_64&amp;distro=alpine-3.16.3</purl>
+      <properties>
+        <property name="syft:package:foundBy">apk-db-cataloger</property>
+        <property name="syft:package:type">apk</property>
+        <property name="syft:package:metadataType">apk-db-entry</property>
+        <property name="syft:location:0:path">/lib/apk/db/installed</property>
+        <property name="syft:metadata:installedSize">0</property>
+        <property name="syft:metadata:originPackage">busybox</property>
+        <property name="syft:metadata:size">0</property>
+      </properties>
+    </component>
+    <component bom-ref="pkg:alpm/arch/gcc-libs@13.2.1-3?arch=x86_64&amp;distro=arch-rolling&amp;package-id=58a2fcf749a9a3cc&amp;upstream=gcc" type="library">
+      <name>gcc-libs</name>
+      <version>13.2.1-3</version>
+      <purl>pkg:alpm/arch/gcc-libs@13.2.1-3?arch=x86_64&amp;distro=arch-rolling&amp;upstream=gcc</purl>
+      <properties>
+        <property name="syft:package:foundBy">alpm-db-cataloger</property>
+        <property name="syft:package:type">alpm</property>
+        <property name="syft:package:metadataType">alpm-db-entry</property>
+        <property name="syft:location:0:path">/var/lib/pacman/local/gcc-libs-13.2.1-3/desc</property>
+        <property name="syft:metadata:architecture">x86_64</property>
+        <property name="syft:metadata:basepackage">gcc</property>
+        <property name="syft:metadata:package">gcc-libs</property>
+        <property name="syft:metadata:size">0</property>
+        <property name="syft:metadata:version">13.2.1-3</property>
+      </properties>
+    </component>
+    <component bom-ref="pkg:apk/alpine/libc-utils@0.7.2-r3?arch=x86_64&amp;distro=alpine-3.16.3&amp;package-id=16a8c7b19fde6f4f&amp;upstream=libc-dev" type="library">
+      <name>libc-utils</name>
+      <version>0.7.2-r3</version>
+      <purl>pkg:apk/alpine/libc-utils@0.7.2-r3?arch=x86_64&amp;distro=alpine-3.16.3&amp;upstream=libc-dev</purl>
+      <properties>
+        <property name="syft:package:foundBy">apk-db-cataloger</property>
+        <property name="syft:package:type">apk</property>
+        <property name="syft:package:metadataType">apk-db-entry</property>
+        <property name="syft:location:0:path">/lib/apk/db/installed</property>
+        <property name="syft:metadata:installedSize">0</property>
+        <property name="syft:metadata:originPackage">libc-dev</property>
+        <property name="syft:metadata:size">0</property>
+      </properties>
+    </component>
+    <component bom-ref="pkg:deb/debian/libpam-runtime@1.5.2-6%2Bdeb12u1?arch=all&amp;distro=debian-12&amp;package-id=7b4ddc97df57aec4&amp;upstream=pam" type="library">
+      <name>libpam-runtime</name>
+      <version>1.5.2-6+deb12u1</version>
+      <purl>pkg:deb/debian/libpam-runtime@1.5.2-6%2Bdeb12u1?arch=all&amp;distro=debian-12&amp;upstream=pam</purl>
+      <externalReferences>
+        <reference type="source-distribution">
+          <url>pkg:deb/debian/pam@1.5.2-6%2Bdeb12u1?arch=source&amp;distro=debian-12</url>
+        </reference>
+      </externalReferences>
+      <properties>
+        <property name="syft:package:foundBy">dpkg-db-cataloger</property>
+        <property name="syft:package:type">deb</property>
+        <property name="syft:package:metadataType">dpkg-db-entry</property>
+        <property name="syft:location:0:path">/var/lib/dpkg/status</property>
+        <property name="syft:metadata:installedSize">0</property>
+        <property name="syft:metadata:source">pam</property>
+      </properties>
+    </component>
+  </components>
+</bom>

syft/format/github/internal/model/model.go

@@ -113,11 +113,7 @@ func toPath(s source.Description, p pkg.Package) string {
 	locations := p.Locations.ToSlice()
 	if len(locations) > 0 {
 		location := locations[0]
-		packagePath := location.RealPath
-		if location.AccessPath != "" {
-			packagePath = location.AccessPath
-		}
-		packagePath = strings.TrimPrefix(packagePath, "/")
+		packagePath := strings.TrimPrefix(location.Path(), "/")
 		switch metadata := s.Metadata.(type) {
 		case source.ImageMetadata:
 			image := strings.ReplaceAll(metadata.UserInput, ":/", "//")

syft/format/github/internal/model/model_test.go

@@ -41,30 +41,21 @@ func sbomFixture() sbom.SBOM {
 			Name:    "pkg-1",
 			Version: "1.0.1",
 			Locations: file.NewLocationSet(
-				file.NewLocationFromCoordinates(file.Coordinates{
-					RealPath:     "/usr/lib",
-					FileSystemID: "fsid-1",
-				}),
+				file.NewLocationFromCoordinates(file.NewCoordinates("/usr/lib", "fsid-1")),
 			),
 		},
 		{
 			Name:    "pkg-2",
 			Version: "2.0.2",
 			Locations: file.NewLocationSet(
-				file.NewLocationFromCoordinates(file.Coordinates{
-					RealPath:     "/usr/lib",
-					FileSystemID: "fsid-1",
-				}),
+				file.NewLocationFromCoordinates(file.NewCoordinates("/usr/lib", "fsid-1")),
 			),
 		},
 		{
 			Name:    "pkg-3",
 			Version: "3.0.3",
 			Locations: file.NewLocationSet(
-				file.NewLocationFromCoordinates(file.Coordinates{
-					RealPath:     "/etc",
-					FileSystemID: "fsid-1",
-				}),
+				file.NewLocationFromCoordinates(file.NewCoordinates("/etc", "fsid-1")),
 			),
 		},
 	} {