fix: unknowns, better full vs local path handling

Signed-off-by: Keith Zantow <kzantow@gmail.com>

internal/archive/extract.go

@@ -16,10 +16,13 @@ import (
 	"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 it can read, and
+// the limiter's bounds. It returns nil when the content is not an archive, ErrUnsupportedFormat when it
-// ErrDiskLimitReached when the archive's own bytes cannot be placed within the disk limit. The caller
+// is one that is not extracted, and ErrDiskLimitReached when the archive's own bytes cannot be placed
-// must Cleanup the result.
+// 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).
@@ -43,9 +46,9 @@ func Extract(ctx context.Context, r io.Reader, archiveCoordinates file.Coordinat
 	// the archive's own bytes are needed only until they are extracted and digested
 	defer release()
 
-	format := identifyFormat(ctx, path.Base(archiveCoordinates.LocalPath()), content)
+	format, err := identifyFormat(ctx, path.Base(archiveCoordinates.LocalPath()), content)
-	if format == nil {
+	if format == nil || err != nil {
-		return nil, nil
+		return nil, err
 	}
 
 	if err := resolver.extract(ctx, format, content, exclusions); err != nil {
@@ -81,20 +84,35 @@ func (r *Resolver) acquire(content io.Reader) (ReaderAtSeeker, func(), error) {
 // 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 {
+func identifyFormat(ctx context.Context, name string, content ReaderAtSeeker) (archives.Extractor, error) {
 	if _, err := content.Seek(0, io.SeekStart); err != nil {
-		return nil
+		return nil, nil
 	}
 	format, _, err := intFile.IdentifyArchive(ctx, name, content)
 	if err == nil {
 		if extractor := supportedExtractor(format); extractor != nil {
-			return extractor
+			return extractor, nil
 		}
 	}
 	if HasZipEndOfCentralDirectory(content) {
-		return archives.Zip{}
+		return archives.Zip{}, nil
 	}
-	return 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

internal/archive/extract_test.go

@@ -36,24 +36,32 @@ func Test_identifyFormat(t *testing.T) {
 		name        string
 		data        []byte
 		want        archives.Extractor
+		unsupported bool
 	}{
-		{"test.zip", zipBytes(t, sampleFiles), archives.Zip{}},
+		{"test.zip", zipBytes(t, sampleFiles), archives.Zip{}, false},
-		{"test.tar.gz", tarGzBytes(t, sampleFiles), archives.CompressedArchive{}},
+		{"test.tar.gz", tarGzBytes(t, sampleFiles), archives.CompressedArchive{}, false},
-		{"plain.txt", []byte("just text"), nil},
+		{"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},
+		{"test.7z", []byte("7z\xbc\xaf\x27\x1c\x00\x04"), nil, true},
-		{"test.rar", []byte("Rar!\x1a\x07\x01\x00"), nil},
+		{"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{}},
+		{"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},
+		{"app.jar", []byte("plain text, no central directory anywhere in it"), nil, false},
-		{"bundle", []byte("plain text, no central directory anywhere in it"), nil},
+		{"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{}},
+		{"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 := identifyFormat(ctx, tt.name, bytes.NewReader(tt.data))
+			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
@@ -227,7 +235,9 @@ func TestResolver_extract_excludedEntriesAreNeverStored(t *testing.T) {
 	r, _ := resolverIn(t, limiter.charge())
 	content := bytes.NewReader(data)
 
-	err := r.extract(context.Background(), identifyFormat(context.Background(), "test.zip", content), content,
+	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)
@@ -314,7 +324,7 @@ func TestExtract_aTruncatedStreamKeepsWhatWasRead(t *testing.T) {
 	assert.Error(t, extracted.Truncated)
 	locations, err := extracted.FilesByGlob("**")
 	require.NoError(t, err)
-	assert.Equal(t, []string{"a.txt"}, localPaths(locations))
+	assert.Equal(t, []string{"/a.txt"}, localPaths(locations))
 }
 
 func TestExtract_aPanicStillReleasesEverything(t *testing.T) {
@@ -536,7 +546,7 @@ func TestExtract_locationsKeepTheTopLevelRealPath(t *testing.T) {
 		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())
+		assert.Equal(t, "/dir/hello.txt", locations[0].LocalPath())
 
 		for _, loc := range []file.Location{
 			locations[0],

internal/archive/helpers_test.go

@@ -109,6 +109,16 @@ func zipFromEntries(t testing.TB, entries []testEntry) []byte {
 	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))
 }
@@ -216,7 +226,8 @@ func extractBytes(t testing.TB, data []byte, name string, charge *charge) (*Reso
 	t.Helper()
 	r, root := resolverIn(t, charge)
 	content := bytes.NewReader(data)
-	format := identifyFormat(context.Background(), name, content)
+	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

internal/archive/resolver.go

@@ -9,6 +9,7 @@ import (
 	"io/fs"
 	"os"
 	"path"
+	"slices"
 	"sort"
 	"strings"
 	"time"
@@ -234,19 +235,39 @@ func entryPath(rooted string) string {
 
 // 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() + "!/" + entryPath(rooted)
+	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) is taken as archive-relative
 // already. The archive's full path with a trailing "!" (what path.Dir gives for an entry at the root)
-// names 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 {
+func (r *Resolver) rootedPath(userPath string) (string, bool) {
-	archivePath := r.archiveCoordinates.FullNestedPath() + "!"
+	if rest, ok := strings.CutPrefix(userPath, r.archiveCoordinates.FullNestedPath()); ok {
-	if userPath == archivePath {
+		if rest == file.ArchivePathSeparator[:1] {
-		return "/"
+			return "/", true
 		}
-	return path.Clean("/" + strings.TrimPrefix(userPath, archivePath+"/"))
+		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
+	}
+	if !strings.HasPrefix(userPath, "/") {
+		userPath = "/" + userPath
+	}
+	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
@@ -272,7 +293,11 @@ func (r *Resolver) location(res stereoscopeFile.Resolution) file.Location {
 // 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) {
-	res, err := r.search.SearchByPath(r.rootedPath(userPath), filetree.FollowBasenameLinks)
+	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
 	}
@@ -292,7 +317,10 @@ func (r *Resolver) FileContentsByLocation(location file.Location) (io.ReadCloser
 }
 
 func (r *Resolver) FileMetadataByLocation(location file.Location) (file.Metadata, error) {
-	rooted := r.rootedPath(location.FullNestedPath())
+	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())
@@ -311,18 +339,19 @@ func (r *Resolver) FileMetadataByLocation(location file.Location) (file.Metadata
 }
 
 func (r *Resolver) HasPath(userPath string) bool {
-	return r.tree.HasPath(stereoscopeFile.Path(r.rootedPath(userPath)))
+	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
-	seen := stereoscopeFile.NewFileReferenceSet()
+	var seen []stereoscopeFile.ID // few paths are asked for at once
 	for _, userPath := range paths {
 		res, ok := r.resolve(userPath)
-		if !ok || seen.Contains(*res.Reference) {
+		if !ok || slices.Contains(seen, res.ID()) {
 			continue
 		}
-		seen.Add(*res.Reference)
+		seen = append(seen, res.ID())
 		out = append(out, r.location(*res))
 	}
 	return out, nil
@@ -332,7 +361,11 @@ func (r *Resolver) FilesByGlob(patterns ...string) ([]file.Location, error) {
 	var out []file.Location
 	seen := stereoscopeFile.NewFileReferenceSet()
 	for _, pattern := range patterns {
-		results, err := r.searchByGlob(r.rootedPath(pattern))
+		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)
 		}
@@ -387,7 +420,7 @@ func (r *Resolver) FilesByMIMEType(types ...string) ([]file.Location, error) {
 	return out, nil
 }
 
-// RelativeFileByPath resolves against the archive root, the only frame an archive has.
+// 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 {

internal/archive/resolver_test.go

@@ -113,6 +113,34 @@ func TestResolver_pathsAndContents(t *testing.T) {
 	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",
@@ -121,7 +149,7 @@ func TestResolver_mimeTypesAreSniffedFromContent(t *testing.T) {
 
 	locations, err := r.FilesByMIMEType("text/x-shellscript")
 	require.NoError(t, err)
-	assert.Equal(t, []string{"run.sh"}, localPaths(locations))
+	assert.Equal(t, []string{"/run.sh"}, localPaths(locations))
 }
 
 func TestResolver_answersAreOrdered(t *testing.T) {
@@ -187,11 +215,11 @@ func TestResolver_globsForADirectorysChildren(t *testing.T) {
 		"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{"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/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/*"))
+	assert.Equal(t, []string{"/META-INF/maven/g/a/pom.xml"}, globPaths(t, r, "**/a/*"))
 }
 
 func TestResolver_invalidGlobIsAnError(t *testing.T) {
@@ -226,7 +254,7 @@ func TestResolver_linksCollapseToOnePath(t *testing.T) {
 				{name: "opt/hard.jar", link: "opt/real.jar", hard: true},
 			},
 			pattern: "**/*.jar",
-			want:    []string{"opt/real.jar"},
+			want:    []string{"/opt/real.jar"},
 			reason:  "one file, so one location - and it is named by the path that holds it",
 		},
 		{
@@ -238,7 +266,7 @@ func TestResolver_linksCollapseToOnePath(t *testing.T) {
 				{name: "opt/m-sym.jar", link: "real.bin"},
 			},
 			pattern: "**/*.jar",
-			want:    []string{"opt/real.bin"},
+			want:    []string{"/opt/real.bin"},
 			reason:  "the content is the target's, so that is the real path the answer carries",
 		},
 		{
@@ -249,7 +277,7 @@ func TestResolver_linksCollapseToOnePath(t *testing.T) {
 				{name: "opt/one-sym.jar", link: "one.jar"},
 			},
 			pattern: "**/*.jar",
-			want:    []string{"opt/one.jar", "opt/two.jar"},
+			want:    []string{"/opt/one.jar", "/opt/two.jar"},
 			reason:  "collapsing is per file, not per pattern",
 		},
 		{
@@ -259,7 +287,7 @@ func TestResolver_linksCollapseToOnePath(t *testing.T) {
 				{name: "opt/gone.jar", link: "missing.jar"},
 			},
 			pattern: "**/*.jar",
-			want:    []string{"opt/real.jar"},
+			want:    []string{"/opt/real.jar"},
 			reason:  "it names no content",
 		},
 		{
@@ -280,7 +308,7 @@ func TestResolver_linksCollapseToOnePath(t *testing.T) {
 				{name: "opt/outer.jar", link: "mid.jar"},
 			},
 			pattern: "**/*.jar",
-			want:    []string{"opt/real.jar"},
+			want:    []string{"/opt/real.jar"},
 			reason:  "following one hop at a time reaches the same file from every path",
 		},
 		{
@@ -300,7 +328,7 @@ func TestResolver_linksCollapseToOnePath(t *testing.T) {
 				{name: "opt/nested/hard.jar", link: "opt/real.jar", hard: true},
 			},
 			pattern: "**/*.jar",
-			want:    []string{"opt/real.jar"},
+			want:    []string{"/opt/real.jar"},
 			reason:  "read as relative it would resolve to opt/nested/opt/real.jar and dangle",
 		},
 	}
@@ -324,7 +352,7 @@ func TestResolver_collapsedLocationReadsTheTarget(t *testing.T) {
 	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, "/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])
@@ -367,7 +395,7 @@ func TestResolver_danglingLinkHasNoContent(t *testing.T) {
 		locations = append(locations, l)
 	}
 	require.Len(t, locations, 1)
-	assert.Equal(t, "opt/gone.jar", locations[0].LocalPath())
+	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")
@@ -394,12 +422,12 @@ func TestResolver_mimeTypeAnswersOnlyWithFiles(t *testing.T) {
 		return localPaths(locations)
 	}
 
-	assert.Equal(t, []string{"opt/real.jar"}, byMIME("application/zip"),
+	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.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"))
+	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
@@ -415,7 +443,7 @@ func TestResolver_allLocationsKeepsEveryPath(t *testing.T) {
 	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,
+	assert.Equal(t, []string{"/opt/gone.jar", "/opt/real.jar", "/opt/sym.jar"}, got,
 		"every path the archive names, links included")
 }
 
@@ -437,7 +465,7 @@ func TestResolver_add_anEntryOverTheCapIsSkippedAndReadNoFurther(t *testing.T) {
 	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))
+	assert.Equal(t, []string{"/ok.txt"}, localPaths(locations))
 }
 
 type countingReader struct {

internal/archive/traversal.go

@@ -2,6 +2,8 @@ package archive
 
 import (
 	"context"
+	"path"
+	"slices"
 	"strings"
 
 	"github.com/anchore/syft/syft/file"
@@ -30,6 +32,52 @@ type Traversal struct {
 	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
+	}
+	if !strings.HasPrefix(entryPath, "/") {
+		entryPath = "/" + entryPath
+	}
+	// cleaning an already clean path allocates nothing
+	return containerPath + file.ArchivePathSeparator + path.Clean(entryPath)[1:]
+}
+
+// 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 {
@@ -75,7 +123,10 @@ func VirtualPath(loc file.Location) string {
 		return accessPath
 	}
 	segments := strings.Split(entries, file.ArchivePathSeparator)
-	segments[len(segments)-1] = strings.TrimPrefix(accessPath, ContainerPath(loc.Coordinates)+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), "/")
 	}
@@ -85,6 +136,9 @@ func VirtualPath(loc file.Location) string {
 var entryPathEscaper = strings.NewReplacer("%", "%25", ":", "%3A")
 
 func escapeEntryPath(p string) string {
+	if !strings.ContainsAny(p, "%:") {
+		return p
+	}
 	return entryPathEscaper.Replace(p)
 }
 

internal/task/archive_tasks.go

@@ -30,27 +30,33 @@ import (
 
 const ArchiveCatalogerTaskName = "archive-cataloger"
 
-// NewArchiveCatalogerTask returns a task that extracts every archive it finds, runs subPipeline
+// 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
+// against the archive's contents as a standalone filesystem, and records
-// from the archive to what was found inside it. It recurses into the archives it extracts up to
+// CONTAINS relationships from the archive to what was found inside it. It recurses into the archives
-// cfg.MaxDepth; the task drops itself from subPipeline so that is the only recursion.
+// 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 means as deep as unboundedArchiveDepth).
-func NewArchiveCatalogerTask(cfg cataloging.ArchiveSearchConfig, subPipeline []Task, exclusions []string) Task {
+func NewArchiveCatalogerTask(cfg cataloging.ArchiveSearchConfig, unknowns cataloging.UnknownsConfig, pkgTasks, fileTasks []Task, exclusions []string) Task {
-	return newArchiveCatalogerTask(cfg.MaxDepth, archiveLimits(cfg), subPipeline, exclusions)
+	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, subPipeline []Task, exclusions []string) Task {
+func newArchiveCatalogerTask(maxDepth int, limits archive.Limits, reportUnsupportedUnknowns bool, pkgTasks, fileTasks []Task, exclusions []string) Task {
 	if maxDepth == 0 {
 		return nil
 	}
-	subPipeline = withoutArchiveCataloger(subPipeline)
+	pkgTasks, fileTasks = withoutArchiveCataloger(pkgTasks), withoutArchiveCataloger(fileTasks)
-	if len(subPipeline) == 0 {
+	if len(pkgTasks)+len(fileTasks) == 0 {
 		return nil
 	}
 
@@ -60,7 +66,9 @@ func newArchiveCatalogerTask(maxDepth int, limits archive.Limits, subPipeline []
 
 		c := &archiveCataloger{
 			maxDepth:                  maxDepth,
-			subPipeline: subPipeline,
+			reportUnsupportedUnknowns: reportUnsupportedUnknowns,
+			pkgTasks:                  pkgTasks,
+			fileTasks:                 fileTasks,
 			limiter:                   archive.NewLimiter(limits),
 			exclusions:                archive.NewExclusions(exclusions),
 			progress:                  bus.StartCatalogerTask(ctx, archiveCatalogerProgressInfo(), -1, ""),
@@ -97,7 +105,9 @@ func withoutArchiveCataloger(tasks []Task) []Task {
 
 type archiveCataloger struct {
 	maxDepth                  int
-	subPipeline []Task
+	reportUnsupportedUnknowns bool
+	pkgTasks                  []Task
+	fileTasks                 []Task
 	limiter                   *archive.Limiter
 	exclusions                archive.Exclusions
 
@@ -164,6 +174,9 @@ func (c *archiveCataloger) catalogCandidates(ctx context.Context, resolver file.
 	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() {
@@ -200,6 +213,12 @@ func (c *archiveCataloger) processArchive(ctx context.Context, parentResolver fi
 	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")
@@ -233,18 +252,33 @@ func (c *archiveCataloger) processArchive(ctx context.Context, parentResolver fi
 	ctx = archive.WithTraversal(ctx, traversal)
 
 	c.progress.Increment()
-	scratch := c.runSubPipeline(ctx, extracted, location.Coordinates)
-	traversal.Packages = packagesAt(scratch, location.Coordinates)
-	children := c.discoverArchives(extracted)
-	mergeArchiveResults(location.Coordinates, archivePath, children, scratch, builder)
-	c.progress.AtomicStage.Set(fmt.Sprintf("%s archives (%s)", humanize.Comma(c.progress.Current()), archivePath))
 
-	// self time stops before descending, so a containing archive is not charged for what it contains
+	// everything found in this archive and the archives nested in it, merged into the parent's SBOM once complete
-	if took := time.Since(started); took > c.slowest {
+	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
+	children := c.discoverArchives(extracted)
+	errs := c.catalogCandidates(ctx, extracted, children, depth+1, foundBuilder)
+
+	started = time.Now()
+	runArchiveTasks(ctx, c.fileTasks, extracted, location.Coordinates, foundBuilder)
+	addContains(location.Coordinates, archivePath, direct, children, found)
+	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 c.catalogCandidates(ctx, extracted, children, depth+1, builder)
+	return errs
 }
 
 // a top-level archive and everything nested in it may decompress to archiveTreeRatio times its size, or
@@ -273,30 +307,37 @@ func (c *archiveCataloger) isAncestor(digests []file.Digest) bool {
 }
 
 // packagesAt returns the packages located at the given coordinates, i.e. those describing the file there.
-func packagesAt(s *sbom.SBOM, coordinates file.Coordinates) []pkg.Package {
+func packagesAt(pkgs []pkg.Package, coordinates file.Coordinates) []pkg.Package {
 	var out []pkg.Package
-	for _, p := range s.Artifacts.Packages.Sorted() {
+	for _, p := range pkgs {
-		if p.Locations.CoordinateSet().Contains(coordinates) {
+		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)}})
 }
 
-// runSubPipeline runs every task against the resolver into a throwaway SBOM, so results can be
+// runArchiveTasks runs each task against the archive's contents.
-// attributed to the containing archive before merging into the shared SBOM.
 //
 // 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 (c *archiveCataloger) runSubPipeline(ctx context.Context, resolver file.Resolver, archiveCoordinates file.Coordinates) *sbom.SBOM {
+func runArchiveTasks(ctx context.Context, tasks []Task, resolver file.Resolver, archiveCoordinates file.Coordinates, builder sbomsync.Builder) {
-	scratch := &sbom.SBOM{Artifacts: sbom.Artifacts{Packages: pkg.NewCollection()}}
+	for _, t := range tasks {
-	scratchBuilder := sbomsync.NewBuilder(scratch)
+		err := runSubTaskSafely(ctx, t, resolver, builder)
-	for _, t := range c.subPipeline {
-		err := runSubTaskSafely(ctx, t, resolver, scratchBuilder)
 		if err == nil {
 			continue
 		}
@@ -306,9 +347,8 @@ func (c *archiveCataloger) runSubPipeline(ctx context.Context, resolver file.Res
 		if remaining != nil {
 			unknowns = append(unknowns, unknown.CoordinateError{Coordinates: archiveCoordinates, Reason: remaining})
 		}
-		appendUnknowns(scratchBuilder, t.Name(), unknowns)
+		appendUnknowns(builder, t.Name(), unknowns)
 	}
-	return scratch
 }
 
 // runSubTaskSafely is runTaskSafely without the task name in a panic's error, since appendUnknowns
@@ -345,10 +385,12 @@ var zipArchiveGlobs = []string{
 	"**/*.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(mimetype.ArchiveMIMETypeSet.List()...)
+	archives, err := resolver.FilesByMIMEType(archiveMIMETypes...)
 	if err != nil {
 		log.WithFields("error", err).Debug("unable to list archive files for recursive cataloging")
 		return nil
@@ -381,44 +423,78 @@ func (c *archiveCataloger) discoverArchives(resolver file.Resolver) []archiveCan
 	return candidates
 }
 
-// mergeArchiveResults copies the throwaway SBOM's packages, files and relationships into the shared
+// mergeArchiveResults copies everything found in an archive into its parent's SBOM.
-// SBOM, adding a CONTAINS relationship from the archive to everything found inside it.
+func mergeArchiveResults(found *sbom.SBOM, builder sbomsync.Builder) {
-//
+	if pkgs := found.Artifacts.Packages.Sorted(); len(pkgs) > 0 {
-// Files inside the archive are those whose container is the archive's own full path, which leaves out the
-// archive itself (a java package or an unknown recorded at its coordinates would otherwise become a
-// self-loop). The nested archives are always included, so the chain of archives is navigable whatever
-// file selection is configured.
-func mergeArchiveResults(archiveCoordinates file.Coordinates, archivePath string, children []archiveCandidate, scratch *sbom.SBOM, builder sbomsync.Builder) {
-	pkgs := scratch.Artifacts.Packages.Sorted()
-	if len(pkgs) > 0 {
 		builder.AddPackages(pkgs...)
 	}
-
 	if accessor, ok := builder.(sbomsync.Accessor); ok {
 		accessor.WriteToSBOM(func(s *sbom.SBOM) {
-			mergeFileArtifacts(&s.Artifacts, &scratch.Artifacts)
+			mergeFileArtifacts(&s.Artifacts, &found.Artifacts)
 		})
 	}
-
+	if len(found.Relationships) > 0 {
-	var rels []artifact.Relationship
+		builder.AddRelationships(found.Relationships...)
-	for _, p := range pkgs {
-		rels = append(rels, artifact.Relationship{From: archiveCoordinates, To: p, Type: artifact.ContainsRelationship})
 	}
+}
+
+// addContains adds a CONTAINS relationship from the archive to each package found directly in it, each
+// file directly in it that the SBOM describes, and each nested archive, so the hierarchy is navigable
+// whatever file selection is configured.
+//
+// Files directly in the archive are those whose container is the archive's own full path, which leaves
+// out the archive itself (a java package or an unknown recorded at its coordinates would otherwise
+// become a self-loop) and the files of nested archives, contained by those.
+func addContains(archiveCoordinates file.Coordinates, archivePath string, direct []pkg.Package, children []archiveCandidate, found *sbom.SBOM) {
 	contained := file.NewCoordinateSet()
 	for _, child := range children {
 		contained.Add(child.location.Coordinates)
 	}
-	for _, coordinates := range scratch.AllCoordinates() {
+	addInside := func(coordinates file.Coordinates) {
 		if archive.ContainerPath(coordinates) == archivePath {
 			contained.Add(coordinates)
 		}
 	}
+	eachFileArtifactCoordinates(&found.Artifacts, addInside)
+	for _, r := range found.Relationships {
+		if c, ok := r.From.(file.Coordinates); ok {
+			addInside(c)
+		}
+		if c, ok := r.To.(file.Coordinates); ok {
+			addInside(c)
+		}
+	}
+
+	var rels []artifact.Relationship
+	for _, p := range direct {
+		rels = append(rels, artifact.Relationship{From: archiveCoordinates, To: p, Type: artifact.ContainsRelationship})
+	}
 	for _, coordinates := range contained.ToSlice() {
 		rels = append(rels, artifact.Relationship{From: archiveCoordinates, To: coordinates, Type: artifact.ContainsRelationship})
 	}
-	rels = append(rels, scratch.Relationships...)
+	found.Relationships = append(found.Relationships, rels...)
-	if len(rels) > 0 {
+}
-		builder.AddRelationships(rels...)
+
+// eachFileArtifactCoordinates calls fn with the coordinates of every file artifact, once per artifact
+// kind describing it.
+func eachFileArtifactCoordinates(a *sbom.Artifacts, fn func(file.Coordinates)) {
+	for c := range a.FileMetadata {
+		fn(c)
+	}
+	for c := range a.FileDigests {
+		fn(c)
+	}
+	for c := range a.FileContents {
+		fn(c)
+	}
+	for c := range a.FileLicenses {
+		fn(c)
+	}
+	for c := range a.Executables {
+		fn(c)
+	}
+	for c := range a.Unknowns {
+		fn(c)
 	}
 }
 

internal/task/archive_tasks_test.go

@@ -104,7 +104,7 @@ func Test_archiveCataloger_aPanicCostsOnlyThatArchive(t *testing.T) {
 
 func newTestTask(t *testing.T, cfg cataloging.ArchiveSearchConfig, subPipeline ...Task) Task {
 	t.Helper()
-	tsk := NewArchiveCatalogerTask(cfg, subPipeline, nil)
+	tsk := NewArchiveCatalogerTask(cfg, cataloging.UnknownsConfig{}, subPipeline, nil, nil)
 	require.NotNil(t, tsk)
 	return tsk
 }
@@ -112,7 +112,7 @@ func newTestTask(t *testing.T, cfg cataloging.ArchiveSearchConfig, subPipeline .
 // 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, subPipeline, nil)
+	tsk := newArchiveCatalogerTask(maxDepth, limits, false, subPipeline, nil, nil)
 	require.NotNil(t, tsk)
 	return tsk
 }
@@ -236,7 +236,7 @@ func Test_NewArchiveCatalogerTask_gating(t *testing.T) {
 
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
-			got := NewArchiveCatalogerTask(tt.cfg, tt.subPipeline, nil)
+			got := NewArchiveCatalogerTask(tt.cfg, cataloging.UnknownsConfig{}, tt.subPipeline, nil, nil)
 			if tt.wantTask {
 				require.NotNil(t, got)
 				assert.Equal(t, ArchiveCatalogerTaskName, got.Name())
@@ -362,7 +362,7 @@ func Test_NewArchiveCatalogerTask_dropsItselfFromSubPipeline(t *testing.T) {
 	var ran int
 	countTask := countingTask(&ran)
 
-	poisoned := []Task{countTask, NewArchiveCatalogerTask(cfg, []Task{countTask}, nil)}
+	poisoned := []Task{countTask, NewArchiveCatalogerTask(cfg, cataloging.UnknownsConfig{}, []Task{countTask}, nil, nil)}
 	require.NotNil(t, poisoned[1])
 
 	tsk := newTestTask(t, cfg, poisoned...)
@@ -371,8 +371,8 @@ func Test_NewArchiveCatalogerTask_dropsItselfFromSubPipeline(t *testing.T) {
 	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, []Task{countTask}, nil)}
+		only := []Task{NewArchiveCatalogerTask(cfg, cataloging.UnknownsConfig{}, []Task{countTask}, nil, nil)}
-		assert.Nil(t, NewArchiveCatalogerTask(cfg, only, nil))
+		assert.Nil(t, NewArchiveCatalogerTask(cfg, cataloging.UnknownsConfig{}, only, nil, nil))
 	})
 }
 
@@ -586,7 +586,7 @@ func Test_archiveCataloger_limitsFallWhenAnArchiveIsReleased(t *testing.T) {
 func newTestCataloger(maxDepth int, limiter *archive.Limiter, subPipeline ...Task) *archiveCataloger {
 	return &archiveCataloger{
 		maxDepth: maxDepth,
-		subPipeline: subPipeline,
+		pkgTasks: subPipeline,
 		limiter:  limiter,
 		progress: bus.StartCatalogerTask(context.Background(), archiveCatalogerProgressInfo(), -1, ""),
 	}

internal/task/file_tasks.go

@@ -4,7 +4,6 @@ import (
 	"context"
 	"crypto"
 
-	"github.com/anchore/syft/internal/archive"
 	"github.com/anchore/syft/internal/sbomsync"
 	"github.com/anchore/syft/syft/artifact"
 	"github.com/anchore/syft/syft/cataloging/filecataloging"
@@ -40,7 +39,7 @@ func newFileDigestCatalogerTask(selection file.Selection, hashers []crypto.Hash,
 
 		accessor := builder.(sbomsync.Accessor)
 
-		coordinates, ok := coordinatesForSelection(ctx, selection, builder.(sbomsync.Accessor))
+		coordinates, ok := coordinatesForSelection(selection, builder.(sbomsync.Accessor))
 		if !ok {
 			return nil
 		}
@@ -71,7 +70,7 @@ func newFileMetadataCatalogerTask(selection file.Selection, tags ...string) Task
 
 		accessor := builder.(sbomsync.Accessor)
 
-		coordinates, ok := coordinatesForSelection(ctx, selection, builder.(sbomsync.Accessor))
+		coordinates, ok := coordinatesForSelection(selection, builder.(sbomsync.Accessor))
 		if !ok {
 			return nil
 		}
@@ -142,12 +141,7 @@ func newExecutableCatalogerTask(selection file.Selection, cfg executable.Config,
 
 // TODO: this should be replaced with a fix that allows passing a coordinate or location iterator to the cataloger
 // Today internal to both cataloger this functions differently: a slice of coordinates vs a channel of locations
-//
+func coordinatesForSelection(selection file.Selection, accessor sbomsync.Accessor) ([]file.Coordinates, bool) {
-// Only coordinates in the resolver's own frame are returned: inside an archive, the files of that archive,
-// and at the scan root, files outside any archive. A package's location can be in another frame (a nested
-// java package is located at the archive in its parent), and looking that path up here would miss or,
-// worse, hit an unrelated file of the same name.
-func coordinatesForSelection(ctx context.Context, selection file.Selection, accessor sbomsync.Accessor) ([]file.Coordinates, bool) {
 	if selection == file.AllFilesSelection {
 		return nil, true
 	}
@@ -175,13 +169,7 @@ func coordinatesForSelection(ctx context.Context, selection file.Selection, acce
 			}
 		})
 
-		frame := archive.TraversalFromContext(ctx).FullTraversalArchivePath()
+		coords := coordinates.ToSlice()
-		var coords []file.Coordinates
-		for _, c := range coordinates.ToSlice() {
-			if archive.ContainerPath(c) == frame {
-				coords = append(coords, c)
-			}
-		}
 
 		if len(coords) == 0 {
 			return nil, false

internal/task/file_tasks_test.go

@@ -1,13 +1,10 @@
 package task
 
 import (
-	"context"
 	"testing"
 
 	"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/syft/artifact"
 	"github.com/anchore/syft/syft/file"
@@ -87,30 +84,9 @@ func Test_coordinatesForSelection(t *testing.T) {
 	}
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
-			files, ok := coordinatesForSelection(context.Background(), tt.selection, sbomsync.NewBuilder(tt.sbom).(sbomsync.Accessor))
+			files, ok := coordinatesForSelection(tt.selection, sbomsync.NewBuilder(tt.sbom).(sbomsync.Accessor))
 			assert.Equal(t, tt.files, files)
 			assert.Equal(t, tt.ok, ok)
 		})
 	}
 }
-
-func Test_coordinatesForSelection_onlyTheResolversFrame(t *testing.T) {
-	// a package located at an archive in its parent's frame must not send the file catalogers looking up
-	// that path inside the archive's own resolver
-	atRoot := file.NewCoordinates("/app.war", "")
-	inWar := file.Coordinates{RealPath: "/app.war", FullPath: "/app.war!/WEB-INF/lib/dep.jar"}
-	s := &sbom.SBOM{Artifacts: sbom.Artifacts{Packages: pkg.NewCollection(
-		pkg.Package{Name: "app", Locations: file.NewLocationSet(file.NewLocationFromCoordinates(atRoot))},
-		pkg.Package{Name: "dep", Locations: file.NewLocationSet(file.NewLocationFromCoordinates(inWar))},
-	)}}
-	accessor := sbomsync.NewBuilder(s).(sbomsync.Accessor)
-
-	got, ok := coordinatesForSelection(context.Background(), file.FilesOwnedByPackageSelection, accessor)
-	require.True(t, ok)
-	assert.Equal(t, []file.Coordinates{atRoot}, got, "at the scan root")
-
-	ctx := archive.WithTraversal(context.Background(), &archive.Traversal{Location: file.NewLocationFromCoordinates(atRoot)})
-	got, ok = coordinatesForSelection(ctx, file.FilesOwnedByPackageSelection, accessor)
-	require.True(t, ok)
-	assert.Equal(t, []file.Coordinates{inWar}, got, "inside app.war")
-}

internal/task/unknowns_tasks.go

@@ -2,8 +2,10 @@ package task
 
 import (
 	"context"
+	"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 +38,20 @@ 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
 			}
+			// 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
 		}
 	}
 
@@ -71,6 +82,7 @@ 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 +95,25 @@ 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() {
+				for _, container := range archives {
+					// an archive's contents are not in this resolver to follow links in
+					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 +1,68 @@
+package task
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+
+	"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_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/unknown/path_error.go

@@ -2,6 +2,7 @@ package unknown
 
 import (
 	"regexp"
+	"strings"
 
 	"github.com/anchore/syft/internal/log"
 	"github.com/anchore/syft/syft/file"
@@ -19,7 +20,7 @@ func ProcessPathErrors(err error) error {
 	if pathErrorRegex.MatchString(errText) {
 		foundPath := pathErrorRegex.ReplaceAllString(err.Error(), "$1")
 		if foundPath != "" {
-			return New(file.NewLocation(foundPath), err)
+			return New(file.NewLocationFromCoordinates(pathCoordinates(foundPath)), err)
 		}
 	}
 	unknowns, remainingErrors := ExtractCoordinateErrors(err)
@@ -31,3 +32,13 @@ func ProcessPathErrors(err error) error {
 	}
 	return Join(out...)
 }
+
+// pathCoordinates names the file at a path from a resolver error, which for a file within an archive is
+// a full path: the real path is what precedes the first archive separator.
+func pathCoordinates(p string) file.Coordinates {
+	realPath, _, nested := strings.Cut(p, file.ArchivePathSeparator)
+	if !nested {
+		return file.NewCoordinates(p, "")
+	}
+	return file.Coordinates{RealPath: realPath, FullPath: p}
+}

syft/archive_cataloger_test.go

@@ -383,6 +383,92 @@ func TestArchiveCataloger_defaultFileSelectionCoversRootJars(t *testing.T) {
 	}
 }
 
+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),
+	}), 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)
+}
+
+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

syft/create_sbom_config.go

@@ -5,7 +5,6 @@ import (
 	"errors"
 	"fmt"
 	"runtime/debug"
-	"slices"
 	"strings"
 
 	"github.com/anchore/syft/internal/log"
@@ -202,7 +201,6 @@ func (c *CreateSBOMConfig) makeTaskGroups(src source.Description, exclusions []s
 	environmentTasks := c.environmentTasks()
 	scopeTasks := c.scopeTasks()
 	relationshipsTasks := c.relationshipTasks(src)
-	unknownTasks := c.unknownsTasks()
 	osFeatureDetectionTasks := c.osFeatureDetectionTasks()
 
 	pkgTasks, fileTasks, selectionEvidence, err := c.selectTasks(src)
@@ -212,7 +210,14 @@ func (c *CreateSBOMConfig) makeTaskGroups(src source.Description, exclusions []s
 
 	// 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, append(slices.Clone(pkgTasks), fileTasks...), exclusions)
+	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
 	switch {
@@ -466,10 +471,10 @@ 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)
 	}
 

syft/file/cataloger/filedigest/cataloger.go

@@ -42,7 +42,7 @@ 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.LocalPath())
+			locs, err := resolver.FilesByPath(c.FullNestedPath())
 			if err != nil {
 				return nil, fmt.Errorf("unable to get file locations for path %q: %w", c.FullNestedPath(), err)
 			}

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.LocalPath())
+					locs, err := resolver.FilesByPath(c.FullNestedPath())
 					if err != nil {
 						errs = unknown.Append(errs, c, err)
 						continue

syft/file/coordinates.go

@@ -30,12 +30,12 @@ func (c Coordinates) FullNestedPath() string {
 	return c.FullPath
 }
 
-// LocalPath is the path within the resolver holding the file: the segment of FullNestedPath after the
+// LocalPath is the rooted path within the resolver holding the file: the segment of FullNestedPath after
-// last archive separator, or RealPath for a file not within an archive.
+// the last archive separator, keeping the separator's slash, or RealPath for a file not within an archive.
 func (c Coordinates) LocalPath() string {
 	fullPath := c.FullNestedPath()
 	if i := strings.LastIndex(fullPath, ArchivePathSeparator); i >= 0 {
-		return fullPath[i+len(ArchivePathSeparator):]
+		return fullPath[i+len(ArchivePathSeparator)-1:]
 	}
 	return fullPath
 }

syft/file/location_test.go

@@ -105,5 +105,5 @@ func TestCoordinates_ID_unchangedByTopLevelFullRealPath(t *testing.T) {
 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, "/META-INF/MANIFEST.MF", Coordinates{RealPath: "/a.war", FullPath: "/a.war!/lib/b.jar!/META-INF/MANIFEST.MF"}.LocalPath())
 }

syft/format/common/spdxhelpers/to_format_model.go

@@ -712,6 +712,26 @@ const (
 	archivePathCommentPrefix = "archivePath: "
 )
 
+// fileComment carries the layer ID and, for a file inside an archive, its archive path. Such a file is
+// named by its full path ("/app.war!/WEB-INF/lib/a.jar!/META-INF/MANIFEST.MF"), so a consumer reading
+// only the name does not mistake it for a file at that path in the scan root; the entry chain after the
+// real path is also kept in the comment so decoding need not guess where it starts.
+func fileComment(c file.Coordinates) string {
+	var entries string
+	if rest, ok := strings.CutPrefix(c.FullPath, c.RealPath); ok {
+		entries, _ = strings.CutPrefix(rest, file.ArchivePathSeparator)
+	}
+	switch {
+	case c.FileSystemID != "" && entries != "":
+		return layerIDCommentPrefix + c.FileSystemID + "\n" + archivePathCommentPrefix + entries
+	case c.FileSystemID != "":
+		return layerIDCommentPrefix + c.FileSystemID
+	case entries != "":
+		return archivePathCommentPrefix + entries
+	}
+	return ""
+}
+
 func toFiles(s sbom.SBOM) (results []*spdx.File) {
 	artifacts := s.Artifacts
 
@@ -742,30 +762,16 @@ func toFiles(s sbom.SBOM) (results []*spdx.File) {
 
 		// TODO: add file classifications (?) and content as a snippet
 
-		var comments []string
-		if c.FileSystemID != "" {
-			comments = append(comments, layerIDCommentPrefix+c.FileSystemID)
-		}
-
-		// a file inside an archive is named by its full path ("/app.war!/WEB-INF/lib/a.jar!/META-INF/MANIFEST.MF"),
-		// so a consumer reading only the name does not mistake it for a file at that path in the scan
-		// root. The entry chain after the real path is also kept in the comment so decoding need not guess
-		// where it starts.
 		name := c.FullNestedPath()
-		if entries, ok := strings.CutPrefix(c.FullNestedPath(), c.RealPath+file.ArchivePathSeparator); ok {
-			comments = append(comments, archivePathCommentPrefix+entries)
-		}
-
 		relativePath, err := convertAbsoluteToRelative(name)
 		if err != nil {
 			log.Debugf("unable to convert relative path '%s' to absolute path: %s", name, err)
 			relativePath = name
 		}
-		comment := strings.Join(comments, "\n")
 
 		results = append(results, &spdx.File{
 			FileSPDXIdentifier: toSPDXID(c),
-			FileComment:        comment,
+			FileComment:        fileComment(c),
 			// required, no attempt made to determine license information
 			LicenseConcluded:  noAssertion,
 			FileCopyrightText: noAssertion,

syft/format/common/spdxhelpers/to_syft_model.go

@@ -530,18 +530,23 @@ func collectPackageFileRelationships(spdxIDMap map[string]any, doc *spdx.Documen
 }
 
 func toSyftCoordinates(f *spdx.File) file.Coordinates {
-	c := file.NewCoordinates(f.FileName, "")
+	return coordinatesFromFile(f.FileName, f.FileComment, string(f.FileSPDXIdentifier))
-	for _, line := range strings.Split(f.FileComment, "\n") {
+}
+
+// coordinatesFromFile decodes what fileComment encodes.
+func coordinatesFromFile(name, comment, id string) file.Coordinates {
+	c := file.NewCoordinates(name, "")
+	for _, line := range strings.Split(comment, "\n") {
 		if v, ok := strings.CutPrefix(line, layerIDCommentPrefix); ok {
 			c.FileSystemID = v
 		}
 		if v, ok := strings.CutPrefix(line, archivePathCommentPrefix); ok {
 			// the name is the full path; the real path is what precedes the entry chain
-			c.RealPath = strings.TrimSuffix(f.FileName, file.ArchivePathSeparator+v)
+			c.RealPath = strings.TrimSuffix(name, file.ArchivePathSeparator+v)
-			c.FullPath = f.FileName
+			c.FullPath = name
 		}
 	}
-	if v, ok := strings.CutPrefix(string(f.FileSPDXIdentifier), layerIDCommentPrefix); ok {
+	if v, ok := strings.CutPrefix(id, layerIDCommentPrefix); ok {
 		c.FileSystemID = v
 	}
 	return c

syft/format/common/spdxhelpers/to_syft_model_v3.go

@@ -393,15 +393,7 @@ func v3collectDocRelationships(spdxMap ptrMap[any], doc *spdx.Document) (out []a
 }
 
 func v3toSyftCoordinates(f spdx.AnyFile) file.Coordinates {
-	const layerIDPrefix = "layerID: "
+	return coordinatesFromFile(f.GetName(), f.GetComment(), f.GetID())
-	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.NewCoordinates(f.GetName(), fileSystemID)
 }
 
 func v3toSyftLocation(f spdx.AnyFile) file.Location {

syft/pkg/cataloger/golang/parse_go_mod.go

@@ -39,16 +39,13 @@ func newGoModCataloger(opts CatalogerConfig) *goModCataloger {
 
 // parseGoModFile takes a go.mod and tries to resolve and lists all packages discovered.
 func (c *goModCataloger) parseGoModFile(ctx context.Context, resolver file.Resolver, _ *generic.Environment, reader file.LocationReadCloser) (pkgs []pkg.Package, relationships []artifact.Relationship, err error) {
+	// the go toolchain needs the go.mod on the host: a location without a reference (such as a file within
+	// an archive) has none, so only the go.mod and go.sum contents are cataloged
 	realPath := string(reader.Location.Reference().RealPath)
-	if realPath == "" {
-		// the Reference().RealPath is used to find full paths when using a directory scan, it does not provide correct paths for archive scanning
-		realPath = reader.LocalPath()
-	}
 	if windows.HostRunningOnWindows() {
 		// directory resolvers hand back volume-encoded posix paths (/c/...), the go toolchain needs the native path
 		realPath = windows.FromPosix(realPath)
 	}
-	modDir := filepath.Dir(realPath)
 	digests, err := parseGoSumFile(resolver, reader)
 	if err != nil {
 		log.Debugf("unable to get go.sum: %v", err)
@@ -69,12 +66,12 @@ func (c *goModCataloger) parseGoModFile(ctx context.Context, resolver file.Resol
 	var sourceModules map[string]*packages.Module
 	var catalogedModules []pkg.Package
 
-	if c.usePackagesLib {
+	if c.usePackagesLib && realPath != "" {
 		var sourcePackages map[string][]pkgInfo
 		var sourceDependencies map[string][]string
 		var sourceModuleToPkg map[string]artifact.Identifiable
 
-		sourcePackages, sourceModules, sourceDependencies, err = c.loadPackages(modDir, reader.Location)
+		sourcePackages, sourceModules, sourceDependencies, err = c.loadPackages(filepath.Dir(realPath), reader.Location)
 		catalogedModules, sourceModuleToPkg = c.catalogModules(ctx, scanRoot, sourcePackages, sourceModules, reader, digests)
 		relationships = buildModuleRelationships(catalogedModules, sourceDependencies, sourceModuleToPkg)
 	}

syft/pkg/cataloger/perl/perllocal.go

@@ -217,7 +217,7 @@ func parsePerllocal(r io.Reader) []perllocalEntry {
 func primaryPath(p pkg.Package) string {
 	for _, location := range p.Locations.ToSlice() {
 		if location.Annotations[pkg.EvidenceAnnotationKey] == pkg.PrimaryEvidenceAnnotation {
-			return location.Path()
+			return location.LocalPath()
 		}
 	}
 	return ""

syft/pkg/cataloger/python/parse_wheel_egg_metadata.go

@@ -48,7 +48,7 @@ func parseWheelOrEggMetadata(locationReader file.LocationReadCloser) (parsedData
 	}
 
 	// add additional metadata not stored in the egg/wheel metadata file
-	metadataPath := locationReader.Path()
+	metadataPath := locationReader.LocalPath()
 
 	pd.SitePackagesRootPath = determineSitePackagesRootPath(metadataPath)
 	if pd.Licenses != "" || pd.LicenseExpression != "" {