[wip]

Signed-off-by: Alex Goodman <wagoodman@users.noreply.github.com>

.binny.yaml

@@ -1,11 +1,21 @@
 tools:
+  # we want to use a pinned version of binny to manage the toolchain (so binny manages itself!)
   - name: binny
     version:
-      want: v0.6.3
+      want: v0.7.0
     method: github-release
     with:
       repo: anchore/binny
 
+  # used to produce SBOMs during release
+  - name: syft
+    version:
+      want: latest
+    method: github-release
+    with:
+      repo: anchore/syft
+
+  # used to sign mac binaries at release
   - name: quill
     version:
       want: v0.4.1
@@ -13,13 +23,15 @@ tools:
     with:
       repo: anchore/quill
 
+  # used for linting
   - name: golangci-lint
     version:
-      want: v1.55.2
+      want: v1.57.2
     method: github-release
     with:
       repo: golangci/golangci-lint
 
+  # used for showing the changelog at release
   - name: glow
     version:
       want: v1.5.1
@@ -27,13 +39,15 @@ tools:
     with:
       repo: charmbracelet/glow
 
+  # used for signing the checksums file at release
   - name: cosign
     version:
-      want: v2.2.2
+      want: v2.2.4
     method: github-release
     with:
       repo: sigstore/cosign
 
+  # used in integration tests to verify JSON schemas
   - name: yajsv
     version:
       want: v1.4.1
@@ -41,13 +55,15 @@ tools:
     with:
       repo: neilpa/yajsv
 
+  # used to release all artifacts
   - name: goreleaser
     version:
-      want: v1.22.1
+      want: v1.25.1
     method: github-release
     with:
       repo: goreleaser/goreleaser
 
+  # used for organizing imports during static analysis
   - name: gosimports
     version:
       want: v0.3.8
@@ -55,6 +71,7 @@ tools:
     with:
       repo: rinchsan/gosimports
 
+  # used at release to generate the changelog
   - name: chronicle
     version:
       want: v0.8.0
@@ -62,6 +79,7 @@ tools:
     with:
       repo: anchore/chronicle
 
+  # used during static analysis for license compliance
   - name: bouncer
     version:
       want: v0.4.0
@@ -69,6 +87,7 @@ tools:
     with:
       repo: wagoodman/go-bouncer
 
+  # used for showing benchmark testing
   - name: benchstat
     version:
       want: latest
@@ -81,16 +100,18 @@ tools:
       entrypoint: cmd/benchstat
       module: golang.org/x/perf
 
+  # used for running all local and CI tasks
   - name: task
     version:
-      want: v3.32.0
+      want: v3.36.0
     method: github-release
     with:
       repo: go-task/task
 
+  # used for triggering a release
   - name: gh
     version:
-      want: v2.40.1
+      want: v2.48.0
     method: github-release
     with:
       repo: cli/cli

.chronicle.yaml

@@ -1,4 +1,4 @@
-enforce-v0: true # don't make breaking-change label bump major version before 1.0.
+enforce-v0: false
 title: ""
 
 github:

.github/dependabot.yml

@@ -1,12 +1,19 @@
 version: 2
+
 updates:
+
   - package-ecosystem: gomod
     directory: "/"
     schedule:
       interval: "daily"
     open-pull-requests-limit: 10
+    labels:
+      - "dependencies"
+
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       interval: "daily"
-    open-pull-requests-limit: 10
+    open-pull-requests-limit: 10
+    labels:
+      - "dependencies"

.github/scripts/check_binary_fixture_size.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+# current limit for fixture size
+size=1000
+
+if [ $# -eq 0 ]; then
+  echo "Usage: $0 <directory>"
+  exit 1
+fi
+
+directory="$1"
+
+# Remove trailing slash using parameter expansion
+directory="${directory%/}"
+
+if [ ! -d "$directory" ]; then
+  echo "Directory not found: $directory"
+  exit 1
+fi
+
+found_large_files=0
+while IFS= read -r -d '' file; do
+  if [ $(wc -c < "$file") -gt $size ]; then
+    echo "File $file is greater than ${size} bytes."
+    found_large_files=1
+  fi
+done < <(find "$directory" -type f -print0)
+
+if [ "$found_large_files" -eq 1 ]; then
+  echo "Script failed: Some files are greater than ${size} bytes."
+  exit 1
+else
+  echo "All files in $directory and its subdirectories are ${size} bytes or smaller. Check passed."
+  exit 0
+fi
+

.github/scripts/labeler.py

@@ -56,6 +56,8 @@ def main(changed_files: str | None = None, merge_base_schema_files: str | None =
 
     pr_json_schema_files = filter_to_schema_files(pr_changed_files)
 
+    pr_labels = get_pr_labels(pr_number)
+
     # print("schema files in pr:   ", summarize_schema_files(pr_json_schema_files))
     # print("og schema files:      ", summarize_schema_files(og_json_schema_files))
 
@@ -76,7 +78,8 @@ def main(changed_files: str | None = None, merge_base_schema_files: str | None =
         add_label(pr_number, JSON_SCHEMA_LABEL)
 
     else:
-        remove_label(pr_number, JSON_SCHEMA_LABEL)
+        if JSON_SCHEMA_LABEL in pr_labels:
+            remove_label(pr_number, JSON_SCHEMA_LABEL)
 
     # new schema files should be scrutinized, comparing the latest and added versions to see if it's a breaking
     # change (major version bump). Warn about it on the PR via adding a breaking-change label...
@@ -84,7 +87,8 @@ def main(changed_files: str | None = None, merge_base_schema_files: str | None =
         print("\nBreaking change detected...")
         add_label(pr_number, BREAKING_CHANGE_LABEL)
     else:
-        remove_label(pr_number, BREAKING_CHANGE_LABEL)
+        if BREAKING_CHANGE_LABEL in pr_labels:        
+            remove_label(pr_number, BREAKING_CHANGE_LABEL)
 
     # modifying an existing schema could be a breaking change, we should warn about it on the PR via a comment...
     # removing schema files should never be allowed, we should warn about it on the PR via a comment...
@@ -119,7 +123,7 @@ def add_label(pr_number: str, label: str):
     # run "gh pr edit --add-label <label>"
     result = run(f"gh pr edit {pr_number} --add-label {label}", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     if result.returncode != 0:
-        print(f"Unable to add  {label!r} label to PR with")
+        print(f"Unable to add '{label!r}' label to PR, error:")
         print(str(result.stderr))
         sys.exit(1)
 
@@ -128,7 +132,7 @@ def remove_label(pr_number: str, label: str):
     # run "gh pr edit --remove-label <label>"
     result = run(f"gh pr edit {pr_number} --remove-label {label}", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     if result.returncode != 0:
-        print(f"Unable to label PR with {label!r}")
+        print(f"Unable to remove '{label!r}' label from PR, error:")
         print(str(result.stderr))
         sys.exit(1)
 
@@ -165,6 +169,17 @@ def get_pr_changed_files(pr_number: str) -> list[str]:
     return list_of_files
 
 
+def get_pr_labels(pr_number: str) -> list[str]:
+    result = run(f"gh pr view {pr_number} --json labels --jq '.labels[].name'", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)
+    if result.returncode != 0:
+        print("Unable to get list of labels on PR")
+        print(str(result.stderr))
+        sys.exit(1)
+    
+    list_of_labels = result.stdout.splitlines()
+    return list_of_labels
+
+
 def filter_to_schema_files(list_of_files: list[str]) -> list[str]:
     # get files matching "schema/json/schema-*.json"
     files = []
@@ -176,7 +191,8 @@ def filter_to_schema_files(list_of_files: list[str]) -> list[str]:
 
 def list_json_schema_files() -> list[str]:
     # list files in "schema/json" directory matching the pattern of "schema-*.json"
-    return sort_json_schema_files(list(glob.glob("schema/json/schema-*.json")))
+    # special case: always ignore the "latest" schema file
+    return sort_json_schema_files([f for f in glob.glob("schema/json/schema-*.json") if "latest" not in f])
 
 
 def run(command: str,  **kwargs) -> subprocess.CompletedProcess:
@@ -197,7 +213,7 @@ def sort_json_schema_files(files: list[str]) -> list[str]:
     # so that "schema/json/schema-1.2.1.json" comes before "schema/json/schema-1.12.1.json".
     versions = [get_semver(file) for file in files if file]
     
-    versions = sorted(versions, key=lambda s: [int(u) for u in s.split('.')])
+    versions = sorted(versions, key=lambda s: [int(u) for u in s.split('.') if "." in s])
 
     return [f"schema/json/schema-{version}.json" for version in versions]
 

.github/scripts/labeler_test.py

@@ -60,6 +60,11 @@ class Labeler(unittest.TestCase):
         expected_sorted_files = ["schema/json/schema-1.2.1.json", "schema/json/schema-1.12.1.json"]
         self.assertEqual(labeler.sort_json_schema_files(files), expected_sorted_files)
 
+        # ensure that "latest" doesn't cause a problem and is ultimately ignored
+        files = ["schema/json/schema-1.12.1.json", "schema/json/schema-_bogus.json"]
+        expected_sorted_files = ["schema/json/schema-_bogus.json", "schema/json/schema-1.12.1.json"]
+        self.assertEqual(labeler.sort_json_schema_files(files), expected_sorted_files)
+
 
 if __name__ == "__main__":
     unittest.main()

.github/workflows/benchmark-testing.yaml

@@ -17,13 +17,13 @@ jobs:
     # the job by event.
     steps:
       - name: Checkout code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4.1.4
 
       - name: Bootstrap environment
         uses: ./.github/actions/bootstrap
 
       - name: Restore base benchmark result
-        uses: actions/cache@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
           path: test/results/benchmark-main.txt
           # use base sha for PR or new commit hash for main push in benchmark result key
@@ -39,13 +39,13 @@ jobs:
           OUTPUT="${OUTPUT//$'\r'/'%0D'}" # URL encode all '\r' characters
           echo "result=$OUTPUT" >> $GITHUB_OUTPUT
 
-      - uses: actions/upload-artifact@c7d193f32edcb7bfad88892161225aeda64e9392 # v4.0.0
+      - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
         with:
           name: benchmark-test-results
           path: test/results/**/*
 
       - name: Update PR benchmark results comment
-        uses: marocchino/sticky-pull-request-comment@efaaab3fd41a9c3de579aba759d2552635e590fd #v2.8.0
+        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 #v2.9.0
         continue-on-error: true
         with:
           header: benchmark

.github/workflows/codeql-analysis.yml

@@ -20,7 +20,7 @@ permissions:
 jobs:
   analyze:
     name: Analyze
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04-4core-16gb
 
     permissions:
       security-events: write
@@ -36,16 +36,16 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
 
     - name: Install Go
-      uses: actions/setup-go@0c52d547c9bc32b1aa3301fd7a9cb496313a4491 #v5.0.0
+      uses: actions/setup-go@cdcb36043654635271a94b9a6d1392de5bb323a7 #v5.0.1
       with:
         go-version-file: go.mod
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@b374143c1149a9115d881581d29b8390bbcbb59c #v3.22.11
+      uses: github/codeql-action/init@d39d31e687223d841ef683f52467bd88e9b21c14 #v3.25.3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -56,7 +56,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@b374143c1149a9115d881581d29b8390bbcbb59c #v3.22.11
+      uses: github/codeql-action/autobuild@d39d31e687223d841ef683f52467bd88e9b21c14 #v3.25.3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -70,4 +70,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@b374143c1149a9115d881581d29b8390bbcbb59c #v3.22.11
+      uses: github/codeql-action/analyze@d39d31e687223d841ef683f52467bd88e9b21c14 #v3.25.3

.github/workflows/dependabot-automation.yaml

@@ -0,0 +1,10 @@
+name: Dependabot Automation
+on:
+  pull_request:
+
+permissions:
+  pull-requests: write
+
+jobs:
+  run:
+    uses: anchore/workflows/.github/workflows/dependabot-automation.yaml@main

.github/workflows/detect-schema-changes.yaml

@@ -30,7 +30,7 @@ jobs:
     runs-on: ubuntu-22.04
     steps:
 
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
 
       - run: python .github/scripts/labeler.py
         env:
@@ -40,7 +40,7 @@ jobs:
 
       - name: Delete existing comment
         if: ${{ hashFiles( env.CI_COMMENT_FILE ) == '' }}
-        uses: marocchino/sticky-pull-request-comment@efaaab3fd41a9c3de579aba759d2552635e590fd #v2.8.0
+        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 #v2.9.0
         with:
           header: ${{ env.COMMENT_HEADER }}
           hide: true
@@ -48,7 +48,7 @@ jobs:
 
       - name: Add comment
         if: ${{ hashFiles( env.CI_COMMENT_FILE ) != '' }}
-        uses: marocchino/sticky-pull-request-comment@efaaab3fd41a9c3de579aba759d2552635e590fd #v2.8.0
+        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 #v2.9.0
         with:
           header: ${{ env.COMMENT_HEADER }}
           path: ${{ env.CI_COMMENT_FILE }}

.github/workflows/release-homebrew.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
 
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
         with:
           # we need to be able to get the commit for a tag
           fetch-depth: 0
@@ -30,7 +30,7 @@ jobs:
           echo -n "commit=$(git rev-parse HEAD)" | tee -a $GITHUB_OUTPUT
 
       - name: Update Homebrew formula
-        uses: dawidd6/action-homebrew-bump-formula@75ed025ff3ad1d617862838b342b06d613a0ddf3 # v3.10.1
+        uses: dawidd6/action-homebrew-bump-formula@baf2b60c51fc1f8453c884b0c61052668a71bd1d # v3.11.0
         with:
           token: ${{ secrets.HOMEBREW_TOKEN }}
           org: anchore
@@ -38,7 +38,7 @@ jobs:
           tag: ${{ steps.release_info.outputs.tag_name }}
           revision: ${{ steps.git_info.outputs.commit }}
 
-      - uses: 8398a7/action-slack@fbd6aa58ba854a740e11a35d0df80cb5d12101d8 #v3.15.1
+      - uses: 8398a7/action-slack@28ba43ae48961b90635b50953d216767a6bea486 #v3.16.2
         if: ${{ failure() }}
         with:
           status: ${{ job.status }}

.github/workflows/release.yaml

@@ -15,7 +15,7 @@ jobs:
     environment: release
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
 
       - name: Check if tag already exists
         # note: this will fail if the tag already exists
@@ -24,7 +24,7 @@ jobs:
           git tag ${{ github.event.inputs.version }}
 
       - name: Check static analysis results
-        uses: fountainhead/action-wait-for-check@297be350cf8393728ea4d4b39435c7d7ae167c93 # v1.1.0
+        uses: fountainhead/action-wait-for-check@5a908a24814494009c4bb27c242ea38c93c593be # v1.2.0
         id: static-analysis
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
@@ -33,7 +33,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha || github.sha }}
 
       - name: Check unit test results
-        uses: fountainhead/action-wait-for-check@297be350cf8393728ea4d4b39435c7d7ae167c93 # v1.1.0
+        uses: fountainhead/action-wait-for-check@5a908a24814494009c4bb27c242ea38c93c593be # v1.2.0
         id: unit
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
@@ -42,7 +42,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha || github.sha }}
 
       - name: Check integration test results
-        uses: fountainhead/action-wait-for-check@297be350cf8393728ea4d4b39435c7d7ae167c93 # v1.1.0
+        uses: fountainhead/action-wait-for-check@5a908a24814494009c4bb27c242ea38c93c593be # v1.2.0
         id: integration
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
@@ -51,7 +51,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha || github.sha }}
 
       - name: Check acceptance test results (linux)
-        uses: fountainhead/action-wait-for-check@297be350cf8393728ea4d4b39435c7d7ae167c93 # v1.1.0
+        uses: fountainhead/action-wait-for-check@5a908a24814494009c4bb27c242ea38c93c593be # v1.2.0
         id: acceptance-linux
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
@@ -60,7 +60,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha || github.sha }}
 
       - name: Check acceptance test results (mac)
-        uses: fountainhead/action-wait-for-check@297be350cf8393728ea4d4b39435c7d7ae167c93 # v1.1.0
+        uses: fountainhead/action-wait-for-check@5a908a24814494009c4bb27c242ea38c93c593be # v1.2.0
         id: acceptance-mac
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
@@ -69,7 +69,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha || github.sha }}
 
       - name: Check cli test results (linux)
-        uses: fountainhead/action-wait-for-check@297be350cf8393728ea4d4b39435c7d7ae167c93 # v1.1.0
+        uses: fountainhead/action-wait-for-check@5a908a24814494009c4bb27c242ea38c93c593be # v1.2.0
         id: cli-linux
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
@@ -94,8 +94,10 @@ jobs:
     permissions:
       contents: write
       packages: write
+      # required for goreleaser signs section with cosign
+      id-token: write
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
         with:
           fetch-depth: 0
 
@@ -103,13 +105,13 @@ jobs:
         uses: ./.github/actions/bootstrap
 
       - name: Login to Docker Hub
-        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d  #v3.0.0
+        uses: docker/login-action@e92390c5fb421da1463c202d546fed0ec5c39f20  #v3.1.0
         with:
-          username: ${{ secrets.TOOLBOX_DOCKER_USER }}
-          password: ${{ secrets.TOOLBOX_DOCKER_PASS }}
+          username: ${{ secrets.ANCHOREOSSWRITE_DH_USERNAME }}
+          password: ${{ secrets.ANCHOREOSSWRITE_DH_PAT }}
 
       - name: Login to GitHub Container Registry
-        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d  #v3.0.0
+        uses: docker/login-action@e92390c5fb421da1463c202d546fed0ec5c39f20  #v3.1.0
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
@@ -136,17 +138,17 @@ jobs:
           # for creating the release (requires write access to packages and content)
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           # for updating brew formula in anchore/homebrew-syft
-          GITHUB_BREW_TOKEN: ${{ secrets.ANCHORE_GIT_READ_TOKEN }}
+          GITHUB_BREW_TOKEN: ${{ secrets.ANCHOREOPS_GITHUB_OSS_WRITE_TOKEN }}
           # for updating the VERSION file in S3...
           AWS_ACCESS_KEY_ID: ${{ secrets.TOOLBOX_AWS_ACCESS_KEY_ID }}
           AWS_SECRET_ACCESS_KEY: ${{ secrets.TOOLBOX_AWS_SECRET_ACCESS_KEY }}
 
-      - uses: anchore/sbom-action@5ecf649a417b8ae17dc8383dc32d46c03f2312df #v0.15.1
+      - uses: anchore/sbom-action@7ccf588e3cf3cc2611714c2eeae48550fbc17552 #v0.15.11
         continue-on-error: true
         with:
           artifact-name: sbom.spdx.json
 
-      - uses: 8398a7/action-slack@fbd6aa58ba854a740e11a35d0df80cb5d12101d8 #v3.15.1
+      - uses: 8398a7/action-slack@28ba43ae48961b90635b50953d216767a6bea486 #v3.16.2
         continue-on-error: true
         with:
           status: ${{ job.status }}

.github/workflows/update-bootstrap-tools.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository == 'anchore/syft' # only run for main repo
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
 
       - name: Bootstrap environment
         uses: ./.github/actions/bootstrap
@@ -50,7 +50,7 @@ jobs:
           app_id: ${{ secrets.TOKEN_APP_ID }}
           private_key: ${{ secrets.TOKEN_APP_PRIVATE_KEY }}
 
-      - uses: peter-evans/create-pull-request@153407881ec5c347639a548ade7d8ad1d6740e38 #v5.0.2
+      - uses: peter-evans/create-pull-request@6d6857d36972b65feb161a90e484f2984215f83e #v6.0.5
         with:
           signoff: true
           delete-branch: true

.github/workflows/update-cpe-dictionary-index.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository == 'anchore/syft' # only run for main repo
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
 
       - name: Bootstrap environment
         uses: ./.github/actions/bootstrap
@@ -33,7 +33,7 @@ jobs:
           app_id: ${{ secrets.TOKEN_APP_ID }}
           private_key: ${{ secrets.TOKEN_APP_PRIVATE_KEY }}
 
-      - uses: peter-evans/create-pull-request@153407881ec5c347639a548ade7d8ad1d6740e38 #v5.0.2
+      - uses: peter-evans/create-pull-request@6d6857d36972b65feb161a90e484f2984215f83e #v6.0.5
         with:
           signoff: true
           delete-branch: true
@@ -45,7 +45,7 @@ jobs:
             Update CPE dictionary index based on the latest available CPE dictionary
           token: ${{ steps.generate-token.outputs.token }}
 
-      - uses: 8398a7/action-slack@fbd6aa58ba854a740e11a35d0df80cb5d12101d8 #v3.15.1
+      - uses: 8398a7/action-slack@28ba43ae48961b90635b50953d216767a6bea486 #v3.16.2
         with:
           status: ${{ job.status }}
           fields: workflow,eventName,job

.github/workflows/update-stereoscope-release.yml

@@ -17,9 +17,9 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository == 'anchore/syft' # only run for main repo
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
 
-      - uses: actions/setup-go@0c52d547c9bc32b1aa3301fd7a9cb496313a4491 #v5.0.0
+      - uses: actions/setup-go@cdcb36043654635271a94b9a6d1392de5bb323a7 #v5.0.1
         with:
           go-version: ${{ env.GO_VERSION }}
           stable: ${{ env.GO_STABLE_VERSION }}
@@ -44,7 +44,7 @@ jobs:
           app_id: ${{ secrets.TOKEN_APP_ID }}
           private_key: ${{ secrets.TOKEN_APP_PRIVATE_KEY }}
 
-      - uses: peter-evans/create-pull-request@153407881ec5c347639a548ade7d8ad1d6740e38 #v5.0.2
+      - uses: peter-evans/create-pull-request@6d6857d36972b65feb161a90e484f2984215f83e #v6.0.5
         with:
           signoff: true
           delete-branch: true

.github/workflows/validations.yaml

@@ -17,7 +17,7 @@ jobs:
     name: "Static analysis"
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
 
       - name: Bootstrap environment
         uses: ./.github/actions/bootstrap
@@ -31,37 +31,49 @@ jobs:
     name: "Unit tests"
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
 
       - name: Bootstrap environment
         uses: ./.github/actions/bootstrap
 
+      - name: Restore file executable test-fixture cache
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
+        with:
+          path: syft/file/cataloger/executable/test-fixtures/elf/bin
+          key: ${{ runner.os }}-unit-file-executable-elf-cache-${{ hashFiles( 'syft/file/cataloger/executable/test-fixtures/elf/cache.fingerprint' ) }}
+
+      - name: Restore file executable shared-info test-fixture cache
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
+        with:
+          path: syft/file/cataloger/executable/test-fixtures/shared-info/bin
+          key: ${{ runner.os }}-unit-file-executable-shared-info-cache-${{ hashFiles( 'syft/file/cataloger/executable/test-fixtures/shared-info/cache.fingerprint' ) }}
+
       - name: Restore Java test-fixture cache
-        uses: actions/cache@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
           path: syft/pkg/cataloger/java/test-fixtures/java-builds/packages
           key: ${{ runner.os }}-unit-java-cache-${{ hashFiles( 'syft/pkg/cataloger/java/test-fixtures/java-builds/cache.fingerprint' ) }}
 
       - name: Restore RPM test-fixture cache
-        uses: actions/cache@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
           path: syft/pkg/cataloger/redhat/test-fixtures/rpms
           key: ${{ runner.os }}-unit-rpm-cache-${{ hashFiles( 'syft/pkg/cataloger/redhat/test-fixtures/rpms.fingerprint' ) }}
 
       - name: Restore go binary test-fixture cache
-        uses: actions/cache@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
           path: syft/pkg/cataloger/golang/test-fixtures/archs/binaries
           key: ${{ runner.os }}-unit-go-binaries-cache-${{ hashFiles( 'syft/pkg/cataloger/golang/test-fixtures/archs/binaries.fingerprint' ) }}
 
       - name: Restore binary cataloger test-fixture cache
-        uses: actions/cache@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
-          path: syft/pkg/cataloger/binary/test-fixtures/classifiers/dynamic
+          path: syft/pkg/cataloger/binary/test-fixtures/classifiers/bin
           key: ${{ runner.os }}-unit-binary-cataloger-cache-${{ hashFiles( 'syft/pkg/cataloger/binary/test-fixtures/cache.fingerprint' ) }}
 
       - name: Restore Kernel test-fixture cache
-        uses: actions/cache@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
           path: syft/pkg/cataloger/kernel/test-fixtures/cache
           key: ${{ runner.os }}-unit-kernel-cache-${{ hashFiles( 'syft/pkg/cataloger/kernel/test-fixtures/cache.fingerprint' ) }}
@@ -75,7 +87,7 @@ jobs:
     name: "Integration tests"
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
 
       - name: Bootstrap environment
         uses: ./.github/actions/bootstrap
@@ -84,10 +96,10 @@ jobs:
         run: make validate-cyclonedx-schema
 
       - name: Restore integration test cache
-        uses: actions/cache@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
-          path: ${{ github.workspace }}/test/integration/test-fixtures/cache
-          key: ${{ runner.os }}-integration-test-cache-${{ hashFiles('test/integration/test-fixtures/cache.fingerprint') }}
+          path: ${{ github.workspace }}/cmd/syft/internal/test/integration/test-fixtures/cache
+          key: ${{ runner.os }}-integration-test-cache-${{ hashFiles('/cmd/syft/internal/test/integration/test-fixtures/cache.fingerprint') }}
 
       - name: Run integration tests
         run: make integration
@@ -97,7 +109,7 @@ jobs:
     name: "Build snapshot artifacts"
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
 
       - name: Bootstrap environment
         uses: ./.github/actions/bootstrap
@@ -110,7 +122,7 @@ jobs:
       # why not use actions/upload-artifact? It is very slow (3 minutes to upload ~600MB of data, vs 10 seconds with this approach).
       # see https://github.com/actions/upload-artifact/issues/199 for more info
       - name: Upload snapshot artifacts
-        uses: actions/cache/save@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache/save@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
           # we need to preserve the snapshot data itself as well as the task data that confirms if the
           # snapshot build is stale or not. Otherwise the downstream jobs will attempt to rebuild the snapshot
@@ -127,14 +139,14 @@ jobs:
     needs: [Build-Snapshot-Artifacts]
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
 
       - name: Bootstrap environment
         uses: ./.github/actions/bootstrap
 
       - name: Download snapshot build
         id: snapshot-cache
-        uses: actions/cache/restore@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache/restore@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
           path: |
             snapshot
@@ -152,7 +164,7 @@ jobs:
 
       - name: Restore install.sh test image cache
         id: install-test-image-cache
-        uses: actions/cache@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
           path: ${{ github.workspace }}/test/install/cache
           key: ${{ runner.os }}-install-test-image-cache-${{ hashFiles('test/install/cache.fingerprint') }}
@@ -175,7 +187,7 @@ jobs:
     needs: [Build-Snapshot-Artifacts]
     runs-on: macos-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
 
       - name: Bootstrap environment
         uses: ./.github/actions/bootstrap
@@ -187,7 +199,7 @@ jobs:
 
       - name: Download snapshot build
         id: snapshot-cache
-        uses: actions/cache/restore@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache/restore@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
           path: |
             snapshot
@@ -202,7 +214,7 @@ jobs:
 
       - name: Restore docker image cache for compare testing
         id: mac-compare-testing-cache
-        uses: actions/cache@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
           path: image.tar
           key: ${{ runner.os }}-${{ hashFiles('test/compare/mac.sh') }}
@@ -220,20 +232,20 @@ jobs:
     needs: [Build-Snapshot-Artifacts]
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 #v4.1.1
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b #v4.1.4
 
       - name: Bootstrap environment
         uses: ./.github/actions/bootstrap
 
       - name: Restore CLI test-fixture cache
-        uses: actions/cache@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
           path: ${{ github.workspace }}/test/cli/test-fixtures/cache
           key: ${{ runner.os }}-cli-test-cache-${{ hashFiles('test/cli/test-fixtures/cache.fingerprint') }}
 
       - name: Download snapshot build
         id: snapshot-cache
-        uses: actions/cache/restore@704facf57e6136b1bc63b828d79edcd491f0ee84 #v3.3.2
+        uses: actions/cache/restore@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 #v4.0.2
         with:
           path: |
             snapshot

.gitignore

@@ -32,7 +32,6 @@ VERSION
 /test/results
 coverage.txt
 *.log
-test/integration/test-fixtures/**/go.sum
 
 # probable archives
 .images

.golangci.yaml

@@ -49,6 +49,9 @@ linters-settings:
     # If lower than 0, disable the check.
     # Default: 40
     statements: 50
+  gocritic:
+    enabled-checks:
+      - deferInLoop
 output:
   uniq-by-line: false
 run:

.goreleaser.yaml

@@ -247,3 +247,28 @@ docker_manifests:
       - ghcr.io/anchore/syft:{{.Tag}}-arm64v8
       - ghcr.io/anchore/syft:{{.Tag}}-ppc64le
       - ghcr.io/anchore/syft:{{.Tag}}-s390x
+
+sboms:
+  - artifacts: archive
+    # this is relative to the snapshot/dist directory, not the root of the repo
+    cmd: ../.tool/syft
+    documents:
+      - "{{ .Binary }}_{{ .Version }}_{{ .Os }}_{{ .Arch }}.sbom"
+    args:
+      - "scan"
+      - "$artifact"
+      - "--output"
+      - "json=$document"
+
+signs:
+  - cmd: .tool/cosign
+    signature: "${artifact}.sig"
+    certificate: "${artifact}.pem"
+    args:
+      - "sign-blob"
+      - "--oidc-issuer=https://token.actions.githubusercontent.com"
+      - "--output-certificate=${certificate}"
+      - "--output-signature=${signature}"
+      - "${artifact}"
+      - "--yes"
+    artifacts: checksum

DEVELOPING.md

@@ -234,7 +234,7 @@ rough outline how that works:
   the `/test` directory. These tests should focus on correctness of functionality in depth. % test coverage metrics 
   only considers unit tests and no other forms of testing.
 
-- `integration`: located within `test/integration`, these tests focus on the behavior surfaced by the common library 
+- `integration`: located within `cmd/syft/internal/test/integration`, these tests focus on the behavior surfaced by the common library 
   entrypoints from the `syft` package and make light assertions about the results surfaced. Additionally, these tests
   tend to make diversity assertions for enum-like objects, ensuring that as enum values are added to a definition
   that integration tests will automatically fail if no test attempts to use that enum value. For more details see 

README.md

@@ -54,6 +54,7 @@ For commercial support options with Syft or Grype, please [contact Anchore](http
 - Ruby (gem)
 - Rust (cargo.lock)
 - Swift (cocoapods, swift-package-manager)
+- Wordpress plugins
 
 ## Installation
 
@@ -109,21 +110,22 @@ nix-shell -p syft
 
 To generate an SBOM for a container image:
 
-```
+```bash
 syft <image>
 ```
 
 The above output includes only software that is visible in the container (i.e., the squashed representation of the image). To include software from all image layers in the SBOM, regardless of its presence in the final image, provide `--scope all-layers`:
 
-```
+```bash
 syft <image> --scope all-layers
 ```
 
 ### Supported sources
 
-Syft can generate an SBOM from a variety of sources:
+Syft can generate an SBOM from a variety of sources including images, files, directories, and archives. Syft will attempt to
+determine the type of source based on provided input, for example:
 
-```
+```bash
 # catalog a container image archive (from the result of `docker image save ...`, `podman save ...`, or `skopeo copy` commands)
 syft path/to/image.tar
 
@@ -134,90 +136,133 @@ syft path/to/image.sif
 syft path/to/dir
 ```
 
-Sources can be explicitly provided with a scheme:
+To explicitly specify the source behavior, use the `--from` flag. Allowable options are:
 
 ```
-docker:yourrepo/yourimage:tag            use images from the Docker daemon
-podman:yourrepo/yourimage:tag            use images from the Podman daemon
-containerd:yourrepo/yourimage:tag        use images from the Containerd daemon
-docker-archive:path/to/yourimage.tar     use a tarball from disk for archives created from "docker save"
-oci-archive:path/to/yourimage.tar        use a tarball from disk for OCI archives (from Skopeo or otherwise)
-oci-dir:path/to/yourimage                read directly from a path on disk for OCI layout directories (from Skopeo or otherwise)
-singularity:path/to/yourimage.sif        read directly from a Singularity Image Format (SIF) container on disk
-dir:path/to/yourproject                  read directly from a path on disk (any directory)
-file:path/to/yourproject/file            read directly from a path on disk (any single file)
-registry:yourrepo/yourimage:tag          pull image directly from a registry (no container runtime required)
+docker             use images from the Docker daemon
+podman             use images from the Podman daemon
+containerd         use images from the Containerd daemon
+docker-archive     use a tarball from disk for archives created from "docker save"
+oci-archive        use a tarball from disk for OCI archives (from Skopeo or otherwise)
+oci-dir            read directly from a path on disk for OCI layout directories (from Skopeo or otherwise)
+singularity        read directly from a Singularity Image Format (SIF) container on disk
+dir                read directly from a path on disk (any directory)
+file               read directly from a path on disk (any single file)
+registry           pull image directly from a registry (no container runtime required)
+```
+If a source is not provided and Syft identifies the input as a potential image reference, Syft will attempt to resolve it using:
+the Docker, Podman, and Containerd daemons followed by direct registry access, in that order.
+
+This default behavior can be overridden with the `default-image-pull-source` configuration option (See [Configuration](#configuration) for more details).
+
+
+### File selection
+
+By default, Syft will catalog file details and digests for files that are owned by discovered packages. You can change this behavior by using the `SYFT_FILE_METADATA_SELECTION` environment variable or the `file.metadata.selection` configuration option. The options are:
+
+- `all`: capture all files from the search space
+- `owned-by-package`: capture only files owned by packages (default)
+- `none`: disable capturing any file information
+
+
+### Package cataloger selection
+
+#### Concepts
+
+> [!IMPORTANT]  
+> Syft uses a different set of catalogers by default when scanning files directly than it does when scanning images
+
+The catalogers for an image scan assumes that package installation steps have already been completed. For example, Syft will identify Python packages that have egg or wheel metadata files under a `site-packages` directory, since this is how the canonical tooling `pip` installs python packages.
+
+The catalogers for a directory scan will look for installed software as well as declared dependencies that are not necessarily installed. For example, dependencies listed in a Python `requirements.txt`.
+
+This default set of catalogers being dynamic is critical as this allows Syft to be used in a variety of contexts while still generating accurate SBOMs.
+Overriding the set of default catalogers is not recommended for most purposes, however, is possible if needed.
+
+Catalogers can be referenced in two different ways:
+- *by name*: the exact cataloger name (e.g. `java-pom-cataloger` or `java-archive-cataloger`)
+- *by tag*: a tag that is associated with a cataloger (e.g. `java`)
+
+Syft can take lists of references on the CLI or in the application configuration to define which catalogers to use.
+
+You can **set** the list of catalogers explicitly to use with the `--override-default-catalogers` CLI flag, accepting a comma-separated list of cataloger names or tags.
+
+You can also **add** to, **remove** from, or **sub-select** catalogers to use within the default set of catalogers by using the `--select-catalogers` CLI flag.
+  - To **sub-select** catalogers simply provide a tag (e.g. `--select-catalogers TAG`). Catalogers will always be selected from the default set of catalogers (e.g. `--select-catalogers java,go` will select all the `java` catalogers in the default set and all the `go` catalogers in the default set).
+  - To **add** a cataloger prefix the cataloger name with `+` (e.g. `--select-catalogers +NAME`). Added catalogers will _always be added_ regardless of removals, filtering, or other defaults.
+  - To **remove** a cataloger prefix the cataloger name or tag with `-` (e.g. `--select-catalogers -NAME_OR_TAG`). Catalogers are removed from the set of default catalogers after processing any sub-selections.
+
+These rules and the dynamic default cataloger sets approximates to the following logic:
+
+```
+image_catalogers = all_catalogers AND catalogers_tagged("image")
+
+directory_catalogers = all_catalogers AND catalogers_tagged("directory")
+
+default_catalogers = image_catalogers OR directory_catalogers
+
+sub_selected_catalogers = default_catalogers INTERSECT catalogers_tagged(TAG) [ UNION sub_selected_catalogers ... ]
+
+base_catalogers = default_catalogers OR sub_selected_catalogers
+
+final_set = (base_catalogers SUBTRACT removed_catalogers) UNION added_catalogers
 ```
 
-If an image source is not provided and cannot be detected from the given reference it is assumed the image should be pulled from the Docker daemon.
-If docker is not present, then the Podman daemon is attempted next, followed by reaching out directly to the image registry last.
 
+#### Examples
 
-This default behavior can be overridden with the `default-image-pull-source` configuration option (See [Configuration](https://github.com/anchore/syft#configuration) for more details).
+Only scan for python related packages with catalogers appropriate for the source type (image or directory):
+```bash
+syft <some container image> --select-catalogers "python"
+# results in the following catalogers being used:
+# - python-installed-package-cataloger
+```
 
-### Default Cataloger Configuration by scan type
+Same command, but the set of catalogers changes based on what is being analyzed (in this case a directory):
+```bash
+syft <a directory> --select-catalogers "python"
+# results in the following catalogers being used:
+# - python-installed-package-cataloger
+# - python-package-cataloger
+```
 
-Syft uses different default sets of catalogers depending on what it is scanning: a container image or a directory on disk. The default catalogers for an image scan assumes that package installation steps have already been completed. For example, Syft will identify Python packages that have egg or wheel metadata files under a site-packages directory, since this indicates software actually installed on an image.
+Use the default set of catalogers and add a cataloger to the set:
+```bash
+syft ... --select-catalogers "+sbom-cataloger"
+```
 
-However, if you are scanning a directory, Syft doesn't assume that all relevant software is installed, and will use catalogers that can identify declared dependencies that may not yet be installed on the final system: for example, dependencies listed in a Python requirements.txt.
+Use the default set of catalogers but remove any catalogers that deal with RPMs:
+```bash
+syft ... --select-catalogers "-rpm"
+```
 
-You can override the list of enabled/disabled catalogers by using the "catalogers" keyword in the [Syft configuration file](https://github.com/anchore/syft#configuration).
+Only scan with catalogers that:
+- are tagged with "go"
+- always use the sbom-cataloger
+- are appropriate for the source type (image or directory)
 
-##### Image Scanning:
-- alpmdb
-- apkdb
-- binary
-- dotnet-deps
-- dotnet-portable-executable
-- dpkgdb
-- go-module-binary
-- graalvm-native-image
-- java
-- javascript-package
-- linux-kernel
-- nix-store
-- php-composer-installed
-- portage
-- python-package
-- rpm-db
-- ruby-gemspec
-- sbom
+```bash
+syft <some container image> --select-catalogers "go,+sbom-cataloger"
+# results in the following catalogers being used:
+# - go-module-binary-cataloger
+# - sbom-cataloger
+```
 
-##### Directory Scanning:
-- alpmdb
-- apkdb
-- binary
-- cocoapods
-- conan
-- dartlang-lock
-- dotnet-deps
-- dotnet-portable-executable
-- dpkgdb
-- elixir-mix-lock
-- erlang-rebar-lock
-- go-mod-file
-- go-module-binary
-- graalvm-native-image
-- haskell
-- java
-- java-gradle-lockfile
-- java-pom
-- javascript-lock
-- linux-kernel
-- nix-store
-- php-composer-lock
-- portage
-- python-index
-- python-package
-- rpm-db
-- rpm-file
-- ruby-gemfile
-- rust-cargo-lock
-- sbom
-- swift-package-manager
+Scan with all catalogers that deal with binary analysis, regardless of the source type:
+```bash
+syft ... --override-default-catalogers "binary"
+# results in the following catalogers being used:
+# - binary-cataloger
+# - cargo-auditable-binary-cataloger
+# - dotnet-portable-executable-cataloger
+# - go-module-binary-cataloger
+```
+
+Only scan with the specific `go-module-binary-cataloger` and `go-module-file-cataloger` catalogers:
+```bash
+syft ... --override-default-catalogers "go-module-binary-cataloger,go-module-file-cataloger"
+```
 
-##### Non Default:
-- cargo-auditable-binary
 
 ### Excluding file paths
 
@@ -260,7 +305,7 @@ Where the `formats` available are:
 
 ## Using templates
 
-Syft lets you define custom output formats, using [Go templates](https://pkg.go.dev/text/template). Here's how it works:
+Syft lets you define custom output formats, using [Go templates](https://pkg.go.dev/text/template) relative to the Syft JSON output. Here's how it works:
 
 - Define your format as a Go template, and save this template as a file.
 
@@ -274,9 +319,9 @@ Syft lets you define custom output formats, using [Go templates](https://pkg.go.
 
 Here's what the `csv.tmpl` file might look like:
 ```gotemplate
-"Package","Version Installed","Found by"
-{{- range .Artifacts}}
-"{{.Name}}","{{.Version}}","{{.FoundBy}}"
+"Package","Version Installed", "Found by"
+{{- range .artifacts}}
+"{{.name}}","{{.version}}","{{.foundBy}}"
 {{- end}}
 ```
 
@@ -293,6 +338,9 @@ Syft also includes a vast array of utility templating functions from [sprig](htt
 
 Lastly, Syft has custom templating functions defined in `./syft/format/template/encoder.go` to help parse the passed-in JSON structs.
 
+> [!NOTE]
+> If you have templates being used before Syft v0.102.0 that are no longer working. This is because templating keys were relative to the internal go structs before this version whereas now the keys are relative to the Syft JSON output. To get the legacy behavior back you can set the `format.template.legacy` option to `true` in your configuration.
+
 ## Multiple outputs
 
 Syft can also output _multiple_ files in differing formats by appending
@@ -457,87 +505,60 @@ Configuration options (example values are the default):
 
 ```yaml
 # the output format(s) of the SBOM report (options: syft-table, syft-text, syft-json, spdx-json, ...)
-# same as -o, --output, and SYFT_OUTPUT env var
 # to specify multiple output files in differing formats, use a list:
 # output:
 #   - "syft-json=<syft-json-output-file>"
 #   - "spdx-json=<spdx-json-output-file>"
-output: "syft-table"
+# SYFT_OUTPUT env var / -o, --output flags
+output: 
+  - "syft-table"
 
 # suppress all output (except for the SBOM report)
-# same as -q ; SYFT_QUIET env var
+# SYFT_QUIET env var / -q flag
 quiet: false
 
-# same as --file; write output report to a file (default is to write to stdout)
-file: ""
-
 # enable/disable checking for application updates on startup
-# same as SYFT_CHECK_FOR_APP_UPDATE env var
+# SYFT_CHECK_FOR_APP_UPDATE env var 
 check-for-app-update: true
 
-# allows users to specify which image source should be used to generate the sbom
-# valid values are: registry, docker, podman
-default-image-pull-source: ""
+# maximum number of workers used to process the list of package catalogers in parallel
+parallelism: 1
 
-# a list of globs to exclude from scanning. same as --exclude ; for example:
+# a list of globs to exclude from scanning, for example:
 # exclude:
 #   - "/etc/**"
 #   - "./out/**/*.json"
+# SYFT_EXCLUDE env var / --exclude flag
 exclude: []
 
-# allows users to exclude synthetic binary packages from the sbom
-# these packages are removed if an overlap with a non-synthetic package is found
-exclude-binary-overlap-by-ownership: true
-
 # os and/or architecture to use when referencing container images (e.g. "windows/armv6" or "arm64")
-# same as --platform; SYFT_PLATFORM env var
+# SYFT_PLATFORM env var / --platform flag
 platform: ""
 
+# the search space to look for file and package data (options: all-layers, squashed)
+# SYFT_SCOPE env var
+scope: "squashed"
+
 # set the list of package catalogers to use when generating the SBOM
 # default = empty (cataloger set determined automatically by the source type [image or file/directory])
-# catalogers:
-#   - alpm-db-cataloger
-#   - apkdb-cataloger
-#   - binary-cataloger
-#   - cargo-auditable-binary-cataloger
-#   - cocoapods-cataloger
-#   - conan-cataloger
-#   - dartlang-lock-cataloger
-#   - dotnet-deps-cataloger
-#   - dotnet-portable-executable-cataloger
-#   - dpkg-db-cataloger
-#   - elixir-mix-lock-cataloger
-#   - erlang-rebar-lock-cataloger
-#   - go-module-file-cataloger
-#   - go-module-binary-cataloger
-#   - graalvm-native-image-cataloger
-#   - haskell-cataloger
-#   - java-cataloger
-#   - java-gradle-lockfile-cataloger
-#   - java-pom-cataloger
-#   - javascript-lock-cataloger
-#   - javascript-package-cataloger
-#   - linux-kernel-cataloger
-#   - nix-store-cataloger
-#   - php-composer-installed-cataloger
-#   - php-composer-lock-cataloger
-#   - portage-cataloger
-#   - python-package-cataloger
-#   - python-installed-package-cataloger
-#   - rpm-db-cataloger
-#   - rpm-archive-cataloger
-#   - ruby-gemfile-cataloger
-#   - ruby-installed-gemspec-cataloger
-#   - rust-cargo-lock-cataloger
-#   - sbom-cataloger
-#   - spm-cataloger
+# Use `syft cataloger list` for a list of catalogers you can specify
+# DEPRECATED: please use default-catalogers and select-catalogers configuration options instead
+# SYFT_CATALOGERS env var / --catalogers flag
 catalogers:
 
+# set the base set of catalogers to use (defaults to 'image' or 'directory' depending on the scan source)
+# SYFT_DEFAULT_CATALOGERS env var / --override-default-catalogers flag
+default-catalogers: []
+
+# add, remove, and filter the catalogers to be used
+# SYFT_SELECT_CATALOGERS env var / --select-catalogers flag;
+select-catalogers: []
 
 # all format configuration
 format:
  
   # default value for all formats that support the "pretty" option (default is unset)
+  # SYFT_FORMAT_PRETTY env var
   pretty: 
 
   # all syft-json format options
@@ -545,6 +566,7 @@ format:
 
     # include space indention and newlines (inherits default value from 'format.pretty' or 'false' if parent is unset)
     # note: inherits default value from 'format.pretty' or 'false' if parent is unset
+    # SYFT_FORMAT_JSON_PRETTY env var
     pretty: false
     
     # transform any syft-json output to conform to an approximation of the v11.0.1 schema. This includes:
@@ -554,21 +576,30 @@ format:
     # that output might not strictly be json schema v11 compliant, however, for consumers that require time to port
     # over to the final syft 1.0 json output this option can be used to ease the transition.
     #
-    # Note: long term support for this option is not guaranteed.
+    # Note: long term support for this option is not guaranteed (it may change or break at any time).
+    # SYFT_FORMAT_JSON_LEGACY env var
     legacy: false
 
   # all template format options
   template:
     # path to the template file to use when rendering the output with the `template` output format. 
     # Note that all template paths are based on the current syft-json schema.
-    # same as -t ; SYFT_TEMPLATE_PATH env var
+    # SYFT_FORMAT_TEMPLATE_PATH env var / -t flag 
     path: ""
+    
+    # if true, uses the go structs for the syft-json format for templating. 
+    # if false, uses the syft-json output for templating (which follows the syft JSON schema exactly).
+    #
+    # Note: long term support for this option is not guaranteed (it may change or break at any time).
+    # SYFT_FORMAT_TEMPLATE_LEGACY env var
+    legacy: false
 
   # all spdx-json format options
   spdx-json:
 
     # include space indention and newlines
     # note: inherits default value from 'format.pretty' or 'false' if parent is unset
+    # SYFT_FORMAT_SPDX_JSON_PRETTY env var
     pretty: false
 
   # all cyclonedx-json format options
@@ -576,6 +607,7 @@ format:
 
      # include space indention and newlines
      # note: inherits default value from 'format.pretty' or 'false' if parent is unset
+     # SYFT_FORMAT_CYCLONEDX_JSON_PRETTY env var
      pretty: false
 
   # all cyclonedx-xml format options
@@ -583,12 +615,41 @@ format:
 
      # include space indention
      # note: inherits default value from 'format.pretty' or 'false' if parent is unset
+     # SYFT_FORMAT_CYCLONEDX_XML_PRETTY env var
      pretty: false
 
 
+file:
+
+   metadata: 
+      # select which files should be captured by the file-metadata cataloger and included in the SBOM. 
+      # Options include:
+      #  - "all": capture all files from the search space
+      #  - "owned-by-package": capture only files owned by packages
+      #  - "none", "": do not capture any files
+      # SYFT_FILE_METADATA_SELECTION env var
+      selection: "owned-by-package"
+
+      # the file digest algorithms to use when cataloging files (options: "md5", "sha1", "sha224", "sha256", "sha384", "sha512")
+      # SYFT_FILE_METADATA_DIGESTS env var
+      digests:
+      - "sha256"
+      - "sha1"
+
+   # capture the contents of select files in the SBOM
+   content:
+      # skip searching a file entirely if it is above the given size (default = 1MB; unit = bytes)
+      # SYFT_FILE_CONTENT_SKIP_FILES_ABOVE_SIZE env var
+      skip-files-above-size: 1048576
+   
+      # file globs for the cataloger to match on
+      # SYFT_FILE_CONTENT_GLOBS env var
+      globs: []
+
+
 # cataloging packages is exposed through the packages and power-user subcommands
 package:
-
+   
   # search within archives that do contain a file index to search against (zip)
   # note: for now this only applies to the java package cataloger
   # SYFT_PACKAGE_SEARCH_INDEXED_ARCHIVES env var
@@ -600,14 +661,11 @@ package:
   # SYFT_PACKAGE_SEARCH_UNINDEXED_ARCHIVES env var
   search-unindexed-archives: false
 
-  cataloger:
-    # enable/disable cataloging of packages
-    # SYFT_PACKAGE_CATALOGER_ENABLED env var
-    enabled: true
+  # allows users to exclude synthetic binary packages from the sbom
+  # these packages are removed if an overlap with a non-synthetic package is found
+  # SYFT_PACKAGE_EXCLUDE_BINARY_OVERLAP_BY_OWNERSHIP env var
+  exclude-binary-overlap-by-ownership: true
 
-    # the search space to look for packages (options: all-layers, squashed)
-    # same as -s ; SYFT_PACKAGE_CATALOGER_SCOPE env var
-    scope: "squashed"
 
 golang:
    # search for go package licences in the GOPATH of the system running Syft, note that this is outside the
@@ -633,6 +691,24 @@ golang:
    # SYFT_GOLANG_NOPROXY env var
    no-proxy: ""
   
+   # the go main module version discovered from binaries built with the go compiler will
+   # always show (devel) as the version. Use these options to control heuristics to guess
+   # a more accurate version from the binary.
+   main-module-version:
+      
+      # look for LD flags that appear to be setting a version (e.g. -X main.version=1.0.0)
+      # SYFT_GOLANG_MAIN_MODULE_VERSION_FROM_LD_FLAGS env var
+      from-ld-flags: true
+      
+      # use the build settings (e.g. vcs.version & vcs.time) to craft a v0 pseudo version 
+      # (e.g. v0.0.0-20220308212642-53e6d0aaf6fb) when a more accurate version cannot be found otherwise.
+      # SYFT_GOLANG_MAIN_MODULE_VERSION_FROM_BUILD_SETTINGS env var
+      from-build-settings: true
+      
+      # search for semver-like strings in the binary contents.
+      # SYFT_GOLANG_MAIN_MODULE_VERSION_FROM_CONTENTS env var
+      from-contents: true
+  
 java:
    maven-url: "https://repo1.maven.org/maven2"
    max-parent-recursive-depth: 5
@@ -657,58 +733,38 @@ python:
    guess-unpinned-requirements: false
 
 javascript:
-   search-remote-licenses: false
-   npm-base-url: "https://registry.npmjs.org"
+  search-remote-licenses: false
+  npm-base-url: "https://registry.npmjs.org"
 
-file-contents:
-  cataloger:
-    # enable/disable cataloging of file contents
-    # SYFT_FILE_CONTENTS_CATALOGER_ENABLED env var
-    enabled: true
 
-    # the search space to look for file contents (options: all-layers, squashed)
-    # SYFT_FILE_CONTENTS_CATALOGER_SCOPE env var
-    scope: "squashed"
-
-  # skip searching a file entirely if it is above the given size (default = 1MB; unit = bytes)
-  # SYFT_FILE_CONTENTS_SKIP_FILES_ABOVE_SIZE env var
-  skip-files-above-size: 1048576
-
-  # file globs for the cataloger to match on
-  # SYFT_FILE_CONTENTS_GLOBS env var
-  globs: []
-
-file-metadata:
-  cataloger:
-    # enable/disable cataloging of file metadata
-    # SYFT_FILE_METADATA_CATALOGER_ENABLED env var
-    enabled: true
-
-    # the search space to look for file metadata (options: all-layers, squashed)
-    # SYFT_FILE_METADATA_CATALOGER_SCOPE env var
-    scope: "squashed"
-
-  # the file digest algorithms to use when cataloging files (options: "md5", "sha1", "sha224", "sha256", "sha384", "sha512")
-  # SYFT_FILE_METADATA_DIGESTS env var
-  digests: ["sha256"]
-
-# maximum number of workers used to process the list of package catalogers in parallel
-parallelism: 1
-
-# options that apply to all scan sources
+# configuration for the source that the SBOM is generated from (e.g. a file, directory, or container image)
 source:
   # alias name for the source
-  # SYFT_SOURCE_NAME env var; --source-name flag
+  # SYFT_SOURCE_NAME env var / --source-name flag
   name: ""
    
   # alias version for the source
-  # SYFT_SOURCE_VERSION env var; --source-version flag
+  # SYFT_SOURCE_VERSION env var / --source-version flag
   version: ""
-   
-  # options affecting the file source type
+
+  # base directory for scanning, no links will be followed above this directory, and all paths will be 
+  # reported relative to this directory
+  # SYFT_SOURCE_BASE_PATH env var
+  base-path: ''
+
+   # options affecting the file source type
   file:
     # the file digest algorithms to use on the scanned file (options: "md5", "sha1", "sha224", "sha256", "sha384", "sha512")
-    digests: ["sha256"]
+    digests: 
+     - "sha256"
+
+  image:
+     
+    # allows users to specify which image source should be used to generate the sbom
+    # valid values are: registry, docker, podman
+    # SYFT_SOURCE_IMAGE_DEFAULT_PULL_SOURCE env var
+    default-pull-source: ""
+
 
 # options when pulling directly from a registry via the "registry:" or "containerd:" scheme
 registry:
@@ -762,15 +818,15 @@ attest:
 
 log:
   # use structured logging
-  # same as SYFT_LOG_STRUCTURED env var
+  # SYFT_LOG_STRUCTURED env var
   structured: false
 
   # the log level; note: detailed logging suppress the ETUI
-  # same as SYFT_LOG_LEVEL env var
+  # SYFT_LOG_LEVEL env var
   level: "error"
 
   # location to write the log file (default is not to have a log file)
-  # same as SYFT_LOG_FILE env var
+  # SYFT_LOG_FILE env var
   file: ""
 ```
 

SECURITY.md

@@ -0,0 +1,32 @@
+# Security Policy
+
+## Supported Versions
+
+<!-- Use this section to tell people about which versions of your project are
+currently being supported with security updates.
+
+| Version | Supported          |
+| ------- | ------------------ |
+| 5.1.x   | :white_check_mark: |
+| 5.0.x   | :x:                |
+| 4.0.x   | :white_check_mark: |
+| < 4.0   | :x:                |
+
+-->
+
+Security updates are applied only to the most recent release, try to always be up to date.
+
+## Reporting a Vulnerability
+
+<!-- Use this section to tell people how to report a vulnerability.
+
+Tell them where to go, how often they can expect to get an update on a
+reported vulnerability, what to expect if the vulnerability is accepted or
+declined, etc. -->
+
+To report a security issue, please email
+[security@anchore.com](mailto:security@anchore.com)
+with a description of the issue, the steps you took to create the issue,
+affected versions, and, if known, mitigations for the issue.
+
+All support will be made on the best effort base, so please indicate the "urgency level" of the vulnerability as Critical, High, Medium or Low.

Taskfile.yaml

@@ -54,6 +54,7 @@ tasks:
       - task: check-licenses
       - task: lint
       - task: check-json-schema-drift
+      - task: check-binary-fixture-size
 
   test:
     desc: Run all levels of test
@@ -169,6 +170,11 @@ tasks:
     cmds:
       - .github/scripts/json-schema-drift-check.sh
 
+  check-binary-fixture-size:
+    desc: Ensure that the binary test fixtures are not too large
+    cmds:
+      - .github/scripts/check_binary_fixture_size.sh syft/pkg/cataloger/binary/test-fixtures/classifiers/snippets
+
 
   ## Testing tasks #################################
 
@@ -179,7 +185,7 @@ tasks:
       - fixtures
     vars:
       TEST_PKGS:
-        sh: "go list ./... | grep -v {{ .OWNER }}/{{ .PROJECT }}/test | tr '\n' ' '"
+        sh: "go list ./... | grep -v {{ .OWNER }}/{{ .PROJECT }}/test | grep -v {{ .OWNER }}/{{ .PROJECT }}/cmd/syft/internal/test | tr '\n' ' '"
 
       # unit test coverage threshold (in % coverage)
       COVERAGE_THRESHOLD: 62
@@ -191,7 +197,7 @@ tasks:
   integration:
     desc: Run integration tests
     cmds:
-      - "go test -v ./test/integration"
+      - "go test -v ./cmd/syft/internal/test/integration"
       # exercise most of the CLI with the data race detector
       - "go run -race cmd/syft/main.go alpine:latest"
 
@@ -259,7 +265,9 @@ tasks:
   fingerprints:
     desc: Generate test fixture fingerprints
     generates:
-      - test/integration/test-fixtures/cache.fingerprint
+      - cmd/syft/internal/test/integration/test-fixtures/cache.fingerprint
+      - syft/file/cataloger/executable/test-fixtures/elf/cache.fingerprint
+      - syft/file/cataloger/executable/test-fixtures/shared-info/cache.fingerprint
       - syft/pkg/cataloger/binary/test-fixtures/cache.fingerprint
       - syft/pkg/cataloger/java/test-fixtures/java-builds/cache.fingerprint
       - syft/pkg/cataloger/golang/test-fixtures/archs/binaries.fingerprint
@@ -268,19 +276,22 @@ tasks:
       - test/install/cache.fingerprint
       - test/cli/test-fixtures/cache.fingerprint
     cmds:
+      # for EXECUTABLE unit test fixtures
+      - "cd syft/file/cataloger/executable/test-fixtures/elf && make cache.fingerprint"
+      - "cd syft/file/cataloger/executable/test-fixtures/shared-info && make cache.fingerprint"
       # for IMAGE integration test fixtures
-      - "cd test/integration/test-fixtures && make cache.fingerprint"
-      # for BINARY test fixtures
+      - "cd cmd/syft/internal/test/integration/test-fixtures && make cache.fingerprint"
+      # for BINARY unit test fixtures
       - "cd syft/pkg/cataloger/binary/test-fixtures && make cache.fingerprint"
-      # for JAVA BUILD test fixtures
+      # for JAVA BUILD unit test fixtures
       - "cd syft/pkg/cataloger/java/test-fixtures/java-builds && make cache.fingerprint"
-      # for GO BINARY test fixtures
+      # for GO BINARY unit test fixtures
       - "cd syft/pkg/cataloger/golang/test-fixtures/archs && make binaries.fingerprint"
-      # for RPM test fixtures
+      # for RPM unit test fixtures
       - "cd syft/pkg/cataloger/redhat/test-fixtures && make rpms.fingerprint"
-      # for Kernel test fixtures
+      # for Kernel unit test fixtures
       - "cd syft/pkg/cataloger/kernel/test-fixtures && make cache.fingerprint"
-      # for INSTALL integration test fixtures
+      # for INSTALL test fixtures
       - "cd test/install && make cache.fingerprint"
       # for CLI test fixtures
       - "cd test/cli/test-fixtures && make cache.fingerprint"
@@ -288,6 +299,8 @@ tasks:
   fixtures:
     desc: Generate test fixtures
     cmds:
+      - "cd syft/file/cataloger/executable/test-fixtures/elf && make"
+      - "cd syft/file/cataloger/executable/test-fixtures/shared-info && make"
       - "cd syft/pkg/cataloger/java/test-fixtures/java-builds && make"
       - "cd syft/pkg/cataloger/redhat/test-fixtures && make"
       - "cd syft/pkg/cataloger/binary/test-fixtures && make"
@@ -377,7 +390,7 @@ tasks:
 
   generate-cpe-dictionary-index:
     desc: Generate the CPE index based off of the latest available CPE dictionary
-    dir: "syft/pkg/cataloger/common/cpe/dictionary"
+    dir: "syft/pkg/cataloger/internal/cpegenerate/dictionary"
     cmds:
       - "go generate"
 

cmd/syft/cli/cli.go

@@ -8,13 +8,8 @@ import (
 	"github.com/spf13/cobra"
 
 	"github.com/anchore/clio"
-	"github.com/anchore/stereoscope"
-	"github.com/anchore/syft/cmd/syft/cli/commands"
-	handler "github.com/anchore/syft/cmd/syft/cli/ui"
-	"github.com/anchore/syft/cmd/syft/internal/ui"
-	"github.com/anchore/syft/internal/bus"
-	"github.com/anchore/syft/internal/log"
-	"github.com/anchore/syft/internal/redact"
+	"github.com/anchore/syft/cmd/syft/internal"
+	"github.com/anchore/syft/cmd/syft/internal/commands"
 )
 
 // Application constructs the `syft packages` command and aliases the root command to `syft packages`.
@@ -34,65 +29,32 @@ func Command(id clio.Identification) *cobra.Command {
 }
 
 func create(id clio.Identification, out io.Writer) (clio.Application, *cobra.Command) {
-	clioCfg := clio.NewSetupConfig(id).
-		WithGlobalConfigFlag().   // add persistent -c <path> for reading an application config from
-		WithGlobalLoggingFlags(). // add persistent -v and -q flags tied to the logging config
-		WithConfigInRootHelp().   // --help on the root command renders the full application config in the help text
-		WithUIConstructor(
-			// select a UI based on the logging configuration and state of stdin (if stdin is a tty)
-			func(cfg clio.Config) ([]clio.UI, error) {
-				noUI := ui.None(out, cfg.Log.Quiet)
-				if !cfg.Log.AllowUI(os.Stdin) || cfg.Log.Quiet {
-					return []clio.UI{noUI}, nil
-				}
-
-				return []clio.UI{
-					ui.New(out, cfg.Log.Quiet,
-						handler.New(handler.DefaultHandlerConfig()),
-					),
-					noUI,
-				}, nil
-			},
-		).
-		WithInitializers(
-			func(state *clio.State) error {
-				// clio is setting up and providing the bus, redact store, and logger to the application. Once loaded,
-				// we can hoist them into the internal packages for global use.
-				stereoscope.SetBus(state.Bus)
-				bus.Set(state.Bus)
-
-				redact.Set(state.RedactStore)
-
-				log.Set(state.Logger)
-				stereoscope.SetLogger(state.Logger)
-
-				return nil
-			},
-		).
-		WithPostRuns(func(state *clio.State, err error) {
-			stereoscope.Cleanup()
-		})
+	clioCfg := internal.AppClioSetupConfig(id, out)
 
 	app := clio.New(*clioCfg)
 
 	// since root is aliased as the packages cmd we need to construct this command first
 	// we also need the command to have information about the `root` options because of this alias
-	packagesCmd := commands.Packages(app)
+	scanCmd := commands.Scan(app)
 
-	// rootCmd is currently an alias for the packages command
-	rootCmd := commands.Root(app, packagesCmd)
+	// root is currently an alias for the scan command
+	rootCmd := commands.Root(app, scanCmd)
 
 	// add sub-commands
 	rootCmd.AddCommand(
-		packagesCmd,
+		scanCmd,
+		commands.Packages(app, scanCmd), // this is currently an alias for the scan command
+		commands.Cataloger(app),
 		commands.Attest(app),
 		commands.Convert(app),
 		clio.VersionCommand(id),
 		cranecmd.NewCmdAuthLogin(id.Name), // syft login uses the same command as crane
 	)
 
-	// explicitly set Cobra output to the real stdout to write things like errors and help
-	rootCmd.SetOut(out)
+	// note: we would direct cobra to use our writer explicitly with rootCmd.SetOut(out) , however this causes
+	// deprecation warnings to be shown to stdout via the writer instead of stderr. This is unfortunate since this
+	// does not appear to be the correct behavior on cobra's part https://github.com/spf13/cobra/issues/1708 .
+	// In the future this functionality should be restored.
 
 	return app, rootCmd
 }

cmd/syft/cli/commands/packages.go

@@ -1,255 +0,0 @@
-package commands
-
-import (
-	"fmt"
-
-	"github.com/hashicorp/go-multierror"
-	"github.com/spf13/cobra"
-
-	"github.com/anchore/clio"
-	"github.com/anchore/stereoscope/pkg/image"
-	"github.com/anchore/syft/cmd/syft/cli/eventloop"
-	"github.com/anchore/syft/cmd/syft/cli/options"
-	"github.com/anchore/syft/cmd/syft/internal/ui"
-	"github.com/anchore/syft/internal"
-	"github.com/anchore/syft/internal/bus"
-	"github.com/anchore/syft/internal/file"
-	"github.com/anchore/syft/internal/log"
-	"github.com/anchore/syft/syft/artifact"
-	"github.com/anchore/syft/syft/sbom"
-	"github.com/anchore/syft/syft/source"
-)
-
-const (
-	packagesExample = `  {{.appName}} {{.command}} alpine:latest                                a summary of discovered packages
-  {{.appName}} {{.command}} alpine:latest -o json                        show all possible cataloging details
-  {{.appName}} {{.command}} alpine:latest -o cyclonedx                   show a CycloneDX formatted SBOM
-  {{.appName}} {{.command}} alpine:latest -o cyclonedx-json              show a CycloneDX JSON formatted SBOM
-  {{.appName}} {{.command}} alpine:latest -o spdx                        show a SPDX 2.3 Tag-Value formatted SBOM
-  {{.appName}} {{.command}} alpine:latest -o spdx@2.2                    show a SPDX 2.2 Tag-Value formatted SBOM
-  {{.appName}} {{.command}} alpine:latest -o spdx-json                   show a SPDX 2.3 JSON formatted SBOM
-  {{.appName}} {{.command}} alpine:latest -o spdx-json@2.2               show a SPDX 2.2 JSON formatted SBOM
-  {{.appName}} {{.command}} alpine:latest -vv                            show verbose debug information
-  {{.appName}} {{.command}} alpine:latest -o template -t my_format.tmpl  show a SBOM formatted according to given template file
-
-  Supports the following image sources:
-    {{.appName}} {{.command}} yourrepo/yourimage:tag     defaults to using images from a Docker daemon. If Docker is not present, the image is pulled directly from the registry.
-    {{.appName}} {{.command}} path/to/a/file/or/dir      a Docker tar, OCI tar, OCI directory, SIF container, or generic filesystem directory
-`
-
-	schemeHelpHeader = "You can also explicitly specify the scheme to use:"
-	imageSchemeHelp  = `    {{.appName}} {{.command}} docker:yourrepo/yourimage:tag            explicitly use the Docker daemon
-    {{.appName}} {{.command}} podman:yourrepo/yourimage:tag            explicitly use the Podman daemon
-    {{.appName}} {{.command}} registry:yourrepo/yourimage:tag          pull image directly from a registry (no container runtime required)
-    {{.appName}} {{.command}} docker-archive:path/to/yourimage.tar     use a tarball from disk for archives created from "docker save"
-    {{.appName}} {{.command}} oci-archive:path/to/yourimage.tar        use a tarball from disk for OCI archives (from Skopeo or otherwise)
-    {{.appName}} {{.command}} oci-dir:path/to/yourimage                read directly from a path on disk for OCI layout directories (from Skopeo or otherwise)
-    {{.appName}} {{.command}} singularity:path/to/yourimage.sif        read directly from a Singularity Image Format (SIF) container on disk
-`
-	nonImageSchemeHelp = `    {{.appName}} {{.command}} dir:path/to/yourproject                  read directly from a path on disk (any directory)
-    {{.appName}} {{.command}} file:path/to/yourproject/file            read directly from a path on disk (any single file)
-`
-	packagesSchemeHelp = "\n  " + schemeHelpHeader + "\n" + imageSchemeHelp + nonImageSchemeHelp
-
-	packagesHelp = packagesExample + packagesSchemeHelp
-)
-
-type packagesOptions struct {
-	options.Config      `yaml:",inline" mapstructure:",squash"`
-	options.Output      `yaml:",inline" mapstructure:",squash"`
-	options.UpdateCheck `yaml:",inline" mapstructure:",squash"`
-	options.Catalog     `yaml:",inline" mapstructure:",squash"`
-}
-
-func defaultPackagesOptions() *packagesOptions {
-	return &packagesOptions{
-		Output:      options.DefaultOutput(),
-		UpdateCheck: options.DefaultUpdateCheck(),
-		Catalog:     options.DefaultCatalog(),
-	}
-}
-
-//nolint:dupl
-func Packages(app clio.Application) *cobra.Command {
-	id := app.ID()
-
-	opts := defaultPackagesOptions()
-
-	return app.SetupCommand(&cobra.Command{
-		Use:   "packages [SOURCE]",
-		Short: "Generate a package SBOM",
-		Long:  "Generate a packaged-based Software Bill Of Materials (SBOM) from container images and filesystems",
-		Example: internal.Tprintf(packagesHelp, map[string]interface{}{
-			"appName": id.Name,
-			"command": "packages",
-		}),
-		Args:    validatePackagesArgs,
-		PreRunE: applicationUpdateCheck(id, &opts.UpdateCheck),
-		RunE: func(cmd *cobra.Command, args []string) error {
-			restoreStdout := ui.CaptureStdoutToTraceLog()
-			defer restoreStdout()
-
-			return runPackages(id, opts, args[0])
-		},
-	}, opts)
-}
-
-func validatePackagesArgs(cmd *cobra.Command, args []string) error {
-	return validateArgs(cmd, args, "an image/directory argument is required")
-}
-
-func validateArgs(cmd *cobra.Command, args []string, error string) error {
-	if len(args) == 0 {
-		// in the case that no arguments are given we want to show the help text and return with a non-0 return code.
-		if err := cmd.Help(); err != nil {
-			return fmt.Errorf("unable to display help: %w", err)
-		}
-		return fmt.Errorf(error)
-	}
-
-	return cobra.MaximumNArgs(1)(cmd, args)
-}
-
-// nolint:funlen
-func runPackages(id clio.Identification, opts *packagesOptions, userInput string) error {
-	writer, err := opts.SBOMWriter()
-	if err != nil {
-		return err
-	}
-
-	src, err := getSource(&opts.Catalog, userInput)
-
-	if err != nil {
-		return err
-	}
-
-	defer func() {
-		if src != nil {
-			if err := src.Close(); err != nil {
-				log.Tracef("unable to close source: %+v", err)
-			}
-		}
-	}()
-
-	s, err := generateSBOM(id, src, &opts.Catalog)
-	if err != nil {
-		return err
-	}
-
-	if s == nil {
-		return fmt.Errorf("no SBOM produced for %q", userInput)
-	}
-
-	if err := writer.Write(*s); err != nil {
-		return fmt.Errorf("failed to write SBOM: %w", err)
-	}
-
-	return nil
-}
-
-func getSource(opts *options.Catalog, userInput string, filters ...func(*source.Detection) error) (source.Source, error) {
-	detection, err := source.Detect(
-		userInput,
-		source.DetectConfig{
-			DefaultImageSource: opts.DefaultImagePullSource,
-		},
-	)
-	if err != nil {
-		return nil, fmt.Errorf("could not deteremine source: %w", err)
-	}
-
-	for _, filter := range filters {
-		if err := filter(detection); err != nil {
-			return nil, err
-		}
-	}
-
-	var platform *image.Platform
-
-	if opts.Platform != "" {
-		platform, err = image.NewPlatform(opts.Platform)
-		if err != nil {
-			return nil, fmt.Errorf("invalid platform: %w", err)
-		}
-	}
-
-	hashers, err := file.Hashers(opts.Source.File.Digests...)
-	if err != nil {
-		return nil, fmt.Errorf("invalid hash: %w", err)
-	}
-
-	src, err := detection.NewSource(
-		source.DetectionSourceConfig{
-			Alias: source.Alias{
-				Name:    opts.Source.Name,
-				Version: opts.Source.Version,
-			},
-			RegistryOptions: opts.Registry.ToOptions(),
-			Platform:        platform,
-			Exclude: source.ExcludeConfig{
-				Paths: opts.Exclusions,
-			},
-			DigestAlgorithms: hashers,
-			BasePath:         opts.BasePath,
-		},
-	)
-
-	if err != nil {
-		if userInput == "power-user" {
-			bus.Notify("Note: the 'power-user' command has been removed.")
-		}
-		return nil, fmt.Errorf("failed to construct source from user input %q: %w", userInput, err)
-	}
-
-	return src, nil
-}
-
-func generateSBOM(id clio.Identification, src source.Source, opts *options.Catalog) (*sbom.SBOM, error) {
-	tasks, err := eventloop.Tasks(opts)
-	if err != nil {
-		return nil, err
-	}
-
-	s := sbom.SBOM{
-		Source: src.Describe(),
-		Descriptor: sbom.Descriptor{
-			Name:          id.Name,
-			Version:       id.Version,
-			Configuration: opts,
-		},
-	}
-
-	err = buildRelationships(&s, src, tasks)
-
-	return &s, err
-}
-
-func buildRelationships(s *sbom.SBOM, src source.Source, tasks []eventloop.Task) error {
-	var errs error
-
-	var relationships []<-chan artifact.Relationship
-	for _, task := range tasks {
-		c := make(chan artifact.Relationship)
-		relationships = append(relationships, c)
-		go func(task eventloop.Task) {
-			err := eventloop.RunTask(task, &s.Artifacts, src, c)
-			if err != nil {
-				errs = multierror.Append(errs, err)
-			}
-		}(task)
-	}
-
-	s.Relationships = append(s.Relationships, mergeRelationships(relationships...)...)
-
-	return errs
-}
-
-func mergeRelationships(cs ...<-chan artifact.Relationship) (relationships []artifact.Relationship) {
-	for _, c := range cs {
-		for n := range c {
-			relationships = append(relationships, n)
-		}
-	}
-
-	return relationships
-}

cmd/syft/cli/eventloop/tasks.go

@@ -1,151 +0,0 @@
-package eventloop
-
-import (
-	"github.com/anchore/syft/cmd/syft/cli/options"
-	"github.com/anchore/syft/internal/file"
-	"github.com/anchore/syft/syft"
-	"github.com/anchore/syft/syft/artifact"
-	"github.com/anchore/syft/syft/file/cataloger/filecontent"
-	"github.com/anchore/syft/syft/file/cataloger/filedigest"
-	"github.com/anchore/syft/syft/file/cataloger/filemetadata"
-	"github.com/anchore/syft/syft/sbom"
-	"github.com/anchore/syft/syft/source"
-)
-
-type Task func(*sbom.Artifacts, source.Source) ([]artifact.Relationship, error)
-
-func Tasks(opts *options.Catalog) ([]Task, error) {
-	var tasks []Task
-
-	generators := []func(opts *options.Catalog) (Task, error){
-		generateCatalogPackagesTask,
-		generateCatalogFileMetadataTask,
-		generateCatalogFileDigestsTask,
-		generateCatalogContentsTask,
-	}
-
-	for _, generator := range generators {
-		task, err := generator(opts)
-		if err != nil {
-			return nil, err
-		}
-
-		if task != nil {
-			tasks = append(tasks, task)
-		}
-	}
-
-	return tasks, nil
-}
-
-func generateCatalogPackagesTask(opts *options.Catalog) (Task, error) {
-	if !opts.Package.Cataloger.Enabled {
-		return nil, nil
-	}
-
-	task := func(results *sbom.Artifacts, src source.Source) ([]artifact.Relationship, error) {
-		packageCatalog, relationships, theDistro, err := syft.CatalogPackages(src, opts.ToCatalogerConfig())
-
-		results.Packages = packageCatalog
-		results.LinuxDistribution = theDistro
-
-		return relationships, err
-	}
-
-	return task, nil
-}
-
-func generateCatalogFileMetadataTask(opts *options.Catalog) (Task, error) {
-	if !opts.FileMetadata.Cataloger.Enabled {
-		return nil, nil
-	}
-
-	metadataCataloger := filemetadata.NewCataloger()
-
-	task := func(results *sbom.Artifacts, src source.Source) ([]artifact.Relationship, error) {
-		resolver, err := src.FileResolver(opts.FileMetadata.Cataloger.GetScope())
-		if err != nil {
-			return nil, err
-		}
-
-		result, err := metadataCataloger.Catalog(resolver)
-		if err != nil {
-			return nil, err
-		}
-		results.FileMetadata = result
-		return nil, nil
-	}
-
-	return task, nil
-}
-
-func generateCatalogFileDigestsTask(opts *options.Catalog) (Task, error) {
-	if !opts.FileMetadata.Cataloger.Enabled {
-		return nil, nil
-	}
-
-	hashes, err := file.Hashers(opts.FileMetadata.Digests...)
-	if err != nil {
-		return nil, err
-	}
-
-	digestsCataloger := filedigest.NewCataloger(hashes)
-
-	task := func(results *sbom.Artifacts, src source.Source) ([]artifact.Relationship, error) {
-		resolver, err := src.FileResolver(opts.FileMetadata.Cataloger.GetScope())
-		if err != nil {
-			return nil, err
-		}
-
-		result, err := digestsCataloger.Catalog(resolver)
-		if err != nil {
-			return nil, err
-		}
-		results.FileDigests = result
-		return nil, nil
-	}
-
-	return task, nil
-}
-
-func generateCatalogContentsTask(opts *options.Catalog) (Task, error) {
-	if !opts.FileContents.Cataloger.Enabled {
-		return nil, nil
-	}
-
-	contentsCataloger, err := filecontent.NewCataloger(opts.FileContents.Globs, opts.FileContents.SkipFilesAboveSize) //nolint:staticcheck
-	if err != nil {
-		return nil, err
-	}
-
-	task := func(results *sbom.Artifacts, src source.Source) ([]artifact.Relationship, error) {
-		resolver, err := src.FileResolver(opts.FileContents.Cataloger.GetScope())
-		if err != nil {
-			return nil, err
-		}
-
-		result, err := contentsCataloger.Catalog(resolver)
-		if err != nil {
-			return nil, err
-		}
-		results.FileContents = result
-		return nil, nil
-	}
-
-	return task, nil
-}
-
-func RunTask(t Task, a *sbom.Artifacts, src source.Source, c chan<- artifact.Relationship) error {
-	defer close(c)
-
-	relationships, err := t(a, src)
-	if err != nil {
-		return err
-	}
-
-	for _, relationship := range relationships {
-		c <- relationship
-	}
-
-	return nil
-}

cmd/syft/cli/options/catalog.go

@@ -1,181 +0,0 @@
-package options
-
-import (
-	"fmt"
-	"sort"
-	"strings"
-
-	"github.com/iancoleman/strcase"
-	"github.com/mitchellh/go-homedir"
-	"github.com/scylladb/go-set/strset"
-
-	"github.com/anchore/clio"
-	"github.com/anchore/fangs"
-	"github.com/anchore/syft/internal/log"
-	"github.com/anchore/syft/syft/cataloging"
-	"github.com/anchore/syft/syft/pkg/cataloger"
-	golangCataloger "github.com/anchore/syft/syft/pkg/cataloger/golang"
-	javaCataloger "github.com/anchore/syft/syft/pkg/cataloger/java"
-	javascriptCataloger "github.com/anchore/syft/syft/pkg/cataloger/javascript"
-	"github.com/anchore/syft/syft/pkg/cataloger/kernel"
-	pythonCataloger "github.com/anchore/syft/syft/pkg/cataloger/python"
-	"github.com/anchore/syft/syft/source"
-)
-
-type Catalog struct {
-	Catalogers                      []string     `yaml:"catalogers" json:"catalogers" mapstructure:"catalogers"`
-	Package                         pkg          `yaml:"package" json:"package" mapstructure:"package"`
-	Golang                          golang       `yaml:"golang" json:"golang" mapstructure:"golang"`
-	Java                            java         `yaml:"java" json:"java" mapstructure:"java"`
-	Javascript                      javascript   `yaml:"javascript" json:"javascript" mapstructure:"javascript"`
-	LinuxKernel                     linuxKernel  `yaml:"linux-kernel" json:"linux-kernel" mapstructure:"linux-kernel"`
-	Python                          python       `yaml:"python" json:"python" mapstructure:"python"`
-	FileMetadata                    fileMetadata `yaml:"file-metadata" json:"file-metadata" mapstructure:"file-metadata"`
-	FileContents                    fileContents `yaml:"file-contents" json:"file-contents" mapstructure:"file-contents"`
-	Registry                        registry     `yaml:"registry" json:"registry" mapstructure:"registry"`
-	Exclusions                      []string     `yaml:"exclude" json:"exclude" mapstructure:"exclude"`
-	Platform                        string       `yaml:"platform" json:"platform" mapstructure:"platform"`
-	Name                            string       `yaml:"name" json:"name" mapstructure:"name"`
-	Source                          sourceCfg    `yaml:"source" json:"source" mapstructure:"source"`
-	Parallelism                     int          `yaml:"parallelism" json:"parallelism" mapstructure:"parallelism"`                                                                         // the number of catalog workers to run in parallel
-	DefaultImagePullSource          string       `yaml:"default-image-pull-source" json:"default-image-pull-source" mapstructure:"default-image-pull-source"`                               // specify default image pull source
-	BasePath                        string       `yaml:"base-path" json:"base-path" mapstructure:"base-path"`                                                                               // specify base path for all file paths
-	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
-}
-
-var _ interface {
-	clio.FlagAdder
-	clio.PostLoader
-} = (*Catalog)(nil)
-
-func DefaultCatalog() Catalog {
-	return Catalog{
-		Package:                         defaultPkg(),
-		LinuxKernel:                     defaultLinuxKernel(),
-		FileMetadata:                    defaultFileMetadata(),
-		FileContents:                    defaultFileContents(),
-		Source:                          defaultSourceCfg(),
-		Parallelism:                     1,
-		ExcludeBinaryOverlapByOwnership: true,
-	}
-}
-
-func (cfg *Catalog) AddFlags(flags clio.FlagSet) {
-	var validScopeValues []string
-	for _, scope := range source.AllScopes {
-		validScopeValues = append(validScopeValues, strcase.ToDelimited(string(scope), '-'))
-	}
-	flags.StringVarP(&cfg.Package.Cataloger.Scope, "scope", "s",
-		fmt.Sprintf("selection of layers to catalog, options=%v", validScopeValues))
-
-	flags.StringVarP(&cfg.Platform, "platform", "",
-		"an optional platform specifier for container image sources (e.g. 'linux/arm64', 'linux/arm64/v8', 'arm64', 'linux')")
-
-	flags.StringArrayVarP(&cfg.Exclusions, "exclude", "",
-		"exclude paths from being scanned using a glob expression")
-
-	flags.StringArrayVarP(&cfg.Catalogers, "catalogers", "",
-		"enable one or more package catalogers")
-
-	flags.StringVarP(&cfg.Source.Name, "name", "",
-		"set the name of the target being analyzed")
-
-	if pfp, ok := flags.(fangs.PFlagSetProvider); ok {
-		flagSet := pfp.PFlagSet()
-		flagSet.Lookup("name").Deprecated = "use: source-name"
-	}
-
-	flags.StringVarP(&cfg.Source.Name, "source-name", "",
-		"set the name of the target being analyzed")
-
-	flags.StringVarP(&cfg.Source.Version, "source-version", "",
-		"set the version of the target being analyzed")
-
-	flags.StringVarP(&cfg.BasePath, "base-path", "",
-		"base directory for scanning, no links will be followed above this directory, and all paths will be reported relative to this directory")
-}
-
-func (cfg *Catalog) PostLoad() error {
-	// parse options on this struct
-	var catalogers []string
-	for _, c := range cfg.Catalogers {
-		for _, f := range strings.Split(c, ",") {
-			catalogers = append(catalogers, strings.TrimSpace(f))
-		}
-	}
-	sort.Strings(catalogers)
-	cfg.Catalogers = catalogers
-
-	if err := checkDefaultSourceValues(cfg.DefaultImagePullSource); err != nil {
-		return err
-	}
-
-	if cfg.Name != "" {
-		log.Warnf("name parameter is deprecated. please use: source-name. name will be removed in a future version")
-		if cfg.Source.Name == "" {
-			cfg.Source.Name = cfg.Name
-		}
-	}
-
-	return nil
-}
-
-func (cfg Catalog) ToCatalogerConfig() cataloger.Config {
-	return cataloger.Config{
-		Search: cataloger.SearchConfig{
-			IncludeIndexedArchives:   cfg.Package.SearchIndexedArchives,
-			IncludeUnindexedArchives: cfg.Package.SearchUnindexedArchives,
-			Scope:                    cfg.Package.Cataloger.GetScope(),
-		},
-		Catalogers:  cfg.Catalogers,
-		Parallelism: cfg.Parallelism,
-		Golang: golangCataloger.DefaultCatalogerConfig().
-			WithSearchLocalModCacheLicenses(cfg.Golang.SearchLocalModCacheLicenses).
-			WithLocalModCacheDir(cfg.Golang.LocalModCacheDir).
-			WithSearchRemoteLicenses(cfg.Golang.SearchRemoteLicenses).
-			WithProxy(cfg.Golang.Proxy).
-			WithNoProxy(cfg.Golang.NoProxy),
-		LinuxKernel: kernel.LinuxKernelCatalogerConfig{
-			CatalogModules: cfg.LinuxKernel.CatalogModules,
-		},
-		Java: javaCataloger.DefaultArchiveCatalogerConfig().
-			WithUseNetwork(cfg.Java.UseNetwork).
-			WithMavenBaseURL(cfg.Java.MavenURL).
-			WithArchiveTraversal(
-				cataloging.ArchiveSearchConfig{
-					IncludeIndexedArchives:   cfg.Package.SearchIndexedArchives,
-					IncludeUnindexedArchives: cfg.Package.SearchUnindexedArchives,
-				},
-				cfg.Java.MaxParentRecursiveDepth),
-		Javascript: javascriptCataloger.DefaultCatalogerConfig().
-			WithSearchRemoteLicenses(cfg.Javascript.SearchRemoteLicenses).
-			WithNpmBaseURL(cfg.Javascript.NpmBaseURL),
-		Python: pythonCataloger.CatalogerConfig{
-			GuessUnpinnedRequirements: cfg.Python.GuessUnpinnedRequirements,
-		},
-		ExcludeBinaryOverlapByOwnership: cfg.ExcludeBinaryOverlapByOwnership,
-	}
-}
-
-var validDefaultSourceValues = []string{"registry", "docker", "podman", ""}
-
-func checkDefaultSourceValues(source string) error {
-	validValues := strset.New(validDefaultSourceValues...)
-	if !validValues.Has(source) {
-		validValuesString := strings.Join(validDefaultSourceValues, ", ")
-		return fmt.Errorf("%s is not a valid default source; please use one of the following: %s''", source, validValuesString)
-	}
-
-	return nil
-}
-
-func expandFilePath(file string) (string, error) {
-	if file != "" {
-		expandedPath, err := homedir.Expand(file)
-		if err != nil {
-			return "", fmt.Errorf("unable to expand file path=%q: %w", file, err)
-		}
-		file = expandedPath
-	}
-	return file, nil
-}

cmd/syft/cli/options/config.go

@@ -1,6 +0,0 @@
-package options
-
-// Config holds a reference to the specific config file that was used to load application configuration
-type Config struct {
-	ConfigFile string `yaml:"config" json:"config" mapstructure:"config"`
-}

cmd/syft/cli/options/file_contents.go

@@ -1,21 +0,0 @@
-package options
-
-import (
-	"github.com/anchore/syft/internal/file"
-	"github.com/anchore/syft/syft/source"
-)
-
-type fileContents struct {
-	Cataloger          scope    `yaml:"cataloger" json:"cataloger" mapstructure:"cataloger"`
-	SkipFilesAboveSize int64    `yaml:"skip-files-above-size" json:"skip-files-above-size" mapstructure:"skip-files-above-size"`
-	Globs              []string `yaml:"globs" json:"globs" mapstructure:"globs"`
-}
-
-func defaultFileContents() fileContents {
-	return fileContents{
-		Cataloger: scope{
-			Scope: source.SquashedScope.String(),
-		},
-		SkipFilesAboveSize: 1 * file.MB,
-	}
-}

cmd/syft/cli/options/file_metadata.go

@@ -1,19 +0,0 @@
-package options
-
-import (
-	"github.com/anchore/syft/syft/source"
-)
-
-type fileMetadata struct {
-	Cataloger scope    `yaml:"cataloger" json:"cataloger" mapstructure:"cataloger"`
-	Digests   []string `yaml:"digests" json:"digests" mapstructure:"digests"`
-}
-
-func defaultFileMetadata() fileMetadata {
-	return fileMetadata{
-		Cataloger: scope{
-			Scope: source.SquashedScope.String(),
-		},
-		Digests: []string{"sha256"},
-	}
-}

cmd/syft/cli/options/format.go

@@ -1,129 +0,0 @@
-package options
-
-import (
-	"fmt"
-
-	"github.com/hashicorp/go-multierror"
-
-	"github.com/anchore/clio"
-	"github.com/anchore/syft/syft/format/cyclonedxjson"
-	"github.com/anchore/syft/syft/format/cyclonedxxml"
-	"github.com/anchore/syft/syft/format/github"
-	"github.com/anchore/syft/syft/format/spdxjson"
-	"github.com/anchore/syft/syft/format/spdxtagvalue"
-	"github.com/anchore/syft/syft/format/syftjson"
-	"github.com/anchore/syft/syft/format/table"
-	"github.com/anchore/syft/syft/format/template"
-	"github.com/anchore/syft/syft/format/text"
-	"github.com/anchore/syft/syft/sbom"
-)
-
-var _ clio.PostLoader = (*Format)(nil)
-
-// Format contains all user configuration for output formatting.
-type Format struct {
-	Pretty        *bool               `yaml:"pretty" json:"pretty" mapstructure:"pretty"`
-	Template      FormatTemplate      `yaml:"template" json:"template" mapstructure:"template"`
-	SyftJSON      FormatSyftJSON      `yaml:"json" json:"json" mapstructure:"json"`
-	SPDXJSON      FormatSPDXJSON      `yaml:"spdx-json" json:"spdx-json" mapstructure:"spdx-json"`
-	CyclonedxJSON FormatCyclonedxJSON `yaml:"cyclonedx-json" json:"cyclonedx-json" mapstructure:"cyclonedx-json"`
-	CyclonedxXML  FormatCyclonedxXML  `yaml:"cyclonedx-xml" json:"cyclonedx-xml" mapstructure:"cyclonedx-xml"`
-}
-
-func (o *Format) PostLoad() error {
-	o.SyftJSON.Pretty = multiLevelOption[bool](false, o.Pretty, o.SyftJSON.Pretty)
-	o.SPDXJSON.Pretty = multiLevelOption[bool](false, o.Pretty, o.SPDXJSON.Pretty)
-	o.CyclonedxJSON.Pretty = multiLevelOption[bool](false, o.Pretty, o.CyclonedxJSON.Pretty)
-	o.CyclonedxXML.Pretty = multiLevelOption[bool](false, o.Pretty, o.CyclonedxXML.Pretty)
-
-	return nil
-}
-
-func DefaultFormat() Format {
-	return Format{
-		Template:      DefaultFormatTemplate(),
-		SyftJSON:      DefaultFormatJSON(),
-		SPDXJSON:      DefaultFormatSPDXJSON(),
-		CyclonedxJSON: DefaultFormatCyclonedxJSON(),
-		CyclonedxXML:  DefaultFormatCyclonedxXML(),
-	}
-}
-
-func (o *Format) Encoders() ([]sbom.FormatEncoder, error) {
-	// setup all encoders based on the configuration
-	var list encoderList
-
-	// in the future there will be application configuration options that can be used to set the default output format
-	list.addWithErr(template.ID)(o.Template.formatEncoders())
-	list.addWithErr(syftjson.ID)(o.SyftJSON.formatEncoders())
-	list.add(table.ID)(table.NewFormatEncoder())
-	list.add(text.ID)(text.NewFormatEncoder())
-	list.add(github.ID)(github.NewFormatEncoder())
-	list.addWithErr(cyclonedxxml.ID)(o.CyclonedxXML.formatEncoders())
-	list.addWithErr(cyclonedxjson.ID)(o.CyclonedxJSON.formatEncoders())
-	list.addWithErr(spdxjson.ID)(o.SPDXJSON.formatEncoders())
-	list.addWithErr(spdxtagvalue.ID)(spdxTagValueEncoders())
-
-	return list.encoders, list.err
-}
-
-// TODO: when application configuration is made for this format then this should be ported to the options object
-// that is created for that configuration (as done with the template output option)
-func spdxTagValueEncoders() ([]sbom.FormatEncoder, error) {
-	var (
-		encs []sbom.FormatEncoder
-		errs error
-	)
-	for _, v := range spdxtagvalue.SupportedVersions() {
-		enc, err := spdxtagvalue.NewFormatEncoderWithConfig(spdxtagvalue.EncoderConfig{Version: v})
-		if err != nil {
-			errs = multierror.Append(errs, err)
-		} else {
-			encs = append(encs, enc)
-		}
-	}
-	return encs, errs
-}
-
-type encoderList struct {
-	encoders []sbom.FormatEncoder
-	err      error
-}
-
-func (l *encoderList) addWithErr(name sbom.FormatID) func([]sbom.FormatEncoder, error) {
-	return func(encs []sbom.FormatEncoder, err error) {
-		if err != nil {
-			l.err = multierror.Append(l.err, fmt.Errorf("unable to configure %q format encoder: %w", name, err))
-			return
-		}
-		for _, enc := range encs {
-			if enc == nil {
-				l.err = multierror.Append(l.err, fmt.Errorf("unable to configure %q format encoder: nil encoder returned", name))
-				continue
-			}
-			l.encoders = append(l.encoders, enc)
-		}
-	}
-}
-
-func (l *encoderList) add(name sbom.FormatID) func(...sbom.FormatEncoder) {
-	return func(encs ...sbom.FormatEncoder) {
-		for _, enc := range encs {
-			if enc == nil {
-				l.err = multierror.Append(l.err, fmt.Errorf("unable to configure %q format encoder: nil encoder returned", name))
-				continue
-			}
-			l.encoders = append(l.encoders, enc)
-		}
-	}
-}
-
-func multiLevelOption[T any](defaultValue T, option ...*T) *T {
-	result := defaultValue
-	for _, opt := range option {
-		if opt != nil {
-			result = *opt
-		}
-	}
-	return &result
-}

cmd/syft/cli/options/format_cyclonedx_json.go

@@ -1,43 +0,0 @@
-package options
-
-import (
-	"github.com/hashicorp/go-multierror"
-
-	"github.com/anchore/syft/syft/format/cyclonedxjson"
-	"github.com/anchore/syft/syft/sbom"
-)
-
-type FormatCyclonedxJSON struct {
-	Pretty *bool `yaml:"pretty" json:"pretty" mapstructure:"pretty"`
-}
-
-func DefaultFormatCyclonedxJSON() FormatCyclonedxJSON {
-	return FormatCyclonedxJSON{}
-}
-
-func (o FormatCyclonedxJSON) formatEncoders() ([]sbom.FormatEncoder, error) {
-	var (
-		encs []sbom.FormatEncoder
-		errs error
-	)
-	for _, v := range cyclonedxjson.SupportedVersions() {
-		enc, err := cyclonedxjson.NewFormatEncoderWithConfig(o.buildConfig(v))
-		if err != nil {
-			errs = multierror.Append(errs, err)
-		} else {
-			encs = append(encs, enc)
-		}
-	}
-	return encs, errs
-}
-
-func (o FormatCyclonedxJSON) buildConfig(version string) cyclonedxjson.EncoderConfig {
-	var pretty bool
-	if o.Pretty != nil {
-		pretty = *o.Pretty
-	}
-	return cyclonedxjson.EncoderConfig{
-		Version: version,
-		Pretty:  pretty,
-	}
-}

cmd/syft/cli/options/format_cyclonedx_xml.go

@@ -1,43 +0,0 @@
-package options
-
-import (
-	"github.com/hashicorp/go-multierror"
-
-	"github.com/anchore/syft/syft/format/cyclonedxxml"
-	"github.com/anchore/syft/syft/sbom"
-)
-
-type FormatCyclonedxXML struct {
-	Pretty *bool `yaml:"pretty" json:"pretty" mapstructure:"pretty"`
-}
-
-func DefaultFormatCyclonedxXML() FormatCyclonedxXML {
-	return FormatCyclonedxXML{}
-}
-
-func (o FormatCyclonedxXML) formatEncoders() ([]sbom.FormatEncoder, error) {
-	var (
-		encs []sbom.FormatEncoder
-		errs error
-	)
-	for _, v := range cyclonedxxml.SupportedVersions() {
-		enc, err := cyclonedxxml.NewFormatEncoderWithConfig(o.buildConfig(v))
-		if err != nil {
-			errs = multierror.Append(errs, err)
-		} else {
-			encs = append(encs, enc)
-		}
-	}
-	return encs, errs
-}
-
-func (o FormatCyclonedxXML) buildConfig(version string) cyclonedxxml.EncoderConfig {
-	var pretty bool
-	if o.Pretty != nil {
-		pretty = *o.Pretty
-	}
-	return cyclonedxxml.EncoderConfig{
-		Version: version,
-		Pretty:  pretty,
-	}
-}

cmd/syft/cli/options/format_spdx_json.go

@@ -1,43 +0,0 @@
-package options
-
-import (
-	"github.com/hashicorp/go-multierror"
-
-	"github.com/anchore/syft/syft/format/spdxjson"
-	"github.com/anchore/syft/syft/sbom"
-)
-
-type FormatSPDXJSON struct {
-	Pretty *bool `yaml:"pretty" json:"pretty" mapstructure:"pretty"`
-}
-
-func DefaultFormatSPDXJSON() FormatSPDXJSON {
-	return FormatSPDXJSON{}
-}
-
-func (o FormatSPDXJSON) formatEncoders() ([]sbom.FormatEncoder, error) {
-	var (
-		encs []sbom.FormatEncoder
-		errs error
-	)
-	for _, v := range spdxjson.SupportedVersions() {
-		enc, err := spdxjson.NewFormatEncoderWithConfig(o.buildConfig(v))
-		if err != nil {
-			errs = multierror.Append(errs, err)
-		} else {
-			encs = append(encs, enc)
-		}
-	}
-	return encs, errs
-}
-
-func (o FormatSPDXJSON) buildConfig(v string) spdxjson.EncoderConfig {
-	var pretty bool
-	if o.Pretty != nil {
-		pretty = *o.Pretty
-	}
-	return spdxjson.EncoderConfig{
-		Version: v,
-		Pretty:  pretty,
-	}
-}

cmd/syft/cli/options/golang.go

@@ -1,9 +0,0 @@
-package options
-
-type golang struct {
-	SearchLocalModCacheLicenses bool   `json:"search-local-mod-cache-licenses" yaml:"search-local-mod-cache-licenses" mapstructure:"search-local-mod-cache-licenses"`
-	LocalModCacheDir            string `json:"local-mod-cache-dir" yaml:"local-mod-cache-dir" mapstructure:"local-mod-cache-dir"`
-	SearchRemoteLicenses        bool   `json:"search-remote-licenses" yaml:"search-remote-licenses" mapstructure:"search-remote-licenses"`
-	Proxy                       string `json:"proxy" yaml:"proxy" mapstructure:"proxy"`
-	NoProxy                     string `json:"no-proxy" yaml:"no-proxy" mapstructure:"no-proxy"`
-}

cmd/syft/cli/options/pkg.go

@@ -1,23 +0,0 @@
-package options
-
-import (
-	"github.com/anchore/syft/syft/pkg/cataloger"
-)
-
-type pkg struct {
-	Cataloger               scope `yaml:"cataloger" json:"cataloger" mapstructure:"cataloger"`
-	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"`
-}
-
-func defaultPkg() pkg {
-	c := cataloger.DefaultSearchConfig()
-	return pkg{
-		SearchIndexedArchives:   c.IncludeIndexedArchives,
-		SearchUnindexedArchives: c.IncludeUnindexedArchives,
-		Cataloger: scope{
-			Enabled: true,
-			Scope:   c.Scope.String(),
-		},
-	}
-}

cmd/syft/cli/options/scope.go

@@ -1,27 +0,0 @@
-package options
-
-import (
-	"fmt"
-
-	"github.com/anchore/clio"
-	"github.com/anchore/syft/syft/source"
-)
-
-type scope struct {
-	Enabled bool   `yaml:"enabled" json:"enabled" mapstructure:"enabled"`
-	Scope   string `yaml:"scope" json:"scope" mapstructure:"scope"`
-}
-
-var _ clio.PostLoader = (*scope)(nil)
-
-func (opt *scope) PostLoad() error {
-	s := opt.GetScope()
-	if s == source.UnknownScope {
-		return fmt.Errorf("bad scope value %v", opt.Scope)
-	}
-	return nil
-}
-
-func (opt scope) GetScope() source.Scope {
-	return source.ParseScope(opt.Scope)
-}

cmd/syft/cli/options/source.go

@@ -1,19 +0,0 @@
-package options
-
-type sourceCfg struct {
-	Name    string     `json:"name" yaml:"name" mapstructure:"name"`
-	Version string     `json:"version" yaml:"version" mapstructure:"version"`
-	File    fileSource `json:"file" yaml:"file" mapstructure:"file"`
-}
-
-type fileSource struct {
-	Digests []string `json:"digests" yaml:"digests" mapstructure:"digests"`
-}
-
-func defaultSourceCfg() sourceCfg {
-	return sourceCfg{
-		File: fileSource{
-			Digests: []string{"sha256"},
-		},
-	}
-}

cmd/syft/cli/ui/__snapshots__/handle_file_digests_cataloger_test.snap

@@ -1,8 +0,0 @@
-
-[TestHandler_handleFileDigestsCatalogerStarted/cataloging_in_progress - 1]
- ⠋ Cataloging file digests         ━━━━━━━━━━━━━━━━━━━━  [current]  
----
-
-[TestHandler_handleFileDigestsCatalogerStarted/cataloging_complete - 1]
- ✔ Cataloged file digests          
----

cmd/syft/cli/ui/__snapshots__/handle_file_metadata_cataloger_test.snap

@@ -1,8 +0,0 @@
-
-[TestHandler_handleFileMetadataCatalogerStarted/cataloging_in_progress - 1]
- ⠋ Cataloging file metadata        ━━━━━━━━━━━━━━━━━━━━  [current]  
----
-
-[TestHandler_handleFileMetadataCatalogerStarted/cataloging_complete - 1]
- ✔ Cataloged file metadata         
----

cmd/syft/cli/ui/__snapshots__/handle_package_cataloger_test.snap

@@ -1,16 +0,0 @@
-
-[TestHandler_handlePackageCatalogerStarted/cataloging_in_progress - 1]
- ⠋ Cataloging packages             [50 packages]  
----
-
-[TestHandler_handlePackageCatalogerStarted/cataloging_only_files_complete - 1]
- ⠋ Cataloging packages             [50 packages]  
----
-
-[TestHandler_handlePackageCatalogerStarted/cataloging_only_packages_complete - 1]
- ⠋ Cataloging packages             [100 packages]  
----
-
-[TestHandler_handlePackageCatalogerStarted/cataloging_complete - 1]
- ✔ Cataloged packages              [100 packages]  
----

cmd/syft/cli/ui/__snapshots__/handle_secrets_cataloger_test.snap

@@ -1,8 +0,0 @@
-
-[TestHandler_handleSecretsCatalogerStarted/cataloging_in_progress - 1]
- ⠋ Cataloging secrets              ━━━━━━━━━━━━━━━━━━━━  [64 secrets]  
----
-
-[TestHandler_handleSecretsCatalogerStarted/cataloging_complete - 1]
- ✔ Cataloged secrets               [64 secrets]  
----

cmd/syft/internal/clio_setup_config.go

@@ -0,0 +1,55 @@
+package internal
+
+import (
+	"io"
+	"os"
+
+	"github.com/anchore/clio"
+	"github.com/anchore/stereoscope"
+	ui2 "github.com/anchore/syft/cmd/syft/cli/ui"
+	"github.com/anchore/syft/cmd/syft/internal/ui"
+	"github.com/anchore/syft/internal/bus"
+	"github.com/anchore/syft/internal/log"
+	"github.com/anchore/syft/internal/redact"
+)
+
+func AppClioSetupConfig(id clio.Identification, out io.Writer) *clio.SetupConfig {
+	clioCfg := clio.NewSetupConfig(id).
+		WithGlobalConfigFlag().   // add persistent -c <path> for reading an application config from
+		WithGlobalLoggingFlags(). // add persistent -v and -q flags tied to the logging config
+		WithConfigInRootHelp().   // --help on the root command renders the full application config in the help text
+		WithUIConstructor(
+			// select a UI based on the logging configuration and state of stdin (if stdin is a tty)
+			func(cfg clio.Config) ([]clio.UI, error) {
+				noUI := ui.None(out, cfg.Log.Quiet)
+				if !cfg.Log.AllowUI(os.Stdin) || cfg.Log.Quiet {
+					return []clio.UI{noUI}, nil
+				}
+
+				return []clio.UI{
+					ui.New(out, cfg.Log.Quiet,
+						ui2.New(ui2.DefaultHandlerConfig()),
+					),
+					noUI,
+				}, nil
+			},
+		).
+		WithInitializers(
+			func(state *clio.State) error {
+				// clio is setting up and providing the bus, redact store, and logger to the application. Once loaded,
+				// we can hoist them into the internal packages for global use.
+				stereoscope.SetBus(state.Bus)
+				bus.Set(state.Bus)
+
+				redact.Set(state.RedactStore)
+
+				log.Set(state.Logger)
+				stereoscope.SetLogger(state.Logger)
+				return nil
+			},
+		).
+		WithPostRuns(func(_ *clio.State, _ error) {
+			stereoscope.Cleanup()
+		})
+	return clioCfg
+}

cmd/syft/internal/commands/attest.go

@@ -1,6 +1,7 @@
 package commands
 
 import (
+	"context"
 	"fmt"
 	"io"
 	"os"
@@ -12,7 +13,8 @@ import (
 	"github.com/wagoodman/go-progress"
 
 	"github.com/anchore/clio"
-	"github.com/anchore/syft/cmd/syft/cli/options"
+	"github.com/anchore/stereoscope"
+	"github.com/anchore/syft/cmd/syft/internal/options"
 	"github.com/anchore/syft/cmd/syft/internal/ui"
 	"github.com/anchore/syft/internal"
 	"github.com/anchore/syft/internal/bus"
@@ -25,11 +27,10 @@ import (
 	"github.com/anchore/syft/syft/format/spdxtagvalue"
 	"github.com/anchore/syft/syft/format/syftjson"
 	"github.com/anchore/syft/syft/sbom"
-	"github.com/anchore/syft/syft/source"
 )
 
 const (
-	attestExample = `  {{.appName}} {{.command}} --output [FORMAT] alpine:latest defaults to using images from a Docker daemon. If Docker is not present, the image is pulled directly from the registry
+	attestExample = `  {{.appName}} {{.command}} --output [FORMAT] alpine:latest            defaults to using images from a Docker daemon. If Docker is not present, the image is pulled directly from the registry
 `
 	attestSchemeHelp = "\n  " + schemeHelpHeader + "\n" + imageSchemeHelp
 	attestHelp       = attestExample + attestSchemeHelp
@@ -41,7 +42,7 @@ type attestOptions struct {
 	options.Output      `yaml:",inline" mapstructure:",squash"`
 	options.UpdateCheck `yaml:",inline" mapstructure:",squash"`
 	options.Catalog     `yaml:",inline" mapstructure:",squash"`
-	options.Attest      `yaml:",inline" mapstructure:",squash"`
+	Attest              options.Attest `yaml:"attest" mapstructure:"attest"`
 }
 
 func Attest(app clio.Application) *cobra.Command {
@@ -60,13 +61,13 @@ func Attest(app clio.Application) *cobra.Command {
 			"appName": id.Name,
 			"command": "attest",
 		}),
-		Args:    validatePackagesArgs,
+		Args:    validateScanArgs,
 		PreRunE: applicationUpdateCheck(id, &opts.UpdateCheck),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			restoreStdout := ui.CaptureStdoutToTraceLog()
 			defer restoreStdout()
 
-			return runAttest(id, &opts, args[0])
+			return runAttest(cmd.Context(), id, &opts, args[0])
 		},
 	}, &opts)
 }
@@ -98,7 +99,7 @@ func defaultAttestOutputOptions() options.Output {
 }
 
 //nolint:funlen
-func runAttest(id clio.Identification, opts *attestOptions, userInput string) error {
+func runAttest(ctx context.Context, id clio.Identification, opts *attestOptions, userInput string) error {
 	// TODO: what other validation here besides binary name?
 	if !commandExists(cosignBinName) {
 		return fmt.Errorf("'syft attest' requires cosign to be installed, however it does not appear to be on PATH")
@@ -111,7 +112,7 @@ func runAttest(id clio.Identification, opts *attestOptions, userInput string) er
 	}
 	defer os.Remove(f.Name())
 
-	s, err := generateSBOMForAttestation(id, &opts.Catalog, userInput)
+	s, err := generateSBOMForAttestation(ctx, id, &opts.Catalog, userInput)
 	if err != nil {
 		return fmt.Errorf("unable to build SBOM: %w", err)
 	}
@@ -231,7 +232,7 @@ func attestCommand(sbomFilepath string, opts *attestOptions, userInput string) (
 }
 
 func predicateType(outputName string) string {
-	// Select Cosign predicate type based on defined output type
+	// select the Cosign predicate type based on defined output type
 	// As orientation, check: https://github.com/sigstore/cosign/blob/main/pkg/cosign/attestation/attestation.go
 	switch strings.ToLower(outputName) {
 	case "cyclonedx-json":
@@ -245,8 +246,12 @@ func predicateType(outputName string) string {
 	}
 }
 
-func generateSBOMForAttestation(id clio.Identification, opts *options.Catalog, userInput string) (*sbom.SBOM, error) {
-	src, err := getSource(opts, userInput, onlyContainerImages)
+func generateSBOMForAttestation(ctx context.Context, id clio.Identification, opts *options.Catalog, userInput string) (*sbom.SBOM, error) {
+	if len(opts.From) > 1 || (len(opts.From) == 1 && opts.From[0] != stereoscope.RegistryTag) {
+		return nil, fmt.Errorf("attest requires use of an OCI registry directly, one or more of the specified sources is unsupported: %v", opts.From)
+	}
+
+	src, err := getSource(ctx, opts, userInput, stereoscope.RegistryTag)
 
 	if err != nil {
 		return nil, err
@@ -260,7 +265,7 @@ func generateSBOMForAttestation(id clio.Identification, opts *options.Catalog, u
 		}
 	}()
 
-	s, err := generateSBOM(id, src, opts)
+	s, err := generateSBOM(ctx, id, src, opts)
 	if err != nil {
 		return nil, err
 	}
@@ -272,13 +277,6 @@ func generateSBOMForAttestation(id clio.Identification, opts *options.Catalog, u
 	return s, nil
 }
 
-func onlyContainerImages(d *source.Detection) error {
-	if !d.IsContainerImage() {
-		return fmt.Errorf("attestations are only supported for oci images at this time")
-	}
-	return nil
-}
-
 func commandExists(cmd string) bool {
 	_, err := exec.LookPath(cmd)
 	return err == nil

cmd/syft/internal/commands/attest_test.go

@@ -2,18 +2,24 @@ package commands
 
 import (
 	"bytes"
+	"context"
 	"fmt"
+	"io"
 	"os/exec"
 	"regexp"
 	"strings"
 	"testing"
 
+	"github.com/google/go-cmp/cmp"
 	"github.com/scylladb/go-set/strset"
+	"github.com/spf13/cobra"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 
 	"github.com/anchore/clio"
-	"github.com/anchore/syft/cmd/syft/cli/options"
+	"github.com/anchore/clio/cliotestutils"
+	"github.com/anchore/syft/cmd/syft/internal"
+	"github.com/anchore/syft/cmd/syft/internal/options"
 	"github.com/anchore/syft/syft/sbom"
 	"github.com/anchore/syft/syft/source"
 )
@@ -258,7 +264,7 @@ func Test_buildSBOMForAttestation(t *testing.T) {
 			if tt.wantErr == nil {
 				tt.wantErr = require.NoError
 			}
-			_, err := generateSBOMForAttestation(tt.args.id, tt.args.opts, tt.args.userInput)
+			_, err := generateSBOMForAttestation(context.Background(), tt.args.id, tt.args.opts, tt.args.userInput)
 			tt.wantErr(t, err)
 			if err != nil {
 				return
@@ -266,3 +272,60 @@ func Test_buildSBOMForAttestation(t *testing.T) {
 		})
 	}
 }
+
+func Test_attestCLIWiring(t *testing.T) {
+	id := clio.Identification{
+		Name:    "syft",
+		Version: "testing",
+	}
+	cfg := internal.AppClioSetupConfig(id, io.Discard)
+	tests := []struct {
+		name          string
+		assertionFunc func(*testing.T, *cobra.Command, []string, ...any)
+		wantOpts      attestOptions
+		args          []string
+		env           map[string]string
+	}{
+		{
+			name:          "key flag is accepted",
+			args:          []string{"some-image:some-tag", "--key", "some-cosign-key.key"},
+			assertionFunc: hasAttestOpts(options.Attest{Key: "some-cosign-key.key"}),
+		},
+		{
+			name: "key password is read from env",
+			args: []string{"some-image:some-tag", "--key", "cosign.key"},
+			env: map[string]string{
+				"SYFT_ATTEST_PASSWORD": "some-password",
+			},
+			assertionFunc: hasAttestOpts(options.Attest{
+				Key:      "cosign.key",
+				Password: "some-password",
+			}),
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if tt.env != nil {
+				for k, v := range tt.env {
+					t.Setenv(k, v)
+				}
+			}
+			app := cliotestutils.NewApplication(t, cfg, tt.assertionFunc)
+			cmd := Attest(app)
+			cmd.SetArgs(tt.args)
+			err := cmd.Execute()
+			assert.NoError(t, err)
+		})
+	}
+}
+
+func hasAttestOpts(wantOpts options.Attest) cliotestutils.AssertionFunc {
+	return func(t *testing.T, _ *cobra.Command, _ []string, cfgs ...any) {
+		assert.Equal(t, len(cfgs), 1)
+		attestOpts, ok := cfgs[0].(*attestOptions)
+		require.True(t, ok)
+		if d := cmp.Diff(wantOpts, attestOpts.Attest); d != "" {
+			t.Errorf("mismatched attest options (-want +got):\n%s", d)
+		}
+	}
+}

cmd/syft/internal/commands/cataloger.go

@@ -0,0 +1,20 @@
+package commands
+
+import (
+	"github.com/spf13/cobra"
+
+	"github.com/anchore/clio"
+)
+
+func Cataloger(app clio.Application) *cobra.Command {
+	cmd := &cobra.Command{
+		Use:   "cataloger",
+		Short: "Show available catalogers and configuration",
+	}
+
+	cmd.AddCommand(
+		CatalogerList(app),
+	)
+
+	return cmd
+}

cmd/syft/internal/commands/cataloger_list.go

@@ -0,0 +1,267 @@
+package commands
+
+import (
+	"encoding/json"
+	"fmt"
+	"sort"
+	"strings"
+
+	"github.com/charmbracelet/lipgloss"
+	"github.com/jedib0t/go-pretty/v6/table"
+	"github.com/scylladb/go-set/strset"
+	"github.com/spf13/cobra"
+
+	"github.com/anchore/clio"
+	"github.com/anchore/syft/internal/bus"
+	"github.com/anchore/syft/internal/task"
+	"github.com/anchore/syft/syft/cataloging/pkgcataloging"
+)
+
+type catalogerListOptions struct {
+	Output            string   `yaml:"output" json:"output" mapstructure:"output"`
+	DefaultCatalogers []string `yaml:"default-catalogers" json:"default-catalogers" mapstructure:"default-catalogers"`
+	SelectCatalogers  []string `yaml:"select-catalogers" json:"select-catalogers" mapstructure:"select-catalogers"`
+	ShowHidden        bool     `yaml:"show-hidden" json:"show-hidden" mapstructure:"show-hidden"`
+}
+
+func (o *catalogerListOptions) AddFlags(flags clio.FlagSet) {
+	flags.StringVarP(&o.Output, "output", "o", "format to output the cataloger list (available: table, json)")
+
+	flags.StringArrayVarP(&o.DefaultCatalogers, "override-default-catalogers", "", "override the default catalogers with an expression")
+
+	flags.StringArrayVarP(&o.SelectCatalogers, "select-catalogers", "", "select catalogers with an expression")
+
+	flags.BoolVarP(&o.ShowHidden, "show-hidden", "s", "show catalogers that have been de-selected")
+}
+
+func defaultCatalogerListOptions() *catalogerListOptions {
+	return &catalogerListOptions{
+		DefaultCatalogers: []string{"all"},
+	}
+}
+
+func CatalogerList(app clio.Application) *cobra.Command {
+	opts := defaultCatalogerListOptions()
+
+	return app.SetupCommand(&cobra.Command{
+		Use:   "list [OPTIONS]",
+		Short: "List available catalogers",
+		RunE: func(_ *cobra.Command, _ []string) error {
+			return runCatalogerList(opts)
+		},
+	}, opts)
+}
+
+func runCatalogerList(opts *catalogerListOptions) error {
+	factories := task.DefaultPackageTaskFactories()
+	allTasks, err := factories.Tasks(task.DefaultCatalogingFactoryConfig())
+	if err != nil {
+		return fmt.Errorf("unable to create cataloger tasks: %w", err)
+	}
+
+	report, err := catalogerListReport(opts, allTasks)
+	if err != nil {
+		return fmt.Errorf("unable to generate cataloger list report: %w", err)
+	}
+
+	bus.Report(report)
+
+	return nil
+}
+
+func catalogerListReport(opts *catalogerListOptions, allTasks []task.Task) (string, error) {
+	selectedTasks, selectionEvidence, err := task.Select(allTasks,
+		pkgcataloging.NewSelectionRequest().
+			WithDefaults(opts.DefaultCatalogers...).
+			WithExpression(opts.SelectCatalogers...),
+	)
+	if err != nil {
+		return "", fmt.Errorf("unable to select catalogers: %w", err)
+	}
+	var report string
+
+	switch opts.Output {
+	case "json":
+		report, err = renderCatalogerListJSON(selectedTasks, selectionEvidence, opts.DefaultCatalogers, opts.SelectCatalogers)
+	case "table", "":
+		if opts.ShowHidden {
+			report = renderCatalogerListTable(allTasks, selectionEvidence, opts.DefaultCatalogers, opts.SelectCatalogers)
+		} else {
+			report = renderCatalogerListTable(selectedTasks, selectionEvidence, opts.DefaultCatalogers, opts.SelectCatalogers)
+		}
+	}
+
+	if err != nil {
+		return "", fmt.Errorf("unable to render cataloger list: %w", err)
+	}
+
+	return report, nil
+}
+
+func renderCatalogerListJSON(tasks []task.Task, selection task.Selection, defaultSelections, selections []string) (string, error) {
+	type node struct {
+		Name string   `json:"name"`
+		Tags []string `json:"tags"`
+	}
+
+	names, tagsByName := extractTaskInfo(tasks)
+
+	nodesByName := make(map[string]node)
+
+	for name := range tagsByName {
+		tagsSelected := selection.TokensByTask[name].SelectedOn.List()
+
+		if len(tagsSelected) == 1 && tagsSelected[0] == "all" {
+			tagsSelected = tagsByName[name]
+		}
+
+		sort.Strings(tagsSelected)
+
+		if tagsSelected == nil {
+			// ensure collections are not null
+			tagsSelected = []string{}
+		}
+
+		nodesByName[name] = node{
+			Name: name,
+			Tags: tagsSelected,
+		}
+	}
+
+	type document struct {
+		DefaultSelection []string `json:"default"`
+		Selection        []string `json:"selection"`
+		Catalogers       []node   `json:"catalogers"`
+	}
+
+	if selections == nil {
+		// ensure collections are not null
+		selections = []string{}
+	}
+
+	doc := document{
+		DefaultSelection: defaultSelections,
+		Selection:        selections,
+	}
+
+	for _, name := range names {
+		doc.Catalogers = append(doc.Catalogers, nodesByName[name])
+	}
+
+	by, err := json.Marshal(doc)
+
+	return string(by), err
+}
+
+func renderCatalogerListTable(tasks []task.Task, selection task.Selection, defaultSelections, selections []string) string {
+	t := table.NewWriter()
+	t.SetStyle(table.StyleLight)
+	t.AppendHeader(table.Row{"Cataloger", "Tags"})
+
+	names, tagsByName := extractTaskInfo(tasks)
+
+	rowsByName := make(map[string]table.Row)
+
+	for name, tags := range tagsByName {
+		rowsByName[name] = formatRow(name, tags, selection)
+	}
+
+	for _, name := range names {
+		t.AppendRow(rowsByName[name])
+	}
+
+	report := t.Render()
+
+	if len(selections) > 0 {
+		header := "Selected by expressions:\n"
+		for _, expr := range selections {
+			header += fmt.Sprintf("  - %q\n", expr)
+		}
+		report = header + report
+	}
+
+	if len(defaultSelections) > 0 {
+		header := "Default selections:\n"
+		for _, expr := range defaultSelections {
+			header += fmt.Sprintf("  - %q\n", expr)
+		}
+		report = header + report
+	}
+
+	return report
+}
+
+func formatRow(name string, tags []string, selection task.Selection) table.Row {
+	isIncluded := selection.Result.Has(name)
+	var selections *task.TokenSelection
+	if s, exists := selection.TokensByTask[name]; exists {
+		selections = &s
+	}
+
+	var formattedTags []string
+	for _, tag := range tags {
+		formattedTags = append(formattedTags, formatToken(tag, selections, isIncluded))
+	}
+
+	var tagStr string
+	if isIncluded {
+		tagStr = strings.Join(formattedTags, ", ")
+	} else {
+		tagStr = strings.Join(formattedTags, grey.Render(", "))
+	}
+
+	// TODO: selection should keep warnings (non-selections) in struct
+
+	return table.Row{
+		formatToken(name, selections, isIncluded),
+		tagStr,
+	}
+}
+
+var (
+	green = lipgloss.NewStyle().Foreground(lipgloss.Color("10")) // hi green
+	grey  = lipgloss.NewStyle().Foreground(lipgloss.Color("8"))  // dark grey
+	red   = lipgloss.NewStyle().Foreground(lipgloss.Color("9"))  // high red
+)
+
+func formatToken(token string, selection *task.TokenSelection, included bool) string {
+	if included && selection != nil {
+		// format all tokens in selection in green
+		if selection.SelectedOn.Has(token) {
+			return green.Render(token)
+		}
+
+		return token
+	}
+
+	// format all tokens in selection in red, all others in grey
+	if selection != nil && selection.DeselectedOn.Has(token) {
+		return red.Render(token)
+	}
+
+	return grey.Render(token)
+}
+
+func extractTaskInfo(tasks []task.Task) ([]string, map[string][]string) {
+	tagsByName := make(map[string][]string)
+	var names []string
+
+	for _, tsk := range tasks {
+		var tags []string
+		name := tsk.Name()
+
+		if s, ok := tsk.(task.Selector); ok {
+			set := strset.New(s.Selectors()...)
+			set.Remove(name)
+			tags = set.List()
+			sort.Strings(tags)
+		}
+
+		tagsByName[name] = tags
+		names = append(names, name)
+	}
+
+	sort.Strings(names)
+
+	return names, tagsByName
+}

cmd/syft/internal/commands/cataloger_list_test.go

@@ -0,0 +1,201 @@
+package commands
+
+import (
+	"context"
+	"strings"
+	"testing"
+
+	"github.com/scylladb/go-set/strset"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/anchore/syft/internal/sbomsync"
+	"github.com/anchore/syft/internal/task"
+	"github.com/anchore/syft/syft/file"
+)
+
+var _ interface {
+	task.Task
+	task.Selector
+} = (*dummyTask)(nil)
+
+type dummyTask struct {
+	name      string
+	selectors []string
+}
+
+func (d dummyTask) HasAllSelectors(s ...string) bool {
+	return strset.New(d.selectors...).Has(s...)
+}
+
+func (d dummyTask) Selectors() []string {
+	return d.selectors
+}
+
+func (d dummyTask) Name() string {
+	return d.name
+}
+
+func (d dummyTask) Execute(_ context.Context, _ file.Resolver, _ sbomsync.Builder) error {
+	panic("implement me")
+}
+
+func testTasks() []task.Task {
+	return []task.Task{
+		dummyTask{
+			name:      "task1",
+			selectors: []string{"image", "a", "b", "1"},
+		},
+		dummyTask{
+			name:      "task2",
+			selectors: []string{"image", "b", "c", "2"},
+		},
+		dummyTask{
+			name:      "task3",
+			selectors: []string{"directory", "c", "d", "3"},
+		},
+		dummyTask{
+			name:      "task4",
+			selectors: []string{"directory", "d", "e", "4"},
+		},
+	}
+}
+
+func Test_catalogerListReport(t *testing.T) {
+	tests := []struct {
+		name    string
+		options *catalogerListOptions
+		want    string
+		wantErr require.ErrorAssertionFunc
+	}{
+		{
+			name: "no expressions, table",
+			options: func() *catalogerListOptions {
+				c := defaultCatalogerListOptions()
+				c.Output = "table"
+				return c
+			}(),
+			want: `
+Default selections:
+  - "all"
+┌───────────┬────────────────────┐
+│ CATALOGER │ TAGS               │
+├───────────┼────────────────────┤
+│ task1     │ 1, a, b, image     │
+│ task2     │ 2, b, c, image     │
+│ task3     │ 3, c, d, directory │
+│ task4     │ 4, d, directory, e │
+└───────────┴────────────────────┘
+`,
+		},
+		{
+			name: "no expressions, json",
+			options: func() *catalogerListOptions {
+				c := defaultCatalogerListOptions()
+				c.Output = "json"
+				return c
+			}(),
+			want: `
+{"default":["all"],"selection":[],"catalogers":[{"name":"task1","tags":["1","a","b","image"]},{"name":"task2","tags":["2","b","c","image"]},{"name":"task3","tags":["3","c","d","directory"]},{"name":"task4","tags":["4","d","directory","e"]}]}
+`,
+		},
+		{
+			name: "no expressions, default selection, table",
+			options: func() *catalogerListOptions {
+				c := defaultCatalogerListOptions()
+				c.Output = "table"
+				c.DefaultCatalogers = []string{
+					"image",
+				}
+				return c
+			}(),
+			want: `
+Default selections:
+  - "image"
+┌───────────┬────────────────┐
+│ CATALOGER │ TAGS           │
+├───────────┼────────────────┤
+│ task1     │ 1, a, b, image │
+│ task2     │ 2, b, c, image │
+└───────────┴────────────────┘
+`,
+		},
+		{
+			name: "no expressions, default selection, json",
+			options: func() *catalogerListOptions {
+				c := defaultCatalogerListOptions()
+				c.Output = "json"
+				c.DefaultCatalogers = []string{
+					"image",
+				}
+				return c
+			}(),
+			want: `
+{"default":["image"],"selection":[],"catalogers":[{"name":"task1","tags":["image"]},{"name":"task2","tags":["image"]}]}
+`,
+		},
+		{
+			name: "with expressions, default selection, table",
+			options: func() *catalogerListOptions {
+				c := defaultCatalogerListOptions()
+				c.Output = "table"
+				c.DefaultCatalogers = []string{
+					"image",
+				}
+				c.SelectCatalogers = []string{
+					"-directory",
+					"+task3",
+					"-c",
+					"b",
+				}
+				return c
+			}(),
+			want: `
+Default selections:
+  - "image"
+Selected by expressions:
+  - "-directory"
+  - "+task3"
+  - "-c"
+  - "b"
+┌───────────┬────────────────────┐
+│ CATALOGER │ TAGS               │
+├───────────┼────────────────────┤
+│ task1     │ 1, a, b, image     │
+│ task3     │ 3, c, d, directory │
+└───────────┴────────────────────┘
+`,
+		},
+		{
+			name: "with expressions, default selection, json",
+			options: func() *catalogerListOptions {
+				c := defaultCatalogerListOptions()
+				c.Output = "json"
+				c.DefaultCatalogers = []string{
+					"image",
+				}
+				c.SelectCatalogers = []string{
+					"-directory",
+					"+task3",
+					"-c",
+					"b",
+				}
+				return c
+			}(),
+			want: `
+{"default":["image"],"selection":["-directory","+task3","-c","b"],"catalogers":[{"name":"task1","tags":["b","image"]},{"name":"task3","tags":["task3"]}]}
+`,
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if tt.wantErr == nil {
+				tt.wantErr = require.NoError
+			}
+
+			got, err := catalogerListReport(tt.options, testTasks())
+			tt.wantErr(t, err)
+			assert.Equal(t, strings.TrimSpace(tt.want), strings.TrimSpace(got))
+		})
+	}
+}

cmd/syft/internal/commands/commands_test.go

@@ -0,0 +1,20 @@
+package commands
+
+import (
+	"os"
+	"testing"
+
+	gologgerredact "github.com/anchore/go-logger/adapter/redact"
+	"github.com/anchore/syft/internal/redact"
+)
+
+func TestMain(m *testing.M) {
+	// Initialize global state needed to test clio/cobra commands directly
+	// Should be kept minimal.
+
+	// Initialize redact store once for all tests in the commands package
+	// Redact store must be wired up here because syft will panic unless
+	// a redact store is wired up exactly once
+	redact.Set(gologgerredact.NewStore())
+	os.Exit(m.Run())
+}

cmd/syft/internal/commands/convert.go

@@ -8,7 +8,7 @@ import (
 	"github.com/spf13/cobra"
 
 	"github.com/anchore/clio"
-	"github.com/anchore/syft/cmd/syft/cli/options"
+	"github.com/anchore/syft/cmd/syft/internal/options"
 	"github.com/anchore/syft/cmd/syft/internal/ui"
 	"github.com/anchore/syft/internal"
 	"github.com/anchore/syft/internal/log"
@@ -47,7 +47,7 @@ func Convert(app clio.Application) *cobra.Command {
 		}),
 		Args:    validateConvertArgs,
 		PreRunE: applicationUpdateCheck(id, &opts.UpdateCheck),
-		RunE: func(cmd *cobra.Command, args []string) error {
+		RunE: func(_ *cobra.Command, args []string) error {
 			restoreStdout := ui.CaptureStdoutToTraceLog()
 			defer restoreStdout()
 

cmd/syft/internal/commands/packages.go

@@ -0,0 +1,37 @@
+package commands
+
+import (
+	"github.com/spf13/cobra"
+
+	"github.com/anchore/clio"
+	"github.com/anchore/syft/cmd/syft/internal/ui"
+	"github.com/anchore/syft/internal"
+)
+
+func Packages(app clio.Application, scanCmd *cobra.Command) *cobra.Command {
+	id := app.ID()
+
+	opts := defaultScanOptions()
+
+	cmd := app.SetupCommand(&cobra.Command{
+		Use:   "packages [SOURCE]",
+		Short: scanCmd.Short,
+		Long:  scanCmd.Long,
+		Args:  scanCmd.Args,
+		Example: internal.Tprintf(scanHelp, map[string]interface{}{
+			"appName": id.Name,
+			"command": "packages",
+		}),
+		PreRunE: applicationUpdateCheck(id, &opts.UpdateCheck),
+		RunE: func(cmd *cobra.Command, args []string) error {
+			restoreStdout := ui.CaptureStdoutToTraceLog()
+			defer restoreStdout()
+
+			return runScan(cmd.Context(), id, opts, args[0])
+		},
+	}, opts)
+
+	cmd.Deprecated = "use `syft scan` instead"
+
+	return cmd
+}

cmd/syft/internal/commands/packages_test.go

@@ -0,0 +1,300 @@
+package commands
+
+import (
+	"errors"
+	"fmt"
+	"testing"
+
+	"github.com/hashicorp/go-multierror"
+	"github.com/stretchr/testify/assert"
+
+	"github.com/anchore/syft/internal/task"
+)
+
+func Test_filterExpressionErrors_expressionErrorsHelp(t *testing.T) {
+	tests := []struct {
+		name        string
+		err         error
+		wantExpErrs []task.ErrInvalidExpression
+		wantErr     assert.ErrorAssertionFunc
+		wantHelp    string
+	}{
+		{
+			name:        "no errors",
+			err:         nil,
+			wantExpErrs: nil,
+			wantErr:     assert.NoError,
+			wantHelp:    "",
+		},
+		{
+			name: "single non-expression error is retained",
+			err:  errors.New("foo"),
+			wantErr: func(t assert.TestingT, err error, i ...interface{}) bool {
+				return assert.Equal(t, "foo", err.Error())
+			},
+			wantHelp: "",
+		},
+		{
+			name: "multiple non-expression sibling errors are retained",
+			err: func() error {
+				var err error
+				err = multierror.Append(err, errors.New("foo"))
+				err = multierror.Append(err, errors.New("bar"))
+				return err
+			}(),
+			wantErr: func(t assert.TestingT, err error, i ...interface{}) bool {
+				// note: this is the default formatting from the hashicorp multierror object
+				expected := `2 errors occurred:
+	* foo
+	* bar
+
+`
+				return assert.Equal(t, expected, err.Error())
+			},
+			wantHelp: "",
+		},
+		{
+			name: "has multiple expression errors (with sibling errors)",
+			err: func() error {
+				var err error
+				err = multierror.Append(err, errors.New("foo"))
+				err = multierror.Append(err, task.ErrInvalidExpression{Expression: "foo", Operation: task.AddOperation, Err: task.ErrTagsNotAllowed})
+				err = multierror.Append(err, errors.New("bar"))
+				err = multierror.Append(err, task.ErrInvalidExpression{Expression: "bar", Operation: task.SubSelectOperation, Err: task.ErrNamesNotAllowed})
+				err = multierror.Append(err, errors.New("last"))
+				return err
+			}(),
+			wantErr: func(t assert.TestingT, err error, i ...interface{}) bool {
+				expected := `5 errors occurred:
+	* foo
+	* invalid expression: "foo": tags are not allowed with this operation (must use exact names)
+	* bar
+	* invalid expression: "bar": names are not allowed with this operation (must use tags)
+	* last
+
+`
+				return assert.Equal(t, expected, err.Error())
+			},
+			wantExpErrs: []task.ErrInvalidExpression{
+				{Expression: "foo", Operation: task.AddOperation, Err: task.ErrTagsNotAllowed},
+				{Expression: "bar", Operation: task.SubSelectOperation, Err: task.ErrNamesNotAllowed},
+			},
+			wantHelp: `Suggestions:
+
+ ❖ Given expression "--select-catalogers foo"
+   However, tags are not allowed with this operation (must use exact names).
+   Adding groups of catalogers may result in surprising behavior (create inaccurate SBOMs).
+   If you are certain this is what you want to do, use "--override-default-catalogers foo" instead.
+
+ ❖ Given expression "--select-catalogers bar"
+   However, names are not allowed with this operation (must use tags).
+   It seems like you are intending to add a cataloger in addition to the default set.
+   ... Did you mean "--select-catalogers +bar" instead?
+`,
+		},
+		{
+			name: "has multiple expression errors (with error chains and sibling errors)",
+			err: func() error {
+				var err error
+				err = multierror.Append(err, fmt.Errorf("foo: %w", fmt.Errorf("bar: %w", errors.New("last"))))
+				err = multierror.Append(err, task.ErrInvalidExpression{Expression: "foo", Operation: task.AddOperation, Err: task.ErrTagsNotAllowed})
+				err = multierror.Append(err, task.ErrInvalidExpression{Expression: "bar", Operation: task.SubSelectOperation, Err: task.ErrNamesNotAllowed})
+				err = multierror.Append(err, errors.New("bottom"))
+
+				return fmt.Errorf("top: %w", fmt.Errorf("middle: %w", err))
+			}(),
+			wantErr: func(t assert.TestingT, err error, i ...interface{}) bool {
+				expected := `top: middle: 4 errors occurred:
+	* foo: bar: last
+	* invalid expression: "foo": tags are not allowed with this operation (must use exact names)
+	* invalid expression: "bar": names are not allowed with this operation (must use tags)
+	* bottom
+
+`
+				return assert.Equal(t, expected, err.Error())
+			},
+			wantExpErrs: []task.ErrInvalidExpression{
+				{Expression: "foo", Operation: task.AddOperation, Err: task.ErrTagsNotAllowed},
+				{Expression: "bar", Operation: task.SubSelectOperation, Err: task.ErrNamesNotAllowed},
+			},
+			wantHelp: `Suggestions:
+
+ ❖ Given expression "--select-catalogers foo"
+   However, tags are not allowed with this operation (must use exact names).
+   Adding groups of catalogers may result in surprising behavior (create inaccurate SBOMs).
+   If you are certain this is what you want to do, use "--override-default-catalogers foo" instead.
+
+ ❖ Given expression "--select-catalogers bar"
+   However, names are not allowed with this operation (must use tags).
+   It seems like you are intending to add a cataloger in addition to the default set.
+   ... Did you mean "--select-catalogers +bar" instead?
+`,
+		},
+		{
+			name: "has multiple expression errors (with error chains and sibling errors)",
+			err: func() error {
+				var err error
+				err = multierror.Append(err, fmt.Errorf("foo: %w", fmt.Errorf("bar: %w", errors.New("last"))))
+				err = multierror.Append(err, task.ErrInvalidExpression{Expression: "foo", Operation: task.AddOperation, Err: task.ErrTagsNotAllowed})
+				err = multierror.Append(err, task.ErrInvalidExpression{Expression: "bar", Operation: task.SubSelectOperation, Err: task.ErrNamesNotAllowed})
+				err = multierror.Append(err, errors.New("bottom"))
+
+				// note we wrap the top error in a chain
+				return fmt.Errorf("top: %w", fmt.Errorf("middle: %w", err))
+			}(),
+			wantErr: func(t assert.TestingT, err error, i ...interface{}) bool {
+				expected := `top: middle: 4 errors occurred:
+	* foo: bar: last
+	* invalid expression: "foo": tags are not allowed with this operation (must use exact names)
+	* invalid expression: "bar": names are not allowed with this operation (must use tags)
+	* bottom
+
+`
+				return assert.Equal(t, expected, err.Error())
+			},
+			wantExpErrs: []task.ErrInvalidExpression{
+				{Expression: "foo", Operation: task.AddOperation, Err: task.ErrTagsNotAllowed},
+				{Expression: "bar", Operation: task.SubSelectOperation, Err: task.ErrNamesNotAllowed},
+			},
+			wantHelp: `Suggestions:
+
+ ❖ Given expression "--select-catalogers foo"
+   However, tags are not allowed with this operation (must use exact names).
+   Adding groups of catalogers may result in surprising behavior (create inaccurate SBOMs).
+   If you are certain this is what you want to do, use "--override-default-catalogers foo" instead.
+
+ ❖ Given expression "--select-catalogers bar"
+   However, names are not allowed with this operation (must use tags).
+   It seems like you are intending to add a cataloger in addition to the default set.
+   ... Did you mean "--select-catalogers +bar" instead?
+`,
+		},
+		{
+			name: "preserve for any errors within ErrInvalidExpression types",
+			err: func() error {
+				var err error
+				err = multierror.Append(err, task.ErrInvalidExpression{Expression: "foo", Operation: task.AddOperation, Err: task.ErrTagsNotAllowed})
+				err = multierror.Append(err, task.ErrInvalidExpression{Expression: "bar", Operation: task.SubSelectOperation, Err: errors.New("explanation")}) // this is what makes this test different...
+
+				return err
+			}(),
+			wantErr: func(t assert.TestingT, err error, i ...interface{}) bool {
+				// note: the errors are removed and the help text shows the enriched error help
+				expected := `2 errors occurred:
+	* invalid expression: "foo": tags are not allowed with this operation (must use exact names)
+	* invalid expression: "bar": explanation
+
+`
+				return assert.Equal(t, expected, err.Error())
+			},
+			wantExpErrs: []task.ErrInvalidExpression{
+				{Expression: "foo", Operation: task.AddOperation, Err: task.ErrTagsNotAllowed},
+				{Expression: "bar", Operation: task.SubSelectOperation, Err: errors.New("explanation")},
+			},
+			wantHelp: `Suggestions:
+
+ ❖ Given expression "--select-catalogers foo"
+   However, tags are not allowed with this operation (must use exact names).
+   Adding groups of catalogers may result in surprising behavior (create inaccurate SBOMs).
+   If you are certain this is what you want to do, use "--override-default-catalogers foo" instead.
+
+`,
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			gotExpErrs := filterExpressionErrors(tt.err)
+			tt.wantErr(t, tt.err) // ensure the error still remains
+			assert.Equal(t, tt.wantExpErrs, gotExpErrs)
+
+			gotHelp := expressionErrorsHelp(gotExpErrs)
+			assert.Equal(t, tt.wantHelp, gotHelp)
+		})
+	}
+}
+
+func Test_expressionSuggestions(t *testing.T) {
+	tests := []struct {
+		name   string
+		expErr task.ErrInvalidExpression
+		want   string
+	}{
+		{
+			name: "no embedded error",
+			expErr: task.ErrInvalidExpression{
+				Expression: "example",
+			},
+			want: ``,
+		},
+		{
+			name: "general error",
+			expErr: task.ErrInvalidExpression{
+				Err:        errors.New("general error message"),
+				Expression: "example",
+			},
+			want: ``,
+		},
+		{
+			name: "ErrUnknownNameOrTag with add operation",
+			expErr: task.ErrInvalidExpression{
+				Err:        task.ErrUnknownNameOrTag,
+				Operation:  task.AddOperation,
+				Expression: "+example",
+			},
+			want: ``,
+		},
+		{
+			name: "ErrUnknownNameOrTag with subselect operation",
+			expErr: task.ErrInvalidExpression{
+				Err:        task.ErrUnknownNameOrTag,
+				Operation:  task.SubSelectOperation,
+				Expression: "example",
+			},
+			want: ``,
+		},
+		{
+			name: "ErrNamesNotAllowed with subselect operator",
+			expErr: task.ErrInvalidExpression{
+				Err:        task.ErrNamesNotAllowed,
+				Operation:  task.SubSelectOperation,
+				Expression: "example",
+			},
+			want: ` ❖ Given expression "--select-catalogers example"
+   However, names are not allowed with this operation (must use tags).
+   It seems like you are intending to add a cataloger in addition to the default set.
+   ... Did you mean "--select-catalogers +example" instead?
+`,
+		},
+		{
+			name: "ErrTagsNotAllowed with add operation",
+			expErr: task.ErrInvalidExpression{
+				Err:        task.ErrTagsNotAllowed,
+				Operation:  task.AddOperation,
+				Expression: "+example",
+			},
+			want: ` ❖ Given expression "--select-catalogers +example"
+   However, tags are not allowed with this operation (must use exact names).
+   Adding groups of catalogers may result in surprising behavior (create inaccurate SBOMs).
+   If you are certain this is what you want to do, use "--override-default-catalogers example" instead.
+`,
+		},
+		{
+			name: "ErrAllNotAllowed with subselect operation",
+			expErr: task.ErrInvalidExpression{
+				Err:        task.ErrAllNotAllowed,
+				Operation:  task.SubSelectOperation,
+				Expression: "example",
+			},
+			want: ` ❖ Given expression "--select-catalogers example"
+   However, you cannot use the 'all' operand in this context.
+   It seems like you are intending to use all catalogers (which is not recommended).
+   ... Did you mean "--override-default-catalogers example" instead?
+`,
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			assert.Equal(t, tt.want, expressionSuggetions(tt.expErr))
+		})
+	}
+}

cmd/syft/internal/commands/root.go

@@ -12,7 +12,7 @@ import (
 func Root(app clio.Application, packagesCmd *cobra.Command) *cobra.Command {
 	id := app.ID()
 
-	opts := defaultPackagesOptions()
+	opts := defaultScanOptions()
 
 	return app.SetupRootCommand(&cobra.Command{
 		Use:     fmt.Sprintf("%s [SOURCE]", app.ID().Name),
@@ -25,7 +25,7 @@ func Root(app clio.Application, packagesCmd *cobra.Command) *cobra.Command {
 			restoreStdout := ui.CaptureStdoutToTraceLog()
 			defer restoreStdout()
 
-			return runPackages(id, opts, args[0])
+			return runScan(cmd.Context(), id, opts, args[0])
 		},
 	}, opts)
 }

cmd/syft/internal/commands/scan.go

@@ -0,0 +1,447 @@
+package commands
+
+import (
+	"context"
+	"errors"
+	"fmt"
+	"os"
+	"reflect"
+	"strings"
+
+	"github.com/hashicorp/go-multierror"
+	"github.com/spf13/cobra"
+	"gopkg.in/yaml.v3"
+
+	"github.com/anchore/clio"
+	"github.com/anchore/go-collections"
+	"github.com/anchore/stereoscope"
+	"github.com/anchore/stereoscope/pkg/image"
+	"github.com/anchore/syft/cmd/syft/internal/options"
+	"github.com/anchore/syft/cmd/syft/internal/ui"
+	"github.com/anchore/syft/internal"
+	"github.com/anchore/syft/internal/bus"
+	"github.com/anchore/syft/internal/file"
+	"github.com/anchore/syft/internal/log"
+	"github.com/anchore/syft/internal/task"
+	"github.com/anchore/syft/syft"
+	"github.com/anchore/syft/syft/sbom"
+	"github.com/anchore/syft/syft/source"
+	"github.com/anchore/syft/syft/source/sourceproviders"
+)
+
+const (
+	scanExample = `  {{.appName}} {{.command}} alpine:latest                                a summary of discovered packages
+  {{.appName}} {{.command}} alpine:latest -o json                        show all possible cataloging details
+  {{.appName}} {{.command}} alpine:latest -o cyclonedx                   show a CycloneDX formatted SBOM
+  {{.appName}} {{.command}} alpine:latest -o cyclonedx-json              show a CycloneDX JSON formatted SBOM
+  {{.appName}} {{.command}} alpine:latest -o spdx                        show a SPDX 2.3 Tag-Value formatted SBOM
+  {{.appName}} {{.command}} alpine:latest -o spdx@2.2                    show a SPDX 2.2 Tag-Value formatted SBOM
+  {{.appName}} {{.command}} alpine:latest -o spdx-json                   show a SPDX 2.3 JSON formatted SBOM
+  {{.appName}} {{.command}} alpine:latest -o spdx-json@2.2               show a SPDX 2.2 JSON formatted SBOM
+  {{.appName}} {{.command}} alpine:latest -vv                            show verbose debug information
+  {{.appName}} {{.command}} alpine:latest -o template -t my_format.tmpl  show a SBOM formatted according to given template file
+
+  Supports the following image sources:
+    {{.appName}} {{.command}} yourrepo/yourimage:tag     defaults to using images from a Docker daemon. If Docker is not present, the image is pulled directly from the registry.
+    {{.appName}} {{.command}} path/to/a/file/or/dir      a Docker tar, OCI tar, OCI directory, SIF container, or generic filesystem directory
+`
+
+	schemeHelpHeader = "You can also explicitly specify the scheme to use:"
+	imageSchemeHelp  = `    {{.appName}} {{.command}} docker:yourrepo/yourimage:tag            explicitly use the Docker daemon
+    {{.appName}} {{.command}} podman:yourrepo/yourimage:tag            explicitly use the Podman daemon
+    {{.appName}} {{.command}} registry:yourrepo/yourimage:tag          pull image directly from a registry (no container runtime required)
+    {{.appName}} {{.command}} docker-archive:path/to/yourimage.tar     use a tarball from disk for archives created from "docker save"
+    {{.appName}} {{.command}} oci-archive:path/to/yourimage.tar        use a tarball from disk for OCI archives (from Skopeo or otherwise)
+    {{.appName}} {{.command}} oci-dir:path/to/yourimage                read directly from a path on disk for OCI layout directories (from Skopeo or otherwise)
+    {{.appName}} {{.command}} singularity:path/to/yourimage.sif        read directly from a Singularity Image Format (SIF) container on disk
+`
+	nonImageSchemeHelp = `    {{.appName}} {{.command}} dir:path/to/yourproject                  read directly from a path on disk (any directory)
+    {{.appName}} {{.command}} file:path/to/yourproject/file            read directly from a path on disk (any single file)
+`
+	scanSchemeHelp = "\n  " + schemeHelpHeader + "\n" + imageSchemeHelp + nonImageSchemeHelp
+
+	scanHelp = scanExample + scanSchemeHelp
+)
+
+type scanOptions struct {
+	options.Config      `yaml:",inline" mapstructure:",squash"`
+	options.Output      `yaml:",inline" mapstructure:",squash"`
+	options.UpdateCheck `yaml:",inline" mapstructure:",squash"`
+	options.Catalog     `yaml:",inline" mapstructure:",squash"`
+}
+
+func defaultScanOptions() *scanOptions {
+	return &scanOptions{
+		Output:      options.DefaultOutput(),
+		UpdateCheck: options.DefaultUpdateCheck(),
+		Catalog:     options.DefaultCatalog(),
+	}
+}
+
+//nolint:dupl
+func Scan(app clio.Application) *cobra.Command {
+	id := app.ID()
+
+	opts := defaultScanOptions()
+
+	return app.SetupCommand(&cobra.Command{
+		Use:   "scan [SOURCE]",
+		Short: "Generate an SBOM",
+		Long:  "Generate a packaged-based Software Bill Of Materials (SBOM) from container images and filesystems",
+		Example: internal.Tprintf(scanHelp, map[string]interface{}{
+			"appName": id.Name,
+			"command": "scan",
+		}),
+		Args:    validateScanArgs,
+		PreRunE: applicationUpdateCheck(id, &opts.UpdateCheck),
+		RunE: func(cmd *cobra.Command, args []string) error {
+			restoreStdout := ui.CaptureStdoutToTraceLog()
+			defer restoreStdout()
+
+			return runScan(cmd.Context(), id, opts, args[0])
+		},
+	}, opts)
+}
+
+func (o *scanOptions) PostLoad() error {
+	return o.validateLegacyOptionsNotUsed()
+}
+
+func (o *scanOptions) validateLegacyOptionsNotUsed() error {
+	if o.Config.ConfigFile == "" {
+		return nil
+	}
+
+	// check for legacy config file shapes that are no longer valid
+	type legacyConfig struct {
+		BasePath                        *string `yaml:"base-path" json:"base-path" mapstructure:"base-path"`
+		DefaultImagePullSource          *string `yaml:"default-image-pull-source" json:"default-image-pull-source" mapstructure:"default-image-pull-source"`
+		ExcludeBinaryOverlapByOwnership *bool   `yaml:"exclude-binary-overlap-by-ownership" json:"exclude-binary-overlap-by-ownership" mapstructure:"exclude-binary-overlap-by-ownership"`
+		File                            any     `yaml:"file" json:"file" mapstructure:"file"`
+	}
+
+	by, err := os.ReadFile(o.Config.ConfigFile)
+	if err != nil {
+		return fmt.Errorf("unable to read config file during validations %q: %w", o.Config.ConfigFile, err)
+	}
+
+	var legacy legacyConfig
+	if err := yaml.Unmarshal(by, &legacy); err != nil {
+		return fmt.Errorf("unable to parse config file during validations %q: %w", o.Config.ConfigFile, err)
+	}
+
+	if legacy.DefaultImagePullSource != nil {
+		return fmt.Errorf("the config file option 'default-image-pull-source' has been removed, please use 'source.image.default-pull-source' instead")
+	}
+
+	if legacy.ExcludeBinaryOverlapByOwnership != nil {
+		return fmt.Errorf("the config file option 'exclude-binary-overlap-by-ownership' has been removed, please use 'package.exclude-binary-overlap-by-ownership' instead")
+	}
+
+	if legacy.BasePath != nil {
+		return fmt.Errorf("the config file option 'base-path' has been removed, please use 'source.base-path' instead")
+	}
+
+	if legacy.File != nil && reflect.TypeOf(legacy.File).Kind() == reflect.String {
+		return fmt.Errorf("the config file option 'file' has been removed, please use 'outputs' instead")
+	}
+
+	return nil
+}
+
+func validateScanArgs(cmd *cobra.Command, args []string) error {
+	return validateArgs(cmd, args, "an image/directory argument is required")
+}
+
+func validateArgs(cmd *cobra.Command, args []string, error string) error {
+	if len(args) == 0 {
+		// in the case that no arguments are given we want to show the help text and return with a non-0 return code.
+		if err := cmd.Help(); err != nil {
+			return fmt.Errorf("unable to display help: %w", err)
+		}
+		return fmt.Errorf(error)
+	}
+
+	return cobra.MaximumNArgs(1)(cmd, args)
+}
+
+func runScan(ctx context.Context, id clio.Identification, opts *scanOptions, userInput string) error {
+	writer, err := opts.SBOMWriter()
+	if err != nil {
+		return err
+	}
+
+	sources := opts.From
+	if len(sources) == 0 {
+		// extract a scheme if it matches any provider tag; this is a holdover for compatibility, using the --from flag is recommended
+		explicitSource, newUserInput := stereoscope.ExtractSchemeSource(userInput, allSourceProviderTags()...)
+		if explicitSource != "" {
+			sources = append(sources, explicitSource)
+			userInput = newUserInput
+		}
+	}
+
+	src, err := getSource(ctx, &opts.Catalog, userInput, sources...)
+
+	if err != nil {
+		return err
+	}
+
+	defer func() {
+		if src != nil {
+			if err := src.Close(); err != nil {
+				log.Tracef("unable to close source: %+v", err)
+			}
+		}
+	}()
+
+	s, err := generateSBOM(ctx, id, src, &opts.Catalog)
+	if err != nil {
+		return err
+	}
+
+	if s == nil {
+		return fmt.Errorf("no SBOM produced for %q", userInput)
+	}
+
+	if err := writer.Write(*s); err != nil {
+		return fmt.Errorf("failed to write SBOM: %w", err)
+	}
+
+	return nil
+}
+
+func getSource(ctx context.Context, opts *options.Catalog, userInput string, sources ...string) (source.Source, error) {
+	cfg := syft.DefaultGetSourceConfig().
+		WithRegistryOptions(opts.Registry.ToOptions()).
+		WithAlias(source.Alias{
+			Name:    opts.Source.Name,
+			Version: opts.Source.Version,
+		}).
+		WithExcludeConfig(source.ExcludeConfig{
+			Paths: opts.Exclusions,
+		}).
+		WithBasePath(opts.Source.BasePath).
+		WithSources(sources...).
+		WithDefaultImagePullSource(opts.Source.Image.DefaultPullSource)
+
+	var err error
+	var platform *image.Platform
+
+	if opts.Platform != "" {
+		platform, err = image.NewPlatform(opts.Platform)
+		if err != nil {
+			return nil, fmt.Errorf("invalid platform: %w", err)
+		}
+		cfg = cfg.WithPlatform(platform)
+	}
+
+	if opts.Source.File.Digests != nil {
+		hashers, err := file.Hashers(opts.Source.File.Digests...)
+		if err != nil {
+			return nil, fmt.Errorf("invalid hash algorithm: %w", err)
+		}
+		cfg = cfg.WithDigestAlgorithms(hashers...)
+	}
+
+	src, err := syft.GetSource(ctx, userInput, cfg)
+	if err != nil {
+		return nil, fmt.Errorf("could not determine source: %w", err)
+	}
+
+	return src, nil
+}
+
+func generateSBOM(ctx context.Context, id clio.Identification, src source.Source, opts *options.Catalog) (*sbom.SBOM, error) {
+	s, err := syft.CreateSBOM(ctx, src, opts.ToSBOMConfig(id))
+	if err != nil {
+		expErrs := filterExpressionErrors(err)
+		notifyExpressionErrors(expErrs)
+		return nil, err
+	}
+	return s, nil
+}
+
+func filterExpressionErrors(err error) []task.ErrInvalidExpression {
+	if err == nil {
+		return nil
+	}
+
+	expErrs := processErrors(err)
+
+	return expErrs
+}
+
+// processErrors traverses error chains and multierror lists and returns all ErrInvalidExpression errors found
+func processErrors(err error) []task.ErrInvalidExpression {
+	var result []task.ErrInvalidExpression
+
+	var processError func(...error)
+	processError = func(errs ...error) {
+		for _, e := range errs {
+			// note: using errors.As will result in surprising behavior (since that will traverse the error chain,
+			// potentially skipping over nodes in a list of errors)
+			if cerr, ok := e.(task.ErrInvalidExpression); ok {
+				result = append(result, cerr)
+				continue
+			}
+			var multiErr *multierror.Error
+			if errors.As(e, &multiErr) {
+				processError(multiErr.Errors...)
+			}
+		}
+	}
+
+	processError(err)
+
+	return result
+}
+
+func notifyExpressionErrors(expErrs []task.ErrInvalidExpression) {
+	helpText := expressionErrorsHelp(expErrs)
+	if helpText == "" {
+		return
+	}
+
+	bus.Notify(helpText)
+}
+
+func expressionErrorsHelp(expErrs []task.ErrInvalidExpression) string {
+	// enrich all errors found with CLI hints
+	if len(expErrs) == 0 {
+		return ""
+	}
+
+	sb := strings.Builder{}
+
+	sb.WriteString("Suggestions:\n\n")
+
+	found := false
+	for i, expErr := range expErrs {
+		help := expressionSuggetions(expErr)
+		if help == "" {
+			continue
+		}
+		found = true
+		sb.WriteString(help)
+		if i != len(expErrs)-1 {
+			sb.WriteString("\n")
+		}
+	}
+
+	if !found {
+		return ""
+	}
+
+	return sb.String()
+}
+
+const expressionHelpTemplate = " ❖ Given expression %q\n%s%s"
+
+func expressionSuggetions(expErr task.ErrInvalidExpression) string {
+	if expErr.Err == nil {
+		return ""
+	}
+
+	hint := getHintPhrase(expErr)
+	if hint == "" {
+		return ""
+	}
+
+	return fmt.Sprintf(expressionHelpTemplate,
+		getExpression(expErr),
+		indentMsg(getExplanation(expErr)),
+		indentMsg(hint),
+	)
+}
+
+func indentMsg(msg string) string {
+	if msg == "" {
+		return ""
+	}
+
+	lines := strings.Split(msg, "\n")
+	for i, line := range lines {
+		lines[i] = "   " + line
+	}
+
+	return strings.Join(lines, "\n") + "\n"
+}
+
+func getExpression(expErr task.ErrInvalidExpression) string {
+	flag := "--select-catalogers"
+	if expErr.Operation == task.SetOperation {
+		flag = "--override-default-catalogers"
+	}
+	return fmt.Sprintf("%s %s", flag, expErr.Expression)
+}
+
+func getExplanation(expErr task.ErrInvalidExpression) string {
+	err := expErr.Err
+	if errors.Is(err, task.ErrUnknownNameOrTag) {
+		noun := ""
+		switch expErr.Operation {
+		case task.AddOperation:
+			noun = "name"
+		case task.SubSelectOperation:
+			noun = "tag"
+		default:
+			noun = "name or tag"
+		}
+
+		return fmt.Sprintf("However, %q is not a recognized cataloger %s.", trimOperation(expErr.Expression), noun)
+	}
+
+	if errors.Is(err, task.ErrNamesNotAllowed) {
+		if expErr.Operation == task.SubSelectOperation {
+			return "However, " + err.Error() + ".\nIt seems like you are intending to add a cataloger in addition to the default set." // nolint:goconst
+		}
+		return "However, " + err.Error() + "." // nolint:goconst
+	}
+
+	if errors.Is(err, task.ErrTagsNotAllowed) {
+		return "However, " + err.Error() + ".\nAdding groups of catalogers may result in surprising behavior (create inaccurate SBOMs)." // nolint:goconst
+	}
+
+	if errors.Is(err, task.ErrAllNotAllowed) {
+		return "However, you " + err.Error() + ".\nIt seems like you are intending to use all catalogers (which is not recommended)."
+	}
+
+	if err != nil {
+		return "However, this is not valid: " + err.Error()
+	}
+
+	return ""
+}
+
+func getHintPhrase(expErr task.ErrInvalidExpression) string {
+	if errors.Is(expErr.Err, task.ErrUnknownNameOrTag) {
+		return ""
+	}
+
+	switch expErr.Operation {
+	case task.AddOperation:
+		if errors.Is(expErr.Err, task.ErrTagsNotAllowed) {
+			return fmt.Sprintf("If you are certain this is what you want to do, use %q instead.", "--override-default-catalogers "+trimOperation(expErr.Expression))
+		}
+
+	case task.SubSelectOperation:
+		didYouMean := "... Did you mean %q instead?"
+		if errors.Is(expErr.Err, task.ErrNamesNotAllowed) {
+			return fmt.Sprintf(didYouMean, "--select-catalogers +"+expErr.Expression)
+		}
+
+		if errors.Is(expErr.Err, task.ErrAllNotAllowed) {
+			return fmt.Sprintf(didYouMean, "--override-default-catalogers "+expErr.Expression)
+		}
+	}
+	return ""
+}
+
+func trimOperation(x string) string {
+	return strings.TrimLeft(x, "+-")
+}
+
+func allSourceProviderTags() []string {
+	return collections.TaggedValueSet[source.Provider]{}.Join(sourceproviders.All("", nil)...).Tags()
+}

cmd/syft/internal/commands/scan_test.go

@@ -0,0 +1,66 @@
+package commands
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+
+	"github.com/anchore/syft/cmd/syft/internal/options"
+)
+
+func Test_scanOptions_validateLegacyOptionsNotUsed(t *testing.T) {
+	tests := []struct {
+		name    string
+		cfg     string
+		wantErr assert.ErrorAssertionFunc
+	}{
+		{
+			name: "no config file",
+		},
+		{
+			name: "config file with no legacy options",
+			cfg:  "test-fixtures/scan-configs/no-legacy-options.yaml",
+		},
+		{
+			name:    "config file with default image pull source legacy option",
+			cfg:     "test-fixtures/scan-configs/with-default-pull-source.yaml",
+			wantErr: assertErrorContains("source.image.default-pull-source"),
+		},
+		{
+			name:    "config file with exclude-binary-overlap-by-ownership legacy option",
+			cfg:     "test-fixtures/scan-configs/with-exclude-binary-overlap-by-ownership.yaml",
+			wantErr: assertErrorContains("package.exclude-binary-overlap-by-ownership"),
+		},
+		{
+			name:    "config file with file string legacy option",
+			cfg:     "test-fixtures/scan-configs/with-file-string.yaml",
+			wantErr: assertErrorContains("outputs"),
+		},
+		{
+			name: "config file with file section",
+			cfg:  "test-fixtures/scan-configs/with-file-section.yaml",
+		},
+		{
+			name:    "config file with base-path legacy option",
+			cfg:     "test-fixtures/scan-configs/with-base-path.yaml",
+			wantErr: assertErrorContains("source.base-path"),
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if tt.wantErr == nil {
+				tt.wantErr = assert.NoError
+			}
+			o := &scanOptions{
+				Config: options.Config{ConfigFile: tt.cfg},
+			}
+			tt.wantErr(t, o.validateLegacyOptionsNotUsed())
+		})
+	}
+}
+
+func assertErrorContains(contains string) assert.ErrorAssertionFunc {
+	return func(t assert.TestingT, err error, i ...interface{}) bool {
+		return assert.ErrorContains(t, err, contains, i...)
+	}
+}

cmd/syft/internal/commands/test-fixtures/scan-configs/no-legacy-options.yaml

@@ -0,0 +1,2 @@
+# simple, valid syft config with no legacy fields used
+parallelism: 5

cmd/syft/internal/commands/test-fixtures/scan-configs/with-base-path.yaml

@@ -0,0 +1 @@
+base-path: "something"

cmd/syft/internal/commands/test-fixtures/scan-configs/with-default-pull-source.yaml

@@ -0,0 +1 @@
+default-image-pull-source: "something"

cmd/syft/internal/commands/test-fixtures/scan-configs/with-exclude-binary-overlap-by-ownership.yaml

@@ -0,0 +1 @@
+exclude-binary-overlap-by-ownership: true

cmd/syft/internal/commands/test-fixtures/scan-configs/with-file-section.yaml

@@ -0,0 +1,2 @@
+file:
+  selection: all

cmd/syft/internal/commands/test-fixtures/scan-configs/with-file-string.yaml

@@ -0,0 +1 @@
+file: path

cmd/syft/internal/commands/update.go

@@ -11,8 +11,8 @@ import (
 
 	"github.com/anchore/clio"
 	hashiVersion "github.com/anchore/go-version"
-	"github.com/anchore/syft/cmd/syft/cli/options"
 	"github.com/anchore/syft/cmd/syft/internal"
+	"github.com/anchore/syft/cmd/syft/internal/options"
 	"github.com/anchore/syft/internal/bus"
 	"github.com/anchore/syft/internal/log"
 	"github.com/anchore/syft/syft/event"
@@ -28,7 +28,7 @@ var latestAppVersionURL = struct {
 }
 
 func applicationUpdateCheck(id clio.Identification, check *options.UpdateCheck) func(cmd *cobra.Command, args []string) error {
-	return func(cmd *cobra.Command, args []string) error {
+	return func(_ *cobra.Command, _ []string) error {
 		if check.CheckForAppUpdate {
 			checkForApplicationUpdate(id)
 		}

cmd/syft/internal/options/attest.go

@@ -4,6 +4,8 @@ import (
 	"github.com/anchore/clio"
 )
 
+var _ clio.FlagAdder = (*Attest)(nil)
+
 type Attest struct {
 	// IMPORTANT: do not show the attestation key/password in any YAML/JSON output (sensitive information)
 	Key      secret `yaml:"key" json:"key" mapstructure:"key"`
@@ -12,6 +14,6 @@ type Attest struct {
 
 var _ clio.FlagAdder = (*Attest)(nil)
 
-func (o Attest) AddFlags(flags clio.FlagSet) {
+func (o *Attest) AddFlags(flags clio.FlagSet) {
 	flags.StringVarP((*string)(&o.Key), "key", "k", "the key to use for the attestation")
 }

cmd/syft/internal/options/catalog.go

@@ -0,0 +1,242 @@
+package options
+
+import (
+	"fmt"
+	"sort"
+	"strings"
+
+	"github.com/iancoleman/strcase"
+
+	"github.com/anchore/clio"
+	"github.com/anchore/fangs"
+	intFile "github.com/anchore/syft/internal/file"
+	"github.com/anchore/syft/internal/log"
+	"github.com/anchore/syft/syft"
+	"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/file/cataloger/executable"
+	"github.com/anchore/syft/syft/file/cataloger/filecontent"
+	"github.com/anchore/syft/syft/pkg/cataloger/binary"
+	"github.com/anchore/syft/syft/pkg/cataloger/golang"
+	"github.com/anchore/syft/syft/pkg/cataloger/java"
+	"github.com/anchore/syft/syft/pkg/cataloger/javascript"
+	"github.com/anchore/syft/syft/pkg/cataloger/kernel"
+	"github.com/anchore/syft/syft/pkg/cataloger/python"
+	"github.com/anchore/syft/syft/source"
+)
+
+type Catalog struct {
+	// high-level cataloger configuration
+	Catalogers        []string            `yaml:"-" json:"catalogers" mapstructure:"catalogers"` // deprecated and not shown in yaml output
+	DefaultCatalogers []string            `yaml:"default-catalogers" json:"default-catalogers" mapstructure:"default-catalogers"`
+	SelectCatalogers  []string            `yaml:"select-catalogers" json:"select-catalogers" mapstructure:"select-catalogers"`
+	Package           packageConfig       `yaml:"package" json:"package" mapstructure:"package"`
+	File              fileConfig          `yaml:"file" json:"file" mapstructure:"file"`
+	Scope             string              `yaml:"scope" json:"scope" mapstructure:"scope"`
+	Parallelism       int                 `yaml:"parallelism" json:"parallelism" mapstructure:"parallelism"` // the number of catalog workers to run in parallel
+	Relationships     relationshipsConfig `yaml:"relationships" json:"relationships" mapstructure:"relationships"`
+
+	// ecosystem-specific cataloger configuration
+	Golang      golangConfig      `yaml:"golang" json:"golang" mapstructure:"golang"`
+	Java        javaConfig        `yaml:"java" json:"java" mapstructure:"java"`
+	JavaScript  javaScriptConfig  `yaml:"javascript" json:"javascript" mapstructure:"javascript"`
+	LinuxKernel linuxKernelConfig `yaml:"linux-kernel" json:"linux-kernel" mapstructure:"linux-kernel"`
+	Python      pythonConfig      `yaml:"python" json:"python" mapstructure:"python"`
+
+	// configuration for the source (the subject being analyzed)
+	Registry   registryConfig `yaml:"registry" json:"registry" mapstructure:"registry"`
+	From       []string       `yaml:"from" json:"from" mapstructure:"from"`
+	Platform   string         `yaml:"platform" json:"platform" mapstructure:"platform"`
+	Source     sourceConfig   `yaml:"source" json:"source" mapstructure:"source"`
+	Exclusions []string       `yaml:"exclude" json:"exclude" mapstructure:"exclude"`
+}
+
+var _ interface {
+	clio.FlagAdder
+	clio.PostLoader
+	fangs.FieldDescriber
+} = (*Catalog)(nil)
+
+func DefaultCatalog() Catalog {
+	return Catalog{
+		Scope:         source.SquashedScope.String(),
+		Package:       defaultPackageConfig(),
+		LinuxKernel:   defaultLinuxKernelConfig(),
+		Golang:        defaultGolangConfig(),
+		File:          defaultFileConfig(),
+		Relationships: defaultRelationshipsConfig(),
+		Source:        defaultSourceConfig(),
+		Parallelism:   1,
+	}
+}
+
+func (cfg Catalog) ToSBOMConfig(id clio.Identification) *syft.CreateSBOMConfig {
+	return syft.DefaultCreateSBOMConfig().
+		WithTool(id.Name, id.Version).
+		WithParallelism(cfg.Parallelism).
+		WithRelationshipsConfig(cfg.ToRelationshipsConfig()).
+		WithSearchConfig(cfg.ToSearchConfig()).
+		WithPackagesConfig(cfg.ToPackagesConfig()).
+		WithFilesConfig(cfg.ToFilesConfig()).
+		WithCatalogerSelection(
+			pkgcataloging.NewSelectionRequest().
+				WithDefaults(cfg.DefaultCatalogers...).
+				WithExpression(cfg.SelectCatalogers...),
+		)
+}
+
+func (cfg Catalog) ToSearchConfig() cataloging.SearchConfig {
+	return cataloging.SearchConfig{
+		Scope: source.ParseScope(cfg.Scope),
+	}
+}
+
+func (cfg Catalog) ToRelationshipsConfig() cataloging.RelationshipsConfig {
+	return cataloging.RelationshipsConfig{
+		PackageFileOwnership:        cfg.Relationships.PackageFileOwnership,
+		PackageFileOwnershipOverlap: cfg.Relationships.PackageFileOwnershipOverlap,
+		// note: this option was surfaced in the syft application configuration before this relationships section was added
+		ExcludeBinaryPackagesWithFileOwnershipOverlap: cfg.Package.ExcludeBinaryOverlapByOwnership,
+	}
+}
+
+func (cfg Catalog) ToFilesConfig() filecataloging.Config {
+	hashers, err := intFile.Hashers(cfg.File.Metadata.Digests...)
+	if err != nil {
+		log.WithFields("error", err).Warn("unable to configure file hashers")
+	}
+
+	return filecataloging.Config{
+		Selection: cfg.File.Metadata.Selection,
+		Hashers:   hashers,
+		Content: filecontent.Config{
+			Globs:              cfg.File.Content.Globs,
+			SkipFilesAboveSize: cfg.File.Content.SkipFilesAboveSize,
+		},
+		Executable: executable.Config{
+			MIMETypes: executable.DefaultConfig().MIMETypes,
+			Globs:     cfg.File.Executable.Globs,
+		},
+	}
+}
+
+func (cfg Catalog) ToPackagesConfig() pkgcataloging.Config {
+	archiveSearch := cataloging.ArchiveSearchConfig{
+		IncludeIndexedArchives:   cfg.Package.SearchIndexedArchives,
+		IncludeUnindexedArchives: cfg.Package.SearchUnindexedArchives,
+	}
+	return pkgcataloging.Config{
+		Binary: binary.DefaultClassifierCatalogerConfig(),
+		Golang: golang.DefaultCatalogerConfig().
+			WithSearchLocalModCacheLicenses(cfg.Golang.SearchLocalModCacheLicenses).
+			WithLocalModCacheDir(cfg.Golang.LocalModCacheDir).
+			WithSearchRemoteLicenses(cfg.Golang.SearchRemoteLicenses).
+			WithProxy(cfg.Golang.Proxy).
+			WithNoProxy(cfg.Golang.NoProxy).
+			WithMainModuleVersion(
+				golang.DefaultMainModuleVersionConfig().
+					WithFromContents(cfg.Golang.MainModuleVersion.FromContents).
+					WithFromBuildSettings(cfg.Golang.MainModuleVersion.FromBuildSettings).
+					WithFromLDFlags(cfg.Golang.MainModuleVersion.FromLDFlags),
+			),
+		JavaScript: javascript.DefaultCatalogerConfig().
+			WithSearchRemoteLicenses(cfg.JavaScript.SearchRemoteLicenses).
+			WithNpmBaseURL(cfg.JavaScript.NpmBaseURL),
+		LinuxKernel: kernel.LinuxKernelCatalogerConfig{
+			CatalogModules: cfg.LinuxKernel.CatalogModules,
+		},
+		Python: python.CatalogerConfig{
+			GuessUnpinnedRequirements: cfg.Python.GuessUnpinnedRequirements,
+		},
+		JavaArchive: java.DefaultArchiveCatalogerConfig().
+			WithUseNetwork(cfg.Java.UseNetwork).
+			WithMavenBaseURL(cfg.Java.MavenURL).
+			WithArchiveTraversal(archiveSearch, cfg.Java.MaxParentRecursiveDepth),
+	}
+}
+
+func (cfg *Catalog) AddFlags(flags clio.FlagSet) {
+	var validScopeValues []string
+	for _, scope := range source.AllScopes {
+		validScopeValues = append(validScopeValues, strcase.ToDelimited(string(scope), '-'))
+	}
+	flags.StringVarP(&cfg.Scope, "scope", "s",
+		fmt.Sprintf("selection of layers to catalog, options=%v", validScopeValues))
+
+	flags.StringArrayVarP(&cfg.From, "from", "",
+		"specify the source behavior to use (e.g. docker, registry, oci-dir, ...)")
+
+	flags.StringVarP(&cfg.Platform, "platform", "",
+		"an optional platform specifier for container image sources (e.g. 'linux/arm64', 'linux/arm64/v8', 'arm64', 'linux')")
+
+	flags.StringArrayVarP(&cfg.Exclusions, "exclude", "",
+		"exclude paths from being scanned using a glob expression")
+
+	flags.StringArrayVarP(&cfg.Catalogers, "catalogers", "",
+		"enable one or more package catalogers")
+
+	if pfp, ok := flags.(fangs.PFlagSetProvider); ok {
+		if err := pfp.PFlagSet().MarkDeprecated("catalogers", "use: override-default-catalogers and select-catalogers"); err != nil {
+			panic(err)
+		}
+	} else {
+		panic("unable to mark flags as deprecated")
+	}
+
+	flags.StringArrayVarP(&cfg.DefaultCatalogers, "override-default-catalogers", "",
+		"set the base set of catalogers to use (defaults to 'image' or 'directory' depending on the scan source)")
+
+	flags.StringArrayVarP(&cfg.SelectCatalogers, "select-catalogers", "",
+		"add, remove, and filter the catalogers to be used")
+
+	flags.StringVarP(&cfg.Source.Name, "source-name", "",
+		"set the name of the target being analyzed")
+
+	flags.StringVarP(&cfg.Source.Version, "source-version", "",
+		"set the version of the target being analyzed")
+
+	flags.StringVarP(&cfg.Source.BasePath, "base-path", "",
+		"base directory for scanning, no links will be followed above this directory, and all paths will be reported relative to this directory")
+}
+
+func (cfg *Catalog) DescribeFields(descriptions fangs.FieldDescriptionSet) {
+	descriptions.Add(&cfg.Parallelism, "number of cataloger workers to run in parallel")
+}
+
+func (cfg *Catalog) PostLoad() error {
+	usingLegacyCatalogers := len(cfg.Catalogers) > 0
+	usingNewCatalogers := len(cfg.DefaultCatalogers) > 0 || len(cfg.SelectCatalogers) > 0
+
+	if usingLegacyCatalogers && usingNewCatalogers {
+		return fmt.Errorf("cannot use both 'catalogers' and 'select-catalogers'/'default-catalogers' flags")
+	}
+
+	flatten := func(l []string) []string {
+		var out []string
+		for _, v := range l {
+			for _, s := range strings.Split(v, ",") {
+				out = append(out, strings.TrimSpace(s))
+			}
+		}
+		sort.Strings(out)
+
+		return out
+	}
+
+	cfg.From = flatten(cfg.From)
+
+	cfg.Catalogers = flatten(cfg.Catalogers)
+	cfg.DefaultCatalogers = flatten(cfg.DefaultCatalogers)
+	cfg.SelectCatalogers = flatten(cfg.SelectCatalogers)
+
+	// for backwards compatibility
+	cfg.DefaultCatalogers = append(cfg.DefaultCatalogers, cfg.Catalogers...)
+
+	s := source.ParseScope(cfg.Scope)
+	if s == source.UnknownScope {
+		return fmt.Errorf("bad scope value %q", cfg.Scope)
+	}
+
+	return nil
+}

cmd/syft/internal/options/catalog_test.go

@@ -0,0 +1,72 @@
+package options
+
+import (
+	"fmt"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestCatalog_PostLoad(t *testing.T) {
+
+	tests := []struct {
+		name    string
+		options Catalog
+		assert  func(t *testing.T, options Catalog)
+		wantErr assert.ErrorAssertionFunc
+	}{
+		{
+			name: "mutually exclusive cataloger flags (cat / def-cat)",
+			options: Catalog{
+				Catalogers:        []string{"foo,bar", "42"},
+				DefaultCatalogers: []string{"some,thing"},
+				Scope:             "squashed",
+			},
+			wantErr: assert.Error,
+		},
+		{
+			name: "mutually exclusive cataloger flags (cat / sel-cat)",
+			options: Catalog{
+				Catalogers:       []string{"foo,bar", "42"},
+				SelectCatalogers: []string{"some,thing"},
+				Scope:            "squashed",
+			},
+			wantErr: assert.Error,
+		},
+		{
+			name: "allow old cataloger flags",
+			options: Catalog{
+				Catalogers: []string{"foo,bar"},
+				Scope:      "squashed",
+			},
+			assert: func(t *testing.T, options Catalog) {
+				assert.Equal(t, []string{"bar", "foo"}, options.DefaultCatalogers) // note: sorted order
+				assert.Equal(t, []string{"bar", "foo"}, options.Catalogers)        // note: sorted order
+			},
+		},
+		{
+			name: "allow new cataloger flags",
+			options: Catalog{
+				SelectCatalogers:  []string{"foo,bar", "42"},
+				DefaultCatalogers: []string{"some,thing"},
+				Scope:             "squashed",
+			},
+			assert: func(t *testing.T, options Catalog) {
+				assert.Equal(t, []string{"42", "bar", "foo"}, options.SelectCatalogers) // note: sorted order
+				assert.Equal(t, []string{"some", "thing"}, options.DefaultCatalogers)   // note: sorted order
+				assert.Empty(t, options.Catalogers)
+			},
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if tt.wantErr == nil {
+				tt.wantErr = assert.NoError
+			}
+			tt.wantErr(t, tt.options.PostLoad(), fmt.Sprintf("PostLoad()"))
+			if tt.assert != nil {
+				tt.assert(t, tt.options)
+			}
+		})
+	}
+}

cmd/syft/internal/options/config.go

@@ -0,0 +1,12 @@
+package options
+
+import "github.com/anchore/fangs"
+
+// Config holds a reference to the specific config file that was used to load application configuration
+type Config struct {
+	ConfigFile string `yaml:"config" json:"config" mapstructure:"config"`
+}
+
+func (cfg *Config) DescribeFields(descriptions fangs.FieldDescriptionSet) {
+	descriptions.Add(&cfg.ConfigFile, "the configuration file that was used to load application configuration")
+}

cmd/syft/internal/options/file.go

@@ -0,0 +1,58 @@
+package options
+
+import (
+	"fmt"
+	"sort"
+
+	"github.com/scylladb/go-set/strset"
+
+	intFile "github.com/anchore/syft/internal/file"
+	"github.com/anchore/syft/syft/file"
+)
+
+type fileConfig struct {
+	Metadata   fileMetadata   `yaml:"metadata" json:"metadata" mapstructure:"metadata"`
+	Content    fileContent    `yaml:"content" json:"content" mapstructure:"content"`
+	Executable fileExecutable `yaml:"executable" json:"executable" mapstructure:"executable"`
+}
+
+type fileMetadata struct {
+	Selection file.Selection `yaml:"selection" json:"selection" mapstructure:"selection"`
+	Digests   []string       `yaml:"digests" json:"digests" mapstructure:"digests"`
+}
+
+type fileContent struct {
+	SkipFilesAboveSize int64    `yaml:"skip-files-above-size" json:"skip-files-above-size" mapstructure:"skip-files-above-size"`
+	Globs              []string `yaml:"globs" json:"globs" mapstructure:"globs"`
+}
+
+type fileExecutable struct {
+	Globs []string `yaml:"globs" json:"globs" mapstructure:"globs"`
+}
+
+func defaultFileConfig() fileConfig {
+	return fileConfig{
+		Metadata: fileMetadata{
+			Selection: file.FilesOwnedByPackageSelection,
+			Digests:   []string{"sha1", "sha256"},
+		},
+		Content: fileContent{
+			SkipFilesAboveSize: 250 * intFile.KB,
+		},
+		Executable: fileExecutable{
+			Globs: nil,
+		},
+	}
+}
+
+func (c *fileConfig) PostLoad() error {
+	digests := strset.New(c.Metadata.Digests...).List()
+	sort.Strings(digests)
+	c.Metadata.Digests = digests
+
+	switch c.Metadata.Selection {
+	case file.NoFilesSelection, file.FilesOwnedByPackageSelection, file.AllFilesSelection:
+		return nil
+	}
+	return fmt.Errorf("invalid file metadata selection: %q", c.Metadata.Selection)
+}

cmd/syft/internal/options/file_test.go

@@ -0,0 +1,56 @@
+package options
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+
+	"github.com/anchore/syft/syft/file"
+)
+
+func Test_fileConfig_PostLoad(t *testing.T) {
+	tests := []struct {
+		name    string
+		cfg     fileConfig
+		assert  func(t *testing.T, cfg fileConfig)
+		wantErr assert.ErrorAssertionFunc
+	}{
+		{
+			name: "deduplicate digests",
+			cfg: fileConfig{
+				Metadata: fileMetadata{
+					Selection: file.NoFilesSelection,
+					Digests:   []string{"sha1", "sha1"},
+				},
+			},
+			assert: func(t *testing.T, cfg fileConfig) {
+				assert.Equal(t, []string{"sha1"}, cfg.Metadata.Digests)
+			},
+		},
+		{
+			name: "error on invalid selection",
+			cfg: fileConfig{
+				Metadata: fileMetadata{
+					Selection: file.Selection("invalid"),
+				},
+			},
+			wantErr: assert.Error,
+		},
+		{
+			name:    "error on empty selection",
+			cfg:     fileConfig{},
+			wantErr: assert.Error,
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if tt.wantErr == nil {
+				tt.wantErr = assert.NoError
+			}
+			tt.wantErr(t, tt.cfg.PostLoad())
+			if tt.assert != nil {
+				tt.assert(t, tt.cfg)
+			}
+		})
+	}
+}

cmd/syft/internal/options/format.go

@@ -0,0 +1,60 @@
+package options
+
+import (
+	"github.com/anchore/clio"
+	"github.com/anchore/syft/syft/format"
+	"github.com/anchore/syft/syft/format/spdxtagvalue"
+	"github.com/anchore/syft/syft/sbom"
+)
+
+var _ clio.PostLoader = (*Format)(nil)
+
+// Format contains all user configuration for output formatting.
+type Format struct {
+	Pretty        *bool               `yaml:"pretty" json:"pretty" mapstructure:"pretty"`
+	Template      FormatTemplate      `yaml:"template" json:"template" mapstructure:"template"`
+	SyftJSON      FormatSyftJSON      `yaml:"json" json:"json" mapstructure:"json"`
+	SPDXJSON      FormatSPDXJSON      `yaml:"spdx-json" json:"spdx-json" mapstructure:"spdx-json"`
+	CyclonedxJSON FormatCyclonedxJSON `yaml:"cyclonedx-json" json:"cyclonedx-json" mapstructure:"cyclonedx-json"`
+	CyclonedxXML  FormatCyclonedxXML  `yaml:"cyclonedx-xml" json:"cyclonedx-xml" mapstructure:"cyclonedx-xml"`
+}
+
+func (o *Format) PostLoad() error {
+	o.SyftJSON.Pretty = multiLevelOption[bool](false, o.Pretty, o.SyftJSON.Pretty)
+	o.SPDXJSON.Pretty = multiLevelOption[bool](false, o.Pretty, o.SPDXJSON.Pretty)
+	o.CyclonedxJSON.Pretty = multiLevelOption[bool](false, o.Pretty, o.CyclonedxJSON.Pretty)
+	o.CyclonedxXML.Pretty = multiLevelOption[bool](false, o.Pretty, o.CyclonedxXML.Pretty)
+
+	return nil
+}
+
+func DefaultFormat() Format {
+	return Format{
+		Template:      DefaultFormatTemplate(),
+		SyftJSON:      DefaultFormatJSON(),
+		SPDXJSON:      DefaultFormatSPDXJSON(),
+		CyclonedxJSON: DefaultFormatCyclonedxJSON(),
+		CyclonedxXML:  DefaultFormatCyclonedxXML(),
+	}
+}
+
+func (o Format) Encoders() ([]sbom.FormatEncoder, error) {
+	return format.EncodersConfig{
+		Template:      o.Template.config(),
+		SyftJSON:      o.SyftJSON.config(),
+		SPDXJSON:      o.SPDXJSON.config(format.AllVersions),                   // we support multiple versions, not just a single version
+		SPDXTagValue:  spdxtagvalue.EncoderConfig{Version: format.AllVersions}, // we support multiple versions, not just a single version
+		CyclonedxJSON: o.CyclonedxJSON.config(format.AllVersions),              // we support multiple versions, not just a single version
+		CyclonedxXML:  o.CyclonedxXML.config(format.AllVersions),               // we support multiple versions, not just a single version
+	}.Encoders()
+}
+
+func multiLevelOption[T any](defaultValue T, option ...*T) *T {
+	result := defaultValue
+	for _, opt := range option {
+		if opt != nil {
+			result = *opt
+		}
+	}
+	return &result
+}

cmd/syft/internal/options/format_cyclonedx_json.go

@@ -0,0 +1,24 @@
+package options
+
+import (
+	"github.com/anchore/syft/syft/format/cyclonedxjson"
+)
+
+type FormatCyclonedxJSON struct {
+	Pretty *bool `yaml:"pretty" json:"pretty" mapstructure:"pretty"`
+}
+
+func DefaultFormatCyclonedxJSON() FormatCyclonedxJSON {
+	return FormatCyclonedxJSON{}
+}
+
+func (o FormatCyclonedxJSON) config(version string) cyclonedxjson.EncoderConfig {
+	var pretty bool
+	if o.Pretty != nil {
+		pretty = *o.Pretty
+	}
+	return cyclonedxjson.EncoderConfig{
+		Version: version,
+		Pretty:  pretty,
+	}
+}

cmd/syft/internal/options/format_cyclonedx_json_test.go

@@ -13,7 +13,7 @@ func TestFormatCyclonedxJSON_buildConfig(t *testing.T) {
 	ft := &FormatCyclonedxJSON{}
 	ft = setAllToNonZero(t, ft).(*FormatCyclonedxJSON)
 
-	subject := ft.buildConfig("Version")
+	subject := ft.config("Version")
 	assertExpectedValue(t, subject)
 }
 

cmd/syft/internal/options/format_cyclonedx_xml.go

@@ -0,0 +1,24 @@
+package options
+
+import (
+	"github.com/anchore/syft/syft/format/cyclonedxxml"
+)
+
+type FormatCyclonedxXML struct {
+	Pretty *bool `yaml:"pretty" json:"pretty" mapstructure:"pretty"`
+}
+
+func DefaultFormatCyclonedxXML() FormatCyclonedxXML {
+	return FormatCyclonedxXML{}
+}
+
+func (o FormatCyclonedxXML) config(version string) cyclonedxxml.EncoderConfig {
+	var pretty bool
+	if o.Pretty != nil {
+		pretty = *o.Pretty
+	}
+	return cyclonedxxml.EncoderConfig{
+		Version: version,
+		Pretty:  pretty,
+	}
+}

cmd/syft/internal/options/format_cyclonedx_xml_test.go

@@ -10,6 +10,6 @@ func TestFormatCyclonedxXML_buildConfig(t *testing.T) {
 	ft := FormatCyclonedxXML{}
 	ftp := setAllToNonZero(t, &ft).(*FormatCyclonedxXML)
 
-	subject := ftp.buildConfig("Version")
+	subject := ftp.config("Version")
 	assertExpectedValue(t, subject)
 }

cmd/syft/internal/options/format_spdx_json.go

@@ -0,0 +1,24 @@
+package options
+
+import (
+	"github.com/anchore/syft/syft/format/spdxjson"
+)
+
+type FormatSPDXJSON struct {
+	Pretty *bool `yaml:"pretty" json:"pretty" mapstructure:"pretty"`
+}
+
+func DefaultFormatSPDXJSON() FormatSPDXJSON {
+	return FormatSPDXJSON{}
+}
+
+func (o FormatSPDXJSON) config(v string) spdxjson.EncoderConfig {
+	var pretty bool
+	if o.Pretty != nil {
+		pretty = *o.Pretty
+	}
+	return spdxjson.EncoderConfig{
+		Version: v,
+		Pretty:  pretty,
+	}
+}

cmd/syft/internal/options/format_spdx_json_test.go

@@ -10,6 +10,6 @@ func TestFormatSPDXJSON_buildConfig(t *testing.T) {
 	ft := &FormatSPDXJSON{}
 	ft = setAllToNonZero(t, ft).(*FormatSPDXJSON)
 
-	subject := ft.buildConfig("Version")
+	subject := ft.config("Version")
 	assertExpectedValue(t, subject)
 }

cmd/syft/internal/options/format_syft_json.go

@@ -2,7 +2,6 @@ package options
 
 import (
 	"github.com/anchore/syft/syft/format/syftjson"
-	"github.com/anchore/syft/syft/sbom"
 )
 
 type FormatSyftJSON struct {
@@ -16,12 +15,7 @@ func DefaultFormatJSON() FormatSyftJSON {
 	}
 }
 
-func (o FormatSyftJSON) formatEncoders() ([]sbom.FormatEncoder, error) {
-	enc, err := syftjson.NewFormatEncoderWithConfig(o.buildConfig())
-	return []sbom.FormatEncoder{enc}, err
-}
-
-func (o FormatSyftJSON) buildConfig() syftjson.EncoderConfig {
+func (o FormatSyftJSON) config() syftjson.EncoderConfig {
 	var pretty bool
 	if o.Pretty != nil {
 		pretty = *o.Pretty

cmd/syft/internal/options/format_syft_json_test.go

@@ -10,6 +10,6 @@ func TestFormatSyftJSON_buildConfig(t *testing.T) {
 	ft := &FormatSyftJSON{}
 	ft = setAllToNonZero(t, ft).(*FormatSyftJSON)
 
-	subject := ft.buildConfig()
+	subject := ft.config()
 	assertExpectedValue(t, subject)
 }

cmd/syft/internal/options/format_template.go

@@ -3,7 +3,6 @@ package options
 import (
 	"github.com/anchore/clio"
 	"github.com/anchore/syft/syft/format/template"
-	"github.com/anchore/syft/syft/sbom"
 )
 
 var _ clio.FlagAdder = (*FormatTemplate)(nil)
@@ -11,6 +10,7 @@ var _ clio.FlagAdder = (*FormatTemplate)(nil)
 type FormatTemplate struct {
 	Enabled bool   `yaml:"-" json:"-" mapstructure:"-"`
 	Path    string `yaml:"path" json:"path" mapstructure:"path"` // -t template file to use for output
+	Legacy  bool   `yaml:"legacy" json:"legacy" mapstructure:"legacy"`
 }
 
 func DefaultFormatTemplate() FormatTemplate {
@@ -26,12 +26,9 @@ func (o *FormatTemplate) AddFlags(flags clio.FlagSet) {
 	}
 }
 
-func (o FormatTemplate) formatEncoders() ([]sbom.FormatEncoder, error) {
-	if !o.Enabled {
-		return nil, nil
-	}
-	enc, err := template.NewFormatEncoder(template.EncoderConfig{
+func (o FormatTemplate) config() template.EncoderConfig {
+	return template.EncoderConfig{
 		TemplatePath: o.Path,
-	})
-	return []sbom.FormatEncoder{enc}, err
+		Legacy:       o.Legacy,
+	}
 }

cmd/syft/internal/options/golang.go

@@ -0,0 +1,38 @@
+package options
+
+import (
+	"strings"
+
+	"github.com/anchore/syft/syft/pkg/cataloger/golang"
+)
+
+type golangConfig struct {
+	SearchLocalModCacheLicenses bool                          `json:"search-local-mod-cache-licenses" yaml:"search-local-mod-cache-licenses" mapstructure:"search-local-mod-cache-licenses"`
+	LocalModCacheDir            string                        `json:"local-mod-cache-dir" yaml:"local-mod-cache-dir" mapstructure:"local-mod-cache-dir"`
+	SearchRemoteLicenses        bool                          `json:"search-remote-licenses" yaml:"search-remote-licenses" mapstructure:"search-remote-licenses"`
+	Proxy                       string                        `json:"proxy" yaml:"proxy" mapstructure:"proxy"`
+	NoProxy                     string                        `json:"no-proxy" yaml:"no-proxy" mapstructure:"no-proxy"`
+	MainModuleVersion           golangMainModuleVersionConfig `json:"main-module-version" yaml:"main-module-version" mapstructure:"main-module-version"`
+}
+
+type golangMainModuleVersionConfig struct {
+	FromLDFlags       bool `json:"from-ld-flags" yaml:"from-ld-flags" mapstructure:"from-ld-flags"`
+	FromContents      bool `json:"from-contents" yaml:"from-contents" mapstructure:"from-contents"`
+	FromBuildSettings bool `json:"from-build-settings" yaml:"from-build-settings" mapstructure:"from-build-settings"`
+}
+
+func defaultGolangConfig() golangConfig {
+	def := golang.DefaultCatalogerConfig()
+	return golangConfig{
+		SearchLocalModCacheLicenses: def.SearchLocalModCacheLicenses,
+		LocalModCacheDir:            def.LocalModCacheDir,
+		SearchRemoteLicenses:        def.SearchRemoteLicenses,
+		Proxy:                       strings.Join(def.Proxies, ","),
+		NoProxy:                     strings.Join(def.NoProxy, ","),
+		MainModuleVersion: golangMainModuleVersionConfig{
+			FromLDFlags:       def.MainModuleVersion.FromLDFlags,
+			FromContents:      def.MainModuleVersion.FromContents,
+			FromBuildSettings: def.MainModuleVersion.FromBuildSettings,
+		},
+	}
+}

cmd/syft/internal/options/java.go

@@ -1,6 +1,6 @@
 package options
 
-type java struct {
+type javaConfig struct {
 	UseNetwork              bool   `yaml:"use-network" json:"use-network" mapstructure:"use-network"`
 	MavenURL                string `yaml:"maven-url" json:"maven-url" mapstructure:"maven-url"`
 	MaxParentRecursiveDepth int    `yaml:"max-parent-recursive-depth" json:"max-parent-recursive-depth" mapstructure:"max-parent-recursive-depth"`

cmd/syft/internal/options/javascript.go

@@ -1,6 +1,6 @@
 package options
 
-type javascript struct {
+type javaScriptConfig struct {
 	SearchRemoteLicenses bool   `json:"search-remote-licenses" yaml:"search-remote-licenses" mapstructure:"search-remote-licenses"`
 	NpmBaseURL           string `json:"npm-base-url" yaml:"npm-base-url" mapstructure:"npm-base-url"`
 }

cmd/syft/internal/options/linux_kernel.go

@@ -1,11 +1,11 @@
 package options
 
-type linuxKernel struct {
+type linuxKernelConfig struct {
 	CatalogModules bool `json:"catalog-modules" yaml:"catalog-modules" mapstructure:"catalog-modules"`
 }
 
-func defaultLinuxKernel() linuxKernel {
-	return linuxKernel{
+func defaultLinuxKernelConfig() linuxKernelConfig {
+	return linuxKernelConfig{
 		CatalogModules: true,
 	}
 }

cmd/syft/internal/options/output.go

@@ -96,7 +96,7 @@ func (o Output) SBOMWriter() (sbom.Writer, error) {
 		}
 	}
 
-	return makeSBOMWriter(o.Outputs, o.File, encoders)
+	return makeSBOMWriter(o.Outputs, o.LegacyFile, encoders)
 }
 
 func (o Output) OutputNameSet() *strset.Set {

cmd/syft/internal/options/output_file.go

@@ -1,6 +1,10 @@
 package options
 
 import (
+	"fmt"
+
+	"github.com/mitchellh/go-homedir"
+
 	"github.com/anchore/clio"
 	"github.com/anchore/fangs"
 	"github.com/anchore/syft/syft/sbom"
@@ -13,13 +17,13 @@ var _ interface {
 
 // Deprecated: OutputFile supports the --file to write the SBOM output to
 type OutputFile struct {
-	Enabled bool   `yaml:"-" json:"-" mapstructure:"-"`
-	File    string `yaml:"file" json:"file" mapstructure:"file"`
+	Enabled    bool   `yaml:"-" json:"-" mapstructure:"-"`
+	LegacyFile string `yaml:"-" json:"-" mapstructure:"legacyFile"`
 }
 
 func (o *OutputFile) AddFlags(flags clio.FlagSet) {
 	if o.Enabled {
-		flags.StringVarP(&o.File, "file", "",
+		flags.StringVarP(&o.LegacyFile, "file", "",
 			"file to write the default report output to (default is STDOUT)")
 
 		if pfp, ok := flags.(fangs.PFlagSetProvider); ok {
@@ -33,12 +37,12 @@ func (o *OutputFile) PostLoad() error {
 	if !o.Enabled {
 		return nil
 	}
-	if o.File != "" {
-		file, err := expandFilePath(o.File)
+	if o.LegacyFile != "" {
+		file, err := expandFilePath(o.LegacyFile)
 		if err != nil {
 			return err
 		}
-		o.File = file
+		o.LegacyFile = file
 	}
 	return nil
 }
@@ -47,10 +51,21 @@ func (o *OutputFile) SBOMWriter(f sbom.FormatEncoder) (sbom.Writer, error) {
 	if !o.Enabled {
 		return nil, nil
 	}
-	writer, err := newSBOMMultiWriter(newSBOMWriterDescription(f, o.File))
+	writer, err := newSBOMMultiWriter(newSBOMWriterDescription(f, o.LegacyFile))
 	if err != nil {
 		return nil, err
 	}
 
 	return writer, nil
 }
+
+func expandFilePath(file string) (string, error) {
+	if file != "" {
+		expandedPath, err := homedir.Expand(file)
+		if err != nil {
+			return "", fmt.Errorf("unable to expand file path=%q: %w", file, err)
+		}
+		file = expandedPath
+	}
+	return file, nil
+}

cmd/syft/internal/options/pkg.go

@@ -0,0 +1,18 @@
+package options
+
+import "github.com/anchore/syft/syft/cataloging"
+
+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
+}
+
+func defaultPackageConfig() packageConfig {
+	c := cataloging.DefaultArchiveSearchConfig()
+	return packageConfig{
+		SearchIndexedArchives:           c.IncludeIndexedArchives,
+		SearchUnindexedArchives:         c.IncludeUnindexedArchives,
+		ExcludeBinaryOverlapByOwnership: true,
+	}
+}

cmd/syft/internal/options/python.go

@@ -1,5 +1,5 @@
 package options
 
-type python struct {
+type pythonConfig struct {
 	GuessUnpinnedRequirements bool `json:"guess-unpinned-requirements" yaml:"guess-unpinned-requirements" mapstructure:"guess-unpinned-requirements"`
 }

cmd/syft/internal/options/registry.go

@@ -18,16 +18,16 @@ type RegistryCredentials struct {
 	TLSKey  string `yaml:"tls-key,omitempty" json:"tls-key,omitempty" mapstructure:"tls-key"`
 }
 
-type registry struct {
+type registryConfig struct {
 	InsecureSkipTLSVerify bool                  `yaml:"insecure-skip-tls-verify" json:"insecure-skip-tls-verify" mapstructure:"insecure-skip-tls-verify"`
 	InsecureUseHTTP       bool                  `yaml:"insecure-use-http" json:"insecure-use-http" mapstructure:"insecure-use-http"`
 	Auth                  []RegistryCredentials `yaml:"auth" json:"auth" mapstructure:"auth"`
 	CACert                string                `yaml:"ca-cert" json:"ca-cert" mapstructure:"ca-cert"`
 }
 
-var _ clio.PostLoader = (*registry)(nil)
+var _ clio.PostLoader = (*registryConfig)(nil)
 
-func (cfg *registry) PostLoad() error {
+func (cfg *registryConfig) PostLoad() error {
 	// there may be additional credentials provided by env var that should be appended to the set of credentials
 	authority, username, password, token, tlsCert, tlsKey :=
 		os.Getenv("SYFT_REGISTRY_AUTH_AUTHORITY"),
@@ -62,7 +62,7 @@ func hasNonEmptyCredentials(username, password, token, tlsCert, tlsKey string) b
 	return hasUserPass || hasToken || hasTLSMaterial
 }
 
-func (cfg *registry) ToOptions() *image.RegistryOptions {
+func (cfg *registryConfig) ToOptions() *image.RegistryOptions {
 	var auth = make([]image.RegistryCredentials, len(cfg.Auth))
 	for i, a := range cfg.Auth {
 		auth[i] = image.RegistryCredentials{

cmd/syft/internal/options/registry_test.go

@@ -72,19 +72,19 @@ func TestHasNonEmptyCredentials(t *testing.T) {
 func Test_registry_ToOptions(t *testing.T) {
 	tests := []struct {
 		name     string
-		input    registry
+		input    registryConfig
 		expected image.RegistryOptions
 	}{
 		{
 			name:  "no registry options",
-			input: registry{},
+			input: registryConfig{},
 			expected: image.RegistryOptions{
 				Credentials: []image.RegistryCredentials{},
 			},
 		},
 		{
 			name: "set InsecureSkipTLSVerify",
-			input: registry{
+			input: registryConfig{
 				InsecureSkipTLSVerify: true,
 			},
 			expected: image.RegistryOptions{
@@ -94,7 +94,7 @@ func Test_registry_ToOptions(t *testing.T) {
 		},
 		{
 			name: "set InsecureUseHTTP",
-			input: registry{
+			input: registryConfig{
 				InsecureUseHTTP: true,
 			},
 			expected: image.RegistryOptions{
@@ -104,7 +104,7 @@ func Test_registry_ToOptions(t *testing.T) {
 		},
 		{
 			name: "set all bool options",
-			input: registry{
+			input: registryConfig{
 				InsecureSkipTLSVerify: true,
 				InsecureUseHTTP:       true,
 			},
@@ -116,7 +116,7 @@ func Test_registry_ToOptions(t *testing.T) {
 		},
 		{
 			name: "provide all tls configuration",
-			input: registry{
+			input: registryConfig{
 				CACert:                "ca.crt",
 				InsecureSkipTLSVerify: true,
 				Auth: []RegistryCredentials{

cmd/syft/internal/options/relationships.go

@@ -0,0 +1,22 @@
+package options
+
+import "github.com/anchore/fangs"
+
+var _ fangs.FieldDescriber = (*relationshipsConfig)(nil)
+
+type relationshipsConfig struct {
+	PackageFileOwnership        bool `mapstructure:"package-file-ownership" json:"package-file-ownership" yaml:"package-file-ownership"`
+	PackageFileOwnershipOverlap bool `mapstructure:"package-file-ownership-overlap" json:"package-file-ownership-overlap" yaml:"package-file-ownership-overlap"`
+}
+
+func defaultRelationshipsConfig() relationshipsConfig {
+	return relationshipsConfig{
+		PackageFileOwnership:        true,
+		PackageFileOwnershipOverlap: true,
+	}
+}
+
+func (r *relationshipsConfig) DescribeFields(descriptions fangs.FieldDescriptionSet) {
+	descriptions.Add(&r.PackageFileOwnership, "include package-to-file relationships that indicate which files are owned by which packages.")
+	descriptions.Add(&r.PackageFileOwnershipOverlap, "include package-to-package relationships that indicate one package is owned by another due to files claimed to be owned by one package are also evidence of another package's existence.")
+}

cmd/syft/internal/options/source.go

@@ -0,0 +1,62 @@
+package options
+
+import (
+	"fmt"
+	"sort"
+	"strings"
+
+	"github.com/scylladb/go-set/strset"
+
+	"github.com/anchore/syft/syft/source/sourceproviders"
+)
+
+type sourceConfig struct {
+	Name     string      `json:"name" yaml:"name" mapstructure:"name"`
+	Version  string      `json:"version" yaml:"version" mapstructure:"version"`
+	BasePath string      `yaml:"base-path" json:"base-path" mapstructure:"base-path"` // specify base path for all file paths
+	File     fileSource  `json:"file" yaml:"file" mapstructure:"file"`
+	Image    imageSource `json:"image" yaml:"image" mapstructure:"image"`
+}
+
+type fileSource struct {
+	Digests []string `json:"digests" yaml:"digests" mapstructure:"digests"`
+}
+
+type imageSource struct {
+	DefaultPullSource string `json:"default-pull-source" yaml:"default-pull-source" mapstructure:"default-pull-source"`
+}
+
+func defaultSourceConfig() sourceConfig {
+	var digests []string
+	for _, alg := range sourceproviders.DefaultConfig().DigestAlgorithms {
+		digests = append(digests, alg.String())
+	}
+	return sourceConfig{
+		File: fileSource{
+			Digests: digests,
+		},
+	}
+}
+
+func (c *fileSource) PostLoad() error {
+	digests := strset.New(c.Digests...).List()
+	sort.Strings(digests)
+	c.Digests = digests
+	return nil
+}
+
+func (c imageSource) PostLoad() error {
+	return checkDefaultSourceValues(c.DefaultPullSource)
+}
+
+var validDefaultSourceValues = []string{"registry", "docker", "podman", ""}
+
+func checkDefaultSourceValues(source string) error {
+	validValues := strset.New(validDefaultSourceValues...)
+	if !validValues.Has(source) {
+		validValuesString := strings.Join(validDefaultSourceValues, ", ")
+		return fmt.Errorf("%s is not a valid default source; please use one of the following: %s''", source, validValuesString)
+	}
+
+	return nil
+}

cmd/syft/internal/options/source_test.go

@@ -0,0 +1,37 @@
+package options
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func Test_fileSource_PostLoad(t *testing.T) {
+	tests := []struct {
+		name    string
+		cfg     fileSource
+		assert  func(t *testing.T, cfg fileSource)
+		wantErr assert.ErrorAssertionFunc
+	}{
+		{
+			name: "deduplicate digests",
+			cfg: fileSource{
+				Digests: []string{"sha1", "sha1"},
+			},
+			assert: func(t *testing.T, cfg fileSource) {
+				assert.Equal(t, []string{"sha1"}, cfg.Digests)
+			},
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if tt.wantErr == nil {
+				tt.wantErr = assert.NoError
+			}
+			tt.wantErr(t, tt.cfg.PostLoad())
+			if tt.assert != nil {
+				tt.assert(t, tt.cfg)
+			}
+		})
+	}
+}

cmd/syft/internal/options/update_check.go

@@ -1,5 +1,7 @@
 package options
 
+import "github.com/anchore/fangs"
+
 type UpdateCheck struct {
 	CheckForAppUpdate bool `yaml:"check-for-app-update" json:"check-for-app-update" mapstructure:"check-for-app-update"` // whether to check for an application update on start up or not
 }
@@ -9,3 +11,7 @@ func DefaultUpdateCheck() UpdateCheck {
 		CheckForAppUpdate: true,
 	}
 }
+
+func (cfg *UpdateCheck) DescribeFields(descriptions fangs.FieldDescriptionSet) {
+	descriptions.Add(&cfg.CheckForAppUpdate, "whether to check for an application update on start up or not")
+}

cmd/syft/internal/test/integration/all_layers_squashed_comparison_test.go

@@ -8,8 +8,8 @@ import (
 
 func Test_AllLayersIncludesSquashed(t *testing.T) {
 	// This is a verification test for issue #894 (https://github.com/anchore/syft/issues/894)
-	allLayers, _ := catalogFixtureImage(t, "image-suse-all-layers", source.AllLayersScope, nil)
-	squashed, _ := catalogFixtureImage(t, "image-suse-all-layers", source.SquashedScope, nil)
+	allLayers, _ := catalogFixtureImage(t, "image-suse-all-layers", source.AllLayersScope)
+	squashed, _ := catalogFixtureImage(t, "image-suse-all-layers", source.SquashedScope)
 
 	lenAllLayers := len(allLayers.Artifacts.Packages.Sorted())
 	lenSquashed := len(squashed.Artifacts.Packages.Sorted())

cmd/syft/internal/test/integration/catalog_packages_cases_test.go

@@ -368,6 +368,14 @@ var dirOnlyTestCases = []testCase{
 			"unicode_util_compat": "0.7.0",
 		},
 	},
+	{
+		name:        "find ErLang OTP applications",
+		pkgType:     pkg.ErlangOTPPkg,
+		pkgLanguage: pkg.Erlang,
+		pkgInfo: map[string]string{
+			"accept": "0.3.5",
+		},
+	},
 	{
 		name:        "find swift package manager packages",
 		pkgType:     pkg.SwiftPkg,
@@ -444,4 +452,20 @@ var commonTestCases = []testCase{
 			"glibc": "2.34-210",
 		},
 	},
+	{
+		name:        "find wordpress plugins",
+		pkgType:     pkg.WordpressPluginPkg,
+		pkgLanguage: pkg.PHP,
+		pkgInfo: map[string]string{
+			"Akismet Anti-spam: Spam Protection": "5.3",
+		},
+	},
+	{
+		name:        "find php pecl package",
+		pkgType:     pkg.PhpPeclPkg,
+		pkgLanguage: pkg.PHP,
+		pkgInfo: map[string]string{
+			"memcached": "3.2.0",
+		},
+	},
 }

cmd/syft/internal/test/integration/catalog_packages_test.go

@@ -1,6 +1,7 @@
 package integration
 
 import (
+	"context"
 	"strings"
 	"testing"
 
@@ -9,53 +10,35 @@ import (
 	"github.com/stretchr/testify/require"
 
 	"github.com/anchore/stereoscope/pkg/imagetest"
-	"github.com/anchore/syft/syft/linux"
+	"github.com/anchore/syft/syft"
 	"github.com/anchore/syft/syft/pkg"
-	"github.com/anchore/syft/syft/pkg/cataloger"
 	"github.com/anchore/syft/syft/source"
 )
 
 func BenchmarkImagePackageCatalogers(b *testing.B) {
+	// get the fixture image tar file
 	fixtureImageName := "image-pkg-coverage"
 	imagetest.GetFixtureImage(b, "docker-archive", fixtureImageName)
 	tarPath := imagetest.GetFixtureImageTarPath(b, fixtureImageName)
 
-	var pc *pkg.Collection
-	for _, c := range cataloger.ImageCatalogers(cataloger.DefaultConfig()) {
-		// in case of future alteration where state is persisted, assume no dependency is safe to reuse
-		userInput := "docker-archive:" + tarPath
-		detection, err := source.Detect(userInput, source.DefaultDetectConfig())
-		require.NoError(b, err)
-		theSource, err := detection.NewSource(source.DefaultDetectionSourceConfig())
-		if err != nil {
-			b.Fatalf("unable to get source: %+v", err)
-		}
-		b.Cleanup(func() {
-			theSource.Close()
-		})
+	// get the source object for the image
+	theSource, err := syft.GetSource(context.Background(), tarPath, syft.DefaultGetSourceConfig().WithSources("docker-archive"))
+	require.NoError(b, err)
 
-		resolver, err := theSource.FileResolver(source.SquashedScope)
-		if err != nil {
-			b.Fatalf("unable to get resolver: %+v", err)
-		}
+	b.Cleanup(func() {
+		require.NoError(b, theSource.Close())
+	})
 
-		theDistro := linux.IdentifyRelease(resolver)
+	// build the SBOM
+	s, err := syft.CreateSBOM(context.Background(), theSource, syft.DefaultCreateSBOMConfig())
 
-		b.Run(c.Name(), func(b *testing.B) {
-			for i := 0; i < b.N; i++ {
-				pc, _, err = cataloger.Catalog(resolver, theDistro, 1, c)
-				if err != nil {
-					b.Fatalf("failure during benchmark: %+v", err)
-				}
-			}
-		})
-
-		b.Logf("catalog for %q number of packages: %d", c.Name(), pc.PackageCount())
-	}
+	// did it work?
+	require.NoError(b, err)
+	require.NotNil(b, s)
 }
 
 func TestPkgCoverageImage(t *testing.T) {
-	sbom, _ := catalogFixtureImage(t, "image-pkg-coverage", source.SquashedScope, nil)
+	sbom, _ := catalogFixtureImage(t, "image-pkg-coverage", source.SquashedScope)
 
 	observedLanguages := strset.New()
 	definedLanguages := strset.New()
@@ -70,8 +53,8 @@ func TestPkgCoverageImage(t *testing.T) {
 	definedLanguages.Remove(pkg.Swift.String())
 	definedLanguages.Remove(pkg.CPP.String())
 	definedLanguages.Remove(pkg.Haskell.String())
-	definedLanguages.Remove(pkg.Erlang.String())
 	definedLanguages.Remove(pkg.Elixir.String())
+	definedLanguages.Remove(pkg.Erlang.String())
 
 	observedPkgs := strset.New()
 	definedPkgs := strset.New()
@@ -84,6 +67,7 @@ func TestPkgCoverageImage(t *testing.T) {
 	definedPkgs.Remove(string(pkg.GoModulePkg))
 	definedPkgs.Remove(string(pkg.RustPkg))
 	definedPkgs.Remove(string(pkg.DartPubPkg))
+	definedPkgs.Remove(string(pkg.ErlangOTPPkg))
 	definedPkgs.Remove(string(pkg.CocoapodsPkg))
 	definedPkgs.Remove(string(pkg.ConanPkg))
 	definedPkgs.Remove(string(pkg.HackagePkg))
@@ -135,7 +119,6 @@ func TestPkgCoverageImage(t *testing.T) {
 				}
 				t.Fatalf("unexpected package count: %d!=%d", pkgCount, len(c.pkgInfo))
 			}
-
 		})
 	}
 
@@ -223,7 +206,6 @@ func TestPkgCoverageDirectory(t *testing.T) {
 				}
 				t.Fatalf("unexpected package count: %d!=%d", actualPkgCount, len(test.pkgInfo))
 			}
-
 		})
 	}
 
@@ -250,29 +232,8 @@ func TestPkgCoverageDirectory(t *testing.T) {
 	}
 }
 
-func TestPkgCoverageCatalogerConfiguration(t *testing.T) {
-	// Check that cataloger configuration can be used to run a cataloger on a source
-	// for which that cataloger isn't enabled by defauly
-	sbom, _ := catalogFixtureImage(t, "image-pkg-coverage", source.SquashedScope, []string{"rust"})
-
-	observedLanguages := strset.New()
-	definedLanguages := strset.New()
-	definedLanguages.Add("rust")
-
-	for actualPkg := range sbom.Artifacts.Packages.Enumerate() {
-		observedLanguages.Add(actualPkg.Language.String())
-	}
-
-	assert.Equal(t, definedLanguages, observedLanguages)
-
-	// Verify that rust isn't actually an image cataloger
-	c := cataloger.DefaultConfig()
-	c.Catalogers = []string{"rust"}
-	assert.Len(t, cataloger.ImageCatalogers(c), 0)
-}
-
 func TestPkgCoverageImage_HasEvidence(t *testing.T) {
-	sbom, _ := catalogFixtureImage(t, "image-pkg-coverage", source.SquashedScope, nil)
+	sbom, _ := catalogFixtureImage(t, "image-pkg-coverage", source.SquashedScope)
 
 	var cases []testCase
 	cases = append(cases, commonTestCases...)
@@ -282,7 +243,6 @@ func TestPkgCoverageImage_HasEvidence(t *testing.T) {
 
 	for _, c := range cases {
 		t.Run(c.name, func(t *testing.T) {
-
 			for a := range sbom.Artifacts.Packages.Enumerate(c.pkgType) {
 				assert.NotEmpty(t, a.Locations.ToSlice(), "package %q has no locations (type=%q)", a.Name, a.Type)
 				for _, l := range a.Locations.ToSlice() {
@@ -292,7 +252,6 @@ func TestPkgCoverageImage_HasEvidence(t *testing.T) {
 					}
 				}
 			}
-
 		})
 	}
 
@@ -312,7 +271,6 @@ func TestPkgCoverageDirectory_HasEvidence(t *testing.T) {
 
 	for _, c := range cases {
 		t.Run(c.name, func(t *testing.T) {
-
 			for a := range sbom.Artifacts.Packages.Enumerate(c.pkgType) {
 				assert.NotEmpty(t, a.Locations.ToSlice(), "package %q has no locations (type=%q)", a.Name, a.Type)
 				for _, l := range a.Locations.ToSlice() {
@@ -322,7 +280,6 @@ func TestPkgCoverageDirectory_HasEvidence(t *testing.T) {
 					}
 				}
 			}
-
 		})
 	}