Merge pull request #2831 from github/cklin/diff-informed-query-filtering

Respect `exclude-from-incremental` query tag for diff-informed analysis

.github/actions/check-codescanning-config/action.yml

@@ -61,11 +61,12 @@ runs:
     - name: Check config
       working-directory: ${{ github.action_path }}
       shell: bash
-      run: ts-node ./index.ts "${{ runner.temp }}/user-config.yaml" '${{ inputs.expected-config-file-contents }}'
-
+      env:
+        EXPECTED_CONFIG_FILE_CONTENTS: '${{ inputs.expected-config-file-contents }}'
+      run: ts-node ./index.ts "$RUNNER_TEMP/user-config.yaml" "$EXPECTED_CONFIG_FILE_CONTENTS"
     - name: Clean up
       shell: bash
       if: always()
       run: |
-        rm -rf ${{ runner.temp }}/codescanning-config-cli-test
-        rm -rf ${{ runner.temp }}/user-config.yaml
+        rm -rf $RUNNER_TEMP/codescanning-config-cli-test
+        rm -rf $RUNNER_TEMP/user-config.yaml

.github/actions/check-codescanning-config/index.ts

@@ -8,7 +8,7 @@ const actualConfig = loadActualConfig()
 
 const rawExpectedConfig = process.argv[3].trim()
 if (!rawExpectedConfig) {
-  core.info('No expected configuration provided')
+  core.setFailed('No expected configuration provided')
 } else {
   core.startGroup('Expected generated user config')
   core.info(yaml.dump(JSON.parse(rawExpectedConfig)))

.github/codeql/codeql-actions-config.yml

@@ -0,0 +1,4 @@
+# Configuration for the CodeQL Actions Queries
+name: "CodeQL Actions Queries config"
+queries:
+  - uses: security-and-quality

.github/releases.ini

@@ -1 +1 @@
-OLDEST_SUPPORTED_MAJOR_VERSION=2
+OLDEST_SUPPORTED_MAJOR_VERSION=3

.github/workflows/__all-platform-bundle.yml

@@ -32,15 +32,10 @@ jobs:
     name: All-platform bundle
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__analyze-ref-input.yml

@@ -36,15 +36,10 @@ jobs:
     name: "Analyze: 'ref' and 'sha' from inputs"
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__autobuild-action.yml

@@ -36,15 +36,10 @@ jobs:
     name: autobuild-action
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__autobuild-direct-tracing-with-working-dir.yml

@@ -38,15 +38,10 @@ jobs:
     name: Autobuild direct tracing (custom working directory)
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__autobuild-direct-tracing.yml

@@ -38,15 +38,10 @@ jobs:
     name: Autobuild direct tracing
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__build-mode-autobuild.yml

@@ -32,15 +32,10 @@ jobs:
     name: Build mode autobuild
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__build-mode-manual.yml

@@ -32,15 +32,10 @@ jobs:
     name: Build mode manual
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__build-mode-none.yml

@@ -34,15 +34,10 @@ jobs:
     name: Build mode none
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__build-mode-rollback.yml

@@ -32,15 +32,10 @@ jobs:
     name: Build mode rollback
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__cleanup-db-cluster-dir.yml

@@ -32,15 +32,10 @@ jobs:
     name: Clean up database cluster directory
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__config-export.yml

@@ -42,15 +42,10 @@ jobs:
     name: Config export
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__config-input.yml

@@ -32,15 +32,10 @@ jobs:
     name: Config input
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__cpp-deptrace-disabled.yml

@@ -36,15 +36,10 @@ jobs:
     name: 'C/C++: disabling autoinstalling dependencies (Linux)'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__cpp-deptrace-enabled-on-macos.yml

@@ -32,15 +32,10 @@ jobs:
     name: 'C/C++: autoinstalling dependencies is skipped (macOS)'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__cpp-deptrace-enabled.yml

@@ -36,15 +36,10 @@ jobs:
     name: 'C/C++: autoinstalling dependencies (Linux)'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__diagnostics-export.yml

@@ -42,15 +42,10 @@ jobs:
     name: Diagnostic export
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__export-file-baseline-information.yml

@@ -36,15 +36,10 @@ jobs:
     name: Export file baseline information
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__extract-direct-to-toolcache.yml

@@ -36,15 +36,10 @@ jobs:
     name: Extract directly to toolcache
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__extractor-ram-threads.yml

@@ -32,15 +32,10 @@ jobs:
     name: Extractor ram and threads options test
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__go-custom-queries.yml

@@ -34,15 +34,10 @@ jobs:
     name: 'Go: Custom queries'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__go-indirect-tracing-workaround-diagnostic.yml

@@ -32,15 +32,10 @@ jobs:
     name: 'Go: diagnostic when Go is changed after init step'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__go-indirect-tracing-workaround-no-file-program.yml

@@ -32,15 +32,10 @@ jobs:
     name: 'Go: diagnostic when `file` is not installed'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__go-indirect-tracing-workaround.yml

@@ -32,15 +32,10 @@ jobs:
     name: 'Go: workaround for indirect tracing'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__go-tracing-autobuilder.yml

@@ -62,15 +62,10 @@ jobs:
     name: 'Go: tracing with autobuilder step'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test
@@ -82,7 +77,7 @@ jobs:
           setup-kotlin: 'true'
       - uses: actions/setup-go@v5
         with:
-          go-version: ~1.23.0
+          go-version: ~1.24.0
       # to avoid potentially misleading autobuilder results where we expect it to download
       # dependencies successfully, but they actually come from a warm cache
           cache: false

.github/workflows/__go-tracing-custom-build-steps.yml

@@ -62,15 +62,10 @@ jobs:
     name: 'Go: tracing with custom build steps'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test
@@ -82,7 +77,7 @@ jobs:
           setup-kotlin: 'true'
       - uses: actions/setup-go@v5
         with:
-          go-version: ~1.23.0
+          go-version: ~1.24.0
       # to avoid potentially misleading autobuilder results where we expect it to download
       # dependencies successfully, but they actually come from a warm cache
           cache: false

.github/workflows/__go-tracing-legacy-workflow.yml

@@ -62,15 +62,10 @@ jobs:
     name: 'Go: tracing with legacy workflow'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test
@@ -82,7 +77,7 @@ jobs:
           setup-kotlin: 'true'
       - uses: actions/setup-go@v5
         with:
-          go-version: ~1.23.0
+          go-version: ~1.24.0
       # to avoid potentially misleading autobuilder results where we expect it to download
       # dependencies successfully, but they actually come from a warm cache
           cache: false

.github/workflows/__init-with-registries.yml

@@ -53,11 +53,6 @@ jobs:
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__javascript-source-root.yml

@@ -36,15 +36,10 @@ jobs:
     name: Custom source root
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__job-run-uuid-sarif.yml

@@ -32,15 +32,10 @@ jobs:
     name: Job run UUID added to SARIF
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__language-aliases.yml

@@ -32,15 +32,10 @@ jobs:
     name: Language aliases
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__multi-language-autodetect.yml

@@ -62,15 +62,10 @@ jobs:
     name: Multi-language repository
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__packaging-codescanning-config-inputs-js.yml

@@ -48,15 +48,10 @@ jobs:
     name: 'Packaging: Config and input passed to the CLI'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__packaging-config-inputs-js.yml

@@ -48,15 +48,10 @@ jobs:
     name: 'Packaging: Config and input'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__packaging-config-js.yml

@@ -48,15 +48,10 @@ jobs:
     name: 'Packaging: Config file'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__packaging-inputs-js.yml

@@ -48,15 +48,10 @@ jobs:
     name: 'Packaging: Action input'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__remote-config.yml

@@ -34,15 +34,10 @@ jobs:
     name: Remote config file
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__resolve-environment-action.yml

@@ -48,15 +48,10 @@ jobs:
     name: Resolve environment
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__rubocop-multi-language.yml

@@ -32,15 +32,10 @@ jobs:
     name: RuboCop multi-language
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test
@@ -51,7 +46,7 @@ jobs:
           use-all-platform-bundle: 'false'
           setup-kotlin: 'true'
       - name: Set up Ruby
-        uses: ruby/setup-ruby@v1
+        uses: ruby/setup-ruby@1a615958ad9d422dd932dc1d5823942ee002799f # v1.227.0
         with:
           ruby-version: 2.6
       - name: Install Code Scanning integration

.github/workflows/__ruby.yml

@@ -42,15 +42,10 @@ jobs:
     name: Ruby analysis
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__rust.yml

@@ -0,0 +1,71 @@
+# Warning: This file is generated automatically, and should not be modified.
+# Instead, please modify the template in the pr-checks directory and run:
+#     (cd pr-checks; pip install ruamel.yaml@0.17.31 && python3 sync.py)
+# to regenerate this file.
+
+name: PR Check - Rust analysis
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  GO111MODULE: auto
+on:
+  push:
+    branches:
+      - main
+      - releases/v*
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+  schedule:
+    - cron: '0 5 * * *'
+  workflow_dispatch: {}
+jobs:
+  rust:
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            version: linked
+          - os: ubuntu-latest
+            version: default
+          - os: ubuntu-latest
+            version: nightly-latest
+    name: Rust analysis
+    permissions:
+      contents: read
+      security-events: read
+    timeout-minutes: 45
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Prepare test
+        id: prepare-test
+        uses: ./.github/actions/prepare-test
+        with:
+          version: ${{ matrix.version }}
+          use-all-platform-bundle: 'false'
+          setup-kotlin: 'true'
+      - uses: ./../action/init
+        with:
+          languages: rust
+          tools: ${{ steps.prepare-test.outputs.tools-url }}
+        env:
+          CODEQL_ACTION_RUST_ANALYSIS: true
+      - uses: ./../action/analyze
+        id: analysis
+        with:
+          upload-database: false
+      - name: Check database
+        shell: bash
+        run: |
+          RUST_DB="${{ fromJson(steps.analysis.outputs.db-locations).rust }}"
+          if [[ ! -d "$RUST_DB" ]]; then
+            echo "Did not create a database for Rust."
+            exit 1
+          fi
+    env:
+      CODEQL_ACTION_TEST_MODE: true

.github/workflows/__split-workflow.yml

@@ -42,15 +42,10 @@ jobs:
     name: Split workflow
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__start-proxy.yml

@@ -36,15 +36,10 @@ jobs:
     name: Start proxy
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__submit-sarif-failure.yml

@@ -36,15 +36,11 @@ jobs:
     name: Submit SARIF after failure
     permissions:
       contents: read
-      security-events: write
+      security-events: write # needed to upload the SARIF file
+
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__swift-autobuild.yml

@@ -32,15 +32,10 @@ jobs:
     name: Swift analysis using autobuild
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__swift-custom-build.yml

@@ -36,15 +36,10 @@ jobs:
     name: Swift analysis using a custom build command
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__test-autobuild-working-dir.yml

@@ -32,15 +32,10 @@ jobs:
     name: Autobuild working directory
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__test-local-codeql.yml

@@ -32,15 +32,10 @@ jobs:
     name: Local CodeQL bundle
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__test-proxy.yml

@@ -34,7 +34,7 @@ jobs:
     name: Proxy test
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
@@ -50,11 +50,6 @@ jobs:
           apt-add-repository https://cli.github.com/packages
           apt install -y gh
         env: {}
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__unset-environment.yml

@@ -34,15 +34,10 @@ jobs:
     name: Test unsetting environment variables
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__upload-ref-sha-input.yml

@@ -36,15 +36,10 @@ jobs:
     name: "Upload-sarif: 'ref' and 'sha' from inputs"
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__with-checkout-path.yml

@@ -36,15 +36,10 @@ jobs:
     name: Use a custom `checkout_path`
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__zstd-bundle-streaming.yml

@@ -34,15 +34,10 @@ jobs:
     name: Zstandard bundle (streaming)
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/__zstd-bundle.yml

@@ -36,15 +36,10 @@ jobs:
     name: Zstandard bundle
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Setup Python on macOS
-        uses: actions/setup-python@v5
-        if: runner.os == 'macOS' && matrix.version == 'stable-v2.14.6'
-        with:
-          python-version: '3.11'
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Prepare test

.github/workflows/check-expected-release-files.yml

@@ -13,6 +13,9 @@ jobs:
   check-expected-release-files:
     runs-on: ubuntu-latest
 
+    permissions:
+      contents: read
+
     steps:
       - name: Checkout CodeQL Action
         uses: actions/checkout@v4

.github/workflows/codeql.yml

@@ -24,7 +24,7 @@ jobs:
       versions: ${{ steps.compare.outputs.versions }}
 
     permissions:
-      security-events: write
+      contents: read
 
     steps:
     - uses: actions/checkout@v4
@@ -70,7 +70,7 @@ jobs:
         echo "Suggested matrix config for analysis job: $VERSIONS_JSON"
         echo "versions=${VERSIONS_JSON}" >> $GITHUB_OUTPUT
 
-  build:
+  analyze-javascript:
     needs: [check-codeql-versions]
     strategy:
       fail-fast: false
@@ -80,6 +80,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     permissions:
+      contents: read
       security-events: write
 
     steps:
@@ -99,3 +100,27 @@ jobs:
       uses: ./analyze
       with:
         category: "/language:javascript"
+
+
+  analyze-actions:
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+
+    permissions:
+      contents: read
+      security-events: write
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+    - name: Initialize CodeQL
+      uses: ./init
+      with:
+        languages: actions
+        config-file: ./.github/codeql/codeql-actions-config.yml
+    - name: Perform CodeQL Analysis
+      uses: ./analyze
+      with:
+        category: "/language:actions"

.github/workflows/codescanning-config-cli.yml

@@ -23,6 +23,11 @@ jobs:
   code-scanning-config-tests:
     continue-on-error: true
 
+    permissions:
+      contents: read
+      packages: read
+      security-events: read
+
     strategy:
       fail-fast: false
       matrix:

.github/workflows/debug-artifacts-failure-safe.yml

@@ -0,0 +1,102 @@
+# Checks logs, SARIF, and database bundle debug artifacts exist
+# when the analyze step fails.
+name: PR Check - Debug artifacts after failure
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+on:
+  push:
+    branches:
+    - main
+    - releases/v*
+  pull_request:
+    types:
+    - opened
+    - synchronize
+    - reopened
+    - ready_for_review
+  schedule:
+    - cron: '0 5 * * *'
+  workflow_dispatch: {}
+jobs:
+  upload-artifacts:
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+        - stable-v2.20.3
+        - default
+        - linked
+        - nightly-latest
+    name: Upload debug artifacts after failure in analyze
+    continue-on-error: true
+    env:
+      CODEQL_ACTION_TEST_MODE: true
+    permissions:
+      contents: read
+    timeout-minutes: 45
+    runs-on: ubuntu-latest
+    steps:
+      - name: Dump GitHub event
+        run: cat "${GITHUB_EVENT_PATH}"
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Prepare test
+        id: prepare-test
+        uses: ./.github/actions/prepare-test
+        with:
+          version: ${{ matrix.version }}
+      - uses: actions/setup-go@v5
+        with:
+          go-version: ^1.13.1
+      - uses: ./../action/init
+        with:
+          tools: ${{ steps.prepare-test.outputs.tools-url }}
+          debug: true
+          debug-artifact-name: my-debug-artifacts
+          debug-database-name: my-db
+      - name: Build code
+        shell: bash
+        run: ./build.sh
+      - uses: ./../action/analyze
+        id: analysis
+        env:
+          # Forces a failure in this step.
+          CODEQL_ACTION_EXTRA_OPTIONS: '{ "database": { "finalize": ["--invalid-option"] } }'
+        with:
+          expect-error: true
+  download-and-check-artifacts:
+    name: Download and check debug artifacts after failure in analyze
+    needs: upload-artifacts
+    timeout-minutes: 45
+    permissions:
+      contents: read
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download all artifacts
+        uses: actions/download-artifact@v4
+      - name: Check expected artifacts exist
+        shell: bash
+        run: |
+          LANGUAGES="cpp csharp go java javascript python"
+          for version in $VERSIONS; do
+            echo "Artifacts from version $version:"
+            pushd "./my-debug-artifacts-${version//./}"
+            for language in $LANGUAGES; do
+              echo "- Checking $language"
+              if [[ ! -f "my-db-$language-partial.zip" ]] ; then
+                echo "Missing a partial database bundle for $language"
+                exit 1
+              fi
+              if [[ ! -d "log" ]] ; then
+                echo "Missing database initialization logs"
+                exit 1
+              fi
+              if [[ ! "$language" == "go" ]] && [[ ! -d "$language/log" ]] ; then
+                echo "Missing logs for $language"
+                exit 1
+              fi
+            done
+            popd
+          done
+        env:
+          GO111MODULE: auto

.github/workflows/debug-artifacts-failure.yml

@@ -1,87 +0,0 @@
-# Checks logs, SARIF, and database bundle debug artifacts exist
-# when the analyze step fails.
-name: PR Check - Debug artifacts after failure
-env:
-  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-on:
-  push:
-    branches:
-    - main
-    - releases/v*
-  pull_request:
-    types:
-    - opened
-    - synchronize
-    - reopened
-    - ready_for_review
-  schedule:
-    - cron: '0 5 * * *'
-  workflow_dispatch: {}
-jobs:
-  upload-artifacts:
-    name: Upload debug artifacts after failure in analyze
-    continue-on-error: true
-    env:
-      CODEQL_ACTION_TEST_MODE: true
-    timeout-minutes: 45
-    runs-on: ubuntu-latest
-    steps:
-      - name: Dump GitHub event
-        run: cat "${GITHUB_EVENT_PATH}"
-      - name: Check out repository
-        uses: actions/checkout@v4
-      - name: Prepare test
-        id: prepare-test
-        uses: ./.github/actions/prepare-test
-        with:
-          version: linked
-      - uses: actions/setup-go@v5
-        with:
-          go-version: ^1.13.1
-      - uses: ./../action/init
-        with:
-          tools: ${{ steps.prepare-test.outputs.tools-url }}
-          debug: true
-          debug-artifact-name: my-debug-artifacts
-          debug-database-name: my-db
-      - name: Build code
-        shell: bash
-        run: ./build.sh
-      - uses: ./../action/analyze
-        id: analysis
-        env:
-          # Forces a failure in this step.
-          CODEQL_ACTION_EXTRA_OPTIONS: '{ "database": { "finalize": ["--invalid-option"] } }'
-        with:
-          expect-error: true
-  download-and-check-artifacts:
-    name: Download and check debug artifacts after failure in analyze
-    needs: upload-artifacts
-    timeout-minutes: 45
-    runs-on: ubuntu-latest
-    steps:
-      - name: Download all artifacts
-        uses: actions/download-artifact@v4
-      - name: Check expected artifacts exist
-        shell: bash
-        run: |
-          LANGUAGES="cpp csharp go java javascript python"
-          cd "./my-debug-artifacts"
-          echo "Artifacts from run:"
-          for language in $LANGUAGES; do
-            echo "- Checking $language"
-            if [[ ! -f "my-db-$language-partial.zip" ]] ; then
-              echo "Missing a partial database bundle for $language"
-              exit 1
-            fi
-            if [[ ! -d "log" ]] ; then
-              echo "Missing database initialization logs"
-              exit 1
-            fi
-            if [[ ! "$language" == "go" ]] && [[ ! -d "$language/log" ]] ; then
-              echo "Missing logs for $language"
-              exit 1
-            fi
-          done
-        env:
-          GO111MODULE: auto

.github/workflows/debug-artifacts-safe.yml

@@ -0,0 +1,97 @@
+# Checks logs, SARIF, and database bundle debug artifacts exist.
+name: PR Check - Debug artifact upload
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+on:
+  push:
+    branches:
+    - main
+    - releases/v*
+  pull_request:
+    types:
+    - opened
+    - synchronize
+    - reopened
+    - ready_for_review
+  schedule:
+    - cron: '0 5 * * *'
+  workflow_dispatch: {}
+jobs:
+  upload-artifacts:
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+        - stable-v2.20.3
+        - default
+        - linked
+        - nightly-latest
+    name: Upload debug artifacts
+    env:
+      CODEQL_ACTION_TEST_MODE: true
+    timeout-minutes: 45
+    permissions:
+      contents: read
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Prepare test
+        id: prepare-test
+        uses: ./.github/actions/prepare-test
+        with:
+          version: ${{ matrix.version }}
+      - uses: actions/setup-go@v5
+        with:
+          go-version: ^1.13.1
+      - uses: ./../action/init
+        id: init
+        with:
+          tools: ${{ steps.prepare-test.outputs.tools-url }}
+          debug: true
+          debug-artifact-name: my-debug-artifacts
+          debug-database-name: my-db
+          # We manually exclude Swift from the languages list here, as it is not supported on Ubuntu
+          languages: cpp,csharp,go,java,javascript,python,ruby
+      - name: Build code
+        shell: bash
+        run: ./build.sh
+      - uses: ./../action/analyze
+        id: analysis
+  download-and-check-artifacts:
+    name: Download and check debug artifacts
+    needs: upload-artifacts
+    timeout-minutes: 45
+    permissions:
+      contents: read
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download all artifacts
+        uses: actions/download-artifact@v4
+      - name: Check expected artifacts exist
+        shell: bash
+        run: |
+          VERSIONS="stable-v2.20.3 default linked nightly-latest"
+          LANGUAGES="cpp csharp go java javascript python"
+          for version in $VERSIONS; do
+            pushd "./my-debug-artifacts-${version//./}"
+            echo "Artifacts from version $version:"
+            for language in $LANGUAGES; do
+              echo "- Checking $language"
+              if [[ ! -f "$language.sarif" ]] ; then
+                echo "Missing a SARIF file for $language"
+                exit 1
+              fi
+              if [[ ! -f "my-db-$language.zip" ]] ; then
+                echo "Missing a database bundle for $language"
+                exit 1
+              fi
+              if [[ ! -d "$language/log" ]] ; then
+                echo "Missing logs for $language"
+                exit 1
+              fi
+            done
+            popd
+          done
+        env:
+          GO111MODULE: auto

.github/workflows/debug-artifacts.yml

@@ -1,97 +0,0 @@
-# Checks logs, SARIF, and database bundle debug artifacts exist.
-name: PR Check - Debug artifact upload
-env:
-  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-on:
-  push:
-    branches:
-    - main
-    - releases/v*
-  pull_request:
-    types:
-    - opened
-    - synchronize
-    - reopened
-    - ready_for_review
-  schedule:
-    - cron: '0 5 * * *'
-  workflow_dispatch: {}
-jobs:
-  upload-artifacts:
-    strategy:
-      fail-fast: false
-      matrix:
-        version:
-        - stable-v2.15.5
-        - stable-v2.16.6
-        - stable-v2.17.6
-        - stable-v2.18.4
-        - stable-v2.19.4
-        - default
-        - linked
-        - nightly-latest
-    name: Upload debug artifacts
-    env:
-      CODEQL_ACTION_TEST_MODE: true
-    timeout-minutes: 45
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out repository
-        uses: actions/checkout@v4
-      - name: Prepare test
-        id: prepare-test
-        uses: ./.github/actions/prepare-test
-        with:
-          version: ${{ matrix.version }}
-      - uses: actions/setup-go@v5
-        with:
-          go-version: ^1.13.1
-      - uses: ./../action/init
-        id: init
-        with:
-          tools: ${{ steps.prepare-test.outputs.tools-url }}
-          debug: true
-          debug-artifact-name: my-debug-artifacts
-          debug-database-name: my-db
-          # We manually exclude Swift from the languages list here, as it is not supported on Ubuntu
-          languages: cpp,csharp,go,java,javascript,python,ruby
-      - name: Build code
-        shell: bash
-        run: ./build.sh
-      - uses: ./../action/analyze
-        id: analysis
-  download-and-check-artifacts:
-    name: Download and check debug artifacts
-    needs: upload-artifacts
-    timeout-minutes: 45
-    runs-on: ubuntu-latest
-    steps:
-      - name: Download all artifacts
-        uses: actions/download-artifact@v4
-      - name: Check expected artifacts exist
-        shell: bash
-        run: |
-          VERSIONS="stable-v2.15.5 stable-v2.16.6 stable-v2.17.6 stable-v2.18.4 stable-v2.19.4 default linked nightly-latest"
-          LANGUAGES="cpp csharp go java javascript python"
-          for version in $VERSIONS; do
-            pushd "./my-debug-artifacts-${version//./}"
-            echo "Artifacts from version $version:"
-            for language in $LANGUAGES; do
-              echo "- Checking $language"
-              if [[ ! -f "$language.sarif" ]] ; then
-                echo "Missing a SARIF file for $language"
-                exit 1
-              fi
-              if [[ ! -f "my-db-$language.zip" ]] ; then
-                echo "Missing a database bundle for $language"
-                exit 1
-              fi
-              if [[ ! -d "$language/log" ]] ; then
-                echo "Missing logs for $language"
-                exit 1
-              fi
-            done
-            popd
-          done
-        env:
-          GO111MODULE: auto

.github/workflows/expected-queries-runs.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     steps:
     - name: Check out repository
       uses: actions/checkout@v4

.github/workflows/post-release-mergeback.yml

@@ -27,6 +27,10 @@ jobs:
       BASE_BRANCH: "${{ github.event.inputs.baseBranch || 'main' }}"
       HEAD_BRANCH: "${{ github.head_ref || github.ref }}"
 
+    permissions:
+      contents: write # needed to create tags and push commits
+      pull-requests: write
+
     steps:
       - name: Dump environment
         run: env
@@ -164,7 +168,7 @@ jobs:
             --draft
 
       - name: Generate token
-        uses: actions/create-github-app-token@c1a285145b9d317df6ced56c09f525b5c2b6f755
+        uses: actions/create-github-app-token@v1.11.7
         id: app-token
         with:
           app-id: ${{ vars.AUTOMATION_APP_ID }}

.github/workflows/pr-checks.yml

@@ -15,12 +15,10 @@ jobs:
     timeout-minutes: 45
     permissions:
       contents: read
-      security-events: write
+      security-events: write # needed to upload ESLint results
 
     strategy:
       fail-fast: false
-      matrix:
-        node-types-version: [16.11, current] # run tests on 16.11 while CodeQL Action v2 is still supported
 
     steps:
       - name: Checkout
@@ -32,40 +30,18 @@ jobs:
 
       - name: Upload sarif
         uses: github/codeql-action/upload-sarif@v3
-        # Only upload SARIF for the latest version of Node.js
-        if: "!cancelled() && matrix.node-types-version == 'current' && !startsWith(github.head_ref, 'dependabot/')"
         with:
           sarif_file: eslint.sarif
           category: eslint
 
-      - name: Update version of @types/node
-        if: matrix.node-types-version != 'current'
-        env:
-          NODE_TYPES_VERSION: ${{ matrix.node-types-version }}
-        run: |
-          # Export `NODE_TYPES_VERSION` so it's available to jq
-          export NODE_TYPES_VERSION="${NODE_TYPES_VERSION}"
-          contents=$(jq '.devDependencies."@types/node" = env.NODE_TYPES_VERSION' package.json)
-          echo "${contents}" > package.json
-          # Usually we run `npm install` on macOS to ensure that we pick up macOS-only dependencies.
-          # However we're not checking in the updated lockfile here, so it's fine to run
-          # `npm install` on Linux.
-          npm install
-
-          if [ ! -z "$(git status --porcelain)" ]; then
-            git config --global user.email "github-actions@github.com"
-            git config --global user.name "github-actions[bot]"
-            # The period in `git add --all .` ensures that we stage deleted files too.
-            git add --all .
-            git commit -m "Use @types/node=${NODE_TYPES_VERSION}"
-          fi
-
       - name: Check generated JS
         run: .github/workflows/script/check-js.sh
 
   check-node-modules:
     if: github.event_name != 'push' || github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/heads/releases/v')
     name: Check modules up to date
+    permissions:
+      contents: read
     runs-on: macos-latest
     timeout-minutes: 45
 
@@ -77,6 +53,8 @@ jobs:
   check-file-contents:
     if: github.event_name != 'push' || github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/heads/releases/v')
     name: Check file contents
+    permissions:
+      contents: read
     runs-on: ubuntu-latest
     timeout-minutes: 45
 
@@ -107,6 +85,8 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
+    permissions:
+      contents: read
     runs-on: ${{ matrix.os }}
     timeout-minutes: 45
 
@@ -127,6 +107,9 @@ jobs:
     env:
       BASE_REF: ${{ github.base_ref }}
 
+    permissions:
+      contents: read
+
     steps:
       - uses: actions/checkout@v4
       - id: head-version

.github/workflows/python312-windows.yml

@@ -17,6 +17,8 @@ jobs:
     env:
       CODEQL_ACTION_TEST_MODE: true
     timeout-minutes: 45
+    permissions:
+      contents: read
     runs-on: windows-latest
 
     steps:

.github/workflows/query-filters.yml

@@ -20,6 +20,8 @@ jobs:
     name: Query Filters Tests
     timeout-minutes: 45
     runs-on: ubuntu-latest
+    permissions:
+      contents: read # This permission is needed to allow the GitHub Actions workflow to read the contents of the repository.
     steps:
     - name: Check out repository
       uses: actions/checkout@v4

.github/workflows/rebuild.yml

@@ -11,6 +11,9 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event.label.name == 'Rebuild'
 
+    permissions:
+      contents: write # needed to push rebuilt commit
+      pull-requests: write # needed to comment on the PR
     steps:
       - name: Checkout
         uses: actions/checkout@v4

.github/workflows/test-codeql-bundle-all.yml

@@ -27,7 +27,7 @@ jobs:
     name: 'CodeQL Bundle All'
     permissions:
       contents: read
-      security-events: write
+      security-events: read
     timeout-minutes: 45
     runs-on: ${{ matrix.os }}
     steps:

.github/workflows/update-bundle.yml

@@ -17,6 +17,9 @@ jobs:
   update-bundle:
     if: github.event.release.prerelease && startsWith(github.event.release.tag_name, 'codeql-bundle-')
     runs-on: ubuntu-latest
+    permissions:
+      contents: write # needed to push commits
+      pull-requests: write # needed to create pull requests
     steps:
       - name: Dump environment
         run: env

.github/workflows/update-dependencies.yml

@@ -9,6 +9,9 @@ jobs:
     timeout-minutes: 45
     runs-on: macos-latest
     if: contains(github.event.pull_request.labels.*.name, 'Update dependencies') && (github.event.pull_request.head.repo.full_name == 'github/codeql-action')
+    permissions:
+      contents: write # needed to push the updated dependencies
+      pull-requests: write # needed to comment on the PR
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4

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

@@ -22,6 +22,8 @@ jobs:
       latest_tag: ${{ steps.versions.outputs.latest_tag }}
       backport_source_branch: ${{ steps.branches.outputs.backport_source_branch }}
       backport_target_branches: ${{ steps.branches.outputs.backport_target_branches }}
+    permissions:
+      contents: read
     steps:
     - uses: actions/checkout@v4
       with:
@@ -63,6 +65,9 @@ jobs:
       REPOSITORY: "${{ github.repository }}"
       MAJOR_VERSION: "${{ needs.prepare.outputs.major_version }}"
       LATEST_TAG: "${{ needs.prepare.outputs.latest_tag }}"
+    permissions:
+      contents: write # needed to push commits
+      pull-requests: write # needed to create pull request
     steps:
     - uses: actions/checkout@v4
       with:
@@ -114,9 +119,12 @@ jobs:
     env:
       SOURCE_BRANCH: ${{ needs.prepare.outputs.backport_source_branch }}
       TARGET_BRANCH: ${{ matrix.target_branch }}
+    permissions:
+      contents: write # needed to push commits
+      pull-requests: write # needed to create pull request
     steps:
     - name: Generate token
-      uses: actions/create-github-app-token@c1a285145b9d317df6ced56c09f525b5c2b6f755
+      uses: actions/create-github-app-token@v1.11.7
       id: app-token
       with:
         app-id: ${{ vars.AUTOMATION_APP_ID }}

.github/workflows/update-supported-enterprise-server-versions.yml

@@ -10,20 +10,23 @@ jobs:
     name: Update Supported Enterprise Server Versions
     timeout-minutes: 45
     runs-on: ubuntu-latest
-    if: ${{ github.repository == 'github/codeql-action' }}
+    if: github.repository == 'github/codeql-action'
+    permissions:
+      contents: write # needed to push commits
+      pull-requests: write # needed to create pull request
 
     steps:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.7"
+          python-version: "3.13"
       - name: Checkout CodeQL Action
         uses: actions/checkout@v4
       - name: Checkout Enterprise Releases
         uses: actions/checkout@v4
         with:
           repository: github/enterprise-releases
-          ssh-key: ${{ secrets.ENTERPRISE_RELEASES_SSH_KEY }}
+          token: ${{ secrets.ENTERPRISE_RELEASE_TOKEN }}
           path: ${{ github.workspace }}/enterprise-releases/
       - name: Update Supported Enterprise Server Versions
         run: |

.pre-commit-config.yaml

@@ -1,20 +1,20 @@
 repos:
   - repo: local
     hooks:
+      - id: lint-ts
+        name: Lint typescript code
+        files: \.ts$
+        language: system
+        entry: npm run lint -- --fix
       - id: compile-ts
         name: Compile typescript
         files: \.[tj]s$
         language: system
         entry: npm run build
         pass_filenames: false
-      - id: lint-ts
-        name: Lint typescript code
-        files: \.ts$
-        language: system
-        entry: npm run lint -- --fix
       - id: pr-checks-sync
         name: Synchronize PR check workflows
         files: ^.github/workflows/__.*\.yml$|^pr-checks
         language: system
-        entry: python3 pr-checks/sync.py
+        entry: pr-checks/sync.sh
         pass_filenames: false

CHANGELOG.md

@@ -2,6 +2,62 @@
 
 See the [releases page](https://github.com/github/codeql-action/releases) for the relevant changes to the CodeQL CLI and language packs.
 
+## [UNRELEASED]
+
+No user facing changes.
+
+## 3.28.13 - 24 Mar 2025
+
+No user facing changes.
+
+## 3.28.12 - 19 Mar 2025
+
+- Dependency caching should now cache more dependencies for Java `build-mode: none` extractions. This should speed up workflows and avoid inconsistent alerts in some cases.
+- Update default CodeQL bundle version to 2.20.7. [#2810](https://github.com/github/codeql-action/pull/2810)
+
+## 3.28.11 - 07 Mar 2025
+
+- Update default CodeQL bundle version to 2.20.6. [#2793](https://github.com/github/codeql-action/pull/2793)
+
+## 3.28.10 - 21 Feb 2025
+
+- Update default CodeQL bundle version to 2.20.5. [#2772](https://github.com/github/codeql-action/pull/2772)
+- Address an issue where the CodeQL Bundle would occasionally fail to decompress on macOS. [#2768](https://github.com/github/codeql-action/pull/2768)
+
+## 3.28.9 - 07 Feb 2025
+
+- Update default CodeQL bundle version to 2.20.4. [#2753](https://github.com/github/codeql-action/pull/2753)
+
+## 3.28.8 - 29 Jan 2025
+
+- Enable support for Kotlin 2.1.10 when running with CodeQL CLI v2.20.3. [#2744](https://github.com/github/codeql-action/pull/2744)
+
+## 3.28.7 - 29 Jan 2025
+
+No user facing changes.
+
+## 3.28.6 - 27 Jan 2025
+
+- Re-enable debug artifact upload for CLI versions 2.20.3 or greater. [#2726](https://github.com/github/codeql-action/pull/2726)
+
+## 3.28.5 - 24 Jan 2025
+
+- Update default CodeQL bundle version to 2.20.3. [#2717](https://github.com/github/codeql-action/pull/2717)
+
+## 3.28.4 - 23 Jan 2025
+
+No user facing changes.
+
+## 3.28.3 - 22 Jan 2025
+
+- Update default CodeQL bundle version to 2.20.2. [#2707](https://github.com/github/codeql-action/pull/2707)
+- Fix an issue downloading the CodeQL Bundle from a GitHub Enterprise Server instance which occurred when the CodeQL Bundle had been synced to the instance using the [CodeQL Action sync tool](https://github.com/github/codeql-action-sync-tool) and the Actions runner did not have Zstandard installed. [#2710](https://github.com/github/codeql-action/pull/2710)
+- Uploading debug artifacts for CodeQL analysis is temporarily disabled. [#2712](https://github.com/github/codeql-action/pull/2712)
+
+## 3.28.2 - 21 Jan 2025
+
+No user facing changes.
+
 ## 3.28.1 - 10 Jan 2025
 
 - CodeQL Action v2 is now deprecated, and is no longer updated or supported. For better performance, improved security, and new features, upgrade to v3. For more information, see [this changelog post](https://github.blog/changelog/2025-01-10-code-scanning-codeql-action-v2-is-now-deprecated/). [#2677](https://github.com/github/codeql-action/pull/2677)
@@ -72,7 +128,7 @@ No user facing changes.
 
 - _Upcoming breaking change_: Add support for using `actions/download-artifact@v4` to programmatically consume CodeQL Action debug artifacts.
 
-  Starting November 30, 2024, GitHub.com customers will [no longer be able to use `actions/download-artifact@v3`](https://github.blog/changelog/2024-04-16-deprecation-notice-v3-of-the-artifact-actions/). Therefore, to avoid breakage, customers who programmatically download the CodeQL Action debug artifacts should set the `CODEQL_ACTION_ARTIFACT_V4_UPGRADE` environment variable to `true` and bump `actions/download-artifact@v3` to `actions/download-artifact@v4` in their workflows. The CodeQL Action will enable this behavior by default in early November and workflows that have not yet bumped to `actions/download-artifact@v3` to `actions/download-artifact@v4` will begin failing then.
+  Starting November 30, 2024, GitHub.com customers will [no longer be able to use `actions/download-artifact@v3`](https://github.blog/changelog/2024-04-16-deprecation-notice-v3-of-the-artifact-actions/). Therefore, to avoid breakage, customers who programmatically download the CodeQL Action debug artifacts should set the `CODEQL_ACTION_ARTIFACT_V4_UPGRADE` environment variable to `true` and bump `actions/download-artifact@v3` to `actions/download-artifact@v4` in their workflows. The CodeQL Action will enable this behavior by default in early November and workflows that have not yet bumped `actions/download-artifact@v3` to `actions/download-artifact@v4` will begin failing then.
 
   This change is currently unavailable for GitHub Enterprise Server customers, as `actions/upload-artifact@v4` and `actions/download-artifact@v4` are not yet compatible with GHES.
 - Update default CodeQL bundle version to 2.19.1. [#2519](https://github.com/github/codeql-action/pull/2519)

CONTRIBUTING.md

@@ -27,7 +27,7 @@ You may want to run `tsc --watch` from the command line or inside of vscode in o
 
 ### Checking in compiled artifacts and `node_modules`
 
-Because CodeQL Action users consume the code directly from this repository, and there can be no build step during an GitHub Actions run, this repository contains all compiled artifacts and node modules. There is a PR check that will fail if any of the compiled artifacts are not up to date. Compiled artifacts are stored in the `lib/` directory. For all day-to-day development purposes, this folder can be ignored.
+Because CodeQL Action users consume the code directly from this repository, and there can be no build step during a GitHub Actions run, this repository contains all compiled artifacts and node modules. There is a PR check that will fail if any of the compiled artifacts are not up to date. Compiled artifacts are stored in the `lib/` directory. For all day-to-day development purposes, this folder can be ignored.
 
 Only run `npm install` if you are explicitly changing the set of dependencies in `package.json`. The `node_modules` directory should be up to date when you check out, but if for some reason, there is an inconsistency use `npm ci && npm run removeNPMAbsolutePaths` to ensure the directory is in a state consistent with the `package-lock.json`. Note that due to a macOS-specific dependency, this command should be run on a macOS machine. There is a PR check to ensure the consistency of the `node_modules` directory.
 
@@ -63,7 +63,7 @@ Here are a few things you can do that will increase the likelihood of your pull
     You can start a release by triggering this workflow via [workflow dispatch](https://github.com/github/codeql-action/actions/workflows/update-release-branch.yml).
 1. The workflow run will open a pull request titled "Merge main into releases/v3". Follow the steps on the checklist in the pull request. Once you've checked off all but the last two of these, approve the PR and automerge it.
 1. When the "Merge main into releases/v3" pull request is merged into the `releases/v3` branch, a mergeback pull request to `main` will be automatically created. This mergeback pull request incorporates the changelog updates into `main`, tags the release using the merge commit of the "Merge main into releases/v3" pull request, and bumps the patch version of the CodeQL Action. 
-1. If a backport to an older major version is required, a pull request targeting that version's branch will also be automatically created
+1. If a backport to an older major version is required, a pull request targeting that version's branch will also be automatically created.
 1. Approve the mergeback and backport pull request (if applicable) and automerge them.
 
 Once the mergeback and backport pull request have been merged, the release is complete.
@@ -109,6 +109,7 @@ To add a new major version of the Action:
 1. Change the `version` field of `package.json` by running `npm version x.y.z` where `x` is the new major version, and `y` and `z` match the latest minor and patch versions of the last release.
 1. Update appropriate documentation to explain the reasoning behind the releases: see [the diff](https://github.com/github/codeql-action/pull/2677/commits/913d60579d4b560addf53ec3c493d491dd3c1378) in our last major version deprecation for examples on which parts of the documentation should be updated.
 1. Consider the timeline behind deprecating the prior Action version: see [CodeQL Action deprecation documentation](#deprecating-a-codeql-action-major-version-write-access-required)
+1. If the new major version runs on a new version of Node, add a PR check to ensure the codebase continues to compile against the previous version of Node. See [Remove Node 16 compilation PR check](https://github.com/github/codeql-action/pull/2695) for an example.
 
 ## Deprecating a CodeQL Action major version (write access required)
 

justfile

@@ -0,0 +1,30 @@
+# Perform all working copy cleanup operations
+all: lint sync
+
+# Lint source typescript
+lint:
+    npm run lint-fix
+
+# Sync generated files (javascript and PR checks)
+sync: build update-pr-checks
+
+# Perform all necessary steps to update the PR checks
+update-pr-checks:
+    pr-checks/sync.sh
+
+# Transpile typescript code into javascript
+build:
+    npm run build
+
+# Build then run all the tests
+test: build
+    npm run test
+
+# Run the tests for a single file
+test_file filename: build
+    npx ava --verbose {{filename}}
+
+[doc("Refresh the .js build artefacts in the lib directory")]
+[confirm]
+refresh-lib:
+    rm -rf lib && npm run build

lib/analyze-action-post.js

@@ -38,11 +38,14 @@ Object.defineProperty(exports, "__esModule", { value: true });
  * It will run after the all steps in this job, in reverse order in relation to
  * other `post:` hooks.
  */
+const fs = __importStar(require("fs"));
 const core = __importStar(require("@actions/core"));
 const actionsUtil = __importStar(require("./actions-util"));
 const api_client_1 = require("./api-client");
+const codeql_1 = require("./codeql");
 const config_utils_1 = require("./config-utils");
 const debugArtifacts = __importStar(require("./debug-artifacts"));
+const dependency_caching_1 = require("./dependency-caching");
 const environment_1 = require("./environment");
 const logging_1 = require("./logging");
 const util_1 = require("./util");
@@ -57,7 +60,21 @@ async function runWrapper() {
         if (process.env[environment_1.EnvVar.INIT_ACTION_HAS_RUN] === "true") {
             const config = await (0, config_utils_1.getConfig)(actionsUtil.getTemporaryDirectory(), logger);
             if (config !== undefined) {
-                await (0, logging_1.withGroup)("Uploading combined SARIF debug artifact", () => debugArtifacts.uploadCombinedSarifArtifacts(logger, config.gitHubVersion.type));
+                const codeql = await (0, codeql_1.getCodeQL)(config.codeQLCmd);
+                const version = await codeql.getVersion();
+                await debugArtifacts.uploadCombinedSarifArtifacts(logger, config.gitHubVersion.type, version.version);
+            }
+        }
+        // If we analysed Java in build-mode: none, we may have downloaded dependencies
+        // to the temp directory. Clean these up so they don't persist unnecessarily
+        // long on self-hosted runners.
+        const javaTempDependencyDir = (0, dependency_caching_1.getJavaTempDependencyDir)();
+        if (fs.existsSync(javaTempDependencyDir)) {
+            try {
+                fs.rmSync(javaTempDependencyDir, { recursive: true });
+            }
+            catch (error) {
+                logger.info(`Failed to remove temporary Java dependencies directory: ${(0, util_1.getErrorMessage)(error)}`);
             }
         }
     }

lib/analyze-action-post.js.map

@@ -1 +1 @@
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+{"version":3,"file":"analyze-action-post.js","sourceRoot":"","sources":["../src/analyze-action-post.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA;;;;GAIG;AACH,uCAAyB;AAEzB,oDAAsC;AAEtC,4DAA8C;AAC9C,6CAAgD;AAChD,qCAAqC;AACrC,iDAA2C;AAC3C,kEAAoD;AACpD,6DAAgE;AAChE,+CAAuC;AACvC,uCAA6C;AAC7C,iCAAoE;AAEpE,KAAK,UAAU,UAAU;IACvB,IAAI,CAAC;QACH,WAAW,CAAC,aAAa,EAAE,CAAC;QAC5B,MAAM,MAAM,GAAG,IAAA,0BAAgB,GAAE,CAAC;QAClC,MAAM,aAAa,GAAG,MAAM,IAAA,6BAAgB,GAAE,CAAC;QAC/C,IAAA,gCAAyB,EAAC,aAAa,EAAE,MAAM,CAAC,CAAC;QAEjD,kFAAkF;QAClF,wFAAwF;QACxF,IAAI,OAAO,CAAC,GAAG,CAAC,oBAAM,CAAC,mBAAmB,CAAC,KAAK,MAAM,EAAE,CAAC;YACvD,MAAM,MAAM,GAAG,MAAM,IAAA,wBAAS,EAC5B,WAAW,CAAC,qBAAqB,EAAE,EACnC,MAAM,CACP,CAAC;YACF,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;gBACzB,MAAM,MAAM,GAAG,MAAM,IAAA,kBAAS,EAAC,MAAM,CAAC,SAAS,CAAC,CAAC;gBACjD,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,UAAU,EAAE,CAAC;gBAC1C,MAAM,cAAc,CAAC,4BAA4B,CAC/C,MAAM,EACN,MAAM,CAAC,aAAa,CAAC,IAAI,EACzB,OAAO,CAAC,OAAO,CAChB,CAAC;YACJ,CAAC;QACH,CAAC;QAED,+EAA+E;QAC/E,4EAA4E;QAC5E,+BAA+B;QAC/B,MAAM,qBAAqB,GAAG,IAAA,6CAAwB,GAAE,CAAC;QACzD,IAAI,EAAE,CAAC,UAAU,CAAC,qBAAqB,CAAC,EAAE,CAAC;YACzC,IAAI,CAAC;gBACH,EAAE,CAAC,MAAM,CAAC,qBAAqB,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;YACxD,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,MAAM,CAAC,IAAI,CACT,2DAA2D,IAAA,sBAAe,EAAC,KAAK,CAAC,EAAE,CACpF,CAAC;YACJ,CAAC;QACH,CAAC;IACH,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,IAAI,CAAC,SAAS,CACZ,oCAAoC,IAAA,sBAAe,EAAC,KAAK,CAAC,EAAE,CAC7D,CAAC;IACJ,CAAC;AACH,CAAC;AAED,KAAK,UAAU,EAAE,CAAC"}

lib/analyze-action.js

@@ -41,7 +41,6 @@ const fs = __importStar(require("fs"));
 const path_1 = __importDefault(require("path"));
 const perf_hooks_1 = require("perf_hooks");
 const core = __importStar(require("@actions/core"));
-const github = __importStar(require("@actions/github"));
 const actionsUtil = __importStar(require("./actions-util"));
 const analyze_1 = require("./analyze");
 const api_client_1 = require("./api-client");
@@ -51,6 +50,7 @@ const codeql_1 = require("./codeql");
 const config_utils_1 = require("./config-utils");
 const database_upload_1 = require("./database-upload");
 const dependency_caching_1 = require("./dependency-caching");
+const diff_informed_analysis_utils_1 = require("./diff-informed-analysis-utils");
 const environment_1 = require("./environment");
 const feature_flags_1 = require("./feature-flags");
 const languages_1 = require("./languages");
@@ -160,6 +160,14 @@ async function run() {
     let dbCreationTimings = undefined;
     let didUploadTrapCaches = false;
     util.initializeEnvironment(actionsUtil.getActionVersion());
+    // Unset the CODEQL_PROXY_* environment variables, as they are not needed
+    // and can cause issues with the CodeQL CLI
+    // Check for CODEQL_PROXY_HOST: and if it is empty but set, unset it
+    if (process.env.CODEQL_PROXY_HOST === "") {
+        delete process.env.CODEQL_PROXY_HOST;
+        delete process.env.CODEQL_PROXY_PORT;
+        delete process.env.CODEQL_PROXY_CA_CERTIFICATE;
+    }
     // Make inputs accessible in the `post` step, details at
     // https://github.com/github/codeql-action/issues/2553
     actionsUtil.persistInputs();
@@ -181,22 +189,24 @@ async function run() {
         const outputDir = actionsUtil.getRequiredInput("output");
         core.exportVariable(environment_1.EnvVar.SARIF_RESULTS_OUTPUT_DIR, outputDir);
         const threads = util.getThreadsFlag(actionsUtil.getOptionalInput("threads") || process.env["CODEQL_THREADS"], logger);
-        const repositoryNwo = (0, repository_1.parseRepositoryNwo)(util.getRequiredEnvParam("GITHUB_REPOSITORY"));
+        const repositoryNwo = (0, repository_1.getRepositoryNwo)();
         const gitHubVersion = await (0, api_client_1.getGitHubVersion)();
         util.checkActionVersion(actionsUtil.getActionVersion(), gitHubVersion);
         const features = new feature_flags_1.Features(gitHubVersion, repositoryNwo, actionsUtil.getTemporaryDirectory(), logger);
         const memory = util.getMemoryFlag(actionsUtil.getOptionalInput("ram") || process.env["CODEQL_RAM"], logger);
-        const pull_request = github.context.payload.pull_request;
-        const diffRangePackDir = pull_request &&
-            (await (0, analyze_1.setupDiffInformedQueryRun)(pull_request.base.ref, pull_request.head.ref, codeql, logger, features));
+        const branches = await (0, diff_informed_analysis_utils_1.getDiffInformedAnalysisBranches)(codeql, features, logger);
+        const diffRangePackDir = branches
+            ? await (0, analyze_1.setupDiffInformedQueryRun)(branches, logger)
+            : undefined;
         await (0, analyze_1.warnIfGoInstalledAfterInit)(config, logger);
         await runAutobuildIfLegacyGoWorkflow(config, logger);
         dbCreationTimings = await (0, analyze_1.runFinalize)(outputDir, threads, memory, codeql, config, logger);
+        const cleanupLevel = actionsUtil.getOptionalInput("cleanup-level") || "brutal";
         if (actionsUtil.getRequiredInput("skip-queries") !== "true") {
-            runStats = await (0, analyze_1.runQueries)(outputDir, memory, util.getAddSnippetsFlag(actionsUtil.getRequiredInput("add-snippets")), threads, diffRangePackDir, actionsUtil.getOptionalInput("category"), config, logger, features);
+            runStats = await (0, analyze_1.runQueries)(outputDir, memory, util.getAddSnippetsFlag(actionsUtil.getRequiredInput("add-snippets")), threads, cleanupLevel, diffRangePackDir, actionsUtil.getOptionalInput("category"), config, logger, features);
         }
-        if (actionsUtil.getOptionalInput("cleanup-level") !== "none") {
-            await (0, analyze_1.runCleanup)(config, actionsUtil.getOptionalInput("cleanup-level") || "brutal", logger);
+        if (cleanupLevel !== "none") {
+            await (0, analyze_1.runCleanup)(config, cleanupLevel, logger);
         }
         const dbLocations = {};
         for (const language of config.languages) {
@@ -230,7 +240,7 @@ async function run() {
         }
         else if (uploadResult !== undefined &&
             actionsUtil.getRequiredInput("wait-for-processing") === "true") {
-            await uploadLib.waitForProcessing((0, repository_1.parseRepositoryNwo)(util.getRequiredEnvParam("GITHUB_REPOSITORY")), uploadResult.sarifID, (0, logging_1.getActionsLogger)());
+            await uploadLib.waitForProcessing((0, repository_1.getRepositoryNwo)(), uploadResult.sarifID, (0, logging_1.getActionsLogger)());
         }
         // If we did not throw an error yet here, but we expect one, throw it.
         if (actionsUtil.getOptionalInput("expect-error") === "true") {

lib/analyze.js

@@ -36,7 +36,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.CodeQLAnalysisError = void 0;
+exports.exportedForTesting = exports.CodeQLAnalysisError = void 0;
 exports.runExtraction = runExtraction;
 exports.dbIsFinalized = dbIsFinalized;
 exports.setupDiffInformedQueryRun = setupDiffInformedQueryRun;
@@ -51,14 +51,17 @@ const io = __importStar(require("@actions/io"));
 const del_1 = __importDefault(require("del"));
 const yaml = __importStar(require("js-yaml"));
 const actionsUtil = __importStar(require("./actions-util"));
+const api_client_1 = require("./api-client");
 const autobuild_1 = require("./autobuild");
 const codeql_1 = require("./codeql");
+const dependency_caching_1 = require("./dependency-caching");
 const diagnostics_1 = require("./diagnostics");
+const diff_informed_analysis_utils_1 = require("./diff-informed-analysis-utils");
 const environment_1 = require("./environment");
 const feature_flags_1 = require("./feature-flags");
-const gitUtils = __importStar(require("./git-utils"));
 const languages_1 = require("./languages");
 const logging_1 = require("./logging");
+const repository_1 = require("./repository");
 const tools_features_1 = require("./tools-features");
 const tracer_config_1 = require("./tracer-config");
 const upload_lib_1 = require("./upload-lib");
@@ -101,6 +104,14 @@ async function runExtraction(codeql, config, logger) {
                     config.buildMode === util_1.BuildMode.Autobuild) {
                     await (0, autobuild_1.setupCppAutobuild)(codeql, logger);
                 }
+                // The Java `build-mode: none` extractor places dependencies (.jar files) in the
+                // database scratch directory by default. For dependency caching purposes, we want
+                // a stable path that caches can be restored into and that we can cache at the
+                // end of the workflow (i.e. that does not get removed when the scratch directory is).
+                if (language === languages_1.Language.java && config.buildMode === util_1.BuildMode.None) {
+                    process.env["CODEQL_EXTRACTOR_JAVA_OPTION_BUILDLESS_DEPENDENCY_DIR"] =
+                        (0, dependency_caching_1.getJavaTempDependencyDir)();
+                }
                 await codeql.extractUsingBuildMode(config, language);
             }
             else {
@@ -151,125 +162,164 @@ async function finalizeDatabaseCreation(codeql, config, threadsFlag, memoryFlag,
 /**
  * Set up the diff-informed analysis feature.
  *
- * @param baseRef The base branch name, used for calculating the diff range.
- * @param headRef The head branch name, used for calculating the diff range.
- * @param codeql
- * @param logger
- * @param features
  * @returns Absolute path to the directory containing the extension pack for
  * the diff range information, or `undefined` if the feature is disabled.
  */
-async function setupDiffInformedQueryRun(baseRef, headRef, codeql, logger, features) {
-    if (!(await features.getValue(feature_flags_1.Feature.DiffInformedQueries, codeql))) {
-        return undefined;
-    }
+async function setupDiffInformedQueryRun(branches, logger) {
     return await (0, logging_1.withGroupAsync)("Generating diff range extension pack", async () => {
-        const diffRanges = await getPullRequestEditedDiffRanges(baseRef, headRef, logger);
-        return writeDiffRangeDataExtensionPack(logger, diffRanges);
+        logger.info(`Calculating diff ranges for ${branches.base}...${branches.head}`);
+        const diffRanges = await getPullRequestEditedDiffRanges(branches, logger);
+        const packDir = writeDiffRangeDataExtensionPack(logger, diffRanges);
+        if (packDir === undefined) {
+            logger.warning("Cannot create diff range extension pack for diff-informed queries; " +
+                "reverting to performing full analysis.");
+        }
+        else {
+            logger.info(`Successfully created diff range extension pack at ${packDir}.`);
+        }
+        return packDir;
     });
 }
 /**
  * Return the file line ranges that were added or modified in the pull request.
  *
- * @param baseRef The base branch name, used for calculating the diff range.
- * @param headRef The head branch name, used for calculating the diff range.
+ * @param branches The base and head branches of the pull request.
  * @param logger
  * @returns An array of tuples, where each tuple contains the absolute path of a
  * file, the start line and the end line (both 1-based and inclusive) of an
  * added or modified range in that file. Returns `undefined` if the action was
  * not triggered by a pull request or if there was an error.
  */
-async function getPullRequestEditedDiffRanges(baseRef, headRef, logger) {
-    const checkoutPath = actionsUtil.getOptionalInput("checkout_path");
-    if (checkoutPath === undefined) {
+async function getPullRequestEditedDiffRanges(branches, logger) {
+    const fileDiffs = await getFileDiffsWithBasehead(branches, logger);
+    if (fileDiffs === undefined) {
         return undefined;
     }
-    // To compute the merge bases between the base branch and the PR topic branch,
-    // we need to fetch the commit graph from the branch heads to those merge
-    // babes. The following 6-step procedure does so while limiting the amount of
-    // history fetched.
-    // Step 1: Deepen from the PR merge commit to the base branch head and the PR
-    // topic branch head, so that the PR merge commit is no longer considered a
-    // grafted commit.
-    await gitUtils.deepenGitHistory();
-    // Step 2: Fetch the base branch shallow history. This step ensures that the
-    // base branch name is present in the local repository. Normally the base
-    // branch name would be added by Step 4. However, if the base branch head is
-    // an ancestor of the PR topic branch head, Step 4 would fail without doing
-    // anything, so we need to fetch the base branch explicitly.
-    await gitUtils.gitFetch(baseRef, ["--depth=1"]);
-    // Step 3: Fetch the PR topic branch history, stopping when we reach commits
-    // that are reachable from the base branch head.
-    await gitUtils.gitFetch(headRef, [`--shallow-exclude=${baseRef}`]);
-    // Step 4: Fetch the base branch history, stopping when we reach commits that
-    // are reachable from the PR topic branch head.
-    await gitUtils.gitFetch(baseRef, [`--shallow-exclude=${headRef}`]);
-    // Step 5: Repack the history to remove the shallow grafts that were added by
-    // the previous fetches. This step works around a bug that causes subsequent
-    // deepening fetches to fail with "fatal: error in object: unshallow <SHA>".
-    // See https://stackoverflow.com/q/63878612
-    await gitUtils.gitRepack(["-d"]);
-    // Step 6: Deepen the history so that we have the merge bases between the base
-    // branch and the PR topic branch.
-    await gitUtils.deepenGitHistory();
-    // To compute the exact same diff as GitHub would compute for the PR, we need
-    // to use the same merge base as GitHub. That is easy to do if there is only
-    // one merge base, which is by far the most common case. If there are multiple
-    // merge bases, we stop without producing a diff range.
-    const mergeBases = await gitUtils.getAllGitMergeBases([baseRef, headRef]);
-    logger.info(`Merge bases: ${mergeBases.join(", ")}`);
-    if (mergeBases.length !== 1) {
-        logger.info("Cannot compute diff range because baseRef and headRef " +
-            `have ${mergeBases.length} merge bases (instead of exactly 1).`);
+    if (fileDiffs.length >= 300) {
+        // The "compare two commits" API returns a maximum of 300 changed files. If
+        // we see that many changed files, it is possible that there could be more,
+        // with the rest being truncated. In this case, we should not attempt to
+        // compute the diff ranges, as the result would be incomplete.
+        logger.warning(`Cannot retrieve the full diff because there are too many ` +
+            `(${fileDiffs.length}) changed files in the pull request.`);
         return undefined;
     }
-    const diffHunkHeaders = await gitUtils.getGitDiffHunkHeaders(mergeBases[0], headRef);
-    if (diffHunkHeaders === undefined) {
-        return undefined;
-    }
-    const results = new Array();
-    let changedFile = "";
-    for (const line of diffHunkHeaders) {
-        if (line.startsWith("+++ ")) {
-            const filePath = gitUtils.decodeGitFilePath(line.substring(4));
-            if (filePath.startsWith("b/")) {
-                // The file was edited: track all hunks in the file
-                changedFile = filePath.substring(2);
-            }
-            else if (filePath === "/dev/null") {
-                // The file was deleted: skip all hunks in the file
-                changedFile = "";
-            }
-            else {
-                logger.warning(`Failed to parse diff hunk header line: ${line}`);
-                return undefined;
-            }
-            continue;
-        }
-        if (line.startsWith("@@ ")) {
-            if (changedFile === "")
-                continue;
-            const match = line.match(/^@@ -\d+(?:,\d+)? \+(\d+)(?:,(\d+))? @@/);
-            if (match === null) {
-                logger.warning(`Failed to parse diff hunk header line: ${line}`);
-                return undefined;
-            }
-            const startLine = parseInt(match[1], 10);
-            const numLines = parseInt(match[2], 10);
-            if (numLines === 0) {
-                // The hunk was a deletion: skip it
-                continue;
-            }
-            const endLine = startLine + (numLines || 1) - 1;
-            results.push({
-                path: path.join(checkoutPath, changedFile),
-                startLine,
-                endLine,
-            });
+    const results = [];
+    for (const filediff of fileDiffs) {
+        const diffRanges = getDiffRanges(filediff, logger);
+        if (diffRanges === undefined) {
+            return undefined;
         }
+        results.push(...diffRanges);
     }
     return results;
 }
+async function getFileDiffsWithBasehead(branches, logger) {
+    // Check CODE_SCANNING_REPOSITORY first. If it is empty or not set, fall back
+    // to GITHUB_REPOSITORY.
+    const repositoryNwo = (0, repository_1.getRepositoryNwoFromEnv)("CODE_SCANNING_REPOSITORY", "GITHUB_REPOSITORY");
+    const basehead = `${branches.base}...${branches.head}`;
+    try {
+        const response = await (0, api_client_1.getApiClient)().rest.repos.compareCommitsWithBasehead({
+            owner: repositoryNwo.owner,
+            repo: repositoryNwo.repo,
+            basehead,
+            per_page: 1,
+        });
+        logger.debug(`Response from compareCommitsWithBasehead(${basehead}):` +
+            `\n${JSON.stringify(response, null, 2)}`);
+        return response.data.files;
+    }
+    catch (error) {
+        if (error.status) {
+            logger.warning(`Error retrieving diff ${basehead}: ${error.message}`);
+            logger.debug(`Error running compareCommitsWithBasehead(${basehead}):` +
+                `\nRequest: ${JSON.stringify(error.request, null, 2)}` +
+                `\nError Response: ${JSON.stringify(error.response, null, 2)}`);
+            return undefined;
+        }
+        else {
+            throw error;
+        }
+    }
+}
+function getDiffRanges(fileDiff, logger) {
+    // Diff-informed queries expect the file path to be absolute. CodeQL always
+    // uses forward slashes as the path separator, so on Windows we need to
+    // replace any backslashes with forward slashes.
+    const filename = path
+        .join(actionsUtil.getRequiredInput("checkout_path"), fileDiff.filename)
+        .replaceAll(path.sep, "/");
+    if (fileDiff.patch === undefined) {
+        if (fileDiff.changes === 0) {
+            // There are situations where a changed file legitimately has no diff.
+            // For example, the file may be a binary file, or that the file may have
+            // been renamed with no changes to its contents. In these cases, the
+            // file would be reported as having 0 changes, and we can return an empty
+            // array to indicate no diff range in this file.
+            return [];
+        }
+        // If a file is reported to have nonzero changes but no patch, that may be
+        // due to the file diff being too large. In this case, we should fall back
+        // to a special diff range that covers the entire file.
+        return [
+            {
+                path: filename,
+                startLine: 0,
+                endLine: 0,
+            },
+        ];
+    }
+    // The 1-based file line number of the current line
+    let currentLine = 0;
+    // The 1-based file line number that starts the current range of added lines
+    let additionRangeStartLine = undefined;
+    const diffRanges = [];
+    const diffLines = fileDiff.patch.split("\n");
+    // Adding a fake context line at the end ensures that the following loop will
+    // always terminate the last range of added lines.
+    diffLines.push(" ");
+    for (const diffLine of diffLines) {
+        if (diffLine.startsWith("-")) {
+            // Ignore deletions completely -- we do not even want to consider them when
+            // calculating consecutive ranges of added lines.
+            continue;
+        }
+        if (diffLine.startsWith("+")) {
+            if (additionRangeStartLine === undefined) {
+                additionRangeStartLine = currentLine;
+            }
+            currentLine++;
+            continue;
+        }
+        if (additionRangeStartLine !== undefined) {
+            // Any line that does not start with a "+" or "-" terminates the current
+            // range of added lines.
+            diffRanges.push({
+                path: filename,
+                startLine: additionRangeStartLine,
+                endLine: currentLine - 1,
+            });
+            additionRangeStartLine = undefined;
+        }
+        if (diffLine.startsWith("@@ ")) {
+            // A new hunk header line resets the current line number.
+            const match = diffLine.match(/^@@ -\d+(?:,\d+)? \+(\d+)(?:,\d+)? @@/);
+            if (match === null) {
+                logger.warning(`Cannot parse diff hunk header for ${fileDiff.filename}: ${diffLine}`);
+                return undefined;
+            }
+            currentLine = parseInt(match[1], 10);
+            continue;
+        }
+        if (diffLine.startsWith(" ")) {
+            // An unchanged context line advances the current line number.
+            currentLine++;
+            continue;
+        }
+    }
+    return diffRanges;
+}
 /**
  * Create an extension pack in the temporary directory that contains the file
  * line ranges that were added or modified in the pull request.
@@ -284,6 +334,14 @@ function writeDiffRangeDataExtensionPack(logger, ranges) {
     if (ranges === undefined) {
         return undefined;
     }
+    if (ranges.length === 0) {
+        // An empty diff range means that there are no added or modified lines in
+        // the pull request. But the `restrictAlertsTo` extensible predicate
+        // interprets an empty data extension differently, as an indication that
+        // all alerts should be included. So we need to specifically set the diff
+        // range to a non-empty list that cannot match any alert location.
+        ranges = [{ path: "", startLine: 0, endLine: 0 }];
+    }
     const diffRangeDir = path.join(actionsUtil.getTemporaryDirectory(), "pr-diff-range");
     fs.mkdirSync(diffRangeDir);
     fs.writeFileSync(path.join(diffRangeDir, "qlpack.yml"), `
@@ -303,7 +361,12 @@ extensions:
     data:
 `;
     let data = ranges
-        .map((range) => `      - ["${range.path}", ${range.startLine}, ${range.endLine}]\n`)
+        .map((range) => 
+    // Using yaml.dump() with `forceQuotes: true` ensures that all special
+    // characters are escaped, and that the path is always rendered as a
+    // quoted string on a single line.
+    `      - [${yaml.dump(range.path, { forceQuotes: true }).trim()}, ` +
+        `${range.startLine}, ${range.endLine}]\n`)
         .join("");
     if (!data) {
         // Ensure that the data extension is not empty, so that a pull request with
@@ -314,22 +377,27 @@ extensions:
     const extensionFilePath = path.join(diffRangeDir, "pr-diff-range.yml");
     fs.writeFileSync(extensionFilePath, extensionContents);
     logger.debug(`Wrote pr-diff-range extension pack to ${extensionFilePath}:\n${extensionContents}`);
+    // Write the diff ranges to a JSON file, for action-side alert filtering by the
+    // upload-lib module.
+    (0, diff_informed_analysis_utils_1.writeDiffRangesJsonFile)(logger, ranges);
     return diffRangeDir;
 }
 // Runs queries and creates sarif files in the given folder
-async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag, diffRangePackDir, automationDetailsId, config, logger, features) {
+async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag, cleanupLevel, diffRangePackDir, automationDetailsId, config, logger, features) {
     const statusReport = {};
-    const dataExtensionFlags = diffRangePackDir
-        ? [
-            `--additional-packs=${diffRangePackDir}`,
-            "--extension-packs=codeql-action/pr-diff-range",
-        ]
-        : [];
+    const queryFlags = [memoryFlag, threadsFlag];
+    if (cleanupLevel !== "overlay") {
+        queryFlags.push("--expect-discarded-cache");
+    }
+    statusReport.analysis_is_diff_informed = diffRangePackDir !== undefined;
+    if (diffRangePackDir) {
+        queryFlags.push(`--additional-packs=${diffRangePackDir}`);
+        queryFlags.push("--extension-packs=codeql-action/pr-diff-range");
+    }
     const sarifRunPropertyFlag = diffRangePackDir
         ? "--sarif-run-property=incrementalMode=diff-informed"
         : undefined;
     const codeql = await (0, codeql_1.getCodeQL)(config.codeQLCmd);
-    const queryFlags = [memoryFlag, threadsFlag, ...dataExtensionFlags];
     for (const language of config.languages) {
         try {
             const sarifFile = path.join(sarifFolder, `${language}.sarif`);
@@ -371,9 +439,6 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
                 }
                 statusReport["event_reports"].push(perQueryAlertCountEventReport);
             }
-            if (!(await util.codeQlVersionAtLeast(codeql, codeql_1.CODEQL_VERSION_ANALYSIS_SUMMARY_V2))) {
-                await runPrintLinesOfCode(language);
-            }
         }
         catch (e) {
             statusReport.analyze_failure_language = language;
@@ -405,10 +470,6 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
         }
         return perQueryAlertCounts;
     }
-    async function runPrintLinesOfCode(language) {
-        const databasePath = util.getCodeQLDatabasePath(config, language);
-        return await codeql.databasePrintBaseline(databasePath);
-    }
 }
 async function runFinalize(outputDir, threadsFlag, memoryFlag, codeql, config, logger) {
     try {
@@ -461,4 +522,7 @@ async function runCleanup(config, cleanupLevel, logger) {
     }
     logger.endGroup();
 }
+exports.exportedForTesting = {
+    getDiffRanges,
+};
 //# sourceMappingURL=analyze.js.map

lib/analyze.test.js

@@ -40,6 +40,7 @@ const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const ava_1 = __importDefault(require("ava"));
 const sinon = __importStar(require("sinon"));
+const actionsUtil = __importStar(require("./actions-util"));
 const analyze_1 = require("./analyze");
 const codeql_1 = require("./codeql");
 const feature_flags_1 = require("./feature-flags");
@@ -113,8 +114,9 @@ const util = __importStar(require("./util"));
             fs.mkdirSync(util.getCodeQLDatabasePath(config, language), {
                 recursive: true,
             });
-            const statusReport = await (0, analyze_1.runQueries)(tmpDir, memoryFlag, addSnippetsFlag, threadsFlag, undefined, undefined, config, (0, logging_1.getRunnerLogger)(true), (0, testing_utils_1.createFeatures)([feature_flags_1.Feature.QaTelemetryEnabled]));
+            const statusReport = await (0, analyze_1.runQueries)(tmpDir, memoryFlag, addSnippetsFlag, threadsFlag, "brutal", undefined, undefined, config, (0, logging_1.getRunnerLogger)(true), (0, testing_utils_1.createFeatures)([feature_flags_1.Feature.QaTelemetryEnabled]));
             t.deepEqual(Object.keys(statusReport).sort(), [
+                "analysis_is_diff_informed",
                 `analyze_builtin_queries_${language}_duration_ms`,
                 "event_reports",
                 `interpret_results_${language}_duration_ms`,
@@ -127,4 +129,188 @@ const util = __importStar(require("./util"));
         }
     });
 });
+function runGetDiffRanges(changes, patch) {
+    sinon
+        .stub(actionsUtil, "getRequiredInput")
+        .withArgs("checkout_path")
+        .returns("/checkout/path");
+    return analyze_1.exportedForTesting.getDiffRanges({
+        filename: "test.txt",
+        changes,
+        patch: patch?.join("\n"),
+    }, (0, logging_1.getRunnerLogger)(true));
+}
+(0, ava_1.default)("getDiffRanges: file unchanged", async (t) => {
+    const diffRanges = runGetDiffRanges(0, undefined);
+    t.deepEqual(diffRanges, []);
+});
+(0, ava_1.default)("getDiffRanges: file diff too large", async (t) => {
+    const diffRanges = runGetDiffRanges(1000000, undefined);
+    t.deepEqual(diffRanges, [
+        {
+            path: "/checkout/path/test.txt",
+            startLine: 0,
+            endLine: 0,
+        },
+    ]);
+});
+(0, ava_1.default)("getDiffRanges: diff thunk with single addition range", async (t) => {
+    const diffRanges = runGetDiffRanges(2, [
+        "@@ -30,6 +50,8 @@",
+        " a",
+        " b",
+        " c",
+        "+1",
+        "+2",
+        " d",
+        " e",
+        " f",
+    ]);
+    t.deepEqual(diffRanges, [
+        {
+            path: "/checkout/path/test.txt",
+            startLine: 53,
+            endLine: 54,
+        },
+    ]);
+});
+(0, ava_1.default)("getDiffRanges: diff thunk with single deletion range", async (t) => {
+    const diffRanges = runGetDiffRanges(2, [
+        "@@ -30,8 +50,6 @@",
+        " a",
+        " b",
+        " c",
+        "-1",
+        "-2",
+        " d",
+        " e",
+        " f",
+    ]);
+    t.deepEqual(diffRanges, []);
+});
+(0, ava_1.default)("getDiffRanges: diff thunk with single update range", async (t) => {
+    const diffRanges = runGetDiffRanges(2, [
+        "@@ -30,7 +50,7 @@",
+        " a",
+        " b",
+        " c",
+        "-1",
+        "+2",
+        " d",
+        " e",
+        " f",
+    ]);
+    t.deepEqual(diffRanges, [
+        {
+            path: "/checkout/path/test.txt",
+            startLine: 53,
+            endLine: 53,
+        },
+    ]);
+});
+(0, ava_1.default)("getDiffRanges: diff thunk with addition ranges", async (t) => {
+    const diffRanges = runGetDiffRanges(2, [
+        "@@ -30,7 +50,9 @@",
+        " a",
+        " b",
+        " c",
+        "+1",
+        " c",
+        "+2",
+        " d",
+        " e",
+        " f",
+    ]);
+    t.deepEqual(diffRanges, [
+        {
+            path: "/checkout/path/test.txt",
+            startLine: 53,
+            endLine: 53,
+        },
+        {
+            path: "/checkout/path/test.txt",
+            startLine: 55,
+            endLine: 55,
+        },
+    ]);
+});
+(0, ava_1.default)("getDiffRanges: diff thunk with mixed ranges", async (t) => {
+    const diffRanges = runGetDiffRanges(2, [
+        "@@ -30,7 +50,7 @@",
+        " a",
+        " b",
+        " c",
+        "-1",
+        " d",
+        "-2",
+        "+3",
+        " e",
+        " f",
+        "+4",
+        "+5",
+        " g",
+        " h",
+        " i",
+    ]);
+    t.deepEqual(diffRanges, [
+        {
+            path: "/checkout/path/test.txt",
+            startLine: 54,
+            endLine: 54,
+        },
+        {
+            path: "/checkout/path/test.txt",
+            startLine: 57,
+            endLine: 58,
+        },
+    ]);
+});
+(0, ava_1.default)("getDiffRanges: multiple diff thunks", async (t) => {
+    const diffRanges = runGetDiffRanges(2, [
+        "@@ -30,6 +50,8 @@",
+        " a",
+        " b",
+        " c",
+        "+1",
+        "+2",
+        " d",
+        " e",
+        " f",
+        "@@ -130,6 +150,8 @@",
+        " a",
+        " b",
+        " c",
+        "+1",
+        "+2",
+        " d",
+        " e",
+        " f",
+    ]);
+    t.deepEqual(diffRanges, [
+        {
+            path: "/checkout/path/test.txt",
+            startLine: 53,
+            endLine: 54,
+        },
+        {
+            path: "/checkout/path/test.txt",
+            startLine: 153,
+            endLine: 154,
+        },
+    ]);
+});
+(0, ava_1.default)("getDiffRanges: no diff context lines", async (t) => {
+    const diffRanges = runGetDiffRanges(2, ["@@ -30 +50,2 @@", "+1", "+2"]);
+    t.deepEqual(diffRanges, [
+        {
+            path: "/checkout/path/test.txt",
+            startLine: 50,
+            endLine: 51,
+        },
+    ]);
+});
+(0, ava_1.default)("getDiffRanges: malformed thunk header", async (t) => {
+    const diffRanges = runGetDiffRanges(2, ["@@ 30 +50,2 @@", "+1", "+2"]);
+    t.deepEqual(diffRanges, undefined);
+});
 //# sourceMappingURL=analyze.test.js.map

lib/api-client.js

@@ -122,14 +122,12 @@ async function getGitHubVersion() {
  * Get the path of the currently executing workflow relative to the repository root.
  */
 async function getWorkflowRelativePath() {
-    const repo_nwo = (0, util_1.getRequiredEnvParam)("GITHUB_REPOSITORY").split("/");
-    const owner = repo_nwo[0];
-    const repo = repo_nwo[1];
+    const repo_nwo = (0, repository_1.getRepositoryNwo)();
     const run_id = Number((0, util_1.getRequiredEnvParam)("GITHUB_RUN_ID"));
     const apiClient = getApiClient();
     const runsResponse = await apiClient.request("GET /repos/:owner/:repo/actions/runs/:run_id?exclude_pull_requests=true", {
-        owner,
-        repo,
+        owner: repo_nwo.owner,
+        repo: repo_nwo.repo,
         run_id,
     });
     const workflowUrl = runsResponse.data.workflow_url;
@@ -187,7 +185,7 @@ function computeAutomationID(analysis_key, environment) {
 }
 /** List all Actions cache entries matching the provided key and ref. */
 async function listActionsCaches(key, ref) {
-    const repositoryNwo = (0, repository_1.parseRepositoryNwo)((0, util_1.getRequiredEnvParam)("GITHUB_REPOSITORY"));
+    const repositoryNwo = (0, repository_1.getRepositoryNwo)();
     return await getApiClient().paginate("GET /repos/{owner}/{repo}/actions/caches", {
         owner: repositoryNwo.owner,
         repo: repositoryNwo.repo,
@@ -197,7 +195,7 @@ async function listActionsCaches(key, ref) {
 }
 /** Delete an Actions cache item by its ID. */
 async function deleteActionsCache(id) {
-    const repositoryNwo = (0, repository_1.parseRepositoryNwo)((0, util_1.getRequiredEnvParam)("GITHUB_REPOSITORY"));
+    const repositoryNwo = (0, repository_1.getRepositoryNwo)();
     await getApiClient().rest.actions.deleteActionsCacheById({
         owner: repositoryNwo.owner,
         repo: repositoryNwo.repo,
@@ -206,9 +204,9 @@ async function deleteActionsCache(id) {
 }
 function wrapApiConfigurationError(e) {
     if ((0, util_1.isHTTPError)(e)) {
-        if (e.message.includes("API rate limit exceeded for site ID installation") ||
+        if (e.message.includes("API rate limit exceeded for installation") ||
             e.message.includes("commit not found") ||
-            /^ref .* not found in this repository$/.test(e.message)) {
+            /ref .* not found in this repository/.test(e.message)) {
             return new util_1.ConfigurationError(e.message);
         }
     }

lib/api-client.test.js

@@ -120,4 +120,30 @@ function mockGetMetaVersionHeader(versionHeader) {
     });
     t.deepEqual({ type: util.GitHubVariant.GHE_DOTCOM }, gheDotcom);
 });
+(0, ava_1.default)("wrapApiConfigurationError correctly wraps specific configuration errors", (t) => {
+    // We don't reclassify arbitrary errors
+    const arbitraryError = new Error("arbitrary error");
+    let res = api.wrapApiConfigurationError(arbitraryError);
+    t.is(res, arbitraryError);
+    // Same goes for arbitrary errors
+    const configError = new util.ConfigurationError("arbitrary error");
+    res = api.wrapApiConfigurationError(configError);
+    t.is(res, configError);
+    // If an HTTP error doesn't contain a specific error message, we don't
+    // wrap is an an API error.
+    const httpError = new util.HTTPError("arbitrary HTTP error", 456);
+    res = api.wrapApiConfigurationError(httpError);
+    t.is(res, httpError);
+    // For other HTTP errors, we wrap them as Configuration errors if they contain
+    // specific error messages.
+    const httpNotFoundError = new util.HTTPError("commit not found", 404);
+    res = api.wrapApiConfigurationError(httpNotFoundError);
+    t.deepEqual(res, new util.ConfigurationError("commit not found"));
+    const refNotFoundError = new util.HTTPError("ref 'refs/heads/jitsi' not found in this repository - https://docs.github.com/rest", 404);
+    res = api.wrapApiConfigurationError(refNotFoundError);
+    t.deepEqual(res, new util.ConfigurationError("ref 'refs/heads/jitsi' not found in this repository - https://docs.github.com/rest"));
+    const apiRateLimitError = new util.HTTPError("API rate limit exceeded for installation", 403);
+    res = api.wrapApiConfigurationError(apiRateLimitError);
+    t.deepEqual(res, new util.ConfigurationError("API rate limit exceeded for installation"));
+});
 //# sourceMappingURL=api-client.test.js.map

lib/api-client.test.js.map

@@ -1 +1 @@
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lib/api-compatibility.json

@@ -1 +1 @@
-{ "maximumVersion": "3.16", "minimumVersion": "3.11" }
+{ "maximumVersion": "3.17", "minimumVersion": "3.12" }

lib/autobuild.js

@@ -123,7 +123,7 @@ async function setupCppAutobuild(codeql, logger) {
     const envVar = feature_flags_1.featureConfig[feature_flags_1.Feature.CppDependencyInstallation].envVar;
     const featureName = "C++ automatic installation of dependencies";
     const gitHubVersion = await (0, api_client_1.getGitHubVersion)();
-    const repositoryNwo = (0, repository_1.parseRepositoryNwo)((0, util_1.getRequiredEnvParam)("GITHUB_REPOSITORY"));
+    const repositoryNwo = (0, repository_1.getRepositoryNwo)();
     const features = new feature_flags_1.Features(gitHubVersion, repositoryNwo, (0, actions_util_1.getTemporaryDirectory)(), logger);
     if (await features.getValue(feature_flags_1.Feature.CppDependencyInstallation, codeql)) {
         // disable autoinstall on self-hosted runners unless explicitly requested

lib/autobuild.js.map

@@ -1 +1 @@
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+{"version":3,"file":"autobuild.js","sourceRoot":"","sources":["../src/autobuild.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAeA,kEAkGC;AAED,8CAmCC;AAED,oCAsBC;AA9KD,oDAAsC;AAEtC,iDAA6E;AAC7E,6CAAgD;AAChD,qCAA6C;AAE7C,uCAAmC;AACnC,+CAAuC;AACvC,mDAAmE;AACnE,2CAAyD;AAEzD,6CAAgD;AAChD,qDAAgD;AAChD,iCAAmC;AAE5B,KAAK,UAAU,2BAA2B,CAC/C,MAAc,EACd,MAA0B,EAC1B,MAAc;IAEd,IACE,CAAC,MAAM,CAAC,SAAS,KAAK,gBAAS,CAAC,IAAI;QAClC,CAAC,MAAM,MAAM,CAAC,eAAe,CAAC,6BAAY,CAAC,wBAAwB,CAAC,CAAC,CAAC;QACxE,MAAM,CAAC,SAAS,KAAK,gBAAS,CAAC,MAAM,EACrC,CAAC;QACD,MAAM,CAAC,IAAI,CACT,qBAAqB,MAAM,CAAC,SAAS,2BAA2B;YAC9D,OAAO,gBAAM,CAAC,kBAAkB,wBAAwB,CAC3D,CAAC;QACF,OAAO,SAAS,CAAC;IACnB,CAAC;IAED,0CAA0C;IAC1C,mFAAmF;IACnF,oFAAoF;IACpF,4EAA4E;IAC5E,MAAM,kBAAkB,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CACvD,IAAA,4BAAgB,EAAC,CAAC,CAAC,CACpB,CAAC;IAEF,IAAI,CAAC,kBAAkB,EAAE,CAAC;QACxB,MAAM,CAAC,IAAI,CACT,iEAAiE,CAClE,CAAC;QACF,OAAO,SAAS,CAAC;IACnB,CAAC;IAED;;;;;;;;;;;;;;;;;;;;;;;;;;OA0BG;IACH,MAAM,2BAA2B,GAAG,kBAAkB,CAAC,MAAM,CAC3D,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,oBAAQ,CAAC,EAAE,CACzB,CAAC;IAEF,MAAM,SAAS,GAAe,EAAE,CAAC;IACjC,yEAAyE;IACzE,UAAU;IACV,IAAI,2BAA2B,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE,CAAC;QACjD,SAAS,CAAC,IAAI,CAAC,2BAA2B,CAAC,CAAC,CAAC,CAAC,CAAC;IACjD,CAAC;IACD,uEAAuE;IACvE,wCAAwC;IACxC,IAAI,kBAAkB,CAAC,MAAM,KAAK,2BAA2B,CAAC,MAAM,EAAE,CAAC;QACrE,SAAS,CAAC,IAAI,CAAC,oBAAQ,CAAC,EAAE,CAAC,CAAC;IAC9B,CAAC;IAED,MAAM,CAAC,KAAK,CAAC,kBAAkB,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;IAE3D,2EAA2E;IAC3E,4EAA4E;IAC5E,2CAA2C;IAC3C,uEAAuE;IACvE,2EAA2E;IAC3E,uEAAuE;IACvE,yCAAyC;IACzC,IAAI,2BAA2B,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC3C,MAAM,CAAC,OAAO,CACZ,oCAAoC,SAAS,CAAC,IAAI,CAChD,OAAO,CACR,8BAA8B,2BAA2B;aACvD,KAAK,CAAC,CAAC,CAAC;aACR,IAAI,CACH,OAAO,CACR,kFAAkF;YACnF,OAAO,gBAAM,CAAC,4BAA4B,wBAAwB,CACrE,CAAC;IACJ,CAAC;IAED,OAAO,SAAS,CAAC;AACnB,CAAC;AAEM,KAAK,UAAU,iBAAiB,CAAC,MAAc,EAAE,MAAc;IACpE,MAAM,MAAM,GAAG,6BAAa,CAAC,uBAAO,CAAC,yBAAyB,CAAC,CAAC,MAAM,CAAC;IACvE,MAAM,WAAW,GAAG,4CAA4C,CAAC;IACjE,MAAM,aAAa,GAAG,MAAM,IAAA,6BAAgB,GAAE,CAAC;IAC/C,MAAM,aAAa,GAAG,IAAA,6BAAgB,GAAE,CAAC;IACzC,MAAM,QAAQ,GAAG,IAAI,wBAAQ,CAC3B,aAAa,EACb,aAAa,EACb,IAAA,oCAAqB,GAAE,EACvB,MAAM,CACP,CAAC;IACF,IAAI,MAAM,QAAQ,CAAC,QAAQ,CAAC,uBAAO,CAAC,yBAAyB,EAAE,MAAM,CAAC,EAAE,CAAC;QACvE,yEAAyE;QACzE,IACE,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,KAAK,aAAa;YACnD,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,EAC9B,CAAC;YACD,MAAM,CAAC,IAAI,CACT,aAAa,WAAW,sCACtB,IAAA,mCAAoB,GAAE,KAAK,SAAS;gBAClC,CAAC,CAAC,8BAA8B,MAAM,yDAAyD,gBAAM,CAAC,oBAAoB,wBAAwB;gBAClJ,CAAC,CAAC,EACN,EAAE,CACH,CAAC;YACF,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;QACvC,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,IAAI,CACT,YAAY,WAAW,yCAAyC,MAAM,yCAAyC,gBAAM,CAAC,oBAAoB,wBAAwB,CACnK,CAAC;YACF,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QACtC,CAAC;IACH,CAAC;SAAM,CAAC;QACN,MAAM,CAAC,IAAI,CAAC,aAAa,WAAW,GAAG,CAAC,CAAC;QACzC,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACvC,CAAC;AACH,CAAC;AAEM,KAAK,UAAU,YAAY,CAChC,MAA0B,EAC1B,QAAkB,EAClB,MAAc;IAEd,MAAM,CAAC,UAAU,CAAC,qCAAqC,QAAQ,OAAO,CAAC,CAAC;IACxE,MAAM,MAAM,GAAG,MAAM,IAAA,kBAAS,EAAC,MAAM,CAAC,SAAS,CAAC,CAAC;IACjD,IAAI,QAAQ,KAAK,oBAAQ,CAAC,GAAG,EAAE,CAAC;QAC9B,MAAM,iBAAiB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC1C,CAAC;IACD,IACE,MAAM,CAAC,SAAS;QAChB,CAAC,MAAM,MAAM,CAAC,eAAe,CAAC,6BAAY,CAAC,wBAAwB,CAAC,CAAC,EACrE,CAAC;QACD,MAAM,MAAM,CAAC,qBAAqB,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;IACvD,CAAC;SAAM,CAAC;QACN,MAAM,MAAM,CAAC,YAAY,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;IAC9C,CAAC;IACD,IAAI,QAAQ,KAAK,oBAAQ,CAAC,EAAE,EAAE,CAAC;QAC7B,IAAI,CAAC,cAAc,CAAC,oBAAM,CAAC,oBAAoB,EAAE,MAAM,CAAC,CAAC;IAC3D,CAAC;IACD,MAAM,CAAC,QAAQ,EAAE,CAAC;AACpB,CAAC"}

lib/cli-errors.js

@@ -110,11 +110,13 @@ function extractAutobuildErrors(error) {
 var CliConfigErrorCategory;
 (function (CliConfigErrorCategory) {
     CliConfigErrorCategory["AutobuildError"] = "AutobuildError";
+    CliConfigErrorCategory["CouldNotCreateTempDir"] = "CouldNotCreateTempDir";
     CliConfigErrorCategory["ExternalRepositoryCloneFailed"] = "ExternalRepositoryCloneFailed";
     CliConfigErrorCategory["GradleBuildFailed"] = "GradleBuildFailed";
     CliConfigErrorCategory["IncompatibleWithActionVersion"] = "IncompatibleWithActionVersion";
     CliConfigErrorCategory["InitCalledTwice"] = "InitCalledTwice";
     CliConfigErrorCategory["InvalidConfigFile"] = "InvalidConfigFile";
+    CliConfigErrorCategory["InvalidExternalRepoSpecifier"] = "InvalidExternalRepoSpecifier";
     CliConfigErrorCategory["InvalidSourceRoot"] = "InvalidSourceRoot";
     CliConfigErrorCategory["MavenBuildFailed"] = "MavenBuildFailed";
     CliConfigErrorCategory["NoBuildCommandAutodetected"] = "NoBuildCommandAutodetected";
@@ -138,6 +140,9 @@ exports.cliErrorsConfig = {
             new RegExp("We were unable to automatically build your code"),
         ],
     },
+    [CliConfigErrorCategory.CouldNotCreateTempDir]: {
+        cliErrorMessageCandidates: [new RegExp("Could not create temp directory")],
+    },
     [CliConfigErrorCategory.ExternalRepositoryCloneFailed]: {
         cliErrorMessageCandidates: [
             new RegExp("Failed to clone external Git repository"),
@@ -166,6 +171,11 @@ exports.cliErrorsConfig = {
             new RegExp("The supplied config file is empty"),
         ],
     },
+    [CliConfigErrorCategory.InvalidExternalRepoSpecifier]: {
+        cliErrorMessageCandidates: [
+            new RegExp("Specifier for external repository is invalid"),
+        ],
+    },
     // Expected source location for database creation does not exist
     [CliConfigErrorCategory.InvalidSourceRoot]: {
         cliErrorMessageCandidates: [new RegExp("Invalid source root")],

lib/codeql.js

@@ -33,7 +33,6 @@ var __importStar = (this && this.__importStar) || (function () {
     };
 })();
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.CODEQL_VERSION_SUBLANGUAGE_FILE_COVERAGE = exports.CODEQL_VERSION_ANALYSIS_SUMMARY_V2 = void 0;
 exports.setupCodeQL = setupCodeQL;
 exports.getCodeQL = getCodeQL;
 exports.setCodeQL = setCodeQL;
@@ -49,7 +48,6 @@ const path = __importStar(require("path"));
 const core = __importStar(require("@actions/core"));
 const toolrunner = __importStar(require("@actions/exec/lib/toolrunner"));
 const yaml = __importStar(require("js-yaml"));
-const semver = __importStar(require("semver"));
 const actions_util_1 = require("./actions-util");
 const cli_errors_1 = require("./cli-errors");
 const doc_url_1 = require("./doc-url");
@@ -57,6 +55,7 @@ const environment_1 = require("./environment");
 const feature_flags_1 = require("./feature-flags");
 const git_utils_1 = require("./git-utils");
 const languages_1 = require("./languages");
+const overlay_database_utils_1 = require("./overlay-database-utils");
 const setupCodeql = __importStar(require("./setup-codeql"));
 const tools_features_1 = require("./tools-features");
 const tracer_config_1 = require("./tracer-config");
@@ -97,18 +96,6 @@ const EXTRACTION_DEBUG_MODE_VERBOSITY = "progress++";
  * For convenience, please keep these in descending order. Once a version
  * flag is older than the oldest supported version above, it may be removed.
  */
-/**
- * Versions 2.15.0+ of the CodeQL CLI support new analysis summaries.
- */
-exports.CODEQL_VERSION_ANALYSIS_SUMMARY_V2 = "2.15.0";
-/**
- * Versions 2.15.0+ of the CodeQL CLI support sub-language file coverage information.
- */
-exports.CODEQL_VERSION_SUBLANGUAGE_FILE_COVERAGE = "2.15.0";
-/**
- * Versions 2.15.2+ of the CodeQL CLI support the `--sarif-include-query-help` option.
- */
-const CODEQL_VERSION_INCLUDE_QUERY_HELP = "2.15.2";
 /**
  * Versions 2.17.1+ of the CodeQL CLI support the `--cache-cleanup` option.
  */
@@ -147,7 +134,11 @@ async function setupCodeQL(toolsInput, apiDetails, tempDir, variant, defaultCliV
         };
     }
     catch (e) {
-        throw new Error(`Unable to download and extract CodeQL CLI: ${(0, util_1.getErrorMessage)(e)}${e instanceof Error && e.stack ? `\n\nDetails: ${e.stack}` : ""}`);
+        const ErrorClass = e instanceof util.ConfigurationError ||
+            (e instanceof Error && e.message.includes("ENOSPC")) // out of disk space
+            ? util.ConfigurationError
+            : Error;
+        throw new ErrorClass(`Unable to download and extract CodeQL CLI: ${(0, util_1.getErrorMessage)(e)}${e instanceof Error && e.stack ? `\n\nDetails: ${e.stack}` : ""}`);
     }
 }
 /**
@@ -264,7 +255,7 @@ async function getCodeQLForCmd(cmd, checkVersion) {
         async supportsFeature(feature) {
             return (0, tools_features_1.isSupportedToolsFeature)(await this.getVersion(), feature);
         },
-        async databaseInitCluster(config, sourceRoot, processName, qlconfigFile, logger) {
+        async databaseInitCluster(config, sourceRoot, processName, qlconfigFile, overlayDatabaseMode, logger) {
             const extraArgs = config.languages.map((language) => `--language=${language}`);
             if (await (0, tracer_config_1.shouldEnableIndirectTracing)(codeql, config)) {
                 extraArgs.push("--begin-tracing");
@@ -272,9 +263,17 @@ async function getCodeQLForCmd(cmd, checkVersion) {
                 extraArgs.push(`--trace-process-name=${processName}`);
             }
             if (config.languages.indexOf(languages_1.Language.actions) >= 0) {
-                extraArgs.push("--search-path");
-                const extractorPath = path.resolve(__dirname, "../actions-extractor");
-                extraArgs.push(extractorPath);
+                // We originally added an embedded version of the Actions extractor to the CodeQL Action
+                // itself in order to deploy the extractor between CodeQL releases. When we did add the
+                // extractor to the CLI, though, its autobuild script was missing the execute bit.
+                // 2.20.6 is the first CLI release with the fully-functional extractor in the CLI. For older
+                // versions, we'll keep using the embedded extractor. We can remove the embedded extractor
+                // once 2.20.6 is deployed in the runner images.
+                if (!(await util.codeQlVersionAtLeast(codeql, "2.20.6"))) {
+                    extraArgs.push("--search-path");
+                    const extractorPath = path.resolve(__dirname, "../actions-extractor");
+                    extraArgs.push(extractorPath);
+                }
             }
             const codeScanningConfigFile = await generateCodeScanningConfig(config, logger);
             const externalRepositoryToken = (0, actions_util_1.getOptionalInput)("external-repository-token");
@@ -289,29 +288,36 @@ async function getCodeQLForCmd(cmd, checkVersion) {
             if (qlconfigFile !== undefined) {
                 extraArgs.push(`--qlconfig-file=${qlconfigFile}`);
             }
-            extraArgs.push("--calculate-language-specific-baseline");
-            if (await isSublanguageFileCoverageEnabled(config, this)) {
-                extraArgs.push("--sublanguage-file-coverage");
-            }
-            else if (await util.codeQlVersionAtLeast(this, exports.CODEQL_VERSION_SUBLANGUAGE_FILE_COVERAGE)) {
-                extraArgs.push("--no-sublanguage-file-coverage");
-            }
             const overwriteFlag = (0, tools_features_1.isSupportedToolsFeature)(await this.getVersion(), tools_features_1.ToolsFeature.ForceOverwrite)
                 ? "--force-overwrite"
                 : "--overwrite";
+            if (overlayDatabaseMode === overlay_database_utils_1.OverlayDatabaseMode.Overlay) {
+                const overlayChangesFile = await (0, overlay_database_utils_1.writeOverlayChangesFile)(config, sourceRoot, logger);
+                extraArgs.push(`--overlay-changes=${overlayChangesFile}`);
+            }
+            else if (overlayDatabaseMode === overlay_database_utils_1.OverlayDatabaseMode.OverlayBase) {
+                extraArgs.push("--overlay-base");
+            }
             await runCli(cmd, [
                 "database",
                 "init",
-                overwriteFlag,
+                ...(overlayDatabaseMode === overlay_database_utils_1.OverlayDatabaseMode.Overlay
+                    ? []
+                    : [overwriteFlag]),
                 "--db-cluster",
                 config.dbLocation,
                 `--source-root=${sourceRoot}`,
+                "--calculate-language-specific-baseline",
                 "--extractor-include-aliases",
+                "--sublanguage-file-coverage",
                 ...extraArgs,
                 ...getExtraOptionsFromEnv(["database", "init"], {
                     ignoringOptions: ["--overwrite"],
                 }),
             ], { stdin: externalRepositoryToken });
+            if (overlayDatabaseMode === overlay_database_utils_1.OverlayDatabaseMode.OverlayBase) {
+                await (0, overlay_database_utils_1.writeBaseDatabaseOidsFile)(config, sourceRoot);
+            }
         },
         async runAutobuild(config, language) {
             applyAutobuildAzurePipelinesTimeoutFix();
@@ -465,16 +471,13 @@ async function getCodeQLForCmd(cmd, checkVersion) {
                 "run-queries",
                 ...flags,
                 databasePath,
-                "--expect-discarded-cache",
+                "--intra-layer-parallelism",
                 "--min-disk-free=1024", // Try to leave at least 1GB free
                 "-v",
                 ...getExtraOptionsFromEnv(["database", "run-queries"], {
                     ignoringOptions: ["--expect-discarded-cache"],
                 }),
             ];
-            if (await util.codeQlVersionAtLeast(this, feature_flags_1.CODEQL_VERSION_FINE_GRAINED_PARALLELISM)) {
-                codeqlArgs.push("--intra-layer-parallelism");
-            }
             await runCli(cmd, codeqlArgs);
         },
         async databaseInterpretResults(databasePath, querySuitePaths, sarifFile, addSnippetsFlag, threadsFlag, verbosityFlag, sarifRunPropertyFlag, automationDetailsId, config, features) {
@@ -492,7 +495,8 @@ async function getCodeQLForCmd(cmd, checkVersion) {
                 "--sarif-add-baseline-file-info",
                 `--sarif-codescanning-config=${getGeneratedCodeScanningConfigPath(config)}`,
                 "--sarif-group-rules-by-pack",
-                ...(await getCodeScanningQueryHelpArguments(this)),
+                "--sarif-include-query-help=always",
+                "--sublanguage-file-coverage",
                 ...(await getJobRunUuidSarifOptions(this)),
                 ...getExtraOptionsFromEnv(["database", "interpret-results"]),
             ];
@@ -502,20 +506,13 @@ async function getCodeQLForCmd(cmd, checkVersion) {
             if (automationDetailsId !== undefined) {
                 codeqlArgs.push("--sarif-category", automationDetailsId);
             }
-            if (await isSublanguageFileCoverageEnabled(config, this)) {
-                codeqlArgs.push("--sublanguage-file-coverage");
-            }
-            else if (await util.codeQlVersionAtLeast(this, exports.CODEQL_VERSION_SUBLANGUAGE_FILE_COVERAGE)) {
-                codeqlArgs.push("--no-sublanguage-file-coverage");
-            }
             if (shouldExportDiagnostics) {
                 codeqlArgs.push("--sarif-include-diagnostics");
             }
             else {
                 codeqlArgs.push("--no-sarif-include-diagnostics");
             }
-            if ((await util.codeQlVersionAtLeast(this, exports.CODEQL_VERSION_ANALYSIS_SUMMARY_V2)) &&
-                !(0, tools_features_1.isSupportedToolsFeature)(await this.getVersion(), tools_features_1.ToolsFeature.AnalysisSummaryV2IsDefault)) {
+            if (!(0, tools_features_1.isSupportedToolsFeature)(await this.getVersion(), tools_features_1.ToolsFeature.AnalysisSummaryV2IsDefault)) {
                 codeqlArgs.push("--new-analysis-summary");
             }
             codeqlArgs.push(databasePath);
@@ -812,6 +809,13 @@ async function generateCodeScanningConfig(config, logger) {
     if (Array.isArray(augmentedConfig.packs) && !augmentedConfig.packs.length) {
         delete augmentedConfig.packs;
     }
+    augmentedConfig["query-filters"] = [
+        ...(config.augmentationProperties.defaultQueryFilters || []),
+        ...(augmentedConfig["query-filters"] || []),
+    ];
+    if (augmentedConfig["query-filters"]?.length === 0) {
+        delete augmentedConfig["query-filters"];
+    }
     logger.info(`Writing augmented user configuration file to ${codeScanningConfigFile}`);
     logger.startGroup("Augmented user configuration file contents");
     logger.info(yaml.dump(augmentedConfig));
@@ -846,19 +850,6 @@ async function getTrapCachingExtractorConfigArgsForLang(config, language) {
 function getGeneratedCodeScanningConfigPath(config) {
     return path.resolve(config.tempDir, "user-config.yaml");
 }
-async function isSublanguageFileCoverageEnabled(config, codeql) {
-    return (
-    // Sub-language file coverage is first supported in GHES 3.12.
-    (config.gitHubVersion.type !== util.GitHubVariant.GHES ||
-        semver.gte(config.gitHubVersion.version, "3.12.0")) &&
-        (await util.codeQlVersionAtLeast(codeql, exports.CODEQL_VERSION_SUBLANGUAGE_FILE_COVERAGE)));
-}
-async function getCodeScanningQueryHelpArguments(codeql) {
-    if (await util.codeQlVersionAtLeast(codeql, CODEQL_VERSION_INCLUDE_QUERY_HELP)) {
-        return ["--sarif-include-query-help=always"];
-    }
-    return ["--sarif-add-query-help"];
-}
 function getExtractionVerbosityArguments(enableDebugLogging) {
     return enableDebugLogging
         ? [`--verbosity=${EXTRACTION_DEBUG_MODE_VERBOSITY}`]

lib/codeql.test.js

@@ -53,6 +53,7 @@ const defaults = __importStar(require("./defaults.json"));
 const doc_url_1 = require("./doc-url");
 const languages_1 = require("./languages");
 const logging_1 = require("./logging");
+const overlay_database_utils_1 = require("./overlay-database-utils");
 const setup_codeql_1 = require("./setup-codeql");
 const testing_utils_1 = require("./testing-utils");
 const tools_features_1 = require("./tools-features");
@@ -335,7 +336,7 @@ const injectedConfigMacro = ava_1.default.macro({
                 tempDir,
                 augmentationProperties,
             };
-            await codeqlObject.databaseInitCluster(thisStubConfig, "", undefined, undefined, (0, logging_1.getRunnerLogger)(true));
+            await codeqlObject.databaseInitCluster(thisStubConfig, "", undefined, undefined, overlay_database_utils_1.OverlayDatabaseMode.None, (0, logging_1.getRunnerLogger)(true));
             const args = runnerConstructorStub.firstCall.args[1];
             // should have used an config file
             const configArg = args.find((arg) => arg.startsWith("--codescanning-config="));
@@ -471,7 +472,7 @@ const injectedConfigMacro = ava_1.default.macro({
         const runnerConstructorStub = stubToolRunnerConstructor();
         const codeqlObject = await codeql.getCodeQLForTesting();
         sinon.stub(codeqlObject, "getVersion").resolves((0, testing_utils_1.makeVersionInfo)("2.17.6"));
-        await codeqlObject.databaseInitCluster({ ...stubConfig, tempDir }, "", undefined, "/path/to/qlconfig.yml", (0, logging_1.getRunnerLogger)(true));
+        await codeqlObject.databaseInitCluster({ ...stubConfig, tempDir }, "", undefined, "/path/to/qlconfig.yml", overlay_database_utils_1.OverlayDatabaseMode.None, (0, logging_1.getRunnerLogger)(true));
         const args = runnerConstructorStub.firstCall.args[1];
         // should have used a config file
         const hasCodeScanningConfigArg = args.some((arg) => arg.startsWith("--codescanning-config="));
@@ -487,7 +488,7 @@ const injectedConfigMacro = ava_1.default.macro({
         const codeqlObject = await codeql.getCodeQLForTesting();
         sinon.stub(codeqlObject, "getVersion").resolves((0, testing_utils_1.makeVersionInfo)("2.17.6"));
         await codeqlObject.databaseInitCluster({ ...stubConfig, tempDir }, "", undefined, undefined, // undefined qlconfigFile
-        (0, logging_1.getRunnerLogger)(true));
+        overlay_database_utils_1.OverlayDatabaseMode.None, (0, logging_1.getRunnerLogger)(true));
         const args = runnerConstructorStub.firstCall.args[1];
         const hasQlconfigArg = args.some((arg) => arg.startsWith("--qlconfig-file="));
         t.false(hasQlconfigArg, "should NOT have injected a qlconfig");
@@ -521,14 +522,6 @@ const NEW_ANALYSIS_SUMMARY_TEST_CASES = [
         flagPassed: true,
         negativeFlagPassed: false,
     },
-    {
-        codeqlVersion: (0, testing_utils_1.makeVersionInfo)("2.14.6"),
-        githubVersion: {
-            type: util.GitHubVariant.DOTCOM,
-        },
-        flagPassed: false,
-        negativeFlagPassed: false,
-    },
 ];
 for (const { codeqlVersion, flagPassed, githubVersion, negativeFlagPassed, } of NEW_ANALYSIS_SUMMARY_TEST_CASES) {
     (0, ava_1.default)(`database interpret-results passes ${flagPassed
@@ -620,7 +613,7 @@ for (const { codeqlVersion, flagPassed, githubVersion, negativeFlagPassed, } of
     sinon.stub(io, "which").resolves("");
     await t.throwsAsync(async () => await codeqlObject.databaseRunQueries(stubConfig.dbLocation, []), {
         instanceOf: cli_errors_1.CliError,
-        message: `Encountered a fatal error while running "codeql-for-testing database run-queries  --expect-discarded-cache --min-disk-free=1024 -v --intra-layer-parallelism". Exit code was 1 and error was: Oops! A fatal internal error occurred. Details:
+        message: `Encountered a fatal error while running "codeql-for-testing database run-queries  --intra-layer-parallelism --min-disk-free=1024 -v". Exit code was 1 and error was: Oops! A fatal internal error occurred. Details:
     com.semmle.util.exception.CatastrophicError: An error occurred while evaluating ControlFlowGraph::ControlFlow::Root.isRootOf/1#dispred#f610e6ed/2@86282cc8
     Severe disk cache trouble (corruption or out of space) at /home/runner/work/_temp/codeql_databases/go/db-go/default/cache/pages/28/33.pack: Failed to write item to disk. See the logs for more details.`,
     });
@@ -646,7 +639,7 @@ for (const { codeqlVersion, flagPassed, githubVersion, negativeFlagPassed, } of
     sinon.stub(io, "which").resolves("");
     process.env["CODEQL_ACTION_EXTRA_OPTIONS"] =
         '{ "database": { "init": ["--overwrite"] } }';
-    await codeqlObject.databaseInitCluster(stubConfig, "sourceRoot", undefined, undefined, (0, logging_1.getRunnerLogger)(false));
+    await codeqlObject.databaseInitCluster(stubConfig, "sourceRoot", undefined, undefined, overlay_database_utils_1.OverlayDatabaseMode.None, (0, logging_1.getRunnerLogger)(false));
     t.true(runnerConstructorStub.calledOnce);
     const args = runnerConstructorStub.firstCall.args[1];
     t.is(args.filter((option) => option === "--overwrite").length, 1, "--overwrite should only be passed once");