Allow query-filters for code-quality

.github/pull_request_template.md

@@ -18,25 +18,14 @@ For internal use only. Please select the risk level of this change:
 
 #### Which use cases does this change impact?
 
-<!-- Delete options that don't apply. If in doubt, do not delete an option. -->
+<!-- Delete options that don't apply. -->
 
-Workflow types:
-
-- **Advanced setup** - Impacts users who have custom CodeQL workflows.
-- **Managed** - Impacts users with `dynamic` workflows (Default Setup, CCR, ...).
-
-Products:
-
-- **Code Scanning** - The changes impact analyses when `analysis-kinds: code-scanning`.
-- **Code Quality** - The changes impact analyses when `analysis-kinds: code-quality`.
-- **CCR** - The changes impact analyses for Copilot Code Reviews.
-- **Third-party analyses** - The changes affect the `upload-sarif` action.
-
-Environments:
-
-- **Dotcom** - Impacts CodeQL workflows on `github.com`.
-- **GHES** - Impacts CodeQL workflows on GitHub Enterprise Server.
-- **Testing/None** - This change does not impact any CodeQL workflows in production.
+- **Advanced setup** - Impacts users who have custom workflows.
+- **Default setup** - Impacts users who use default setup.
+- **Code Scanning** - Impacts Code Scanning (i.e. `analysis-kinds: code-scanning`).
+- **Code Quality** - Impacts Code Quality (i.e. `analysis-kinds: code-quality`).
+- **Third-party analyses** - Impacts third-party analyses (i.e. `upload-sarif`).
+- **GHES** - Impacts GitHub Enterprise Server.
 
 #### How did/will you validate this change?
 
@@ -65,15 +54,6 @@ Environments:
     - **Alerts** - New or existing monitors will trip if something goes wrong with this change.
 - **Other** - Please provide details.
 
-#### Are there any special considerations for merging or releasing this change?
-
-<!--
-    Consider whether this change depends on a different change in another repository that should be released first.
--->
-
-- **No special considerations** - This change can be merged at any time.
-- **Special considerations** - This change should only be merged once certain preconditions are met. Please provide details of those or link to this PR from an internal issue.
-
 ### Merge / deployment checklist
 
 - Confirm this change is backwards compatible with existing workflows.

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

@@ -27,11 +27,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -39,11 +34,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -84,10 +74,6 @@ jobs:
         with:
           go-version: ${{ inputs.go-version || '>=1.21.0' }}
           cache: false
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - id: init
         uses: ./../action/init
         with:

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

@@ -32,11 +32,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -49,11 +44,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -95,10 +85,6 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ inputs.python-version || '3.13' }}
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         with:
           tools: ${{ steps.prepare-test.outputs.tools-url }}

.github/workflows/__autobuild-action.yml

@@ -21,19 +21,9 @@ on:
   schedule:
     - cron: '0 5 * * *'
   workflow_dispatch:
-    inputs:
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
+    inputs: {}
   workflow_call:
-    inputs:
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
+    inputs: {}
 defaults:
   run:
     shell: bash
@@ -69,10 +59,6 @@ jobs:
           version: ${{ matrix.version }}
           use-all-platform-bundle: 'false'
           setup-kotlin: 'true'
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         with:
           languages: csharp

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

@@ -27,11 +27,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -39,11 +34,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -80,10 +70,6 @@ jobs:
         with:
           go-version: ${{ inputs.go-version || '>=1.21.0' }}
           cache: false
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         id: init
         with:

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

@@ -27,11 +27,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -39,11 +34,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -84,10 +74,6 @@ jobs:
         with:
           go-version: ${{ inputs.go-version || '>=1.21.0' }}
           cache: false
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         id: init
         with:

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

@@ -27,11 +27,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -39,11 +34,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -82,10 +72,6 @@ jobs:
         with:
           go-version: ${{ inputs.go-version || '>=1.21.0' }}
           cache: false
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         with:
           languages: go

.github/workflows/__go.yml

@@ -18,11 +18,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 jobs:
   go-custom-queries:
     name: 'Go: Custom queries'
@@ -32,7 +27,6 @@ jobs:
     uses: ./.github/workflows/__go-custom-queries.yml
     with:
       go-version: ${{ inputs.go-version }}
-      dotnet-version: ${{ inputs.dotnet-version }}
   go-indirect-tracing-workaround-diagnostic:
     name: 'Go: diagnostic when Go is changed after init step'
     permissions:

.github/workflows/__local-bundle.yml

@@ -32,11 +32,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -49,11 +44,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -95,10 +85,6 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ inputs.python-version || '3.13' }}
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - name: Fetch latest CodeQL bundle
         run: |
           wget https://github.com/github/codeql-action/releases/latest/download/codeql-bundle-linux64.tar.zst

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

@@ -32,11 +32,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -49,11 +44,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -129,10 +119,6 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ inputs.python-version || '3.13' }}
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - name: Use Xcode 16
         if: runner.os == 'macOS' && matrix.version != 'nightly-latest'
         run: sudo xcode-select -s "/Applications/Xcode_16.app"

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

@@ -32,11 +32,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -49,11 +44,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -106,10 +96,6 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ inputs.python-version || '3.13' }}
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         with:
           config-file: .github/codeql/codeql-config-packaging3.yml

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

@@ -27,11 +27,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -39,11 +34,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -91,10 +81,6 @@ jobs:
         with:
           go-version: ${{ inputs.go-version || '>=1.21.0' }}
           cache: false
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         with:
           config-file: .github/codeql/codeql-config-packaging3.yml

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

@@ -27,11 +27,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -39,11 +34,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -91,10 +81,6 @@ jobs:
         with:
           go-version: ${{ inputs.go-version || '>=1.21.0' }}
           cache: false
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         with:
           config-file: .github/codeql/codeql-config-packaging.yml

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

@@ -27,11 +27,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -39,11 +34,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -91,10 +81,6 @@ jobs:
         with:
           go-version: ${{ inputs.go-version || '>=1.21.0' }}
           cache: false
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         with:
           config-file: .github/codeql/codeql-config-packaging2.yml

.github/workflows/__remote-config.yml

@@ -32,11 +32,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -49,11 +44,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -97,10 +87,6 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ inputs.python-version || '3.13' }}
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         with:
           tools: ${{ steps.prepare-test.outputs.tools-url }}

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

@@ -56,7 +56,7 @@ jobs:
           use-all-platform-bundle: 'false'
           setup-kotlin: 'true'
       - name: Set up Ruby
-        uses: ruby/setup-ruby@8aeb6ff8030dd539317f8e1769a044873b56ea71 # v1.268.0
+        uses: ruby/setup-ruby@d5126b9b3579e429dd52e51e68624dda2e05be25 # v1.267.0
         with:
           ruby-version: 2.6
       - name: Install Code Scanning integration

.github/workflows/__split-workflow.yml

@@ -27,11 +27,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -39,11 +34,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -90,10 +80,6 @@ jobs:
         with:
           go-version: ${{ inputs.go-version || '>=1.21.0' }}
           cache: false
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         with:
           config-file: .github/codeql/codeql-config-packaging3.yml

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

@@ -27,11 +27,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -39,11 +34,6 @@ on:
         description: The version of Go to install
         required: false
         default: '>=1.21.0'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -84,10 +74,6 @@ jobs:
         with:
           go-version: ${{ inputs.go-version || '>=1.21.0' }}
           cache: false
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - name: Use Xcode 16
         if: runner.os == 'macOS' && matrix.version != 'nightly-latest'
         run: sudo xcode-select -s "/Applications/Xcode_16.app"

.github/workflows/__unset-environment.yml

@@ -32,11 +32,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -49,11 +44,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -97,10 +87,6 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ inputs.python-version || '3.13' }}
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         id: init
         with:

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

@@ -32,11 +32,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -49,11 +44,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -95,10 +85,6 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ inputs.python-version || '3.13' }}
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         with:
           tools: ${{ steps.prepare-test.outputs.tools-url }}

.github/workflows/__upload-sarif.yml

@@ -32,11 +32,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -49,11 +44,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -102,10 +92,6 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ inputs.python-version || '3.13' }}
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - uses: ./../action/init
         with:
           tools: ${{ steps.prepare-test.outputs.tools-url }}

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

@@ -32,11 +32,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
   workflow_call:
     inputs:
       go-version:
@@ -49,11 +44,6 @@ on:
         description: The version of Python to install
         required: false
         default: '3.13'
-      dotnet-version:
-        type: string
-        description: The version of .NET to install
-        required: false
-        default: 9.x
 defaults:
   run:
     shell: bash
@@ -95,10 +85,6 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ inputs.python-version || '3.13' }}
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: ${{ inputs.dotnet-version || '9.x' }}
       - name: Delete original checkout
         run: |
           # delete the original checkout so we don't accidentally use it.

.github/workflows/codeql.yml

@@ -81,7 +81,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04,ubuntu-24.04,windows-2022,windows-2025,macos-14,macos-15]
+        os: [ubuntu-22.04,ubuntu-24.04,windows-2022,windows-2025,macos-13,macos-14,macos-15]
         tools: ${{ fromJson(needs.check-codeql-versions.outputs.versions) }}
     runs-on: ${{ matrix.os }}
 

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

@@ -54,10 +54,6 @@ jobs:
       - uses: actions/setup-go@v6
         with:
           go-version: ^1.13.1
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: '9.x'
       - uses: ./../action/init
         with:
           tools: ${{ steps.prepare-test.outputs.tools-url }}

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

@@ -50,10 +50,6 @@ jobs:
       - uses: actions/setup-go@v6
         with:
           go-version: ^1.13.1
-      - name: Install .NET
-        uses: actions/setup-dotnet@v5
-        with:
-          dotnet-version: '9.x'
       - uses: ./../action/init
         id: init
         with:

.github/workflows/script/bundle_changelog.py

@@ -1,18 +0,0 @@
-import os
-import re
-
-# Get the PR number from the PR URL.
-pr_number = os.environ['PR_URL'].split('/')[-1]
-changelog_note = f"- Update default CodeQL bundle version to {os.environ['CLI_VERSION']}. [#{pr_number}]({os.environ['PR_URL']})"
-
-# If the "[UNRELEASED]" section starts with "no user facing changes", remove that line.
-with open('CHANGELOG.md', 'r') as f:
-    changelog = f.read()
-
-changelog = changelog.replace('## [UNRELEASED]\n\nNo user facing changes.', '## [UNRELEASED]\n')
-
-# Add the changelog note to the bottom of the "[UNRELEASED]" section.
-changelog = re.sub(r'\n## (\d+\.\d+\.\d+)', f'{changelog_note}\n\n## \\1', changelog, count=1)
-
-with open('CHANGELOG.md', 'w') as f:
-    f.write(changelog)

.github/workflows/script/update-required-checks.sh

@@ -29,7 +29,7 @@ fi
 echo "Getting checks for $GITHUB_SHA"
 
 # Ignore any checks with "https://", CodeQL, LGTM, Update, and ESLint checks.
-CHECKS="$(gh api repos/github/codeql-action/commits/"${GITHUB_SHA}"/check-runs --paginate | jq --slurp --compact-output --raw-output '[.[].check_runs.[] | select(.conclusion != "skipped") | .name | select(contains("https://") or . == "CodeQL" or . == "Dependabot" or . == "check-expected-release-files" or contains("Update") or contains("ESLint") or contains("update") or contains("test-setup-python-scripts") or . == "Agent" or . == "Cleanup artifacts" or . == "Prepare" or . == "Upload results" | not)] | unique | sort')"
+CHECKS="$(gh api repos/github/codeql-action/commits/"${GITHUB_SHA}"/check-runs --paginate | jq --slurp --compact-output --raw-output '[.[].check_runs.[] | select(.conclusion != "skipped") | .name | select(contains("https://") or . == "CodeQL" or . == "Dependabot" or . == "check-expected-release-files" or contains("Update") or contains("ESLint") or contains("update") or contains("test-setup-python-scripts") | not)] | unique | sort')"
 
 echo "$CHECKS" | jq
 

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

@@ -43,10 +43,6 @@ jobs:
       with:
         version: ${{ matrix.version }}
         use-all-platform-bundle: true
-    - name: Install .NET
-      uses: actions/setup-dotnet@v5
-      with:
-        dotnet-version: '9.x'
     - id: init
       uses: ./../action/init
       with:

.github/workflows/update-bundle.yml

@@ -40,11 +40,6 @@ jobs:
           git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
           git config --global user.name "github-actions[bot]"
 
-      - name: Set up Python
-        uses: actions/setup-python@v6
-        with:
-          python-version: '3.12'
-
       - name: Set up Node.js
         uses: actions/setup-node@v6
         with:
@@ -83,8 +78,28 @@ jobs:
           echo "PR_URL=$pr_url" | tee -a "$GITHUB_ENV"
 
       - name: Create changelog note
+        shell: python
         run: |
-          python .github/workflows/script/bundle_changelog.py
+          import os
+          import re
+
+          # Get the PR number from the PR URL.
+          pr_number = os.environ['PR_URL'].split('/')[-1]
+          changelog_note = f"- Update default CodeQL bundle version to {os.environ['CLI_VERSION']}. [#{pr_number}]({os.environ['PR_URL']})"
+
+          # If the "[UNRELEASED]" section starts with "no user facing changes", remove that line.
+          # Use perl to avoid having to escape the newline character.
+
+          with open('CHANGELOG.md', 'r') as f:
+              changelog = f.read()
+
+          changelog = changelog.replace('## [UNRELEASED]\n\nNo user facing changes.', '## [UNRELEASED]\n')
+
+          # Add the changelog note to the bottom of the "[UNRELEASED]" section.
+          changelog = re.sub(r'\n## (\d+\.\d+\.\d+)', f'{changelog_note}\n\n## \\1', changelog, count=1)
+
+          with open('CHANGELOG.md', 'w') as f:
+              f.write(changelog)
 
       - name: Push changelog note
         run: |

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

@@ -4,12 +4,6 @@ on:
   schedule:
     - cron: "0 0 * * *"
   workflow_dispatch:
-  pull_request:
-    branches:
-      - main
-    paths:
-      - .github/workflows/update-supported-enterprise-server-versions.yml
-      - .github/workflows/update-supported-enterprise-server-versions/update.py
 
 jobs:
   update-supported-enterprise-server-versions:
@@ -34,7 +28,6 @@ jobs:
           repository: github/enterprise-releases
           token: ${{ secrets.ENTERPRISE_RELEASE_TOKEN }}
           path: ${{ github.workspace }}/enterprise-releases/
-          sparse-checkout: releases.json
       - name: Update Supported Enterprise Server Versions
         run: |
           cd ./.github/workflows/update-supported-enterprise-server-versions/
@@ -42,7 +35,6 @@ jobs:
           pipenv install
           pipenv run ./update.py
           rm --recursive "$ENTERPRISE_RELEASES_PATH"
-          npm ci
           npm run build
         env:
           ENTERPRISE_RELEASES_PATH: ${{ github.workspace }}/enterprise-releases/
@@ -52,33 +44,25 @@ jobs:
           git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
           git config --global user.name "github-actions[bot]"
 
-      - name: Commit changes
-        id: prepare-commit
+      - name: Commit changes and open PR
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           if [[ -z $(git status --porcelain) ]]; then
             echo "No changes to commit"
-            echo "committed=false" >> $GITHUB_OUTPUT
           else
             git checkout -b update-supported-enterprise-server-versions
             git add .
             git commit --message "Update supported GitHub Enterprise Server versions"
+            git push origin update-supported-enterprise-server-versions
 
-            echo "committed=true" >> $GITHUB_OUTPUT
+            body="This PR updates the list of supported GitHub Enterprise Server versions, either because a new "
+            body+="version is about to be feature frozen, or because an old release has been deprecated."
+            body+=$'\n\n'
+            body+="If an old release has been deprecated, please follow the instructions in CONTRIBUTING.md to "
+            body+="deprecate the corresponding version of CodeQL."
+
+            gh pr create --draft \
+              --title "Update supported GitHub Enterprise Server versions" \
+              --body "$body"
           fi
-
-      - name: Open PR
-        if: github.event_name != 'pull_request' && steps.prepare-commit.outputs.committed == 'true'
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          git push origin update-supported-enterprise-server-versions
-
-          body="This PR updates the list of supported GitHub Enterprise Server versions, either because a new "
-          body+="version is about to be feature frozen, or because an old release has been deprecated."
-          body+=$'\n\n'
-          body+="If an old release has been deprecated, please follow the instructions in CONTRIBUTING.md to "
-          body+="deprecate the corresponding version of CodeQL."
-
-          gh pr create --draft \
-            --title "Update supported GitHub Enterprise Server versions" \
-            --body "$body"

CHANGELOG.md

@@ -6,15 +6,6 @@ See the [releases page](https://github.com/github/codeql-action/releases) for th
 
 No user facing changes.
 
-## 4.31.4 - 18 Nov 2025
-
-No user facing changes.
-
-## 4.31.3 - 13 Nov 2025
-
-- CodeQL Action v3 will be deprecated in December 2026.  The Action now logs a warning for customers who are running v3 but could be running v4. For more information, see [Upcoming deprecation of CodeQL Action v3](https://github.blog/changelog/2025-10-28-upcoming-deprecation-of-codeql-action-v3/).
-- Update default CodeQL bundle version to 2.23.5. [#3288](https://github.com/github/codeql-action/pull/3288)
-
 ## 4.31.2 - 30 Oct 2025
 
 No user facing changes.

eslint.config.mjs

@@ -12,7 +12,6 @@ import filenames from "eslint-plugin-filenames";
 import github from "eslint-plugin-github";
 import _import from "eslint-plugin-import";
 import noAsyncForeach from "eslint-plugin-no-async-foreach";
-import jsdoc from "eslint-plugin-jsdoc";
 import globals from "globals";
 
 const __filename = fileURLToPath(import.meta.url);
@@ -53,7 +52,6 @@ export default [
       github: fixupPluginRules(github),
       import: fixupPluginRules(_import),
       "no-async-foreach": noAsyncForeach,
-      "jsdoc": jsdoc,
     },
 
     languageOptions: {
@@ -135,16 +133,6 @@ export default [
       "@typescript-eslint/no-shadow": "error",
       "@typescript-eslint/prefer-optional-chain": "error",
       "one-var": ["error", "never"],
-
-      // Check param names to ensure that we don't have outdated JSDocs.
-      "jsdoc/check-param-names": [
-        "error",
-        {
-          // We don't currently require full JSDoc coverage, so this rule
-          // should not error on missing @param annotations.
-          disableMissingParamChecks: true,
-        }
-      ],
     },
   },
   {

lib/defaults.json

@@ -1,6 +1,6 @@
 {
-  "bundleVersion": "codeql-bundle-v2.23.5",
-  "cliVersion": "2.23.5",
-  "priorBundleVersion": "codeql-bundle-v2.23.3",
-  "priorCliVersion": "2.23.3"
+  "bundleVersion": "codeql-bundle-v2.23.3",
+  "cliVersion": "2.23.3",
+  "priorBundleVersion": "codeql-bundle-v2.23.2",
+  "priorCliVersion": "2.23.2"
 }

package.json

@@ -1,6 +1,6 @@
 {
   "name": "codeql",
-  "version": "4.31.5",
+  "version": "4.31.3",
   "private": true,
   "description": "CodeQL action",
   "scripts": {
@@ -35,44 +35,45 @@
     "@actions/io": "^2.0.0",
     "@actions/tool-cache": "^2.0.2",
     "@octokit/plugin-retry": "^6.0.0",
+    "@octokit/request-error": "^7.0.2",
     "@schemastore/package": "0.0.10",
     "archiver": "^7.0.1",
     "fast-deep-equal": "^3.1.3",
     "follow-redirects": "^1.15.11",
     "get-folder-size": "^5.0.0",
-    "js-yaml": "^4.1.1",
+    "js-yaml": "^4.1.0",
     "jsonschema": "1.4.1",
     "long": "^5.3.2",
     "node-forge": "^1.3.1",
+    "octokit": "^5.0.5",
     "semver": "^7.7.3",
     "uuid": "^13.0.0"
   },
   "devDependencies": {
     "@ava/typescript": "6.0.0",
-    "@eslint/compat": "^2.0.0",
+    "@eslint/compat": "^1.4.1",
     "@eslint/eslintrc": "^3.3.1",
-    "@eslint/js": "^9.39.1",
+    "@eslint/js": "^9.39.0",
     "@microsoft/eslint-formatter-sarif": "^3.1.0",
     "@octokit/types": "^16.0.0",
     "@types/archiver": "^7.0.0",
     "@types/follow-redirects": "^1.14.4",
     "@types/js-yaml": "^4.0.9",
-    "@types/node": "^20.19.9",
+    "@types/node": "20.19.9",
     "@types/node-forge": "^1.3.14",
     "@types/semver": "^7.7.1",
-    "@types/sinon": "^21.0.0",
-    "@typescript-eslint/eslint-plugin": "^8.46.4",
+    "@types/sinon": "^17.0.4",
+    "@typescript-eslint/eslint-plugin": "^8.46.3",
     "@typescript-eslint/parser": "^8.41.0",
     "ava": "^6.4.1",
-    "esbuild": "^0.27.0",
+    "esbuild": "^0.25.12",
     "eslint": "^8.57.1",
     "eslint-import-resolver-typescript": "^3.8.7",
     "eslint-plugin-filenames": "^1.3.2",
     "eslint-plugin-github": "^5.1.8",
     "eslint-plugin-import": "2.29.1",
-    "eslint-plugin-jsdoc": "^61.2.1",
     "eslint-plugin-no-async-foreach": "^0.1.1",
-    "glob": "^11.1.0",
+    "glob": "^11.0.3",
     "nock": "^14.0.10",
     "sinon": "^21.0.0",
     "typescript": "^5.9.3"
@@ -96,7 +97,6 @@
     "eslint-plugin-jsx-a11y": {
       "semver": ">=6.3.1"
     },
-    "brace-expansion@2.0.1": "2.0.2",
-    "glob": "^11.1.0"
+    "brace-expansion@2.0.1": "2.0.2"
   }
 }

pr-checks/checks/all-platform-bundle.yml

@@ -4,7 +4,6 @@ operatingSystems: ["ubuntu", "macos", "windows"]
 versions: ["nightly-latest"]
 useAllPlatformBundle: "true"
 installGo: true
-installDotNet: true
 steps:
   - id: init
     uses: ./../action/init

pr-checks/checks/analyze-ref-input.yml

@@ -3,7 +3,6 @@ description: "Checks that specifying 'ref' and 'sha' as inputs works"
 versions: ["default"]
 installGo: true
 installPython: true
-installDotNet: true
 steps:
   - uses: ./../action/init
     with:

pr-checks/checks/autobuild-action.yml

@@ -2,7 +2,6 @@ name: "autobuild-action"
 description: "Tests that the C# autobuild action works"
 operatingSystems: ["ubuntu", "macos", "windows"]
 versions: ["linked"]
-installDotNet: true
 steps:
   - uses: ./../action/init
     with:

pr-checks/checks/build-mode-manual.yml

@@ -2,7 +2,6 @@ name: "Build mode manual"
 description: "An end-to-end integration test of a Java repository built using 'build-mode: manual'"
 versions: ["nightly-latest"]
 installGo: true
-installDotNet: true
 steps:
   - uses: ./../action/init
     id: init

pr-checks/checks/export-file-baseline-information.yml

@@ -3,7 +3,6 @@ description: "Tests that file baseline information is exported when the feature
 operatingSystems: ["ubuntu", "macos", "windows"]
 versions: ["nightly-latest"]
 installGo: true
-installDotNet: true
 env:
   CODEQL_ACTION_SUBLANGUAGE_FILE_COVERAGE: true
 steps:

pr-checks/checks/go-custom-queries.yml

@@ -7,7 +7,6 @@ versions:
   - linked
   - nightly-latest
 installGo: true
-installDotNet: true
 env:
   DOTNET_GENERATE_ASPNET_CERTIFICATE: "false"
 steps:

pr-checks/checks/local-bundle.yml

@@ -3,7 +3,6 @@ description: "Tests using a CodeQL bundle from a local file rather than a URL"
 versions: ["linked"]
 installGo: true
 installPython: true
-installDotNet: true
 steps:
   - name: Fetch latest CodeQL bundle
     run: |

pr-checks/checks/multi-language-autodetect.yml

@@ -5,7 +5,6 @@ env:
   CODEQL_ACTION_RESOLVE_SUPPORTED_LANGUAGES_USING_CLI: true
 installGo: true
 installPython: true
-installDotNet: true
 steps:
   - name: Use Xcode 16
     if: runner.os == 'macOS' && matrix.version != 'nightly-latest'

pr-checks/checks/packaging-codescanning-config-inputs-js.yml

@@ -4,7 +4,6 @@ versions: ["linked", "default", "nightly-latest"] # This feature is not compatib
 installGo: true
 installNode: true
 installPython: true
-installDotNet: true
 steps:
   - uses: ./../action/init
     with:

pr-checks/checks/packaging-config-inputs-js.yml

@@ -3,7 +3,6 @@ description: "Checks that specifying packages using a combination of a config fi
 versions: ["linked", "default", "nightly-latest"] # This feature is not compatible with old CLIs
 installGo: true
 installNode: true
-installDotNet: true
 steps:
   - uses: ./../action/init
     with:

pr-checks/checks/packaging-config-js.yml

@@ -3,7 +3,6 @@ description: "Checks that specifying packages using only a config file works"
 versions: ["linked", "default", "nightly-latest"] # This feature is not compatible with old CLIs
 installGo: true
 installNode: true
-installDotNet: true
 steps:
   - uses: ./../action/init
     with:

pr-checks/checks/packaging-inputs-js.yml

@@ -3,7 +3,6 @@ description: "Checks that specifying packages using the input to the Action work
 versions: ["linked", "default", "nightly-latest"] # This feature is not compatible with old CLIs
 installGo: true
 installNode: true
-installDotNet: true
 steps:
   - uses: ./../action/init
     with:

pr-checks/checks/remote-config.yml

@@ -7,7 +7,6 @@ versions:
   - nightly-latest
 installGo: true
 installPython: true
-installDotNet: true
 steps:
   - uses: ./../action/init
     with:

pr-checks/checks/rubocop-multi-language.yml

@@ -4,7 +4,7 @@ description: "Tests using RuboCop to analyze a multi-language repository and the
 versions: ["default"]
 steps:
   - name: Set up Ruby
-    uses: ruby/setup-ruby@8aeb6ff8030dd539317f8e1769a044873b56ea71 # v1.268.0
+    uses: ruby/setup-ruby@d5126b9b3579e429dd52e51e68624dda2e05be25 # v1.267.0
     with:
       ruby-version: 2.6
   - name: Install Code Scanning integration

pr-checks/checks/split-workflow.yml

@@ -3,7 +3,6 @@ description: "Tests a split-up workflow in which we first build a database and l
 operatingSystems: ["ubuntu", "macos"]
 versions: ["linked", "default", "nightly-latest"] # This feature is not compatible with old CLIs
 installGo: true
-installDotNet: true
 steps:
   - uses: ./../action/init
     with:

pr-checks/checks/swift-custom-build.yml

@@ -3,7 +3,6 @@ description: "Tests creation of a Swift database using custom build"
 versions: ["linked", "default", "nightly-latest"]
 operatingSystems: ["macos"]
 installGo: true
-installDotNet: true
 env:
   DOTNET_GENERATE_ASPNET_CERTIFICATE: "false"
 steps:

pr-checks/checks/unset-environment.yml

@@ -7,7 +7,6 @@ versions:
   - nightly-latest
 installGo: true
 installPython: true
-installDotNet: true
 steps:
   - uses: ./../action/init
     id: init

pr-checks/checks/upload-ref-sha-input.yml

@@ -3,7 +3,6 @@ description: "Checks that specifying 'ref' and 'sha' as inputs works"
 versions: ["default"]
 installGo: true
 installPython: true
-installDotNet: true
 steps:
   - uses: ./../action/init
     with:

pr-checks/checks/upload-sarif.yml

@@ -4,7 +4,6 @@ versions: ["default"]
 analysisKinds: ["code-scanning", "code-quality", "code-scanning,code-quality"]
 installGo: true
 installPython: true
-installDotNet: true
 steps:
   - uses: ./../action/init
     with:

pr-checks/checks/with-checkout-path.yml

@@ -3,7 +3,6 @@ description: "Checks that a custom `checkout_path` will find the proper commit_o
 versions: ["linked"]
 installGo: true
 installPython: true
-installDotNet: true
 steps:
   # This ensures we don't accidentally use the original checkout for any part of the test.
   - name: Delete original checkout

pr-checks/sync.py

@@ -204,25 +204,6 @@ for file in sorted((this_dir / 'checks').glob('*.yml')):
             }
         })
 
-    installDotNet = is_truthy(checkSpecification.get('installDotNet', ''))
-
-    if installDotNet:
-        baseDotNetVersionExpr = '9.x'
-        workflowInputs['dotnet-version'] = {
-            'type': 'string',
-            'description': 'The version of .NET to install',
-            'required': False,
-            'default': baseDotNetVersionExpr,
-        }
-
-        steps.append({
-            'name': 'Install .NET',
-            'uses': 'actions/setup-dotnet@v5',
-            'with': {
-                'dotnet-version': '${{ inputs.dotnet-version || \'' + baseDotNetVersionExpr + '\' }}'
-            }
-        })
-
     # If container initialisation steps are present in the check specification,
     # make sure to execute them first.
     if 'container' in checkSpecification and 'container-init-steps' in checkSpecification:

src/actions-util.ts

@@ -80,7 +80,7 @@ export function isRunningLocalAction(): boolean {
  *
  * This can be used to get the Action's name or tell if we're running a local Action.
  */
-function getRelativeScriptPath(): string {
+export function getRelativeScriptPath(): string {
   const runnerTemp = getRequiredEnvParam("RUNNER_TEMP");
   const actionsDirectory = path.join(path.dirname(runnerTemp), "_actions");
   return path.relative(actionsDirectory, __filename);

src/analyses.ts

@@ -98,7 +98,7 @@ export async function getAnalysisKinds(
 export const codeQualityQueries: string[] = ["code-quality"];
 
 // Enumerates API endpoints that accept SARIF files.
-enum SARIF_UPLOAD_ENDPOINT {
+export enum SARIF_UPLOAD_ENDPOINT {
   CODE_SCANNING = "PUT /repos/:owner/:repo/code-scanning/analysis",
   CODE_QUALITY = "PUT /repos/:owner/:repo/code-quality/analysis",
 }

src/analyze-action.ts

@@ -25,7 +25,7 @@ import {
   isCodeQualityEnabled,
   isCodeScanningEnabled,
 } from "./config-utils";
-import { cleanupAndUploadDatabases } from "./database-upload";
+import { uploadDatabases } from "./database-upload";
 import {
   DependencyCacheUploadStatusReport,
   uploadDependencyCaches,
@@ -35,7 +35,7 @@ import { EnvVar } from "./environment";
 import { Feature, Features } from "./feature-flags";
 import { KnownLanguage } from "./languages";
 import { getActionsLogger, Logger } from "./logging";
-import { cleanupAndUploadOverlayBaseDatabaseToCache } from "./overlay-database-utils";
+import { uploadOverlayBaseDatabaseToCache } from "./overlay-database-utils";
 import { getRepositoryNwo } from "./repository";
 import * as statusReport from "./status-report";
 import {
@@ -417,21 +417,12 @@ async function run() {
     }
 
     // Possibly upload the overlay-base database to actions cache.
-    // Note: Take care with the ordering of this call since databases may be cleaned up
-    // at the `overlay` level.
-    await cleanupAndUploadOverlayBaseDatabaseToCache(codeql, config, logger);
+    // If databases are to be uploaded, they will first be cleaned up at the overlay level.
+    await uploadOverlayBaseDatabaseToCache(codeql, config, logger);
 
     // Possibly upload the database bundles for remote queries.
-    // Note: Take care with the ordering of this call since databases may be cleaned up
-    // at the `overlay` or `clear` level.
-    await cleanupAndUploadDatabases(
-      repositoryNwo,
-      codeql,
-      config,
-      apiDetails,
-      features,
-      logger,
-    );
+    // If databases are to be uploaded, they will first be cleaned up at the clear level.
+    await uploadDatabases(repositoryNwo, codeql, config, apiDetails, logger);
 
     // Possibly upload the TRAP caches for later re-use
     const trapCacheUploadStartTime = performance.now();
@@ -447,11 +438,14 @@ async function run() {
 
     // Store dependency cache(s) if dependency caching is enabled.
     if (shouldStoreCache(config.dependencyCachingEnabled)) {
-      dependencyCacheResults = await uploadDependencyCaches(
+      const minimizeJavaJars = await features.getValue(
+        Feature.JavaMinimizeDependencyJars,
         codeql,
-        features,
+      );
+      dependencyCacheResults = await uploadDependencyCaches(
         config,
         logger,
+        minimizeJavaJars,
       );
     }
 

src/analyze.ts

@@ -38,26 +38,89 @@ export class CodeQLAnalysisError extends Error {
   }
 }
 
-type KnownLanguageKey = keyof typeof KnownLanguage;
-
-type RunQueriesDurationStatusReport = {
+export interface QueriesStatusReport {
   /**
-   * Time taken in ms to run queries for the language (or undefined if this language was not analyzed).
+   * Time taken in ms to run queries for actions (or undefined if this language was not analyzed).
    *
    * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
    * taken to run _all_ the queries.
    */
-  [L in KnownLanguageKey as `analyze_builtin_queries_${L}_duration_ms`]?: number;
-};
+  analyze_builtin_queries_actions_duration_ms?: number;
+  /**
+   * Time taken in ms to run queries for cpp (or undefined if this language was not analyzed).
+   *
+   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
+   * taken to run _all_ the queries.
+   */
+  analyze_builtin_queries_cpp_duration_ms?: number;
+  /**
+   * Time taken in ms to run queries for csharp (or undefined if this language was not analyzed).
+   *
+   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
+   * taken to run _all_ the queries.
+   */
+  analyze_builtin_queries_csharp_duration_ms?: number;
+  /**
+   * Time taken in ms to run queries for go (or undefined if this language was not analyzed).
+   *
+   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
+   * taken to run _all_ the queries.
+   */
+  analyze_builtin_queries_go_duration_ms?: number;
+  /**
+   * Time taken in ms to run queries for java (or undefined if this language was not analyzed).
+   *
+   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
+   * taken to run _all_ the queries.
+   */
+  analyze_builtin_queries_java_duration_ms?: number;
+  /**
+   * Time taken in ms to run queries for javascript (or undefined if this language was not analyzed).
+   *
+   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
+   * taken to run _all_ the queries.
+   */
+  analyze_builtin_queries_javascript_duration_ms?: number;
+  /**
+   * Time taken in ms to run queries for python (or undefined if this language was not analyzed).
+   *
+   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
+   * taken to run _all_ the queries.
+   */
+  analyze_builtin_queries_python_duration_ms?: number;
+  /**
+   * Time taken in ms to run queries for ruby (or undefined if this language was not analyzed).
+   *
+   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
+   * taken to run _all_ the queries.
+   */
+  analyze_builtin_queries_ruby_duration_ms?: number;
+  /** Time taken in ms to run queries for swift (or undefined if this language was not analyzed).
+   *
+   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
+   * taken to run _all_ the queries.
+   */
+  analyze_builtin_queries_swift_duration_ms?: number;
 
-type InterpretResultsDurationStatusReport = {
-  /** Time taken in ms to interpret results for the language (or undefined if this language was not analyzed). */
-  [L in KnownLanguageKey as `interpret_results_${L}_duration_ms`]?: number;
-};
+  /** Time taken in ms to interpret results for actions (or undefined if this language was not analyzed). */
+  interpret_results_actions_duration_ms?: number;
+  /** Time taken in ms to interpret results for cpp (or undefined if this language was not analyzed). */
+  interpret_results_cpp_duration_ms?: number;
+  /** Time taken in ms to interpret results for csharp (or undefined if this language was not analyzed). */
+  interpret_results_csharp_duration_ms?: number;
+  /** Time taken in ms to interpret results for go (or undefined if this language was not analyzed). */
+  interpret_results_go_duration_ms?: number;
+  /** Time taken in ms to interpret results for java (or undefined if this language was not analyzed). */
+  interpret_results_java_duration_ms?: number;
+  /** Time taken in ms to interpret results for javascript (or undefined if this language was not analyzed). */
+  interpret_results_javascript_duration_ms?: number;
+  /** Time taken in ms to interpret results for python (or undefined if this language was not analyzed). */
+  interpret_results_python_duration_ms?: number;
+  /** Time taken in ms to interpret results for ruby (or undefined if this language was not analyzed). */
+  interpret_results_ruby_duration_ms?: number;
+  /** Time taken in ms to interpret results for swift (or undefined if this language was not analyzed). */
+  interpret_results_swift_duration_ms?: number;
 
-export interface QueriesStatusReport
-  extends RunQueriesDurationStatusReport,
-    InterpretResultsDurationStatusReport {
   /**
    * Whether the analysis is diff-informed (in the sense that the action generates a diff-range data
    * extension for the analysis, regardless of whether the data extension is actually used by queries).

src/api-client.ts

@@ -18,6 +18,11 @@ import {
 
 const GITHUB_ENTERPRISE_VERSION_HEADER = "x-github-enterprise-version";
 
+export enum DisallowedAPIVersionReason {
+  ACTION_TOO_OLD,
+  ACTION_TOO_NEW,
+}
+
 export type GitHubApiCombinedDetails = GitHubApiDetails &
   GitHubApiExternalRepoDetails;
 

src/caching-utils.ts

@@ -1,5 +1,3 @@
-import * as crypto from "crypto";
-
 import * as core from "@actions/core";
 
 import { getOptionalInput, isDefaultSetup } from "./actions-util";
@@ -73,33 +71,6 @@ export function getCachingKind(input: string | undefined): CachingKind {
   }
 }
 
-// The length to which `createCacheKeyHash` truncates hash strings.
-export const cacheKeyHashLength = 16;
-
-/**
- * Creates a SHA-256 hash of the cache key components to ensure uniqueness
- * while keeping the cache key length manageable.
- *
- * @param components Object containing all components that should influence cache key uniqueness
- * @returns A short SHA-256 hash (first 16 characters) of the components
- */
-export function createCacheKeyHash(components: Record<string, any>): string {
-  // From https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/JSON/stringify
-  //
-  // "Properties are visited using the same algorithm as Object.keys(), which
-  // has a well-defined order and is stable across implementations. For example,
-  // JSON.stringify on the same object will always produce the same string, and
-  // JSON.parse(JSON.stringify(obj)) would produce an object with the same key
-  // ordering as the original (assuming the object is completely
-  // JSON-serializable)."
-  const componentsJson = JSON.stringify(components);
-  return crypto
-    .createHash("sha256")
-    .update(componentsJson)
-    .digest("hex")
-    .substring(0, cacheKeyHashLength);
-}
-
 /** Determines whether dependency caching is enabled. */
 export function getDependencyCachingEnabled(): CachingKind {
   // If the workflow specified something always respect that

src/cli-errors.ts

@@ -159,7 +159,10 @@ type CliErrorConfiguration = {
  * All of our caught CLI error messages that we handle specially: ie. if we
  * would like to categorize an error as a configuration error or not.
  */
-const cliErrorsConfig: Record<CliConfigErrorCategory, CliErrorConfiguration> = {
+export const cliErrorsConfig: Record<
+  CliConfigErrorCategory,
+  CliErrorConfiguration
+> = {
   [CliConfigErrorCategory.AutobuildError]: {
     cliErrorMessageCandidates: [
       new RegExp("We were unable to automatically build your code"),

src/codeql.ts

@@ -35,7 +35,7 @@ import { ToolsDownloadStatusReport } from "./tools-download";
 import { ToolsFeature, isSupportedToolsFeature } from "./tools-features";
 import { shouldEnableIndirectTracing } from "./tracer-config";
 import * as util from "./util";
-import { BuildMode, CleanupLevel, getErrorMessage } from "./util";
+import { BuildMode, getErrorMessage } from "./util";
 
 type Options = Array<string | number | boolean>;
 
@@ -141,10 +141,7 @@ export interface CodeQL {
   /**
    * Clean up all the databases within a database cluster.
    */
-  databaseCleanupCluster(
-    config: Config,
-    cleanupLevel: CleanupLevel,
-  ): Promise<void>;
+  databaseCleanupCluster(config: Config, cleanupLevel: string): Promise<void>;
   /**
    * Run 'codeql database bundle'.
    */
@@ -516,7 +513,7 @@ export async function getCodeQLForTesting(
  *        version requirement. Must be set to true outside tests.
  * @returns A new CodeQL object
  */
-async function getCodeQLForCmd(
+export async function getCodeQLForCmd(
   cmd: string,
   checkVersion: boolean,
 ): Promise<CodeQL> {
@@ -881,7 +878,7 @@ async function getCodeQLForCmd(
     },
     async databaseCleanupCluster(
       config: Config,
-      cleanupLevel: CleanupLevel,
+      cleanupLevel: string,
     ): Promise<void> {
       const cacheCleanupFlag = (await util.codeQlVersionAtLeast(
         this,
@@ -1074,11 +1071,8 @@ async function getCodeQLForCmd(
 /**
  * Gets the options for `path` of `options` as an array of extra option strings.
  *
- * @param paths The CLI command components to get extra options for.
- * @param args Additional arguments for this function.
- * @param args.ignoringOptions
- *   Options that should be ignored, for example because they have already
- *   been passed and it is an error to pass them more than once.
+ * @param ignoringOptions Options that should be ignored, for example because they have already
+ *                        been passed and it is an error to pass them more than once.
  */
 function getExtraOptionsFromEnv(
   paths: string[],
@@ -1160,9 +1154,8 @@ async function runCli(
 /**
  * Writes the code scanning configuration that is to be used by the CLI.
  *
- * @param config The CodeQL Action state to write.
- * @param logger The logger to use.
- *
+ * @param codeql The CodeQL object to use.
+ * @param config The CodeQL Action state to use.
  * @returns The path to the generated user configuration file.
  */
 async function writeCodeScanningConfigFile(
@@ -1225,7 +1218,7 @@ export async function getTrapCachingExtractorConfigArgsForLang(
  *
  * This will not exist if the configuration is being parsed in the Action.
  */
-function getGeneratedCodeScanningConfigPath(config: Config): string {
+export function getGeneratedCodeScanningConfigPath(config: Config): string {
   return path.resolve(config.tempDir, "user-config.yaml");
 }
 

src/config-utils.test.ts

@@ -37,9 +37,7 @@ import {
   ConfigurationError,
   withTmpDir,
   BuildMode,
-  DiskUsage,
 } from "./util";
-import * as util from "./util";
 
 setupTests(test);
 
@@ -202,14 +200,16 @@ test("load code quality config", async (t) => {
     );
 
     // And the config we expect it to result in
-    const expectedConfig = createTestConfig({
+    const expectedConfig: configUtils.Config = {
+      version: actionsUtil.getActionVersion(),
       analysisKinds: [AnalysisKind.CodeQuality],
       languages: [KnownLanguage.actions],
+      buildMode: undefined,
+      originalUserInput: {},
       // This gets set because we only have `AnalysisKind.CodeQuality`
       computedConfig: {
         "disable-default-queries": true,
         queries: [{ uses: "code-quality" }],
-        "query-filters": [],
       },
       tempDir,
       codeQLCmd: codeql.getPath(),
@@ -218,7 +218,14 @@ test("load code quality config", async (t) => {
       debugMode: false,
       debugArtifactName: "",
       debugDatabaseName: "",
-    });
+      trapCaches: {},
+      trapCacheDownloadTime: 0,
+      dependencyCachingEnabled: CachingKind.None,
+      extraQueryExclusions: [],
+      overlayDatabaseMode: OverlayDatabaseMode.None,
+      useOverlayDatabaseCaching: false,
+      repositoryProperties: {},
+    };
 
     t.deepEqual(config, expectedConfig);
   });
@@ -248,7 +255,6 @@ test("initActionState doesn't throw if there are queries configured in the repos
     const computedConfig: configUtils.UserConfig = {
       "disable-default-queries": true,
       queries: [{ uses: "code-quality" }],
-      "query-filters": [],
     };
 
     const expectedConfig = createTestConfig({
@@ -499,7 +505,9 @@ test("load non-empty input", async (t) => {
     };
 
     // And the config we expect it to parse to
-    const expectedConfig = createTestConfig({
+    const expectedConfig: configUtils.Config = {
+      version: actionsUtil.getActionVersion(),
+      analysisKinds: [AnalysisKind.CodeScanning],
       languages: [KnownLanguage.javascript],
       buildMode: BuildMode.None,
       originalUserInput: userConfig,
@@ -511,7 +519,14 @@ test("load non-empty input", async (t) => {
       debugMode: false,
       debugArtifactName: "my-artifact",
       debugDatabaseName: "my-db",
-    });
+      trapCaches: {},
+      trapCacheDownloadTime: 0,
+      dependencyCachingEnabled: CachingKind.None,
+      extraQueryExclusions: [],
+      overlayDatabaseMode: OverlayDatabaseMode.None,
+      useOverlayDatabaseCaching: false,
+      repositoryProperties: {},
+    };
 
     const languagesInput = "javascript";
     const configFilePath = createConfigFile(inputFileContents, tempDir);
@@ -856,62 +871,71 @@ const mockRepositoryNwo = parseRepositoryNwo("owner/repo");
     expectedLanguages: ["javascript"],
   },
 ].forEach((args) => {
-  test(`getLanguages: ${args.name}`, async (t) => {
-    const mockRequest = mockLanguagesInRepo(args.languagesInRepository);
-    const stubExtractorEntry = {
-      extractor_root: "",
-    };
-    const codeQL = createStubCodeQL({
-      betterResolveLanguages: (options) =>
-        Promise.resolve({
-          aliases: {
-            "c#": KnownLanguage.csharp,
-            c: KnownLanguage.cpp,
-            kotlin: KnownLanguage.java,
-            typescript: KnownLanguage.javascript,
-          },
-          extractors: {
-            cpp: [stubExtractorEntry],
-            csharp: [stubExtractorEntry],
-            java: [stubExtractorEntry],
-            javascript: [stubExtractorEntry],
-            python: [stubExtractorEntry],
-            ...(options?.filterToLanguagesWithQueries
-              ? {}
-              : {
-                  html: [stubExtractorEntry],
-                }),
-          },
-        }),
+  for (const resolveSupportedLanguagesUsingCli of [true, false]) {
+    test(`getLanguages${resolveSupportedLanguagesUsingCli ? " (supported languages via CLI)" : ""}: ${args.name}`, async (t) => {
+      const features = createFeatures(
+        resolveSupportedLanguagesUsingCli
+          ? [Feature.ResolveSupportedLanguagesUsingCli]
+          : [],
+      );
+      const mockRequest = mockLanguagesInRepo(args.languagesInRepository);
+      const stubExtractorEntry = {
+        extractor_root: "",
+      };
+      const codeQL = createStubCodeQL({
+        betterResolveLanguages: (options) =>
+          Promise.resolve({
+            aliases: {
+              "c#": KnownLanguage.csharp,
+              c: KnownLanguage.cpp,
+              kotlin: KnownLanguage.java,
+              typescript: KnownLanguage.javascript,
+            },
+            extractors: {
+              cpp: [stubExtractorEntry],
+              csharp: [stubExtractorEntry],
+              java: [stubExtractorEntry],
+              javascript: [stubExtractorEntry],
+              python: [stubExtractorEntry],
+              ...(options?.filterToLanguagesWithQueries
+                ? {}
+                : {
+                    html: [stubExtractorEntry],
+                  }),
+            },
+          }),
+      });
+
+      if (args.expectedLanguages) {
+        // happy path
+        const actualLanguages = await configUtils.getLanguages(
+          codeQL,
+          args.languagesInput,
+          mockRepositoryNwo,
+          ".",
+          features,
+          mockLogger,
+        );
+
+        t.deepEqual(actualLanguages.sort(), args.expectedLanguages.sort());
+      } else {
+        // there is an error
+        await t.throwsAsync(
+          async () =>
+            await configUtils.getLanguages(
+              codeQL,
+              args.languagesInput,
+              mockRepositoryNwo,
+              ".",
+              features,
+              mockLogger,
+            ),
+          { message: args.expectedError },
+        );
+      }
+      t.deepEqual(mockRequest.called, args.expectedApiCall);
     });
-
-    if (args.expectedLanguages) {
-      // happy path
-      const actualLanguages = await configUtils.getLanguages(
-        codeQL,
-        args.languagesInput,
-        mockRepositoryNwo,
-        ".",
-        mockLogger,
-      );
-
-      t.deepEqual(actualLanguages.sort(), args.expectedLanguages.sort());
-    } else {
-      // there is an error
-      await t.throwsAsync(
-        async () =>
-          await configUtils.getLanguages(
-            codeQL,
-            args.languagesInput,
-            mockRepositoryNwo,
-            ".",
-            mockLogger,
-          ),
-        { message: args.expectedError },
-      );
-    }
-    t.deepEqual(mockRequest.called, args.expectedApiCall);
-  });
+  }
 });
 
 for (const { displayName, language, feature } of [
@@ -973,12 +997,12 @@ interface OverlayDatabaseModeTestSetup {
   features: Feature[];
   isPullRequest: boolean;
   isDefaultBranch: boolean;
+  repositoryOwner: string;
   buildMode: BuildMode | undefined;
   languages: Language[];
   codeqlVersion: string;
   gitRoot: string | undefined;
   codeScanningConfig: configUtils.UserConfig;
-  diskUsage: DiskUsage | undefined;
 }
 
 const defaultOverlayDatabaseModeTestSetup: OverlayDatabaseModeTestSetup = {
@@ -986,15 +1010,12 @@ const defaultOverlayDatabaseModeTestSetup: OverlayDatabaseModeTestSetup = {
   features: [],
   isPullRequest: false,
   isDefaultBranch: false,
+  repositoryOwner: "github",
   buildMode: BuildMode.None,
   languages: [KnownLanguage.javascript],
   codeqlVersion: CODEQL_OVERLAY_MINIMUM_VERSION,
   gitRoot: "/some/git/root",
   codeScanningConfig: {},
-  diskUsage: {
-    numAvailableBytes: 50_000_000_000,
-    numTotalBytes: 100_000_000_000,
-  },
 };
 
 const getOverlayDatabaseModeMacro = test.macro({
@@ -1027,8 +1048,6 @@ const getOverlayDatabaseModeMacro = test.macro({
             setup.overlayDatabaseEnvVar;
         }
 
-        sinon.stub(util, "checkDiskUsage").resolves(setup.diskUsage);
-
         // Mock feature flags
         const features = createFeatures(setup.features);
 
@@ -1037,6 +1056,12 @@ const getOverlayDatabaseModeMacro = test.macro({
           .stub(actionsUtil, "isAnalyzingPullRequest")
           .returns(setup.isPullRequest);
 
+        // Mock repository owner
+        const repository = {
+          owner: setup.repositoryOwner,
+          repo: "test-repo",
+        };
+
         // Set up CodeQL mock
         const codeql = mockCodeQLVersion(setup.codeqlVersion);
 
@@ -1059,6 +1084,7 @@ const getOverlayDatabaseModeMacro = test.macro({
 
         const result = await configUtils.getOverlayDatabaseMode(
           codeql,
+          repository,
           features,
           setup.languages,
           tempDir, // sourceRoot
@@ -1186,45 +1212,6 @@ test(
   },
 );
 
-test(
-  getOverlayDatabaseModeMacro,
-  "No overlay-base database on default branch if runner disk space is too low",
-  {
-    languages: [KnownLanguage.javascript],
-    features: [
-      Feature.OverlayAnalysis,
-      Feature.OverlayAnalysisCodeScanningJavascript,
-    ],
-    isDefaultBranch: true,
-    diskUsage: {
-      numAvailableBytes: 1_000_000_000,
-      numTotalBytes: 100_000_000_000,
-    },
-  },
-  {
-    overlayDatabaseMode: OverlayDatabaseMode.None,
-    useOverlayDatabaseCaching: false,
-  },
-);
-
-test(
-  getOverlayDatabaseModeMacro,
-  "No overlay-base database on default branch if we can't determine runner disk space",
-  {
-    languages: [KnownLanguage.javascript],
-    features: [
-      Feature.OverlayAnalysis,
-      Feature.OverlayAnalysisCodeScanningJavascript,
-    ],
-    isDefaultBranch: true,
-    diskUsage: undefined,
-  },
-  {
-    overlayDatabaseMode: OverlayDatabaseMode.None,
-    useOverlayDatabaseCaching: false,
-  },
-);
-
 test(
   getOverlayDatabaseModeMacro,
   "No overlay-base database on default branch when code-scanning feature enabled with disable-default-queries",
@@ -1395,45 +1382,6 @@ test(
   },
 );
 
-test(
-  getOverlayDatabaseModeMacro,
-  "No overlay analysis on PR if runner disk space is too low",
-  {
-    languages: [KnownLanguage.javascript],
-    features: [
-      Feature.OverlayAnalysis,
-      Feature.OverlayAnalysisCodeScanningJavascript,
-    ],
-    isPullRequest: true,
-    diskUsage: {
-      numAvailableBytes: 1_000_000_000,
-      numTotalBytes: 100_000_000_000,
-    },
-  },
-  {
-    overlayDatabaseMode: OverlayDatabaseMode.None,
-    useOverlayDatabaseCaching: false,
-  },
-);
-
-test(
-  getOverlayDatabaseModeMacro,
-  "No overlay analysis on PR if we can't determine runner disk space",
-  {
-    languages: [KnownLanguage.javascript],
-    features: [
-      Feature.OverlayAnalysis,
-      Feature.OverlayAnalysisCodeScanningJavascript,
-    ],
-    isPullRequest: true,
-    diskUsage: undefined,
-  },
-  {
-    overlayDatabaseMode: OverlayDatabaseMode.None,
-    useOverlayDatabaseCaching: false,
-  },
-);
-
 test(
   getOverlayDatabaseModeMacro,
   "No overlay analysis on PR when code-scanning feature enabled with disable-default-queries",
@@ -1558,9 +1506,10 @@ test(
 
 test(
   getOverlayDatabaseModeMacro,
-  "Overlay PR analysis by env",
+  "Overlay PR analysis by env for dsp-testing",
   {
     overlayDatabaseEnvVar: "overlay",
+    repositoryOwner: "dsp-testing",
   },
   {
     overlayDatabaseMode: OverlayDatabaseMode.Overlay,
@@ -1570,10 +1519,10 @@ test(
 
 test(
   getOverlayDatabaseModeMacro,
-  "Overlay PR analysis by env on a runner with low disk space",
+  "Overlay PR analysis by env for other-org",
   {
     overlayDatabaseEnvVar: "overlay",
-    diskUsage: { numAvailableBytes: 0, numTotalBytes: 100_000_000_000 },
+    repositoryOwner: "other-org",
   },
   {
     overlayDatabaseMode: OverlayDatabaseMode.Overlay,
@@ -1583,11 +1532,12 @@ test(
 
 test(
   getOverlayDatabaseModeMacro,
-  "Overlay PR analysis by feature flag",
+  "Overlay PR analysis by feature flag for dsp-testing",
   {
     languages: [KnownLanguage.javascript],
     features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
     isPullRequest: true,
+    repositoryOwner: "dsp-testing",
   },
   {
     overlayDatabaseMode: OverlayDatabaseMode.Overlay,
@@ -1595,6 +1545,21 @@ test(
   },
 );
 
+test(
+  getOverlayDatabaseModeMacro,
+  "No overlay PR analysis by feature flag for other-org",
+  {
+    languages: [KnownLanguage.javascript],
+    features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
+    isPullRequest: true,
+    repositoryOwner: "other-org",
+  },
+  {
+    overlayDatabaseMode: OverlayDatabaseMode.None,
+    useOverlayDatabaseCaching: false,
+  },
+);
+
 test(
   getOverlayDatabaseModeMacro,
   "Fallback due to autobuild with traced language",

src/config-utils.ts

@@ -34,7 +34,6 @@ import {
   OverlayDatabaseMode,
 } from "./overlay-database-utils";
 import { RepositoryNwo } from "./repository";
-import { ToolsFeature } from "./tools-features";
 import { downloadTrapCaches } from "./trap-caching";
 import {
   GitHubVersion,
@@ -43,22 +42,10 @@ import {
   codeQlVersionAtLeast,
   cloneObject,
   isDefined,
-  checkDiskUsage,
 } from "./util";
 
 export * from "./config/db-config";
 
-/**
- * The minimum available disk space (in MB) required to perform overlay analysis.
- * If the available disk space on the runner is below the threshold when deciding
- * whether to perform overlay analysis, then the action will not perform overlay
- * analysis unless overlay analysis has been explicitly enabled via environment
- * variable.
- */
-const OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 20000;
-const OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES =
-  OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1_000_000;
-
 export type RegistryConfigWithCredentials = RegistryConfigNoCredentials & {
   // Token to use when downloading packs from this registry.
   token: string;
@@ -160,9 +147,6 @@ export interface Config {
   /** A value indicating how dependency caching should be used. */
   dependencyCachingEnabled: CachingKind;
 
-  /** The keys of caches that we restored, if any. */
-  dependencyCachingRestoredKeys: string[];
-
   /**
    * Extra query exclusions to append to the config.
    */
@@ -191,12 +175,14 @@ export interface Config {
   repositoryProperties: RepositoryProperties;
 }
 
-async function getSupportedLanguageMap(
+export async function getSupportedLanguageMap(
   codeql: CodeQL,
+  features: FeatureEnablement,
   logger: Logger,
 ): Promise<Record<string, string>> {
-  const resolveSupportedLanguagesUsingCli = await codeql.supportsFeature(
-    ToolsFeature.BuiltinExtractorsSpecifyDefaultQueries,
+  const resolveSupportedLanguagesUsingCli = await features.getValue(
+    Feature.ResolveSupportedLanguagesUsingCli,
+    codeql,
   );
   const resolveResult = await codeql.betterResolveLanguages({
     filterToLanguagesWithQueries: resolveSupportedLanguagesUsingCli,
@@ -254,7 +240,7 @@ export function hasActionsWorkflows(sourceRoot: string): boolean {
 /**
  * Gets the set of languages in the current repository.
  */
-async function getRawLanguagesInRepo(
+export async function getRawLanguagesInRepo(
   repository: RepositoryNwo,
   sourceRoot: string,
   logger: Logger,
@@ -297,6 +283,7 @@ export async function getLanguages(
   languagesInput: string | undefined,
   repository: RepositoryNwo,
   sourceRoot: string,
+  features: FeatureEnablement,
   logger: Logger,
 ): Promise<Language[]> {
   // Obtain languages without filtering them.
@@ -307,7 +294,7 @@ export async function getLanguages(
     logger,
   );
 
-  const languageMap = await getSupportedLanguageMap(codeql, logger);
+  const languageMap = await getSupportedLanguageMap(codeql, features, logger);
   const languagesSet = new Set<Language>();
   const unknownLanguages: string[] = [];
 
@@ -363,7 +350,7 @@ export function getRawLanguagesNoAutodetect(
  * @returns A tuple containing a list of languages in this repository that might be
  * analyzable and whether or not this list was determined automatically.
  */
-async function getRawLanguages(
+export async function getRawLanguages(
   languagesInput: string | undefined,
   repository: RepositoryNwo,
   sourceRoot: string,
@@ -444,6 +431,7 @@ export async function initActionState(
     languagesInput,
     repository,
     sourceRoot,
+    features,
     logger,
   );
 
@@ -511,7 +499,6 @@ export async function initActionState(
     trapCaches,
     trapCacheDownloadTime,
     dependencyCachingEnabled: getCachingKind(dependencyCachingEnabled),
-    dependencyCachingRestoredKeys: [],
     extraQueryExclusions: [],
     overlayDatabaseMode: OverlayDatabaseMode.None,
     useOverlayDatabaseCaching: false,
@@ -595,11 +582,17 @@ const OVERLAY_ANALYSIS_CODE_SCANNING_FEATURES: Record<Language, Feature> = {
 };
 
 async function isOverlayAnalysisFeatureEnabled(
+  repository: RepositoryNwo,
   features: FeatureEnablement,
   codeql: CodeQL,
   languages: Language[],
   codeScanningConfig: UserConfig,
 ): Promise<boolean> {
+  // TODO: Remove the repository owner check once support for overlay analysis
+  // stabilizes, and no more backward-incompatible changes are expected.
+  if (!["github", "dsp-testing"].includes(repository.owner)) {
+    return false;
+  }
   if (!(await features.getValue(Feature.OverlayAnalysis, codeql))) {
     return false;
   }
@@ -657,6 +650,7 @@ async function isOverlayAnalysisFeatureEnabled(
  */
 export async function getOverlayDatabaseMode(
   codeql: CodeQL,
+  repository: RepositoryNwo,
   features: FeatureEnablement,
   languages: Language[],
   sourceRoot: string,
@@ -685,43 +679,27 @@ export async function getOverlayDatabaseMode(
     );
   } else if (
     await isOverlayAnalysisFeatureEnabled(
+      repository,
       features,
       codeql,
       languages,
       codeScanningConfig,
     )
   ) {
-    const diskUsage = await checkDiskUsage(logger);
-    if (
-      diskUsage === undefined ||
-      diskUsage.numAvailableBytes < OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES
-    ) {
-      const diskSpaceMb =
-        diskUsage === undefined
-          ? 0
-          : Math.round(diskUsage.numAvailableBytes / 1_000_000);
-      overlayDatabaseMode = OverlayDatabaseMode.None;
-      useOverlayDatabaseCaching = false;
+    if (isAnalyzingPullRequest()) {
+      overlayDatabaseMode = OverlayDatabaseMode.Overlay;
+      useOverlayDatabaseCaching = true;
       logger.info(
         `Setting overlay database mode to ${overlayDatabaseMode} ` +
-          `due to insufficient disk space (${diskSpaceMb} MB).`,
+          "with caching because we are analyzing a pull request.",
+      );
+    } else if (await isAnalyzingDefaultBranch()) {
+      overlayDatabaseMode = OverlayDatabaseMode.OverlayBase;
+      useOverlayDatabaseCaching = true;
+      logger.info(
+        `Setting overlay database mode to ${overlayDatabaseMode} ` +
+          "with caching because we are analyzing the default branch.",
       );
-    } else {
-      if (isAnalyzingPullRequest()) {
-        overlayDatabaseMode = OverlayDatabaseMode.Overlay;
-        useOverlayDatabaseCaching = true;
-        logger.info(
-          `Setting overlay database mode to ${overlayDatabaseMode} ` +
-            "with caching because we are analyzing a pull request.",
-        );
-      } else if (await isAnalyzingDefaultBranch()) {
-        overlayDatabaseMode = OverlayDatabaseMode.OverlayBase;
-        useOverlayDatabaseCaching = true;
-        logger.info(
-          `Setting overlay database mode to ${overlayDatabaseMode} ` +
-            "with caching because we are analyzing the default branch.",
-        );
-      }
     }
   }
 
@@ -798,8 +776,7 @@ function userConfigFromActionPath(tempDir: string): string {
 function hasQueryCustomisation(userConfig: UserConfig): boolean {
   return (
     isDefined(userConfig["disable-default-queries"]) ||
-    isDefined(userConfig.queries) ||
-    isDefined(userConfig["query-filters"])
+    isDefined(userConfig.queries)
   );
 }
 
@@ -861,7 +838,6 @@ export async function initConfig(
     // Set the query customisation options for Code Quality only analysis.
     config.computedConfig["disable-default-queries"] = true;
     config.computedConfig.queries = queries;
-    config.computedConfig["query-filters"] = [];
   }
 
   // The choice of overlay database mode depends on the selection of languages
@@ -871,6 +847,7 @@ export async function initConfig(
   const { overlayDatabaseMode, useOverlayDatabaseCaching } =
     await getOverlayDatabaseMode(
       inputs.codeql,
+      inputs.repository,
       inputs.features,
       config.languages,
       inputs.sourceRoot,
@@ -1057,6 +1034,7 @@ export async function getConfig(
  * pack.
  *
  * @param registriesInput The value of the `registries` input.
+ * @param codeQL a codeQL object, used only for checking the version of CodeQL.
  * @param tempDir a temporary directory to store the generated qlconfig.yml file.
  * @param logger a logger object.
  * @returns The path to the generated `qlconfig.yml` file and the auth tokens to
@@ -1259,7 +1237,7 @@ export function isCodeQualityEnabled(config: Config): boolean {
  * @returns Returns `AnalysisKind.CodeScanning` if `AnalysisKind.CodeScanning` is enabled;
  * otherwise `AnalysisKind.CodeQuality`.
  */
-function getPrimaryAnalysisKind(config: Config): AnalysisKind {
+export function getPrimaryAnalysisKind(config: Config): AnalysisKind {
   return isCodeScanningEnabled(config)
     ? AnalysisKind.CodeScanning
     : AnalysisKind.CodeQuality;

src/config/db-config.ts

@@ -160,6 +160,7 @@ const PACK_IDENTIFIER_PATTERN = (function () {
  * Version and path are optional.
  *
  * @param packStr the package specification to verify.
+ * @param configFile Config file to use for error reporting
  */
 export function parsePacksSpecification(packStr: string): Pack {
   if (typeof packStr !== "string") {

src/database-upload.test.ts

@@ -10,12 +10,11 @@ import { GitHubApiDetails } from "./api-client";
 import * as apiClient from "./api-client";
 import { createStubCodeQL } from "./codeql";
 import { Config } from "./config-utils";
-import { cleanupAndUploadDatabases } from "./database-upload";
+import { uploadDatabases } from "./database-upload";
 import * as gitUtils from "./git-utils";
 import { KnownLanguage } from "./languages";
 import { RepositoryNwo } from "./repository";
 import {
-  createFeatures,
   createTestConfig,
   getRecordingLogger,
   LoggedMessage,
@@ -92,12 +91,11 @@ test("Abort database upload if 'upload-database' input set to false", async (t)
     sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);
 
     const loggedMessages = [];
-    await cleanupAndUploadDatabases(
+    await uploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
       testApiDetails,
-      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
     t.assert(
@@ -123,7 +121,7 @@ test("Abort database upload if 'analysis-kinds: code-scanning' is not enabled",
     await mockHttpRequests(201);
 
     const loggedMessages = [];
-    await cleanupAndUploadDatabases(
+    await uploadDatabases(
       testRepoName,
       getCodeQL(),
       {
@@ -131,7 +129,6 @@ test("Abort database upload if 'analysis-kinds: code-scanning' is not enabled",
         analysisKinds: [AnalysisKind.CodeQuality],
       },
       testApiDetails,
-      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
     t.assert(
@@ -158,12 +155,11 @@ test("Abort database upload if running against GHES", async (t) => {
     config.gitHubVersion = { type: GitHubVariant.GHES, version: "3.0" };
 
     const loggedMessages = [];
-    await cleanupAndUploadDatabases(
+    await uploadDatabases(
       testRepoName,
       getCodeQL(),
       config,
       testApiDetails,
-      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
     t.assert(
@@ -187,12 +183,11 @@ test("Abort database upload if not analyzing default branch", async (t) => {
     sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(false);
 
     const loggedMessages = [];
-    await cleanupAndUploadDatabases(
+    await uploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
       testApiDetails,
-      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
     t.assert(
@@ -217,12 +212,11 @@ test("Don't crash if uploading a database fails", async (t) => {
     await mockHttpRequests(500);
 
     const loggedMessages = [] as LoggedMessage[];
-    await cleanupAndUploadDatabases(
+    await uploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
       testApiDetails,
-      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
 
@@ -249,12 +243,11 @@ test("Successfully uploading a database to github.com", async (t) => {
     await mockHttpRequests(201);
 
     const loggedMessages = [] as LoggedMessage[];
-    await cleanupAndUploadDatabases(
+    await uploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
       testApiDetails,
-      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
     t.assert(
@@ -279,7 +272,7 @@ test("Successfully uploading a database to GHEC-DR", async (t) => {
     const databaseUploadSpy = await mockHttpRequests(201);
 
     const loggedMessages = [] as LoggedMessage[];
-    await cleanupAndUploadDatabases(
+    await uploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
@@ -288,7 +281,6 @@ test("Successfully uploading a database to GHEC-DR", async (t) => {
         url: "https://tenant.ghe.com",
         apiURL: undefined,
       },
-      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
     t.assert(

src/database-upload.ts

@@ -5,20 +5,17 @@ import { AnalysisKind } from "./analyses";
 import { getApiClient, GitHubApiDetails } from "./api-client";
 import { type CodeQL } from "./codeql";
 import { Config } from "./config-utils";
-import { Feature, FeatureEnablement } from "./feature-flags";
 import * as gitUtils from "./git-utils";
 import { Logger, withGroupAsync } from "./logging";
-import { OverlayDatabaseMode } from "./overlay-database-utils";
 import { RepositoryNwo } from "./repository";
 import * as util from "./util";
-import { bundleDb, CleanupLevel, parseGitHubUrl } from "./util";
+import { bundleDb, parseGitHubUrl } from "./util";
 
-export async function cleanupAndUploadDatabases(
+export async function uploadDatabases(
   repositoryNwo: RepositoryNwo,
   codeql: CodeQL,
   config: Config,
   apiDetails: GitHubApiDetails,
-  features: FeatureEnablement,
   logger: Logger,
 ): Promise<void> {
   if (actionsUtil.getRequiredInput("upload-database") !== "true") {
@@ -53,16 +50,10 @@ export async function cleanupAndUploadDatabases(
     return;
   }
 
-  const cleanupLevel =
-    config.overlayDatabaseMode === OverlayDatabaseMode.OverlayBase &&
-    (await features.getValue(Feature.UploadOverlayDbToApi))
-      ? CleanupLevel.Overlay
-      : CleanupLevel.Clear;
-
   // Clean up the database, since intermediate results may still be written to the
   // database if there is high RAM pressure.
   await withGroupAsync("Cleaning up databases", async () => {
-    await codeql.databaseCleanupCluster(config, cleanupLevel);
+    await codeql.databaseCleanupCluster(config, "clear");
   });
 
   const client = getApiClient();

src/defaults.json

@@ -1,6 +1,6 @@
 {
-  "bundleVersion": "codeql-bundle-v2.23.5",
-  "cliVersion": "2.23.5",
-  "priorBundleVersion": "codeql-bundle-v2.23.3",
-  "priorCliVersion": "2.23.3"
+  "bundleVersion": "codeql-bundle-v2.23.3",
+  "cliVersion": "2.23.3",
+  "priorBundleVersion": "codeql-bundle-v2.23.2",
+  "priorCliVersion": "2.23.2"
 }

src/dependency-caching.test.ts

@@ -1,627 +0,0 @@
-import * as fs from "fs";
-import path from "path";
-
-import * as actionsCache from "@actions/cache";
-import * as glob from "@actions/glob";
-import test from "ava";
-import * as sinon from "sinon";
-
-import { cacheKeyHashLength } from "./caching-utils";
-import * as cachingUtils from "./caching-utils";
-import { createStubCodeQL } from "./codeql";
-import {
-  CacheConfig,
-  checkHashPatterns,
-  getCsharpHashPatterns,
-  getFeaturePrefix,
-  makePatternCheck,
-  internal,
-  CSHARP_BASE_PATTERNS,
-  CSHARP_EXTRA_PATTERNS,
-  downloadDependencyCaches,
-  CacheHitKind,
-  cacheKey,
-  uploadDependencyCaches,
-  CacheStoreResult,
-} from "./dependency-caching";
-import { Feature } from "./feature-flags";
-import { KnownLanguage } from "./languages";
-import {
-  setupTests,
-  createFeatures,
-  getRecordingLogger,
-  checkExpectedLogMessages,
-  LoggedMessage,
-  createTestConfig,
-} from "./testing-utils";
-import { withTmpDir } from "./util";
-
-setupTests(test);
-
-function makeAbsolutePatterns(tmpDir: string, patterns: string[]): string[] {
-  return patterns.map((pattern) => path.join(tmpDir, pattern));
-}
-
-test("makePatternCheck - returns undefined if no patterns match", async (t) => {
-  await withTmpDir(async (tmpDir) => {
-    fs.writeFileSync(path.join(tmpDir, "test.java"), "");
-    const result = await makePatternCheck(
-      makeAbsolutePatterns(tmpDir, ["**/*.cs"]),
-    );
-    t.is(result, undefined);
-  });
-});
-
-test("makePatternCheck - returns all patterns if any pattern matches", async (t) => {
-  await withTmpDir(async (tmpDir) => {
-    fs.writeFileSync(path.join(tmpDir, "test.java"), "");
-    const patterns = makeAbsolutePatterns(tmpDir, ["**/*.cs", "**/*.java"]);
-    const result = await makePatternCheck(patterns);
-    t.deepEqual(result, patterns);
-  });
-});
-
-test("getCsharpHashPatterns - returns base patterns if any pattern matches", async (t) => {
-  const codeql = createStubCodeQL({});
-  const features = createFeatures([]);
-  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
-
-  makePatternCheckStub
-    .withArgs(CSHARP_BASE_PATTERNS)
-    .resolves(CSHARP_BASE_PATTERNS);
-  makePatternCheckStub.withArgs(CSHARP_EXTRA_PATTERNS).rejects();
-
-  await t.notThrowsAsync(async () => {
-    const result = await getCsharpHashPatterns(codeql, features);
-    t.deepEqual(result, CSHARP_BASE_PATTERNS);
-  });
-});
-
-test("getCsharpHashPatterns - returns base patterns if any base pattern matches and CsharpNewCacheKey is enabled", async (t) => {
-  const codeql = createStubCodeQL({});
-  const features = createFeatures([Feature.CsharpNewCacheKey]);
-  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
-
-  makePatternCheckStub
-    .withArgs(CSHARP_BASE_PATTERNS)
-    .resolves(CSHARP_BASE_PATTERNS);
-  makePatternCheckStub
-    .withArgs(CSHARP_EXTRA_PATTERNS)
-    .resolves(CSHARP_EXTRA_PATTERNS);
-
-  await t.notThrowsAsync(async () => {
-    const result = await getCsharpHashPatterns(codeql, features);
-    t.deepEqual(result, CSHARP_BASE_PATTERNS);
-  });
-});
-
-test("getCsharpHashPatterns - returns extra patterns if any extra pattern matches and CsharpNewCacheKey is enabled", async (t) => {
-  const codeql = createStubCodeQL({});
-  const features = createFeatures([Feature.CsharpNewCacheKey]);
-  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
-
-  makePatternCheckStub.withArgs(CSHARP_BASE_PATTERNS).resolves(undefined);
-  makePatternCheckStub
-    .withArgs(CSHARP_EXTRA_PATTERNS)
-    .resolves(CSHARP_EXTRA_PATTERNS);
-
-  await t.notThrowsAsync(async () => {
-    const result = await getCsharpHashPatterns(codeql, features);
-    t.deepEqual(result, CSHARP_EXTRA_PATTERNS);
-  });
-});
-
-test("getCsharpHashPatterns - returns undefined if neither base nor extra patterns match", async (t) => {
-  const codeql = createStubCodeQL({});
-  const features = createFeatures([Feature.CsharpNewCacheKey]);
-  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
-
-  makePatternCheckStub.withArgs(CSHARP_BASE_PATTERNS).resolves(undefined);
-  makePatternCheckStub.withArgs(CSHARP_EXTRA_PATTERNS).resolves(undefined);
-
-  await t.notThrowsAsync(async () => {
-    const result = await getCsharpHashPatterns(codeql, features);
-    t.deepEqual(result, undefined);
-  });
-});
-
-test("checkHashPatterns - logs when no patterns match", async (t) => {
-  const codeql = createStubCodeQL({});
-  const features = createFeatures([]);
-  const messages: LoggedMessage[] = [];
-  const config: CacheConfig = {
-    getDependencyPaths: () => [],
-    getHashPatterns: async () => undefined,
-  };
-
-  const result = await checkHashPatterns(
-    codeql,
-    features,
-    KnownLanguage.csharp,
-    config,
-    "download",
-    getRecordingLogger(messages),
-  );
-
-  t.is(result, undefined);
-  checkExpectedLogMessages(t, messages, [
-    "Skipping download of dependency cache",
-  ]);
-});
-
-test("checkHashPatterns - returns patterns when patterns match", async (t) => {
-  await withTmpDir(async (tmpDir) => {
-    const codeql = createStubCodeQL({});
-    const features = createFeatures([]);
-    const messages: LoggedMessage[] = [];
-    const patterns = makeAbsolutePatterns(tmpDir, ["**/*.cs", "**/*.java"]);
-
-    fs.writeFileSync(path.join(tmpDir, "test.java"), "");
-
-    const config: CacheConfig = {
-      getDependencyPaths: () => [],
-      getHashPatterns: async () => makePatternCheck(patterns),
-    };
-
-    const result = await checkHashPatterns(
-      codeql,
-      features,
-      KnownLanguage.csharp,
-      config,
-      "upload",
-      getRecordingLogger(messages),
-    );
-
-    t.deepEqual(result, patterns);
-    t.deepEqual(messages, []);
-  });
-});
-
-type RestoreCacheFunc = (
-  paths: string[],
-  primaryKey: string,
-  restoreKeys: string[] | undefined,
-) => Promise<string | undefined>;
-
-/**
- * Constructs a function that `actionsCache.restoreCache` can be stubbed with.
- *
- * @param mockCacheKeys The keys of caches that we want to exist in the Actions cache.
- *
- * @returns Returns a function that `actionsCache.restoreCache` can be stubbed with.
- */
-function makeMockCacheCheck(mockCacheKeys: string[]): RestoreCacheFunc {
-  return async (
-    _paths: string[],
-    primaryKey: string,
-    restoreKeys: string[] | undefined,
-  ) => {
-    // The behaviour here mirrors what the real `restoreCache` would do:
-    // - Starting with the primary restore key, check all caches for a match:
-    //   even for the primary restore key, this only has to be a prefix match.
-    // - If the primary restore key doesn't prefix-match any cache, then proceed
-    //   in the same way for each restore key in turn.
-    for (const restoreKey of [primaryKey, ...(restoreKeys || [])]) {
-      for (const mockCacheKey of mockCacheKeys) {
-        if (mockCacheKey.startsWith(restoreKey)) {
-          return mockCacheKey;
-        }
-      }
-    }
-    // Only if no restore key matches any cache key prefix, there is no matching
-    // cache and we return `undefined`.
-    return undefined;
-  };
-}
-
-test("downloadDependencyCaches - does not restore caches with feature keys if no features are enabled", async (t) => {
-  process.env["RUNNER_OS"] = "Linux";
-
-  const codeql = createStubCodeQL({});
-  const messages: LoggedMessage[] = [];
-  const logger = getRecordingLogger(messages);
-
-  sinon.stub(glob, "hashFiles").resolves("abcdef");
-
-  const keyWithFeature = await cacheKey(
-    codeql,
-    createFeatures([Feature.CsharpNewCacheKey]),
-    KnownLanguage.csharp,
-    // Patterns don't matter here because we have stubbed `hashFiles` to always return a specific hash above.
-    [],
-  );
-
-  const restoreCacheStub = sinon
-    .stub(actionsCache, "restoreCache")
-    .callsFake(makeMockCacheCheck([keyWithFeature]));
-
-  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
-  makePatternCheckStub
-    .withArgs(CSHARP_BASE_PATTERNS)
-    .resolves(CSHARP_BASE_PATTERNS);
-  makePatternCheckStub.withArgs(CSHARP_EXTRA_PATTERNS).resolves(undefined);
-
-  const result = await downloadDependencyCaches(
-    codeql,
-    createFeatures([]),
-    [KnownLanguage.csharp],
-    logger,
-  );
-  const statusReport = result.statusReport;
-  t.is(statusReport.length, 1);
-  t.is(statusReport[0].language, KnownLanguage.csharp);
-  t.is(statusReport[0].hit_kind, CacheHitKind.Miss);
-  t.deepEqual(result.restoredKeys, []);
-  t.assert(restoreCacheStub.calledOnce);
-});
-
-test("downloadDependencyCaches - restores caches with feature keys if features are enabled", async (t) => {
-  process.env["RUNNER_OS"] = "Linux";
-
-  const codeql = createStubCodeQL({});
-  const messages: LoggedMessage[] = [];
-  const logger = getRecordingLogger(messages);
-  const features = createFeatures([Feature.CsharpNewCacheKey]);
-
-  const mockHash = "abcdef";
-  sinon.stub(glob, "hashFiles").resolves(mockHash);
-
-  const keyWithFeature = await cacheKey(
-    codeql,
-    features,
-    KnownLanguage.csharp,
-    // Patterns don't matter here because we have stubbed `hashFiles` to always return a specific hash above.
-    [],
-  );
-
-  const restoreCacheStub = sinon
-    .stub(actionsCache, "restoreCache")
-    .callsFake(makeMockCacheCheck([keyWithFeature]));
-
-  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
-  makePatternCheckStub
-    .withArgs(CSHARP_BASE_PATTERNS)
-    .resolves(CSHARP_BASE_PATTERNS);
-  makePatternCheckStub.withArgs(CSHARP_EXTRA_PATTERNS).resolves(undefined);
-
-  const result = await downloadDependencyCaches(
-    codeql,
-    features,
-    [KnownLanguage.csharp],
-    logger,
-  );
-
-  // Check that the status report for telemetry indicates that one cache was restored with an exact match.
-  const statusReport = result.statusReport;
-  t.is(statusReport.length, 1);
-  t.is(statusReport[0].language, KnownLanguage.csharp);
-  t.is(statusReport[0].hit_kind, CacheHitKind.Exact);
-
-  // Check that the restored key has been returned.
-  const restoredKeys = result.restoredKeys;
-  t.is(restoredKeys.length, 1);
-  t.assert(
-    restoredKeys[0].endsWith(mockHash),
-    "Expected restored key to end with hash returned by `hashFiles`",
-  );
-
-  // `restoreCache` should have been called exactly once.
-  t.assert(restoreCacheStub.calledOnce);
-});
-
-test("downloadDependencyCaches - restores caches with feature keys if features are enabled for partial matches", async (t) => {
-  process.env["RUNNER_OS"] = "Linux";
-
-  const codeql = createStubCodeQL({});
-  const messages: LoggedMessage[] = [];
-  const logger = getRecordingLogger(messages);
-  const features = createFeatures([Feature.CsharpNewCacheKey]);
-
-  // We expect two calls to `hashFiles`: the first by the call to `cacheKey` below,
-  // and the second by `downloadDependencyCaches`. We use the result of the first
-  // call as part of the cache key that identifies a mock, existing cache. The result
-  // of the second call is for the primary restore key, which we don't want to match
-  // the first key so that we can test the restore keys logic.
-  const restoredHash = "abcdef";
-  const hashFilesStub = sinon.stub(glob, "hashFiles");
-  hashFilesStub.onFirstCall().resolves(restoredHash);
-  hashFilesStub.onSecondCall().resolves("123456");
-
-  const keyWithFeature = await cacheKey(
-    codeql,
-    features,
-    KnownLanguage.csharp,
-    // Patterns don't matter here because we have stubbed `hashFiles` to always return a specific hash above.
-    [],
-  );
-
-  const restoreCacheStub = sinon
-    .stub(actionsCache, "restoreCache")
-    .callsFake(makeMockCacheCheck([keyWithFeature]));
-
-  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
-  makePatternCheckStub
-    .withArgs(CSHARP_BASE_PATTERNS)
-    .resolves(CSHARP_BASE_PATTERNS);
-  makePatternCheckStub.withArgs(CSHARP_EXTRA_PATTERNS).resolves(undefined);
-
-  const result = await downloadDependencyCaches(
-    codeql,
-    features,
-    [KnownLanguage.csharp],
-    logger,
-  );
-
-  // Check that the status report for telemetry indicates that one cache was restored with a partial match.
-  const statusReport = result.statusReport;
-  t.is(statusReport.length, 1);
-  t.is(statusReport[0].language, KnownLanguage.csharp);
-  t.is(statusReport[0].hit_kind, CacheHitKind.Partial);
-
-  // Check that the restored key has been returned.
-  const restoredKeys = result.restoredKeys;
-  t.is(restoredKeys.length, 1);
-  t.assert(
-    restoredKeys[0].endsWith(restoredHash),
-    "Expected restored key to end with hash returned by `hashFiles`",
-  );
-
-  t.assert(restoreCacheStub.calledOnce);
-});
-
-test("uploadDependencyCaches - skips upload for a language with no cache config", async (t) => {
-  const codeql = createStubCodeQL({});
-  const messages: LoggedMessage[] = [];
-  const logger = getRecordingLogger(messages);
-  const features = createFeatures([]);
-  const config = createTestConfig({
-    languages: [KnownLanguage.actions],
-  });
-
-  const result = await uploadDependencyCaches(codeql, features, config, logger);
-  t.is(result.length, 0);
-  checkExpectedLogMessages(t, messages, [
-    "Skipping upload of dependency cache for actions",
-  ]);
-});
-
-test("uploadDependencyCaches - skips upload if no files for the hash exist", async (t) => {
-  const codeql = createStubCodeQL({});
-  const messages: LoggedMessage[] = [];
-  const logger = getRecordingLogger(messages);
-  const features = createFeatures([]);
-  const config = createTestConfig({
-    languages: [KnownLanguage.go],
-  });
-
-  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
-  makePatternCheckStub.resolves(undefined);
-
-  const result = await uploadDependencyCaches(codeql, features, config, logger);
-  t.is(result.length, 1);
-  t.is(result[0].language, KnownLanguage.go);
-  t.is(result[0].result, CacheStoreResult.NoHash);
-});
-
-test("uploadDependencyCaches - skips upload if we know the cache already exists", async (t) => {
-  process.env["RUNNER_OS"] = "Linux";
-
-  const codeql = createStubCodeQL({});
-  const messages: LoggedMessage[] = [];
-  const logger = getRecordingLogger(messages);
-  const features = createFeatures([]);
-
-  const mockHash = "abcdef";
-  sinon.stub(glob, "hashFiles").resolves(mockHash);
-
-  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
-  makePatternCheckStub
-    .withArgs(CSHARP_BASE_PATTERNS)
-    .resolves(CSHARP_BASE_PATTERNS);
-
-  const primaryCacheKey = await cacheKey(
-    codeql,
-    features,
-    KnownLanguage.csharp,
-    CSHARP_BASE_PATTERNS,
-  );
-
-  const config = createTestConfig({
-    languages: [KnownLanguage.csharp],
-    dependencyCachingRestoredKeys: [primaryCacheKey],
-  });
-
-  const result = await uploadDependencyCaches(codeql, features, config, logger);
-  t.is(result.length, 1);
-  t.is(result[0].language, KnownLanguage.csharp);
-  t.is(result[0].result, CacheStoreResult.Duplicate);
-});
-
-test("uploadDependencyCaches - skips upload if cache size is 0", async (t) => {
-  process.env["RUNNER_OS"] = "Linux";
-
-  const codeql = createStubCodeQL({});
-  const messages: LoggedMessage[] = [];
-  const logger = getRecordingLogger(messages);
-  const features = createFeatures([]);
-
-  const mockHash = "abcdef";
-  sinon.stub(glob, "hashFiles").resolves(mockHash);
-
-  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
-  makePatternCheckStub
-    .withArgs(CSHARP_BASE_PATTERNS)
-    .resolves(CSHARP_BASE_PATTERNS);
-
-  sinon.stub(cachingUtils, "getTotalCacheSize").resolves(0);
-
-  const config = createTestConfig({
-    languages: [KnownLanguage.csharp],
-  });
-
-  const result = await uploadDependencyCaches(codeql, features, config, logger);
-  t.is(result.length, 1);
-  t.is(result[0].language, KnownLanguage.csharp);
-  t.is(result[0].result, CacheStoreResult.Empty);
-
-  checkExpectedLogMessages(t, messages, [
-    "Skipping upload of dependency cache",
-  ]);
-});
-
-test("uploadDependencyCaches - uploads caches when all requirements are met", async (t) => {
-  process.env["RUNNER_OS"] = "Linux";
-
-  const codeql = createStubCodeQL({});
-  const messages: LoggedMessage[] = [];
-  const logger = getRecordingLogger(messages);
-  const features = createFeatures([]);
-
-  const mockHash = "abcdef";
-  sinon.stub(glob, "hashFiles").resolves(mockHash);
-
-  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
-  makePatternCheckStub
-    .withArgs(CSHARP_BASE_PATTERNS)
-    .resolves(CSHARP_BASE_PATTERNS);
-
-  sinon.stub(cachingUtils, "getTotalCacheSize").resolves(1024);
-  sinon.stub(actionsCache, "saveCache").resolves();
-
-  const config = createTestConfig({
-    languages: [KnownLanguage.csharp],
-  });
-
-  const result = await uploadDependencyCaches(codeql, features, config, logger);
-  t.is(result.length, 1);
-  t.is(result[0].language, KnownLanguage.csharp);
-  t.is(result[0].result, CacheStoreResult.Stored);
-  t.is(result[0].upload_size_bytes, 1024);
-
-  checkExpectedLogMessages(t, messages, ["Uploading cache of size"]);
-});
-
-test("uploadDependencyCaches - catches `ReserveCacheError` exceptions", async (t) => {
-  process.env["RUNNER_OS"] = "Linux";
-
-  const codeql = createStubCodeQL({});
-  const messages: LoggedMessage[] = [];
-  const logger = getRecordingLogger(messages);
-  const features = createFeatures([]);
-
-  const mockHash = "abcdef";
-  sinon.stub(glob, "hashFiles").resolves(mockHash);
-
-  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
-  makePatternCheckStub
-    .withArgs(CSHARP_BASE_PATTERNS)
-    .resolves(CSHARP_BASE_PATTERNS);
-
-  sinon.stub(cachingUtils, "getTotalCacheSize").resolves(1024);
-  sinon
-    .stub(actionsCache, "saveCache")
-    .throws(new actionsCache.ReserveCacheError("Already in use"));
-
-  const config = createTestConfig({
-    languages: [KnownLanguage.csharp],
-  });
-
-  await t.notThrowsAsync(async () => {
-    const result = await uploadDependencyCaches(
-      codeql,
-      features,
-      config,
-      logger,
-    );
-    t.is(result.length, 1);
-    t.is(result[0].language, KnownLanguage.csharp);
-    t.is(result[0].result, CacheStoreResult.Duplicate);
-
-    checkExpectedLogMessages(t, messages, ["Not uploading cache for"]);
-  });
-});
-
-test("uploadDependencyCaches - throws other exceptions", async (t) => {
-  process.env["RUNNER_OS"] = "Linux";
-
-  const codeql = createStubCodeQL({});
-  const messages: LoggedMessage[] = [];
-  const logger = getRecordingLogger(messages);
-  const features = createFeatures([]);
-
-  const mockHash = "abcdef";
-  sinon.stub(glob, "hashFiles").resolves(mockHash);
-
-  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
-  makePatternCheckStub
-    .withArgs(CSHARP_BASE_PATTERNS)
-    .resolves(CSHARP_BASE_PATTERNS);
-
-  sinon.stub(cachingUtils, "getTotalCacheSize").resolves(1024);
-  sinon.stub(actionsCache, "saveCache").throws();
-
-  const config = createTestConfig({
-    languages: [KnownLanguage.csharp],
-  });
-
-  await t.throwsAsync(async () => {
-    await uploadDependencyCaches(codeql, features, config, logger);
-  });
-});
-
-test("getFeaturePrefix - returns empty string if no features are enabled", async (t) => {
-  const codeql = createStubCodeQL({});
-  const features = createFeatures([]);
-
-  for (const knownLanguage of Object.values(KnownLanguage)) {
-    const result = await getFeaturePrefix(codeql, features, knownLanguage);
-    t.deepEqual(result, "", `Expected no feature prefix for ${knownLanguage}`);
-  }
-});
-
-test("getFeaturePrefix - Java - returns 'minify-' if JavaMinimizeDependencyJars is enabled", async (t) => {
-  const codeql = createStubCodeQL({});
-  const features = createFeatures([Feature.JavaMinimizeDependencyJars]);
-
-  const result = await getFeaturePrefix(codeql, features, KnownLanguage.java);
-  t.deepEqual(result, "minify-");
-});
-
-test("getFeaturePrefix - non-Java - returns '' if JavaMinimizeDependencyJars is enabled", async (t) => {
-  const codeql = createStubCodeQL({});
-  const features = createFeatures([Feature.JavaMinimizeDependencyJars]);
-
-  for (const knownLanguage of Object.values(KnownLanguage)) {
-    // Skip Java since we expect a result for it, which is tested in the previous test.
-    if (knownLanguage === KnownLanguage.java) {
-      continue;
-    }
-    const result = await getFeaturePrefix(codeql, features, knownLanguage);
-    t.deepEqual(result, "", `Expected no feature prefix for ${knownLanguage}`);
-  }
-});
-
-test("getFeaturePrefix - C# - returns prefix if CsharpNewCacheKey is enabled", async (t) => {
-  const codeql = createStubCodeQL({});
-  const features = createFeatures([Feature.CsharpNewCacheKey]);
-
-  const result = await getFeaturePrefix(codeql, features, KnownLanguage.csharp);
-  t.notDeepEqual(result, "");
-  t.assert(result.endsWith("-"));
-  // Check the length of the prefix, which should correspond to `cacheKeyHashLength` + 1 for the trailing `-`.
-  t.is(result.length, cacheKeyHashLength + 1);
-});
-
-test("getFeaturePrefix - non-C# - returns '' if CsharpNewCacheKey is enabled", async (t) => {
-  const codeql = createStubCodeQL({});
-  const features = createFeatures([Feature.CsharpNewCacheKey]);
-
-  for (const knownLanguage of Object.values(KnownLanguage)) {
-    // Skip C# since we expect a result for it, which is tested in the previous test.
-    if (knownLanguage === KnownLanguage.csharp) {
-      continue;
-    }
-    const result = await getFeaturePrefix(codeql, features, knownLanguage);
-    t.deepEqual(result, "", `Expected no feature prefix for ${knownLanguage}`);
-  }
-});

src/dependency-caching.ts

@@ -6,11 +6,9 @@ import * as glob from "@actions/glob";
 
 import { getTemporaryDirectory } from "./actions-util";
 import { listActionsCaches } from "./api-client";
-import { createCacheKeyHash, getTotalCacheSize } from "./caching-utils";
-import { CodeQL } from "./codeql";
+import { getTotalCacheSize } from "./caching-utils";
 import { Config } from "./config-utils";
 import { EnvVar } from "./environment";
-import { Feature, FeatureEnablement } from "./feature-flags";
 import { KnownLanguage, Language } from "./languages";
 import { Logger } from "./logging";
 import { getErrorMessage, getRequiredEnvParam } from "./util";
@@ -18,21 +16,15 @@ import { getErrorMessage, getRequiredEnvParam } from "./util";
 /**
  * Caching configuration for a particular language.
  */
-export interface CacheConfig {
-  /** Gets the paths of directories on the runner that should be included in the cache. */
-  getDependencyPaths: () => string[];
+interface CacheConfig {
+  /** The paths of directories on the runner that should be included in the cache. */
+  paths: string[];
   /**
-   * Gets an array of glob patterns for the paths of files whose contents affect which dependencies are used
-   * by a project. This function also checks whether there are any matching files and returns
-   * `undefined` if no files match.
-   *
-   * The glob patterns are intended to be used for cache keys, where we find all files which match these
-   * patterns, calculate a hash for their contents, and use that hash as part of the cache key.
+   * Patterns for the paths of files whose contents affect which dependencies are used
+   * by a project. We find all files which match these patterns, calculate a hash for
+   * their contents, and use that hash as part of the cache key.
    */
-  getHashPatterns: (
-    codeql: CodeQL,
-    features: FeatureEnablement,
-  ) => Promise<string[] | undefined>;
+  hash: string[];
 }
 
 const CODEQL_DEPENDENCY_CACHE_PREFIX = "codeql-dependencies";
@@ -47,105 +39,21 @@ export function getJavaTempDependencyDir(): string {
   return join(getTemporaryDirectory(), "codeql_java", "repository");
 }
 
-/**
- * Returns an array of paths of directories on the runner that should be included in a dependency cache
- * for a Java analysis. It is important that this is a function, because we call `getTemporaryDirectory`
- * which would otherwise fail in tests if we haven't had a chance to initialise `RUNNER_TEMP`.
- *
- * @returns The paths of directories on the runner that should be included in a dependency cache
- * for a Java analysis.
- */
-function getJavaDependencyDirs(): string[] {
-  return [
-    // Maven
-    join(os.homedir(), ".m2", "repository"),
-    // Gradle
-    join(os.homedir(), ".gradle", "caches"),
-    // CodeQL Java build-mode: none
-    getJavaTempDependencyDir(),
-  ];
-}
-
-/**
- * Checks that there are files which match `patterns`. If there are matching files for any of the patterns,
- * this function returns all `patterns`. Otherwise, `undefined` is returned.
- *
- * @param patterns The glob patterns to find matching files for.
- * @returns The array of glob patterns if there are matching files, or `undefined` otherwise.
- */
-export async function makePatternCheck(
-  patterns: string[],
-): Promise<string[] | undefined> {
-  const globber = await makeGlobber(patterns);
-
-  if ((await globber.glob()).length === 0) {
-    return undefined;
-  }
-
-  return patterns;
-}
-
-/** These files contain accurate information about dependencies, including the exact versions
- * that the relevant package manager has determined for the project. Using these gives us
- * stable hashes unless the dependencies change.
- */
-export const CSHARP_BASE_PATTERNS = [
-  // NuGet
-  "**/packages.lock.json",
-  // Paket
-  "**/paket.lock",
-];
-
-/** These are less accurate for use in cache key calculations, because they:
- *
- * - Don't contain the exact versions used. They may only contain version ranges or none at all.
- * - They contain information unrelated to dependencies, which we don't care about.
- *
- * As a result, the hash we compute from these files may change, even if
- * the dependencies haven't changed.
- */
-export const CSHARP_EXTRA_PATTERNS = [
-  "**/*.csproj",
-  "**/packages.config",
-  "**/nuget.config",
-];
-
-/**
- * Returns the list of glob patterns that should be used to calculate the cache key hash
- * for a C# dependency cache. This will try to use `CSHARP_BASE_PATTERNS` whenever possible.
- * As a fallback, it will also use `CSHARP_EXTRA_PATTERNS` if the corresponding FF is enabled.
- *
- * @param codeql The CodeQL instance to use.
- * @param features Information about which FFs are enabled.
- * @returns A list of glob patterns to use for hashing.
- */
-export async function getCsharpHashPatterns(
-  codeql: CodeQL,
-  features: FeatureEnablement,
-): Promise<string[] | undefined> {
-  const basePatterns = await internal.makePatternCheck(CSHARP_BASE_PATTERNS);
-
-  if (basePatterns !== undefined) {
-    return basePatterns;
-  }
-
-  if (await features.getValue(Feature.CsharpNewCacheKey, codeql)) {
-    return internal.makePatternCheck(CSHARP_EXTRA_PATTERNS);
-  }
-
-  // If we get to this point, we didn't find any files with `CSHARP_BASE_PATTERNS`,
-  // and `Feature.CsharpNewCacheKey` is not enabled.
-  return undefined;
-}
-
 /**
  * Default caching configurations per language.
  */
-const defaultCacheConfigs: { [language: string]: CacheConfig } = {
-  java: {
-    getDependencyPaths: getJavaDependencyDirs,
-    getHashPatterns: async () =>
-      internal.makePatternCheck([
+function getDefaultCacheConfig(): { [language: string]: CacheConfig } {
+  return {
+    java: {
+      paths: [
+        // Maven
+        join(os.homedir(), ".m2", "repository"),
+        // Gradle
+        join(os.homedir(), ".gradle", "caches"),
+        // CodeQL Java build-mode: none
+        getJavaTempDependencyDir(),
+      ],
+      hash: [
         // Maven
         "**/pom.xml",
         // Gradle
@@ -155,17 +63,23 @@ const defaultCacheConfigs: { [language: string]: CacheConfig } = {
         "buildSrc/**/Dependencies.kt",
         "gradle/*.versions.toml",
         "**/versions.properties",
-      ]),
-  },
-  csharp: {
-    getDependencyPaths: () => [join(os.homedir(), ".nuget", "packages")],
-    getHashPatterns: getCsharpHashPatterns,
-  },
-  go: {
-    getDependencyPaths: () => [join(os.homedir(), "go", "pkg", "mod")],
-    getHashPatterns: async () => internal.makePatternCheck(["**/go.sum"]),
-  },
-};
+      ],
+    },
+    csharp: {
+      paths: [join(os.homedir(), ".nuget", "packages")],
+      hash: [
+        // NuGet
+        "**/packages.lock.json",
+        // Paket
+        "**/paket.lock",
+      ],
+    },
+    go: {
+      paths: [join(os.homedir(), "go", "pkg", "mod")],
+      hash: ["**/go.sum"],
+    },
+  };
+}
 
 async function makeGlobber(patterns: string[]): Promise<glob.Globber> {
   return glob.create(patterns.join("\n"));
@@ -193,66 +107,23 @@ export interface DependencyCacheRestoreStatus {
 /** An array of `DependencyCacheRestoreStatus` objects for each analysed language with a caching configuration. */
 export type DependencyCacheRestoreStatusReport = DependencyCacheRestoreStatus[];
 
-/** Represents the results of `downloadDependencyCaches`. */
-export interface DownloadDependencyCachesResult {
-  /** The status report for telemetry */
-  statusReport: DependencyCacheRestoreStatusReport;
-  /** An array of cache keys that we have restored and therefore know to exist. */
-  restoredKeys: string[];
-}
-
-/**
- * A wrapper around `cacheConfig.getHashPatterns` which logs when there are no files to calculate
- * a hash for the cache key from.
- *
- * @param codeql The CodeQL instance to use.
- * @param features Information about which FFs are enabled.
- * @param language The language the `CacheConfig` is for. For use in the log message.
- * @param cacheConfig The caching configuration to call `getHashPatterns` on.
- * @param checkType Whether we are checking the patterns for a download or upload.
- * @param logger The logger to write the log message to if there is an error.
- * @returns An array of glob patterns to use for hashing files, or `undefined` if there are no matching files.
- */
-export async function checkHashPatterns(
-  codeql: CodeQL,
-  features: FeatureEnablement,
-  language: Language,
-  cacheConfig: CacheConfig,
-  checkType: "download" | "upload",
-  logger: Logger,
-): Promise<string[] | undefined> {
-  const patterns = await cacheConfig.getHashPatterns(codeql, features);
-
-  if (patterns === undefined) {
-    logger.info(
-      `Skipping ${checkType} of dependency cache for ${language} as we cannot calculate a hash for the cache key.`,
-    );
-  }
-
-  return patterns;
-}
-
 /**
  * Attempts to restore dependency caches for the languages being analyzed.
  *
- * @param codeql The CodeQL instance to use.
- * @param features Information about which FFs are enabled.
  * @param languages The languages being analyzed.
  * @param logger A logger to record some informational messages to.
- *
+ * @param minimizeJavaJars Whether the Java extractor should rewrite downloaded JARs to minimize their size.
  * @returns An array of `DependencyCacheRestoreStatus` objects for each analysed language with a caching configuration.
  */
 export async function downloadDependencyCaches(
-  codeql: CodeQL,
-  features: FeatureEnablement,
   languages: Language[],
   logger: Logger,
-): Promise<DownloadDependencyCachesResult> {
+  minimizeJavaJars: boolean,
+): Promise<DependencyCacheRestoreStatusReport> {
   const status: DependencyCacheRestoreStatusReport = [];
-  const restoredKeys: string[] = [];
 
   for (const language of languages) {
-    const cacheConfig = defaultCacheConfigs[language];
+    const cacheConfig = getDefaultCacheConfig()[language];
 
     if (cacheConfig === undefined) {
       logger.info(
@@ -263,22 +134,19 @@ export async function downloadDependencyCaches(
 
     // Check that we can find files to calculate the hash for the cache key from, so we don't end up
     // with an empty string.
-    const patterns = await checkHashPatterns(
-      codeql,
-      features,
-      language,
-      cacheConfig,
-      "download",
-      logger,
-    );
-    if (patterns === undefined) {
+    const globber = await makeGlobber(cacheConfig.hash);
+
+    if ((await globber.glob()).length === 0) {
       status.push({ language, hit_kind: CacheHitKind.NoHash });
+      logger.info(
+        `Skipping download of dependency cache for ${language} as we cannot calculate a hash for the cache key.`,
+      );
       continue;
     }
 
-    const primaryKey = await cacheKey(codeql, features, language, patterns);
+    const primaryKey = await cacheKey(language, cacheConfig, minimizeJavaJars);
     const restoreKeys: string[] = [
-      await cachePrefix(codeql, features, language),
+      await cachePrefix(language, minimizeJavaJars),
     ];
 
     logger.info(
@@ -289,7 +157,7 @@ export async function downloadDependencyCaches(
 
     const start = performance.now();
     const hitKey = await actionsCache.restoreCache(
-      cacheConfig.getDependencyPaths(),
+      cacheConfig.paths,
       primaryKey,
       restoreKeys,
     );
@@ -297,27 +165,16 @@ export async function downloadDependencyCaches(
 
     if (hitKey !== undefined) {
       logger.info(`Cache hit on key ${hitKey} for ${language}.`);
-
-      // We have a partial cache hit, unless the key of the restored cache matches the
-      // primary restore key.
-      let hit_kind = CacheHitKind.Partial;
-      if (hitKey === primaryKey) {
-        hit_kind = CacheHitKind.Exact;
-      }
-
-      status.push({
-        language,
-        hit_kind,
-        download_duration_ms,
-      });
-      restoredKeys.push(hitKey);
+      const hit_kind =
+        hitKey === primaryKey ? CacheHitKind.Exact : CacheHitKind.Partial;
+      status.push({ language, hit_kind, download_duration_ms });
     } else {
       status.push({ language, hit_kind: CacheHitKind.Miss });
       logger.info(`No suitable cache found for ${language}.`);
     }
   }
 
-  return { statusReport: status, restoredKeys };
+  return status;
 }
 
 /** Enumerates possible outcomes for storing caches. */
@@ -346,22 +203,20 @@ export type DependencyCacheUploadStatusReport = DependencyCacheUploadStatus[];
 /**
  * Attempts to store caches for the languages that were analyzed.
  *
- * @param codeql The CodeQL instance to use.
- * @param features Information about which FFs are enabled.
  * @param config The configuration for this workflow.
  * @param logger A logger to record some informational messages to.
+ * @param minimizeJavaJars Whether the Java extractor should rewrite downloaded JARs to minimize their size.
  *
  * @returns An array of `DependencyCacheUploadStatus` objects for each analysed language with a caching configuration.
  */
 export async function uploadDependencyCaches(
-  codeql: CodeQL,
-  features: FeatureEnablement,
   config: Config,
   logger: Logger,
+  minimizeJavaJars: boolean,
 ): Promise<DependencyCacheUploadStatusReport> {
   const status: DependencyCacheUploadStatusReport = [];
   for (const language of config.languages) {
-    const cacheConfig = defaultCacheConfigs[language];
+    const cacheConfig = getDefaultCacheConfig()[language];
 
     if (cacheConfig === undefined) {
       logger.info(
@@ -372,28 +227,13 @@ export async function uploadDependencyCaches(
 
     // Check that we can find files to calculate the hash for the cache key from, so we don't end up
     // with an empty string.
-    const patterns = await checkHashPatterns(
-      codeql,
-      features,
-      language,
-      cacheConfig,
-      "upload",
-      logger,
-    );
-    if (patterns === undefined) {
+    const globber = await makeGlobber(cacheConfig.hash);
+
+    if ((await globber.glob()).length === 0) {
       status.push({ language, result: CacheStoreResult.NoHash });
-      continue;
-    }
-
-    // Now that we have verified that there are suitable files, compute the hash for the cache key.
-    const key = await cacheKey(codeql, features, language, patterns);
-
-    // Check that we haven't previously restored this exact key. If a cache with this key
-    // already exists in the Actions Cache, performing the next steps is pointless as the cache
-    // will not get overwritten. We can therefore skip the expensive work of measuring the size
-    // of the cache contents and attempting to upload it if we know that the cache already exists.
-    if (config.dependencyCachingRestoredKeys.includes(key)) {
-      status.push({ language, result: CacheStoreResult.Duplicate });
+      logger.info(
+        `Skipping upload of dependency cache for ${language} as we cannot calculate a hash for the cache key.`,
+      );
       continue;
     }
 
@@ -407,11 +247,7 @@ export async function uploadDependencyCaches(
     //   use the cache quota that we compete with. In that case, we do not wish to use up all of the quota
     //   with the dependency caches. For this, we could use the Cache API to check whether other workflows
     //   are using the quota and how full it is.
-    const size = await getTotalCacheSize(
-      cacheConfig.getDependencyPaths(),
-      logger,
-      true,
-    );
+    const size = await getTotalCacheSize(cacheConfig.paths, logger, true);
 
     // Skip uploading an empty cache.
     if (size === 0) {
@@ -422,13 +258,15 @@ export async function uploadDependencyCaches(
       continue;
     }
 
+    const key = await cacheKey(language, cacheConfig, minimizeJavaJars);
+
     logger.info(
       `Uploading cache of size ${size} for ${language} with key ${key}...`,
     );
 
     try {
       const start = performance.now();
-      await actionsCache.saveCache(cacheConfig.getDependencyPaths(), key);
+      await actionsCache.saveCache(cacheConfig.paths, key);
       const upload_duration_ms = Math.round(performance.now() - start);
 
       status.push({
@@ -461,86 +299,31 @@ export async function uploadDependencyCaches(
 /**
  * Computes a cache key for the specified language.
  *
- * @param codeql The CodeQL instance to use.
- * @param features Information about which FFs are enabled.
  * @param language The language being analyzed.
- * @param patterns The file patterns to hash.
- *
+ * @param cacheConfig The cache configuration for the language.
+ * @param minimizeJavaJars Whether the Java extractor should rewrite downloaded JARs to minimize their size.
  * @returns A cache key capturing information about the project(s) being analyzed in the specified language.
  */
-export async function cacheKey(
-  codeql: CodeQL,
-  features: FeatureEnablement,
+async function cacheKey(
   language: Language,
-  patterns: string[],
+  cacheConfig: CacheConfig,
+  minimizeJavaJars: boolean = false,
 ): Promise<string> {
-  const hash = await glob.hashFiles(patterns.join("\n"));
-  return `${await cachePrefix(codeql, features, language)}${hash}`;
-}
-
-/**
- * If experimental features which the cache contents depend on are enabled for the current language,
- * this function returns a prefix that uniquely identifies the set of enabled features. The purpose of
- * this is to avoid restoring caches whose contents depended on experimental features, if those
- * experimental features are later disabled.
- *
- * @param codeql The CodeQL instance.
- * @param features Information about enabled features.
- * @param language The language we are creating the key for.
- *
- * @returns A cache key prefix identifying the enabled, experimental features that the cache depends on.
- */
-export async function getFeaturePrefix(
-  codeql: CodeQL,
-  features: FeatureEnablement,
-  language: Language,
-): Promise<string> {
-  const enabledFeatures: Feature[] = [];
-
-  const addFeatureIfEnabled = async (feature: Feature) => {
-    if (await features.getValue(feature, codeql)) {
-      enabledFeatures.push(feature);
-    }
-  };
-
-  if (language === KnownLanguage.java) {
-    // To ensure a safe rollout of JAR minimization, we change the key when the feature is enabled.
-    const minimizeJavaJars = await features.getValue(
-      Feature.JavaMinimizeDependencyJars,
-      codeql,
-    );
-
-    // To maintain backwards compatibility with this, we return "minify-" instead of a hash.
-    if (minimizeJavaJars) {
-      return "minify-";
-    }
-  } else if (language === KnownLanguage.csharp) {
-    await addFeatureIfEnabled(Feature.CsharpNewCacheKey);
-  }
-
-  // If any features that affect the cache are enabled, return a feature prefix by
-  // computing a hash of the feature array.
-  if (enabledFeatures.length > 0) {
-    return `${createCacheKeyHash(enabledFeatures)}-`;
-  }
-
-  // No feature prefix.
-  return "";
+  const hash = await glob.hashFiles(cacheConfig.hash.join("\n"));
+  return `${await cachePrefix(language, minimizeJavaJars)}${hash}`;
 }
 
 /**
  * Constructs a prefix for the cache key, comprised of a CodeQL-specific prefix, a version number that
  * can be changed to invalidate old caches, the runner's operating system, and the specified language name.
  *
- * @param codeql The CodeQL instance to use.
- * @param features Information about which FFs are enabled.
  * @param language The language being analyzed.
+ * @param minimizeJavaJars Whether the Java extractor should rewrite downloaded JARs to minimize their size.
  * @returns The prefix that identifies what a cache is for.
  */
 async function cachePrefix(
-  codeql: CodeQL,
-  features: FeatureEnablement,
   language: Language,
+  minimizeJavaJars: boolean,
 ): Promise<string> {
   const runnerOs = getRequiredEnvParam("RUNNER_OS");
   const customPrefix = process.env[EnvVar.DEPENDENCY_CACHING_PREFIX];
@@ -550,18 +333,12 @@ async function cachePrefix(
     prefix = `${prefix}-${customPrefix}`;
   }
 
-  // Calculate the feature prefix for the cache, if any. This is a hash that identifies
-  // experimental features that affect the cache contents.
-  const featurePrefix = await getFeaturePrefix(codeql, features, language);
-
-  // Assemble the cache key. For backwards compatibility with the JAR minification experiment's existing
-  // feature prefix usage, we add that feature prefix at the start. Other feature prefixes are inserted
-  // after the general CodeQL dependency cache prefix.
-  if (featurePrefix === "minify-") {
-    return `${featurePrefix}${prefix}-${CODEQL_DEPENDENCY_CACHE_VERSION}-${runnerOs}-${language}-`;
-  } else {
-    return `${prefix}-${featurePrefix}${CODEQL_DEPENDENCY_CACHE_VERSION}-${runnerOs}-${language}-`;
+  // To ensure a safe rollout of JAR minimization, we change the key when the feature is enabled.
+  if (language === KnownLanguage.java && minimizeJavaJars) {
+    prefix = `minify-${prefix}`;
   }
+
+  return `${prefix}-${CODEQL_DEPENDENCY_CACHE_VERSION}-${runnerOs}-${language}-`;
 }
 
 /** Represents information about our overall cache usage for CodeQL dependency caches. */
@@ -594,7 +371,3 @@ export async function getDependencyCacheUsage(
 
   return undefined;
 }
-
-export const internal = {
-  makePatternCheck,
-};

src/environment.ts

@@ -20,6 +20,12 @@ export enum EnvVar {
   /** Whether the CodeQL Action has invoked the Go autobuilder. */
   DID_AUTOBUILD_GOLANG = "CODEQL_ACTION_DID_AUTOBUILD_GOLANG",
 
+  /**
+   * Whether to disable the SARIF post-processing in the Action that removes duplicate locations from
+   * notifications in the `run[].invocations[].toolExecutionNotifications` SARIF property.
+   */
+  DISABLE_DUPLICATE_LOCATION_FIX = "CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX",
+
   /**
    * Whether the CodeQL Action is using its own deprecated and non-standard way of scanning for
    * multiple languages.
@@ -50,12 +56,20 @@ export enum EnvVar {
   /** Whether the error for a deprecated version of the CodeQL Action was logged. */
   LOG_VERSION_DEPRECATION = "CODEQL_ACTION_DID_LOG_VERSION_DEPRECATION",
 
+  /**
+   * For macOS. Result of `csrutil status` to determine whether System Integrity
+   * Protection is enabled.
+   */
+  IS_SIP_ENABLED = "CODEQL_ACTION_IS_SIP_ENABLED",
+
   /** UUID representing the current job run. */
   JOB_RUN_UUID = "JOB_RUN_UUID",
 
   /** Status for the entire job, submitted to the status report in `init-post` */
   JOB_STATUS = "CODEQL_ACTION_JOB_STATUS",
 
+  ODASA_TRACER_CONFIGURATION = "ODASA_TRACER_CONFIGURATION",
+
   /** The value of the `output` input for the analyze action. */
   SARIF_RESULTS_OUTPUT_DIR = "CODEQL_ACTION_SARIF_RESULTS_OUTPUT_DIR",
 

src/feature-flags.ts

@@ -47,7 +47,6 @@ export enum Feature {
   AnalyzeUseNewUpload = "analyze_use_new_upload",
   CleanupTrapCaches = "cleanup_trap_caches",
   CppDependencyInstallation = "cpp_dependency_installation_enabled",
-  CsharpNewCacheKey = "csharp_new_cache_key",
   DiffInformedQueries = "diff_informed_queries",
   DisableCsharpBuildless = "disable_csharp_buildless",
   DisableJavaBuildlessEnabled = "disable_java_buildless_enabled",
@@ -77,7 +76,7 @@ export enum Feature {
   OverlayAnalysisSwift = "overlay_analysis_swift",
   PythonDefaultIsToNotExtractStdlib = "python_default_is_to_not_extract_stdlib",
   QaTelemetryEnabled = "qa_telemetry_enabled",
-  UploadOverlayDbToApi = "upload_overlay_db_to_api",
+  ResolveSupportedLanguagesUsingCli = "resolve_supported_languages_using_cli",
   UseRepositoryProperties = "use_repository_properties",
   ValidateDbConfig = "validate_db_config",
 }
@@ -134,11 +133,6 @@ export const featureConfig: Record<
     legacyApi: true,
     minimumVersion: "2.15.0",
   },
-  [Feature.CsharpNewCacheKey]: {
-    defaultValue: false,
-    envVar: "CODEQL_ACTION_CSHARP_NEW_CACHE_KEY",
-    minimumVersion: undefined,
-  },
   [Feature.DiffInformedQueries]: {
     defaultValue: true,
     envVar: "CODEQL_ACTION_DIFF_INFORMED_QUERIES",
@@ -167,10 +161,11 @@ export const featureConfig: Record<
     legacyApi: true,
     minimumVersion: undefined,
   },
-  [Feature.JavaMinimizeDependencyJars]: {
+  [Feature.ResolveSupportedLanguagesUsingCli]: {
     defaultValue: false,
-    envVar: "CODEQL_ACTION_JAVA_MINIMIZE_DEPENDENCY_JARS",
-    minimumVersion: "2.23.0",
+    envVar: "CODEQL_ACTION_RESOLVE_SUPPORTED_LANGUAGES_USING_CLI",
+    minimumVersion: undefined,
+    toolsFeature: ToolsFeature.BuiltinExtractorsSpecifyDefaultQueries,
   },
   [Feature.OverlayAnalysis]: {
     defaultValue: false,
@@ -283,21 +278,21 @@ export const featureConfig: Record<
     minimumVersion: undefined,
     toolsFeature: ToolsFeature.PythonDefaultIsToNotExtractStdlib,
   },
+  [Feature.UseRepositoryProperties]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_USE_REPOSITORY_PROPERTIES",
+    minimumVersion: undefined,
+  },
   [Feature.QaTelemetryEnabled]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_QA_TELEMETRY",
     legacyApi: true,
     minimumVersion: undefined,
   },
-  [Feature.UploadOverlayDbToApi]: {
+  [Feature.JavaMinimizeDependencyJars]: {
     defaultValue: false,
-    envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
-    minimumVersion: undefined,
-  },
-  [Feature.UseRepositoryProperties]: {
-    defaultValue: false,
-    envVar: "CODEQL_ACTION_USE_REPOSITORY_PROPERTIES",
-    minimumVersion: undefined,
+    envVar: "CODEQL_ACTION_JAVA_MINIMIZE_DEPENDENCY_JARS",
+    minimumVersion: "2.23.0",
   },
   [Feature.ValidateDbConfig]: {
     defaultValue: false,

src/git-utils.ts

@@ -122,6 +122,67 @@ export const determineBaseBranchHeadCommitOid = async function (
   }
 };
 
+/**
+ * Deepen the git history of HEAD by one level. Errors are logged.
+ *
+ * This function uses the `checkout_path` to determine the repository path and
+ * works only when called from `analyze` or `upload-sarif`.
+ */
+export const deepenGitHistory = async function () {
+  try {
+    await runGitCommand(
+      getOptionalInput("checkout_path"),
+      [
+        "fetch",
+        "origin",
+        "HEAD",
+        "--no-tags",
+        "--no-recurse-submodules",
+        "--deepen=1",
+      ],
+      "Cannot deepen the shallow repository.",
+    );
+  } catch {
+    // Errors are already logged by runGitCommand()
+  }
+};
+
+/**
+ * Fetch the given remote branch. Errors are logged.
+ *
+ * This function uses the `checkout_path` to determine the repository path and
+ * works only when called from `analyze` or `upload-sarif`.
+ */
+export const gitFetch = async function (branch: string, extraFlags: string[]) {
+  try {
+    await runGitCommand(
+      getOptionalInput("checkout_path"),
+      ["fetch", "--no-tags", ...extraFlags, "origin", `${branch}:${branch}`],
+      `Cannot fetch ${branch}.`,
+    );
+  } catch {
+    // Errors are already logged by runGitCommand()
+  }
+};
+
+/**
+ * Repack the git repository, using with the given flags. Errors are logged.
+ *
+ * This function uses the `checkout_path` to determine the repository path and
+ * works only when called from `analyze` or `upload-sarif`.
+ */
+export const gitRepack = async function (flags: string[]) {
+  try {
+    await runGitCommand(
+      getOptionalInput("checkout_path"),
+      ["repack", ...flags],
+      "Cannot repack the repository.",
+    );
+  } catch {
+    // Errors are already logged by runGitCommand()
+  }
+};
+
 /**
  * Decode, if necessary, a file path produced by Git. See
  * https://git-scm.com/docs/git-config#Documentation/git-config.txt-corequotePath

src/init-action.ts

@@ -371,7 +371,7 @@ async function run() {
   }
 
   let overlayBaseDatabaseStats: OverlayBaseDatabaseDownloadStats | undefined;
-  let dependencyCachingStatus: DependencyCacheRestoreStatusReport | undefined;
+  let dependencyCachingResults: DependencyCacheRestoreStatusReport | undefined;
   try {
     if (
       config.overlayDatabaseMode === OverlayDatabaseMode.Overlay &&
@@ -578,16 +578,16 @@ async function run() {
     }
 
     // Restore dependency cache(s), if they exist.
+    const minimizeJavaJars = await features.getValue(
+      Feature.JavaMinimizeDependencyJars,
+      codeql,
+    );
     if (shouldRestoreCache(config.dependencyCachingEnabled)) {
-      const dependencyCachingResult = await downloadDependencyCaches(
-        codeql,
-        features,
+      dependencyCachingResults = await downloadDependencyCaches(
         config.languages,
         logger,
+        minimizeJavaJars,
       );
-      dependencyCachingStatus = dependencyCachingResult.statusReport;
-      config.dependencyCachingRestoredKeys =
-        dependencyCachingResult.restoredKeys;
     }
 
     // Suppress warnings about disabled Python library extraction.
@@ -648,7 +648,7 @@ async function run() {
         `${EnvVar.JAVA_EXTRACTOR_MINIMIZE_DEPENDENCY_JARS} is already set to '${process.env[EnvVar.JAVA_EXTRACTOR_MINIMIZE_DEPENDENCY_JARS]}', so the Action will not override it.`,
       );
     } else if (
-      (await features.getValue(Feature.JavaMinimizeDependencyJars, codeql)) &&
+      minimizeJavaJars &&
       config.dependencyCachingEnabled &&
       config.buildMode === BuildMode.None &&
       config.languages.includes(KnownLanguage.java)
@@ -735,7 +735,7 @@ async function run() {
       toolsSource,
       toolsVersion,
       overlayBaseDatabaseStats,
-      dependencyCachingStatus,
+      dependencyCachingResults,
       logger,
       error,
     );
@@ -758,7 +758,7 @@ async function run() {
     toolsSource,
     toolsVersion,
     overlayBaseDatabaseStats,
-    dependencyCachingStatus,
+    dependencyCachingResults,
     logger,
   );
 }

src/overlay-database-utils.ts

@@ -1,3 +1,4 @@
+import * as crypto from "crypto";
 import * as fs from "fs";
 import * as path from "path";
 
@@ -10,13 +11,11 @@ import {
   getWorkflowRunID,
 } from "./actions-util";
 import { getAutomationID } from "./api-client";
-import { createCacheKeyHash } from "./caching-utils";
 import { type CodeQL } from "./codeql";
 import { type Config } from "./config-utils";
 import { getCommitOid, getFileOidsUnderPath } from "./git-utils";
 import { Logger, withGroupAsync } from "./logging";
 import {
-  CleanupLevel,
   getErrorMessage,
   isInTestMode,
   tryGetFolderBytes,
@@ -29,7 +28,7 @@ export enum OverlayDatabaseMode {
   None = "none",
 }
 
-export const CODEQL_OVERLAY_MINIMUM_VERSION = "2.23.5";
+export const CODEQL_OVERLAY_MINIMUM_VERSION = "2.22.4";
 
 /**
  * The maximum (uncompressed) size of the overlay base database that we will
@@ -176,7 +175,7 @@ const MAX_CACHE_OPERATION_MS = 600_000;
  * @param warningPrefix Prefix for the check failure warning message
  * @returns True if the verification succeeded, false otherwise
  */
-function checkOverlayBaseDatabase(
+export function checkOverlayBaseDatabase(
   config: Config,
   logger: Logger,
   warningPrefix: string,
@@ -205,7 +204,7 @@ function checkOverlayBaseDatabase(
  * @returns A promise that resolves to true if the upload was performed and
  * successfully completed, or false otherwise
  */
-export async function cleanupAndUploadOverlayBaseDatabaseToCache(
+export async function uploadOverlayBaseDatabaseToCache(
   codeql: CodeQL,
   config: Config,
   logger: Logger,
@@ -243,7 +242,7 @@ export async function cleanupAndUploadOverlayBaseDatabaseToCache(
 
   // Clean up the database using the overlay cleanup level.
   await withGroupAsync("Cleaning up databases", async () => {
-    await codeql.databaseCleanupCluster(config, CleanupLevel.Overlay);
+    await codeql.databaseCleanupCluster(config, "overlay");
   });
 
   const dbLocation = config.dbLocation;
@@ -515,3 +514,27 @@ export async function getCacheRestoreKeyPrefix(
   // easier to debug and understand the cache key structure.
   return `${CACHE_PREFIX}-${CACHE_VERSION}-${componentsHash}-${languages}-${codeQlVersion}-`;
 }
+
+/**
+ * Creates a SHA-256 hash of the cache key components to ensure uniqueness
+ * while keeping the cache key length manageable.
+ *
+ * @param components Object containing all components that should influence cache key uniqueness
+ * @returns A short SHA-256 hash (first 16 characters) of the components
+ */
+function createCacheKeyHash(components: Record<string, any>): string {
+  // From https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/JSON/stringify
+  //
+  // "Properties are visited using the same algorithm as Object.keys(), which
+  // has a well-defined order and is stable across implementations. For example,
+  // JSON.stringify on the same object will always produce the same string, and
+  // JSON.parse(JSON.stringify(obj)) would produce an object with the same key
+  // ordering as the original (assuming the object is completely
+  // JSON-serializable)."
+  const componentsJson = JSON.stringify(components);
+  return crypto
+    .createHash("sha256")
+    .update(componentsJson)
+    .digest("hex")
+    .substring(0, 16);
+}

src/setup-codeql.ts

@@ -34,7 +34,7 @@ export enum ToolsSource {
   Download = "DOWNLOAD",
 }
 
-const CODEQL_DEFAULT_ACTION_REPOSITORY = "github/codeql-action";
+export const CODEQL_DEFAULT_ACTION_REPOSITORY = "github/codeql-action";
 const CODEQL_NIGHTLIES_REPOSITORY_OWNER = "dsp-testing";
 const CODEQL_NIGHTLIES_REPOSITORY_NAME = "codeql-cli-nightlies";
 
@@ -180,6 +180,17 @@ export function tryGetTagNameFromUrl(
   return match[1];
 }
 
+export function tryGetBundleVersionFromUrl(
+  url: string,
+  logger: Logger,
+): string | undefined {
+  const tagName = tryGetTagNameFromUrl(url, logger);
+  if (tagName === undefined) {
+    return undefined;
+  }
+  return tryGetBundleVersionFromTagName(tagName, logger);
+}
+
 export function convertToSemVer(version: string, logger: Logger): string {
   if (!semver.valid(version)) {
     logger.debug(
@@ -569,7 +580,7 @@ export async function getCodeQLSource(
  * Gets a fallback version number to use when looking for CodeQL in the toolcache if we didn't find
  * the `x.y.z` version. This is to support old versions of the toolcache.
  */
-async function tryGetFallbackToolcacheVersion(
+export async function tryGetFallbackToolcacheVersion(
   cliVersion: string | undefined,
   tagName: string,
   logger: Logger,
@@ -718,7 +729,7 @@ function getCanonicalToolcacheVersion(
   return cliVersion;
 }
 
-interface SetupCodeQLResult {
+export interface SetupCodeQLResult {
   codeqlFolder: string;
   toolsDownloadStatusReport?: ToolsDownloadStatusReport;
   toolsSource: ToolsSource;
@@ -739,7 +750,7 @@ export async function setupCodeQLBundle(
   defaultCliVersion: CodeQLDefaultVersionInfo,
   features: FeatureEnablement,
   logger: Logger,
-): Promise<SetupCodeQLResult> {
+) {
   if (!(await util.isBinaryAccessible("tar", logger))) {
     throw new util.ConfigurationError(
       "Could not find tar in PATH, so unable to extract CodeQL bundle.",

src/start-proxy.ts

@@ -8,7 +8,7 @@ import { ConfigurationError, getErrorMessage, isDefined } from "./util";
 
 export const UPDATEJOB_PROXY = "update-job-proxy";
 export const UPDATEJOB_PROXY_VERSION = "v2.0.20250624110901";
-const UPDATEJOB_PROXY_URL_PREFIX =
+export const UPDATEJOB_PROXY_URL_PREFIX =
   "https://github.com/github/codeql-action/releases/download/codeql-bundle-v2.22.0/";
 
 export type Credential = {
@@ -202,7 +202,7 @@ export function getFallbackUrl(proxyPackage: string): string {
  *
  * @returns The response from the GitHub API.
  */
-async function getLinkedRelease() {
+export async function getLinkedRelease() {
   return getApiClient().rest.repos.getReleaseByTag({
     owner: "github",
     repo: "codeql-action",

src/status-report.ts

@@ -54,7 +54,7 @@ export enum ActionName {
  * considered to be a third party analysis and is treated differently when calculating SLOs. To ensure
  * misconfigured workflows are not treated as third party, only the upload-sarif action can return false.
  */
-function isFirstPartyAnalysis(actionName: ActionName): boolean {
+export function isFirstPartyAnalysis(actionName: ActionName): boolean {
   if (actionName !== ActionName.UploadSarif) {
     return true;
   }
@@ -252,7 +252,7 @@ export interface EventReport {
  *
  * @param actionName The name of the action, e.g. 'init', 'finish', 'upload-sarif'
  * @param status The status. Must be 'success', 'failure', or 'starting'
- * @param actionStartedAt The time this action started executing.
+ * @param startedAt The time this action started executing.
  * @param cause  Cause of failure (only supply if status is 'failure')
  * @param exception Exception (only supply if status is 'failure')
  * @returns undefined if an exception was thrown.

src/testing-utils.ts

@@ -392,7 +392,6 @@ export function createTestConfig(overrides: Partial<Config>): Config {
       trapCaches: {},
       trapCacheDownloadTime: 0,
       dependencyCachingEnabled: CachingKind.None,
-      dependencyCachingRestoredKeys: [],
       extraQueryExclusions: [],
       overlayDatabaseMode: OverlayDatabaseMode.None,
       useOverlayDatabaseCaching: false,

src/tools-download.ts

@@ -17,7 +17,7 @@ import { cleanUpPath, getErrorMessage, getRequiredEnvParam } from "./util";
 /**
  * High watermark to use when streaming the download and extraction of the CodeQL tools.
  */
-const STREAMING_HIGH_WATERMARK_BYTES = 4 * 1024 * 1024; // 4 MiB
+export const STREAMING_HIGH_WATERMARK_BYTES = 4 * 1024 * 1024; // 4 MiB
 
 /**
  * The name of the tool cache directory for the CodeQL tools.

src/tracer-config.ts

@@ -76,7 +76,7 @@ export async function endTracingForCluster(
   }
 }
 
-async function getTracerConfigForCluster(
+export async function getTracerConfigForCluster(
   config: Config,
 ): Promise<TracerConfig> {
   const tracingEnvVariables = JSON.parse(

src/upload-lib.ts

@@ -412,7 +412,7 @@ export function findSarifFilesInDir(
   return sarifFiles;
 }
 
-function getSarifFilePaths(
+export function getSarifFilePaths(
   sarifPath: string,
   isSarif: (name: string) => boolean,
 ) {
@@ -738,7 +738,7 @@ export async function postProcessSarifFiles(
  * @param logger The logger to use.
  * @param pathInput The input provided for `post-processed-sarif-path`.
  * @param uploadTarget The upload target.
- * @param postProcessingResults The results of post-processing SARIF files.
+ * @param processingResults The results of post-processing SARIF files.
  */
 export async function writePostProcessedFiles(
   logger: Logger,

src/util.test.ts

@@ -447,21 +447,13 @@ const CHECK_ACTION_VERSION_TESTS: Array<[string, util.GitHubVersion, boolean]> =
     ["2.2.1", { type: util.GitHubVariant.DOTCOM }, true],
     ["2.2.1", { type: util.GitHubVariant.GHE_DOTCOM }, true],
     ["2.2.1", { type: util.GitHubVariant.GHES, version: "3.10" }, false],
-    ["2.2.1", { type: util.GitHubVariant.GHES, version: "3.11" }, false],
-    ["2.2.1", { type: util.GitHubVariant.GHES, version: "3.12" }, false],
-    ["3.2.1", { type: util.GitHubVariant.DOTCOM }, true],
-    ["3.2.1", { type: util.GitHubVariant.GHE_DOTCOM }, true],
+    ["2.2.1", { type: util.GitHubVariant.GHES, version: "3.11" }, true],
+    ["2.2.1", { type: util.GitHubVariant.GHES, version: "3.12" }, true],
+    ["3.2.1", { type: util.GitHubVariant.DOTCOM }, false],
+    ["3.2.1", { type: util.GitHubVariant.GHE_DOTCOM }, false],
     ["3.2.1", { type: util.GitHubVariant.GHES, version: "3.10" }, false],
     ["3.2.1", { type: util.GitHubVariant.GHES, version: "3.11" }, false],
     ["3.2.1", { type: util.GitHubVariant.GHES, version: "3.12" }, false],
-    ["3.2.1", { type: util.GitHubVariant.GHES, version: "3.19" }, false],
-    ["3.2.1", { type: util.GitHubVariant.GHES, version: "3.20" }, true],
-    ["3.2.1", { type: util.GitHubVariant.GHES, version: "3.21" }, true],
-    ["4.2.1", { type: util.GitHubVariant.DOTCOM }, false],
-    ["4.2.1", { type: util.GitHubVariant.GHE_DOTCOM }, false],
-    ["4.2.1", { type: util.GitHubVariant.GHES, version: "3.19" }, false],
-    ["4.2.1", { type: util.GitHubVariant.GHES, version: "3.20" }, false],
-    ["4.2.1", { type: util.GitHubVariant.GHES, version: "3.21" }, false],
   ];
 
 for (const [
@@ -476,7 +468,7 @@ for (const [
     githubVersion,
   )}`;
   test(`checkActionVersion ${reportErrorDescription} for ${versionsDescription}`, async (t) => {
-    const warningSpy = sinon.spy(core, "warning");
+    const warningSpy = sinon.spy(core, "error");
     const versionStub = sinon
       .stub(api, "getGitHubVersion")
       .resolves(githubVersion);
@@ -488,7 +480,9 @@ for (const [
     if (shouldReportError) {
       t.true(
         warningSpy.calledOnceWithExactly(
-          sinon.match("CodeQL Action v3 will be deprecated in December 2026."),
+          sinon.match(
+            "CodeQL Action major versions v1 and v2 have been deprecated.",
+          ),
         ),
       );
     } else {

src/util.ts

@@ -4,6 +4,7 @@ import * as os from "os";
 import * as path from "path";
 
 import * as core from "@actions/core";
+import * as exec from "@actions/exec/lib/exec";
 import * as io from "@actions/io";
 import getFolderSize from "get-folder-size";
 import * as yaml from "js-yaml";
@@ -1025,6 +1026,34 @@ export function fixInvalidNotifications(
   return newSarif;
 }
 
+/**
+ * Removes duplicates from the sarif file.
+ *
+ * When `CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX` is set to true, this will
+ * simply rename the input file to the output file. Otherwise, it will parse the
+ * input file as JSON, remove duplicate locations from the SARIF notification
+ * objects, and write the result to the output file.
+ *
+ * For context, see documentation of:
+ * `CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX`. */
+export function fixInvalidNotificationsInFile(
+  inputPath: string,
+  outputPath: string,
+  logger: Logger,
+): void {
+  if (process.env[EnvVar.DISABLE_DUPLICATE_LOCATION_FIX] === "true") {
+    logger.info(
+      "SARIF notification object duplicate location fix disabled by the " +
+        `${EnvVar.DISABLE_DUPLICATE_LOCATION_FIX} environment variable.`,
+    );
+    fs.renameSync(inputPath, outputPath);
+  } else {
+    let sarif = JSON.parse(fs.readFileSync(inputPath, "utf8")) as SarifFile;
+    sarif = fixInvalidNotifications(sarif, logger);
+    fs.writeFileSync(outputPath, JSON.stringify(sarif));
+  }
+}
+
 export function wrapError(error: unknown): Error {
   return error instanceof Error ? error : new Error(String(error));
 }
@@ -1085,38 +1114,38 @@ export async function checkDiskUsage(
 }
 
 /**
- * Prompt the customer to upgrade to CodeQL Action v4, if appropriate.
+ * Prompt the customer to upgrade to CodeQL Action v3, if appropriate.
  *
- * Check whether a customer is running v3. If they are, and we can determine that the GitHub
- * instance supports v4, then log an error prompting the customer to upgrade to v4.
+ * Check whether a customer is running v1 or v2. If they are, and we can determine that the GitHub
+ * instance supports v3, then log an error prompting the customer to upgrade to v3.
  */
 export function checkActionVersion(
   version: string,
   githubVersion: GitHubVersion,
 ) {
   if (
-    !semver.satisfies(version, ">=4") && // do not log error if the customer is already running v4
+    !semver.satisfies(version, ">=3") && // do not log error if the customer is already running v3
     !process.env[EnvVar.LOG_VERSION_DEPRECATION] // do not log error if we have already
   ) {
-    // Only error for versions of GHES that are compatible with CodeQL Action version 4.
+    // Only error for versions of GHES that are compatible with CodeQL Action version 3.
     //
-    // GHES 3.20 is the first version to ship with the v4 tag and this warning message code.
-    // Therefore, users who are seeing this warning message code are running on GHES 3.20 or newer,
-    // and should update to CodeQL Action v4.
+    // GHES 3.11 shipped without the v3 tag, but it also shipped without this warning message code.
+    // Therefore users who are seeing this warning message code have pulled in a new version of the
+    // Action, and with it the v3 tag.
     if (
       githubVersion.type === GitHubVariant.DOTCOM ||
       githubVersion.type === GitHubVariant.GHE_DOTCOM ||
       (githubVersion.type === GitHubVariant.GHES &&
         semver.satisfies(
           semver.coerce(githubVersion.version) ?? "0.0.0",
-          ">=3.20",
+          ">=3.11",
         ))
     ) {
-      core.warning(
-        "CodeQL Action v3 will be deprecated in December 2026. " +
-          "Please update all occurrences of the CodeQL Action in your workflow files to v4. " +
+      core.error(
+        "CodeQL Action major versions v1 and v2 have been deprecated. " +
+          "Please update all occurrences of the CodeQL Action in your workflow files to v3. " +
           "For more information, see " +
-          "https://github.blog/changelog/2025-10-28-upcoming-deprecation-of-codeql-action-v3/",
+          "https://github.blog/changelog/2025-01-10-code-scanning-codeql-action-v2-is-now-deprecated/",
       );
       // set LOG_VERSION_DEPRECATION env var to prevent the warning from being logged multiple times
       core.exportVariable(EnvVar.LOG_VERSION_DEPRECATION, "true");
@@ -1168,6 +1197,49 @@ export function cloneObject<T>(obj: T): T {
   return JSON.parse(JSON.stringify(obj)) as T;
 }
 
+// The first time this function is called, it runs `csrutil status` to determine
+// whether System Integrity Protection is enabled; and saves the result in an
+// environment variable. Afterwards, simply return the value of the environment
+// variable.
+export async function checkSipEnablement(
+  logger: Logger,
+): Promise<boolean | undefined> {
+  if (
+    process.env[EnvVar.IS_SIP_ENABLED] !== undefined &&
+    ["true", "false"].includes(process.env[EnvVar.IS_SIP_ENABLED])
+  ) {
+    return process.env[EnvVar.IS_SIP_ENABLED] === "true";
+  }
+
+  try {
+    const sipStatusOutput = await exec.getExecOutput("csrutil status");
+    if (sipStatusOutput.exitCode === 0) {
+      if (
+        sipStatusOutput.stdout.includes(
+          "System Integrity Protection status: enabled.",
+        )
+      ) {
+        core.exportVariable(EnvVar.IS_SIP_ENABLED, "true");
+        return true;
+      }
+      if (
+        sipStatusOutput.stdout.includes(
+          "System Integrity Protection status: disabled.",
+        )
+      ) {
+        core.exportVariable(EnvVar.IS_SIP_ENABLED, "false");
+        return false;
+      }
+    }
+    return undefined;
+  } catch (e) {
+    logger.warning(
+      `Failed to determine if System Integrity Protection was enabled: ${e}`,
+    );
+    return undefined;
+  }
+}
+
 export async function cleanUpPath(file: string, name: string, logger: Logger) {
   logger.debug(`Cleaning up ${name}.`);
   try {
@@ -1219,6 +1291,17 @@ export function isDefined<T>(value: T | null | undefined): value is T {
   return value !== undefined && value !== null;
 }
 
+/** Like `Object.keys`, but typed so that the elements of the resulting array have the
+ * same type as the keys of the input object. Note that this may not be sound if the input
+ * object has been cast to `T` from a subtype of `T` and contains additional keys that
+ * are not represented by `keyof T`.
+ */
+export function unsafeKeysInvariant<T extends Record<string, any>>(
+  object: T,
+): Array<keyof T> {
+  return Object.keys(object) as Array<keyof T>;
+}
+
 /** Like `Object.entries`, but typed so that the key elements of the result have the
  * same type as the keys of the input object. Note that this may not be sound if the input
  * object has been cast to `T` from a subtype of `T` and contains additional keys that
@@ -1231,8 +1314,3 @@ export function unsafeEntriesInvariant<T extends Record<string, any>>(
     ([_, val]) => val !== undefined,
   ) as Array<[keyof T, Exclude<T[keyof T], undefined>]>;
 }
-
-export enum CleanupLevel {
-  Clear = "clear",
-  Overlay = "overlay",
-}

tests/multi-language-repo/global.json

@@ -1,6 +0,0 @@
-{
-  "sdk": {
-    "version": "9.0.307",
-    "rollForward": "latestFeature"
-  }
-}