Address review

Action size: Reduce duplication between `upload-lib` and `entry-points`

.github/actions/prepare-mergeback-branch/action.yml

@@ -41,7 +41,38 @@ runs:
         git add .
         git commit -m "Update changelog and version after ${VERSION}"
 
-        git push origin "${NEW_BRANCH}"
+    # Update the build artifacts with the new version number
+    - name: Rebuild the Action
+      shell: bash
+      run: |
+        set -exu
+        npm ci
+        npm run build
+
+    - name: Check for rebuild changes
+      id: rebuild_changes
+      shell: bash
+      run: |
+        set -exu
+        git add --all
+        if git diff --cached --quiet; then
+          echo "has_changes=false" >> "${GITHUB_OUTPUT}"
+        else
+          echo "has_changes=true" >> "${GITHUB_OUTPUT}"
+        fi
+
+    - name: Commit rebuild
+      if: steps.rebuild_changes.outputs.has_changes == 'true'
+      shell: bash
+      run: |
+        set -exu
+        git commit -m "Rebuild"
+
+    - name: Push mergeback branch
+      shell: bash
+      env:
+        NEW_BRANCH: "${{ inputs.branch }}"
+      run: git push origin "${NEW_BRANCH}"
 
     - name: Create PR
       shell: bash
@@ -60,8 +91,6 @@ runs:
 
           Please do the following:
 
-          - [ ] Remove and re-add the "Rebuild" label to the PR to trigger just this workflow.
-          - [ ] Wait for the "Rebuild" workflow to push a commit updating the distribution files.
           - [ ] Mark the PR as ready for review to trigger the full set of PR checks.
           - [ ] Approve and merge the PR. When merging the PR, make sure "Create a merge commit" is
                 selected rather than "Squash and merge" or "Rebase and merge".
@@ -74,7 +103,6 @@ runs:
           --head "${NEW_BRANCH}" \
           --base "${BASE_BRANCH}" \
           --title "${pr_title}" \
-          --label "Rebuild" \
           --body "${pr_body}" \
           --assignee "${GITHUB_ACTOR}" \
           --draft

.github/actions/release-initialise/action.yml

@@ -18,7 +18,7 @@ runs:
     - name: Set up Node
       uses: actions/setup-node@v6
       with:
-        node-version: 20
+        node-version: 24
         cache: 'npm'
 
     - name: Set up Python

.github/update-release-branch.py

@@ -16,12 +16,27 @@ No user facing changes.
 """
 
 # NB: This exact commit message is used to find commits for reverting during backports.
-# Changing it requires a transition period where both old and new versions are supported.
+# Changing it requires a transition period where both old and new versions are supported.
 BACKPORT_COMMIT_MESSAGE = 'Update version and changelog for v'
 
+# Commit message used for rebuild commits, both those produced by this script and those produced
+# by the `Rebuild Action` workflow (`.github/workflows/rebuild.yml`).
+REBUILD_COMMIT_MESSAGE = 'Rebuild'
+
 # Name of the remote
 ORIGIN = 'origin'
 
+# Environment variables to check for a GitHub API token.
+TOKEN_ENVIRONMENT_VARIABLES = ('GH_TOKEN', 'GITHUB_TOKEN')
+
+# Gets a GitHub API token from one of the supported environment variables.
+def get_github_token():
+  for variable_name in TOKEN_ENVIRONMENT_VARIABLES:
+    token = os.environ.get(variable_name, '').strip()
+    if token:
+      return token
+  raise Exception('Missing GitHub token. Set GITHUB_TOKEN or GH_TOKEN.')
+
 # Runs git with the given args and returns the stdout.
 # Raises an error if git does not exit successfully (unless passed
 # allow_non_zero_exit_code=True).
@@ -32,6 +47,28 @@ def run_git(*args, allow_non_zero_exit_code=False):
     raise Exception(f'Call to {" ".join(cmd)} exited with code {p.returncode} stderr: {p.stderr.decode("ascii")}.')
   return p.stdout.decode('ascii')
 
+# Runs the given command, streaming output to the console.
+# Raises an error if the command does not exit successfully.
+def run_command(*args):
+  cmd = list(args)
+  print(f'Running `{" ".join(cmd)}`.')
+  subprocess.run(cmd, check=True)
+
+# Rebuilds the action and commits any changes.
+def rebuild_action():
+  # For backports, the only source-level change vs the source branch is the new version number,
+  # so we just need to refresh the version embedded in `lib/`.
+  run_command('npm', 'ci')
+  run_command('npm', 'run', 'build')
+
+  run_git('add', '--all')
+  # `git diff --cached --quiet` exits 0 if there are no staged changes, 1 if there are.
+  if subprocess.run(['git', 'diff', '--cached', '--quiet']).returncode == 0:
+    print('Rebuild produced no changes; skipping Rebuild commit.')
+  else:
+    run_git('commit', '-m', REBUILD_COMMIT_MESSAGE)
+    print('Created Rebuild commit.')
+
 # Returns true if the given branch exists on the origin remote
 def branch_exists_on_remote(branch_name):
   return run_git('ls-remote', '--heads', ORIGIN, branch_name).strip() != ''
@@ -87,9 +124,11 @@ def open_pr(
   body.append('Please do the following:')
   if len(conflicted_files) > 0:
     body.append(' - [ ] Ensure `package.json` file contains the correct version.')
-    body.append(' - [ ] Add commits to this branch to resolve the merge conflicts ' +
+    body.append(' - [ ] Add a commit to this branch to resolve the merge conflicts ' +
       'in the following files:')
-    body.extend([f'    - [ ] `{file}`' for file in conflicted_files])
+    body.extend([f'    - `{file}`' for file in conflicted_files])
+    body.append(' - [ ] Rebuild the Action locally (`npm run build`) and push any changes to the ' +
+      f'built output in `lib` as a separate commit named exactly `{REBUILD_COMMIT_MESSAGE}`.')
     body.append(' - [ ] Ensure another maintainer has reviewed the additional commits you added to this ' +
       'branch to resolve the merge conflicts.')
   body.append(' - [ ] Ensure the CHANGELOG displays the correct version and date.')
@@ -97,10 +136,6 @@ def open_pr(
   body.append(f' - [ ] Check that there are not any unexpected commits being merged into the `{target_branch}` branch.')
   body.append(' - [ ] Ensure the docs team is aware of any documentation changes that need to be released.')
 
-  if not is_primary_release:
-    body.append(' - [ ] Remove and re-add the "Rebuild" label to the PR to trigger just this workflow.')
-    body.append(' - [ ] Wait for the "Rebuild" workflow to push a commit updating the distribution files.')
-
   body.append(' - [ ] Mark the PR as ready for review to trigger the full set of PR checks.')
   body.append(' - [ ] Approve and merge this PR. Make sure `Create a merge commit` is selected rather than `Squash and merge` or `Rebase and merge`.')
 
@@ -109,13 +144,11 @@ def open_pr(
     body.append(' - [ ] Merge all backport PRs to older release branches, that will automatically be created once this PR is merged.')
 
   title = f'Merge {source_branch} into {target_branch}'
-  labels = ['Rebuild'] if not is_primary_release else []
 
   # Create the pull request
   # PR checks won't be triggered on PRs created by Actions. Therefore mark the PR as draft so that
   # a maintainer can take the PR out of draft, thereby triggering the PR checks.
   pr = repo.create_pull(title=title, body='\n'.join(body), head=new_branch_name, base=target_branch, draft=True)
-  pr.add_to_labels(*labels)
   print(f'Created PR #{str(pr.number)}')
 
   # Assign the conductor
@@ -270,12 +303,6 @@ def update_changelog(version):
 def main():
   parser = argparse.ArgumentParser('update-release-branch.py')
 
-  parser.add_argument(
-    '--github-token',
-    type=str,
-    required=True,
-    help='GitHub token, typically from GitHub Actions.'
-  )
   parser.add_argument(
     '--repository-nwo',
     type=str,
@@ -313,7 +340,7 @@ def main():
   target_branch = args.target_branch
   is_primary_release = args.is_primary_release
 
-  repo = Github(args.github_token).get_repo(args.repository_nwo)
+  repo = Github(get_github_token()).get_repo(args.repository_nwo)
 
   # the target branch will be of the form releases/vN, where N is the major version number
   target_branch_major_version = target_branch.strip('releases/v')
@@ -380,8 +407,9 @@ def main():
       # releases.
       run_git('revert', vOlder_update_commits[0], '--no-edit')
 
-      # Also revert the "Rebuild" commit created by Actions.
+      # Also revert the "Rebuild" commit, whether created by this script or by the
-      rebuild_commit = run_git('log', '--grep', '^Rebuild$', '--format=%H').split()[0]
+      # `Rebuild Action` workflow.
+      rebuild_commit = run_git('log', '--grep', f'^{REBUILD_COMMIT_MESSAGE}$', '--format=%H').split()[0]
       print(f'  Reverting {rebuild_commit}')
       run_git('revert', rebuild_commit, '--no-edit')
 
@@ -396,9 +424,10 @@ def main():
       run_git('add', '.')
       run_git('commit', '--no-edit')
 
-    # Migrate the package version number from a vLatest version number to a vOlder version number
+    # Migrate the package version number from a vLatest version number to a vOlder version number.
+    # `package-lock.json` is updated as part of the subsequent rebuild step (see `rebuild_action`).
     print(f'Setting version number to {version} in package.json')
-    replace_version_package_json(get_current_version(), version) # We rely on the `Rebuild` workflow to update package-lock.json
+    replace_version_package_json(get_current_version(), version)
     run_git('add', 'package.json')
 
     # Migrate the changelog notes from vLatest version numbers to vOlder version numbers
@@ -421,6 +450,13 @@ def main():
     run_git('add', 'CHANGELOG.md')
     run_git('commit', '-m', f'Update changelog for v{version}')
 
+  if not is_primary_release:
+    if len(conflicted_files) == 0:
+      print('Rebuilding the Action.')
+      rebuild_action()
+    else:
+      print(f'Skipping automatic rebuild because the merge produced conflicts in {conflicted_files}.')
+
   run_git('push', ORIGIN, new_branch_name)
 
   # Open a PR to update the branch

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

@@ -49,10 +49,6 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - os: ubuntu-latest
-            version: stable-v2.17.6
-          - os: ubuntu-latest
-            version: stable-v2.18.4
           - os: ubuntu-latest
             version: stable-v2.19.4
           - os: ubuntu-latest
@@ -61,6 +57,10 @@ jobs:
             version: stable-v2.21.4
           - os: ubuntu-latest
             version: stable-v2.22.4
+          - os: ubuntu-latest
+            version: stable-v2.23.9
+          - os: ubuntu-latest
+            version: stable-v2.24.3
           - os: ubuntu-latest
             version: default
           - os: ubuntu-latest

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

@@ -49,10 +49,6 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - os: ubuntu-latest
-            version: stable-v2.17.6
-          - os: ubuntu-latest
-            version: stable-v2.18.4
           - os: ubuntu-latest
             version: stable-v2.19.4
           - os: ubuntu-latest
@@ -61,6 +57,10 @@ jobs:
             version: stable-v2.21.4
           - os: ubuntu-latest
             version: stable-v2.22.4
+          - os: ubuntu-latest
+            version: stable-v2.23.9
+          - os: ubuntu-latest
+            version: stable-v2.24.3
           - os: ubuntu-latest
             version: default
           - os: ubuntu-latest

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

@@ -49,10 +49,6 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - os: ubuntu-latest
-            version: stable-v2.17.6
-          - os: ubuntu-latest
-            version: stable-v2.18.4
           - os: ubuntu-latest
             version: stable-v2.19.4
           - os: ubuntu-latest
@@ -61,6 +57,10 @@ jobs:
             version: stable-v2.21.4
           - os: ubuntu-latest
             version: stable-v2.22.4
+          - os: ubuntu-latest
+            version: stable-v2.23.9
+          - os: ubuntu-latest
+            version: stable-v2.24.3
           - os: ubuntu-latest
             version: default
           - os: ubuntu-latest

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

@@ -59,41 +59,41 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - os: ubuntu-latest
-            version: stable-v2.17.6
-          - os: macos-latest
-            version: stable-v2.17.6
-          - os: ubuntu-latest
-            version: stable-v2.18.4
-          - os: macos-latest
-            version: stable-v2.18.4
           - os: ubuntu-latest
             version: stable-v2.19.4
-          - os: macos-latest
+          - os: macos-latest-xlarge
             version: stable-v2.19.4
           - os: ubuntu-latest
             version: stable-v2.20.7
-          - os: macos-latest
+          - os: macos-latest-xlarge
             version: stable-v2.20.7
           - os: ubuntu-latest
             version: stable-v2.21.4
-          - os: macos-latest
+          - os: macos-latest-xlarge
             version: stable-v2.21.4
           - os: ubuntu-latest
             version: stable-v2.22.4
-          - os: macos-latest
+          - os: macos-latest-xlarge
             version: stable-v2.22.4
+          - os: ubuntu-latest
+            version: stable-v2.23.9
+          - os: macos-latest-xlarge
+            version: stable-v2.23.9
+          - os: ubuntu-latest
+            version: stable-v2.24.3
+          - os: macos-latest-xlarge
+            version: stable-v2.24.3
           - os: ubuntu-latest
             version: default
-          - os: macos-latest
+          - os: macos-latest-xlarge
             version: default
           - os: ubuntu-latest
             version: linked
-          - os: macos-latest
+          - os: macos-latest-xlarge
             version: linked
           - os: ubuntu-latest
             version: nightly-latest
-          - os: macos-latest
+          - os: macos-latest-xlarge
             version: nightly-latest
     name: Multi-language repository
     if: github.triggering_actor != 'dependabot[bot]'

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

@@ -59,7 +59,7 @@ jobs:
           use-all-platform-bundle: 'false'
           setup-kotlin: 'true'
       - name: Set up Ruby
-        uses: ruby/setup-ruby@0cb964fd540e0a24c900370abf38a33466142735 # v1.305.0
+        uses: ruby/setup-ruby@c4e5b1316158f92e3d49443a9d58b31d25ac0f8f # v1.306.0
         with:
           ruby-version: 2.6
       - name: Install Code Scanning integration

.github/workflows/__rust.yml

@@ -40,7 +40,7 @@ jobs:
       matrix:
         include:
           - os: ubuntu-latest
-            version: stable-v2.19.3
+            version: stable-v2.19.4
           - os: ubuntu-latest
             version: stable-v2.22.1
           - os: ubuntu-latest

.github/workflows/__swift-autobuild.yml

@@ -39,7 +39,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - os: macos-latest
+          - os: macos-latest-xlarge
             version: nightly-latest
     name: Swift analysis using autobuild
     if: github.triggering_actor != 'dependabot[bot]'

.github/workflows/codeql.yml

@@ -77,7 +77,7 @@ 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-14-xlarge,macos-15-xlarge]
         tools: ${{ fromJson(needs.check-codeql-versions.outputs.versions) }}
     runs-on: ${{ matrix.os }}
 

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

@@ -6,13 +6,6 @@ env:
   # Diff informed queries add an additional query filter which is not yet
   # taken into account by these tests.
   CODEQL_ACTION_DIFF_INFORMED_QUERIES: false
-  # Specify overlay enablement manually to ensure stability around the exclude-from-incremental
-  # query filter. Here we only enable for the default code scanning suite.
-  CODEQL_ACTION_OVERLAY_ANALYSIS: true
-  CODEQL_ACTION_OVERLAY_ANALYSIS_JAVASCRIPT: false
-  CODEQL_ACTION_OVERLAY_ANALYSIS_CODE_SCANNING_JAVASCRIPT: true
-  CODEQL_ACTION_OVERLAY_ANALYSIS_STATUS_CHECK: false
-  CODEQL_ACTION_OVERLAY_ANALYSIS_SKIP_RESOURCE_CHECKS: true
 
 on:
   push:
@@ -79,33 +72,13 @@ jobs:
       with:
         version: ${{ matrix.version }}
 
-    # On PRs, overlay analysis may change the config that is passed to the CLI.
+    - name: Empty file
-    # Therefore, we have two variants of the following test, one for PRs and one for other events.
-    - name: Empty file (non-PR)
-      if: github.event_name != 'pull_request'
       uses: ./../action/.github/actions/check-codescanning-config
       with:
         expected-config-file-contents: "{}"
         languages: javascript
         tools: ${{ steps.prepare-test.outputs.tools-url }}
 
-    - name: Empty file (PR)
-      if: github.event_name == 'pull_request'
-      uses: ./../action/.github/actions/check-codescanning-config
-      with:
-        expected-config-file-contents: |
-          {
-            "query-filters": [
-              {
-                "exclude": {
-                  "tags": "exclude-from-incremental"
-                }
-              }
-            ]
-          }
-        languages: javascript
-        tools: ${{ steps.prepare-test.outputs.tools-url }}
-
     - name: Packs from input
       if: success() || failure()
       uses: ./../action/.github/actions/check-codescanning-config

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

@@ -48,6 +48,9 @@ jobs:
         with:
           fetch-depth: 0  # ensure we have all tags and can push commits
       - uses: actions/setup-node@v6
+        with:
+          node-version: 24
+          cache: 'npm'
       - uses: actions/setup-python@v6
         with:
           python-version: '3.12'
@@ -131,7 +134,7 @@ jobs:
           echo "::endgroup::"
 
       - name: Generate token
-        uses: actions/create-github-app-token@v3.1.1
+        uses: actions/create-github-app-token@v3.2.0
         id: app-token
         with:
           app-id: ${{ vars.AUTOMATION_APP_ID }}

.github/workflows/pr-checks.yml

@@ -105,10 +105,10 @@ jobs:
         run: npx tsx --test
 
   check-node-version:
-    if: github.triggering_actor != 'dependabot[bot]'
+    if: github.triggering_actor != 'dependabot[bot]' && startsWith(github.head_ref, 'backport-')
-    name: Check Action Node versions
+    name: Check Action Node versions for Backport
     runs-on: ubuntu-latest
-    timeout-minutes: 45
+    timeout-minutes: 5
     env:
       BASE_REF: ${{ github.base_ref }}
 
@@ -116,31 +116,40 @@ jobs:
       contents: read
 
     steps:
-      - uses: actions/checkout@v6
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 1
+
       - id: head-version
-        name: Verify all Actions use the same Node version
+        name: Determine Node version for HEAD
         run: |
-          NODE_VERSION=$(find . -name "action.yml" -exec yq -e '.runs.using' {} \; | grep node | sort | uniq)
+          if [[ ! -f ".nvmrc" ]]; then
-          echo "NODE_VERSION: ${NODE_VERSION}"
+            echo "::error::Cannot find .nvmrc in the HEAD commit."
-          if [[ $(echo "$NODE_VERSION" | wc -l) -gt 1 ]]; then
-            echo "::error::More than one node version used in 'action.yml' files."
             exit 1
           fi
+
+          NODE_VERSION=$(cat .nvmrc)
+          echo "NODE_VERSION: ${NODE_VERSION}"
           echo "node_version=${NODE_VERSION}" >> $GITHUB_OUTPUT
 
       - id: checkout-base
         name: 'Backport: Check out base ref'
-        if: ${{ startsWith(github.head_ref, 'backport-') }}
         uses: actions/checkout@v6
         with:
           ref: ${{ env.BASE_REF }}
+          fetch-depth: 1
 
       - name: 'Backport: Verify Node versions unchanged'
-        if: steps.checkout-base.outcome == 'success'
         env:
           HEAD_VERSION: ${{ steps.head-version.outputs.node_version }}
         run: |
-          BASE_VERSION=$(find . -name "action.yml" -exec yq -e '.runs.using' {} \; | grep node | sort | uniq)
+          if [[ ! -f ".nvmrc" ]]; then
+            echo "::error::Cannot find .nvmrc in the base commit."
+            exit 1
+          fi
+
+          BASE_VERSION=$(cat .nvmrc)
           echo "HEAD_VERSION: ${HEAD_VERSION}"
           echo "BASE_VERSION: ${BASE_VERSION}"
           if [[ "$BASE_VERSION" != "$HEAD_VERSION" ]]; then

.github/workflows/rollback-release.yml

@@ -136,7 +136,7 @@ jobs:
 
       - name: Generate token
         if: github.event_name == 'workflow_dispatch'
-        uses: actions/create-github-app-token@v3.1.1
+        uses: actions/create-github-app-token@v3.2.0
         id: app-token
         with:
           app-id: ${{ vars.AUTOMATION_APP_ID }}

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

@@ -64,11 +64,12 @@ jobs:
 
     - name: Update current release branch
       if: github.event_name == 'workflow_dispatch'
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       run: |
         echo SOURCE_BRANCH=${REF_NAME}
         echo TARGET_BRANCH=releases/${MAJOR_VERSION}
         python .github/update-release-branch.py \
-          --github-token ${{ secrets.GITHUB_TOKEN }} \
           --repository-nwo ${{ github.repository }} \
           --source-branch '${{ env.REF_NAME }}' \
           --target-branch 'releases/${{ env.MAJOR_VERSION }}' \
@@ -93,7 +94,7 @@ jobs:
       pull-requests: write # needed to create pull request
     steps:
     - name: Generate token
-      uses: actions/create-github-app-token@v3.1.1
+      uses: actions/create-github-app-token@v3.2.0
       id: app-token
       with:
         app-id: ${{ vars.AUTOMATION_APP_ID }}
@@ -107,11 +108,12 @@ jobs:
     - uses: ./.github/actions/release-initialise
 
     - name: Update older release branch
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       run: |
         echo SOURCE_BRANCH=${SOURCE_BRANCH}
         echo TARGET_BRANCH=${TARGET_BRANCH}
         python .github/update-release-branch.py \
-          --github-token ${{ secrets.GITHUB_TOKEN }} \
           --repository-nwo ${{ github.repository }} \
           --source-branch ${SOURCE_BRANCH} \
           --target-branch ${TARGET_BRANCH} \

.nvmrc

@@ -0,0 +1 @@
+24

.vscode/tests.code-snippets

@@ -19,7 +19,7 @@
     "scope": "javascript, typescript",
     "prefix": "testMacro",
     "body": [
-      "const ${1:nameMacro} = test.macro({",
+      "const ${1:nameMacro} = makeMacro({",
       "  exec: async (t: ExecutionContext<unknown>) => {},",
       "",
       "  title: (providedTitle = \"\") => `${2:common title} - \\${providedTitle}`,",

CHANGELOG.md

@@ -4,7 +4,19 @@ See the [releases page](https://github.com/github/codeql-action/releases) for th
 
 ## [UNRELEASED]
 
-No user facing changes.
+- _Breaking change_: Bump the minimum required CodeQL bundle version to 2.19.4. [#3894](https://github.com/github/codeql-action/pull/3894)
+- Add support for SHA-256 Git object IDs. [#3893](https://github.com/github/codeql-action/pull/3893)
+
+## 4.35.5 - 15 May 2026
+
+- We have improved how the JavaScript bundles for the CodeQL Action are generated to avoid duplication across bundles and reduce the size of the repository by around 70%. This should have no effect on the runtime behaviour of the CodeQL Action. [#3899](https://github.com/github/codeql-action/pull/3899)
+- For performance and accuracy reasons, [improved incremental analysis](https://github.com/github/roadmap/issues/1158) will now only be enabled on a pull request when diff-informed analysis is also enabled for that run. If diff-informed analysis is unavailable (for example, because the PR diff ranges could not be computed), the action will fall back to a full analysis. [#3791](https://github.com/github/codeql-action/pull/3791)
+- If multiple inputs are provided for the GitHub-internal `analysis-kinds` input, only `code-scanning` will be enabled. The `analysis-kinds` input is experimental, for GitHub-internal use only, and may change without notice at any time. [#3892](https://github.com/github/codeql-action/pull/3892)
+- Added an experimental change which, when running a Code Scanning analysis for a PR with [improved incremental analysis](https://github.com/github/roadmap/issues/1158) enabled, prefers CodeQL CLI versions that have a cached overlay-base database for the configured languages. This speeds up analysis for a repository when there is not yet a cached overlay-base database for the latest CLI version. We expect to roll this change out to everyone in May. [#3880](https://github.com/github/codeql-action/pull/3880)
+
+## 4.35.4 - 07 May 2026
+
+- Update default CodeQL bundle version to [2.25.4](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.25.4). [#3881](https://github.com/github/codeql-action/pull/3881)
 
 ## 4.35.3 - 01 May 2026
 

CONTRIBUTING.md

@@ -71,7 +71,7 @@ Once the mergeback and backport pull request have been merged, the release is co
 
 Since the `codeql-action` runs most of its testing through individual Actions workflows, there are over two hundred required jobs that need to pass in order for a PR to turn green. It would be too tedious to maintain that list manually. You can regenerate the set of required checks automatically by running the [sync-checks.ts](pr-checks/sync-checks.ts) script:
 
-- At a minimum, you must provide an argument for the `--token` input. For example, `--token "$(gh auth token)"` to use the same token that `gh` uses. If no token is provided or the token has insufficient permissions, the script will fail.
+- At a minimum, you must provide a token with permissions to update branch protection rules. For example, `gh auth token | pr-checks/sync-checks.ts --token-stdin` uses the same token that `gh` uses. You can also set the `GH_TOKEN` or `GITHUB_TOKEN` environment variable. If no token is provided or the token has insufficient permissions, the script will fail.
 - By default, the script performs a dry run and outputs information about the changes it would make to the branch protection rules. To actually apply the changes, specify the `--apply` flag.
 - If you run the script without any other arguments, it will retrieve the set of workflows that ran for the latest commit on `main`.
 - You can specify a different git ref with the `--ref` input. You will likely want to use this if you have a PR that removes or adds PR checks. For example, `--ref "some/branch/name"` to use the HEAD of the `some/branch/name` branch.

README.md

@@ -78,8 +78,6 @@ We typically release new minor versions of the CodeQL Action and Bundle when a n
 | `v3.28.21` | `2.21.3` | Enterprise Server 3.18 | |
 | `v3.28.12` | `2.20.7` | Enterprise Server 3.17 | |
 | `v3.28.6` | `2.20.3` | Enterprise Server 3.16 | |
-| `v3.28.6` | `2.20.3` | Enterprise Server 3.15 | |
-| `v3.28.6` | `2.20.3` | Enterprise Server 3.14 | |
 
 See the full list of GHES release and deprecation dates at [GitHub Enterprise Server releases](https://docs.github.com/en/enterprise-server/admin/all-releases#releases-of-github-enterprise-server).
 

analyze/action.yml

@@ -95,5 +95,5 @@ outputs:
     description: The ID of the uploaded SARIF file.
 runs:
   using: node24
-  main: "../lib/analyze-action.js"
+  main: "../lib/analyze-entry.js"
-  post: "../lib/analyze-action-post.js"
+  post: "../lib/analyze-post-entry.js"

autobuild/action.yml

@@ -16,4 +16,4 @@ inputs:
     required: false
 runs:
   using: node24
-  main: '../lib/autobuild-action.js'
+  main: '../lib/autobuild-entry.js'

build.mjs

@@ -1,9 +1,10 @@
-import { copyFile, rm, writeFile } from "node:fs/promises";
+import { copyFile, readFile, rm, writeFile } from "node:fs/promises";
-import { dirname, join } from "node:path";
+import { basename, dirname, join } from "node:path";
 import { fileURLToPath } from "node:url";
 
 import * as esbuild from "esbuild";
 import { globSync } from "glob";
+import * as yaml from "js-yaml";
 
 import pkg from "./package.json" with { type: "json" };
 
@@ -27,6 +28,70 @@ const cleanPlugin = {
   },
 };
 
+/** A plugin that checks that the Node versions in all `action.yml` files are the same. */
+const checkNodeVersionsPlugin = {
+  name: "check-node-versions",
+  setup(build) {
+    build.onStart(async () => {
+      // Find all the `action.yml` files. We don't care about the stub in the repository root,
+      // since that is a `composite` action.
+      const actionSpecifications = globSync("*/action.yml");
+
+      // Track the Node versions we find for each file.
+      const nodeVersions = {};
+
+      // We will store the first Node version we find and use it to compare against the others.
+      // If there's any disagreement, we set `versionMismatch` to `true` and throw an error
+      // that includes all the discovered Node versions at the end.
+      let nodeVersion = undefined;
+      let versionMismatch = false;
+
+      for (const actionSpecification of actionSpecifications) {
+        // Read the contents of the action.yml file.
+        const contents = await readFile(actionSpecification, "utf-8");
+        const specification = yaml.load(contents);
+
+        // Find the `runs.using` value in the specification.
+        const using = specification.runs.using;
+        if (using === undefined || using === null) {
+          throw new Error(
+            `Couldn't find 'runs.using' in ${actionSpecification}`,
+          );
+        }
+
+        if (typeof using !== "string" || !using.startsWith("node")) {
+          throw new Error(
+            `Expected 'runs.using' to be a string starting with 'node' in ${actionSpecification}`,
+          );
+        }
+
+        if (nodeVersion === undefined) {
+          // First one we found: set it as the baseline.
+          nodeVersion = using;
+        } else if (nodeVersion !== using) {
+          // Disagreement: set `versionMismatch` to indicate that we should throw an error later.
+          versionMismatch = true;
+        }
+        nodeVersions[actionSpecification] = using;
+      }
+
+      // Throw an error if there was a version mismatch.
+      if (versionMismatch) {
+        throw new Error(
+          `More than one node version used in 'action.yml' files: ${JSON.stringify(nodeVersions)}`,
+        );
+      }
+
+      // Write the node version to `.nvmrc`.
+      await writeFile(
+        join(__dirname, ".nvmrc"),
+        nodeVersion.substring("node".length) + "\n",
+        "utf-8",
+      );
+    });
+  },
+};
+
 /**
  * Copy defaults.json to the output directory since other projects depend on it.
  *
@@ -62,18 +127,159 @@ const onEndPlugin = {
   },
 };
 
+/** The name of the virtual `entry-points` module. */
+const SHARED_ENTRYPOINT = "entry-points";
+
+/** The property name under which `upload-lib`'s namespace is exposed in `entry-points`. */
+const UPLOAD_LIB_EXPORT = "uploadLib";
+
+/** The relative source path of the `upload-lib` module that we re-export from `entry-points`. */
+const UPLOAD_LIB_SRC = "./src/upload-lib";
+
+/**
+ * This plugin finds all source files that contain Action entry points. It then generates the
+ * virtual `entry-points` module which imports all identified files, and re-exports their
+ * `runWrapper` functions with suitable aliases.
+ *
+ * The virtual module additionally re-exports `upload-lib` under the `uploadLib` namespace so that
+ * external consumers can access it via the small `lib/upload-lib.js` stub emitted below.
+ *
+ * A tiny stub file is emitted for each Action entrypoint, and one for `upload-lib`. Each stub
+ * imports the shared bundle and calls/re-exports from the respective entry point.
+ *
+ * @type {esbuild.Plugin}
+ */
+const entryPointsPlugin = {
+  name: "entry-points",
+  setup(build) {
+    const namespace = "actions";
+    const actions = [];
+
+    const toPascal = (s) =>
+      s.replace(/(^|-)([a-z0-9])/gi, (_, __, c) => c.toUpperCase());
+
+    // Find the source files containing Action entry points.
+    build.onStart(() => {
+      const actionFiles = globSync("src/*-action{,-post}.ts");
+      for (const actionFile of actionFiles) {
+        const match = basename(actionFile).match(/(.*)-action(-post)?/);
+
+        if (match.length < 2) {
+          throw new Error(`'${actionFile}' didn't match expected pattern.`);
+        }
+
+        const actionName = match[1];
+        const isPost = match[2] !== undefined;
+
+        actions.push({
+          path: actionFile,
+          name: actionName,
+          isPost,
+          pascalCaseName: `${toPascal(actionName)}${isPost ? "Post" : ""}Action`,
+        });
+      }
+    });
+
+    // Resolve the virtual `entry-points` file and set the corresponding namespace.
+    // Ideally, we'd `RegExp.escape` the entrypoint here, but that API isn't supported in Node 20.
+    // Since we're dealing with a hardcoded string, this isn't too much of a problem.
+    build.onResolve({ filter: new RegExp(`^${SHARED_ENTRYPOINT}$`) }, () => {
+      return { path: SHARED_ENTRYPOINT, namespace };
+    });
+
+    // Generate the virtual `entry-points` file based on the Actions we discovered.
+    // Restrict using the namespace. The path filter does not need to discriminate any further.
+    build.onLoad({ filter: /.*/, namespace }, async () => {
+      const wrapperTemplatePath = "entry-wrapper.js.tpl";
+      const wrapperTemplate = await readFile(
+        join(SRC_DIR, wrapperTemplatePath),
+        "utf-8",
+      );
+
+      const actionsSorted = actions.sort((a, b) =>
+        a.name.localeCompare(b.name),
+      );
+      const imports = actionsSorted
+        .map(
+          (action) =>
+            `import * as ${action.pascalCaseName} from "./src/${basename(action.path)}";`,
+        )
+        .join("\n");
+      const wrappers = actionsSorted
+        .map((action) =>
+          wrapperTemplate.replaceAll("__ACTION__", action.pascalCaseName),
+        )
+        .join("\n\n");
+
+      // Also re-export the `upload-lib` namespace so that external consumers can reach it
+      // via the `lib/upload-lib.js` stub without us having to bundle a second copy.
+      const uploadLibReExport = `export * as ${UPLOAD_LIB_EXPORT} from "${UPLOAD_LIB_SRC}";`;
+
+      return {
+        contents: `"use strict";\n${imports}\n\n${uploadLibReExport}\n\n${wrappers}\n`,
+        resolveDir: ".",
+        loader: "ts",
+      };
+    });
+
+    // Emit entry point stubs for each Action using the entry template.
+    build.onEnd(async () => {
+      const makeHeader = (templatePath, sourceFile) =>
+        `// Automatically generated from '${templatePath}' for 'src/${basename(sourceFile)}'.\n\n`;
+
+      // Read the entry point template.
+      const actionTemplatePath = "action-entry.js.tpl";
+      const actionTemplate = await readFile(
+        join(SRC_DIR, actionTemplatePath),
+        "utf-8",
+      );
+
+      // Write entry point stubs for each Action.
+      for (const action of actions) {
+        await writeFile(
+          join(
+            OUT_DIR,
+            `${action.name}${action.isPost ? "-post" : ""}-entry.js`,
+          ),
+          makeHeader(actionTemplatePath, action.path) +
+            actionTemplate.replaceAll("__ACTION__", action.pascalCaseName),
+        );
+      }
+
+      // Write a small stub for `upload-lib` that re-exports it from the shared bundle.
+      // External callers (e.g. internal testing environments) `require("./lib/upload-lib")`
+      // and expect the same shape as before, so we expose the namespace as `module.exports`.
+      const uploadLibStubTemplatePath = "upload-lib-stub.js.tpl";
+      const uploadLibStubTemplate = await readFile(
+        join(SRC_DIR, uploadLibStubTemplatePath),
+        "utf-8",
+      );
+      await writeFile(
+        join(OUT_DIR, "upload-lib.js"),
+        makeHeader(uploadLibStubTemplatePath, `${UPLOAD_LIB_SRC}.ts`) +
+          uploadLibStubTemplate.replaceAll(
+            "__UPLOAD_LIB_EXPORT__",
+            UPLOAD_LIB_EXPORT,
+          ),
+      );
+    });
+  },
+};
+
 const context = await esbuild.context({
-  // Include upload-lib.ts as an entry point for use in testing environments.
+  entryPoints: [{ in: SHARED_ENTRYPOINT, out: SHARED_ENTRYPOINT }],
-  entryPoints: globSync([
-    `${SRC_DIR}/*-action.ts`,
-    `${SRC_DIR}/*-action-post.ts`,
-    "src/upload-lib.ts",
-  ]),
   bundle: true,
   format: "cjs",
   outdir: OUT_DIR,
   platform: "node",
-  plugins: [cleanPlugin, copyDefaultsPlugin, onEndPlugin],
+  external: ["./entry-points"],
+  plugins: [
+    cleanPlugin,
+    checkNodeVersionsPlugin,
+    copyDefaultsPlugin,
+    entryPointsPlugin,
+    onEndPlugin,
+  ],
   target: ["node20"],
   define: {
     __CODEQL_ACTION_VERSION__: JSON.stringify(pkg.version),

init/action.yml

@@ -171,5 +171,5 @@ outputs:
     description: The version of the CodeQL binary used for analysis
 runs:
   using: node24
-  main: '../lib/init-action.js'
+  main: '../lib/init-entry.js'
-  post: '../lib/init-action-post.js'
+  post: '../lib/init-post-entry.js'

lib/analyze-entry.js

@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/analyze-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runAnalyzeAction)();

lib/analyze-post-entry.js

@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/analyze-action-post.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runAnalyzePostAction)();

lib/autobuild-entry.js

@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/autobuild-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runAutobuildAction)();

lib/defaults.json

@@ -1,6 +1,6 @@
 {
-  "bundleVersion": "codeql-bundle-v2.25.3",
+  "bundleVersion": "codeql-bundle-v2.25.4",
-  "cliVersion": "2.25.3",
+  "cliVersion": "2.25.4",
-  "priorBundleVersion": "codeql-bundle-v2.25.2",
+  "priorBundleVersion": "codeql-bundle-v2.25.3",
-  "priorCliVersion": "2.25.2"
+  "priorCliVersion": "2.25.3"
 }

lib/init-entry.js

@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/init-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runInitAction)();

lib/init-post-entry.js

@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/init-action-post.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runInitPostAction)();

lib/resolve-environment-entry.js

@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/resolve-environment-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runResolveEnvironmentAction)();

lib/setup-codeql-entry.js

@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/setup-codeql-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runSetupCodeqlAction)();

lib/start-proxy-entry.js

@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/start-proxy-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runStartProxyAction)();

lib/start-proxy-post-entry.js

@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/start-proxy-action-post.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runStartProxyPostAction)();

lib/upload-sarif-entry.js

@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/upload-sarif-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runUploadSarifAction)();

lib/upload-sarif-post-entry.js

@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/upload-sarif-action-post.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runUploadSarifPostAction)();

package.json

@@ -1,18 +1,19 @@
 {
   "name": "codeql",
-  "version": "4.35.4",
+  "version": "4.36.0",
   "private": true,
   "description": "CodeQL action",
   "scripts": {
     "_build_comment": "echo 'Run the full build so we typecheck the project and can reuse the transpiled files in npm test'",
-    "build": "./scripts/check-node-modules.sh && npm run transpile && node build.mjs && npx tsx ./pr-checks/bundle-metadata.ts",
+    "build": "./scripts/check-node-modules.sh && npm run transpile && node build.mjs",
     "lint": "eslint --report-unused-disable-directives --max-warnings=0 .",
     "lint-ci": "SARIF_ESLINT_IGNORE_SUPPRESSED=true eslint --report-unused-disable-directives --max-warnings=0 . --format @microsoft/eslint-formatter-sarif --output-file=eslint.sarif",
     "lint-fix": "eslint --report-unused-disable-directives --max-warnings=0 . --fix",
     "ava": "npm run transpile && ava --verbose",
     "test": "npm run ava -- src/",
     "test-debug": "npm run test -- --timeout=20m",
-    "transpile": "tsc --build --verbose tsconfig.json"
+    "transpile": "tsc --build --verbose tsconfig.json",
+    "update-pr-checks": "./pr-checks/sync.sh"
   },
   "license": "MIT",
   "workspaces": [
@@ -43,32 +44,32 @@
     "uuid": "^14.0.0"
   },
   "devDependencies": {
-    "@ava/typescript": "7.0.0",
+    "@ava/typescript": "6.0.0",
     "@eslint/compat": "^2.0.5",
     "@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": "^20.19.39",
     "@types/node-forge": "^1.3.14",
     "@types/sarif": "^2.1.7",
     "@types/semver": "^7.7.1",
     "@types/sinon": "^21.0.1",
-    "ava": "^7.0.0",
+    "ava": "^6.4.1",
     "esbuild": "^0.28.0",
-    "eslint": "^9.39.2",
+    "eslint": "^9.39.4",
     "eslint-import-resolver-typescript": "^4.4.4",
     "eslint-plugin-github": "^6.0.0",
     "eslint-plugin-import-x": "^4.16.2",
     "eslint-plugin-jsdoc": "^62.9.0",
     "eslint-plugin-no-async-foreach": "^0.1.1",
     "glob": "^11.1.0",
-    "globals": "^17.5.0",
+    "globals": "^17.6.0",
     "nock": "^14.0.12",
-    "sinon": "^21.1.2",
+    "sinon": "^22.0.0",
-    "typescript": "^6.0.2",
+    "typescript": "^6.0.3",
-    "typescript-eslint": "^8.58.2"
+    "typescript-eslint": "^8.59.2"
   },
   "overrides": {
     "@actions/tool-cache": {
@@ -89,7 +90,6 @@
     "eslint-plugin-jsx-a11y": {
       "semver": ">=6.3.1"
     },
-    "brace-expansion@2.0.1": "2.0.2",
     "glob": "^11.1.0",
     "undici": "^6.24.0"
   }

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

@@ -2,7 +2,8 @@ name: "Multi-language repository"
 description: "An end-to-end integration test of a multi-language repository using automatic language detection"
 operatingSystems:
   - ubuntu
-  - macos
+  - os: macos
+    runner-image: macos-latest-xlarge
 env:
   CODEQL_ACTION_RESOLVE_SUPPORTED_LANGUAGES_USING_CLI: true
 installGo: true

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

@@ -5,7 +5,7 @@ versions:
   - default
 steps:
   - name: Set up Ruby
-    uses: ruby/setup-ruby@0cb964fd540e0a24c900370abf38a33466142735 # v1.305.0
+    uses: ruby/setup-ruby@c4e5b1316158f92e3d49443a9d58b31d25ac0f8f # v1.306.0
     with:
       ruby-version: 2.6
   - name: Install Code Scanning integration

pr-checks/checks/rust.yml

@@ -2,7 +2,7 @@ name: "Rust analysis"
 description: "Tests creation of a Rust database"
 versions:
   # experimental rust support introduced, requires action to set `CODEQL_ENABLE_EXPERIMENTAL_FEATURES`
-  - stable-v2.19.3
+  - stable-v2.19.4
   # first public preview version
   - stable-v2.22.1
   - linked

pr-checks/checks/swift-autobuild.yml

@@ -3,7 +3,8 @@ description: "Tests creation of a Swift database using autobuild"
 versions:
   - nightly-latest
 operatingSystems:
-  - macos
+  - os: macos
+    runner-image: macos-latest-xlarge
 steps:
   - uses: ./../action/init
     id: init

pr-checks/package.json

@@ -7,10 +7,10 @@
     "@octokit/core": "^7.0.6",
     "@octokit/plugin-paginate-rest": ">=9.2.2",
     "@octokit/plugin-rest-endpoint-methods": "^17.0.0",
-    "yaml": "^2.8.3"
+    "yaml": "^2.8.4"
   },
   "devDependencies": {
-    "@types/node": "^20.19.9",
+    "@types/node": "^20.19.39",
     "tsx": "^4.21.0"
   }
 }

pr-checks/sync-checks.test.ts

@@ -7,7 +7,13 @@ Tests for the sync-checks.ts script
 import * as assert from "node:assert/strict";
 import { describe, it } from "node:test";
 
-import { CheckInfo, Exclusions, Options, removeExcluded } from "./sync-checks";
+import {
+  CheckInfo,
+  Exclusions,
+  Options,
+  removeExcluded,
+  resolveToken,
+} from "./sync-checks";
 
 const defaultOptions: Options = {
   apply: false,
@@ -58,3 +64,46 @@ describe("removeExcluded", async () => {
     assert.deepEqual(retained, expectedExactMatches);
   });
 });
+
+describe("resolveToken", async () => {
+  await it("reads the token from standard input", async () => {
+    const token = await resolveToken(
+      { tokenStdin: true },
+      { env: {}, readStdin: async () => " stdin-token\n" },
+    );
+    assert.equal(token, "stdin-token");
+  });
+
+  await it("reads the token from the GH_TOKEN environment variable", async () => {
+    const token = await resolveToken(
+      {},
+      { env: { GH_TOKEN: "env-token" }, readStdin: async () => "" },
+    );
+    assert.equal(token, "env-token");
+  });
+
+  await it("reads the token from the GITHUB_TOKEN environment variable", async () => {
+    const token = await resolveToken(
+      {},
+      { env: { GITHUB_TOKEN: "env-token" }, readStdin: async () => "" },
+    );
+    assert.equal(token, "env-token");
+  });
+
+  await it("rejects an empty standard input token", async () => {
+    await assert.rejects(
+      resolveToken(
+        { tokenStdin: true },
+        { env: {}, readStdin: async () => "\n" },
+      ),
+      /No token received on standard input/,
+    );
+  });
+
+  await it("rejects missing token sources", async () => {
+    await assert.rejects(
+      resolveToken({}, { env: {}, readStdin: async () => "" }),
+      /Missing authentication token/,
+    );
+  });
+});

pr-checks/sync-checks.ts

@@ -15,8 +15,8 @@ import {
 
 /** Represents the command-line options. */
 export interface Options {
-  /** The token to use to authenticate to the GitHub API. */
+  /** Whether to read the GitHub API token from standard input. */
-  token?: string;
+  tokenStdin?: boolean;
   /** The git ref to use the checks for. */
   ref?: string;
   /** Whether to actually apply the changes or not. */
@@ -31,6 +31,65 @@ const codeqlActionRepo = {
   repo: "codeql-action",
 };
 
+/** Environment variables to check for a GitHub API token. */
+const TOKEN_ENVIRONMENT_VARIABLES = ["GH_TOKEN", "GITHUB_TOKEN"];
+
+/** Represents the sources from which we can retrieve the GitHub API token. */
+interface TokenSource {
+  /** Environment variables to inspect. */
+  env: NodeJS.ProcessEnv;
+  /** Reads a token from standard input. */
+  readStdin: () => Promise<string>;
+}
+
+/** Reads the GitHub API token from standard input. */
+async function readTokenFromStdin(): Promise<string> {
+  let token = "";
+  process.stdin.setEncoding("utf8");
+  for await (const chunk of process.stdin) {
+    token += chunk;
+  }
+  return token.trim();
+}
+
+/** Gets a GitHub API token from one of the supported environment variables. */
+function getTokenFromEnvironment(env: NodeJS.ProcessEnv): string | undefined {
+  for (const variableName of TOKEN_ENVIRONMENT_VARIABLES) {
+    const token = env[variableName]?.trim();
+    if (token) {
+      return token;
+    }
+  }
+  return undefined;
+}
+
+/** Gets the token to use to authenticate to the GitHub API. */
+export async function resolveToken(
+  options: Pick<Options, "tokenStdin">,
+  tokenSource: TokenSource = {
+    env: process.env,
+    readStdin: readTokenFromStdin,
+  },
+): Promise<string> {
+  if (options.tokenStdin) {
+    const token = (await tokenSource.readStdin()).trim();
+    if (token.length === 0) {
+      throw new Error("No token received on standard input.");
+    }
+    return token;
+  }
+
+  const environmentToken = getTokenFromEnvironment(tokenSource.env);
+  if (environmentToken !== undefined) {
+    return environmentToken;
+  }
+
+  throw new Error(
+    "Missing authentication token. Set GH_TOKEN/GITHUB_TOKEN or pipe a token " +
+      "to --token-stdin.",
+  );
+}
+
 /** Represents a configuration of which checks should not be set up as required checks. */
 export interface Exclusions {
   /** A list of strings that, if contained in a check name, are excluded. */
@@ -205,9 +264,10 @@ async function updateBranch(
 async function main(): Promise<void> {
   const { values: options } = parseArgs({
     options: {
-      // The token to use to authenticate to the API.
+      // Read the token to use to authenticate to the API from standard input.
-      token: {
+      "token-stdin": {
-        type: "string",
+        type: "boolean",
+        default: false,
       },
       // The git ref for which to retrieve the check runs.
       ref: {
@@ -228,16 +288,16 @@ async function main(): Promise<void> {
     strict: true,
   });
 
-  if (options.token === undefined) {
+  const token = await resolveToken({
-    throw new Error("Missing --token");
+    tokenStdin: options["token-stdin"],
-  }
+  });
 
   console.info(
     `Oldest supported major version is: ${OLDEST_SUPPORTED_MAJOR_VERSION}`,
   );
 
   // Initialise the API client.
-  const client = getApiClient(options.token);
+  const client = getApiClient(token);
 
   // Find the check runs for the specified `ref` that we will later set as the required checks
   // for the main and release branches.

pr-checks/sync.ts

@@ -28,6 +28,24 @@ interface WorkflowInput {
 /** A partial mapping from known input names to input definitions. */
 type WorkflowInputs = Partial<Record<KnownInputName, WorkflowInput>>;
 
+/** An operating system identifier. */
+type OperatingSystemIdentifier = "ubuntu" | "macos" | "windows";
+
+/**
+ * Represents an operating system matrix entry for a generated PR check workflow.
+ *
+ * Either a string containing the OS identifier or an object containing the OS identifier and an
+ * optional runner image label.
+ */
+type OperatingSystem =
+  | OperatingSystemIdentifier
+  | {
+      /** OS identifier. */
+      os: OperatingSystemIdentifier;
+      /** Optional runner image label. */
+      "runner-image"?: string;
+    };
+
 /**
  * Represents PR check specifications.
  */
@@ -36,8 +54,8 @@ interface Specification extends JobSpecification {
   inputs?: Record<string, WorkflowInput>;
   /** CodeQL bundle versions to test against. Defaults to `DEFAULT_TEST_VERSIONS`. */
   versions?: string[];
-  /** Operating system prefixes used to select runner images (e.g. `["ubuntu", "macos"]`). */
+  /** Operating system prefixes, either as strings or with explicit runner image labels. */
-  operatingSystems?: string[];
+  operatingSystems?: OperatingSystem[];
   /** Per-OS version overrides. If specified for an OS, only those versions are tested on that OS. */
   osCodeQlVersions?: Record<string, string[]>;
   /** Whether to use the all-platform CodeQL bundle. */
@@ -97,10 +115,6 @@ type LanguageSetups = Partial<Record<BuiltInLanguage, LanguageSetup>>;
 // The default set of CodeQL Bundle versions to use for the PR checks.
 const defaultTestVersions = [
   // The oldest supported CodeQL version. If bumping, update `CODEQL_MINIMUM_VERSION` in `codeql.ts`
-  "stable-v2.17.6",
-  // The last CodeQL release in the 2.18 series.
-  "stable-v2.18.4",
-  // The last CodeQL release in the 2.19 series.
   "stable-v2.19.4",
   // The last CodeQL release in the 2.20 series.
   "stable-v2.20.7",
@@ -108,6 +122,10 @@ const defaultTestVersions = [
   "stable-v2.21.4",
   // The last CodeQL release in the 2.22 series.
   "stable-v2.22.4",
+  // The last CodeQL release in the 2.23 series.
+  "stable-v2.23.9",
+  // The last CodeQL release in the 2.24 series.
+  "stable-v2.24.3",
   // The default version of CodeQL for Dotcom, as determined by feature flags.
   "default",
   // The version of CodeQL shipped with the Action in `defaults.json`. During the release process
@@ -311,10 +329,19 @@ function generateJobMatrix(
       );
     }
 
-    const runnerImages = ["ubuntu-latest", "macos-latest", "windows-latest"];
+    const defaultRunnerImages = [
+      "ubuntu-latest",
+      "macos-latest",
+      "windows-latest",
+    ];
     const operatingSystems = checkSpecification.operatingSystems ?? ["ubuntu"];
 
-    for (const operatingSystem of operatingSystems) {
+    for (const operatingSystemConfig of operatingSystems) {
+      const operatingSystem =
+        typeof operatingSystemConfig === "string"
+          ? operatingSystemConfig
+          : operatingSystemConfig.os;
+
       // If osCodeQlVersions is set for this OS, only include the specified CodeQL versions.
       const allowedVersions =
         checkSpecification.osCodeQlVersions?.[operatingSystem];
@@ -322,9 +349,13 @@ function generateJobMatrix(
         continue;
       }
 
-      const runnerImagesForOs = runnerImages.filter((image) =>
+      const runnerImagesForOs =
-        image.startsWith(operatingSystem),
+        typeof operatingSystemConfig === "string" ||
-      );
+        operatingSystemConfig["runner-image"] === undefined
+          ? defaultRunnerImages.filter((image) =>
+              image.startsWith(operatingSystem),
+            )
+          : [operatingSystemConfig["runner-image"]];
 
       for (const runnerImage of runnerImagesForOs) {
         matrix.push({

resolve-environment/action.yml

@@ -22,4 +22,4 @@ outputs:
     description: The inferred build environment configuration.
 runs:
   using: node24
-  main: '../lib/resolve-environment-action.js'
+  main: '../lib/resolve-environment-entry.js'

setup-codeql/action.yml

@@ -19,6 +19,25 @@ inputs:
       If not specified, the Action will check in several places until it finds
       the CodeQL tools.
     required: false
+  languages:
+    description: >-
+      A comma-separated list of CodeQL languages that will be analyzed in subsequent
+      `github/codeql-action/init` and `github/codeql-action/analyze` invocations. If specified, the
+      Action may use this list to select a CodeQL CLI version that is best suited to analyzing those
+      languages, for example by preferring a version that has a cached overlay-base database for the
+      specified languages. This input is not remembered and must also be passed to
+      `github/codeql-action/init`.
+    required: false
+  analysis-kinds:
+    description: >-
+      [Internal] A comma-separated list of analysis kinds that subsequent
+      `github/codeql-action/init` invocations will enable. If specified, the Action may use this
+      list to select a CodeQL CLI version that is best suited to those analysis kinds. This input is
+      not remembered and must also be passed to `github/codeql-action/init`.
+
+      Available options are the same as for the `analysis-kinds` input on the `init` Action.
+    default: 'code-scanning'
+    required: true
   token:
     description: GitHub token to use for authenticating with this instance of GitHub.
     default: ${{ github.token }}
@@ -36,4 +55,4 @@ outputs:
     description: The version of the CodeQL binary that was installed.
 runs:
   using: node24
-  main: '../lib/setup-codeql-action.js'
+  main: '../lib/setup-codeql-entry.js'

src/action-entry.js.tpl

@@ -0,0 +1,4 @@
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.run__ACTION__)();

src/analyses.test.ts

@@ -16,7 +16,12 @@ import {
 } from "./analyses";
 import { EnvVar } from "./environment";
 import { getRunnerLogger } from "./logging";
-import { setupTests } from "./testing-utils";
+import {
+  createFeatures,
+  RecordingLogger,
+  setupBaseActionsVars,
+  setupTests,
+} from "./testing-utils";
 import { AssessmentPayload } from "./upload-lib/types";
 import { ConfigurationError } from "./util";
 
@@ -53,24 +58,91 @@ test("Parsing analysis kinds requires at least one analysis kind", async (t) =>
 test.serial(
   "getAnalysisKinds - returns expected analysis kinds for `analysis-kinds` input",
   async (t) => {
+    process.env[EnvVar.TEST_MODE] = "true";
+    const features = createFeatures([]);
     const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
     requiredInputStub
       .withArgs("analysis-kinds")
       .returns("code-scanning,code-quality");
-    const result = await getAnalysisKinds(getRunnerLogger(true), true);
+    const result = await getAnalysisKinds(
+      getRunnerLogger(true),
+      features,
+      true,
+    );
     t.assert(result.includes(AnalysisKind.CodeScanning));
     t.assert(result.includes(AnalysisKind.CodeQuality));
   },
 );
 
+test.serial(
+  "getAnalysisKinds - only use `code-scanning` for multiple analysis kinds outside of test mode",
+  async (t) => {
+    setupBaseActionsVars();
+    process.env[EnvVar.TEST_MODE] = "false";
+    const features = createFeatures([]);
+    const logger = new RecordingLogger();
+    const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
+    requiredInputStub
+      .withArgs("analysis-kinds")
+      .returns("code-scanning,code-quality");
+    const result = await getAnalysisKinds(logger, features, true);
+    t.deepEqual(result, [AnalysisKind.CodeScanning]);
+    t.assert(
+      logger.hasMessage(
+        "Continuing with only `analysis-kinds: code-scanning`.",
+      ),
+    );
+  },
+);
+
+test.serial(
+  "getAnalysisKinds - logs error for non-default `analysis-kinds` in custom workflow",
+  async (t) => {
+    setupBaseActionsVars({ GITHUB_EVENT_NAME: "push" });
+    process.env[EnvVar.TEST_MODE] = "false";
+    const features = createFeatures([]);
+    const logger = new RecordingLogger();
+    const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
+    requiredInputStub.withArgs("analysis-kinds").returns("code-quality");
+    const result = await getAnalysisKinds(logger, features, true);
+    t.deepEqual(result, [AnalysisKind.CodeQuality]);
+    t.assert(
+      logger.hasMessage(
+        "An analysis kind other than `code-scanning` was specified in a custom workflow.",
+      ),
+    );
+  },
+);
+
+test.serial(
+  "getAnalysisKinds - no error for non-default `analysis-kinds` in managed workflow",
+  async (t) => {
+    setupBaseActionsVars({ GITHUB_EVENT_NAME: "dynamic" });
+    process.env[EnvVar.TEST_MODE] = "false";
+    const features = createFeatures([]);
+    const logger = new RecordingLogger();
+    const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
+    requiredInputStub.withArgs("analysis-kinds").returns("code-quality");
+    const result = await getAnalysisKinds(logger, features, true);
+    t.deepEqual(result, [AnalysisKind.CodeQuality]);
+    t.deepEqual(logger.messages, []);
+  },
+);
+
 test.serial(
   "getAnalysisKinds - includes `code-quality` when deprecated `quality-queries` input is used",
   async (t) => {
+    process.env[EnvVar.TEST_MODE] = "true";
+    const features = createFeatures([]);
     const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
     requiredInputStub.withArgs("analysis-kinds").returns("code-scanning");
     const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
     optionalInputStub.withArgs("quality-queries").returns("code-quality");
-    const result = await getAnalysisKinds(getRunnerLogger(true), true);
+    const result = await getAnalysisKinds(
+      getRunnerLogger(true),
+      features,
+      true,
+    );
     t.assert(result.includes(AnalysisKind.CodeScanning));
     t.assert(result.includes(AnalysisKind.CodeQuality));
   },
@@ -79,9 +151,12 @@ test.serial(
 test.serial(
   "getAnalysisKinds - throws if `analysis-kinds` input is invalid",
   async (t) => {
+    const features = createFeatures([]);
     const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
     requiredInputStub.withArgs("analysis-kinds").returns("no-such-thing");
-    await t.throwsAsync(getAnalysisKinds(getRunnerLogger(true), true));
+    await t.throwsAsync(
+      getAnalysisKinds(getRunnerLogger(true), features, true),
+    );
   },
 );
 
@@ -98,11 +173,18 @@ for (let i = 0; i < analysisKinds.length; i++) {
       test.serial(
         `getAnalysisKinds - allows ${analysisKind} with ${otherAnalysis}`,
         async (t) => {
+          setupBaseActionsVars();
+          process.env[EnvVar.TEST_MODE] = "true";
+          const features = createFeatures([]);
           const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
           requiredInputStub
             .withArgs("analysis-kinds")
             .returns([analysisKind, otherAnalysis].join(","));
-          const result = await getAnalysisKinds(getRunnerLogger(true), true);
+          const result = await getAnalysisKinds(
+            getRunnerLogger(true),
+            features,
+            true,
+          );
           t.is(result.length, 2);
         },
       );
@@ -110,14 +192,19 @@ for (let i = 0; i < analysisKinds.length; i++) {
       test.serial(
         `getAnalysisKinds - throws if ${analysisKind} is enabled with ${otherAnalysis}`,
         async (t) => {
+          setupBaseActionsVars();
+          const features = createFeatures([]);
           const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
           requiredInputStub
             .withArgs("analysis-kinds")
             .returns([analysisKind, otherAnalysis].join(","));
-          await t.throwsAsync(getAnalysisKinds(getRunnerLogger(true), true), {
+          await t.throwsAsync(
-            instanceOf: ConfigurationError,
+            getAnalysisKinds(getRunnerLogger(true), features, true),
-            message: `${analysisKind} and ${otherAnalysis} cannot be enabled at the same time`,
+            {
-          });
+              instanceOf: ConfigurationError,
+              message: `${analysisKind} and ${otherAnalysis} cannot be enabled at the same time`,
+            },
+          );
         },
       );
     }

src/analyses.ts

@@ -2,15 +2,17 @@ import {
   fixCodeQualityCategory,
   getOptionalInput,
   getRequiredInput,
+  isDynamicWorkflow,
 } from "./actions-util";
 import { EnvVar } from "./environment";
+import { Feature, FeatureEnablement } from "./feature-flags";
 import { Logger } from "./logging";
 import {
   AssessmentPayload,
   BasePayload,
   UploadPayload,
 } from "./upload-lib/types";
-import { ConfigurationError, getRequiredEnvParam } from "./util";
+import { ConfigurationError, getRequiredEnvParam, isInTestMode } from "./util";
 
 export enum AnalysisKind {
   CodeScanning = "code-scanning",
@@ -64,6 +66,21 @@ export async function parseAnalysisKinds(
 // Used to avoid re-parsing the input after we have done it once.
 let cachedAnalysisKinds: AnalysisKind[] | undefined;
 
+/** Determines whether `code-scanning` is the only enabled analysis kind in `analysisKinds`. */
+function isOnlyCodeScanningEnabled(analysisKinds: AnalysisKind[]) {
+  return (
+    analysisKinds.length === 1 && analysisKinds[0] === AnalysisKind.CodeScanning
+  );
+}
+
+/** Prepends a generic message about the intended usage for `analysis-kinds` to `message`. */
+function makeAnalysisKindUsageError(message: string) {
+  return (
+    "The `analysis-kinds` input is experimental and for GitHub-internal use only. " +
+    `Its behaviour may change at any time or be removed entirely. ${message}`
+  );
+}
+
 /**
  * Initialises the analysis kinds for the analysis based on the `analysis-kinds` input.
  * This function will also use the deprecated `quality-queries` input as an indicator to enable `code-quality`.
@@ -77,6 +94,7 @@ let cachedAnalysisKinds: AnalysisKind[] | undefined;
  */
 export async function getAnalysisKinds(
   logger: Logger,
+  features: FeatureEnablement,
   skipCache: boolean = false,
 ): Promise<AnalysisKind[]> {
   if (!skipCache && cachedAnalysisKinds !== undefined) {
@@ -87,6 +105,26 @@ export async function getAnalysisKinds(
     getRequiredInput("analysis-kinds"),
   );
 
+  // Log an error if we are outside of a GitHub-managed workflow and an analysis kind
+  // other than `code-scanning` is enabled.
+  if (
+    !isInTestMode() &&
+    !isDynamicWorkflow() &&
+    !isOnlyCodeScanningEnabled(analysisKinds)
+  ) {
+    const codeQualityHint = analysisKinds.includes(AnalysisKind.CodeQuality)
+      ? " If your intention is to use quality queries outside of Code Quality, " +
+        "use the `queries` input with `code-quality` instead."
+      : "";
+
+    logger.error(
+      makeAnalysisKindUsageError(
+        "An analysis kind other than `code-scanning` was specified in a custom workflow. " +
+          `This is not supported and will become a fatal error in a future version of the CodeQL Action.${codeQualityHint}`,
+      ),
+    );
+  }
+
   // Warn that `quality-queries` is deprecated if there is an argument for it.
   const qualityQueriesInput = getOptionalInput("quality-queries");
 
@@ -120,6 +158,25 @@ export async function getAnalysisKinds(
     }
   }
 
+  // Log an error if we have multiple inputs for `analysis-kinds` outside of test mode,
+  // and enable only `code-scanning`.
+  if (
+    !isInTestMode() &&
+    analysisKinds.length > 1 &&
+    !(await features.getValue(Feature.AllowMultipleAnalysisKinds))
+  ) {
+    logger.error(
+      makeAnalysisKindUsageError(
+        "Specifying multiple values as input is no longer supported. " +
+          "Continuing with only `analysis-kinds: code-scanning`.",
+      ),
+    );
+
+    // Only enable Code Scanning.
+    cachedAnalysisKinds = [AnalysisKind.CodeScanning];
+    return cachedAnalysisKinds;
+  }
+
   // Cache the analysis kinds and return them.
   cachedAnalysisKinds = analysisKinds;
   return cachedAnalysisKinds;

src/analyze-action-env.test.ts

@@ -1,90 +0,0 @@
-import test from "ava";
-import * as sinon from "sinon";
-
-import * as actionsUtil from "./actions-util";
-import * as analyze from "./analyze";
-import * as api from "./api-client";
-import * as configUtils from "./config-utils";
-import * as gitUtils from "./git-utils";
-import * as statusReport from "./status-report";
-import {
-  setupTests,
-  setupActionsVars,
-  mockFeatureFlagApiEndpoint,
-} from "./testing-utils";
-import * as util from "./util";
-
-setupTests(test);
-
-// This test needs to be in its own file so that ava would run it in its own
-// nodejs process. The code being tested is in analyze-action.ts, which runs
-// immediately on load. So the file needs to be loaded during part of the test,
-// and that can happen only once per nodejs process. If multiple such tests are
-// in the same test file, ava would run them in the same nodejs process, and all
-// but the first test would fail.
-
-test("analyze action with RAM & threads from environment variables", async (t) => {
-  // This test frequently times out on Windows with the default timeout, so we bump
-  // it a bit to 20s.
-  t.timeout(1000 * 20);
-  await util.withTmpDir(async (tmpDir) => {
-    setupActionsVars(tmpDir, tmpDir);
-    sinon
-      .stub(statusReport, "createStatusReportBase")
-      .resolves({} as statusReport.StatusReportBase);
-    sinon.stub(statusReport, "sendStatusReport").resolves();
-    sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);
-
-    const gitHubVersion: util.GitHubVersion = {
-      type: util.GitHubVariant.DOTCOM,
-    };
-    sinon.stub(configUtils, "getConfig").resolves({
-      gitHubVersion,
-      augmentationProperties: {},
-      languages: [],
-      packs: [],
-      trapCaches: {},
-    } as unknown as configUtils.Config);
-    const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
-    requiredInputStub.withArgs("token").returns("fake-token");
-    requiredInputStub.withArgs("upload-database").returns("false");
-    requiredInputStub.withArgs("output").returns("out");
-    const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
-    optionalInputStub.withArgs("expect-error").returns("false");
-    sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
-    mockFeatureFlagApiEndpoint(200, {});
-
-    // When there are no action inputs for RAM and threads, the action uses
-    // environment variables (passed down from the init action) to set RAM and
-    // threads usage.
-    process.env["CODEQL_THREADS"] = "-1";
-    process.env["CODEQL_RAM"] = "4992";
-
-    const runFinalizeStub = sinon.stub(analyze, "runFinalize");
-    const runQueriesStub = sinon.stub(analyze, "runQueries");
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    const analyzeAction = require("./analyze-action");
-
-    // When analyze-action.ts loads, it runs an async function from the top
-    // level but does not wait for it to finish. To ensure that calls to
-    // runFinalize and runQueries are correctly captured by spies, we explicitly
-    // wait for the action promise to complete before starting verification.
-    await analyzeAction.runPromise;
-
-    t.assert(
-      runFinalizeStub.calledOnceWith(
-        sinon.match.any,
-        sinon.match.any,
-        "--threads=-1",
-        "--ram=4992",
-      ),
-    );
-    t.assert(
-      runQueriesStub.calledOnceWith(
-        sinon.match.any,
-        "--ram=4992",
-        "--threads=-1",
-      ),
-    );
-  });
-});

src/analyze-action-input.test.ts

@@ -1,88 +0,0 @@
-import test from "ava";
-import * as sinon from "sinon";
-
-import * as actionsUtil from "./actions-util";
-import * as analyze from "./analyze";
-import * as api from "./api-client";
-import * as configUtils from "./config-utils";
-import * as gitUtils from "./git-utils";
-import * as statusReport from "./status-report";
-import {
-  setupTests,
-  setupActionsVars,
-  mockFeatureFlagApiEndpoint,
-} from "./testing-utils";
-import * as util from "./util";
-
-setupTests(test);
-
-// This test needs to be in its own file so that ava would run it in its own
-// nodejs process. The code being tested is in analyze-action.ts, which runs
-// immediately on load. So the file needs to be loaded during part of the test,
-// and that can happen only once per nodejs process. If multiple such tests are
-// in the same test file, ava would run them in the same nodejs process, and all
-// but the first test would fail.
-
-test("analyze action with RAM & threads from action inputs", async (t) => {
-  t.timeout(1000 * 20);
-  await util.withTmpDir(async (tmpDir) => {
-    setupActionsVars(tmpDir, tmpDir);
-    sinon
-      .stub(statusReport, "createStatusReportBase")
-      .resolves({} as statusReport.StatusReportBase);
-    sinon.stub(statusReport, "sendStatusReport").resolves();
-    const gitHubVersion: util.GitHubVersion = {
-      type: util.GitHubVariant.DOTCOM,
-    };
-    sinon.stub(configUtils, "getConfig").resolves({
-      gitHubVersion,
-      augmentationProperties: {},
-      languages: [],
-      packs: [],
-      trapCaches: {},
-    } as unknown as configUtils.Config);
-    const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
-    requiredInputStub.withArgs("token").returns("fake-token");
-    requiredInputStub.withArgs("upload-database").returns("false");
-    requiredInputStub.withArgs("output").returns("out");
-    const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
-    optionalInputStub.withArgs("expect-error").returns("false");
-    sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
-    sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);
-    mockFeatureFlagApiEndpoint(200, {});
-
-    process.env["CODEQL_THREADS"] = "1";
-    process.env["CODEQL_RAM"] = "4992";
-
-    // Action inputs have precedence over environment variables.
-    optionalInputStub.withArgs("threads").returns("-1");
-    optionalInputStub.withArgs("ram").returns("3012");
-
-    const runFinalizeStub = sinon.stub(analyze, "runFinalize");
-    const runQueriesStub = sinon.stub(analyze, "runQueries");
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    const analyzeAction = require("./analyze-action");
-
-    // When analyze-action.ts loads, it runs an async function from the top
-    // level but does not wait for it to finish. To ensure that calls to
-    // runFinalize and runQueries are correctly captured by spies, we explicitly
-    // wait for the action promise to complete before starting verification.
-    await analyzeAction.runPromise;
-
-    t.assert(
-      runFinalizeStub.calledOnceWith(
-        sinon.match.any,
-        sinon.match.any,
-        "--threads=-1",
-        "--ram=3012",
-      ),
-    );
-    t.assert(
-      runQueriesStub.calledOnceWith(
-        sinon.match.any,
-        "--ram=3012",
-        "--threads=-1",
-      ),
-    );
-  });
-});

src/analyze-action-post.ts

@@ -20,7 +20,7 @@ import { EnvVar } from "./environment";
 import { getActionsLogger } from "./logging";
 import { checkGitHubVersionInRange, getErrorMessage } from "./util";
 
-async function runWrapper() {
+export async function runWrapper() {
   // To capture errors appropriately, keep as much code within the try-catch as
   // possible, and only use safe functions outside.
 
@@ -72,5 +72,3 @@ async function runWrapper() {
     );
   }
 }
-
-void runWrapper();

src/analyze-action.test.ts

@@ -0,0 +1,142 @@
+import test from "ava";
+import * as sinon from "sinon";
+
+import * as actionsUtil from "./actions-util";
+import * as analyze from "./analyze";
+import { runWrapper } from "./analyze-action";
+import * as api from "./api-client";
+import * as configUtils from "./config-utils";
+import * as gitUtils from "./git-utils";
+import * as statusReport from "./status-report";
+import {
+  setupTests,
+  setupActionsVars,
+  mockFeatureFlagApiEndpoint,
+} from "./testing-utils";
+import * as util from "./util";
+
+setupTests(test);
+
+test.serial(
+  "analyze action with RAM & threads from environment variables",
+  async (t) => {
+    // This test frequently times out on Windows with the default timeout, so we bump
+    // it a bit to 20s.
+    t.timeout(1000 * 20);
+    await util.withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      sinon
+        .stub(statusReport, "createStatusReportBase")
+        .resolves({} as statusReport.StatusReportBase);
+      sinon.stub(statusReport, "sendStatusReport").resolves();
+      sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);
+
+      const gitHubVersion: util.GitHubVersion = {
+        type: util.GitHubVariant.DOTCOM,
+      };
+      sinon.stub(configUtils, "getConfig").resolves({
+        gitHubVersion,
+        augmentationProperties: {},
+        languages: [],
+        packs: [],
+        trapCaches: {},
+      } as unknown as configUtils.Config);
+      const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
+      requiredInputStub.withArgs("token").returns("fake-token");
+      requiredInputStub.withArgs("upload-database").returns("false");
+      requiredInputStub.withArgs("output").returns("out");
+      const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
+      optionalInputStub.withArgs("expect-error").returns("false");
+      sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
+      mockFeatureFlagApiEndpoint(200, {});
+
+      // When there are no action inputs for RAM and threads, the action uses
+      // environment variables (passed down from the init action) to set RAM and
+      // threads usage.
+      process.env["CODEQL_THREADS"] = "-1";
+      process.env["CODEQL_RAM"] = "4992";
+
+      const runFinalizeStub = sinon.stub(analyze, "runFinalize");
+      const runQueriesStub = sinon.stub(analyze, "runQueries");
+
+      await runWrapper();
+
+      t.assert(
+        runFinalizeStub.calledOnceWith(
+          sinon.match.any,
+          sinon.match.any,
+          "--threads=-1",
+          "--ram=4992",
+        ),
+      );
+      t.assert(
+        runQueriesStub.calledOnceWith(
+          sinon.match.any,
+          "--ram=4992",
+          "--threads=-1",
+        ),
+      );
+    });
+  },
+);
+
+test.serial(
+  "analyze action with RAM & threads from action inputs",
+  async (t) => {
+    t.timeout(1000 * 20);
+    await util.withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      sinon
+        .stub(statusReport, "createStatusReportBase")
+        .resolves({} as statusReport.StatusReportBase);
+      sinon.stub(statusReport, "sendStatusReport").resolves();
+      const gitHubVersion: util.GitHubVersion = {
+        type: util.GitHubVariant.DOTCOM,
+      };
+      sinon.stub(configUtils, "getConfig").resolves({
+        gitHubVersion,
+        augmentationProperties: {},
+        languages: [],
+        packs: [],
+        trapCaches: {},
+      } as unknown as configUtils.Config);
+      const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
+      requiredInputStub.withArgs("token").returns("fake-token");
+      requiredInputStub.withArgs("upload-database").returns("false");
+      requiredInputStub.withArgs("output").returns("out");
+      const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
+      optionalInputStub.withArgs("expect-error").returns("false");
+      sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
+      sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);
+      mockFeatureFlagApiEndpoint(200, {});
+
+      process.env["CODEQL_THREADS"] = "1";
+      process.env["CODEQL_RAM"] = "4992";
+
+      // Action inputs have precedence over environment variables.
+      optionalInputStub.withArgs("threads").returns("-1");
+      optionalInputStub.withArgs("ram").returns("3012");
+
+      const runFinalizeStub = sinon.stub(analyze, "runFinalize");
+      const runQueriesStub = sinon.stub(analyze, "runQueries");
+
+      await runWrapper();
+
+      t.assert(
+        runFinalizeStub.calledOnceWith(
+          sinon.match.any,
+          sinon.match.any,
+          "--threads=-1",
+          "--ram=3012",
+        ),
+      );
+      t.assert(
+        runQueriesStub.calledOnceWith(
+          sinon.match.any,
+          "--ram=3012",
+          "--threads=-1",
+        ),
+      );
+    });
+  },
+);

src/analyze-action.ts

@@ -523,14 +523,11 @@ async function run(startedAt: Date) {
   }
 }
 
-// Module-level startedAt so it can be accessed by runWrapper for error reporting
+export async function runWrapper() {
-const startedAt = new Date();
+  const startedAt = new Date();
-export const runPromise = run(startedAt);
-
-async function runWrapper() {
   const logger = getActionsLogger();
   try {
-    await runPromise;
+    await run(startedAt);
   } catch (error) {
     core.setFailed(`analyze action failed: ${util.getErrorMessage(error)}`);
     await sendUnhandledErrorStatusReport(
@@ -542,5 +539,3 @@ async function runWrapper() {
   }
   await util.checkForTimeout();
 }
-
-void runWrapper();

src/artifact-scanner.test.ts

@@ -141,9 +141,9 @@ test("scanArtifactsForTokens handles files without tokens", async (t) => {
   }
 });
 
+// `scanArchiveFile` does not support Windows, so we skip this test there.
 if (os.platform() !== "win32") {
   test("scanArtifactsForTokens finds token in debug artifacts", async (t) => {
-    t.timeout(15000); // 15 seconds
     const messages: LoggedMessage[] = [];
     const logger = getRecordingLogger(messages, { logToConsole: false });
     // The zip here is a regression test based on

src/artifact-scanner.ts

@@ -156,6 +156,10 @@ async function scanArchiveFile(
     );
   }
 
+  if (process.platform === "win32") {
+    throw new Error("Scanning archives is not supported on Windows.");
+  }
+
   const result: ScanResult = {
     scannedFiles: 0,
     findings: [],

src/autobuild-action.ts

@@ -142,7 +142,7 @@ async function run(startedAt: Date) {
   await sendCompletedStatusReport(config, logger, startedAt, languages ?? []);
 }
 
-async function runWrapper() {
+export async function runWrapper() {
   const startedAt = new Date();
   const logger = getActionsLogger();
   try {
@@ -157,5 +157,3 @@ async function runWrapper() {
     );
   }
 }
-
-void runWrapper();

src/codeql.test.ts

@@ -33,6 +33,7 @@ import {
   mockBundleDownloadApi,
   makeVersionInfo,
   createTestConfig,
+  makeMacro,
 } from "./testing-utils";
 import { ToolsDownloadStatusReport } from "./tools-download";
 import * as util from "./util";
@@ -70,8 +71,10 @@ async function installIntoToolcache({
     tmpDir,
     util.GitHubVariant.GHES,
     cliVersion !== undefined
-      ? { cliVersion, tagName }
+      ? { enabledVersions: [{ cliVersion, tagName }] }
       : SAMPLE_DEFAULT_CLI_VERSION,
+    undefined, // rawLanguages
+    false, // useOverlayAwareDefaultCliVersion
     createFeatures([]),
     getRunnerLogger(true),
     false,
@@ -143,6 +146,8 @@ test.serial(
           tmpDir,
           util.GitHubVariant.DOTCOM,
           SAMPLE_DEFAULT_CLI_VERSION,
+          undefined, // rawLanguages
+          false, // useOverlayAwareDefaultCliVersion
           features,
           getRunnerLogger(true),
           false,
@@ -175,6 +180,8 @@ test.serial(
         tmpDir,
         util.GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         features,
         getRunnerLogger(true),
         false,
@@ -214,6 +221,8 @@ test.serial(
         tmpDir,
         util.GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         features,
         getRunnerLogger(true),
         false,
@@ -264,6 +273,8 @@ for (const {
           tmpDir,
           util.GitHubVariant.DOTCOM,
           SAMPLE_DEFAULT_CLI_VERSION,
+          undefined, // rawLanguages
+          false, // useOverlayAwareDefaultCliVersion
           features,
           getRunnerLogger(true),
           false,
@@ -284,11 +295,11 @@ for (const {
 for (const toolcacheVersion of [
   // Test that we use the tools from the toolcache when `SAMPLE_DEFAULT_CLI_VERSION` is requested
   // and `SAMPLE_DEFAULT_CLI_VERSION-` is in the toolcache.
-  SAMPLE_DEFAULT_CLI_VERSION.cliVersion,
+  SAMPLE_DEFAULT_CLI_VERSION.enabledVersions[0].cliVersion,
-  `${SAMPLE_DEFAULT_CLI_VERSION.cliVersion}-20230101`,
+  `${SAMPLE_DEFAULT_CLI_VERSION.enabledVersions[0].cliVersion}-20230101`,
 ]) {
   test.serial(
-    `uses tools from toolcache when ${SAMPLE_DEFAULT_CLI_VERSION.cliVersion} is requested and ` +
+    `uses tools from toolcache when ${SAMPLE_DEFAULT_CLI_VERSION.enabledVersions[0].cliVersion} is requested and ` +
       `${toolcacheVersion} is installed`,
     async (t) => {
       const features = createFeatures([]);
@@ -308,11 +319,16 @@ for (const toolcacheVersion of [
           tmpDir,
           util.GitHubVariant.DOTCOM,
           SAMPLE_DEFAULT_CLI_VERSION,
+          undefined, // rawLanguages
+          false, // useOverlayAwareDefaultCliVersion
           features,
           getRunnerLogger(true),
           false,
         );
-        t.is(result.toolsVersion, SAMPLE_DEFAULT_CLI_VERSION.cliVersion);
+        t.is(
+          result.toolsVersion,
+          SAMPLE_DEFAULT_CLI_VERSION.enabledVersions[0].cliVersion,
+        );
         t.is(result.toolsSource, ToolsSource.Toolcache);
         t.is(result.toolsDownloadStatusReport?.combinedDurationMs, undefined);
         t.is(result.toolsDownloadStatusReport?.downloadDurationMs, undefined);
@@ -342,9 +358,15 @@ test.serial(
         tmpDir,
         util.GitHubVariant.GHES,
         {
-          cliVersion: defaults.cliVersion,
+          enabledVersions: [
-          tagName: defaults.bundleVersion,
+            {
+              cliVersion: defaults.cliVersion,
+              tagName: defaults.bundleVersion,
+            },
+          ],
         },
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         features,
         getRunnerLogger(true),
         false,
@@ -384,9 +406,15 @@ test.serial(
         tmpDir,
         util.GitHubVariant.GHES,
         {
-          cliVersion: defaults.cliVersion,
+          enabledVersions: [
-          tagName: defaults.bundleVersion,
+            {
+              cliVersion: defaults.cliVersion,
+              tagName: defaults.bundleVersion,
+            },
+          ],
         },
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         features,
         getRunnerLogger(true),
         false,
@@ -426,6 +454,8 @@ test.serial(
         tmpDir,
         util.GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         features,
         getRunnerLogger(true),
         false,
@@ -467,6 +497,8 @@ test.serial(
         tmpDir,
         util.GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         features,
         getRunnerLogger(true),
         false,
@@ -540,7 +572,7 @@ test.serial("getExtraOptions throws for bad content", (t) => {
 });
 
 // Test macro for ensuring different variants of injected augmented configurations
-const injectedConfigMacro = test.macro({
+const injectedConfigMacro = makeMacro({
   exec: async (
     t: ExecutionContext<unknown>,
     augmentationProperties: AugmentationProperties,
@@ -590,9 +622,8 @@ const injectedConfigMacro = test.macro({
     `databaseInitCluster() injected config: ${providedTitle}`,
 });
 
-test.serial(
+injectedConfigMacro.serial(
   "basic",
-  injectedConfigMacro,
   {
     ...defaultAugmentationProperties,
   },
@@ -600,9 +631,8 @@ test.serial(
   {},
 );
 
-test.serial(
+injectedConfigMacro.serial(
   "injected packs from input",
-  injectedConfigMacro,
   {
     ...defaultAugmentationProperties,
     packsInput: ["xxx", "yyy"],
@@ -613,9 +643,8 @@ test.serial(
   },
 );
 
-test.serial(
+injectedConfigMacro.serial(
   "injected packs from input with existing packs combines",
-  injectedConfigMacro,
   {
     ...defaultAugmentationProperties,
     packsInputCombines: true,
@@ -635,9 +664,8 @@ test.serial(
   },
 );
 
-test.serial(
+injectedConfigMacro.serial(
   "injected packs from input with existing packs overrides",
-  injectedConfigMacro,
   {
     ...defaultAugmentationProperties,
     packsInput: ["xxx", "yyy"],
@@ -655,9 +683,8 @@ test.serial(
 );
 
 // similar, but with queries
-test.serial(
+injectedConfigMacro.serial(
   "injected queries from input",
-  injectedConfigMacro,
   {
     ...defaultAugmentationProperties,
     queriesInput: [{ uses: "xxx" }, { uses: "yyy" }],
@@ -675,9 +702,8 @@ test.serial(
   },
 );
 
-test.serial(
+injectedConfigMacro.serial(
   "injected queries from input overrides",
-  injectedConfigMacro,
   {
     ...defaultAugmentationProperties,
     queriesInput: [{ uses: "xxx" }, { uses: "yyy" }],
@@ -699,9 +725,8 @@ test.serial(
   },
 );
 
-test.serial(
+injectedConfigMacro.serial(
   "injected queries from input combines",
-  injectedConfigMacro,
   {
     ...defaultAugmentationProperties,
     queriesInputCombines: true,
@@ -727,9 +752,8 @@ test.serial(
   },
 );
 
-test.serial(
+injectedConfigMacro.serial(
   "injected queries from input combines 2",
-  injectedConfigMacro,
   {
     ...defaultAugmentationProperties,
     queriesInputCombines: true,
@@ -749,9 +773,8 @@ test.serial(
   },
 );
 
-test.serial(
+injectedConfigMacro.serial(
   "injected queries and packs, but empty",
-  injectedConfigMacro,
   {
     ...defaultAugmentationProperties,
     queriesInputCombines: true,
@@ -768,9 +791,8 @@ test.serial(
   {},
 );
 
-test.serial(
+injectedConfigMacro.serial(
   "repo property queries have the highest precedence",
-  injectedConfigMacro,
   {
     ...defaultAugmentationProperties,
     queriesInputCombines: true,
@@ -790,9 +812,8 @@ test.serial(
   },
 );
 
-test.serial(
+injectedConfigMacro.serial(
   "repo property queries combines with queries input",
-  injectedConfigMacro,
   {
     ...defaultAugmentationProperties,
     queriesInputCombines: false,
@@ -817,9 +838,8 @@ test.serial(
   },
 );
 
-test.serial(
+injectedConfigMacro.serial(
   "repo property queries combines everything else",
-  injectedConfigMacro,
   {
     ...defaultAugmentationProperties,
     queriesInputCombines: true,
@@ -1052,7 +1072,7 @@ test.serial(
 );
 
 test.serial(
-  "Avoids duplicating --overwrite flag if specified in CODEQL_ACTION_EXTRA_OPTIONS",
+  "Avoids duplicating --force-overwrite flag if specified in CODEQL_ACTION_EXTRA_OPTIONS",
   async (t) => {
     const runnerConstructorStub = stubToolRunnerConstructor();
     const codeqlObject = await stubCodeql();
@@ -1060,7 +1080,7 @@ test.serial(
     sinon.stub(io, "which").resolves("");
 
     process.env["CODEQL_ACTION_EXTRA_OPTIONS"] =
-      '{ "database": { "init": ["--overwrite"] } }';
+      '{ "database": { "init": ["--force-overwrite"] } }';
 
     await codeqlObject.databaseInitCluster(
       stubConfig,
@@ -1073,9 +1093,9 @@ test.serial(
     t.true(runnerConstructorStub.calledOnce);
     const args = runnerConstructorStub.firstCall.args[1] as string[];
     t.is(
-      args.filter((option: string) => option === "--overwrite").length,
+      args.filter((option: string) => option === "--force-overwrite").length,
       1,
-      "--overwrite should only be passed once",
+      "--force-overwrite should only be passed once",
     );
 
     // Clean up

src/codeql.ts

@@ -277,7 +277,7 @@ let cachedCodeQL: CodeQL | undefined = undefined;
  * The version flags below can be used to conditionally enable certain features
  * on versions newer than this.
  */
-const CODEQL_MINIMUM_VERSION = "2.17.6";
+const CODEQL_MINIMUM_VERSION = "2.19.4";
 
 /**
  * This version will shortly become the oldest version of CodeQL that the Action will run with.
@@ -305,6 +305,8 @@ const EXTRACTION_DEBUG_MODE_VERBOSITY = "progress++";
  * @param tempDir
  * @param variant
  * @param defaultCliVersion
+ * @param rawLanguages Raw set of languages.
+ * @param useOverlayAwareDefaultCliVersion Whether to select an overlay-aware default CLI version.
  * @param features Information about the features that are enabled.
  * @param logger
  * @param checkVersion Whether to check that CodeQL CLI meets the minimum
@@ -317,6 +319,8 @@ export async function setupCodeQL(
   tempDir: string,
   variant: util.GitHubVariant,
   defaultCliVersion: CodeQLDefaultVersionInfo,
+  rawLanguages: string[] | undefined,
+  useOverlayAwareDefaultCliVersion: boolean,
   features: FeatureEnablement,
   logger: Logger,
   checkVersion: boolean,
@@ -340,6 +344,8 @@ export async function setupCodeQL(
       tempDir,
       variant,
       defaultCliVersion,
+      rawLanguages,
+      useOverlayAwareDefaultCliVersion,
       features,
       logger,
     );
@@ -586,13 +592,6 @@ async function getCodeQLForCmd(
         extraArgs.push(`--qlconfig-file=${qlconfigFile}`);
       }
 
-      const overwriteFlag = isSupportedToolsFeature(
-        await this.getVersion(),
-        ToolsFeature.ForceOverwrite,
-      )
-        ? "--force-overwrite"
-        : "--overwrite";
-
       const overlayDatabaseMode = config.overlayDatabaseMode;
       if (overlayDatabaseMode === OverlayDatabaseMode.Overlay) {
         const overlayChangesFile = await writeOverlayChangesFile(
@@ -619,7 +618,7 @@ async function getCodeQLForCmd(
           "init",
           ...(overlayDatabaseMode === OverlayDatabaseMode.Overlay
             ? []
-            : [overwriteFlag]),
+            : ["--force-overwrite"]),
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
@@ -630,7 +629,14 @@ async function getCodeQLForCmd(
             // Some user configs specify `--no-calculate-baseline` as an additional
             // argument to `codeql database init`. Therefore ignore the baseline file
             // options here to avoid specifying the same argument twice and erroring.
-            ignoringOptions: ["--overwrite", ...baselineFilesOptions],
+            //
+            // Ignore `--overwrite` to avoid passing both `--force-overwrite` and `--overwrite` if
+            // the user has configured `--overwrite`.
+            ignoringOptions: [
+              "--force-overwrite",
+              "--overwrite",
+              ...baselineFilesOptions,
+            ],
           }),
         ],
         { stdin: externalRepositoryToken },
@@ -847,7 +853,7 @@ async function getCodeQLForCmd(
         "--sarif-group-rules-by-pack",
         "--sarif-include-query-help=always",
         "--sublanguage-file-coverage",
-        ...(await getJobRunUuidSarifOptions(this)),
+        ...(await getJobRunUuidSarifOptions()),
         ...getExtraOptionsFromEnv(["database", "interpret-results"]),
       ];
       if (sarifRunPropertyFlag !== undefined) {
@@ -1277,13 +1283,8 @@ function applyAutobuildAzurePipelinesTimeoutFix() {
   ].join(" ");
 }
 
-async function getJobRunUuidSarifOptions(codeql: CodeQL) {
+async function getJobRunUuidSarifOptions() {
   const jobRunUuid = process.env[EnvVar.JOB_RUN_UUID];
 
-  return jobRunUuid &&
+  return jobRunUuid ? [`--sarif-run-property=jobRunUuid=${jobRunUuid}`] : [];
-    (await codeql.supportsFeature(
-      ToolsFeature.DatabaseInterpretResultsSupportsSarifRunProperty,
-    ))
-    ? [`--sarif-run-property=jobRunUuid=${jobRunUuid}`]
-    : [];
 }

src/config-utils.test.ts

@@ -21,6 +21,7 @@ import { GitVersionInfo } from "./git-utils";
 import { BuiltInLanguage, Language } from "./languages";
 import { getRunnerLogger } from "./logging";
 import { CODEQL_OVERLAY_MINIMUM_VERSION } from "./overlay";
+import * as overlayDiagnostics from "./overlay/diagnostics";
 import { OverlayDisabledReason } from "./overlay/diagnostics";
 import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import * as overlayStatus from "./overlay/status";
@@ -34,6 +35,7 @@ import {
   LoggedMessage,
   mockCodeQLVersion,
   createTestConfig,
+  makeMacro,
 } from "./testing-utils";
 import {
   GitHubVariant,
@@ -1034,10 +1036,9 @@ const defaultOverlayDatabaseModeTestSetup: OverlayDatabaseModeTestSetup = {
   repositoryProperties: {},
 };
 
-const checkOverlayEnablementMacro = test.macro({
+const checkOverlayEnablementMacro = makeMacro({
   exec: async (
     t: ExecutionContext,
-    _title: string,
     setupOverrides: Partial<OverlayDatabaseModeTestSetup>,
     expected:
       | {
@@ -1131,11 +1132,10 @@ const checkOverlayEnablementMacro = test.macro({
       }
     });
   },
-  title: (_, title) => `checkOverlayEnablement: ${title}`,
+  title: (title) => `checkOverlayEnablement: ${title}`,
 });
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Environment variable override - Overlay",
   {
     overlayDatabaseEnvVar: "overlay",
@@ -1146,8 +1146,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Environment variable override - OverlayBase",
   {
     overlayDatabaseEnvVar: "overlay-base",
@@ -1158,8 +1157,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Environment variable override - None",
   {
     overlayDatabaseEnvVar: "none",
@@ -1169,8 +1167,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Ignore invalid environment variable",
   {
     overlayDatabaseEnvVar: "invalid-mode",
@@ -1180,8 +1177,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Ignore feature flag when analyzing non-default branch",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1192,8 +1188,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay-base database on default branch when feature enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1206,15 +1201,14 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay-base database on default branch when feature enabled with custom analysis",
   {
     languages: [BuiltInLanguage.javascript],
     features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
     codeScanningConfig: {
       packs: ["some-custom-pack@1.0.0"],
-    } as UserConfig,
+    },
     isDefaultBranch: true,
   },
   {
@@ -1223,8 +1217,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay-base database on default branch when code-scanning feature enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1240,8 +1233,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay-base database on default branch if runner disk space is too low",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1260,8 +1252,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay-base database on default branch if we can't determine runner disk space",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1277,8 +1268,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay-base database on default branch if runner disk space is too low and skip resource checks flag is enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1299,8 +1289,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay-base database on default branch if runner disk space is below v2 limit and v2 resource checks enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1320,8 +1309,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay-base database on default branch if runner disk space is between v2 and v1 limits and v2 resource checks enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1342,8 +1330,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay-base database on default branch if runner disk space is between v2 and v1 limits and v2 resource checks not enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1362,8 +1349,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay-base database on default branch if memory flag is too low",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1379,8 +1365,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay-base database on default branch if memory flag is too low but CodeQL >= 2.24.3",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1398,8 +1383,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay-base database on default branch if memory flag is too low and skip resource checks flag is enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1417,8 +1401,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay-base database on default branch when cached status indicates previous failure",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1435,8 +1418,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay analysis on PR when cached status indicates previous failure",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1453,8 +1435,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay-base database on default branch when code-scanning feature enabled with disable-default-queries",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1464,7 +1445,7 @@ test.serial(
     ],
     codeScanningConfig: {
       "disable-default-queries": true,
-    } as UserConfig,
+    },
     isDefaultBranch: true,
   },
   {
@@ -1472,8 +1453,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay-base database on default branch when code-scanning feature enabled with packs",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1483,7 +1463,7 @@ test.serial(
     ],
     codeScanningConfig: {
       packs: ["some-custom-pack@1.0.0"],
-    } as UserConfig,
+    },
     isDefaultBranch: true,
   },
   {
@@ -1491,8 +1471,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay-base database on default branch when code-scanning feature enabled with queries",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1502,7 +1481,7 @@ test.serial(
     ],
     codeScanningConfig: {
       queries: [{ uses: "some-query.ql" }],
-    } as UserConfig,
+    },
     isDefaultBranch: true,
   },
   {
@@ -1510,8 +1489,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay-base database on default branch when code-scanning feature enabled with query-filters",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1521,7 +1499,7 @@ test.serial(
     ],
     codeScanningConfig: {
       "query-filters": [{ include: { "security-severity": "high" } }],
-    } as UserConfig,
+    },
     isDefaultBranch: true,
   },
   {
@@ -1529,8 +1507,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay-base database on default branch when only language-specific feature enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1542,8 +1519,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay-base database on default branch when only code-scanning feature enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1555,8 +1531,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay-base database on default branch when language-specific feature disabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1568,8 +1543,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay analysis on PR when feature enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1582,15 +1556,14 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay analysis on PR when feature enabled with custom analysis",
   {
     languages: [BuiltInLanguage.javascript],
     features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
     codeScanningConfig: {
       packs: ["some-custom-pack@1.0.0"],
-    } as UserConfig,
+    },
     isPullRequest: true,
   },
   {
@@ -1599,8 +1572,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay analysis on PR when code-scanning feature enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1616,8 +1588,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay analysis on PR if runner disk space is too low",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1636,8 +1607,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay analysis on PR if runner disk space is too low and skip resource checks flag is enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1658,8 +1628,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay analysis on PR if we can't determine runner disk space",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1675,8 +1644,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay analysis on PR if memory flag is too low",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1692,8 +1660,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay analysis on PR if memory flag is too low but CodeQL >= 2.24.3",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1711,8 +1678,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay analysis on PR if memory flag is too low and skip resource checks flag is enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1730,8 +1696,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay analysis on PR when code-scanning feature enabled with disable-default-queries",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1741,7 +1706,7 @@ test.serial(
     ],
     codeScanningConfig: {
       "disable-default-queries": true,
-    } as UserConfig,
+    },
     isPullRequest: true,
   },
   {
@@ -1749,8 +1714,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay analysis on PR when code-scanning feature enabled with packs",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1760,7 +1724,7 @@ test.serial(
     ],
     codeScanningConfig: {
       packs: ["some-custom-pack@1.0.0"],
-    } as UserConfig,
+    },
     isPullRequest: true,
   },
   {
@@ -1768,8 +1732,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay analysis on PR when code-scanning feature enabled with queries",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1779,7 +1742,7 @@ test.serial(
     ],
     codeScanningConfig: {
       queries: [{ uses: "some-query.ql" }],
-    } as UserConfig,
+    },
     isPullRequest: true,
   },
   {
@@ -1787,8 +1750,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay analysis on PR when code-scanning feature enabled with query-filters",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1798,7 +1760,7 @@ test.serial(
     ],
     codeScanningConfig: {
       "query-filters": [{ include: { "security-severity": "high" } }],
-    } as UserConfig,
+    },
     isPullRequest: true,
   },
   {
@@ -1806,8 +1768,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay analysis on PR when only language-specific feature enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1819,8 +1780,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay analysis on PR when only code-scanning feature enabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1832,8 +1792,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay analysis on PR when language-specific feature disabled",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1845,8 +1804,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay PR analysis by env",
   {
     overlayDatabaseEnvVar: "overlay",
@@ -1857,8 +1815,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay PR analysis by env on a runner with low disk space",
   {
     overlayDatabaseEnvVar: "overlay",
@@ -1870,8 +1827,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay PR analysis by feature flag",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1884,8 +1840,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Fallback due to autobuild with traced language",
   {
     overlayDatabaseEnvVar: "overlay",
@@ -1897,8 +1852,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Fallback due to no build mode with traced language",
   {
     overlayDatabaseEnvVar: "overlay",
@@ -1910,8 +1864,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Fallback due to old CodeQL version",
   {
     overlayDatabaseEnvVar: "overlay",
@@ -1922,8 +1875,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Fallback due to missing git root",
   {
     overlayDatabaseEnvVar: "overlay",
@@ -1934,8 +1886,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Fallback due to old git version with submodules",
   {
     overlayDatabaseEnvVar: "overlay",
@@ -1947,8 +1898,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Fallback when git version cannot be determined and repo has submodules",
   {
     overlayDatabaseEnvVar: "overlay",
@@ -1960,8 +1910,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay enabled when git version cannot be determined and repo has no submodules",
   {
     overlayDatabaseEnvVar: "overlay",
@@ -1974,8 +1923,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay when disabled via repository property",
   {
     languages: [BuiltInLanguage.javascript],
@@ -1990,8 +1938,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Overlay not disabled when repository property is false",
   {
     languages: [BuiltInLanguage.javascript],
@@ -2007,8 +1954,7 @@ test.serial(
   },
 );
 
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "Environment variable override takes precedence over repository property",
   {
     overlayDatabaseEnvVar: "overlay",
@@ -2024,8 +1970,7 @@ test.serial(
 
 // Exercise language-specific overlay analysis features code paths
 for (const language in BuiltInLanguage) {
-  test.serial(
+  checkOverlayEnablementMacro.serial(
-    checkOverlayEnablementMacro,
     `Check default overlay analysis feature for ${language}`,
     {
       languages: [language],
@@ -2042,8 +1987,7 @@ for (const language in BuiltInLanguage) {
 // overlay analysis enabled, even when the base overlay feature flag is on.
 // Using swift here as it doesn't currently have overlay support — update this if
 // swift gains overlay support.
-test.serial(
+checkOverlayEnablementMacro.serial(
-  checkOverlayEnablementMacro,
   "No overlay analysis for language without per-language overlay feature flag",
   {
     languages: [BuiltInLanguage.swift],
@@ -2200,3 +2144,87 @@ test.serial(
     });
   },
 );
+
+test("applyIncrementalAnalysisSettings: no-op when mode is not Overlay and diff ranges are unavailable", async (t) => {
+  const config = createTestConfig({});
+  config.overlayDatabaseMode = OverlayDatabaseMode.None;
+  const codeql = createStubCodeQL({});
+  const logger = getRunnerLogger(true);
+
+  await configUtils.applyIncrementalAnalysisSettings(
+    config,
+    false,
+    codeql,
+    logger,
+  );
+
+  t.is(config.overlayDatabaseMode, OverlayDatabaseMode.None);
+  t.deepEqual(config.extraQueryExclusions, []);
+});
+
+test("applyIncrementalAnalysisSettings: keeps overlay mode and adds exclusions when diff ranges are available", async (t) => {
+  const config = createTestConfig({
+    overlayDatabaseMode: OverlayDatabaseMode.Overlay,
+  });
+  const codeql = createStubCodeQL({});
+  const logger = getRunnerLogger(true);
+
+  await configUtils.applyIncrementalAnalysisSettings(
+    config,
+    true,
+    codeql,
+    logger,
+  );
+
+  t.is(config.overlayDatabaseMode, OverlayDatabaseMode.Overlay);
+  t.deepEqual(config.extraQueryExclusions, [
+    { exclude: { tags: "exclude-from-incremental" } },
+  ]);
+});
+
+test("applyIncrementalAnalysisSettings: disables overlay analysis when diff ranges are unavailable", async (t) => {
+  const config = createTestConfig({
+    overlayDatabaseMode: OverlayDatabaseMode.Overlay,
+  });
+  config.useOverlayDatabaseCaching = true;
+  const codeql = createStubCodeQL({});
+  const logger = getRunnerLogger(true);
+  const addDiagnosticsStub = sinon
+    .stub(overlayDiagnostics, "addOverlayDisablementDiagnostics")
+    .resolves();
+
+  await configUtils.applyIncrementalAnalysisSettings(
+    config,
+    false,
+    codeql,
+    logger,
+  );
+
+  t.is(config.overlayDatabaseMode, OverlayDatabaseMode.None);
+  t.is(config.useOverlayDatabaseCaching, false);
+  t.deepEqual(config.extraQueryExclusions, []);
+  t.true(addDiagnosticsStub.calledOnce);
+  t.is(
+    addDiagnosticsStub.firstCall.args[2],
+    OverlayDisabledReason.DiffInformedAnalysisNotEnabled,
+  );
+});
+
+test("applyIncrementalAnalysisSettings: adds exclusions for diff-informed-only runs", async (t) => {
+  const config = createTestConfig({});
+  config.overlayDatabaseMode = OverlayDatabaseMode.None;
+  const codeql = createStubCodeQL({});
+  const logger = getRunnerLogger(true);
+
+  await configUtils.applyIncrementalAnalysisSettings(
+    config,
+    true,
+    codeql,
+    logger,
+  );
+
+  t.is(config.overlayDatabaseMode, OverlayDatabaseMode.None);
+  t.deepEqual(config.extraQueryExclusions, [
+    { exclude: { tags: "exclude-from-incremental" } },
+  ]);
+});

src/config-utils.ts

@@ -31,7 +31,7 @@ import {
   addNoLanguageDiagnostic,
   makeTelemetryDiagnostic,
 } from "./diagnostics";
-import { shouldPerformDiffInformedAnalysis } from "./diff-informed-analysis-utils";
+import { prepareDiffInformedAnalysis } from "./diff-informed-analysis-utils";
 import { EnvVar } from "./environment";
 import * as errorMessages from "./error-messages";
 import { Feature, FeatureEnablement } from "./feature-flags";
@@ -407,6 +407,7 @@ export async function getLanguages(
   return languages;
 }
 
+/** Splits the `languages` input into a list of raw languages without checking if they are supported by CodeQL. */
 export function getRawLanguagesNoAutodetect(
   languagesInput: string | undefined,
 ): string[] {
@@ -1076,6 +1077,48 @@ function hasQueryCustomisation(userConfig: UserConfig): boolean {
   );
 }
 
+/**
+ * Finalize the incremental-analysis configuration for this run.
+ *
+ * Overlay analysis has only been validated in combination with diff-informed
+ * analysis, so if `Overlay` mode was selected for a pull request but the diff
+ * ranges could not be computed, fall back to a full non-overlay analysis.
+ *
+ * Query exclusions for incremental-only queries are then applied whenever the
+ * diff ranges are available — which, after the fallback above, is exactly the
+ * set of runs where any kind of incremental analysis (overlay or
+ * diff-informed) is in effect.
+ */
+export async function applyIncrementalAnalysisSettings(
+  config: Config,
+  hasDiffRanges: boolean,
+  codeql: CodeQL,
+  logger: Logger,
+): Promise<void> {
+  if (
+    config.overlayDatabaseMode === OverlayDatabaseMode.Overlay &&
+    !hasDiffRanges
+  ) {
+    logger.info(
+      `Reverting overlay database mode to ${OverlayDatabaseMode.None} ` +
+        "because the PR diff ranges could not be computed.",
+    );
+    config.overlayDatabaseMode = OverlayDatabaseMode.None;
+    config.useOverlayDatabaseCaching = false;
+    await addOverlayDisablementDiagnostics(
+      config,
+      codeql,
+      OverlayDisabledReason.DiffInformedAnalysisNotEnabled,
+    );
+  }
+
+  if (hasDiffRanges) {
+    config.extraQueryExclusions.push({
+      exclude: { tags: "exclude-from-incremental" },
+    });
+  }
+}
+
 /**
  * Load and return the config.
  *
@@ -1230,18 +1273,18 @@ export async function initConfig(
     );
   }
 
-  if (
+  const hasDiffRanges = await prepareDiffInformedAnalysis(
-    config.overlayDatabaseMode === OverlayDatabaseMode.Overlay ||
+    inputs.codeql,
-    (await shouldPerformDiffInformedAnalysis(
+    inputs.features,
-      inputs.codeql,
+    logger,
-      inputs.features,
+  );
-      logger,
+
-    ))
+  await applyIncrementalAnalysisSettings(
-  ) {
+    config,
-    config.extraQueryExclusions.push({
+    hasDiffRanges,
-      exclude: { tags: "exclude-from-incremental" },
+    inputs.codeql,
-    });
+    logger,
-  }
+  );
 
   if (await isTrapCachingEnabled(features, config.overlayDatabaseMode)) {
     const { trapCaches, trapCacheDownloadTime } = await downloadCacheWithTime(

src/config/db-config.test.ts

@@ -7,6 +7,7 @@ import {
   checkExpectedLogMessages,
   getRecordingLogger,
   LoggedMessage,
+  makeMacro,
 } from "../testing-utils";
 import { ConfigurationError, prettyPrintPack } from "../util";
 
@@ -15,7 +16,7 @@ import * as dbConfig from "./db-config";
 /**
  * Test macro for ensuring the packs block is valid
  */
-const parsePacksMacro = test.macro({
+const parsePacksMacro = makeMacro({
   exec: (
     t: ExecutionContext<unknown>,
     packsInput: string,
@@ -33,7 +34,7 @@ const parsePacksMacro = test.macro({
 /**
  * Test macro for testing when the packs block is invalid
  */
-const parsePacksErrorMacro = test.macro({
+const parsePacksErrorMacro = makeMacro({
   exec: (
     t: ExecutionContext<unknown>,
     packsInput: string,
@@ -49,34 +50,32 @@ const parsePacksErrorMacro = test.macro({
 /**
  * Test macro for testing when the packs block is invalid
  */
-const invalidPackNameMacro = test.macro({
+const invalidPackNameMacro = makeMacro({
-  exec: (t: ExecutionContext, name: string) =>
+  exec: (t: ExecutionContext, arg: string) =>
-    parsePacksErrorMacro.exec(
+    parsePacksErrorMacro.fn(
       t,
-      name,
+      arg,
       [BuiltInLanguage.cpp],
-      new RegExp(`^"${name}" is not a valid pack$`),
+      new RegExp(`^"${arg}" is not a valid pack$`),
     ),
   title: (_providedTitle: string | undefined, arg: string | undefined) =>
     `Invalid pack string: ${arg}`,
 });
 
-test("no packs", parsePacksMacro, "", [], undefined);
+parsePacksMacro("no packs", "", [], undefined);
-test("two packs", parsePacksMacro, "a/b,c/d@1.2.3", [BuiltInLanguage.cpp], {
+parsePacksMacro("two packs", "a/b,c/d@1.2.3", [BuiltInLanguage.cpp], {
   [BuiltInLanguage.cpp]: ["a/b", "c/d@1.2.3"],
 });
-test(
+parsePacksMacro(
   "two packs with spaces",
-  parsePacksMacro,
   " a/b , c/d@1.2.3 ",
   [BuiltInLanguage.cpp],
   {
     [BuiltInLanguage.cpp]: ["a/b", "c/d@1.2.3"],
   },
 );
-test(
+parsePacksErrorMacro(
   "two packs with language",
-  parsePacksErrorMacro,
   "a/b,c/d@1.2.3",
   [BuiltInLanguage.cpp, BuiltInLanguage.java],
   new RegExp(
@@ -85,9 +84,8 @@ test(
   ),
 );
 
-test(
+parsePacksMacro(
   "packs with other valid names",
-  parsePacksMacro,
   [
     // ranges are ok
     "c/d@1.0",
@@ -123,23 +121,23 @@ test(
   },
 );
 
-test(invalidPackNameMacro, "c"); // all packs require at least a scope and a name
+invalidPackNameMacro.test("c"); // all packs require at least a scope and a name
-test(invalidPackNameMacro, "c-/d");
+invalidPackNameMacro.test("c-/d");
-test(invalidPackNameMacro, "-c/d");
+invalidPackNameMacro.test("-c/d");
-test(invalidPackNameMacro, "c/d_d");
+invalidPackNameMacro.test("c/d_d");
-test(invalidPackNameMacro, "c/d@@");
+invalidPackNameMacro.test("c/d@@");
-test(invalidPackNameMacro, "c/d@1.0.0:");
+invalidPackNameMacro.test("c/d@1.0.0:");
-test(invalidPackNameMacro, "c/d:");
+invalidPackNameMacro.test("c/d:");
-test(invalidPackNameMacro, "c/d:/a");
+invalidPackNameMacro.test("c/d:/a");
-test(invalidPackNameMacro, "@1.0.0:a");
+invalidPackNameMacro.test("@1.0.0:a");
-test(invalidPackNameMacro, "c/d@../a");
+invalidPackNameMacro.test("c/d@../a");
-test(invalidPackNameMacro, "c/d@b/../a");
+invalidPackNameMacro.test("c/d@b/../a");
-test(invalidPackNameMacro, "c/d:z@1");
+invalidPackNameMacro.test("c/d:z@1");
 
 /**
  * Test macro for pretty printing pack specs
  */
-const packSpecPrettyPrintingMacro = test.macro({
+const packSpecPrettyPrintingMacro = makeMacro({
   exec: (t: ExecutionContext, packStr: string, packObj: dbConfig.Pack) => {
     const parsed = dbConfig.parsePacksSpecification(packStr);
     t.deepEqual(parsed, packObj, "parsed pack spec is correct");
@@ -163,36 +161,35 @@ const packSpecPrettyPrintingMacro = test.macro({
   ) => `Prettyprint pack spec: '${packStr}'`,
 });
 
-test(packSpecPrettyPrintingMacro, "a/b", {
+packSpecPrettyPrintingMacro.test("a/b", {
   name: "a/b",
   version: undefined,
   path: undefined,
 });
-test(packSpecPrettyPrintingMacro, "a/b@~1.2.3", {
+packSpecPrettyPrintingMacro.test("a/b@~1.2.3", {
   name: "a/b",
   version: "~1.2.3",
   path: undefined,
 });
-test(packSpecPrettyPrintingMacro, "a/b@~1.2.3:abc/def", {
+packSpecPrettyPrintingMacro.test("a/b@~1.2.3:abc/def", {
   name: "a/b",
   version: "~1.2.3",
   path: "abc/def",
 });
-test(packSpecPrettyPrintingMacro, "a/b:abc/def", {
+packSpecPrettyPrintingMacro.test("a/b:abc/def", {
   name: "a/b",
   version: undefined,
   path: "abc/def",
 });
-test(packSpecPrettyPrintingMacro, "    a/b:abc/def    ", {
+packSpecPrettyPrintingMacro.test("    a/b:abc/def    ", {
   name: "a/b",
   version: undefined,
   path: "abc/def",
 });
 
-const calculateAugmentationMacro = test.macro({
+const calculateAugmentationMacro = makeMacro({
   exec: async (
     t: ExecutionContext,
-    _title: string,
     rawPacksInput: string | undefined,
     rawQueriesInput: string | undefined,
     languages: Language[],
@@ -207,11 +204,10 @@ const calculateAugmentationMacro = test.macro({
     );
     t.deepEqual(actualAugmentationProperties, expectedAugmentationProperties);
   },
-  title: (_, title) => `Calculate Augmentation: ${title}`,
+  title: (title) => `Calculate Augmentation: ${title}`,
 });
 
-test(
+calculateAugmentationMacro(
-  calculateAugmentationMacro,
   "All empty",
   undefined,
   undefined,
@@ -222,8 +218,7 @@ test(
   },
 );
 
-test(
+calculateAugmentationMacro(
-  calculateAugmentationMacro,
   "With queries",
   undefined,
   " a, b , c, d",
@@ -235,8 +230,7 @@ test(
   },
 );
 
-test(
+calculateAugmentationMacro(
-  calculateAugmentationMacro,
   "With queries combining",
   undefined,
   "   +   a, b , c, d ",
@@ -249,8 +243,7 @@ test(
   },
 );
 
-test(
+calculateAugmentationMacro(
-  calculateAugmentationMacro,
   "With packs",
   "   codeql/a , codeql/b   , codeql/c  , codeql/d  ",
   undefined,
@@ -262,8 +255,7 @@ test(
   },
 );
 
-test(
+calculateAugmentationMacro(
-  calculateAugmentationMacro,
   "With packs combining",
   "   +   codeql/a, codeql/b, codeql/c, codeql/d",
   undefined,
@@ -276,8 +268,7 @@ test(
   },
 );
 
-test(
+calculateAugmentationMacro(
-  calculateAugmentationMacro,
   "With repo property queries",
   undefined,
   undefined,
@@ -294,8 +285,7 @@ test(
   },
 );
 
-test(
+calculateAugmentationMacro(
-  calculateAugmentationMacro,
   "With repo property queries combining",
   undefined,
   undefined,
@@ -312,10 +302,9 @@ test(
   },
 );
 
-const calculateAugmentationErrorMacro = test.macro({
+const calculateAugmentationErrorMacro = makeMacro({
   exec: async (
     t: ExecutionContext,
-    _title: string,
     rawPacksInput: string | undefined,
     rawQueriesInput: string | undefined,
     languages: Language[],
@@ -333,11 +322,10 @@ const calculateAugmentationErrorMacro = test.macro({
       { message: expectedError },
     );
   },
-  title: (_, title) => `Calculate Augmentation Error: ${title}`,
+  title: (title) => `Calculate Augmentation Error: ${title}`,
 });
 
-test(
+calculateAugmentationErrorMacro(
-  calculateAugmentationErrorMacro,
   "Plus (+) with nothing else (queries)",
   undefined,
   "   +   ",
@@ -346,8 +334,7 @@ test(
   /The workflow property "queries" is invalid/,
 );
 
-test(
+calculateAugmentationErrorMacro(
-  calculateAugmentationErrorMacro,
   "Plus (+) with nothing else (packs)",
   "   +   ",
   undefined,
@@ -356,8 +343,7 @@ test(
   /The workflow property "packs" is invalid/,
 );
 
-test(
+calculateAugmentationErrorMacro(
-  calculateAugmentationErrorMacro,
   "Plus (+) with nothing else (repo property queries)",
   undefined,
   undefined,
@@ -368,8 +354,7 @@ test(
   /The repository property "github-codeql-extra-queries" is invalid/,
 );
 
-test(
+calculateAugmentationErrorMacro(
-  calculateAugmentationErrorMacro,
   "Packs input with multiple languages",
   "   +  a/b, c/d ",
   undefined,
@@ -378,8 +363,7 @@ test(
   /Cannot specify a 'packs' input in a multi-language analysis/,
 );
 
-test(
+calculateAugmentationErrorMacro(
-  calculateAugmentationErrorMacro,
   "Packs input with no languages",
   "   +  a/b, c/d ",
   undefined,
@@ -388,8 +372,7 @@ test(
   /No languages specified/,
 );
 
-test(
+calculateAugmentationErrorMacro(
-  calculateAugmentationErrorMacro,
   "Invalid packs",
   " a-pack-without-a-scope ",
   undefined,

src/debug-artifacts.ts

@@ -263,7 +263,7 @@ export function getArtifactSuffix(matrix: string | undefined): string {
     try {
       const matrixObject = JSON.parse(matrix);
       if (json.isObject(matrixObject)) {
-        for (const matrixKey of Object.keys(matrixObject as object).sort())
+        for (const matrixKey of Object.keys(matrixObject).sort())
           suffix += `-${matrixObject[matrixKey]}`;
       } else {
         core.warning("User-specified `matrix` input is not an object.");

src/defaults.json

@@ -1,6 +1,6 @@
 {
-  "bundleVersion": "codeql-bundle-v2.25.3",
+  "bundleVersion": "codeql-bundle-v2.25.4",
-  "cliVersion": "2.25.3",
+  "cliVersion": "2.25.4",
-  "priorBundleVersion": "codeql-bundle-v2.25.2",
+  "priorBundleVersion": "codeql-bundle-v2.25.3",
-  "priorCliVersion": "2.25.2"
+  "priorCliVersion": "2.25.3"
 }

src/diff-informed-analysis-utils.test.ts

@@ -5,17 +5,20 @@ import * as actionsUtil from "./actions-util";
 import type { PullRequestBranches } from "./actions-util";
 import * as apiClient from "./api-client";
 import {
-  shouldPerformDiffInformedAnalysis,
+  getDiffInformedAnalysisBranches,
+  prepareDiffInformedAnalysis,
   exportedForTesting,
 } from "./diff-informed-analysis-utils";
-import { Feature, initFeatures } from "./feature-flags";
+import { Feature, FeatureEnablement, initFeatures } from "./feature-flags";
 import { getRunnerLogger } from "./logging";
 import { parseRepositoryNwo } from "./repository";
 import {
   setupTests,
+  createFeatures,
   mockCodeQLVersion,
   mockFeatureFlagApiEndpoint,
   setupActionsVars,
+  makeMacro,
 } from "./testing-utils";
 import { GitHubVariant, withTmpDir } from "./util";
 import type { GitHubVersion } from "./util";
@@ -42,10 +45,9 @@ const defaultTestCase: DiffInformedAnalysisTestCase = {
   codeQLVersion: "2.21.0",
 };
 
-const testShouldPerformDiffInformedAnalysis = test.macro({
+const testShouldPerformDiffInformedAnalysis = makeMacro({
   exec: async (
     t: ExecutionContext,
-    _title: string,
     partialTestCase: Partial<DiffInformedAnalysisTestCase>,
     expectedResult: boolean,
   ) => {
@@ -73,39 +75,34 @@ const testShouldPerformDiffInformedAnalysis = test.macro({
         [Feature.DiffInformedQueries]: testCase.featureEnabled,
       });
 
-      const getGitHubVersionStub = sinon
+      sinon
         .stub(apiClient, "getGitHubVersion")
         .resolves(testCase.gitHubVersion);
-      const getPullRequestBranchesStub = sinon
+      sinon
         .stub(actionsUtil, "getPullRequestBranches")
         .returns(testCase.pullRequestBranches);
 
-      const result = await shouldPerformDiffInformedAnalysis(
+      const branches = await getDiffInformedAnalysisBranches(
         codeql,
         features,
         logger,
       );
 
-      t.is(result, expectedResult);
+      t.is(branches !== undefined, expectedResult);
 
       delete process.env.CODEQL_ACTION_DIFF_INFORMED_QUERIES;
-
-      getGitHubVersionStub.restore();
-      getPullRequestBranchesStub.restore();
     });
   },
-  title: (_, title) => `shouldPerformDiffInformedAnalysis: ${title}`,
+  title: (title) => `getDiffInformedAnalysisBranches: ${title}`,
 });
 
-test.serial(
+testShouldPerformDiffInformedAnalysis.serial(
-  testShouldPerformDiffInformedAnalysis,
   "returns true in the default test case",
   {},
   true,
 );
 
-test.serial(
+testShouldPerformDiffInformedAnalysis.serial(
-  testShouldPerformDiffInformedAnalysis,
   "returns false when feature flag is disabled from the API",
   {
     featureEnabled: false,
@@ -113,8 +110,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testShouldPerformDiffInformedAnalysis.serial(
-  testShouldPerformDiffInformedAnalysis,
   "returns false when CODEQL_ACTION_DIFF_INFORMED_QUERIES is set to false",
   {
     featureEnabled: true,
@@ -123,8 +119,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testShouldPerformDiffInformedAnalysis.serial(
-  testShouldPerformDiffInformedAnalysis,
   "returns true when CODEQL_ACTION_DIFF_INFORMED_QUERIES is set to true",
   {
     featureEnabled: false,
@@ -133,8 +128,7 @@ test.serial(
   true,
 );
 
-test.serial(
+testShouldPerformDiffInformedAnalysis.serial(
-  testShouldPerformDiffInformedAnalysis,
   "returns false for CodeQL version 2.20.0",
   {
     codeQLVersion: "2.20.0",
@@ -142,8 +136,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testShouldPerformDiffInformedAnalysis.serial(
-  testShouldPerformDiffInformedAnalysis,
   "returns false for invalid GHES version",
   {
     gitHubVersion: {
@@ -154,8 +147,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testShouldPerformDiffInformedAnalysis.serial(
-  testShouldPerformDiffInformedAnalysis,
   "returns false for GHES version 3.18.5",
   {
     gitHubVersion: {
@@ -166,8 +158,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testShouldPerformDiffInformedAnalysis.serial(
-  testShouldPerformDiffInformedAnalysis,
   "returns true for GHES version 3.19.0",
   {
     gitHubVersion: {
@@ -178,8 +169,7 @@ test.serial(
   true,
 );
 
-test.serial(
+testShouldPerformDiffInformedAnalysis.serial(
-  testShouldPerformDiffInformedAnalysis,
   "returns false when not a pull request",
   {
     pullRequestBranches: undefined,
@@ -187,6 +177,135 @@ test.serial(
   false,
 );
 
+test.serial(
+  "prepareDiffInformedAnalysis: returns false when not a pull request",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      const logger = getRunnerLogger(true);
+      const codeql = mockCodeQLVersion("2.21.0");
+      const features = createFeatures([Feature.DiffInformedQueries]);
+
+      sinon.stub(actionsUtil, "getPullRequestBranches").returns(undefined);
+      sinon
+        .stub(apiClient, "getGitHubVersion")
+        .resolves({ type: GitHubVariant.DOTCOM });
+
+      const result = await prepareDiffInformedAnalysis(
+        codeql,
+        features,
+        logger,
+      );
+
+      t.false(result);
+    });
+  },
+);
+
+test.serial(
+  "prepareDiffInformedAnalysis: returns false when applicability check throws",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      const logger = getRunnerLogger(true);
+      const codeql = mockCodeQLVersion("2.21.0");
+      // A features implementation whose getValue rejects, simulating an
+      // unexpected failure when determining whether diff-informed analysis
+      // should run.
+      const features: FeatureEnablement = {
+        getEnabledDefaultCliVersions: async () => {
+          throw new Error("not implemented");
+        },
+        getValue: async () => {
+          throw new Error("feature flag lookup failed");
+        },
+      };
+
+      const result = await prepareDiffInformedAnalysis(
+        codeql,
+        features,
+        logger,
+      );
+
+      t.false(result);
+    });
+  },
+);
+
+test.serial(
+  "prepareDiffInformedAnalysis: returns true when the diff is fetched successfully",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      const logger = getRunnerLogger(true);
+      const codeql = mockCodeQLVersion("2.21.0");
+      const features = createFeatures([Feature.DiffInformedQueries]);
+
+      sinon
+        .stub(actionsUtil, "getPullRequestBranches")
+        .returns({ base: "main", head: "feature" });
+      sinon
+        .stub(apiClient, "getGitHubVersion")
+        .resolves({ type: GitHubVariant.DOTCOM });
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-argument
+      sinon.stub(apiClient, "getApiClient").returns({
+        rest: {
+          repos: {
+            compareCommitsWithBasehead: sinon
+              .stub()
+              .resolves({ data: { files: [] } }),
+          },
+        },
+      } as any);
+
+      const result = await prepareDiffInformedAnalysis(
+        codeql,
+        features,
+        logger,
+      );
+
+      t.true(result);
+    });
+  },
+);
+
+test.serial(
+  "prepareDiffInformedAnalysis: returns false when the diff API call fails",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      const logger = getRunnerLogger(true);
+      const codeql = mockCodeQLVersion("2.21.0");
+      const features = createFeatures([Feature.DiffInformedQueries]);
+
+      sinon
+        .stub(actionsUtil, "getPullRequestBranches")
+        .returns({ base: "main", head: "feature" });
+      sinon
+        .stub(apiClient, "getGitHubVersion")
+        .resolves({ type: GitHubVariant.DOTCOM });
+      const notFoundError: any = new Error("Not Found");
+      notFoundError.status = 404;
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-argument
+      sinon.stub(apiClient, "getApiClient").returns({
+        rest: {
+          repos: {
+            compareCommitsWithBasehead: sinon.stub().rejects(notFoundError),
+          },
+        },
+      } as any);
+
+      const result = await prepareDiffInformedAnalysis(
+        codeql,
+        features,
+        logger,
+      );
+
+      t.false(result);
+    });
+  },
+);
+
 function runGetDiffRanges(changes: number, patch: string[] | undefined): any {
   return exportedForTesting.getDiffRanges(
     {

src/diff-informed-analysis-utils.ts

@@ -5,9 +5,9 @@ import type { PullRequestBranches } from "./actions-util";
 import { getApiClient, getGitHubVersion } from "./api-client";
 import type { CodeQL } from "./codeql";
 import { Feature, FeatureEnablement } from "./feature-flags";
-import { Logger } from "./logging";
+import { Logger, withGroupAsync } from "./logging";
 import { getRepositoryNwoFromEnv } from "./repository";
-import { GitHubVariant, satisfiesGHESVersion } from "./util";
+import { getErrorMessage, GitHubVariant, satisfiesGHESVersion } from "./util";
 
 /**
  * This interface is an abbreviated version of the file diff object returned by
@@ -21,20 +21,6 @@ interface FileDiff {
   patch?: string | undefined;
 }
 
-/**
- * Check if the action should perform diff-informed analysis.
- */
-export async function shouldPerformDiffInformedAnalysis(
-  codeql: CodeQL,
-  features: FeatureEnablement,
-  logger: Logger,
-): Promise<boolean> {
-  return (
-    (await getDiffInformedAnalysisBranches(codeql, features, logger)) !==
-    undefined
-  );
-}
-
 /**
  * Get the branches to use for diff-informed analysis.
  *
@@ -69,6 +55,46 @@ export async function getDiffInformedAnalysisBranches(
   return branches;
 }
 
+/**
+ * Prepares the diff ranges needed for diff-informed analysis for the current
+ * run.
+ *
+ * @returns `true` if the diff ranges were successfully computed and persisted
+ *   and are therefore available for use, `false` otherwise.
+ */
+export async function prepareDiffInformedAnalysis(
+  codeql: CodeQL,
+  features: FeatureEnablement,
+  logger: Logger,
+): Promise<boolean> {
+  let branches: PullRequestBranches | undefined;
+  try {
+    branches = await getDiffInformedAnalysisBranches(codeql, features, logger);
+  } catch (e) {
+    // If we cannot determine whether diff-informed analysis applies (for
+    // example, because a feature-flag lookup failed), treat it as not
+    // applicable rather than triggering the overlay fallback.
+    logger.warning(
+      `Failed to determine branch information for diff-informed analysis: ${getErrorMessage(e)}`,
+    );
+    return false;
+  }
+  if (!branches) {
+    return false;
+  }
+
+  return await withGroupAsync("Computing PR diff ranges", async () => {
+    try {
+      return await computeAndPersistDiffRanges(branches, logger);
+    } catch (e) {
+      logger.warning(
+        `Failed to compute diff-informed analysis ranges: ${getErrorMessage(e)}`,
+      );
+      return false;
+    }
+  });
+}
+
 export interface DiffThunkRange {
   /** Relative path from the repository root, using forward slashes as separators. */
   path: string;
@@ -151,6 +177,33 @@ export async function getPullRequestEditedDiffRanges(
   return results;
 }
 
+/**
+ * Compute and persist the diff ranges for a pull request. This fetches the
+ * diff from the GitHub API and writes it to the diff ranges JSON file so that
+ * CodeQL can use it for diff-informed analysis.
+ *
+ * @param branches The base and head branches of the pull request, as returned
+ *   by `getDiffInformedAnalysisBranches`.
+ * @param logger
+ * @returns `true` if the diff ranges were successfully computed and persisted,
+ *   otherwise `false`.
+ */
+export async function computeAndPersistDiffRanges(
+  branches: PullRequestBranches,
+  logger: Logger,
+): Promise<boolean> {
+  const ranges = await getPullRequestEditedDiffRanges(branches, logger);
+  if (ranges === undefined) {
+    return false;
+  }
+  writeDiffRangesJsonFile(logger, ranges);
+  const distinctFiles = new Set(ranges.map((r) => r.path)).size;
+  logger.info(
+    `Persisted ${ranges.length} diff range(s) across ${distinctFiles} file(s).`,
+  );
+  return true;
+}
+
 async function getFileDiffsWithBasehead(
   branches: PullRequestBranches,
   logger: Logger,

src/entry-wrapper.js.tpl

@@ -0,0 +1,3 @@
+export async function run__ACTION__() {
+  return await __ACTION__.runWrapper();
+}

src/feature-flags.test.ts

@@ -451,12 +451,16 @@ test.serial(`selects CLI from defaults.json on GHES`, async (t) => {
   await withTmpDir(async (tmpDir) => {
     const features = setUpFeatureFlagTests(tmpDir);
 
-    const defaultCliVersion = await features.getDefaultCliVersion(
+    const defaultCliVersion = await features.getEnabledDefaultCliVersions(
       GitHubVariant.GHES,
     );
     t.deepEqual(defaultCliVersion, {
-      cliVersion: defaults.cliVersion,
+      enabledVersions: [
-      tagName: defaults.bundleVersion,
+        {
+          cliVersion: defaults.cliVersion,
+          tagName: defaults.bundleVersion,
+        },
+      ],
     });
   });
 });
@@ -482,10 +486,13 @@ for (const variant of [GitHubVariant.DOTCOM, GitHubVariant.GHEC_DR]) {
           false;
         mockFeatureFlagApiEndpoint(200, expectedFeatureEnablement);
 
-        const defaultCliVersion = await features.getDefaultCliVersion(variant);
+        const defaultCliVersion =
+          await features.getEnabledDefaultCliVersions(variant);
         t.deepEqual(defaultCliVersion, {
-          cliVersion: "2.20.1",
+          enabledVersions: [
-          tagName: "codeql-bundle-v2.20.1",
+            { cliVersion: "2.20.1", tagName: "codeql-bundle-v2.20.1" },
+            { cliVersion: "2.20.0", tagName: "codeql-bundle-v2.20.0" },
+          ],
           toolsFeatureFlagsValid: true,
         });
       });
@@ -500,10 +507,15 @@ for (const variant of [GitHubVariant.DOTCOM, GitHubVariant.GHEC_DR]) {
         const expectedFeatureEnablement = initializeFeatures(true);
         mockFeatureFlagApiEndpoint(200, expectedFeatureEnablement);
 
-        const defaultCliVersion = await features.getDefaultCliVersion(variant);
+        const defaultCliVersion =
+          await features.getEnabledDefaultCliVersions(variant);
         t.deepEqual(defaultCliVersion, {
-          cliVersion: defaults.cliVersion,
+          enabledVersions: [
-          tagName: defaults.bundleVersion,
+            {
+              cliVersion: defaults.cliVersion,
+              tagName: defaults.bundleVersion,
+            },
+          ],
           toolsFeatureFlagsValid: false,
         });
       });
@@ -529,10 +541,13 @@ for (const variant of [GitHubVariant.DOTCOM, GitHubVariant.GHEC_DR]) {
         ] = true;
         mockFeatureFlagApiEndpoint(200, expectedFeatureEnablement);
 
-        const defaultCliVersion = await features.getDefaultCliVersion(variant);
+        const defaultCliVersion =
+          await features.getEnabledDefaultCliVersions(variant);
         t.deepEqual(defaultCliVersion, {
-          cliVersion: "2.20.1",
+          enabledVersions: [
-          tagName: "codeql-bundle-v2.20.1",
+            { cliVersion: "2.20.1", tagName: "codeql-bundle-v2.20.1" },
+            { cliVersion: "2.20.0", tagName: "codeql-bundle-v2.20.0" },
+          ],
           toolsFeatureFlagsValid: true,
         });
 

src/feature-flags.ts

@@ -26,12 +26,38 @@ const DEFAULT_VERSION_FEATURE_FLAG_SUFFIX = "_enabled";
 
 /**
  * The first version of the CodeQL Bundle that shipped with zstd-compressed bundles.
+ *
+ * This is now below the minimum version of CodeQL, but we keep this around because we currently set
+ * up CodeQL before checking that the version is new enough.
  */
 export const CODEQL_VERSION_ZSTD_BUNDLE = "2.19.0";
 
-export interface CodeQLDefaultVersionInfo {
+const LINKED_CODEQL_VERSION: CodeQLVersionInfo = {
+  cliVersion: defaults.cliVersion,
+  tagName: defaults.bundleVersion,
+};
+
+export interface CodeQLVersionInfo {
+  /** The version number of the CodeQL CLI, e.g. `2.19.0`. */
   cliVersion: string;
+  /**
+   * The tag name of the CodeQL Bundle associated with this version, e.g. `codeql-bundle-v2.19.0`.
+   */
   tagName: string;
+}
+
+export interface CodeQLDefaultVersionInfo {
+  /**
+   * CodeQL CLI versions that are enabled as defaults, sorted from highest to lowest.
+   *
+   * Guaranteed to be non-empty. When feature flags are unavailable, this falls back to a single
+   * entry containing the version pinned in `defaults.json`.
+   */
+  enabledVersions: CodeQLVersionInfo[];
+  /**
+   * If accessed, whether the tools feature flags are valid, i.e. contain at least one enabled
+   * version.
+   */
   toolsFeatureFlagsValid?: boolean;
 }
 
@@ -44,6 +70,8 @@ export interface CodeQLDefaultVersionInfo {
  * Legacy features should end with `_enabled`.
  */
 export enum Feature {
+  /** Controls whether we allow multiple values for the `analysis-kinds` input. */
+  AllowMultipleAnalysisKinds = "allow_multiple_analysis_kinds",
   AllowToolcacheInput = "allow_toolcache_input",
   CleanupTrapCaches = "cleanup_trap_caches",
   CppDependencyInstallation = "cpp_dependency_installation_enabled",
@@ -72,6 +100,19 @@ export enum Feature {
   OverlayAnalysisGo = "overlay_analysis_go",
   OverlayAnalysisJava = "overlay_analysis_java",
   OverlayAnalysisJavascript = "overlay_analysis_javascript",
+  /**
+   * When set, chooses the default CodeQL CLI version as the highest version that is both enabled by
+   * feature flags and present as an overlay-base database in the Actions cache for the configured
+   * languages. Falls back to the highest feature flagged version if no intersecting overlay-base
+   * database exists in the cache.
+   */
+  OverlayAnalysisMatchCodeqlVersion = "overlay_analysis_match_codeql_version",
+  /**
+   * Like `OverlayAnalysisMatchCodeqlVersion`, but only logs a diagnostic with the version that
+   * would have been chosen instead of actually changing the default CodeQL CLI version.
+   * `OverlayAnalysisMatchCodeqlVersion` overrides this flag.
+   */
+  OverlayAnalysisMatchCodeqlVersionDryRun = "overlay_analysis_match_codeql_version_dry_run",
   OverlayAnalysisPython = "overlay_analysis_python",
   /**
    * Controls whether lower disk space requirements are used for overlay hardware checks.
@@ -124,6 +165,11 @@ export type FeatureConfig = {
 };
 
 export const featureConfig = {
+  [Feature.AllowMultipleAnalysisKinds]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_ALLOW_MULTIPLE_ANALYSIS_KINDS",
+    minimumVersion: undefined,
+  },
   [Feature.AllowToolcacheInput]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_ALLOW_TOOLCACHE_INPUT",
@@ -277,6 +323,16 @@ export const featureConfig = {
     envVar: "CODEQL_ACTION_OVERLAY_ANALYSIS_DISABLE_TRAP_CACHING",
     minimumVersion: undefined,
   },
+  [Feature.OverlayAnalysisMatchCodeqlVersion]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_OVERLAY_ANALYSIS_MATCH_CODEQL_VERSION",
+    minimumVersion: undefined,
+  },
+  [Feature.OverlayAnalysisMatchCodeqlVersionDryRun]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_OVERLAY_ANALYSIS_MATCH_CODEQL_VERSION_DRY_RUN",
+    minimumVersion: undefined,
+  },
   [Feature.OverlayAnalysisResourceChecksV2]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_OVERLAY_ANALYSIS_RESOURCE_CHECKS_V2",
@@ -346,8 +402,12 @@ export type FeatureWithoutCLI = {
 }[keyof typeof featureConfig];
 
 export interface FeatureEnablement {
-  /** Gets the default version of the CodeQL tools. */
+  /**
-  getDefaultCliVersion(
+   * Returns the set of default CodeQL CLI versions to consider, sorted from
+   * highest to lowest. The first entry is the version that the CodeQL Action
+   * will use by default. The list is always non-empty.
+   */
+  getEnabledDefaultCliVersions(
     variant: util.GitHubVariant,
   ): Promise<CodeQLDefaultVersionInfo>;
   getValue(feature: FeatureWithoutCLI): Promise<boolean>;
@@ -371,12 +431,11 @@ export const FEATURE_FLAGS_FILE_NAME = "cached-feature-flags.json";
 class OfflineFeatures implements FeatureEnablement {
   constructor(protected readonly logger: Logger) {}
 
-  async getDefaultCliVersion(
+  async getEnabledDefaultCliVersions(
     _variant: util.GitHubVariant,
   ): Promise<CodeQLDefaultVersionInfo> {
     return {
-      cliVersion: defaults.cliVersion,
+      enabledVersions: [LINKED_CODEQL_VERSION],
-      tagName: defaults.bundleVersion,
     };
   }
 
@@ -386,7 +445,7 @@ class OfflineFeatures implements FeatureEnablement {
   getFeatureConfig(feature: Feature): FeatureConfig {
     // Narrow the type to FeatureConfig to avoid type errors. To avoid unsafe use of `as`, we
     // check that the required properties exist using `satisfies`.
-    return featureConfig[feature] satisfies FeatureConfig as FeatureConfig;
+    return featureConfig[feature] satisfies FeatureConfig;
   }
 
   /**
@@ -518,13 +577,13 @@ class Features extends OfflineFeatures {
     );
   }
 
-  async getDefaultCliVersion(
+  async getEnabledDefaultCliVersions(
     variant: util.GitHubVariant,
   ): Promise<CodeQLDefaultVersionInfo> {
     if (supportsFeatureFlags(variant)) {
-      return await this.gitHubFeatureFlags.getDefaultCliVersionFromFlags();
+      return await this.gitHubFeatureFlags.getEnabledDefaultCliVersionsFromFlags();
     }
-    return super.getDefaultCliVersion(variant);
+    return super.getEnabledDefaultCliVersions(variant);
   }
 
   /**
@@ -600,16 +659,22 @@ class GitHubFeatureFlags {
     return version;
   }
 
-  async getDefaultCliVersionFromFlags(): Promise<CodeQLDefaultVersionInfo> {
+  /**
+   * Returns CLI versions enabled by `default_codeql_version_*_enabled` feature
+   * flags, sorted from highest to lowest. Falls back to the version pinned in
+   * `defaults.json` if no such flags are enabled.
+   */
+  async getEnabledDefaultCliVersionsFromFlags(): Promise<CodeQLDefaultVersionInfo> {
     const response = await this.getAllFeatures();
 
-    const enabledFeatureFlagCliVersions = Object.entries(response)
+    const sortedCliVersions = Object.entries(response)
       .map(([f, isEnabled]) =>
         isEnabled ? this.getCliVersionFromFeatureFlag(f) : undefined,
       )
-      .filter((f): f is string => f !== undefined);
+      .filter((f): f is string => f !== undefined)
+      .sort(semver.rcompare);
 
-    if (enabledFeatureFlagCliVersions.length === 0) {
+    if (sortedCliVersions.length === 0) {
       // We expect at least one default CLI version to be enabled on Dotcom at any time. However if
       // the feature flags are misconfigured, rather than crashing, we fall back to the CLI version
       // shipped with the Action in defaults.json. This has the effect of immediately rolling out
@@ -625,8 +690,7 @@ class GitHubFeatureFlags {
           `shipped with the Action. This is ${defaults.cliVersion}.`,
       );
       const result: CodeQLDefaultVersionInfo = {
-        cliVersion: defaults.cliVersion,
+        enabledVersions: [LINKED_CODEQL_VERSION],
-        tagName: defaults.bundleVersion,
       };
       if (this.hasAccessedRemoteFeatureFlags) {
         result.toolsFeatureFlagsValid = false;
@@ -634,17 +698,14 @@ class GitHubFeatureFlags {
       return result;
     }
 
-    const maxCliVersion = enabledFeatureFlagCliVersions.reduce(
-      (maxVersion, currentVersion) =>
-        currentVersion > maxVersion ? currentVersion : maxVersion,
-      enabledFeatureFlagCliVersions[0],
-    );
     this.logger.debug(
-      `Derived default CLI version of ${maxCliVersion} from feature flags.`,
+      `Derived default CLI version of ${sortedCliVersions[0]} from feature flags.`,
     );
     return {
-      cliVersion: maxCliVersion,
+      enabledVersions: sortedCliVersions.map((cliVersion) => ({
-      tagName: `codeql-bundle-v${maxCliVersion}`,
+        cliVersion,
+        tagName: `codeql-bundle-v${cliVersion}`,
+      })),
       toolsFeatureFlagsValid: true,
     };
   }

src/git-utils.test.ts

@@ -33,7 +33,6 @@ test.serial(
 
       const actualRef = await gitUtils.getRef();
       t.deepEqual(actualRef, expectedRef);
-      callback.restore();
     });
   },
 );
@@ -54,7 +53,6 @@ test.serial(
 
       const actualRef = await gitUtils.getRef();
       t.deepEqual(actualRef, expectedRef);
-      callback.restore();
     });
   },
 );
@@ -73,7 +71,6 @@ test.serial(
 
       const actualRef = await gitUtils.getRef();
       t.deepEqual(actualRef, "refs/pull/1/head");
-      callback.restore();
     });
   },
 );
@@ -100,8 +97,6 @@ test.serial(
 
       const actualRef = await gitUtils.getRef();
       t.deepEqual(actualRef, "refs/pull/2/merge");
-      callback.restore();
-      getAdditionalInputStub.restore();
     });
   },
 );
@@ -161,7 +156,6 @@ test.serial(
             "Both 'ref' and 'sha' are required if one of them is provided.",
         },
       );
-      getAdditionalInputStub.restore();
     });
   },
 );
@@ -188,7 +182,6 @@ test.serial(
             "Both 'ref' and 'sha' are required if one of them is provided.",
         },
       );
-      getAdditionalInputStub.restore();
     });
   },
 );
@@ -242,7 +235,6 @@ test.serial("isAnalyzingDefaultBranch()", async (t) => {
     process.env["GITHUB_EVENT_NAME"] = "schedule";
     process.env["GITHUB_REF"] = "refs/heads/main";
     t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(), false);
-    getAdditionalInputStub.restore();
   });
 });
 
@@ -254,8 +246,6 @@ test.serial("determineBaseBranchHeadCommitOid non-pullrequest", async (t) => {
   const result = await gitUtils.determineBaseBranchHeadCommitOid(__dirname);
   t.deepEqual(result, undefined);
   t.deepEqual(0, infoStub.callCount);
-
-  infoStub.restore();
 });
 
 test.serial(
@@ -276,8 +266,6 @@ test.serial(
       "git call failed. Will calculate the base branch SHA on the server. Error: " +
         "The checkout path provided to the action does not appear to be a git repository.",
     );
-
-    infoStub.restore();
   },
 );
 
@@ -301,10 +289,27 @@ test.serial("determineBaseBranchHeadCommitOid other error", async (t) => {
       "The checkout path provided to the action does not appear to be a git repository.",
     ),
   );
-
-  infoStub.restore();
 });
 
+test.serial(
+  "determineBaseBranchHeadCommitOid accepts SHA-256 OIDs",
+  async (t) => {
+    const mergeSha = "a".repeat(64);
+    const baseOid = "b".repeat(64);
+    const headOid = "c".repeat(64);
+
+    process.env["GITHUB_EVENT_NAME"] = "pull_request";
+    process.env["GITHUB_SHA"] = mergeSha;
+
+    sinon
+      .stub(gitUtils as any, "runGitCommand")
+      .resolves(`commit ${mergeSha}\nparent ${baseOid}\nparent ${headOid}\n`);
+
+    const result = await gitUtils.determineBaseBranchHeadCommitOid(__dirname);
+    t.deepEqual(result, baseOid);
+  },
+);
+
 test.serial("decodeGitFilePath unquoted strings", async (t) => {
   t.deepEqual(gitUtils.decodeGitFilePath("foo"), "foo");
   t.deepEqual(gitUtils.decodeGitFilePath("foo bar"), "foo bar");
@@ -436,6 +441,64 @@ test.serial("getFileOidsUnderPath handles quoted paths", async (t) => {
   });
 });
 
+test.serial("getFileOidsUnderPath handles SHA-256 OIDs", async (t) => {
+  await withTmpDir(async (tmpDir) => {
+    const sha256OidA =
+      "9f86d081884c7d659a2feaa0c55ad015a3bf4f1b2c0d4b7e8f9a1234567890ab";
+    const sha256OidB =
+      "aabbccddeeff00112233445566778899aabbccddeeff00112233445566778899";
+
+    sinon
+      .stub(gitUtils as any, "runGitCommand")
+      .callsFake(async (_cwd: any, args: any) => {
+        if (args[0] === "rev-parse") {
+          return `${tmpDir}\n`;
+        }
+        return (
+          `100644 ${sha256OidA} 0\tlib/sha256-file-a.js\n` +
+          `100644 ${sha256OidB} 0\tsrc/sha256-file-b.ts`
+        );
+      });
+
+    const result = await gitUtils.getFileOidsUnderPath("/fake/path");
+
+    t.deepEqual(result, {
+      "lib/sha256-file-a.js": sha256OidA,
+      "src/sha256-file-b.ts": sha256OidB,
+    });
+  });
+});
+
+test.serial(
+  "getFileOidsUnderPath rejects OIDs of unsupported length",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      // 50-char OID: not a valid SHA-1 (40) or SHA-256 (64) length. The regex
+      // must not accept this even though every character is a valid hex digit.
+      const invalidLine =
+        "100644 30d998ded095371488be3a729eb61d86ed721a1830d998ded0 0\tlib/bad.js";
+      sinon
+        .stub(gitUtils as any, "runGitCommand")
+        .callsFake(async (_cwd: any, args: any) => {
+          if (args[0] === "rev-parse") {
+            return `${tmpDir}\n`;
+          }
+          return invalidLine;
+        });
+
+      await t.throwsAsync(
+        async () => {
+          await gitUtils.getFileOidsUnderPath("/fake/path");
+        },
+        {
+          instanceOf: Error,
+          message: `Unexpected "git ls-files" output: ${invalidLine}`,
+        },
+      );
+    });
+  },
+);
+
 test.serial("getFileOidsUnderPath handles empty output", async (t) => {
   await withTmpDir(async (tmpDir) => {
     sinon

src/git-utils.ts

@@ -163,11 +163,12 @@ export const determineBaseBranchHeadCommitOid = async function (
       }
     }
 
-    // Let's confirm our assumptions: We had a merge commit and the parsed parent data looks correct
+    // Let's confirm our assumptions: We had a merge commit and the parsed parent
+    // data looks correct. OIDs are either 40 (SHA-1) or 64 (SHA-256) hex characters.
     if (
       commitOid === mergeSha &&
-      headOid.length === 40 &&
+      (headOid.length === 40 || headOid.length === 64) &&
-      baseOid.length === 40
+      (baseOid.length === 40 || baseOid.length === 64)
     ) {
       return baseOid;
     }
@@ -296,7 +297,8 @@ export const getFileOidsUnderPath = async function (
   // 100644 4c51bc1d9e86cd86e01b0f340cb8ce095c33b283 0\tsrc/git-utils.test.ts
   // 100644 6b792ea543ce75d7a8a03df591e3c85311ecb64f 0\tsrc/git-utils.ts
   // The fields are: <mode> <oid> <stage>\t<path>
-  const regex = /^[0-9]+ ([0-9a-f]{40}) [0-9]+\t(.+)$/;
+  // The OID is either 40 (SHA-1) or 64 (SHA-256) hex characters.
+  const regex = /^[0-9]+ ([0-9a-f]{40}|[0-9a-f]{64}) [0-9]+\t(.+)$/;
   for (const line of stdout.split("\n")) {
     if (line) {
       const match = line.match(regex);

src/init-action-post-helper.test.ts

@@ -19,6 +19,7 @@ import {
   createFeatures,
   createTestConfig,
   DEFAULT_ACTIONS_VARS,
+  makeMacro,
   makeVersionInfo,
   RecordingLogger,
   setupActionsVars,
@@ -601,7 +602,7 @@ async function testFailedSarifUpload(
   uploadFiles.resolves({
     sarifID: "42",
     statusReport: { raw_upload_size_bytes: 20, zipped_upload_size_bytes: 10 },
-  } as uploadLib.UploadResult);
+  });
   const waitForProcessing = sinon.stub(uploadLib, "waitForProcessing");
 
   const features = [] as Feature[];
@@ -796,7 +797,7 @@ test.serial(
   },
 );
 
-const skippedUploadTest = test.macro({
+const skippedUploadTest = makeMacro({
   exec: async (
     t: ExecutionContext<unknown>,
     config: Partial<configUtils.Config>,
@@ -823,9 +824,8 @@ const skippedUploadTest = test.macro({
     `tryUploadSarifIfRunFailed - skips upload ${providedTitle}`,
 });
 
-test.serial(
+skippedUploadTest.serial(
   "without CodeQL command",
-  skippedUploadTest,
   // No codeQLCmd
   {
     analysisKinds: [AnalysisKind.RiskAssessment],
@@ -834,9 +834,8 @@ test.serial(
   "CodeQL command not found",
 );
 
-test.serial(
+skippedUploadTest.serial(
   "if no language is configured",
-  skippedUploadTest,
   // No explicit language configuration
   {
     analysisKinds: [AnalysisKind.RiskAssessment],
@@ -845,9 +844,8 @@ test.serial(
   "Unexpectedly, the configuration is not for a single language.",
 );
 
-test.serial(
+skippedUploadTest.serial(
   "if multiple languages is configured",
-  skippedUploadTest,
   // Multiple explicit languages configured
   {
     analysisKinds: [AnalysisKind.RiskAssessment],

src/init-action-post.ts

@@ -207,7 +207,7 @@ function getJobStatusFromEnvironment(): JobStatus | undefined {
   return undefined;
 }
 
-async function runWrapper() {
+export async function runWrapper() {
   const startedAt = new Date();
   const logger = getActionsLogger();
   try {
@@ -222,5 +222,3 @@ async function runWrapper() {
     );
   }
 }
-
-void runWrapper();

src/init-action.ts

@@ -37,11 +37,6 @@ import {
   makeDiagnostic,
   makeTelemetryDiagnostic,
 } from "./diagnostics";
-import {
-  getDiffInformedAnalysisBranches,
-  getPullRequestEditedDiffRanges,
-  writeDiffRangesJsonFile,
-} from "./diff-informed-analysis-utils";
 import { EnvVar } from "./environment";
 import { Feature, FeatureEnablement, initFeatures } from "./feature-flags";
 import {
@@ -281,7 +276,7 @@ async function run(startedAt: Date) {
     // successful, the results are cached so that we don't duplicate the work in normal runs.
     let analysisKinds: AnalysisKind[] | undefined;
     try {
-      analysisKinds = await getAnalysisKinds(logger);
+      analysisKinds = await getAnalysisKinds(logger, features);
     } catch (err) {
       logger.debug(
         `Failed to parse analysis kinds for 'starting' status report: ${getErrorMessage(err)}`,
@@ -298,16 +293,23 @@ async function run(startedAt: Date) {
       );
     }
 
-    const codeQLDefaultVersionInfo = await features.getDefaultCliVersion(
+    const codeQLDefaultVersionInfo =
-      gitHubVersion.type,
+      await features.getEnabledDefaultCliVersions(gitHubVersion.type);
-    );
     toolsFeatureFlagsValid = codeQLDefaultVersionInfo.toolsFeatureFlagsValid;
+    const rawLanguages = configUtils.getRawLanguagesNoAutodetect(
+      getOptionalInput("languages"),
+    );
+    const useOverlayAwareDefaultCliVersion =
+      analysisKinds?.length === 1 &&
+      analysisKinds[0] === AnalysisKind.CodeScanning;
     const initCodeQLResult = await initCodeQL(
       getOptionalInput("tools"),
       apiDetails,
       getTemporaryDirectory(),
       gitHubVersion.type,
       codeQLDefaultVersionInfo,
+      rawLanguages,
+      useOverlayAwareDefaultCliVersion,
       features,
       logger,
     );
@@ -346,7 +348,7 @@ async function run(startedAt: Date) {
       }
     }
 
-    analysisKinds = await getAnalysisKinds(logger);
+    analysisKinds = await getAnalysisKinds(logger, features);
     const debugMode = getOptionalInput("debug") === "true" || core.isDebug();
     const repositoryProperties = repositoryPropertiesResult.orElse({});
     const fileCoverageResult = await getFileCoverageInformationEnabled(
@@ -427,7 +429,6 @@ async function run(startedAt: Date) {
     }
 
     await checkInstallPython311(config.languages, codeql);
-    await computeAndPersistDiffRanges(codeql, features, logger);
   } catch (unwrappedError) {
     const error = wrapError(unwrappedError);
     core.setFailed(error.message);
@@ -823,42 +824,6 @@ async function loadRepositoryProperties(
   }
 }
 
-/**
- * Compute and persist diff ranges when diff-informed analysis is enabled
- * (feature flag + PR context). This writes the standard pr-diff-range.json
- * file for later reuse in the analyze step. Failures are logged but non-fatal.
- */
-async function computeAndPersistDiffRanges(
-  codeql: CodeQL,
-  features: FeatureEnablement,
-  logger: Logger,
-): Promise<void> {
-  await withGroupAsync("Computing PR diff ranges", async () => {
-    try {
-      const branches = await getDiffInformedAnalysisBranches(
-        codeql,
-        features,
-        logger,
-      );
-      if (!branches) {
-        return;
-      }
-      const ranges = await getPullRequestEditedDiffRanges(branches, logger);
-      if (ranges === undefined) {
-        return;
-      }
-      writeDiffRangesJsonFile(logger, ranges);
-      const distinctFiles = new Set(ranges.map((r) => r.path)).size;
-      logger.info(
-        `Persisted ${ranges.length} diff range(s) across ${distinctFiles} file(s).`,
-      );
-    } catch (e) {
-      logger.warning(
-        `Failed to compute and persist PR diff ranges: ${getErrorMessage(e)}`,
-      );
-    }
-  });
-}
 async function recordZstdAvailability(
   config: configUtils.Config,
   zstdAvailability: ZstdAvailability,
@@ -873,7 +838,7 @@ async function recordZstdAvailability(
   );
 }
 
-async function runWrapper() {
+export async function runWrapper() {
   const startedAt = new Date();
   const logger = getActionsLogger();
   try {
@@ -889,5 +854,3 @@ async function runWrapper() {
   }
   await checkForTimeout();
 }
-
-void runWrapper();

src/init.test.ts

@@ -22,6 +22,7 @@ import {
   createTestConfig,
   getRecordingLogger,
   setupTests,
+  makeMacro,
 } from "./testing-utils";
 import { ConfigurationError, withTmpDir } from "./util";
 
@@ -158,10 +159,9 @@ type PackInfo = {
   qlpackFileName?: string;
 };
 
-const testCheckPacksForOverlayCompatibility = test.macro({
+const testCheckPacksForOverlayCompatibility = makeMacro({
   exec: async (
     t: ExecutionContext,
-    _title: string,
     {
       cliOverlayVersion,
       languages,
@@ -234,11 +234,10 @@ const testCheckPacksForOverlayCompatibility = test.macro({
       );
     });
   },
-  title: (_, title) => `checkPacksForOverlayCompatibility: ${title}`,
+  title: (title) => `checkPacksForOverlayCompatibility: ${title}`,
 });
 
-test(
+testCheckPacksForOverlayCompatibility(
-  testCheckPacksForOverlayCompatibility,
   "returns false when CLI does not support overlay",
   {
     cliOverlayVersion: undefined,
@@ -253,8 +252,7 @@ test(
   },
 );
 
-test(
+testCheckPacksForOverlayCompatibility(
-  testCheckPacksForOverlayCompatibility,
   "returns true when there are no query packs",
   {
     cliOverlayVersion: 2,
@@ -264,8 +262,7 @@ test(
   },
 );
 
-test(
+testCheckPacksForOverlayCompatibility(
-  testCheckPacksForOverlayCompatibility,
   "returns true when query pack has not been compiled",
   {
     cliOverlayVersion: 2,
@@ -281,8 +278,7 @@ test(
   },
 );
 
-test(
+testCheckPacksForOverlayCompatibility(
-  testCheckPacksForOverlayCompatibility,
   "returns true when query pack has expected overlay version",
   {
     cliOverlayVersion: 2,
@@ -297,8 +293,7 @@ test(
   },
 );
 
-test(
+testCheckPacksForOverlayCompatibility(
-  testCheckPacksForOverlayCompatibility,
   "returns true when query packs for all languages to analyze are compatible",
   {
     cliOverlayVersion: 2,
@@ -317,8 +312,7 @@ test(
   },
 );
 
-test(
+testCheckPacksForOverlayCompatibility(
-  testCheckPacksForOverlayCompatibility,
   "returns true when query pack for a language not analyzed is incompatible",
   {
     cliOverlayVersion: 2,
@@ -337,8 +331,7 @@ test(
   },
 );
 
-test(
+testCheckPacksForOverlayCompatibility(
-  testCheckPacksForOverlayCompatibility,
   "returns false when query pack for a language to analyze is incompatible",
   {
     cliOverlayVersion: 2,
@@ -357,8 +350,7 @@ test(
   },
 );
 
-test(
+testCheckPacksForOverlayCompatibility(
-  testCheckPacksForOverlayCompatibility,
   "returns false when query pack is missing .packinfo",
   {
     cliOverlayVersion: 2,
@@ -377,8 +369,7 @@ test(
   },
 );
 
-test(
+testCheckPacksForOverlayCompatibility(
-  testCheckPacksForOverlayCompatibility,
   "returns false when query pack has different overlay version",
   {
     cliOverlayVersion: 2,
@@ -397,8 +388,7 @@ test(
   },
 );
 
-test(
+testCheckPacksForOverlayCompatibility(
-  testCheckPacksForOverlayCompatibility,
   "returns false when query pack is missing overlayVersion in .packinfo",
   {
     cliOverlayVersion: 2,
@@ -417,8 +407,7 @@ test(
   },
 );
 
-test(
+testCheckPacksForOverlayCompatibility(
-  testCheckPacksForOverlayCompatibility,
   "returns false when .packinfo is not valid JSON",
   {
     cliOverlayVersion: 2,
@@ -437,8 +426,7 @@ test(
   },
 );
 
-test(
+testCheckPacksForOverlayCompatibility(
-  testCheckPacksForOverlayCompatibility,
   "returns true when query pack uses codeql-pack.yml filename",
   {
     cliOverlayVersion: 2,

src/init.ts

@@ -39,6 +39,8 @@ export async function initCodeQL(
   tempDir: string,
   variant: util.GitHubVariant,
   defaultCliVersion: CodeQLDefaultVersionInfo,
+  rawLanguages: string[] | undefined,
+  useOverlayAwareDefaultCliVersion: boolean,
   features: FeatureEnablement,
   logger: Logger,
 ): Promise<{
@@ -61,6 +63,8 @@ export async function initCodeQL(
     tempDir,
     variant,
     defaultCliVersion,
+    rawLanguages,
+    useOverlayAwareDefaultCliVersion,
     features,
     logger,
     true,

src/overlay/caching.test.ts

@@ -13,6 +13,7 @@ import { BuiltInLanguage } from "../languages";
 import { getRunnerLogger } from "../logging";
 import {
   createTestConfig,
+  makeMacro,
   mockCodeQLVersion,
   setupTests,
 } from "../testing-utils";
@@ -51,10 +52,9 @@ const defaultDownloadTestCase: DownloadOverlayBaseDatabaseTestCase = {
   resolveDatabaseOutput: { overlayBaseSpecifier: "20250626:XXX" },
 };
 
-const testDownloadOverlayBaseDatabaseFromCache = test.macro({
+const testDownloadOverlayBaseDatabaseFromCache = makeMacro({
   exec: async (
     t,
-    _title: string,
     partialTestCase: Partial<DownloadOverlayBaseDatabaseTestCase>,
     expectDownloadSuccess: boolean,
   ) => {
@@ -80,80 +80,59 @@ const testDownloadOverlayBaseDatabaseFromCache = test.macro({
         await fs.promises.writeFile(baseDatabaseOidsFile, JSON.stringify({}));
       }
 
-      const stubs: sinon.SinonStub[] = [];
+      sinon.stub(apiClient, "getAutomationID").resolves("test-automation-id/");
 
-      const getAutomationIDStub = sinon
+      sinon.stub(utils, "isInTestMode").returns(testCase.isInTestMode);
-        .stub(apiClient, "getAutomationID")
-        .resolves("test-automation-id/");
-      stubs.push(getAutomationIDStub);
-
-      const isInTestModeStub = sinon
-        .stub(utils, "isInTestMode")
-        .returns(testCase.isInTestMode);
-      stubs.push(isInTestModeStub);
 
       if (testCase.restoreCacheResult instanceof Error) {
-        const restoreCacheStub = sinon
+        sinon
           .stub(actionsCache, "restoreCache")
           .rejects(testCase.restoreCacheResult);
-        stubs.push(restoreCacheStub);
       } else {
-        const restoreCacheStub = sinon
+        sinon
           .stub(actionsCache, "restoreCache")
           .resolves(testCase.restoreCacheResult);
-        stubs.push(restoreCacheStub);
       }
 
-      const tryGetFolderBytesStub = sinon
+      sinon
         .stub(utils, "tryGetFolderBytes")
         .resolves(testCase.tryGetFolderBytesSucceeds ? 1024 * 1024 : undefined);
-      stubs.push(tryGetFolderBytesStub);
 
       const codeql = mockCodeQLVersion(testCase.codeQLVersion);
 
       if (testCase.resolveDatabaseOutput instanceof Error) {
-        const resolveDatabaseStub = sinon
+        sinon
           .stub(codeql, "resolveDatabase")
           .rejects(testCase.resolveDatabaseOutput);
-        stubs.push(resolveDatabaseStub);
       } else {
-        const resolveDatabaseStub = sinon
+        sinon
           .stub(codeql, "resolveDatabase")
           .resolves(testCase.resolveDatabaseOutput);
-        stubs.push(resolveDatabaseStub);
       }
 
-      try {
+      const result = await downloadOverlayBaseDatabaseFromCache(
-        const result = await downloadOverlayBaseDatabaseFromCache(
+        codeql,
-          codeql,
+        config,
-          config,
+        logger,
-          logger,
+      );
-        );
 
-        if (expectDownloadSuccess) {
+      if (expectDownloadSuccess) {
-          t.truthy(result);
+        t.truthy(result);
-        } else {
+      } else {
-          t.is(result, undefined);
+        t.is(result, undefined);
-        }
-      } finally {
-        for (const stub of stubs) {
-          stub.restore();
-        }
       }
     });
   },
-  title: (_, title) => `downloadOverlayBaseDatabaseFromCache: ${title}`,
+  title: (title) => `downloadOverlayBaseDatabaseFromCache: ${title}`,
 });
 
-test.serial(
+testDownloadOverlayBaseDatabaseFromCache.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
   "returns stats when successful",
   {},
   true,
 );
 
-test.serial(
+testDownloadOverlayBaseDatabaseFromCache.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
   "returns undefined when mode is OverlayDatabaseMode.OverlayBase",
   {
     overlayDatabaseMode: OverlayDatabaseMode.OverlayBase,
@@ -161,8 +140,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testDownloadOverlayBaseDatabaseFromCache.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
   "returns undefined when mode is OverlayDatabaseMode.None",
   {
     overlayDatabaseMode: OverlayDatabaseMode.None,
@@ -170,8 +148,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testDownloadOverlayBaseDatabaseFromCache.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
   "returns undefined when caching is disabled",
   {
     useOverlayDatabaseCaching: false,
@@ -179,8 +156,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testDownloadOverlayBaseDatabaseFromCache.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
   "returns undefined in test mode",
   {
     isInTestMode: true,
@@ -188,8 +164,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testDownloadOverlayBaseDatabaseFromCache.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
   "returns undefined when cache miss",
   {
     restoreCacheResult: undefined,
@@ -197,8 +172,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testDownloadOverlayBaseDatabaseFromCache.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
   "returns undefined when download fails",
   {
     restoreCacheResult: new Error("Download failed"),
@@ -206,8 +180,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testDownloadOverlayBaseDatabaseFromCache.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
   "returns undefined when downloaded database is invalid",
   {
     hasBaseDatabaseOidsFile: false,
@@ -215,8 +188,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testDownloadOverlayBaseDatabaseFromCache.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
   "returns undefined when downloaded database doesn't have an overlayBaseSpecifier",
   {
     resolveDatabaseOutput: {},
@@ -224,8 +196,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testDownloadOverlayBaseDatabaseFromCache.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
   "returns undefined when resolving database metadata fails",
   {
     resolveDatabaseOutput: new Error("Failed to resolve database metadata"),
@@ -233,8 +204,7 @@ test.serial(
   false,
 );
 
-test.serial(
+testDownloadOverlayBaseDatabaseFromCache.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
   "returns undefined when filesystem error occurs",
   {
     tryGetFolderBytesSucceeds: false,
@@ -391,6 +361,32 @@ test.serial(
   },
 );
 
+test.serial(
+  "getCodeQlVersionsForOverlayBaseDatabases de-duplicates resolved language aliases",
+  async (t) => {
+    const logger = getRunnerLogger(true);
+
+    sinon.stub(apiClient, "getAutomationID").resolves("test-automation-id/");
+    const listActionsCachesStub = sinon
+      .stub(apiClient, "listActionsCaches")
+      .resolves([
+        {
+          key: "codeql-overlay-base-database-1-c5666c509a2d9895-javascript_python-2.25.0-abc123-1-1",
+        },
+      ]);
+
+    const result = await getCodeQlVersionsForOverlayBaseDatabases(
+      ["javascript", "typescript", "Python", "python"],
+      logger,
+    );
+    t.deepEqual(result, ["2.25.0"]);
+    sinon.assert.calledOnceWithExactly(
+      listActionsCachesStub,
+      "codeql-overlay-base-database-1-c5666c509a2d9895-javascript_python-",
+    );
+  },
+);
+
 test.serial(
   "getCodeQlVersionsForOverlayBaseDatabases ignores nightly versions with build metadata",
   async (t) => {

src/overlay/caching.ts

@@ -461,9 +461,10 @@ export async function getCodeQlVersionsForOverlayBaseDatabases(
     );
     return undefined;
   }
-  const cacheKeyPrefix = await getCacheKeyPrefixBase(
+  const dedupedLanguages = [
-    languages.filter((l) => l !== undefined),
+    ...new Set(languages.filter((l) => l !== undefined)),
-  );
+  ];
+  const cacheKeyPrefix = await getCacheKeyPrefixBase(dedupedLanguages);
 
   logger.debug(
     `Searching for overlay-base databases in Actions cache with ` +

src/overlay/diagnostics.ts

@@ -39,6 +39,15 @@ export enum OverlayDisabledReason {
   NotPullRequestOrDefaultBranch = "not-pull-request-or-default-branch",
   /** The top-level overlay analysis feature flag is not enabled. */
   OverallFeatureNotEnabled = "overall-feature-not-enabled",
+  /**
+   * Overlay analysis was selected for a pull request, but diff-informed
+   * analysis was not enabled for the run (for example, because the
+   * `DiffInformedQueries` feature flag is off, the GHES version is too old,
+   * or the PR diff ranges could not be computed). Overlay analysis has only
+   * been validated in combination with diff-informed analysis, so we fall
+   * back to a non-overlay analysis in this case.
+   */
+  DiffInformedAnalysisNotEnabled = "diff-informed-analysis-not-enabled",
   /** Overlay analysis was skipped because it previously failed with similar hardware resources. */
   SkippedDueToCachedStatus = "skipped-due-to-cached-status",
   /** Disk usage could not be determined during the overlay status check. */

src/overlay/index.test.ts

@@ -50,31 +50,21 @@ test.serial(
         "modified.js": "ddd444", // Changed OID
         "added.js": "eee555", // New file
       };
-      const getFileOidsStubForOverlay = sinon
+      sinon.stub(gitUtils, "getFileOidsUnderPath").resolves(currentOids);
-        .stub(gitUtils, "getFileOidsUnderPath")
-        .resolves(currentOids);
 
       // Write the overlay changes file, which uses the mocked overlay OIDs
       // and the base database OIDs file
       const diffRangeFilePath = path.join(tempDir, "pr-diff-range.json");
-      const getTempDirStub = sinon
+      sinon.stub(actionsUtil, "getTemporaryDirectory").returns(tempDir);
-        .stub(actionsUtil, "getTemporaryDirectory")
+      sinon
-        .returns(tempDir);
-      const getDiffRangesStub = sinon
         .stub(actionsUtil, "getDiffRangesJsonFilePath")
         .returns(diffRangeFilePath);
-      const getGitRootStub = sinon
+      sinon.stub(gitUtils, "getGitRoot").resolves(sourceRoot);
-        .stub(gitUtils, "getGitRoot")
-        .resolves(sourceRoot);
       const changesFilePath = await writeOverlayChangesFile(
         config,
         sourceRoot,
         logger,
       );
-      getFileOidsStubForOverlay.restore();
-      getTempDirStub.restore();
-      getDiffRangesStub.restore();
-      getGitRootStub.restore();
 
       const fileContent = await fs.promises.readFile(changesFilePath, "utf-8");
       const parsedContent = JSON.parse(fileContent) as { changes: string[] };
@@ -128,20 +118,14 @@ test.serial(
         "modified.js": "ddd444", // Changed OID
         "reverted.js": "eee555", // Same OID as base -- not detected by OID comparison
       };
-      const getFileOidsStubForOverlay = sinon
+      sinon.stub(gitUtils, "getFileOidsUnderPath").resolves(currentOids);
-        .stub(gitUtils, "getFileOidsUnderPath")
-        .resolves(currentOids);
 
       const diffRangeFilePath = path.join(tempDir, "pr-diff-range.json");
-      const getTempDirStub = sinon
+      sinon.stub(actionsUtil, "getTemporaryDirectory").returns(tempDir);
-        .stub(actionsUtil, "getTemporaryDirectory")
+      sinon
-        .returns(tempDir);
-      const getDiffRangesStub = sinon
         .stub(actionsUtil, "getDiffRangesJsonFilePath")
         .returns(diffRangeFilePath);
-      const getGitRootStub = sinon
+      sinon.stub(gitUtils, "getGitRoot").resolves(sourceRoot);
-        .stub(gitUtils, "getGitRoot")
-        .resolves(sourceRoot);
 
       // Write a pr-diff-range.json file with diff ranges including
       // "reverted.js" (unchanged OIDs) and "modified.js" (already in OID changes)
@@ -159,10 +143,6 @@ test.serial(
         sourceRoot,
         logger,
       );
-      getFileOidsStubForOverlay.restore();
-      getTempDirStub.restore();
-      getDiffRangesStub.restore();
-      getGitRootStub.restore();
 
       const fileContent = await fs.promises.readFile(changesFilePath, "utf-8");
       const parsedContent = JSON.parse(fileContent) as { changes: string[] };
@@ -208,20 +188,14 @@ test.serial(
         "unchanged.js": "aaa111",
         "modified.js": "ddd444",
       };
-      const getFileOidsStubForOverlay = sinon
+      sinon.stub(gitUtils, "getFileOidsUnderPath").resolves(currentOids);
-        .stub(gitUtils, "getFileOidsUnderPath")
-        .resolves(currentOids);
 
       const diffRangeFilePath = path.join(tempDir, "pr-diff-range.json");
-      const getTempDirStub = sinon
+      sinon.stub(actionsUtil, "getTemporaryDirectory").returns(tempDir);
-        .stub(actionsUtil, "getTemporaryDirectory")
+      sinon
-        .returns(tempDir);
-      const getDiffRangesStub = sinon
         .stub(actionsUtil, "getDiffRangesJsonFilePath")
         .returns(diffRangeFilePath);
-      const getGitRootStub = sinon
+      sinon.stub(gitUtils, "getGitRoot").resolves(sourceRoot);
-        .stub(gitUtils, "getGitRoot")
-        .resolves(sourceRoot);
 
       // No pr-diff-range.json file exists - should work the same as before
       const changesFilePath = await writeOverlayChangesFile(
@@ -229,10 +203,6 @@ test.serial(
         sourceRoot,
         logger,
       );
-      getFileOidsStubForOverlay.restore();
-      getTempDirStub.restore();
-      getDiffRangesStub.restore();
-      getGitRootStub.restore();
 
       const fileContent = await fs.promises.readFile(changesFilePath, "utf-8");
       const parsedContent = JSON.parse(fileContent) as { changes: string[] };
@@ -281,21 +251,15 @@ test.serial(
         "app.js": "aaa111",
         "lib/util.js": "bbb222",
       };
-      const getFileOidsStubForOverlay = sinon
+      sinon.stub(gitUtils, "getFileOidsUnderPath").resolves(currentOids);
-        .stub(gitUtils, "getFileOidsUnderPath")
-        .resolves(currentOids);
 
       const diffRangeFilePath = path.join(tempDir, "pr-diff-range.json");
-      const getTempDirStub = sinon
+      sinon.stub(actionsUtil, "getTemporaryDirectory").returns(tempDir);
-        .stub(actionsUtil, "getTemporaryDirectory")
+      sinon
-        .returns(tempDir);
-      const getDiffRangesStub = sinon
         .stub(actionsUtil, "getDiffRangesJsonFilePath")
         .returns(diffRangeFilePath);
       // getGitRoot returns the repo root (parent of sourceRoot)
-      const getGitRootStub = sinon
+      sinon.stub(gitUtils, "getGitRoot").resolves(repoRoot);
-        .stub(gitUtils, "getGitRoot")
-        .resolves(repoRoot);
 
       // Diff ranges use repo-root-relative paths (as returned by the GitHub compare API)
       await fs.promises.writeFile(
@@ -312,10 +276,6 @@ test.serial(
         sourceRoot,
         logger,
       );
-      getFileOidsStubForOverlay.restore();
-      getTempDirStub.restore();
-      getDiffRangesStub.restore();
-      getGitRootStub.restore();
 
       const fileContent = await fs.promises.readFile(changesFilePath, "utf-8");
       const parsedContent = JSON.parse(fileContent) as { changes: string[] };

src/resolve-environment-action.ts

@@ -117,7 +117,7 @@ async function run(startedAt: Date) {
   }
 }
 
-async function runWrapper() {
+export async function runWrapper() {
   const startedAt = new Date();
   const logger = getActionsLogger();
   try {
@@ -137,5 +137,3 @@ async function runWrapper() {
   }
   await checkForTimeout();
 }
-
-void runWrapper();

src/setup-codeql-action.ts

@@ -7,8 +7,10 @@ import {
   getRequiredInput,
   getTemporaryDirectory,
 } from "./actions-util";
+import { AnalysisKind, getAnalysisKinds } from "./analyses";
 import { getGitHubVersion } from "./api-client";
 import { CodeQL } from "./codeql";
+import { getRawLanguagesNoAutodetect } from "./config-utils";
 import { EnvVar } from "./environment";
 import { initFeatures } from "./feature-flags";
 import { initCodeQL } from "./init";
@@ -136,16 +138,22 @@ async function run(startedAt: Date): Promise<void> {
     if (statusReportBase !== undefined) {
       await sendStatusReport(statusReportBase);
     }
-    const codeQLDefaultVersionInfo = await features.getDefaultCliVersion(
+    const codeQLDefaultVersionInfo =
-      gitHubVersion.type,
+      await features.getEnabledDefaultCliVersions(gitHubVersion.type);
-    );
     toolsFeatureFlagsValid = codeQLDefaultVersionInfo.toolsFeatureFlagsValid;
+    const rawLanguages = getRawLanguagesNoAutodetect(
+      getOptionalInput("languages"),
+    );
+    const analysisKinds = await getAnalysisKinds(logger, features);
     const initCodeQLResult = await initCodeQL(
       getOptionalInput("tools"),
       apiDetails,
       getTemporaryDirectory(),
       gitHubVersion.type,
       codeQLDefaultVersionInfo,
+      rawLanguages,
+      analysisKinds.length === 1 &&
+        analysisKinds[0] === AnalysisKind.CodeScanning,
       features,
       logger,
     );
@@ -188,7 +196,7 @@ async function run(startedAt: Date): Promise<void> {
 }
 
 /** Run the action and catch any unhandled errors. */
-async function runWrapper(): Promise<void> {
+export async function runWrapper(): Promise<void> {
   const startedAt = new Date();
   const logger = getActionsLogger();
   try {
@@ -204,5 +212,3 @@ async function runWrapper(): Promise<void> {
   }
   await checkForTimeout();
 }
-
-void runWrapper();

src/setup-codeql.test.ts

@@ -7,8 +7,9 @@ import * as sinon from "sinon";
 
 import * as actionsUtil from "./actions-util";
 import * as api from "./api-client";
-import { Feature, FeatureEnablement } from "./feature-flags";
+import { Feature } from "./feature-flags";
 import { getRunnerLogger } from "./logging";
+import { getCacheRestoreKeyPrefix } from "./overlay/caching";
 import * as setupCodeql from "./setup-codeql";
 import * as tar from "./tar";
 import {
@@ -18,8 +19,9 @@ import {
   SAMPLE_DOTCOM_API_DETAILS,
   checkExpectedLogMessages,
   createFeatures,
+  createTestConfig,
   getRecordingLogger,
-  initializeFeatures,
+  makeMacro,
   mockBundleDownloadApi,
   setupActionsVars,
   setupTests,
@@ -33,14 +35,6 @@ import {
 
 setupTests(test);
 
-// TODO: Remove when when we no longer need to pass in features (https://github.com/github/codeql-action/issues/2600)
-const expectedFeatureEnablement: FeatureEnablement = initializeFeatures(
-  true,
-) as FeatureEnablement;
-expectedFeatureEnablement.getValue = function (feature: Feature) {
-  // eslint-disable-next-line @typescript-eslint/no-unsafe-return
-  return expectedFeatureEnablement[feature];
-};
 test.beforeEach(() => {
   initializeEnvironment("1.2.3");
 });
@@ -107,6 +101,8 @@ test.serial(
       const source = await setupCodeql.getCodeQLSource(
         `https://github.com/github/codeql-action/releases/download/${tagName}/codeql-bundle-linux64.tar.gz`,
         SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
         false,
@@ -130,6 +126,8 @@ test.serial(
       const source = await setupCodeql.getCodeQLSource(
         "linked",
         SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
         false,
@@ -155,6 +153,8 @@ test.serial(
       const source = await setupCodeql.getCodeQLSource(
         "latest",
         SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
         false,
@@ -211,6 +211,8 @@ test.serial(
         "tmp/codeql_action_test/",
         GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         features,
         logger,
       );
@@ -266,6 +268,8 @@ test.serial(
         "tmp/codeql_action_test/",
         GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         features,
         logger,
       );
@@ -317,6 +321,8 @@ test.serial(
       const source = await setupCodeql.getCodeQLSource(
         "nightly",
         SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
         false,
@@ -378,6 +384,8 @@ test.serial(
       const source = await setupCodeql.getCodeQLSource(
         undefined,
         SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
         false,
@@ -432,6 +440,8 @@ test.serial(
       const source = await setupCodeql.getCodeQLSource(
         "toolcache",
         SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
         false,
@@ -473,7 +483,7 @@ test.serial(
   },
 );
 
-const toolcacheInputFallbackMacro = test.macro({
+const toolcacheInputFallbackMacro = makeMacro({
   exec: async (
     t: ExecutionContext<unknown>,
     featureList: Feature[],
@@ -499,6 +509,8 @@ const toolcacheInputFallbackMacro = test.macro({
       const source = await setupCodeql.getCodeQLSource(
         "toolcache",
         SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
         false,
@@ -514,7 +526,10 @@ const toolcacheInputFallbackMacro = test.macro({
 
       // Check that `sourceType` and `toolsVersion` match expectations.
       t.is(source.sourceType, "download");
-      t.is(source.toolsVersion, SAMPLE_DEFAULT_CLI_VERSION.cliVersion);
+      t.is(
+        source.toolsVersion,
+        SAMPLE_DEFAULT_CLI_VERSION.enabledVersions[0].cliVersion,
+      );
 
       // Check that key messages we would expect to find in the log are present.
       for (const expectedMessage of expectedMessages) {
@@ -533,9 +548,8 @@ const toolcacheInputFallbackMacro = test.macro({
     `getCodeQLSource falls back to downloading the CLI if ${providedTitle}`,
 });
 
-test.serial(
+toolcacheInputFallbackMacro.serial(
   "the toolcache doesn't have a CodeQL CLI when tools == toolcache",
-  toolcacheInputFallbackMacro,
   [Feature.AllowToolcacheInput],
   { GITHUB_EVENT_NAME: "dynamic" },
   [],
@@ -545,9 +559,8 @@ test.serial(
   ],
 );
 
-test.serial(
+toolcacheInputFallbackMacro.serial(
   "the workflow trigger is not `dynamic`",
-  toolcacheInputFallbackMacro,
   [Feature.AllowToolcacheInput],
   { GITHUB_EVENT_NAME: "pull_request" },
   [],
@@ -556,9 +569,8 @@ test.serial(
   ],
 );
 
-test.serial(
+toolcacheInputFallbackMacro.serial(
   "the feature flag is not enabled",
-  toolcacheInputFallbackMacro,
   [],
   { GITHUB_EVENT_NAME: "dynamic" },
   [],
@@ -598,3 +610,288 @@ test.serial(
     t.is(setupCodeql.getLatestToolcacheVersion(getRunnerLogger(true)), "3.2.1");
   },
 );
+
+const overlayMatchEnabledVersions = {
+  enabledVersions: [
+    { cliVersion: "2.20.2", tagName: "codeql-bundle-v2.20.2" },
+    { cliVersion: "2.20.1", tagName: "codeql-bundle-v2.20.1" },
+    { cliVersion: "2.20.0", tagName: "codeql-bundle-v2.20.0" },
+  ],
+  toolsFeatureFlagsValid: true,
+};
+
+async function fakeOverlayBaseCacheKey(
+  language: string,
+  cliVersion: string,
+  suffix: string,
+): Promise<string> {
+  const prefix = await getCacheRestoreKeyPrefix(
+    createTestConfig({ languages: [language] }),
+    cliVersion,
+  );
+  return `${prefix}${suffix}`;
+}
+
+test.serial(
+  "getCodeQLSource uses overlay-aware default version when requested for a PR",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      process.env["CODE_SCANNING_REF"] = "refs/heads/feature-branch";
+      process.env["CODE_SCANNING_BASE_BRANCH"] = "main";
+
+      sinon.stub(api, "getAutomationID").resolves("test/");
+      const listStub = sinon.stub(api, "listActionsCaches").resolves([
+        {
+          key: await fakeOverlayBaseCacheKey("javascript", "2.20.1", "abc-1-1"),
+        },
+      ]);
+      sinon
+        .stub(toolcache, "find")
+        .withArgs("CodeQL", "2.20.1")
+        .returns("/path/to/codeql-2.20.1");
+
+      const source = await setupCodeql.getCodeQLSource(
+        undefined,
+        overlayMatchEnabledVersions,
+        ["javascript"],
+        true,
+        SAMPLE_DOTCOM_API_DETAILS,
+        GitHubVariant.DOTCOM,
+        false,
+        createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+        getRunnerLogger(true),
+      );
+
+      t.assert(listStub.calledOnce);
+      t.is(source.sourceType, "toolcache");
+      t.is(source.toolsVersion, "2.20.1");
+    });
+  },
+);
+
+test.serial(
+  "getCodeQLSource skips overlay-aware default version when not requested",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      process.env["CODE_SCANNING_REF"] = "refs/heads/feature-branch";
+      process.env["CODE_SCANNING_BASE_BRANCH"] = "main";
+
+      sinon.stub(api, "getAutomationID").resolves("test/");
+      const listStub = sinon.stub(api, "listActionsCaches").resolves([
+        {
+          key: await fakeOverlayBaseCacheKey("javascript", "2.20.1", "abc-1-1"),
+        },
+      ]);
+      sinon
+        .stub(toolcache, "find")
+        .withArgs("CodeQL", "2.20.2")
+        .returns("/path/to/codeql-2.20.2");
+
+      const source = await setupCodeql.getCodeQLSource(
+        undefined,
+        overlayMatchEnabledVersions,
+        ["javascript"],
+        false,
+        SAMPLE_DOTCOM_API_DETAILS,
+        GitHubVariant.DOTCOM,
+        false,
+        createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+        getRunnerLogger(true),
+      );
+
+      t.assert(listStub.notCalled);
+      t.is(source.sourceType, "toolcache");
+      t.is(source.toolsVersion, "2.20.2");
+    });
+  },
+);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases returns flag-enabled versions present in cache, sorted desc",
+  async (t) => {
+    sinon.stub(api, "getAutomationID").resolves("test/");
+    sinon.stub(api, "listActionsCaches").resolves([
+      // Flag-enabled versions present in the cache, listed in non-descending
+      // order so the test exercises the sort.
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.20.0", "ghi-3-1"),
+      },
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.20.1", "def-2-1"),
+      },
+      // Newer than any flag-enabled version: should be filtered out.
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.21.0", "abc-1-1"),
+      },
+    ]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, [
+      { cliVersion: "2.20.1", tagName: "codeql-bundle-v2.20.1" },
+      { cliVersion: "2.20.0", tagName: "codeql-bundle-v2.20.0" },
+    ]);
+  },
+);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases returns empty when no cached version is flag-enabled",
+  async (t) => {
+    sinon.stub(api, "getAutomationID").resolves("test/");
+    sinon.stub(api, "listActionsCaches").resolves([
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.19.0", "abc-1-1"),
+      },
+    ]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, []);
+  },
+);
+
+const noLanguagesMacro = makeMacro({
+  exec: async (
+    t: ExecutionContext<unknown>,
+    rawLanguages: string[] | undefined,
+  ) => {
+    const listStub = sinon.stub(api, "listActionsCaches").resolves([]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      rawLanguages,
+      createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, []);
+    t.assert(
+      listStub.notCalled,
+      "Should not list Actions caches without any rawLanguages.",
+    );
+  },
+  title: (providedTitle = "") =>
+    `getEnabledVersionsWithOverlayBaseDatabases does not list caches when rawLanguages is ${providedTitle}`,
+});
+
+noLanguagesMacro.serial("undefined", undefined);
+noLanguagesMacro.serial("an empty array", []);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases returns empty when listing caches throws",
+  async (t) => {
+    sinon.stub(api, "getAutomationID").resolves("test/");
+    sinon.stub(api, "listActionsCaches").rejects(new Error("listing failed"));
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, []);
+  },
+);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases returns versions present in the cache",
+  async (t) => {
+    sinon.stub(api, "getAutomationID").resolves("test/");
+    sinon.stub(api, "listActionsCaches").resolves([
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.20.2", "abc-1-1"),
+      },
+    ]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, [
+      { cliVersion: "2.20.2", tagName: "codeql-bundle-v2.20.2" },
+    ]);
+  },
+);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases does not list caches when both gates are off",
+  async (t) => {
+    const listStub = sinon.stub(api, "listActionsCaches").resolves([]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, []);
+    t.assert(
+      listStub.notCalled,
+      "Should not list Actions caches when both gating feature flags are off.",
+    );
+  },
+);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases dry-run returns empty but lists caches",
+  async (t) => {
+    sinon.stub(api, "getAutomationID").resolves("test/");
+    const listStub = sinon.stub(api, "listActionsCaches").resolves([
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.20.1", "abc-1-1"),
+      },
+    ]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([Feature.OverlayAnalysisMatchCodeqlVersionDryRun]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(
+      result,
+      [],
+      "Dry-run should return an empty list so the caller falls back.",
+    );
+    t.assert(
+      listStub.calledOnce,
+      "Dry-run should still list Actions caches to populate the diagnostic.",
+    );
+  },
+);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases match flag wins over dry-run",
+  async (t) => {
+    sinon.stub(api, "getAutomationID").resolves("test/");
+    sinon.stub(api, "listActionsCaches").resolves([
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.20.1", "abc-1-1"),
+      },
+    ]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([
+        Feature.OverlayAnalysisMatchCodeqlVersion,
+        Feature.OverlayAnalysisMatchCodeqlVersionDryRun,
+      ]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, [
+      { cliVersion: "2.20.1", tagName: "codeql-bundle-v2.20.1" },
+    ]);
+  },
+);

src/setup-codeql.ts

@@ -7,17 +7,27 @@ import { default as deepEqual } from "fast-deep-equal";
 import * as semver from "semver";
 import { v4 as uuidV4 } from "uuid";
 
-import { isDynamicWorkflow, isRunningLocalAction } from "./actions-util";
+import {
+  isAnalyzingPullRequest,
+  isDynamicWorkflow,
+  isRunningLocalAction,
+} from "./actions-util";
 import * as api from "./api-client";
 import * as defaults from "./defaults.json";
-import { addNoLanguageDiagnostic, makeDiagnostic } from "./diagnostics";
+import {
+  addNoLanguageDiagnostic,
+  makeDiagnostic,
+  makeTelemetryDiagnostic,
+} from "./diagnostics";
 import {
   CODEQL_VERSION_ZSTD_BUNDLE,
   CodeQLDefaultVersionInfo,
+  CodeQLVersionInfo,
   Feature,
   FeatureEnablement,
 } from "./feature-flags";
 import { Logger } from "./logging";
+import { getCodeQlVersionsForOverlayBaseDatabases } from "./overlay/caching";
 import * as tar from "./tar";
 import {
   downloadAndExtract,
@@ -264,12 +274,131 @@ async function findOverridingToolsInCache(
   return undefined;
 }
 
+/**
+ * Returns the sorted set of enabled versions that have cached overlay-base databases for the
+ * given languages, or an empty list if neither the `OverlayAnalysisMatchCodeqlVersion` nor the
+ * `OverlayAnalysisMatchCodeqlVersionDryRun` feature flag is enabled. When only the dry-run flag
+ * is enabled, this performs the lookup and emits a telemetry diagnostic with the version that
+ * would have been chosen, but still returns an empty list so the caller falls back.
+ */
+export async function getEnabledVersionsWithOverlayBaseDatabases(
+  defaultCliVersion: CodeQLDefaultVersionInfo,
+  rawLanguages: string[] | undefined,
+  features: FeatureEnablement,
+  logger: Logger,
+): Promise<CodeQLVersionInfo[]> {
+  if (rawLanguages === undefined || rawLanguages.length === 0) {
+    return [];
+  }
+  const isEnabled = await features.getValue(
+    Feature.OverlayAnalysisMatchCodeqlVersion,
+  );
+  const isDryRun =
+    !isEnabled &&
+    (await features.getValue(Feature.OverlayAnalysisMatchCodeqlVersionDryRun));
+  if (!isEnabled && !isDryRun) {
+    return [];
+  }
+
+  let cachedVersions: string[] | undefined;
+  try {
+    cachedVersions = await getCodeQlVersionsForOverlayBaseDatabases(
+      rawLanguages,
+      logger,
+    );
+  } catch (e) {
+    logger.warning(
+      "Could not list overlay-base databases in the Actions cache while choosing a default " +
+        `CodeQL CLI version, falling back to the highest enabled version. Details: ${util.getErrorMessage(e)}`,
+    );
+    return [];
+  }
+
+  if (cachedVersions === undefined || cachedVersions.length === 0) {
+    return [];
+  }
+
+  const cachedVersionsSet = new Set(cachedVersions);
+  const overlayVersions = defaultCliVersion.enabledVersions.filter((v) =>
+    cachedVersionsSet.has(v.cliVersion),
+  );
+
+  if (overlayVersions.length === 0) {
+    return [];
+  }
+
+  const isCachedVersionDifferent =
+    overlayVersions[0].cliVersion !==
+    defaultCliVersion.enabledVersions[0].cliVersion;
+
+  if (isCachedVersionDifferent) {
+    addNoLanguageDiagnostic(
+      undefined,
+      makeTelemetryDiagnostic(
+        "codeql-action/overlay-aware-default-codeql-version",
+        "Overlay-aware default CodeQL version selection",
+        {
+          cachedVersions,
+          enabledVersions: defaultCliVersion.enabledVersions.map(
+            (v) => v.cliVersion,
+          ),
+          isDryRun,
+          overlayAwareVersion: overlayVersions[0].cliVersion,
+        },
+      ),
+    );
+  }
+
+  if (isDryRun) {
+    logger.debug(
+      `Overlay-aware default CodeQL version selection is running in dry-run mode. Would have used version ${overlayVersions[0].cliVersion}.`,
+    );
+    return [];
+  }
+
+  return overlayVersions;
+}
+
+/**
+ * Resolves the newest enabled default CLI version that has a cached overlay-base database for the
+ * relevant languages, if running a Code Scanning analysis for a pull request and one exists.
+ * Otherwise, falls back to the newest enabled default CLI version.
+ */
+async function resolveDefaultCliVersion(
+  defaultCliVersion: CodeQLDefaultVersionInfo,
+  rawLanguages: string[] | undefined,
+  useOverlayAwareDefaultCliVersion: boolean,
+  features: FeatureEnablement,
+  logger: Logger,
+): Promise<CodeQLVersionInfo> {
+  if (!useOverlayAwareDefaultCliVersion || !isAnalyzingPullRequest()) {
+    return defaultCliVersion.enabledVersions[0];
+  }
+
+  const overlayVersions = await getEnabledVersionsWithOverlayBaseDatabases(
+    defaultCliVersion,
+    rawLanguages,
+    features,
+    logger,
+  );
+  if (overlayVersions.length > 0) {
+    logger.info(
+      `Using CodeQL version ${overlayVersions[0].cliVersion} since this is the ` +
+        `highest enabled version that has a cached overlay-base database.`,
+    );
+    return overlayVersions[0];
+  }
+  return defaultCliVersion.enabledVersions[0];
+}
+
 /**
  * Determines where the CodeQL CLI we want to use comes from. This can be from a local file,
  * the Actions toolcache, or a download.
  *
  * @param toolsInput The argument provided for the `tools` input, if any.
  * @param defaultCliVersion The default CLI version that's linked to the CodeQL Action.
+ * @param rawLanguages Raw set of languages.
+ * @param useOverlayAwareDefaultCliVersion Whether to select an overlay-aware default CLI version.
  * @param apiDetails Information about the GitHub API.
  * @param variant The GitHub variant we are running on.
  * @param tarSupportsZstd Whether zstd is supported by `tar`.
@@ -281,6 +410,8 @@ async function findOverridingToolsInCache(
 export async function getCodeQLSource(
   toolsInput: string | undefined,
   defaultCliVersion: CodeQLDefaultVersionInfo,
+  rawLanguages: string[] | undefined,
+  useOverlayAwareDefaultCliVersion: boolean,
   apiDetails: api.GitHubApiDetails,
   variant: util.GitHubVariant,
   tarSupportsZstd: boolean,
@@ -438,8 +569,15 @@ export async function getCodeQLSource(
         }
       }
 
-      cliVersion = defaultCliVersion.cliVersion;
+      const version = await resolveDefaultCliVersion(
-      tagName = defaultCliVersion.tagName;
+        defaultCliVersion,
+        rawLanguages,
+        useOverlayAwareDefaultCliVersion,
+        features,
+        logger,
+      );
+      cliVersion = version.cliVersion;
+      tagName = version.tagName;
     }
   } else if (toolsInput !== undefined) {
     // If a tools URL was provided, then use that.
@@ -454,9 +592,15 @@ export async function getCodeQLSource(
       }
     }
   } else {
-    // Otherwise, use the default CLI version passed in.
+    const version = await resolveDefaultCliVersion(
-    cliVersion = defaultCliVersion.cliVersion;
+      defaultCliVersion,
-    tagName = defaultCliVersion.tagName;
+      rawLanguages,
+      useOverlayAwareDefaultCliVersion,
+      features,
+      logger,
+    );
+    cliVersion = version.cliVersion;
+    tagName = version.tagName;
   }
 
   const bundleVersion =
@@ -791,6 +935,8 @@ export async function setupCodeQLBundle(
   tempDir: string,
   variant: util.GitHubVariant,
   defaultCliVersion: CodeQLDefaultVersionInfo,
+  rawLanguages: string[] | undefined,
+  useOverlayAwareDefaultCliVersion: boolean,
   features: FeatureEnablement,
   logger: Logger,
 ): Promise<SetupCodeQLResult> {
@@ -804,6 +950,8 @@ export async function setupCodeQLBundle(
   const source = await getCodeQLSource(
     toolsInput,
     defaultCliVersion,
+    rawLanguages,
+    useOverlayAwareDefaultCliVersion,
     apiDetails,
     variant,
     zstdAvailability.available,

src/start-proxy-action-post.ts

@@ -12,7 +12,7 @@ import { uploadArtifacts } from "./debug-artifacts";
 import { getActionsLogger } from "./logging";
 import { checkGitHubVersionInRange, getErrorMessage } from "./util";
 
-async function runWrapper() {
+export async function runWrapper() {
   // To capture errors appropriately, keep as much code within the try-catch as
   // possible, and only use safe functions outside.
 
@@ -62,5 +62,3 @@ async function runWrapper() {
     );
   }
 }
-
-void runWrapper();