Add InstanceApiClient and incorporate getAuthorizationHeaderFor into it

Include apiDetails in CodeQLDownloadSource
Use instance in DownloadSource and pass it on to getApiClient
2026-10-15 20:05:33 +03:00 · 2026-10-14 20:49:06 +01:00 · 2026-10-14 20:48:44 +01:00 · 2026-10-14 20:48:40 +01:00 · 2026-10-14 20:31:06 +01:00 · 2026-10-14 20:03:19 +01:00
136 changed files with 42368 additions and 15851 deletions
@@ -92,8 +92,7 @@ runs:
          Please do the following:

          - [ ] Approve running 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".
+          - [ ] 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".
        EOF
        )

@@ -8,8 +8,6 @@ updates:
      interval: weekly
    cooldown:
      default-days: 7
-      exclude:
-        - "@actions/*"
    labels:
      - Rebuild
    # Ignore incompatible dependency updates
@@ -33,8 +31,6 @@ updates:
      interval: weekly
    cooldown:
      default-days: 7
-      exclude:
-        - "actions/*"
    labels:
      - Rebuild
    groups:
@@ -51,6 +51,8 @@ jobs:
        with:
          node-version: 20.x
          cache: npm
+      - name: Install newer npm
+        run: npm install -g npm@11.19.1
      - name: Install dependencies
        run: npm ci
      - name: Prepare test
@@ -124,4 +124,5 @@ jobs:
    env:
      CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS: false
      CODEQL_ACTION_SUBLANGUAGE_FILE_COVERAGE: true
+      CODEQL_ACTION_PER_LANGUAGE_BUNDLES: false
      CODEQL_ACTION_TEST_MODE: true
@@ -44,8 +44,6 @@ jobs:
      fail-fast: false
      matrix:
        include:
-          - os: ubuntu-latest
-            version: stable-v2.19.4
          - os: ubuntu-latest
            version: stable-v2.20.7
          - os: ubuntu-latest
@@ -56,6 +54,8 @@ jobs:
            version: stable-v2.23.9
          - os: ubuntu-latest
            version: stable-v2.24.3
+          - os: ubuntu-latest
+            version: stable-v2.25.6
          - os: ubuntu-latest
            version: default
          - os: ubuntu-latest
@@ -44,8 +44,6 @@ jobs:
      fail-fast: false
      matrix:
        include:
-          - os: ubuntu-latest
-            version: stable-v2.19.4
          - os: ubuntu-latest
            version: stable-v2.20.7
          - os: ubuntu-latest
@@ -56,6 +54,8 @@ jobs:
            version: stable-v2.23.9
          - os: ubuntu-latest
            version: stable-v2.24.3
+          - os: ubuntu-latest
+            version: stable-v2.25.6
          - os: ubuntu-latest
            version: default
          - os: ubuntu-latest
@@ -44,8 +44,6 @@ jobs:
      fail-fast: false
      matrix:
        include:
-          - os: ubuntu-latest
-            version: stable-v2.19.4
          - os: ubuntu-latest
            version: stable-v2.20.7
          - os: ubuntu-latest
@@ -56,6 +54,8 @@ jobs:
            version: stable-v2.23.9
          - os: ubuntu-latest
            version: stable-v2.24.3
+          - os: ubuntu-latest
+            version: stable-v2.25.6
          - os: ubuntu-latest
            version: default
          - os: ubuntu-latest
@@ -54,10 +54,6 @@ jobs:
      fail-fast: false
      matrix:
        include:
-          - os: ubuntu-latest
-            version: stable-v2.19.4
-          - os: macos-15-xlarge
-            version: stable-v2.19.4
          - os: ubuntu-latest
            version: stable-v2.20.7
          - os: macos-15-xlarge
@@ -78,6 +74,10 @@ jobs:
            version: stable-v2.24.3
          - os: macos-latest-xlarge
            version: stable-v2.24.3
+          - os: ubuntu-latest
+            version: stable-v2.25.6
+          - os: macos-latest-xlarge
+            version: stable-v2.25.6
          - os: ubuntu-latest
            version: default
          - os: macos-latest-xlarge
@@ -116,13 +116,14 @@ jobs:
          version: ${{ matrix.version }}
          use-all-platform-bundle: 'false'
          setup-kotlin: 'true'
-      - name: Install Python 3.13 for older CLI versions
-        # We need Python 3.13 for older CLI versions because they are not compatible with Python 3.14 or newer.
+      - name: Install Python 3.13.15 for older CLI versions
+        # Older CLI versions don't work with Python 3.13.16 or newer because their Python extractor
+        # imports `importlib._bootstrap._ERR_MSG`, which those Python versions no longer define.
        # See https://github.com/github/codeql-action/pull/3212
        if: matrix.version != 'nightly-latest' && matrix.version != 'linked'
        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
        with:
-          python-version: '3.13'
+          python-version: '3.13.15'

      - name: Use Xcode 16
        # Only the older CodeQL CLI versions need Xcode 16, and these run on macOS 15.
@@ -84,6 +84,8 @@ jobs:
        with:
          node-version: 20.x
          cache: npm
+      - name: Install newer npm
+        run: npm install -g npm@11.19.1
      - name: Install dependencies
        run: npm ci
      - name: Prepare test
@@ -84,6 +84,8 @@ jobs:
        with:
          node-version: 20.x
          cache: npm
+      - name: Install newer npm
+        run: npm install -g npm@11.19.1
      - name: Install dependencies
        run: npm ci
      - name: Prepare test
@@ -84,6 +84,8 @@ jobs:
        with:
          node-version: 20.x
          cache: npm
+      - name: Install newer npm
+        run: npm install -g npm@11.19.1
      - name: Install dependencies
        run: npm ci
      - name: Prepare test
@@ -84,6 +84,8 @@ jobs:
        with:
          node-version: 20.x
          cache: npm
+      - name: Install newer npm
+        run: npm install -g npm@11.19.1
      - name: Install dependencies
        run: npm ci
      - name: Prepare test
@@ -54,7 +54,7 @@ jobs:
          use-all-platform-bundle: 'false'
          setup-kotlin: 'true'
      - name: Set up Ruby
-        uses: ruby/setup-ruby@95ef2b042f9d7a56d8268cba8559e2842e2ad01b # v1.321.0
+        uses: ruby/setup-ruby@14594264cd68ce8a2345dd349bc3d138a4ef85c8 # v1.327.0
        with:
          ruby-version: 2.6
      - name: Install Code Scanning integration
@@ -35,7 +35,7 @@ jobs:
      matrix:
        include:
          - os: ubuntu-latest
-            version: stable-v2.19.4
+            version: stable-v2.20.7
          - os: ubuntu-latest
            version: stable-v2.22.1
          - os: ubuntu-latest
@@ -30,7 +30,7 @@ jobs:
      fail-fast: false
      matrix:
        version:
-        - stable-v2.20.3
+        - stable-v2.20.7
        - default
        - linked
        - nightly-latest
@@ -29,7 +29,7 @@ jobs:
      fail-fast: false
      matrix:
        version:
-        - stable-v2.20.3
+        - stable-v2.20.7
        - default
        - linked
        - nightly-latest
@@ -85,7 +85,7 @@ jobs:
        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
      - name: Check expected artifacts exist
        run: |
-          VERSIONS="stable-v2.20.3 default linked nightly-latest"
+          VERSIONS="stable-v2.20.7 default linked nightly-latest"
          LANGUAGES="cpp csharp go java javascript python"
          for version in $VERSIONS; do
            pushd "./my-debug-artifacts-${version//./}"
@@ -47,6 +47,12 @@ jobs:
          node-version: ${{ matrix.node-version }}
          cache: "npm"

+      # Install a new enough version of `npm` to understand `min-release-age`
+      # that is still compatible with Node 20.
+      - name: Install newer npm
+        if: matrix.node-version == 20
+        run: npm install -g npm@11.19.1
+
      - name: Install dependencies
        run: |
          # Use the system Bash shell to ensure we can run commands like `npm ci`
@@ -95,6 +101,14 @@ jobs:
      - name: Checkout repository
        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1

+      - name: Check for incorrect addresses in package-lock.json
+        run: |
+          if git grep -nE '(pkgs\.visualstudio\.com|pkgs\.dev\.azure\.com|packagefeedproxy\.microsoft\.io)' -- \
+              'package-lock.json'; then
+            echo "::error::package-lock.json contains internal package feed URLs. Replace them with public registry URLs."
+            exit 1
+          fi
+
      - name: Set up Node.js
        uses: actions/setup-node@820762786026740c76f36085b0efc47a31fe5020 # v7.0.0
        with:
@@ -114,9 +128,9 @@ jobs:
        working-directory: pr-checks
        run: npx tsx --test

-      - name: Run `pr-checks/changenotes.mts` to ensure that all unreleased change notes are valid
+      - name: Run `pr-checks/changenotes.ts` to ensure that all unreleased change notes are valid
        if: ${{ !cancelled() && steps.install-deps.outcome == 'success' }}
-        run: npx tsx pr-checks/changenotes.mts validate
+        run: npx tsx pr-checks/changenotes.ts validate

      - name: Verify all Actions use the same Node version
        id: head-version
@@ -28,7 +28,7 @@ defaults:

 jobs:
  prepare:
-    name: "Prepare release"
+    name: "Release info"
    runs-on: ubuntu-latest
    if: github.repository == 'github/codeql-action'

@@ -54,32 +54,27 @@ jobs:
        run: |
          git fetch origin "$BASE_BRANCH"

-          # Allow merge conflicts in `lib`, since rebuilding should resolve them.
-          git merge "origin/$BASE_BRANCH"
-          MERGE_RESULT=$?
-
-          if [ "$MERGE_RESULT" -eq 0 ]; then
+          # Allow merge conflicts in `lib`, since rebuilding should resolve them. Conflicts leave the
+          # merge in progress, so check for `MERGE_HEAD` to tell them apart from failures that don't.
+          if git merge "origin/$BASE_BRANCH"; then
            echo "Merge succeeded cleanly."
-          elif [ "$MERGE_RESULT" -eq 1 ]; then
-            echo "Merge conflicts detected (exit code $MERGE_RESULT), continuing."
-          else
-            echo "git merge failed with unexpected exit code $MERGE_RESULT."
-            exit 1
-          fi
-
-          if [ "$MERGE_RESULT" -ne 0 ]; then
+          elif git rev-parse --verify MERGE_HEAD >/dev/null 2>&1; then
+            echo "Merge conflicts detected, continuing."
            echo "merge-in-progress=true" >> $GITHUB_OUTPUT

-            # Check for merge conflicts outside of `lib`. Disable git diff's trailing whitespace check
-            # since `node_modules/@types/semver/README.md` fails it.
-            if git -c core.whitespace=-trailing-space diff --check | grep --invert-match '^lib/'; then
+            # Check for merge conflicts outside of `lib`.
+            CONFLICTS_OUTSIDE_LIB=$(git diff --name-only --diff-filter=U | grep --invert-match '^lib/' || true)
+            if [ -n "$CONFLICTS_OUTSIDE_LIB" ]; then
              echo "Merge conflicts were detected outside of the lib directory. Please resolve them manually."
-              git -c core.whitespace=-trailing-space diff --check | grep --invert-match '^lib/' || true
+              echo "$CONFLICTS_OUTSIDE_LIB"
              exit 1
            fi

            echo "No merge conflicts found outside the lib directory. We should be able to resolve all of" \
              "these by rebuilding the Action."
+          else
+            echo "git merge failed for a reason other than merge conflicts."
+            exit 1
          fi

      - name: Compile TypeScript
@@ -10,8 +10,7 @@ on:
        required: true
  # Only for dry-runs of changes to the workflow.
  push:
-    # Don't run dry-run on release branches, to avoid an issue where the
-    # "new" tag determined by the "Prepare release" job already exists.
+    # Don't run dry-run on release branches, since that's unnecessary.
    branches-ignore:
      - releases/v*
    paths:
@@ -24,7 +23,7 @@ defaults:

 jobs:
  prepare:
-    name: "Prepare release"
+    name: "Prepare"
    if: github.repository == 'github/codeql-action'

    permissions:
@@ -107,8 +106,10 @@ jobs:
          # We usually expect to checkout `inputs.rollback-tag` (required for `workflow_dispatch`),
          # but use `v0.0.0` for testing.
          ROLLBACK_TAG: ${{ inputs.rollback-tag || 'v0.0.0' }}
-          RELEASE_TAG: ${{ needs.prepare.outputs.version }}
-          MAJOR_VERSION_TAG: ${{ needs.prepare.outputs.major_version }}
+          # Use `needs.prepare.outputs.version` for actual runs and `v0.0.1` for testing.
+          RELEASE_TAG: ${{ case(github.event_name == 'workflow_dispatch', needs.prepare.outputs.version, 'v0.0.1') }}
+          # Use `needs.prepare.outputs.major_version` for actual runs and `v0` for testing.
+          MAJOR_VERSION_TAG: ${{ case(github.event_name == 'workflow_dispatch', needs.prepare.outputs.major_version, 'v0') }}
        run: |
          git checkout "refs/tags/${ROLLBACK_TAG}"
          git tag --annotate "${RELEASE_TAG}" --message "${RELEASE_TAG}"
@@ -184,4 +185,3 @@ jobs:
          # Setting this to `true` for non-workflow_dispatch events will
          # still push the `branch`, but won't create a corresponding PR
          dry-run: "${{ github.event_name != 'workflow_dispatch' }}"
-
@@ -16,15 +16,15 @@ defaults:
    shell: bash

 jobs:
-
  prepare:
-    name: "Prepare release"
+    name: "Prepare"
    permissions:
      contents: read

    uses: ./.github/workflows/prepare-release.yml

  update:
+    name: "Update release branch"
    timeout-minutes: 45
    runs-on: ubuntu-latest
    if: github.event_name == 'workflow_dispatch'
@@ -77,6 +77,7 @@ jobs:
          --conductor ${GITHUB_ACTOR}

  backport:
+    name: "Create backport"
    timeout-minutes: 45
    runs-on: ubuntu-latest
    environment: Automation
@@ -1 +1,2 @@
 lockfile-version=3
+min-release-age=7
@@ -7,6 +7,10 @@
    // transpiled JavaScript
    "build": true,
    "lib": true,
+
+    // exclude "tests" by default because it causes VSCode to start language-specific extensions
+    // that are not typically needed during development (or indeed may not work correctly)
+    "tests": true
  },
  "search.exclude": {
    "**/node_modules": true,
@@ -18,7 +22,7 @@
  "git.ignoreLimitWarning": true,
  // Use the vendored TypeScript version to have a consistent development experience across
  // machines.
-  "typescript.tsdk": "node_modules/typescript/lib",
+  "js/ts.tsdk.path": "node_modules/typescript/lib",
  "[typescript]": {
    "editor.defaultFormatter": "esbenp.prettier-vscode"
  },
@@ -2,6 +2,20 @@

 See the [releases page](https://github.com/github/codeql-action/releases) for the relevant changes to the CodeQL CLI and language packs.

+## [UNRELEASED]
+
+- _Breaking change_: Bump the minimum required CodeQL bundle version to 2.20.7. [#4205](https://github.com/github/codeql-action/pull/4205)
+
+## 4.38.3 - 08 Oct 2026
+
+- _Upcoming breaking change_: CodeQL version 2.21.2 and earlier were discontinued on 24 September 2026 alongside GitHub Enterprise Server 3.17, and will be unsupported by the next minor release of the CodeQL Action. Added a deprecation warning for customers using these versions of CodeQL. [#4188](https://github.com/github/codeql-action/pull/4188)
+- Update default CodeQL bundle version to [2.27.2](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.27.2). [#4203](https://github.com/github/codeql-action/pull/4203)
+- Fixed a bug where the decision of whether to use a per-language bundle did not account for custom configurations that reference queries outside of compiled CodeQL packs. This issue was caught during internal testing and did not affect any customer repositories. We will resume the roll out of per-language bundles in the coming weeks. [#4184](https://github.com/github/codeql-action/pull/4184)
+
+## 4.38.2 - 24 Sept 2026
+
+- Update default CodeQL bundle version to [2.27.1](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.27.1). [#4160](https://github.com/github/codeql-action/pull/4160)
+
 ## 4.38.1 - 18 Sept 2026

 - The CodeQL Action now has experimental support for CodeQL releases for which per-language bundles are available. Per-language bundles support analysis for a single language and are therefore smaller than the combined bundles that allow analysis for all supported languages. As a result, per-language bundles take up less space on disk and are faster to download. We expect to roll this change out to everyone in the coming weeks. [#4146](https://github.com/github/codeql-action/pull/4146)
@@ -53,6 +53,7 @@ Here are a few things you can do that will increase the likelihood of your pull
 - Write tests.
 - Keep your change as focused as possible. If there are multiple changes you would like to make that are not dependent upon each other, consider submitting them as separate pull requests.
 - Write a [good commit message](http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html).
+- For user-facing changes, add a change-note file. See [unreleased-change-notes/README.md](unreleased-change-notes/README.md).

 ## Releasing (write access required)

@@ -72,12 +72,11 @@ We typically release new minor versions of the CodeQL Action and Bundle when a n

 | Minimum CodeQL Action | Minimum CodeQL Bundle Version | GitHub Environment | Notes |
 |-----------------------|-------------------------------|--------------------|-------|
+| `v4.36.2` | `2.25.6` | Enterprise Server 3.22 | |
 | `v4.33.0` | `2.24.3` | Enterprise Server 3.21 | |
 | `v4.31.10` | `2.23.9` | Enterprise Server 3.20 | |
 | `v3.29.11` | `2.22.4` | Enterprise Server 3.19 | |
 | `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 | |

 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).

@@ -1,3 +1,4 @@
 import pkg from "./package.json" with { type: "json" };

 globalThis.__CODEQL_ACTION_VERSION__ = pkg.version;
+globalThis.__CODEQL_ACTION_TEST_ENV__ = "unit-test";
@@ -78,7 +78,7 @@ const UPLOAD_LIB_SRC = "./src/upload-lib";
 *
 * 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.
 *
@@ -212,6 +212,7 @@ const context = await esbuild.context({
  target: ["node20"],
  define: {
    __CODEQL_ACTION_VERSION__: JSON.stringify(pkg.version),
+    __CODEQL_ACTION_TEST_ENV__: JSON.stringify(""),
  },
  metafile: true,
 });
@@ -140,6 +140,17 @@ export default [
      "no-async-foreach/no-async-foreach": "error",
      "no-sequences": "error",
      "no-shadow": "off",
+
+      // A basic check that we don't use `exportVariable` from `@actions/core`.
+      "no-restricted-syntax": [
+        "error",
+        {
+          selector: "MemberExpression[property.name='exportVariable']",
+          message:
+            "Use the `export` method of an `Env` instance or `exportEnvVar` from `environment.ts` instead.",
+        },
+      ],
+
      // This is overly restrictive with unsetting `EnvVar`s
      "@typescript-eslint/no-dynamic-delete": "off",
      "@typescript-eslint/no-shadow": "error",
@@ -158,7 +169,16 @@ export default [
    },
  },
  {
-    files: ["**/*.ts", "**/*.js", "**/*.mts"],
+    files: ["src/environment.ts"],
+
+    // We allow `exportVariable` from `@actions/core` to be used in this file
+    // since it defines the wrapper around it that other modules use.
+    rules: {
+      "no-restricted-syntax": "off",
+    },
+  },
+  {
+    files: ["**/*.ts", "**/*.js"],

    rules: {
      "@typescript-eslint/no-explicit-any": "off",
@@ -180,7 +200,7 @@ export default [
    },
  },
  {
-    files: ["pr-checks/**/*.ts", "pr-checks/**/*.mts"],
+    files: ["pr-checks/**/*.ts"],

    languageOptions: {
      parserOptions: {
@@ -1,6 +1,6 @@
 {
-  "bundleVersion": "codeql-bundle-v2.27.0",
-  "cliVersion": "2.27.0",
-  "priorBundleVersion": "codeql-bundle-v2.26.4",
-  "priorCliVersion": "2.26.4"
+  "bundleVersion": "codeql-bundle-v2.27.2",
+  "cliVersion": "2.27.2",
+  "priorBundleVersion": "codeql-bundle-v2.27.1",
+  "priorCliVersion": "2.27.1"
 }
@@ -1,6 +1,6 @@
 {
  "name": "codeql",
-  "version": "4.38.1",
+  "version": "4.39.0",
  "private": true,
  "description": "CodeQL action",
  "scripts": {
@@ -22,7 +22,7 @@
  "dependencies": {
    "@actions/artifact": "^5.0.3",
    "@actions/artifact-legacy": "npm:@actions/artifact@^1.1.2",
-    "@actions/cache": "^5.2.0",
+    "@actions/cache": "^5.3.0",
    "@actions/core": "^2.0.3",
    "@actions/exec": "^2.0.0",
    "@actions/github": "^8.0.1",
@@ -31,21 +31,20 @@
    "@actions/io": "^2.0.0",
    "@actions/tool-cache": "^3.0.1",
    "@octokit/core": "^7.0.8",
-    "@octokit/plugin-paginate-rest": "^15.0.0",
+    "@octokit/plugin-paginate-rest": "^16.0.0",
    "@octokit/plugin-rest-endpoint-methods": "^18.0.0",
    "@octokit/plugin-retry": "^8.1.1",
    "archiver": "^8.0.0",
-    "fast-deep-equal": "^3.1.3",
-    "follow-redirects": "^1.16.0",
+    "follow-redirects": "^1.16.1",
    "get-folder-size": "^5.0.0",
    "https-proxy-agent": "^7.0.6",
-    "js-yaml": "^5.4.1",
+    "js-yaml": "^5.4.3",
    "jsonschema": "1.5.0",
    "long": "^5.3.2",
    "node-forge": "^1.4.0",
    "semver": "^7.8.5",
-    "uuid": "^14.0.2",
-    "undici": "^6.28.0"
+    "undici": "^6.28.0",
+    "uuid": "^14.0.2"
  },
  "devDependencies": {
    "@ava/typescript": "6.0.0",
@@ -66,14 +65,14 @@
    "eslint-import-resolver-typescript": "^4.4.5",
    "eslint-plugin-github": "^6.1.2",
    "eslint-plugin-import-x": "^4.17.1",
-    "eslint-plugin-jsdoc": "^64.3.8",
+    "eslint-plugin-jsdoc": "^65.2.0",
    "eslint-plugin-no-async-foreach": "^0.1.1",
    "glob": "^13.0.6",
-    "globals": "^17.12.0",
+    "globals": "^17.13.0",
    "nock": "^14.0.17",
    "sinon": "^22.1.0",
    "typescript": "^6.0.3",
-    "typescript-eslint": "^8.70.0"
+    "typescript-eslint": "^8.71.1"
  },
  "overrides": {
    "@actions/tool-cache": {
@@ -0,0 +1 @@
+24
@@ -112,7 +112,7 @@ ${NO_CHANGES_STR}`;
 describe("updateChangelog", async () => {
  await it("removes `NO_CHANGES_STR` if present in [UNRELEASED] section", async () => {
    const result = updateChangelog(EMPTY_CHANGELOG, "");
-    assert.ok(!result.includes(NO_CHANGES_STR.trim()));
+    assert.ok(!result.includes(NO_CHANGES_STR));
  });

  await it("doesn't remove `NO_CHANGES_STR` if present in versioned section", async () => {
@@ -120,7 +120,7 @@ describe("updateChangelog", async () => {
      EMPTY_CHANGELOG.replace(UNRELEASED_PLACEHOLDER, "1.2.3"),
      "",
    );
-    assert.ok(result.includes(NO_CHANGES_STR.trim()));
+    assert.ok(result.includes(NO_CHANGES_STR));
  });

  await it("throws if there are no sections", async () => {
@@ -122,6 +122,6 @@ function main() {
 }

 // Only call `main` if this script was run directly.
-if (require.main === module) {
+if (import.meta.main) {
  process.exit(main());
 }
@@ -43,6 +43,6 @@ async function main() {
 }

 // Only call `main` if this script was run directly.
-if (require.main === module) {
+if (import.meta.main) {
  void main();
 }
@@ -9,17 +9,46 @@ import * as fs from "node:fs";
 import { describe, it } from "node:test";

 import {
+  addBodyLinesToUnreleasedSection,
+  ChangelogSection,
  EMPTY_CHANGELOG,
+  getHeader,
  getReleaseDateString,
+  NO_CHANGES_STR,
  parseChangelog,
  processChangelogForBackports,
  renderChangelog,
  setVersionAndDate,
+  UNRELEASED_PLACEHOLDER,
 } from "./changelog";
 import { CHANGELOG_FILE } from "./config";

 const testDate = new Date(2026, 7, 14);

+describe("getHeader", async () => {
+  function Section(headerLine: string): ChangelogSection {
+    return {
+      headerLine,
+      bodyLines: [],
+    };
+  }
+  await it("returns non-headers unchanged", () => {
+    assert.equal("foo", getHeader(Section("foo")));
+    assert.equal("- bar", getHeader(Section("- bar")));
+  });
+  await it("strips octothorpes", async () => {
+    assert.equal("foo", getHeader(Section("# foo")));
+    assert.equal("foo", getHeader(Section("## foo")));
+    assert.equal("foo", getHeader(Section("### foo")));
+    assert.equal("foo", getHeader(Section("#### foo")));
+    assert.equal("foo", getHeader(Section("##### foo")));
+    assert.equal("foo", getHeader(Section("###### foo")));
+  });
+  await it("strips whitespace", async () => {
+    assert.equal("foo", getHeader(Section("# foo  ")));
+  });
+});
+
 describe("getReleaseDateString", async () => {
  await it("formats dates as expected", async () => {
    assert.equal(getReleaseDateString(testDate), "14 Aug 2026");
@@ -70,3 +99,73 @@ describe("processChangelogForBackports", async () => {
    assert.deepEqual(result.split("\n"), testChangelogResult.split("\n"));
  });
 });
+
+describe("addBodyLinesToUnreleasedSection", async () => {
+  function newChangelogWithSections(sections: ChangelogSection[]) {
+    return {
+      preamble: [],
+      sections,
+    };
+  }
+
+  await it("throws error if '[UNRELEASED]' section is not first", async () => {
+    const invalidChangelog = newChangelogWithSections([
+      {
+        headerLine: "## Release 1.0.0",
+        bodyLines: [],
+      },
+      {
+        headerLine: `## ${UNRELEASED_PLACEHOLDER}`,
+        bodyLines: [],
+      },
+    ]);
+    assert.throws(() =>
+      addBodyLinesToUnreleasedSection(invalidChangelog, ["foo"]),
+    );
+  });
+
+  await it("overwrites 'No user facing changes.'", async () => {
+    const changelog = newChangelogWithSections([
+      {
+        headerLine: `## ${UNRELEASED_PLACEHOLDER}`,
+        bodyLines: ["", NO_CHANGES_STR, ""],
+      },
+    ]);
+
+    addBodyLinesToUnreleasedSection(changelog, ["- foo"]);
+
+    assert.equal(changelog.sections[0].bodyLines.length, 3);
+    assert.deepEqual(changelog.sections[0].bodyLines, ["", "- foo", ""]);
+  });
+
+  await it("does nothing if lines is empty", async () => {
+    const changelog = newChangelogWithSections([
+      {
+        headerLine: `## ${UNRELEASED_PLACEHOLDER}`,
+        bodyLines: ["", NO_CHANGES_STR, ""],
+      },
+    ]);
+    const changelogClone = structuredClone(changelog);
+
+    addBodyLinesToUnreleasedSection(changelog, []);
+
+    assert.deepEqual(changelog, changelogClone);
+  });
+
+  await it("inserts a line", async () => {
+    const changelog = newChangelogWithSections([
+      {
+        headerLine: `## ${UNRELEASED_PLACEHOLDER}`,
+        bodyLines: ["", "- Added a new dependency.", ""],
+      },
+    ]);
+    const lineToInsert = "- foo";
+
+    addBodyLinesToUnreleasedSection(changelog, [lineToInsert]);
+
+    assert.equal(changelog.sections[0].bodyLines.length, 4);
+    assert.ok(
+      changelog.sections[0].bodyLines.some((line) => line === lineToInsert),
+    );
+  });
+});
@@ -6,14 +6,16 @@ import { CHANGELOG_FILE, DryRunOption } from "./config";
 export const UNRELEASED_PLACEHOLDER = "[UNRELEASED]";

 /** The default contents for a section in the changelog. */
-export const NO_CHANGES_STR = "No user facing changes.\n\n";
+export const NO_CHANGES_STR = "No user facing changes.";

 /** Placeholder changelog content for a new release. */
 export const EMPTY_CHANGELOG = `# CodeQL Action Changelog

 ## ${UNRELEASED_PLACEHOLDER}

-${NO_CHANGES_STR}`;
+${NO_CHANGES_STR}
+
+`;

 /**
 * Represents sections in a changelog.
@@ -31,6 +33,13 @@ export interface Changelog {
  sections: ChangelogSection[];
 }

+/**
+ * Returns the text of the header (without the '## ' prefix) of the given section.
+ * */
+export function getHeader(section: ChangelogSection): string {
+  return section.headerLine.replace(/^#+\s+/, "").trimEnd();
+}
+
 /** Returns `date` formatted as `DD Mon YYYY`. */
 export function getReleaseDateString(today: Date = new Date()): string {
  return today.toLocaleDateString("en-GB", {
@@ -125,6 +134,42 @@ export function parseChangelog(content: string): Changelog {
  return { preamble, sections };
 }

+/**
+ * Inserts the changenotes `lines` in the `[UNRELEASED]` section of `changelog`.
+ * If the section contains the stock message {@link NO_CHANGES_STR}, then
+ * `lines` will be inserted in place and the stock message will be deleted.
+ *
+ * @throws Error -- if the [UNRELEASED] section does not exist.
+ *
+ * @param changelog The CHANGELOG object to modify.
+ * @param lines The changenotes to insert.
+ */
+export function addBodyLinesToUnreleasedSection(
+  changelog: Changelog,
+  lines: string[],
+) {
+  // Do nothing if there is nothing to insert.
+  if (lines.length === 0) return;
+
+  const unreleasedSection = changelog.sections[0];
+  if (getHeader(unreleasedSection) !== UNRELEASED_PLACEHOLDER) {
+    throw Error(
+      `'${UNRELEASED_PLACEHOLDER}' is not the first section of 'CHANGELOG.md'`,
+    );
+  }
+
+  if (unreleasedSection.bodyLines.includes(NO_CHANGES_STR)) {
+    unreleasedSection.bodyLines = ["", ...lines, ""];
+    return;
+  }
+
+  // The last body line should be a blank line (for spacing).
+  // Remove it so that we can add `lines` and then add the blank line back.
+  unreleasedSection.bodyLines.pop();
+  unreleasedSection.bodyLines.push(...lines);
+  unreleasedSection.bodyLines.push("");
+}
+
 /**
 * Combines an array of lines into a single string by adding line breaks.
 */
@@ -204,7 +249,7 @@ export function processChangelogForBackports(

    // Add an entry if we didn't keep any.
    if (!foundContent) {
-      section.bodyLines.push(NO_CHANGES_STR.trim());
+      section.bodyLines.push(NO_CHANGES_STR);
    }
  }

@@ -1,18 +1,15 @@
 import assert from "node:assert/strict";
-import * as fs from "node:fs";
-import * as path from "node:path";
 import { describe, it } from "node:test";

-import { withTmpDir, withTmpFile } from "../../src/util";
+import { withTmpFile } from "../../src/util";

 import {
  hasValidChangenoteCategory,
-  isValidAllChangenoteFiles,
  isValidChangenoteContent,
  isValidChangenoteFile,
  isValidChangenoteFilename,
  VALID_CHANGE_NOTE_CATEGORIES,
-} from "./validate.mjs";
+} from "./validate";

 await describe("isValidChangenoteContent", async () => {
  await it("recognizes an unordered Markdown list", () => {
@@ -157,26 +154,6 @@ await describe("isValidChangenoteFile", async () => {
    assert.equal(isValidChangenoteFile("non-existent-file.md"), false);
  });

-  await it("rejects invalid filename", async () => {
-    await withTmpFile(
-      "fix-bug.md",
-      "---\ncategory: fix\n---\n- Fixed a bug\n",
-      (filePath) => {
-        assert.equal(isValidChangenoteFile(filePath), false);
-      },
-    );
-  });
-
-  await it("rejects missing frontmatter", async () => {
-    await withTmpFile(
-      "2026-01-01-fix-bug.md",
-      "- Fixed a bug\n",
-      (filePath) => {
-        assert.equal(isValidChangenoteFile(filePath), false);
-      },
-    );
-  });
-
  await it("rejects invalid Markdown", async () => {
    await withTmpFile(
      "2026-01-01-fix-bug.md",
@@ -187,39 +164,3 @@ await describe("isValidChangenoteFile", async () => {
    );
  });
 });
-
-await describe("isValidAllChangenoteFiles", async () => {
-  await it("accepts list of file paths of valid change-notes", async () => {
-    await withTmpDir(async (tmpDir) => {
-      const fileName1 = path.join(tmpDir, "2026-01-01-fix-bug.md");
-      const fileName2 = path.join(tmpDir, "2026-01-02-add-feature.md");
-      fs.writeFileSync(fileName1, "---\ncategory: fix\n---\n- Fixed a bug\n");
-      fs.writeFileSync(
-        fileName2,
-        "---\ncategory: feature\n---\n- Added a feature\n",
-      );
-      assert.equal(isValidAllChangenoteFiles([fileName1, fileName2]), true);
-    });
-  });
-
-  await it("accepts the empty list", async () => {
-    assert.equal(isValidAllChangenoteFiles([]), true);
-  });
-
-  await it("accepts list of .gitkeep", async () => {
-    assert.equal(isValidAllChangenoteFiles([".gitkeep"]), true);
-  });
-
-  await it("rejects list containing a file path to an invalid change-note", async () => {
-    await withTmpDir(async (tmpDir) => {
-      const fileName1 = path.join(tmpDir, "2026-01-01-fix-bug.md");
-      const fileName2 = path.join(tmpDir, "2026-01-02-wrong-category.md");
-      fs.writeFileSync(fileName1, "---\ncategory: fix\n---\n- Fixed a bug\n");
-      fs.writeFileSync(
-        fileName2,
-        "---\ncategory: foobar\n---\n- Added a feature\n",
-      );
-      assert.equal(isValidAllChangenoteFiles([fileName1, fileName2]), false);
-    });
-  });
-});
@@ -1,5 +1,4 @@
 import * as fs from "node:fs";
-import * as path from "node:path";

 import { matter } from "lite-matter";
 import type { List, ListItem } from "mdast";
@@ -95,21 +94,7 @@ export function isValidChangenoteFile(filename: string): boolean {
    return false;
  }

-  const { data: frontmatter, content } = matter(fileData);
-
-  if (!isValidChangenoteFilename(path.basename(filename))) {
-    isValid = false;
-    console.error(
-      `${filename}: invalid filename; must match pattern YYYY-MM-DD-id.md`,
-    );
-  }
-  if (!hasValidChangenoteCategory(frontmatter)) {
-    isValid = false;
-    const categories = Object.keys(VALID_CHANGE_NOTE_CATEGORIES).join(", ");
-    console.error(
-      `${filename}: invalid category; must be one of: ${categories}`,
-    );
-  }
+  const { content } = matter(fileData);
  if (!isValidChangenoteContent(content)) {
    isValid = false;
    console.error(
@@ -119,14 +104,3 @@ export function isValidChangenoteFile(filename: string): boolean {

  return isValid;
 }
-
-/**
- * Validates the change-note files of the given list of file paths, ignoring ".gitkeep".
- * @param filepaths A list of filepaths to validate
- * @returns True if all the paths are valid, false otherwise.
- */
-export function isValidAllChangenoteFiles(filepaths: string[]): boolean {
-  return filepaths
-    .filter((f) => f !== ".gitkeep")
-    .reduce((r, filePath) => r && isValidChangenoteFile(filePath), true);
-}
@@ -1,56 +0,0 @@
-#!/usr/bin/env npx tsx
-
-import * as fs from "node:fs";
-import { pathToFileURL } from "node:url";
-import { parseArgs } from "node:util";
-
-import { isValidAllChangenoteFiles } from "./changelog/validate.mjs";
-import { CHANGENOTES_DIR } from "./config";
-
-const entryPoint = process.argv[1];
-if (entryPoint && import.meta.url === pathToFileURL(entryPoint).href) {
-  try {
-    process.exit(main());
-  } catch (error) {
-    console.error(error);
-    process.exit(1);
-  }
-}
-
-function main(): number {
-  const { positionals } = parseArgs({
-    allowPositionals: true,
-    strict: true,
-  });
-  const [command] = positionals;
-  switch (command) {
-    case undefined:
-    case "help":
-      return usage();
-    case "validate":
-      return validate();
-    default:
-      console.error(`Unknown command: ${command}`);
-      return 1;
-  }
-}
-
-function usage(): number {
-  console.log(`Usage: changenotes.mts validate`);
-  return 0;
-}
-
-function validate(): number {
-  try {
-    if (isValidAllChangenoteFiles(fs.readdirSync(CHANGENOTES_DIR))) {
-      console.log(`All changenotes in '${CHANGENOTES_DIR}' are valid.`);
-      return 0;
-    }
-  } catch (error) {
-    console.error(
-      `Failed to read changenotes directory '${CHANGENOTES_DIR}'`,
-      error,
-    );
-  }
-  return 1;
-}
@@ -0,0 +1,134 @@
+#!/usr/bin/env npx tsx
+
+import * as fs from "node:fs";
+import { pathToFileURL } from "node:url";
+import { parseArgs } from "node:util";
+import path from "path";
+
+import { ExitCode } from "@actions/core";
+import { matter } from "lite-matter";
+
+import {
+  addBodyLinesToUnreleasedSection,
+  parseChangelog,
+  renderChangelog,
+  withChangelog,
+} from "./changelog";
+import { isValidChangenoteFile } from "./changelog/validate";
+import { CHANGENOTES_DIR } from "./config";
+
+/**
+ * Describes a changenote file, including its file path, frontmatter, and content.
+ */
+interface ChangenoteFile {
+  absolutePath: string;
+  data: Record<string, any>;
+  content: string;
+}
+
+/**
+ * Returns the absolute file paths of all files in
+ * {@link CHANGENOTES_DIR} (except ".gitkeep" and "README.md").
+ * */
+function listUnreleasedChangenoteDir(): string[] {
+  return fs
+    .readdirSync(CHANGENOTES_DIR)
+    .filter((name) => ![".gitkeep", "README.md"].includes(name))
+    .map((name) => path.join(CHANGENOTES_DIR, name));
+}
+
+/**
+ * Scans the {@link CHANGENOTES_DIR} directory for changenote files
+ * and returns a parsed listing of those changenote files.
+ */
+function getChangenotes(): ChangenoteFile[] {
+  return listUnreleasedChangenoteDir().map((absolutePath) => {
+    return {
+      absolutePath,
+      ...matter(fs.readFileSync(absolutePath, "utf-8")),
+    };
+  });
+}
+
+const entryPoint = process.argv[1];
+if (entryPoint && import.meta.url === pathToFileURL(entryPoint).href) {
+  try {
+    process.exit(main());
+  } catch (error) {
+    console.error(error);
+    process.exit(ExitCode.Failure);
+  }
+}
+
+function main(): ExitCode {
+  const { positionals } = parseArgs({
+    allowPositionals: true,
+    strict: true,
+  });
+  const [command] = positionals;
+  switch (command) {
+    case undefined:
+    case "help":
+      return usage();
+    case "assemble":
+      return assemble();
+    case "validate":
+      return validate();
+    default:
+      console.error(`Unknown command: ${command}`);
+      return ExitCode.Failure;
+  }
+}
+
+function usage(): ExitCode {
+  const message =
+    "Usage: changenotes.ts assemble\n" +
+    "       changenotes.ts validate\n" +
+    "       changenotes.ts help";
+  console.log(message);
+  return ExitCode.Success;
+}
+
+function assemble(): ExitCode {
+  try {
+    const changenotes = getChangenotes();
+    const changenoteBodies = changenotes.map((c) => c.content);
+    const changenotePaths = changenotes.map((c) => c.absolutePath);
+
+    withChangelog((contents) => {
+      const changelog = parseChangelog(contents);
+      addBodyLinesToUnreleasedSection(changelog, changenoteBodies);
+      return renderChangelog(changelog);
+    }, {});
+
+    // Delete changenotes only after successful processing.
+    for (const p of changenotePaths) {
+      fs.unlinkSync(p);
+    }
+
+    return ExitCode.Success;
+  } catch (e) {
+    console.error("Failed to assemble changenotes to 'CHANGELOG.md'", e);
+  }
+
+  return ExitCode.Failure;
+}
+
+function validate(): ExitCode {
+  try {
+    const allChangenotesValid = getChangenotes().reduce(
+      (r, changenote) => r && isValidChangenoteFile(changenote.absolutePath),
+      true,
+    );
+    if (allChangenotesValid) {
+      console.log(`All changenotes in '${CHANGENOTES_DIR}' are valid.`);
+      return ExitCode.Success;
+    }
+  } catch (error) {
+    console.error(
+      `Failed to read changenotes directory '${CHANGENOTES_DIR}'`,
+      error,
+    );
+  }
+  return ExitCode.Failure;
+}
@@ -218,6 +218,6 @@ async function run(): Promise<void> {
  }
 }

-if (require.main === module) {
+if (import.meta.main) {
  void run();
 }
@@ -11,6 +11,10 @@ installDotNet: true
 env:
  CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS: false
  CODEQL_ACTION_SUBLANGUAGE_FILE_COVERAGE: true
+  # To balance speed and coverage, we analyze only a single language (JavaScript), but use the
+  # combined bundle so we can test that baseline information is reported for each language in the
+  # multi-language source directory.
+  CODEQL_ACTION_PER_LANGUAGE_BUNDLES: false
 steps:
  - uses: ./../action/init
    id: init
@@ -10,7 +10,6 @@ operatingSystems:
  - os: macos
    runner-image: macos-15-xlarge
    codeql-versions:
-      - stable-v2.19.4
      - stable-v2.20.7
      - stable-v2.21.4
      - stable-v2.22.4
@@ -20,13 +19,14 @@ env:
 installGo: true
 installDotNet: true
 steps:
-  - name: Install Python 3.13 for older CLI versions
-    # We need Python 3.13 for older CLI versions because they are not compatible with Python 3.14 or newer.
+  - name: Install Python 3.13.15 for older CLI versions
+    # Older CLI versions don't work with Python 3.13.16 or newer because their Python extractor
+    # imports `importlib._bootstrap._ERR_MSG`, which those Python versions no longer define.
    # See https://github.com/github/codeql-action/pull/3212
    if: matrix.version != 'nightly-latest' && matrix.version != 'linked'
    uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
    with:
-      python-version: "3.13"
+      python-version: "3.13.15"

  - name: Use Xcode 16
    # Only the older CodeQL CLI versions need Xcode 16, and these run on macOS 15.
@@ -5,7 +5,7 @@ versions:
  - default
 steps:
  - name: Set up Ruby
-    uses: ruby/setup-ruby@95ef2b042f9d7a56d8268cba8559e2842e2ad01b # v1.321.0
+    uses: ruby/setup-ruby@14594264cd68ce8a2345dd349bc3d138a4ef85c8 # v1.327.0
    with:
      ruby-version: 2.6
  - name: Install Code Scanning integration
@@ -1,8 +1,8 @@
 name: "Rust analysis"
 description: "Tests creation of a Rust database"
 versions:
-  # experimental rust support introduced, requires action to set `CODEQL_ENABLE_EXPERIMENTAL_FEATURES`
-  - stable-v2.19.4
+  # oldest CodeQL version supported by the Action, where Rust support is experimental and requires the Action to set `CODEQL_ENABLE_EXPERIMENTAL_FEATURES`
+  - stable-v2.20.7
  # first public preview version
  - stable-v2.22.1
  - linked
@@ -1,4 +1,9 @@
 import path from "path";
+import { fileURLToPath } from "url";
+
+// For backwards-compatibility.
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = path.dirname(__filename);

 /** The oldest supported major version of the CodeQL Action. */
 export const OLDEST_SUPPORTED_MAJOR_VERSION = 3;
@@ -5,6 +5,8 @@ contains:
  - "test-setup-python-scripts"
  - "update"
  - "Update"
+  # Matrix-ed job; the name starts with this
+  - "Create backport"
 is:
  - "Agent"
  - "check-expected-release-files"
@@ -15,4 +17,6 @@ is:
  - "Label PR with size"
  - "Post repo size comment"
  - "Prepare"
+  - "Release info"
  - "Upload results"
+  - "Update release branch"
@@ -1,19 +1,20 @@
 {
  "private": true,
  "description": "Dependencies for codeql-action scripts",
+  "type": "module",
  "dependencies": {
    "@actions/core": "^2.0.3",
    "@actions/github": "^8.0.1",
    "@octokit/core": "^7.0.8",
-    "@octokit/plugin-paginate-rest": ">=15.0.0",
+    "@octokit/plugin-paginate-rest": ">=16.0.0",
    "@octokit/plugin-rest-endpoint-methods": "^18.0.0",
    "lite-matter": "^0.1.2",
-    "mdast-util-from-markdown": "^2.0.3",
+    "mdast-util-from-markdown": "^2.1.0",
    "semver": "^7.8.5",
-    "yaml": "^2.9.0"
+    "yaml": "^2.9.1"
  },
  "devDependencies": {
-    "@types/node": "^20.19.43",
-    "tsx": "^4.23.13"
+    "@types/node": "^24.19.0",
+    "tsx": "^4.23.15"
  }
 }
@@ -77,6 +77,6 @@ function main() {
 }

 // Only call `main` if this script was run directly.
-if (require.main === module) {
+if (import.meta.main) {
  process.exit(main());
 }
@@ -116,6 +116,6 @@ async function main() {
 }

 // Only call `main` if this script was run directly.
-if (require.main === module) {
+if (import.meta.main) {
  void main();
 }
@@ -79,6 +79,6 @@ function main() {
 }

 // Only call `main` if this script was run directly.
-if (require.main === module) {
+if (import.meta.main) {
  process.exit(main());
 }
@@ -21,10 +21,11 @@ import * as fs from "fs";
 import { parseArgs } from "node:util";
 import * as path from "path";

-const THIS_DIR = __dirname;
-const CHECKS_DIR = path.join(THIS_DIR, "checks");
-const WORKFLOW_DIR = path.join(THIS_DIR, "..", ".github", "workflows");
-const SYNC_TS_PATH = path.join(THIS_DIR, "sync.ts");
+import { PR_CHECKS_DIR, REPO_ROOT } from "./config";
+
+const CHECKS_DIR = path.join(PR_CHECKS_DIR, "checks");
+const WORKFLOW_DIR = path.join(REPO_ROOT, ".github", "workflows");
+const SYNC_TS_PATH = path.join(PR_CHECKS_DIR, "sync.ts");

 /**
 * Scan generated workflow files to extract the latest action versions.
@@ -232,6 +233,6 @@ function main(): number {
 }

 // Only call `main` if this script was run directly.
-if (require.main === module) {
+if (import.meta.main) {
  process.exit(main());
 }
@@ -342,6 +342,6 @@ async function main(): Promise<void> {
 }

 // Only call `main` if this script was run directly.
-if (require.main === module) {
+if (import.meta.main) {
  void main();
 }
@@ -7,6 +7,8 @@ import * as yaml from "yaml";

 import { BuiltInLanguage } from "../src/languages";

+import { PR_CHECKS_DIR, REPO_ROOT } from "./config";
+
 /**
 * Returns a `uses` value for `action` pinned to a commit SHA, with the
 * human-readable version recorded in a trailing comment.
@@ -134,8 +136,6 @@ 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-v2.19.4",
-  // The last CodeQL release in the 2.20 series.
  "stable-v2.20.7",
  // The last CodeQL release in the 2.21 series.
  "stable-v2.21.4",
@@ -145,6 +145,8 @@ const defaultTestVersions = [
  "stable-v2.23.9",
  // The last CodeQL release in the 2.24 series.
  "stable-v2.24.3",
+  // The last CodeQL release in the 2.25 series.
+  "stable-v2.25.6",
  // 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
@@ -221,6 +223,12 @@ const languageSetups: LanguageSetups = {
          cache: "npm",
        },
      },
+      // Install a new enough version of `npm` to understand `min-release-age`
+      // that is still compatible with Node 20.
+      {
+        name: "Install newer npm",
+        run: "npm install -g npm@11.19.1",
+      },
      {
        name: "Install dependencies",
        run: "npm ci",
@@ -306,9 +314,8 @@ const languageSetups: LanguageSetups = {
 // See https://github.com/github/codeql-action/pull/3423
 const YQ_VERSION = "v4.50.1";

-const THIS_DIR = __dirname;
-const CHECKS_DIR = path.join(THIS_DIR, "checks");
-const OUTPUT_DIR = path.join(THIS_DIR, "..", ".github", "workflows");
+const CHECKS_DIR = path.join(PR_CHECKS_DIR, "checks");
+const OUTPUT_DIR = path.join(REPO_ROOT, ".github", "workflows");

 /**
 * Loads and parses a YAML file.
@@ -8,6 +8,6 @@
    "sourceMap": false,
    "noEmit": true
  },
-  "include": ["./**/*.ts", "./**/*.mts", "../src/**/*.ts"],
+  "include": ["./**/*.ts", "../src/**/*.ts"],
  "exclude": ["node_modules"]
 }
@@ -238,6 +238,6 @@ function main() {
 }

 // Only call `main` if this script was run directly.
-if (require.main === module) {
+if (import.meta.main) {
  main();
 }
@@ -835,6 +835,6 @@ async function main(): Promise<void> {
 }

 // Only call `main` if this script was run directly.
-if (require.main === module) {
+if (import.meta.main) {
  void main();
 }
@@ -23,7 +23,8 @@ predicate isSafeForDefaultSetup(string envVar) {
      "GITHUB_BASE_REF", "GITHUB_EVENT_NAME", "GITHUB_JOB", "GITHUB_RUN_ATTEMPT", "GITHUB_RUN_ID",
      "GITHUB_SHA", "GITHUB_REPOSITORY", "GITHUB_SERVER_URL", "GITHUB_TOKEN", "GITHUB_WORKFLOW",
      "GITHUB_WORKSPACE", "GOFLAGS", "ImageVersion", "JAVA_TOOL_OPTIONS", "RUNNER_ARCH",
-      "RUNNER_ENVIRONMENT", "RUNNER_NAME", "RUNNER_OS", "RUNNER_TEMP", "RUNNER_TOOL_CACHE"
+      "RUNNER_ENVIRONMENT", "RUNNER_NAME", "RUNNER_OS", "RUNNER_TEMP", "RUNNER_TOOL_CACHE",
+      "NODE_ENV"
    ]
 }

@@ -21,19 +21,16 @@ inputs:
    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`.
+      A comma-separated list of CodeQL languages that the installed CodeQL CLI will be used to
+      analyze. 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.
    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`.
+      [Internal] A comma-separated list of analysis kinds that the installed CodeQL CLI will be used
+      for. If specified, the Action may use this list to select a CodeQL CLI version that is best
+      suited to those analysis kinds.

      Available options are the same as for the `analysis-kinds` input on the `init` Action.
    default: 'code-scanning'
@@ -19,6 +19,24 @@ import { getErrorMessage } from "./util";

 setupTests(test);

+for (const [key, displayName] of Object.entries(
+  statusReport.ACTION_DISPLAY_NAMES,
+)) {
+  test(`getDisplayActionName - '${displayName}' instead of '${key}'`, (t) => {
+    t.is(statusReport.getDisplayActionName(key as ActionName), displayName);
+  });
+}
+
+test("getDisplayActionName - returns action name", (t) => {
+  for (const actionName of Object.values(ActionName)) {
+    if (statusReport.ACTION_DISPLAY_NAMES[actionName]) {
+      continue;
+    }
+
+    t.is(statusReport.getDisplayActionName(actionName), actionName);
+  }
+});
+
 interface RunInActionsTestOpts {
  runFn?: () => Promise<any>;
  expectedErrorMessage?: string;
@@ -19,6 +19,10 @@ export interface BaseState {
  name: ActionName;
  /** When the Action was started. */
  startedAt: Date;
+  /** The platform the Action is running on. */
+  platform: NodeJS.Platform;
+  /** The architecture of the host. */
+  arch: NodeJS.Architecture;
 }

 /** Describes different state features that an Action may have. */
@@ -52,6 +56,29 @@ export interface FeatureState {
 /** Identifies a type of state an Action may have. */
 export type StateFeature = keyof FeatureState;

+/**
+ * The `Env` feature implies the availability of the `ReadOnlyEnv` feature.
+ *
+ * If `T` is `Env`, this returns `Env | ReadOnlyEnv`.
+ * Otherwise, it is the identity and returns T.
+ */
+type ImpliedFeatures<T extends StateFeature> = T extends "Env"
+  ? "Env" | "ReadOnlyEnv"
+  : T;
+
+/**
+ * Given an object type `Obj`, this tries to lookup a corresponding `StateFeature`
+ * to which the object type belongs in `FeatureState`. Resolves to `never` if there
+ * is no match.
+ */
+type FeatureNameFor<Obj extends object> = {
+  [K in StateFeature]: [Obj] extends [FeatureState[K]]
+    ? [FeatureState[K]] extends [Obj]
+      ? K
+      : never
+    : never;
+}[StateFeature];
+
 /** Constructs the intersection of all state types identifies by `Fs`. */
 export type FieldsOf<Fs extends readonly StateFeature[]> = Fs extends []
  ? Record<never, never>
@@ -62,8 +89,54 @@ export type FieldsOf<Fs extends readonly StateFeature[]> = Fs extends []
    ? FeatureState[Head] & FieldsOf<Tail>
    : never;

+/**
+ * Symbol used for a field in `ActionState` that carries the type array of state features.
+ * This is a Symbol so that it doesn't clash with any property names we might want to have.
+ */
+const stateFeatures = Symbol();
+
 /** Describes the state of an Action that has access to the state corresponding to `Fs`. */
-export type ActionState<Fs extends readonly StateFeature[]> = FieldsOf<Fs>;
+export type ActionState<Fs extends readonly StateFeature[]> = FieldsOf<Fs> & {
+  /**
+   * When given a chance, TypeScript will simplify an `ActionState<Fs>` type as much as possible,
+   * which results in a concrete object type that doesn't mention `Fs`.
+   *
+   * That causes problems for functions which accept `ActionState<Fs>` values, but need to know the
+   * feature keys `Fs`. This property here explicitly captures `Fs` in the concrete object type
+   * that results from simplifying `ActionState<Fs>`.
+   *
+   * This is a function rather than a field, because we want to be able to provide values of type
+   * `ActionState<Fs>` to functions expecting `ActionState<As>` where `As` is a subset of `Fs`.
+   *
+   * Since function types are contravariant in the types of their parameters, using a function
+   * type here allows that to happen.
+   *
+   * Because the field is optional, we don't have to explicitly provide a value
+   * for it anywhere while the type is still inferred.
+   *
+   * `Fs[number]` returns the union of all features in `Fs`. We wrap it in `ImpliedFeatures`
+   * so that `Env` is expanded into `Env | ReadOnlyEnv`, allowing functions that expect the
+   * `ReadOnlyEnv` feature to be provided with an `ActionState` that has the `Env` feature
+   * without requiring this to be made explicit.
+   */
+  readonly [stateFeatures]?: (ts: ImpliedFeatures<Fs[number]>) => void;
+};
+
+/** Extends `state` with an `extra` feature. */
+export function extendActionState<
+  // In first position, so that it can be explicitly provided if `FeatureNameFor`
+  // should not work on `extra`.
+  F extends StateFeature,
+  Fs extends readonly StateFeature[],
+  E extends FeatureState[F],
+>(
+  state: ActionState<Fs>,
+  extra: E,
+): ActionState<[...Fs, FeatureNameFor<E> & F]> {
+  return { ...state, ...extra } as unknown as ActionState<
+    [...Fs, FeatureNameFor<E> & F]
+  >;
+}

 /** The type of an Action's main entry point. This is a function that is provided
 * with a basic `ActionState` object with features that are always available.
@@ -98,6 +171,8 @@ export async function runInActions(action: Action) {
    const actionState = {
      name: action.name,
      startedAt,
+      platform: process.platform,
+      arch: process.arch,
      logger,
      env,
      actions: actionsEnv,
@@ -7,12 +7,13 @@ import {
  isAnalyzingPullRequest,
  isDefaultSetup,
  isDynamicWorkflow,
+  printDebugLogs,
 } from "./actions-util";
 import { computeAutomationID } from "./api-client";
 import { EnvVar } from "./environment";
 import { getRunnerLogger } from "./logging";
-import { setupTests } from "./testing-utils";
-import { initializeEnvironment } from "./util";
+import { RecordingLogger, setupTests } from "./testing-utils";
+import { initializeEnvironment, withTmpDir } from "./util";

 setupTests(test);

@@ -100,6 +101,21 @@ test("computeAutomationID()", async (t) => {
  );
 });

+test("printDebugLogs - doesn't throw when config doesn't have needed properties", async (t) => {
+  const logger = new RecordingLogger();
+  await t.notThrowsAsync(printDebugLogs(logger, {}));
+  await t.notThrowsAsync(printDebugLogs(logger, { languages: [] }));
+  await t.notThrowsAsync(printDebugLogs(logger, { dbLocation: "nowhere" }));
+});
+
+test("printDebugLogs - doesn't throw when language db doesn't exist", async (t) =>
+  withTmpDir(async (tmpDir) => {
+    const logger = new RecordingLogger();
+    await t.notThrowsAsync(
+      printDebugLogs(logger, { dbLocation: tmpDir, languages: ["javascript"] }),
+    );
+  }));
+
 test.serial("getPullRequestBranches() with pull request context", (t) => {
  withMockedContext(
    {
@@ -6,7 +6,7 @@ import * as toolrunner from "@actions/exec/lib/toolrunner";
 import * as github from "@actions/github";
 import * as io from "@actions/io";

-import type { Config } from "./config-utils";
+import { hasConfigKey, type Config } from "./config/action-config";
 import { Env, EnvVar, ActionsEnvVars, ReadOnlyEnv } from "./environment";
 import { Logger } from "./logging";
 import {
@@ -14,6 +14,7 @@ import {
  getCodeQLDatabasePath,
  ConfigurationError,
  getEnv,
+  getErrorMessage,
 } from "./util";

 /**
@@ -29,7 +30,6 @@ declare const __CODEQL_ACTION_VERSION__: string;
 export interface ActionsEnv {
  getRequiredInput: (name: string) => string;
  getOptionalInput: (name: string) => string | undefined;
-  exportVariable: (name: string, value: string) => void;
 }

 /**
@@ -39,7 +39,6 @@ export function getActionsEnv(): ActionsEnv {
  return {
    getRequiredInput,
    getOptionalInput,
-    exportVariable: core.exportVariable,
  };
 }

@@ -94,7 +93,7 @@ export function getActionVersion(): string {
 *
 * This will be "dynamic" for default setup workflow runs.
 */
-export function getWorkflowEventName(env: Env = getEnv()) {
+export function getWorkflowEventName(env: ReadOnlyEnv = getEnv()) {
  return env.getRequired(ActionsEnvVars.GITHUB_EVENT_NAME);
 }

@@ -102,7 +101,7 @@ export function getWorkflowEventName(env: Env = getEnv()) {
 * Returns whether the current workflow is executing a local copy of the Action, e.g. we're running
 * a workflow on the codeql-action repo itself.
 */
-export function isRunningLocalAction(env: Env = getEnv()): boolean {
+export function isRunningLocalAction(env: ReadOnlyEnv = getEnv()): boolean {
  const relativeScriptPath = getRelativeScriptPath(env);
  return (
    relativeScriptPath.startsWith("..") || path.isAbsolute(relativeScriptPath)
@@ -114,14 +113,14 @@ export function isRunningLocalAction(env: Env = getEnv()): boolean {
 *
 * This can be used to get the Action's name or tell if we're running a local Action.
 */
-function getRelativeScriptPath(env: Env): string {
+function getRelativeScriptPath(env: ReadOnlyEnv): string {
  const runnerTemp = env.getRequired(ActionsEnvVars.RUNNER_TEMP);
  const actionsDirectory = path.join(path.dirname(runnerTemp), "_actions");
  return path.relative(actionsDirectory, __filename);
 }

 /** Returns the contents of `GITHUB_EVENT_PATH` as a JSON object. */
-export function getWorkflowEvent(env: Env = getEnv()): any {
+export function getWorkflowEvent(env: ReadOnlyEnv = getEnv()): any {
  const eventJsonFile = env.getRequired(ActionsEnvVars.GITHUB_EVENT_PATH);
  try {
    return JSON.parse(fs.readFileSync(eventJsonFile, "utf-8"));
@@ -132,28 +131,38 @@ export function getWorkflowEvent(env: Env = getEnv()): any {
  }
 }

-export async function printDebugLogs(config: Config) {
+export async function printDebugLogs(logger: Logger, config: Partial<Config>) {
+  if (
+    !hasConfigKey(config, "languages") ||
+    !hasConfigKey(config, "dbLocation")
+  ) {
+    logger.debug(
+      `Not printing debug logs, because the configuration does not include the 'languages' or 'dbLocation' fields.`,
+    );
+    return;
+  }
+
  for (const language of config.languages) {
    const databaseDirectory = getCodeQLDatabasePath(config, language);
    const logsDirectory = path.join(databaseDirectory, "log");
    if (!doesDirectoryExist(logsDirectory)) {
-      core.info(`Directory ${logsDirectory} does not exist.`);
+      logger.info(`Directory ${logsDirectory} does not exist.`);
      continue; // Skip this language database.
    }

    const walkLogFiles = (dir: string) => {
      const entries = fs.readdirSync(dir, { withFileTypes: true });
      if (entries.length === 0) {
-        core.info(`No debug logs found at directory ${logsDirectory}.`);
+        logger.info(`No debug logs found at directory ${logsDirectory}.`);
      }
      for (const entry of entries) {
        if (entry.isFile()) {
          const absolutePath = path.resolve(dir, entry.name);
-          core.startGroup(
+          logger.startGroup(
            `CodeQL Debug Logs - ${language} - ${entry.name} from file at path ${absolutePath}`,
          );
-          process.stdout.write(fs.readFileSync(absolutePath));
-          core.endGroup();
+          logger.info(fs.readFileSync(absolutePath, "utf-8"));
+          logger.endGroup();
        } else if (entry.isDirectory()) {
          walkLogFiles(path.resolve(dir, entry.name));
        }
@@ -412,14 +421,23 @@ export const persistInputs = function (env: Env = getEnv()) {
 /**
 * Restores all inputs to the action from the persisted state.
 */
-export const restoreInputs = function () {
-  const persistedInputs = core.getState(persistedInputsKey);
-  if (persistedInputs) {
-    for (const [name, value] of JSON.parse(persistedInputs)) {
-      process.env[name] = value;
+export function restoreInputs(logger: Logger) {
+  try {
+    const persistedInputsValue = core.getState(persistedInputsKey);
+    if (persistedInputsValue) {
+      const persistedInputs = JSON.parse(persistedInputsValue);
+
+      for (const [name, value] of persistedInputs) {
+        process.env[name] = value;
+      }
    }
+  } catch (err) {
+    logger.error(`Unable to restore inputs: ${getErrorMessage(err)}`);
+    throw new Error(
+      "Failed to restore inputs from the state set by this action's main execution.",
+    );
  }
-};
+}

 export interface PullRequestBranches {
  base: string;
@@ -9,7 +9,6 @@ import * as core from "@actions/core";

 import * as actionsUtil from "./actions-util";
 import { getGitHubVersion } from "./api-client";
-import { getCodeQL } from "./codeql";
 import { getConfig } from "./config-utils";
 import * as debugArtifacts from "./debug-artifacts";
 import {
@@ -25,8 +24,8 @@ export async function runWrapper() {
  // possible, and only use safe functions outside.

  try {
-    actionsUtil.restoreInputs();
    const logger = getActionsLogger();
+    actionsUtil.restoreInputs(logger);
    const gitHubVersion = await getGitHubVersion();
    checkGitHubVersionInRange(gitHubVersion, logger);

@@ -38,12 +37,9 @@ export async function runWrapper() {
        logger,
      );
      if (config !== undefined) {
-        const codeql = await getCodeQL(logger, config.codeQLCmd);
-        const version = await codeql.getVersion();
        await debugArtifacts.uploadCombinedSarifArtifacts(
          logger,
          config.gitHubVersion.type,
-          version.version,
        );
      }
    }
@@ -45,6 +45,7 @@ test.serial(
      requiredInputStub.withArgs("token").returns("fake-token");
      requiredInputStub.withArgs("upload-database").returns("false");
      requiredInputStub.withArgs("output").returns("out");
+      requiredInputStub.withArgs("checkout_path").returns("");
      const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
      optionalInputStub.withArgs("expect-error").returns("false");
      sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
@@ -104,6 +105,7 @@ test.serial(
      requiredInputStub.withArgs("token").returns("fake-token");
      requiredInputStub.withArgs("upload-database").returns("false");
      requiredInputStub.withArgs("output").returns("out");
+      requiredInputStub.withArgs("checkout_path").returns("");
      const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
      optionalInputStub.withArgs("expect-error").returns("false");
      sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
@@ -4,12 +4,18 @@ import { performance } from "perf_hooks";

 import * as core from "@actions/core";

-import { Action, ActionState, runInActions } from "./action-common";
+import {
+  Action,
+  ActionState,
+  extendActionState,
+  runInActions,
+} from "./action-common";
 import * as actionsUtil from "./actions-util";
 import * as analyses from "./analyses";
 import {
  CodeQLAnalysisError,
  dbIsFinalized,
+  determineCheckoutPath,
  QueriesStatusReport,
  runFinalize,
  runQueries,
@@ -212,9 +218,11 @@ async function runAutobuildIfLegacyGoWorkflow(config: Config, logger: Logger) {
  await runAutobuild(config, BuiltInLanguage.go, logger);
 }

-async function run({ startedAt, logger }: ActionState<["Base", "Logger"]>) {
+async function run(action: ActionState<["Base", "Logger", "Env", "Actions"]>) {
  // To capture errors appropriately, keep as much code within the try-catch as
  // possible, and only use safe functions outside.
+  const startedAt = action.startedAt;
+  const logger = action.logger;

  let uploadResults:
    | Partial<Record<analyses.AnalysisKind, UploadResult>>
@@ -263,17 +271,6 @@ async function run({ startedAt, logger }: ActionState<["Base", "Logger"]>) {
      );
    }

-    // Unset the CODEQL_PROXY_* environment variables when using older CodeQL
-    // CLIs, as they are not needed and can cause issues.
-    if (
-      process.env.CODEQL_PROXY_HOST === "" &&
-      !(await util.codeQlVersionAtLeast(codeql, "2.20.7"))
-    ) {
-      delete process.env.CODEQL_PROXY_HOST;
-      delete process.env.CODEQL_PROXY_PORT;
-      delete process.env.CODEQL_PROXY_CA_CERTIFICATE;
-    }
-
    if (actionsUtil.getOptionalInput("cleanup-level")) {
      logger.info(
        "The 'cleanup-level' input is ignored since the CodeQL Action now automatically " +
@@ -283,7 +280,7 @@ async function run({ startedAt, logger }: ActionState<["Base", "Logger"]>) {

    const apiDetails = getApiDetails();
    const outputDir = actionsUtil.getRequiredInput("output");
-    core.exportVariable(EnvVar.SARIF_RESULTS_OUTPUT_DIR, outputDir);
+    action.env.export(EnvVar.SARIF_RESULTS_OUTPUT_DIR, outputDir);
    const threads = util.getThreadsFlag(
      actionsUtil.getOptionalInput("threads") || process.env["CODEQL_THREADS"],
      logger,
@@ -307,8 +304,13 @@ async function run({ startedAt, logger }: ActionState<["Base", "Logger"]>) {
      logger,
    );

+    const checkoutPath = await determineCheckoutPath(action, config);
+
    // Setup diff informed analysis if needed (based on whether init created the file)
-    const diffRangePackDir = await setupDiffInformedQueryRun(logger);
+    const diffRangePackDir = await setupDiffInformedQueryRun(
+      logger,
+      checkoutPath,
+    );

    await warnIfGoInstalledAfterInit(config, logger);
    await runAutobuildIfLegacyGoWorkflow(config, logger);
@@ -354,7 +356,6 @@ async function run({ startedAt, logger }: ActionState<["Base", "Logger"]>) {
      actionsUtil.getOptionalInput("upload"),
    );
    if (runStats) {
-      const checkoutPath = actionsUtil.getRequiredInput("checkout_path");
      const category = actionsUtil.getOptionalInput("category");

      uploadResults = await postProcessAndUploadSarif(
@@ -388,18 +389,25 @@ async function run({ startedAt, logger }: ActionState<["Base", "Logger"]>) {
    // Possibly upload the overlay-base database to actions cache.
    // Note: Take care with the ordering of this call since databases may be cleaned up
    // at the `overlay` level.
-    await cleanupAndUploadOverlayBaseDatabaseToCache(codeql, config, logger);
+    await cleanupAndUploadOverlayBaseDatabaseToCache(
+      codeql,
+      config,
+      logger,
+      checkoutPath,
+    );
+
+    const actionWithFeatures = extendActionState(action, { features });

    // Possibly upload the database bundles for remote queries.
    // Note: Take care with the ordering of this call since databases may be cleaned up
    // at the `overlay` or `clear` level.
    databaseUploadResults = await cleanupAndUploadDatabases(
+      actionWithFeatures,
      repositoryNwo,
      codeql,
      config,
      apiDetails,
-      features,
-      logger,
+      checkoutPath,
    );

    // Possibly upload the TRAP caches for later re-use
@@ -443,7 +451,7 @@ async function run({ startedAt, logger }: ActionState<["Base", "Logger"]>) {
        `expect-error input was set to true but no error was thrown.`,
      );
    }
-    core.exportVariable(EnvVar.ANALYZE_DID_COMPLETE_SUCCESSFULLY, "true");
+    action.env.export(EnvVar.ANALYZE_DID_COMPLETE_SUCCESSFULLY, "true");
  } catch (unwrappedError) {
    const error = util.wrapError(unwrappedError);
    if (
@@ -7,13 +7,15 @@ import * as sinon from "sinon";
 import { CodeQuality, CodeScanning, RiskAssessment } from "./analyses";
 import {
  runQueries,
-  defaultSuites,
  resolveQuerySuiteAlias,
  addSarifExtension,
  diffRangeExtensionPackContents,
+  determineCheckoutPath,
 } from "./analyze";
 import { createStubCodeQL } from "./codeql";
+import { defaultSuites } from "./config/db-config";
 import { Feature } from "./feature-flags";
+import * as gitUtils from "./git-utils";
 import { BuiltInLanguage } from "./languages";
 import { getRunnerLogger } from "./logging";
 import {
@@ -21,12 +23,98 @@ import {
  setupActionsVars,
  createFeatures,
  createTestConfig,
+  callee,
 } from "./testing-utils";
 import * as uploadLib from "./upload-lib";
 import * as util from "./util";

 setupTests(test);

+test.serial(
+  "determineCheckoutPath - logs when checkout_path is not in a work tree",
+  async (t) => {
+    const expectedPath = path.resolve("/checkout/path");
+    const target = callee(determineCheckoutPath)
+      .withActions((actions) => {
+        sinon
+          .stub(actions, "getRequiredInput")
+          .withArgs("checkout_path")
+          .returns(expectedPath);
+      })
+      .withArgs(createTestConfig({}));
+    sinon.stub(gitUtils, "getGitRoot").resolves(undefined);
+
+    await target
+      .logs(t, "is not in the work tree of a git repository")
+      .passes(t.is, expectedPath);
+  },
+);
+
+test.serial(
+  "determineCheckoutPath - logs when checkout_path is not a repo root",
+  async (t) => {
+    const expectedPath = path.resolve("/checkout/path");
+    const target = callee(determineCheckoutPath)
+      .withActions((actions) => {
+        sinon
+          .stub(actions, "getRequiredInput")
+          .withArgs("checkout_path")
+          .returns(expectedPath);
+      })
+      .withArgs(createTestConfig({}));
+    sinon.stub(gitUtils, "getGitRoot").resolves("/checkout");
+
+    await target
+      .logs(t, "is not the root of the repository")
+      .passes(t.is, expectedPath);
+  },
+);
+
+test.serial(
+  "determineCheckoutPath - logs when checkout_path is not the same as repo root in config",
+  async (t) => {
+    const expectedPath = path.resolve("/checkout/path");
+    const target = callee(determineCheckoutPath)
+      .withActions((actions) => {
+        sinon
+          .stub(actions, "getRequiredInput")
+          .withArgs("checkout_path")
+          .returns(expectedPath);
+      })
+      .withArgs(createTestConfig({ repositoryRoot: "/some/other/path" }));
+    sinon.stub(gitUtils, "getGitRoot").resolves(expectedPath);
+
+    await target
+      .logs(t, "does not match that found by the 'codeql-action/init' step")
+      .passes(t.is, expectedPath);
+  },
+);
+
+test.serial(
+  "determineCheckoutPath - doesn't log any of the messages when all is as expected",
+  async (t) => {
+    const expectedPath = path.resolve("/checkout/path");
+    const target = callee(determineCheckoutPath)
+      .withActions((actions) => {
+        sinon
+          .stub(actions, "getRequiredInput")
+          .withArgs("checkout_path")
+          .returns(expectedPath);
+      })
+      .withArgs(createTestConfig({ repositoryRoot: expectedPath }));
+    sinon.stub(gitUtils, "getGitRoot").resolves(expectedPath);
+
+    await target
+      .notLogs(
+        t,
+        "is not in the work tree of a git repository",
+        "is not the root of the repository",
+        "does not match that found by the 'codeql-action/init' step",
+      )
+      .passes(t.is, expectedPath);
+  },
+);
+
 /**
 * Checks the status report produced by the analyze Action.
 *
@@ -5,10 +5,13 @@ import { performance } from "perf_hooks";
 import * as io from "@actions/io";
 import * as yaml from "js-yaml";

-import { getTemporaryDirectory, getRequiredInput } from "./actions-util";
+import type { ActionState } from "./action-common";
+import { getTemporaryDirectory } from "./actions-util";
 import * as analyses from "./analyses";
 import { setupCppAutobuild } from "./autobuild";
 import { type CodeQL } from "./codeql";
+import type { ActionConfig } from "./config/action-config";
+import { defaultSuites } from "./config/db-config";
 import * as configUtils from "./config-utils";
 import {
  getCsharpTempDependencyDir,
@@ -21,6 +24,7 @@ import {
 } from "./diff-informed-analysis-utils";
 import { EnvVar } from "./environment";
 import { FeatureEnablement, Feature } from "./feature-flags";
+import { getGitRoot } from "./git-utils";
 import { BuiltInLanguage, Language } from "./languages";
 import { Logger, withGroupAsync } from "./logging";
 import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
@@ -85,6 +89,58 @@ export interface QueriesStatusReport
  event_reports?: EventReport[];
 }

+/**
+ * Determines the path at which the repository being analysed is checked out at.
+ * Returns the value of the required `checkout_path` input and validates that it
+ * refers to the root of a repository.
+ *
+ * @param action The action state.
+ * @param config The CodeQL Action configuration state.
+ */
+export async function determineCheckoutPath(
+  action: ActionState<["Logger", "Actions"]>,
+  config: configUtils.Config,
+) {
+  const checkoutPathInput = action.actions.getRequiredInput("checkout_path");
+
+  // Try to obtain the root path of the repository and validate that it matches the input.
+  const absCheckoutPathInput = path.resolve(checkoutPathInput);
+  const repositoryRoot = await getGitRoot(absCheckoutPathInput);
+
+  if (repositoryRoot === undefined) {
+    action.logger.warning(
+      [
+        `The directory at '${absCheckoutPathInput}' is not in the work tree of a git repository.`,
+        "If the repository being analyzed is checked out elsewhere,",
+        "you must explicitly set the 'checkout_path' input for the 'codeql-action/analyze' step to",
+        "the checkout path.",
+      ].join(" "),
+    );
+  } else if (repositoryRoot !== absCheckoutPathInput) {
+    action.logger.warning(
+      [
+        `The directory at '${absCheckoutPathInput}' is not the root of the repository ('${repositoryRoot}').`,
+        "Set the 'checkout_path' input for the 'codeql-action/analyze' step to the root path of the checkout.",
+      ].join(" "),
+    );
+  } else if (
+    config.repositoryRoot !== undefined &&
+    repositoryRoot !== config.repositoryRoot
+  ) {
+    // The repository root that was persisted by the `init` step doesn't match the one we have found here.
+    action.logger.warning(
+      [
+        `The repository path at '${repositoryRoot}' does not match that found by the 'codeql-action/init' step: '${config.repositoryRoot}'.`,
+        "Ensure that the 'checkout_path' input for the 'codeql-action/analyze' step is set to the path of the same repository that",
+        "the 'codeql-action/init' step determined. This is either the GitHub Actions workspace or the repository root corresponding to",
+        "the 'source-root' input if that was provided.",
+      ].join(" "),
+    );
+  }
+
+  return absCheckoutPathInput;
+}
+
 async function setupPythonExtractor(logger: Logger) {
  const codeqlPython = process.env["CODEQL_PYTHON"];
  if (codeqlPython === undefined || codeqlPython.length === 0) {
@@ -123,7 +179,7 @@ export async function runExtraction(
          language === BuiltInLanguage.cpp &&
          config.buildMode === BuildMode.Autobuild
        ) {
-          await setupCppAutobuild(codeql, logger);
+          await setupCppAutobuild(logger);
        }

        // The Java and C# `build-mode: none` extractors place dependencies in the
@@ -170,7 +226,7 @@ async function shouldExtractLanguage(
 }

 export function dbIsFinalized(
-  config: configUtils.Config,
+  config: ActionConfig<"dbLocation">,
  language: Language,
  logger: Logger,
 ) {
@@ -233,6 +289,7 @@ async function finalizeDatabaseCreation(
 */
 export async function setupDiffInformedQueryRun(
  logger: Logger,
+  checkoutPath: string,
 ): Promise<string | undefined> {
  return await withGroupAsync(
    "Generating diff range extension pack",
@@ -245,7 +302,6 @@ export async function setupDiffInformedQueryRun(
        return undefined;
      }

-      const checkoutPath = getRequiredInput("checkout_path");
      const packDir = writeDiffRangeDataExtensionPack(
        logger,
        diffRanges,
@@ -357,15 +413,6 @@ dataExtensions:
  return diffRangeDir;
 }

-// A set of default query suite names that are understood by the CLI.
-export const defaultSuites: Set<string> = new Set([
-  "security-experimental",
-  "security-extended",
-  "security-and-quality",
-  "code-quality",
-  "code-scanning",
-]);
-
 /**
 * If `maybeSuite` is the name of a default query suite, it is resolved into the corresponding
 * query suite name for the given `language`. Otherwise, `maybeSuite` is returned as is.
@@ -8,7 +8,14 @@ import * as actionsUtil from "./actions-util";
 import * as api from "./api-client";
 import { DO_NOT_RETRY_STATUSES } from "./api-client";
 import { ActionsEnvVars, RegistryProxyVars } from "./environment";
-import { callee, getTestEnv, setupTests } from "./testing-utils";
+import { GITHUB_DOTCOM_API_URL, GITHUB_DOTCOM_URL } from "./github";
+import {
+  callee,
+  getTestEnv,
+  RecordingLogger,
+  SAMPLE_DOTCOM_API_DETAILS,
+  setupTests,
+} from "./testing-utils";
 import * as util from "./util";

 setupTests(test);
@@ -111,103 +118,115 @@ test.serial("getGitHubVersion for GHEC-DR", async (t) => {
  t.deepEqual({ type: util.GitHubVariant.GHEC_DR }, gheDotcom);
 });

-test.serial(
-  "wrapApiConfigurationError correctly wraps specific configuration errors",
-  (t) => {
+test("wrapApiConfigurationError doesn't wrap errors it isn't supposed to", (t) => {
+  const unwrappedErrors = [
    // We don't reclassify arbitrary errors
-    const arbitraryError = new Error("arbitrary error");
-    let res = api.wrapApiConfigurationError(arbitraryError);
-    t.is(res, arbitraryError);
+    new Error("arbitrary error"),
+    // Same goes for arbitrary strings
+    "arbitrary error",
+    // If an HTTP error doesn't contain a specific error message, we don't wrap it.
+    new util.HTTPError("arbitrary HTTP error", 456),
+  ];

-    // Same goes for arbitrary errors
-    const configError = new util.ConfigurationError("arbitrary error");
-    res = api.wrapApiConfigurationError(configError);
-    t.is(res, configError);
-
-    // If an HTTP error doesn't contain a specific error message, we don't
-    // wrap is an an API error.
-    const httpError = new util.HTTPError("arbitrary HTTP error", 456);
-    res = api.wrapApiConfigurationError(httpError);
-    t.is(res, httpError);
-
-    // For other HTTP errors, we wrap them as Configuration errors if they contain
-    // specific error messages.
-    const httpNotFoundError = new util.HTTPError("commit not found", 404);
-    res = api.wrapApiConfigurationError(httpNotFoundError);
-    t.deepEqual(res, new util.ConfigurationError("commit not found"));
-
-    const refNotFoundError = new util.HTTPError(
-      "ref 'refs/heads/jitsi' not found in this repository - https://docs.github.com/rest",
-      404,
-    );
-    res = api.wrapApiConfigurationError(refNotFoundError);
-    t.deepEqual(
+  for (const unwrappedError of unwrappedErrors) {
+    const res = api.wrapApiConfigurationError(unwrappedError);
+    t.is(
      res,
-      new util.ConfigurationError(
-        "ref 'refs/heads/jitsi' not found in this repository - https://docs.github.com/rest",
-      ),
+      unwrappedError,
+      `${util.getErrorMessage(unwrappedError)} should not be wrapped by wrapApiConfigurationError`,
    );
+  }
+});

-    const apiRateLimitError = new util.HTTPError(
-      "API rate limit exceeded for installation",
-      403,
-    );
-    res = api.wrapApiConfigurationError(apiRateLimitError);
-    t.deepEqual(
-      res,
-      new util.ConfigurationError("API rate limit exceeded for installation"),
-    );
+test("wrapApiConfigurationError correctly wraps specific configuration errors", (t) => {
+  // For other HTTP errors, we wrap them as Configuration errors if they contain
+  // specific error messages.
+  const httpNotFoundError = new util.HTTPError("commit not found", 404);
+  const refNotFoundError = new util.HTTPError(
+    "ref 'refs/heads/jitsi' not found in this repository - https://docs.github.com/rest",
+    404,
+  );
+  const apiRateLimitError = new util.HTTPError(
+    "API rate limit exceeded for installation",
+    403,
+  );
+  const resourceNotAccessibleError = new util.HTTPError(
+    "Resource not accessible by integration",
+    403,
+  );
+  const errorsToWrap = [
+    httpNotFoundError,
+    refNotFoundError,
+    apiRateLimitError,
+    resourceNotAccessibleError,
+  ];

-    const tokenSuggestionMessage =
-      "Please check that your token is valid and has the required permissions: contents: read, security-events: write";
-    const badCredentialsError = new util.HTTPError("Bad credentials", 401);
-    res = api.wrapApiConfigurationError(badCredentialsError);
+  for (const errorToWrap of errorsToWrap) {
+    const res = api.wrapApiConfigurationError(errorToWrap);
+    t.deepEqual(res, new util.ConfigurationError(errorToWrap.message));
+  }
+});
+
+test("wrapApiConfigurationError wraps token errors", async (t) => {
+  const tokenSuggestionMessage =
+    "Please check that your token is valid and has the required permissions: contents: read, security-events: write";
+  const badCredentialsError = new util.HTTPError("Bad credentials", 401);
+  const notFoundError = new util.HTTPError("Not Found", 404);
+  const errorsToWrap = [badCredentialsError, notFoundError];
+
+  for (const errorToWrap of errorsToWrap) {
+    const res = api.wrapApiConfigurationError(errorToWrap);
    t.deepEqual(res, new util.ConfigurationError(tokenSuggestionMessage));
+  }
+});

-    const notFoundError = new util.HTTPError("Not Found", 404);
-    res = api.wrapApiConfigurationError(notFoundError);
-    t.deepEqual(res, new util.ConfigurationError(tokenSuggestionMessage));
+test("wrapApiConfigurationError wraps enablement errors", async (t) => {
+  // Enablement errors.
+  const enablementErrorMessages = [
+    "Code Security must be enabled for this repository to use code scanning",
+    "Advanced Security must be enabled for this repository to use code scanning",
+    "Code Scanning is not enabled for this repository. Please enable code scanning in the repository settings.",
+    "Code quality is not enabled for this repository. Please enable code quality in the repository settings.",
+  ];
+  const transforms = [
+    (msg: string) => msg,
+    (msg: string) => msg.toLowerCase(),
+    (msg: string) => msg.toLocaleUpperCase(),
+  ];

-    const resourceNotAccessibleError = new util.HTTPError(
-      "Resource not accessible by integration",
-      403,
-    );
-    res = api.wrapApiConfigurationError(resourceNotAccessibleError);
-    t.deepEqual(
-      res,
-      new util.ConfigurationError("Resource not accessible by integration"),
-    );
-
-    // Enablement errors.
-    const enablementErrorMessages = [
-      "Code Security must be enabled for this repository to use code scanning",
-      "Advanced Security must be enabled for this repository to use code scanning",
-      "Code Scanning is not enabled for this repository. Please enable code scanning in the repository settings.",
-      "Code quality is not enabled for this repository. Please enable code quality in the repository settings.",
-    ];
-    const transforms = [
-      (msg: string) => msg,
-      (msg: string) => msg.toLowerCase(),
-      (msg: string) => msg.toLocaleUpperCase(),
-    ];
-
-    for (const enablementErrorMessage of enablementErrorMessages) {
-      for (const transform of transforms) {
-        const enablementError = new util.HTTPError(
-          transform(enablementErrorMessage),
-          403,
-        );
-        res = api.wrapApiConfigurationError(enablementError);
-        t.deepEqual(
-          res,
-          new util.ConfigurationError(
-            api.getFeatureEnablementError(enablementError.message),
-          ),
-        );
-      }
+  for (const enablementErrorMessage of enablementErrorMessages) {
+    for (const transform of transforms) {
+      const enablementError = new util.HTTPError(
+        transform(enablementErrorMessage),
+        403,
+      );
+      const res = api.wrapApiConfigurationError(enablementError);
+      t.deepEqual(
+        res,
+        new util.ConfigurationError(
+          api.getFeatureEnablementError(enablementError.message),
+        ),
+      );
    }
-  },
-);
+  }
+});
+
+test("wrapApiConfigurationError doesn't double-wrap errors", async (t) => {
+  // This test checks that errors don't get wrapped a second time if `wrapApiConfigurationError`
+  // is called on an error that was already wrapped by a previous call to `wrapApiConfigurationError`.
+  // Start by calling `wrapApiConfigurationError` on an unwrapped error that should be wrapped:
+  const unwrappedError = new util.HTTPError("commit not found", 404);
+  const wrappedError = api.wrapApiConfigurationError(unwrappedError);
+
+  // Sanity-check that it was wrapped, as expected.
+  t.deepEqual(
+    wrappedError,
+    new util.ConfigurationError(unwrappedError.message),
+  );
+
+  // The result of the second call should be exactly `wrappedError`:
+  t.is(api.wrapApiConfigurationError(wrappedError), wrappedError);
+});

 test("getRegistryProxy - returns undefined if the proxy is not configured", async (t) => {
  const target = callee(api.getRegistryProxy).withArgs();
@@ -272,3 +291,62 @@ test("makeProxyRequestOptions - returns fetch with custom proxy", async (t) => {
    githubUtils.defaults.request,
  );
 });
+
+test.serial(
+  "getApiClientWithExternalAuth constructs clients with or without tokens",
+  (t) => {
+    t.notThrows(() => {
+      api.getApiClientWithExternalAuth(SAMPLE_DOTCOM_API_DETAILS);
+      api.getApiClientWithExternalAuth({
+        ...SAMPLE_DOTCOM_API_DETAILS,
+        auth: undefined,
+      });
+    });
+  },
+);
+
+test("getAuthorizationHeaderFor - returns undefined if there's no token", (t) => {
+  const logger = new RecordingLogger();
+
+  for (const authValue of [undefined, "", "    "]) {
+    const client = new api.InstanceApiClient({
+      ...SAMPLE_DOTCOM_API_DETAILS,
+      auth: authValue,
+    });
+    t.is(
+      client.getAuthorizationHeaderFor(logger, `${GITHUB_DOTCOM_URL}/github`),
+      undefined,
+    );
+  }
+});
+
+test("getAuthorizationHeaderFor - returns header value with token if url is allowed", (t) => {
+  const logger = new RecordingLogger();
+  const client = new api.InstanceApiClient({
+    ...SAMPLE_DOTCOM_API_DETAILS,
+  });
+
+  for (const url of [
+    `${GITHUB_DOTCOM_URL}/github`,
+    `${GITHUB_DOTCOM_API_URL}/github`,
+  ]) {
+    t.is(
+      client.getAuthorizationHeaderFor(logger, url),
+      `token ${SAMPLE_DOTCOM_API_DETAILS.auth}`,
+    );
+  }
+});
+
+test("getAuthorizationHeaderFor - returns undefined if url is not allowed", (t) => {
+  const logger = new RecordingLogger();
+  const client = new api.InstanceApiClient({
+    ...SAMPLE_DOTCOM_API_DETAILS,
+  });
+
+  for (const url of [
+    `https://localhost/github`,
+    `https://api.localhost/github`,
+  ]) {
+    t.is(client.getAuthorizationHeaderFor(logger, url), undefined);
+  }
+});
@@ -1,5 +1,6 @@
 import * as core from "@actions/core";
 import * as githubUtils from "@actions/github/lib/utils";
+import type { OctokitOptions } from "@octokit/core";
 import * as retry from "@octokit/plugin-retry";
 import { RequestRequestOptions } from "@octokit/types";
 import {
@@ -12,25 +13,34 @@ import {
 import type { ActionState } from "./action-common";
 import { getActionVersion, getRequiredInput } from "./actions-util";
 import {
-  ActionsEnvVars,
  EnvVar,
  ReadOnlyEnv,
  RegistryProxyVars,
  getEnv,
+  exportEnvVar,
+  ActionsEnvVars,
 } from "./environment";
+import {
+  getCurrentInstance,
+  getDotcomInstance,
+  GITHUB_DOTCOM_URL,
+  parseGitHubUrl,
+  type GitHubApiCombinedDetails,
+  type GitHubApiDetails,
+} from "./github";
 import { Logger } from "./logging";
 import { getRepositoryNwo, RepositoryNwo } from "./repository";
 import {
  asHTTPError,
  ConfigurationError,
  getRequiredEnvParam,
-  GITHUB_DOTCOM_URL,
  GitHubVariant,
  GitHubVersion,
-  parseGitHubUrl,
  parseMatrixInput,
 } from "./util";

+export type { GitHubApiDetails, GitHubApiCombinedDetails } from "./github";
+
 const GITHUB_ENTERPRISE_VERSION_HEADER = "x-github-enterprise-version";

 /**
@@ -42,21 +52,6 @@ const GITHUB_ENTERPRISE_VERSION_HEADER = "x-github-enterprise-version";
 */
 export const DO_NOT_RETRY_STATUSES = [400, 410, 422, 451];

-export type GitHubApiCombinedDetails = GitHubApiDetails &
-  GitHubApiExternalRepoDetails;
-
-export interface GitHubApiDetails {
-  auth: string;
-  url: string;
-  apiURL: string | undefined;
-}
-
-export interface GitHubApiExternalRepoDetails {
-  externalRepoAuth?: string;
-  url: string;
-  apiURL: string | undefined;
-}
-
 /**
 * Gets the configuration for the private registry authentication proxy,
 * if it is available in the environment.
@@ -127,6 +122,61 @@ export function makeProxyRequestOptions(
 /** The type of GitHub API client we use. */
 export type ApiClient = InstanceType<typeof githubUtils.GitHub>;

+/**
+ * Encapsulates a {@link GitHubApiCombinedDetails} along with operations which ensure that any credentials
+ * are only used with the GitHub instance that is represented by the {@link GitHubApiCombinedDetails} value.
+ */
+export class InstanceApiClient {
+  private readonly client: ApiClient;
+  private readonly apiDetails: GitHubApiCombinedDetails;
+  private readonly authorizationHeader: string | undefined;
+
+  constructor(
+    apiDetails: GitHubApiCombinedDetails,
+    clientOptions: CreateApiClientOptions = {},
+  ) {
+    this.apiDetails = apiDetails;
+    this.client = createApiClientWithDetails(apiDetails, clientOptions);
+
+    // Compute the Authorization header value if we have a token.
+    const token = this.apiDetails.auth?.trim();
+    if (token !== undefined && token !== "") {
+      this.authorizationHeader = `token ${token}`;
+    }
+  }
+
+  /**
+   * Gets a value for the `Authorization` header for a request to `url`; or `undefined` if the
+   * `Authorization` header should not be set for `url`.
+   *
+   * @param logger The logger to use for debugging messages.
+   * @param url The URL for which we want to add an `Authorization` header.
+   */
+  public getAuthorizationHeaderFor(
+    logger: Logger,
+    url: string,
+  ): string | undefined {
+    // We don't have to check the `url` if we don't have a token to begin with.
+    if (this.authorizationHeader === undefined) {
+      return undefined;
+    }
+
+    // We only want to provide an authorization header if we are downloading
+    // from the same GitHub instance the Action is running on.
+    // This avoids leaking Enterprise tokens to dotcom.
+    if (
+      url.startsWith(`${this.apiDetails.url}/`) ||
+      (this.apiDetails.apiURL && url.startsWith(`${this.apiDetails.apiURL}/`))
+    ) {
+      logger.debug(`Providing an authorization token.`);
+      return this.authorizationHeader;
+    }
+
+    logger.debug(`Not using an authorization token.`);
+    return undefined;
+  }
+}
+
 /** Options for `createApiClientWithDetails`. */
 interface CreateApiClientOptions {
  allowExternal?: boolean;
@@ -138,37 +188,82 @@ function createApiClientWithDetails(
  { allowExternal = false, proxy = undefined }: CreateApiClientOptions = {},
 ): ApiClient {
  const auth =
-    (allowExternal && apiDetails.externalRepoAuth) || apiDetails.auth;
+    allowExternal && apiDetails.externalRepoAuth !== undefined
+      ? apiDetails.externalRepoAuth
+      : apiDetails.auth;
  const retryingOctokit = githubUtils.GitHub.plugin(retry.retry);
  const requestOptions = makeProxyRequestOptions(proxy);
-  return new retryingOctokit(
-    githubUtils.getOctokitOptions(auth, {
-      baseUrl: apiDetails.apiURL,
-      userAgent: `CodeQL-Action/${getActionVersion()}`,
-      log: {
-        debug: core.debug,
-        info: core.info,
-        warn: core.warning,
-        error: core.error,
-      },
-      request: requestOptions,
-      retry: {
-        doNotRetry: DO_NOT_RETRY_STATUSES,
-      },
-    }),
-  );
+
+  const opts: OctokitOptions = {
+    auth:
+      auth !== undefined && auth.trim() !== "" ? `token ${auth}` : undefined,
+    baseUrl: apiDetails.apiURL,
+    userAgent: `CodeQL-Action/${getActionVersion()}`,
+    log: {
+      debug: core.debug,
+      info: core.info,
+      warn: core.warning,
+      error: core.error,
+    },
+    request: requestOptions,
+    retry: {
+      doNotRetry: DO_NOT_RETRY_STATUSES,
+    },
+  };
+
+  return new retryingOctokit(opts);
 }

+/**
+ * Gets a `GitHubApiDetails` object describing the GitHub instance we are currently running on.
+ *
+ * @param env The environment variables to read.
+ */
 export function getApiDetails(env: ReadOnlyEnv = getEnv()): GitHubApiDetails {
  return {
    auth: getRequiredInput("token"),
-    url: env.getRequired(ActionsEnvVars.GITHUB_SERVER_URL),
-    apiURL: env.getRequired(ActionsEnvVars.GITHUB_API_URL),
+    ...getCurrentInstance(env),
  };
 }

-export function getApiClient(env: ReadOnlyEnv = getEnv()) {
-  return createApiClientWithDetails(getApiDetails(env));
+/**
+ * Constructs an {@link ApiClient} using {@link apiDetails}.
+ *
+ * If {@link apiDetails} is not specified, then the GitHub instance URLs and auth token
+ * are taken from {@link env}.
+ *
+ * If {@link env} is not specified, then the process environment is used.
+ *
+ * @param env The environment to obtain the GitHub instance URLs from.
+ * @param apiDetails The {@link GitHubApiDetails} to construct the {@link ApiClient} for.
+ */
+export function getApiClient(
+  env: ReadOnlyEnv = getEnv(),
+  apiDetails?: GitHubApiDetails,
+) {
+  return createApiClientWithDetails(apiDetails ?? getApiDetails(env));
+}
+
+/*
+ * Gets a `GitHubApiDetails` object describing the GitHub Dotcom instance.
+ *
+ * @param env The environment variables to read.
+ */
+export function getDotcomApiDetails(env: ReadOnlyEnv): GitHubApiDetails {
+  // If we are currently running on dotcom, then just call `getApiDetails` which will
+  // construct the appropriate `GitHubApiDetails` from the environment and include the
+  // value of the `token` input. The `token` input relates to the GitHub instance that
+  // we are running on only. Therefore, if we are not currently running on dotcom,
+  // then we construct `GitHubApiDetails` without the `token` value and using the
+  // hard-coded instance and API URLs.
+  if (env.getRequired(ActionsEnvVars.GITHUB_SERVER_URL) === GITHUB_DOTCOM_URL) {
+    return getApiDetails(env);
+  } else {
+    return {
+      auth: undefined,
+      ...getDotcomInstance(),
+    };
+  }
 }

 export function getApiClientWithExternalAuth(
@@ -178,36 +273,6 @@ export function getApiClientWithExternalAuth(
  return createApiClientWithDetails(apiDetails, { allowExternal: true, proxy });
 }

-/**
- * Gets a value for the `Authorization` header for a request to `url`; or `undefined` if the
- * `Authorization` header should not be set for `url`.
- *
- * @param logger The logger to use for debugging messages.
- * @param apiDetails Details of the GitHub API we are using.
- * @param url The URL for which we want to add an `Authorization` header.
- *
- * @returns The value for the `Authorization` header or `undefined` if it shouldn't be populated.
- */
-export function getAuthorizationHeaderFor(
-  logger: Logger,
-  apiDetails: GitHubApiDetails,
-  url: string,
-): string | undefined {
-  // We only want to provide an authorization header if we are downloading
-  // from the same GitHub instance the Action is running on.
-  // This avoids leaking Enterprise tokens to dotcom.
-  if (
-    url.startsWith(`${apiDetails.url}/`) ||
-    (apiDetails.apiURL && url.startsWith(`${apiDetails.apiURL}/`))
-  ) {
-    logger.debug(`Providing an authorization token.`);
-    return `token ${apiDetails.auth}`;
-  }
-
-  logger.debug(`Not using an authorization token.`);
-  return undefined;
-}
-
 let cachedGitHubVersion: GitHubVersion | undefined = undefined;

 export async function getGitHubVersionFromApi(
@@ -219,25 +284,31 @@ export async function getGitHubVersionFromApi(
    return { type: GitHubVariant.DOTCOM };
  }

-  // Doesn't strictly have to be the meta endpoint as we're only
-  // using the response headers which are available on every request.
-  //
-  // See https://docs.github.com/en/rest/meta/meta#get-github-meta-information.
-  // eslint-disable-next-line @typescript-eslint/no-unsafe-call
-  const response = await apiClient.rest.meta.get();
+  try {
+    // Doesn't strictly have to be the meta endpoint as we're only
+    // using the response headers which are available on every request.
+    //
+    // See https://docs.github.com/en/rest/meta/meta#get-github-meta-information.
+    // eslint-disable-next-line @typescript-eslint/no-unsafe-call
+    const response = await apiClient.rest.meta.get();

-  // This happens on dotcom, although we expect to have already returned in that
-  // case. This can also serve as a fallback in cases we haven't foreseen.
-  if (response.headers[GITHUB_ENTERPRISE_VERSION_HEADER] === undefined) {
-    return { type: GitHubVariant.DOTCOM };
+    // This happens on dotcom, although we expect to have already returned in that
+    // case. This can also serve as a fallback in cases we haven't foreseen.
+    if (response.headers[GITHUB_ENTERPRISE_VERSION_HEADER] === undefined) {
+      return { type: GitHubVariant.DOTCOM };
+    }
+
+    if (response.headers[GITHUB_ENTERPRISE_VERSION_HEADER] === "ghe.com") {
+      return { type: GitHubVariant.GHEC_DR };
+    }
+
+    const version = response.headers[
+      GITHUB_ENTERPRISE_VERSION_HEADER
+    ] as string;
+    return { type: GitHubVariant.GHES, version };
+  } catch (err) {
+    throw wrapApiConfigurationError(err);
  }
-
-  if (response.headers[GITHUB_ENTERPRISE_VERSION_HEADER] === "ghe.com") {
-    return { type: GitHubVariant.GHEC_DR };
-  }
-
-  const version = response.headers[GITHUB_ENTERPRISE_VERSION_HEADER] as string;
-  return { type: GitHubVariant.GHES, version };
 }

 /**
@@ -249,9 +320,10 @@ export async function getGitHubVersionFromApi(
 */
 export async function getGitHubVersion(): Promise<GitHubVersion> {
  if (cachedGitHubVersion === undefined) {
+    const apiDetails = getApiDetails();
    cachedGitHubVersion = await getGitHubVersionFromApi(
-      getApiClient(),
-      getApiDetails(),
+      createApiClientWithDetails(apiDetails),
+      apiDetails,
    );
  }
  return cachedGitHubVersion;
@@ -309,7 +381,7 @@ export async function getAnalysisKey(): Promise<string> {
  const jobName = getRequiredEnvParam("GITHUB_JOB");

  analysisKey = `${workflowPath}:${jobName}`;
-  core.exportVariable(EnvVar.ANALYSIS_KEY, analysisKey);
+  exportEnvVar(EnvVar.ANALYSIS_KEY, analysisKey);
  return analysisKey;
 }

@@ -414,7 +486,14 @@ export function getFeatureEnablementError(message: string): string {
  return `Please verify that the necessary features are enabled: ${message}`;
 }

-export function wrapApiConfigurationError(e: unknown) {
+/**
+ * Decides whether `e` is a known error returned by the GitHub API that we should
+ * classify as a `ConfigurationError`.
+ *
+ * @param e The error to classify.
+ * @returns Either `e` or a corresponding `ConfigurationError`.
+ */
+export function wrapApiConfigurationError<T>(e: T): T | ConfigurationError {
  const httpError = asHTTPError(e);
  if (httpError !== undefined) {
    if (
@@ -1 +1 @@
-{"maximumVersion":"3.23","minimumVersion":"3.17"}
+{"maximumVersion":"3.23","minimumVersion":"3.18"}
@@ -68,7 +68,11 @@ async function sendCompletedStatusReport(
  }
 }

-async function run({ startedAt, logger }: ActionState<["Base", "Logger"]>) {
+async function run({
+  startedAt,
+  env,
+  logger,
+}: ActionState<["Base", "Env", "Logger"]>) {
  // To capture errors appropriately, keep as much code within the try-catch as
  // possible, and only use safe functions outside.

@@ -135,7 +139,7 @@ async function run({ startedAt, logger }: ActionState<["Base", "Logger"]>) {
    return;
  }

-  core.exportVariable(EnvVar.AUTOBUILD_DID_COMPLETE_SUCCESSFULLY, "true");
+  env.export(EnvVar.AUTOBUILD_DID_COMPLETE_SUCCESSFULLY, "true");

  await sendCompletedStatusReport(config, logger, startedAt, languages ?? []);
 }
@@ -1,11 +1,9 @@
-import * as core from "@actions/core";
-
 import { getTemporaryDirectory, getWorkflowEventName } from "./actions-util";
 import { getGitHubVersion } from "./api-client";
 import { CodeQL, getCodeQL } from "./codeql";
 import * as configUtils from "./config-utils";
 import { DocUrl } from "./doc-url";
-import { ActionsEnvVars, EnvVar } from "./environment";
+import { ActionsEnvVars, EnvVar, exportEnvVar } from "./environment";
 import { Feature, featureConfig, initFeatures } from "./feature-flags";
 import { BuiltInLanguage, Language } from "./languages";
 import { Logger } from "./logging";
@@ -112,7 +110,7 @@ export async function determineAutobuildLanguages(
  return languages;
 }

-export async function setupCppAutobuild(codeql: CodeQL, logger: Logger) {
+export async function setupCppAutobuild(logger: Logger) {
  const envVar = featureConfig[Feature.CppDependencyInstallation].envVar;
  const featureName = "C++ automatic installation of dependencies";
  const gitHubVersion = await getGitHubVersion();
@@ -123,7 +121,7 @@ export async function setupCppAutobuild(codeql: CodeQL, logger: Logger) {
    getTemporaryDirectory(),
    logger,
  );
-  if (await features.getValue(Feature.CppDependencyInstallation, codeql)) {
+  if (await features.getValue(Feature.CppDependencyInstallation)) {
    // disable autoinstall on self-hosted runners unless explicitly requested
    if (
      process.env[ActionsEnvVars.RUNNER_ENVIRONMENT] === "self-hosted" &&
@@ -136,16 +134,16 @@ export async function setupCppAutobuild(codeql: CodeQL, logger: Logger) {
            : ""
        }`,
      );
-      core.exportVariable(envVar, "false");
+      exportEnvVar(envVar, "false");
    } else {
      logger.info(
        `Enabling ${featureName}. This can be disabled by setting the ${envVar} environment variable to 'false'. See ${DocUrl.DEFINE_ENV_VARIABLES} for more information.`,
      );
-      core.exportVariable(envVar, "true");
+      exportEnvVar(envVar, "true");
    }
  } else {
    logger.info(`Disabling ${featureName}.`);
-    core.exportVariable(envVar, "false");
+    exportEnvVar(envVar, "false");
  }
 }

@@ -157,7 +155,7 @@ export async function runAutobuild(
  logger.startGroup(`Attempting to automatically build ${language} code`);
  const codeQL = await getCodeQL(logger, config.codeQLCmd);
  if (language === BuiltInLanguage.cpp) {
-    await setupCppAutobuild(codeQL, logger);
+    await setupCppAutobuild(logger);
  }
  if (config.buildMode) {
    await codeQL.extractUsingBuildMode(config, language);
@@ -165,7 +163,7 @@ export async function runAutobuild(
    await codeQL.runAutobuild(config, language);
  }
  if (language === BuiltInLanguage.go) {
-    core.exportVariable(EnvVar.DID_AUTOBUILD_GOLANG, "true");
+    exportEnvVar(EnvVar.DID_AUTOBUILD_GOLANG, "true");
  }
  logger.endGroup();
 }
@@ -1,7 +1,26 @@
 import test from "ava";

-import { getCodeQLBundleFromUrl } from "./codeql-bundle";
+import { getCodeQLBundleFromUrl, getCodeQLBundleName } from "./codeql-bundle";
 import { BuiltInLanguage } from "./languages";
+import { BundlePlatform } from "./platform";
+
+test("getCodeQLBundleName returns a per-language bundle name only when a language is specified", (t) => {
+  t.is(
+    getCodeQLBundleName("zstd", BundlePlatform.Linux64, BuiltInLanguage.java),
+    "codeql-bundle-java-linux64.tar.zst",
+  );
+  t.is(
+    getCodeQLBundleName("zstd", BundlePlatform.Linux64),
+    "codeql-bundle-linux64.tar.zst",
+  );
+});
+
+test("getCodeQLBundleName names the Swift bundle for macOS", (t) => {
+  t.is(
+    getCodeQLBundleName("zstd", BundlePlatform.Osx64, BuiltInLanguage.swift),
+    "codeql-bundle-swift-osx64.tar.zst",
+  );
+});

 for (const [assetName, language] of [
  ["codeql-bundle-java-linux64.tar.zst", BuiltInLanguage.java],
@@ -1,4 +1,7 @@
+import type { GitHubApiDetails } from "./github";
 import { BuiltInLanguage, parseBuiltInLanguage } from "./languages";
+import { BundlePlatform } from "./platform";
+import type { CompressionMethod } from "./tar";

 /** Describes the contents and location of a downloadable CodeQL bundle. */
 export type CodeQLBundle =
@@ -11,6 +14,44 @@ export type CodeQLBundle =
      combinedBundleURL?: string;
    };

+/** A resolved download, including its bundle identity and version. */
+export interface CodeQLDownloadSource {
+  /** Distinguishes downloads from local archives and cached installations. */
+  sourceType: "download";
+  /** Information about the GitHub instance that contains the asset. */
+  apiDetails: GitHubApiDetails;
+  /** The bundle to download. */
+  bundle: CodeQLBundle;
+  /** The compression format of the bundle archive. */
+  compressionMethod: CompressionMethod;
+  /** Bundle version of the tools, if known. */
+  bundleVersion?: string;
+  /** Requested CLI version, if known. */
+  cliVersion?: string;
+  /** Resolved version for telemetry, independent of whether the bundle can be cached. */
+  toolsVersion: string;
+}
+
+/** Returns the exact bundle asset name for a platform and optional language. */
+export function getCodeQLBundleName(
+  compressionMethod: CompressionMethod,
+  platform: BundlePlatform | undefined,
+  language?: BuiltInLanguage,
+): string {
+  const extensions: Record<CompressionMethod, string> = {
+    gzip: ".tar.gz",
+    zstd: ".tar.zst",
+  };
+  const extension = extensions[compressionMethod];
+  if (platform === undefined) {
+    return `codeql-bundle${extension}`;
+  }
+  if (language !== undefined) {
+    return `codeql-bundle-${language}-${platform}${extension}`;
+  }
+  return `codeql-bundle-${platform}${extension}`;
+}
+
 const PER_LANGUAGE_BUNDLE_NAME =
  /^codeql-bundle-(.+)-(?:linux64|osx64|win64)\.tar\.(?:gz|zst)$/;

@@ -34,6 +34,7 @@ import {
  makeVersionInfo,
  createTestConfig,
  makeMacro,
+  mockApiDetails,
 } from "./testing-utils";
 import { ToolsDownloadStatusReport } from "./tools-download";
 import * as util from "./util";
@@ -99,6 +100,7 @@ async function installIntoToolcache({
      ? { enabledVersions: [{ cliVersion, tagName }] }
      : SAMPLE_DEFAULT_CLI_VERSION,
    undefined, // rawLanguages
+    undefined, // otherLanguagePacksReason
    false, // useOverlayAwareDefaultCliVersion
    createFeatures([]),
    getRunnerLogger(true),
@@ -125,19 +127,6 @@ function mockReleaseApi({
    });
 }

-function mockApiDetails(apiDetails: GitHubApiDetails) {
-  // This is a workaround to mock `api.getApiDetails()` since it doesn't seem to be possible to
-  // mock this directly. The difficulty is that `getApiDetails()` is called locally in
-  // `api-client.ts`, but `sinon.stub(api, "getApiDetails")` only affects calls to
-  // `getApiDetails()` via an imported `api` module.
-  sinon
-    .stub(actionsUtil, "getRequiredInput")
-    .withArgs("token")
-    .returns(apiDetails.auth);
-  process.env["GITHUB_SERVER_URL"] = apiDetails.url;
-  process.env["GITHUB_API_URL"] = apiDetails.apiURL || "";
-}
-
 async function stubCodeql(): Promise<codeql.CodeQL> {
  const codeqlObject = await codeql.getCodeQLForTesting();
  sinon.stub(codeqlObject, "getVersion").resolves(makeVersionInfo("2.17.6"));
@@ -172,6 +161,7 @@ test.serial(
          util.GitHubVariant.DOTCOM,
          SAMPLE_DEFAULT_CLI_VERSION,
          undefined, // rawLanguages
+          undefined, // otherLanguagePacksReason
          false, // useOverlayAwareDefaultCliVersion
          features,
          getRunnerLogger(true),
@@ -207,6 +197,7 @@ test.serial(
        util.GitHubVariant.DOTCOM,
        SAMPLE_DEFAULT_CLI_VERSION,
        undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
        false, // useOverlayAwareDefaultCliVersion
        features,
        getRunnerLogger(true),
@@ -246,6 +237,7 @@ test.serial(
        util.GitHubVariant.DOTCOM,
        SAMPLE_DEFAULT_CLI_VERSION,
        undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
        false, // useOverlayAwareDefaultCliVersion
        features,
        getRunnerLogger(true),
@@ -286,6 +278,7 @@ for (const { cliVersion, tagName, expectedToolcacheVersion } of [
    async (t) => {
      await util.withTmpDir(async (tmpDir) => {
        setupActionsVars(tmpDir, tmpDir);
+        mockApiDetails(SAMPLE_DOTCOM_API_DETAILS);

        const result = await installIntoToolcache({
          cliVersion,
@@ -355,6 +348,7 @@ for (const {
          util.GitHubVariant.DOTCOM,
          SAMPLE_DEFAULT_CLI_VERSION,
          undefined, // rawLanguages
+          undefined, // otherLanguagePacksReason
          false, // useOverlayAwareDefaultCliVersion
          features,
          getRunnerLogger(true),
@@ -397,6 +391,7 @@ for (const toolcacheVersion of [
          util.GitHubVariant.DOTCOM,
          SAMPLE_DEFAULT_CLI_VERSION,
          undefined, // rawLanguages
+          undefined, // otherLanguagePacksReason
          false, // useOverlayAwareDefaultCliVersion
          features,
          getRunnerLogger(true),
@@ -441,6 +436,7 @@ test.serial(
          ],
        },
        undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
        false, // useOverlayAwareDefaultCliVersion
        features,
        getRunnerLogger(true),
@@ -463,6 +459,7 @@ test.serial(

    await util.withTmpDir(async (tmpDir) => {
      setupActionsVars(tmpDir, tmpDir);
+      mockApiDetails(SAMPLE_DOTCOM_API_DETAILS);

      await installIntoToolcache({
        tagName: "codeql-bundle-20200601",
@@ -487,6 +484,7 @@ test.serial(
          ],
        },
        undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
        false, // useOverlayAwareDefaultCliVersion
        features,
        getRunnerLogger(true),
@@ -509,6 +507,7 @@ test.serial(

    await util.withTmpDir(async (tmpDir) => {
      setupActionsVars(tmpDir, tmpDir);
+      mockApiDetails(SAMPLE_DOTCOM_API_DETAILS);

      await installIntoToolcache({
        tagName: "codeql-bundle-20200601",
@@ -526,6 +525,7 @@ test.serial(
        util.GitHubVariant.DOTCOM,
        SAMPLE_DEFAULT_CLI_VERSION,
        undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
        false, // useOverlayAwareDefaultCliVersion
        features,
        getRunnerLogger(true),
@@ -567,6 +567,7 @@ test.serial(
        util.GitHubVariant.DOTCOM,
        SAMPLE_DEFAULT_CLI_VERSION,
        undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
        false, // useOverlayAwareDefaultCliVersion
        features,
        getRunnerLogger(true),
@@ -15,9 +15,10 @@ import * as api from "./api-client";
 import * as outputCache from "./cli/output-cache";
 import type { VersionInfo } from "./cli/types";
 import { CliError, wrapCliConfigurationError } from "./cli-errors";
+import type { ActionConfig } from "./config/action-config";
 import { appendExtraQueryExclusions, type Config } from "./config-utils";
 import { DocUrl } from "./doc-url";
-import { EnvVar, getEnv } from "./environment";
+import { EnvVar, getEnv, exportEnvVar } from "./environment";
 import {
  CodeQLDefaultVersionInfo,
  Feature,
@@ -197,7 +198,7 @@ export interface CodeQL {
  diagnosticsExport(
    sarifFile: string,
    automationDetailsId: string | undefined,
-    config: Config,
+    config: ActionConfig<"tempDir">,
  ): Promise<void>;
  /** Get the location of an extractor for the specified language. */
  resolveExtractor(language: Language): Promise<string>;
@@ -253,22 +254,22 @@ 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 = "2.19.4";
+const CODEQL_MINIMUM_VERSION = "2.20.7";

 /**
 * This version will shortly become the oldest version of CodeQL that the Action will run with.
 */
-const CODEQL_NEXT_MINIMUM_VERSION = "2.20.7";
+const CODEQL_NEXT_MINIMUM_VERSION = "2.21.3";

 /**
 * This is the version of GHES that was most recently deprecated.
 */
-const GHES_VERSION_MOST_RECENTLY_DEPRECATED = "3.16";
+const GHES_VERSION_MOST_RECENTLY_DEPRECATED = "3.17";

 /**
 * This is the deprecation date for the version of GHES that was most recently deprecated.
 */
-const GHES_MOST_RECENT_DEPRECATION_DATE = "2026-07-01";
+const GHES_MOST_RECENT_DEPRECATION_DATE = "2026-09-24";

 /** The CLI verbosity level to use for extraction in debug mode. */
 const EXTRACTION_DEBUG_MODE_VERBOSITY = "progress++";
@@ -302,6 +303,9 @@ export function isDiskConfigurationError(e: unknown): boolean {
 * @param variant
 * @param defaultCliVersion
 * @param rawLanguages Raw set of languages.
+ * @param otherLanguagePacksReason Why the CodeQL CLI may need packs for languages other than
+ *   `rawLanguages`, or `undefined` if it won't. If defined, the combined bundle is used. See
+ *   `PerLanguageBundleOptions.otherLanguagePacksReason`.
 * @param useOverlayAwareDefaultCliVersion Whether to select an overlay-aware default CLI version.
 * @param features Information about the features that are enabled.
 * @param logger
@@ -316,6 +320,7 @@ export async function setupCodeQL(
  variant: util.GitHubVariant,
  defaultCliVersion: CodeQLDefaultVersionInfo,
  rawLanguages: string[] | undefined,
+  otherLanguagePacksReason: string | undefined,
  useOverlayAwareDefaultCliVersion: boolean,
  features: FeatureEnablement,
  logger: Logger,
@@ -339,6 +344,7 @@ export async function setupCodeQL(
      variant,
      defaultCliVersion,
      rawLanguages,
+      otherLanguagePacksReason,
      useOverlayAwareDefaultCliVersion,
      features,
      logger,
@@ -908,7 +914,7 @@ async function getCodeQLForCmd(
    async diagnosticsExport(
      sarifFile: string,
      automationDetailsId: string | undefined,
-      config: Config,
+      config: ActionConfig<"tempDir">,
    ): Promise<void> {
      const args = [
        "diagnostics",
@@ -937,6 +943,7 @@ async function getCodeQLForCmd(
          "--format=json",
          `--language=${language}`,
          "--extractor-include-aliases",
+          "-J-XX:-UsePerfData",
          ...getExtraOptionsFromEnv(["resolve", "extractor"]),
        ],
        {
@@ -951,7 +958,13 @@ async function getCodeQLForCmd(
          },
        },
      ).exec();
-      return JSON.parse(extractorPath) as string;
+      try {
+        return JSON.parse(extractorPath) as string;
+      } catch (err) {
+        throw new Error(
+          `Failed to parse extractor path for '${language}' from CLI: ${getErrorMessage(err)}\nOutput was: ${extractorPath}`,
+        );
+      }
    },
    async resolveQueriesStartingPacks(queries: string[]): Promise<string[]> {
      const codeqlArgs = [
@@ -1042,7 +1055,7 @@ async function getCodeQLForCmd(
        }' by 'github/codeql-action/*@v${getActionVersion()}' in your code scanning workflow to ` +
        "continue using this version of the CodeQL Action.",
    );
-    core.exportVariable(EnvVar.SUPPRESS_DEPRECATED_SOON_WARNING, "true");
+    exportEnvVar(EnvVar.SUPPRESS_DEPRECATED_SOON_WARNING, "true");
  }
  return codeql;
 }
@@ -1212,7 +1225,7 @@ export async function getTrapCachingExtractorConfigArgsForLang(
 ): Promise<string[]> {
  const cacheDir = config.trapCaches[language];
  if (cacheDir === undefined) return [];
-  const write = await isAnalyzingDefaultBranch();
+  const write = await isAnalyzingDefaultBranch(getEnv(), config.repositoryRoot);
  return [
    `-O=${language}.trap.cache.dir=${cacheDir}`,
    `-O=${language}.trap.cache.bound=${TRAP_CACHE_SIZE_MB}`,
@@ -1225,7 +1238,9 @@ export async function getTrapCachingExtractorConfigArgsForLang(
 *
 * This will not exist if the configuration is being parsed in the Action.
 */
-function getGeneratedCodeScanningConfigPath(config: Config): string {
+function getGeneratedCodeScanningConfigPath(
+  config: ActionConfig<"tempDir">,
+): string {
  return path.resolve(config.tempDir, "user-config.yaml");
 }

@@ -172,6 +172,7 @@ test.serial("load empty config", async (t) => {
      createTestInitConfigInputs({
        languagesInput: languages,
        repository: { owner: "github", repo: "example" },
+        sourceRoot: tempDir,
        tempDir,
        codeql,
        logger,
@@ -186,6 +187,7 @@ test.serial("load empty config", async (t) => {
        logger,
      }),
      {},
+      undefined,
    );

    t.deepEqual(config, expectedConfig);
@@ -216,6 +218,7 @@ test.serial("load code quality config", async (t) => {
        analysisKinds: [AnalysisKind.CodeQuality],
        languagesInput: languages,
        repository: { owner: "github", repo: "example" },
+        sourceRoot: tempDir,
        tempDir,
        codeql,
        logger,
@@ -296,6 +299,7 @@ test.serial(
            analysisKinds: [AnalysisKind.CodeQuality],
            languagesInput: languages,
            repository: { owner: "github", repo: "example" },
+            sourceRoot: tempDir,
            tempDir,
            codeql,
            repositoryProperties,
@@ -473,6 +477,12 @@ const simpleConfigFileContents = `
  queries:
    - uses: ./foo_file`;

+/** The configuration in `simpleConfigFileContents`. */
+const simpleConfigInput: UserConfig = {
+  name: "my config",
+  queries: [{ uses: "./foo_file" }],
+};
+
 /** A less minimal configuration file. */
 const otherConfigFileContents = `
  name: my config
@@ -512,6 +522,7 @@ test.serial("load non-empty input", async (t) => {
    // And the config we expect it to parse to
    const expectedConfig = createTestConfig({
      languages: [BuiltInLanguage.javascript],
+      repositoryRoot: undefined,
      buildMode: BuildMode.None,
      originalUserInput: userConfig,
      computedConfig: userConfig,
@@ -532,6 +543,7 @@ test.serial("load non-empty input", async (t) => {
      state,
      createTestInitConfigInputs({
        languagesInput,
+        sourceRoot: tempDir,
        buildModeInput: "none",
        configFile: configFilePath,
        debugArtifactName: "my-artifact",
@@ -558,16 +570,14 @@ test.serial(
        tempDir,
      );

-      const configInput = `
-      name: my config
-      queries:
-        - uses: ./foo
-      packs:
-        javascript:
-          - a/b@1.2.3
-        python:
-          - c/d@1.2.3
-    `;
+      const configInput: UserConfig = {
+        name: "my config",
+        queries: [{ uses: "./foo" }],
+        packs: {
+          javascript: ["a/b@1.2.3"],
+          python: ["c/d@1.2.3"],
+        },
+      };

      fs.mkdirSync(path.join(tempDir, "foo"));

@@ -598,7 +608,16 @@ test.serial(
        }),
      );

-      t.deepEqual(config.originalUserInput, yaml.load(configInput));
+      // Compare with a separate object rather than `configInput` itself, so that the test catches
+      // changes made to the input in place.
+      t.deepEqual(config.originalUserInput, {
+        name: "my config",
+        queries: [{ uses: "./foo" }],
+        packs: {
+          javascript: ["a/b@1.2.3"],
+          python: ["c/d@1.2.3"],
+        },
+      });
    });
  },
 );
@@ -1092,11 +1111,6 @@ const checkOverlayEnablementMacro = makeMacro({
            return lang === BuiltInLanguage.java;
          });

-        // Mock git root detection
-        if (setup.gitRoot !== undefined) {
-          sinon.stub(gitUtils, "getGitRoot").resolves(setup.gitRoot);
-        }
-
        // Mock submodule detection
        sinon.stub(gitUtils, "hasSubmodules").returns(setup.hasSubmodules);

@@ -1109,6 +1123,7 @@ const checkOverlayEnablementMacro = makeMacro({
          codeql,
          features,
          setup.languages,
+          setup.gitRoot, // repositoryRoot
          tempDir, // sourceRoot
          setup.buildMode,
          undefined,
@@ -2413,7 +2428,7 @@ test("determineUserConfig - loads config input", async (t) => {
    const expectedConfigPath = configUtils.userConfigFromActionPath(tmpDir);

    const inputs = createTestInitConfigInputs({
-      configInput: simpleConfigFileContents,
+      configInput: simpleConfigInput,
      configFile: undefined,
      workspacePath: tmpDir,
    });
@@ -2423,17 +2438,15 @@ test("determineUserConfig - loads config input", async (t) => {

    await target
      // The input source and path of the generated config file should have been logged.
-      .logs(
-        t,
-        "Using config from action input:",
-        `Using configuration file: ${expectedConfigPath}`,
-      )
-      // The message about no configuration input and
-      // the warning about both inputs should not have been logged.
+      .logs(t, `Using config from action input: ${expectedConfigPath}`)
+      // The message about no configuration input and the warning about both inputs should not have
+      // been logged. The generated config file isn't loaded, since the `config` input has already
+      // been parsed.
      .notLogs(
        t,
        "No configuration file was provided",
        "Both a config file and config input were provided. Ignoring config file.",
+        `Using configuration file: ${expectedConfigPath}`,
      )
      // The loaded configuration should match `simpleConfigFileContents`.
      .passes(t.deepEqual, {
@@ -2452,7 +2465,7 @@ test("determineUserConfig - ignores config file input when both specified", asyn
    const expectedConfigPath = configUtils.userConfigFromActionPath(tmpDir);

    const inputs = createTestInitConfigInputs({
-      configInput: simpleConfigFileContents,
+      configInput: simpleConfigInput,
      configFile: configFilePath,
      workspacePath: tmpDir,
    });
@@ -2466,10 +2479,14 @@ test("determineUserConfig - ignores config file input when both specified", asyn
      .logs(
        t,
        `Using config from action input: ${expectedConfigPath}`,
-        `Using configuration file: ${expectedConfigPath}`,
        "Both a config file and config input were provided. Ignoring config file.",
      )
-      .notLogs(t, "No configuration file was provided")
+      // The generated config file isn't loaded, since the `config` input has already been parsed.
+      .notLogs(
+        t,
+        "No configuration file was provided",
+        `Using configuration file: ${expectedConfigPath}`,
+      )
      // The loaded configuration should match `simpleConfigFileContents`.
      .passes(t.deepEqual, {
        name: "my config",
@@ -2482,11 +2499,14 @@ test("determineUserConfig - ignores config file input when both specified", asyn
 });

 /** A `config` input that we might get from Default Setup. */
-const defaultSetupConfigInput = `
-  threat-models: [local, remote]
-  default-setup:
-    org:
-      model-packs: [foo, bar]`;
+const defaultSetupConfigInput: UserConfig = {
+  "threat-models": ["local", "remote"],
+  "default-setup": {
+    org: {
+      "model-packs": ["foo", "bar"],
+    },
+  },
+};

 test("determineUserConfig - merges configs if FF is enabled in Default Setup", async (t) => {
  await withTmpDir(async (tmpDir) => {
@@ -2555,7 +2575,7 @@ test("determineUserConfig - ignores config file input in Default Setup if FF is
      .withArgs(
        tmpDir,
        createTestInitConfigInputs({
-          configInput: simpleConfigFileContents,
+          configInput: simpleConfigInput,
          configFile: configFilePath,
          workspacePath: tmpDir,
        }),
@@ -2565,10 +2585,14 @@ test("determineUserConfig - ignores config file input in Default Setup if FF is
      .logs(
        t,
        `Using config from action input: ${expectedConfigPath}`,
-        `Using configuration file: ${expectedConfigPath}`,
        "Both a config file and config input were provided. Ignoring config file.",
      )
-      .notLogs(t, "No configuration file was provided")
+      // The generated config file isn't loaded, since the `config` input has already been parsed.
+      .notLogs(
+        t,
+        "No configuration file was provided",
+        `Using configuration file: ${expectedConfigPath}`,
+      )
      .passes(t.deepEqual, {
        name: "my config",
        queries: [{ uses: "./foo_file" }],
@@ -2587,7 +2611,7 @@ test("determineUserConfig - ignores config file input outside Default Setup if F
      .withArgs(
        tmpDir,
        createTestInitConfigInputs({
-          configInput: simpleConfigFileContents,
+          configInput: simpleConfigInput,
          configFile: configFilePath,
          workspacePath: tmpDir,
        }),
@@ -2597,10 +2621,14 @@ test("determineUserConfig - ignores config file input outside Default Setup if F
      .logs(
        t,
        `Using config from action input: ${expectedConfigPath}`,
-        `Using configuration file: ${expectedConfigPath}`,
        "Both a config file and config input were provided. Ignoring config file.",
      )
-      .notLogs(t, "No configuration file was provided")
+      // The generated config file isn't loaded, since the `config` input has already been parsed.
+      .notLogs(
+        t,
+        "No configuration file was provided",
+        `Using configuration file: ${expectedConfigPath}`,
+      )
      .passes(t.deepEqual, {
        name: "my config",
        queries: [{ uses: "./foo_file" }],
@@ -2,7 +2,6 @@ import * as fs from "fs";
 import * as path from "path";
 import { performance } from "perf_hooks";

-import * as core from "@actions/core";
 import * as yaml from "js-yaml";

 import { ActionState } from "./action-common";
@@ -22,7 +21,11 @@ import {
 import * as api from "./api-client";
 import { getCachingKind } from "./caching-utils";
 import { type CodeQL } from "./codeql";
-import { type Config } from "./config/action-config";
+import {
+  type AbortedInitConfig,
+  type ActionConfig,
+  type Config,
+} from "./config/action-config";
 import {
  calculateAugmentation,
  ExcludeQueryFilter,
@@ -46,7 +49,7 @@ import {
  makeTelemetryDiagnostic,
 } from "./diagnostics";
 import { prepareDiffInformedAnalysis } from "./diff-informed-analysis-utils";
-import { EnvVar } from "./environment";
+import { EnvVar, exportEnvVar, getEnv } from "./environment";
 import * as errorMessages from "./error-messages";
 import { Feature, FeatureEnablement, FeatureWithoutCLI } from "./feature-flags";
 import {
@@ -72,6 +75,7 @@ import {
 import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import { shouldSkipOverlayAnalysis } from "./overlay/status";
 import { RepositoryNwo } from "./repository";
+import { ActionName } from "./status-report";
 import { ToolsFeature } from "./tools-features";
 import { downloadTrapCaches } from "./trap-caching";
 import {
@@ -337,7 +341,8 @@ export interface InitConfigInputs {
  packsInput: string | undefined;
  configFile: string | undefined;
  dbLocation: string | undefined;
-  configInput: string | undefined;
+  /** The configuration from the `config` input. */
+  configInput: UserConfig | undefined;
  buildModeInput: string | undefined;
  ramInput: string | undefined;
  dependencyCachingEnabled: string | undefined;
@@ -385,6 +390,7 @@ export async function initActionState(
    enableFileCoverageInformation,
  }: InitConfigInputs,
  userConfig: UserConfig,
+  repositoryRoot: string | undefined,
 ): Promise<Config> {
  const languages = await getLanguages(
    codeql,
@@ -436,6 +442,7 @@ export async function initActionState(

  return {
    version: getActionVersion(),
+    repositoryRoot,
    analysisKinds,
    languages,
    buildMode,
@@ -465,12 +472,18 @@ async function downloadCacheWithTime(
  codeQL: CodeQL,
  languages: Language[],
  logger: Logger,
+  repositoryRoot: string | undefined,
 ): Promise<{
  trapCaches: { [language: string]: string };
  trapCacheDownloadTime: number;
 }> {
  const start = performance.now();
-  const trapCaches = await downloadTrapCaches(codeQL, languages, logger);
+  const trapCaches = await downloadTrapCaches(
+    codeQL,
+    languages,
+    logger,
+    repositoryRoot,
+  );
  const trapCacheDownloadTime = performance.now() - start;
  return { trapCaches, trapCacheDownloadTime };
 }
@@ -718,6 +731,7 @@ export async function checkOverlayEnablement(
  codeql: CodeQL,
  features: FeatureEnablement,
  languages: Language[],
+  repositoryRoot: string | undefined,
  sourceRoot: string,
  buildMode: BuildMode | undefined,
  ramInput: string | undefined,
@@ -747,6 +761,7 @@ export async function checkOverlayEnablement(
      true,
      codeql,
      languages,
+      repositoryRoot,
      sourceRoot,
      buildMode,
      gitVersion,
@@ -820,7 +835,7 @@ export async function checkOverlayEnablement(
      `Setting overlay database mode to ${overlayDatabaseMode} ` +
        "with caching because we are analyzing a pull request.",
    );
-  } else if (await isAnalyzingDefaultBranch()) {
+  } else if (await isAnalyzingDefaultBranch(getEnv(), repositoryRoot)) {
    overlayDatabaseMode = OverlayDatabaseMode.OverlayBase;
    logger.info(
      `Setting overlay database mode to ${overlayDatabaseMode} ` +
@@ -836,6 +851,7 @@ export async function checkOverlayEnablement(
    false,
    codeql,
    languages,
+    repositoryRoot,
    sourceRoot,
    buildMode,
    gitVersion,
@@ -855,6 +871,7 @@ async function validateOverlayDatabaseMode(
  overlayModeSetExplicitly: boolean,
  codeql: CodeQL,
  languages: Language[],
+  repositoryRoot: string | undefined,
  sourceRoot: string,
  buildMode: BuildMode | undefined,
  gitVersion: GitVersionInfo | undefined,
@@ -890,8 +907,7 @@ async function validateOverlayDatabaseMode(
    );
    return new Failure(OverlayDisabledReason.IncompatibleCodeQl);
  }
-  const gitRoot = await getGitRoot(sourceRoot);
-  if (gitRoot === undefined) {
+  if (repositoryRoot === undefined) {
    logger.warning(
      `Cannot build an ${overlayDatabaseMode} database because ` +
        `the source root "${sourceRoot}" is not inside a git repository. ` +
@@ -899,7 +915,7 @@ async function validateOverlayDatabaseMode(
    );
    return new Failure(OverlayDisabledReason.NoGitRoot);
  }
-  if (hasSubmodules(gitRoot)) {
+  if (hasSubmodules(repositoryRoot)) {
    if (gitVersion === undefined) {
      logger.warning(
        `Cannot build an ${overlayDatabaseMode} database because ` +
@@ -964,10 +980,10 @@ async function setCppTrapCachingEnvironmentVariables(
      );
    } else if (config.trapCaches[BuiltInLanguage.cpp]) {
      logger.info("Enabling TRAP caching for C/C++.");
-      core.exportVariable(envVar, "true");
+      exportEnvVar(envVar, "true");
    } else {
      logger.debug(`Disabling TRAP caching for C/C++.`);
-      core.exportVariable(envVar, "false");
+      exportEnvVar(envVar, "false");
    }
  }
 }
@@ -1057,17 +1073,13 @@ export async function determineUserConfig(
  tempDir: string,
  inputs: InitConfigInputs,
 ): Promise<UserConfig> {
-  const validateConfig = await action.features.getValue(
-    Feature.ValidateDbConfig,
-  );
-
  // We have the following cases:
  // 1. A `config` or `config-file` input is provided, but not both: use the provided one.
  // 2. Both are provided and we are in an advanced workflow: ignore the `config-file` input.
  // 3. Both are provided and we are in Default Setup: the `config` input uses a limited
  //    set of options, which are supported by `mergeDefaultSetupAndUserConfigs`,
  //    and we merge the two configs.
-  if (inputs.configInput) {
+  if (inputs.configInput !== undefined) {
    const computedConfigPath = userConfigFromActionPath(tempDir);

    // Get a function which enables us to determine whether the FF that allows us to
@@ -1084,12 +1096,6 @@ export async function determineUserConfig(
    ) {
      // If the FF is enabled and we are in Default Setup, combine the supported
      // configuration file properties and write the result to disk.
-      const fromConfigInput = parseUserConfig(
-        action.logger,
-        "`config` input",
-        inputs.configInput,
-        validateConfig,
-      );
      const fromConfigFile = await loadUserConfig(
        action,
        inputs.configFile,
@@ -1102,7 +1108,7 @@ export async function determineUserConfig(
      // the CLI or other CodeQL Action steps.
      const mergedConfig = mergeDefaultSetupAndUserConfigs(
        action.logger,
-        fromConfigInput,
+        inputs.configInput,
        fromConfigFile,
      );
      fs.writeFileSync(computedConfigPath, yaml.dump(mergedConfig));
@@ -1122,12 +1128,13 @@ export async function determineUserConfig(
        );
      }

-      // Write the `config` input straight to disk.
-      fs.writeFileSync(computedConfigPath, inputs.configInput);
+      // Write the `config` input to disk without merging it with a configuration file.
+      fs.writeFileSync(computedConfigPath, yaml.dump(inputs.configInput));
      inputs.configFile = computedConfigPath;
      action.logger.debug(
        `Using config from action input: ${inputs.configFile}`,
      );
+      return inputs.configInput;
    }
  }

@@ -1160,9 +1167,11 @@ export async function initConfig(
  const { logger, features } = actionState;
  const { tempDir } = inputs;

+  const repositoryRoot = await getGitRoot(inputs.sourceRoot);
+
  const userConfig = await determineUserConfig(actionState, tempDir, inputs);

-  const config = await initActionState(inputs, userConfig);
+  const config = await initActionState(inputs, userConfig, repositoryRoot);

  // If Code Quality analysis is the only enabled analysis kind, then we will initialise
  // the database for Code Quality. That entails disabling the default queries and only
@@ -1244,6 +1253,7 @@ export async function initConfig(
    inputs.codeql,
    inputs.features,
    config.languages,
+    repositoryRoot,
    inputs.sourceRoot,
    config.buildMode,
    inputs.ramInput,
@@ -1297,6 +1307,7 @@ export async function initConfig(
      inputs.codeql,
      config.languages,
      logger,
+      repositoryRoot,
    );
    config.trapCaches = trapCaches;
    config.trapCacheDownloadTime = trapCacheDownloadTime;
@@ -1388,31 +1399,86 @@ export function getPathToParsedConfigFile(tempDir: string): string {
  return path.join(tempDir, "config");
 }

+function getPathToFailedConfigFile(tempDir: string): string {
+  return path.join(tempDir, "failed-config");
+}
+
 /**
- * Store the given config to the path returned from getPathToParsedConfigFile.
+ * Writes {@link config} to {@link configFilePath}.
+ *
+ * This function is not intended to be called, other than by
+ * {@link saveConfig} and {@link saveAbortedInitConfig} below.
 */
-export async function saveConfig(config: Config, logger: Logger) {
+function saveConfigFile(
+  logger: Logger,
+  configFilePath: string,
+  config: Partial<Config>,
+) {
  const configString = JSON.stringify(config);
-  const configFile = getPathToParsedConfigFile(config.tempDir);
-  fs.mkdirSync(path.dirname(configFile), { recursive: true });
-  fs.writeFileSync(configFile, configString, "utf8");
+  fs.mkdirSync(path.dirname(configFilePath), { recursive: true });
+  fs.writeFileSync(configFilePath, configString, "utf8");
  logger.debug("Saved config:");
  logger.debug(configString);
 }

 /**
- * Get the config that has been saved to the given temp dir.
- * If the config could not be found then returns undefined.
+ * Store the given config to the path returned from getPathToParsedConfigFile.
 */
-export async function getConfig(
-  tempDir: string,
+export async function saveConfig(config: Config, logger: Logger) {
+  const configFile = getPathToParsedConfigFile(config.tempDir);
+  saveConfigFile(logger, configFile, config);
+}
+
+/**
+ * Store parts of {@link config} as a failed configuration file.
+ *
+ * The file will only contain parts of {@link config} that are relevant to
+ * the `init-post` step in the workflow.
+ */
+export function saveAbortedInitConfig(
+  action: ActionState<["Base", "Logger"]>,
+  config: Config,
+) {
+  // Should only be called by init.
+  if (action.name !== ActionName.Init) {
+    throw new Error(
+      `Internal error: 'saveAbortedInitConfig' should only be called by '${ActionName.Init}', but was called by '${action.name}'.`,
+    );
+  }
+
+  // Create a copy of the input `Config` that only contains the keys we want.
+  const failedConfig: AbortedInitConfig = {
+    version: config.version,
+    tempDir: config.tempDir,
+    codeQLCmd: config.codeQLCmd,
+    debugMode: config.debugMode,
+    gitHubVersion: config.gitHubVersion,
+    languages: config.languages,
+    analysisKinds: config.analysisKinds,
+  };
+
+  action.logger.debug(`Saving config for failed init step.`);
+  saveConfigFile(
+    action.logger,
+    getPathToFailedConfigFile(config.tempDir),
+    failedConfig,
+  );
+}
+
+/**
+ * Attempts to read a {@link Config} from {@link configFilePath}.
+ *
+ * This function is not intended to be called, other than by
+ * {@link getConfig} and {@link getAbortedInitConfig} below.
+ */
+function readConfigFile(
  logger: Logger,
-): Promise<Config | undefined> {
-  const configFile = getPathToParsedConfigFile(tempDir);
-  if (!fs.existsSync(configFile)) {
+  configFilePath: string,
+): Config | undefined {
+  if (!fs.existsSync(configFilePath)) {
    return undefined;
  }
-  const configString = fs.readFileSync(configFile, "utf8");
+  const configString = fs.readFileSync(configFilePath, "utf8");
  logger.debug("Loaded config:");
  logger.debug(configString);

@@ -1425,13 +1491,50 @@ export async function getConfig(
  }
  if (config.version !== getActionVersion()) {
    throw new ConfigurationError(
-      `Loaded a configuration file for version '${config.version}', but running version '${getActionVersion()}'`,
+      [
+        `Loaded a configuration file for version '${config.version}', but running version '${getActionVersion()}'.`,
+        "All steps in a workflow that use `github/codeql-action` must use the same version to work correctly.",
+        "If you are using Dependabot to manage dependency updates, you can configure a dependency group to update all `github/codeql-action` steps at the same time.",
+        "For more information, see https://docs.github.com/en/code-security/reference/supply-chain-security/dependabot-options-reference#groups--",
+      ].join(" "),
    );
  }

  return config as Config;
 }

+/**
+ * Get the config that has been saved to the given temp dir.
+ * If the config could not be found then returns undefined.
+ */
+export async function getConfig(
+  tempDir: string,
+  logger: Logger,
+): Promise<Config | undefined> {
+  const configFile = getPathToParsedConfigFile(tempDir);
+  return readConfigFile(logger, configFile);
+}
+
+/**
+ * Loads a {@link AbortedInitConfig} from a failed `init` step if it exists.
+ *
+ * The result will only contain parts of a {@link Config} that are relevant to
+ * the `init-post` step in the workflow.
+ */
+export function getAbortedInitConfig(
+  action: ActionState<["Base", "Logger"]>,
+  tempDir: string,
+): AbortedInitConfig | undefined {
+  // Only intended to be called by the `init-post` action.
+  if (action.name !== ActionName.InitPost) {
+    throw new Error(
+      `Internal error: 'getAbortedInitConfig' should only be called by '${ActionName.InitPost}', but was called by '${action.name}'.`,
+    );
+  }
+
+  return readConfigFile(action.logger, getPathToFailedConfigFile(tempDir));
+}
+
 /**
 * Generate a `qlconfig.yml` file from the `registries` input.
 * This file is used by the CodeQL CLI to list the registries to use for each
@@ -1622,21 +1725,27 @@ export function appendExtraQueryExclusions(
 /**
 * Returns `true` if Code Scanning analysis is enabled, or `false` if not.
 */
-export function isCodeScanningEnabled(config: Config): boolean {
+export function isCodeScanningEnabled(
+  config: ActionConfig<"analysisKinds">,
+): boolean {
  return config.analysisKinds.includes(AnalysisKind.CodeScanning);
 }

 /**
 * Returns `true` if Code Quality analysis is enabled, or `false` if not.
 */
-export function isCodeQualityEnabled(config: Config): boolean {
+export function isCodeQualityEnabled(
+  config: ActionConfig<"analysisKinds">,
+): boolean {
  return config.analysisKinds.includes(AnalysisKind.CodeQuality);
 }

 /**
 * Returns `true` if Code Scanning Risk Assessment analysis is enabled, or `false` if not.
 */
-export function isRiskAssessmentEnabled(config: Config): boolean {
+export function isRiskAssessmentEnabled(
+  config: ActionConfig<"analysisKinds">,
+): boolean {
  return config.analysisKinds.includes(AnalysisKind.RiskAssessment);
 }

@@ -16,6 +16,11 @@ export interface Config {
   * The version of the CodeQL Action that the configuration is for.
   */
  version: string;
+  /**
+   * The path at which the repository being analysed is checked out at, if available.
+   * Persisted in the CodeQL Action configuration state, so that we can consult it in later workflow steps.
+   */
+  repositoryRoot: string | undefined;
  /**
   * Set of analysis kinds that are enabled.
   */
@@ -126,3 +131,38 @@ export interface Config {
   */
  enableFileCoverageInformation: boolean;
 }
+
+/** Properties available in `Config`. */
+export type ActionConfigProperties = keyof Config;
+
+/**
+ * The CodeQL Action configuration state that is persisted
+ * between steps of the CodeQL Action in a CodeQL workflow.
+ *
+ * By default, this is equivalent to `Config`. By explicitly
+ * providing required property names for `T` this can be restricted
+ * to requiring only those. For example, in `ActionConfig<"codeQLCmd">`
+ * all properties except `codeqlCmd` are optional.
+ */
+export type ActionConfig<
+  T extends ActionConfigProperties = ActionConfigProperties,
+> = Partial<Config> & Pick<Config, T>;
+
+/** Helper function to check whether `config` has `key` to narrow the type of `config`. */
+export function hasConfigKey<Key extends ActionConfigProperties>(
+  config: Partial<Config>,
+  key: Key,
+): config is ActionConfig<Key> {
+  return config[key] !== undefined;
+}
+
+/** A minimal configuration that we can make available even when `init` aborts. */
+export type AbortedInitConfig = ActionConfig<
+  | "version"
+  | "tempDir"
+  | "gitHubVersion"
+  | "debugMode"
+  | "languages"
+  | "analysisKinds"
+  | "codeQLCmd"
+>;
@@ -625,3 +625,73 @@ test("mergeDefaultSetupAndUserConfigs - warns about invalid keys from Default Se
    `Invalid keys in Default Setup configuration: ${expectedInvalidKeys}`,
  ]);
 });
+
+/** Parses `contents` as a configuration without validating it. */
+function parseUnvalidatedConfig(contents: string): dbConfig.UserConfig {
+  return dbConfig.parseUserConfig(
+    getRunnerLogger(true),
+    "test",
+    contents,
+    false,
+  );
+}
+
+test("matchesDefaultSetupConfigSchema - returns true for configurations that only use Default Setup properties", (t) => {
+  for (const contents of [
+    [
+      "default-setup:",
+      "  org:",
+      "    model-packs: [ github/immutable-actions-list@0.0.1 ]",
+      "threat-models: [  ]",
+    ].join("\n"),
+    "threat-models: [ local ]",
+    "{}",
+  ]) {
+    t.true(
+      dbConfig.matchesDefaultSetupConfigSchema(
+        parseUnvalidatedConfig(contents),
+      ),
+      contents,
+    );
+  }
+});
+
+test("matchesDefaultSetupConfigSchema - returns false for configurations that use other properties", (t) => {
+  for (const contents of [
+    "queries: [ { uses: ./queries/show_ifs.ql } ]",
+    "paths-ignore: [ tests ]",
+    "default-setup: { org: { model-packs: [], queries: [] } }",
+  ]) {
+    t.false(
+      dbConfig.matchesDefaultSetupConfigSchema(
+        parseUnvalidatedConfig(contents),
+      ),
+      contents,
+    );
+  }
+});
+
+test("matchesDefaultSetupConfigSchema - returns false for invalid Default Setup properties", (t) => {
+  for (const contents of [
+    "threat-models: local",
+    "default-setup: { org: { model-packs: [ 1 ] } }",
+  ]) {
+    t.false(
+      dbConfig.matchesDefaultSetupConfigSchema(
+        parseUnvalidatedConfig(contents),
+      ),
+      contents,
+    );
+  }
+});
+
+test("matchesDefaultSetupConfigSchema - returns false for configurations that aren't mappings", (t) => {
+  for (const contents of ["- threat-models", "local", "null"]) {
+    t.false(
+      dbConfig.matchesDefaultSetupConfigSchema(
+        parseUnvalidatedConfig(contents),
+      ),
+      contents,
+    );
+  }
+});
@@ -33,6 +33,15 @@ export interface QuerySpec {
  uses: string;
 }

+// A set of default query suite names that are understood by the CLI.
+export const defaultSuites: Set<string> = new Set([
+  "security-experimental",
+  "security-extended",
+  "security-and-quality",
+  "code-quality",
+  "code-scanning",
+]);
+
 const ORG_SCHEMA = {
  /** An array of model pack names. */
  "model-packs": json.optional(json.array(json.string)),
@@ -77,7 +86,11 @@ export interface UserConfig {
  "default-setup"?: DefaultSetupConfig;
 }

-/** A subset of the `UserConfig` schema that is used by Default Setup. */
+/**
+ * A subset of the `UserConfig` schema that is known to be used by Default Setup. None of these
+ * properties may add queries, since a per-language CodeQL bundle can be used with a `config` input
+ * that only sets them.
+ */
 const DEFAULT_SETUP_CONFIG_SCHEMA = {
  "threat-models": json.optional(json.array(json.string)),
  "default-setup": json.optional<DefaultSetupConfig>(
@@ -85,6 +98,24 @@ const DEFAULT_SETUP_CONFIG_SCHEMA = {
  ),
 } as const satisfies json.Schema;

+/**
+ * Returns whether `config` matches what we expect Default Setup to send in the `config` input: a
+ * mapping that only sets properties in `DEFAULT_SETUP_CONFIG_SCHEMA`, with values of the expected
+ * types.
+ */
+export function matchesDefaultSetupConfigSchema(config: UserConfig): boolean {
+  // Unless validation is enabled, `parseUserConfig` doesn't check that the YAML is a mapping.
+  if (!json.isObject(config)) {
+    return false;
+  }
+  const result = json.checkSchema(
+    DEFAULT_SETUP_CONFIG_SCHEMA,
+    config as json.UnvalidatedObject<any>,
+  );
+  // `valid` doesn't account for unknown properties.
+  return result.valid && result.unknownKeys.length === 0;
+}
+
 /**
 * Merges supported properties from two configuration files. This is intended only for
 * use with merging the `config` input provided by Default Setup with a potentially
@@ -437,63 +468,60 @@ export async function calculateAugmentation(
    languages,
    packsInputCombines,
  );
-  const queriesInputCombines = shouldCombine(rawQueriesInput);
-  const queriesInput = parseQueriesFromInput(
-    rawQueriesInput,
-    queriesInputCombines,
+  const queries = parseQueriesFromInput(rawQueriesInput);
+  const repoPropertyQueries = parseQueriesFromInput(
+    repositoryProperties[RepositoryPropertyName.EXTRA_QUERIES],
+    RepositoryPropertyName.EXTRA_QUERIES,
  );

-  const repoExtraQueries =
-    repositoryProperties[RepositoryPropertyName.EXTRA_QUERIES];
-  const repoExtraQueriesCombines = shouldCombine(repoExtraQueries);
-  const repoPropertyQueries = {
-    combines: repoExtraQueriesCombines,
-    input: parseQueriesFromInput(
-      repoExtraQueries,
-      repoExtraQueriesCombines,
-      new ConfigurationError(
-        errorMessages.getRepoPropertyError(
-          RepositoryPropertyName.EXTRA_QUERIES,
-          errorMessages.getEmptyCombinesError(),
-        ),
-      ),
-    ),
-  };
-
  return {
    packsInputCombines,
    packsInput: packsInput?.[languages[0]],
-    queriesInput,
-    queriesInputCombines,
+    queriesInput: queries.input,
+    queriesInputCombines: queries.combines,
    repoPropertyQueries,
  };
 }

-function parseQueriesFromInput(
-  rawQueriesInput: string | undefined,
-  queriesInputCombines: boolean,
-  errorToThrow?: ConfigurationError,
-) {
-  if (!rawQueriesInput) {
-    return undefined;
+/**
+ * Parses a comma-separated list of queries, which may have a '+' prefix. Entries aren't validated,
+ * so an empty entry becomes `{ uses: "" }`.
+ *
+ * @param value The list of queries.
+ * @param repositoryProperty The repository property that `value` comes from, if any. Error messages
+ *   refer to this property, or to the `queries` input if no property is given.
+ * @returns An `Augmentation` containing the parsed queries and whether `value` has a '+' prefix.
+ *   The queries are `undefined` if `value` is unset or empty.
+ * @throws A `ConfigurationError` if `value` is a '+' with no queries after it.
+ */
+export function parseQueriesFromInput(
+  value: string | undefined,
+  repositoryProperty?: RepositoryPropertyName,
+): Augmentation<QuerySpec[]> {
+  if (!value) {
+    return { combines: false, input: undefined };
  }

-  const trimmedInput = queriesInputCombines
-    ? rawQueriesInput.trim().slice(1).trim()
-    : (rawQueriesInput?.trim() ?? "");
-  if (queriesInputCombines && trimmedInput.length === 0) {
-    if (errorToThrow) {
-      throw errorToThrow;
-    }
+  const combines = shouldCombine(value);
+  const trimmedInput = combines ? value.trim().slice(1).trim() : value.trim();
+  if (combines && trimmedInput.length === 0) {
    throw new ConfigurationError(
-      errorMessages.getConfigFilePropertyError(
-        undefined,
-        "queries",
-        "A '+' was used in the 'queries' input to specify that you wished to add some packs to your CodeQL analysis. However, no packs were specified. Please either remove the '+' or specify some packs.",
-      ),
+      repositoryProperty !== undefined
+        ? errorMessages.getRepoPropertyError(
+            repositoryProperty,
+            errorMessages.getEmptyCombinesError(),
+          )
+        : errorMessages.getConfigFilePropertyError(
+            undefined,
+            "queries",
+            "A '+' was used in the 'queries' input to specify that you wished to add some packs to your CodeQL analysis. However, no packs were specified. Please either remove the '+' or specify some packs.",
+          ),
    );
  }
-  return trimmedInput.split(",").map((query) => ({ uses: query.trim() }));
+  return {
+    combines,
+    input: trimmedInput.split(",").map((query) => ({ uses: query.trim() })),
+  };
 }

 /**
@@ -610,11 +638,13 @@ export function generateCodeScanningConfig(
 * Attempts to parse `contents` into a `UserConfig` value.
 *
 * @param logger The logger to use.
- * @param pathInput The path to the file where `contents` was obtained from, for use in error messages.
- * @param contents The string contents of a YAML file to try and parse as a `UserConfig`.
- * @param validateConfig Whether to validate the configuration file against the schema.
- * @returns The `UserConfig` corresponding to `contents`, if parsing was successful.
- * @throws A `ConfigurationError` if parsing failed.
+ * @param pathInput Where `contents` came from, such as the path to a file, for use in error messages.
+ * @param contents The YAML to try and parse as a `UserConfig`.
+ * @param validateConfig Whether to validate the configuration against the schema.
+ * @returns The `UserConfig` corresponding to `contents`, if parsing was successful. Unless
+ *   `validateConfig` is set, the result might not be a mapping.
+ * @throws A `ConfigurationError` if `contents` isn't valid YAML or, when `validateConfig` is set,
+ *   isn't a valid configuration.
 */
 export function parseUserConfig(
  logger: Logger,
@@ -1,4 +1,5 @@
-import * as fs from "fs";
+import fs from "fs";
+import path from "path";

 import * as github from "@actions/github";
 import test from "ava";
@@ -10,7 +11,10 @@ import { GitHubApiDetails } from "./api-client";
 import * as apiClient from "./api-client";
 import { createStubCodeQL } from "./codeql";
 import { Config } from "./config-utils";
-import { cleanupAndUploadDatabases } from "./database-upload";
+import {
+  cleanupAndUploadDatabases,
+  uploadBundledDatabase,
+} from "./database-upload";
 import { Feature } from "./feature-flags";
 import * as gitUtils from "./git-utils";
 import { BuiltInLanguage } from "./languages";
@@ -20,8 +24,10 @@ import {
  checkExpectedLogMessages,
  createFeatures,
  createTestConfig,
-  getRecordingLogger,
-  LoggedMessage,
+  getTestEnv,
+  initAllState,
+  RecordingLogger,
+  SAMPLE_DOTCOM_API_DETAILS,
  setupActionsVars,
  setupTests,
 } from "./testing-utils";
@@ -90,23 +96,24 @@ test.serial(
  "Abort database upload if 'upload-database' input set to false",
  async (t) => {
    await withTmpDir(async (tmpDir) => {
-      setupActionsVars(tmpDir, tmpDir);
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
      sinon
        .stub(actionsUtil, "getRequiredInput")
        .withArgs("upload-database")
        .returns("false");
      sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);

-      const loggedMessages: LoggedMessage[] = [];
+      const logger = new RecordingLogger();
      await cleanupAndUploadDatabases(
+        initAllState({ env, logger }),
        testRepoName,
        getCodeQL(),
        getTestConfig(tmpDir),
        testApiDetails,
-        createFeatures([]),
-        getRecordingLogger(loggedMessages),
+        "",
      );
-      checkExpectedLogMessages(t, loggedMessages, [
+      checkExpectedLogMessages(t, logger.messages, [
        "Database upload disabled in workflow. Skipping upload.",
      ]);
    });
@@ -117,7 +124,8 @@ test.serial(
  "Abort database upload if 'analysis-kinds: code-scanning' is not enabled",
  async (t) => {
    await withTmpDir(async (tmpDir) => {
-      setupActionsVars(tmpDir, tmpDir);
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
      sinon
        .stub(actionsUtil, "getRequiredInput")
        .withArgs("upload-database")
@@ -126,8 +134,9 @@ test.serial(

      await mockHttpRequests(201);

-      const loggedMessages: LoggedMessage[] = [];
+      const logger = new RecordingLogger();
      await cleanupAndUploadDatabases(
+        initAllState({ env, logger }),
        testRepoName,
        getCodeQL(),
        {
@@ -135,10 +144,9 @@ test.serial(
          analysisKinds: [AnalysisKind.CodeQuality],
        },
        testApiDetails,
-        createFeatures([]),
-        getRecordingLogger(loggedMessages),
+        "",
      );
-      checkExpectedLogMessages(t, loggedMessages, [
+      checkExpectedLogMessages(t, logger.messages, [
        "Not uploading database because 'analysis-kinds: code-scanning' is not enabled.",
      ]);
    });
@@ -147,7 +155,8 @@ test.serial(

 test.serial("Abort database upload if running against GHES", async (t) => {
  await withTmpDir(async (tmpDir) => {
-    setupActionsVars(tmpDir, tmpDir);
+    const env = getTestEnv();
+    setupActionsVars(tmpDir, tmpDir, {}, env);
    sinon
      .stub(actionsUtil, "getRequiredInput")
      .withArgs("upload-database")
@@ -157,16 +166,16 @@ test.serial("Abort database upload if running against GHES", async (t) => {
    const config = getTestConfig(tmpDir);
    config.gitHubVersion = { type: GitHubVariant.GHES, version: "3.0" };

-    const loggedMessages: LoggedMessage[] = [];
+    const logger = new RecordingLogger();
    await cleanupAndUploadDatabases(
+      initAllState({ env, logger }),
      testRepoName,
      getCodeQL(),
      config,
      testApiDetails,
-      createFeatures([]),
-      getRecordingLogger(loggedMessages),
+      "",
    );
-    checkExpectedLogMessages(t, loggedMessages, [
+    checkExpectedLogMessages(t, logger.messages, [
      "Not running against github.com or GHEC-DR. Skipping upload.",
    ]);
  });
@@ -176,23 +185,24 @@ test.serial(
  "Abort database upload if not analyzing default branch",
  async (t) => {
    await withTmpDir(async (tmpDir) => {
-      setupActionsVars(tmpDir, tmpDir);
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
      sinon
        .stub(actionsUtil, "getRequiredInput")
        .withArgs("upload-database")
        .returns("true");
      sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(false);

-      const loggedMessages: LoggedMessage[] = [];
+      const logger = new RecordingLogger();
      await cleanupAndUploadDatabases(
+        initAllState({ env, logger }),
        testRepoName,
        getCodeQL(),
        getTestConfig(tmpDir),
        testApiDetails,
-        createFeatures([]),
-        getRecordingLogger(loggedMessages),
+        "",
      );
-      checkExpectedLogMessages(t, loggedMessages, [
+      checkExpectedLogMessages(t, logger.messages, [
        "Not analyzing default branch. Skipping upload.",
      ]);
    });
@@ -203,7 +213,8 @@ test.serial(
  "Don't crash if uploading a database fails with a non-retryable error",
  async (t) => {
    await withTmpDir(async (tmpDir) => {
-      setupActionsVars(tmpDir, tmpDir);
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
      sinon
        .stub(actionsUtil, "getRequiredInput")
        .withArgs("upload-database")
@@ -212,17 +223,17 @@ test.serial(

      const databaseUploadSpy = await mockHttpRequests(422);

-      const loggedMessages: LoggedMessage[] = [];
+      const logger = new RecordingLogger();
      await cleanupAndUploadDatabases(
+        initAllState({ env, logger }),
        testRepoName,
        getCodeQL(),
        getTestConfig(tmpDir),
        testApiDetails,
-        createFeatures([]),
-        getRecordingLogger(loggedMessages),
+        "",
      );

-      checkExpectedLogMessages(t, loggedMessages, [
+      checkExpectedLogMessages(t, logger.messages, [
        "Failed to upload database for javascript: some error message",
      ]);

@@ -236,7 +247,8 @@ test.serial(
  "Don't crash if uploading a database fails with a retryable error",
  async (t) => {
    await withTmpDir(async (tmpDir) => {
-      setupActionsVars(tmpDir, tmpDir);
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
      sinon
        .stub(actionsUtil, "getRequiredInput")
        .withArgs("upload-database")
@@ -251,17 +263,17 @@ test.serial(
        .stub(global, "setTimeout")
        .callsFake((fn: () => void) => originalSetTimeout(fn, 0));

-      const loggedMessages: LoggedMessage[] = [];
+      const logger = new RecordingLogger();
      await cleanupAndUploadDatabases(
+        initAllState({ env, logger }),
        testRepoName,
        getCodeQL(),
        getTestConfig(tmpDir),
        testApiDetails,
-        createFeatures([]),
-        getRecordingLogger(loggedMessages),
+        "",
      );

-      checkExpectedLogMessages(t, loggedMessages, [
+      checkExpectedLogMessages(t, logger.messages, [
        "Failed to upload database for javascript: some error message",
      ]);

@@ -279,7 +291,8 @@ test.serial(

 test.serial("Successfully uploading a database to github.com", async (t) => {
  await withTmpDir(async (tmpDir) => {
-    setupActionsVars(tmpDir, tmpDir);
+    const env = getTestEnv();
+    setupActionsVars(tmpDir, tmpDir, {}, env);
    sinon
      .stub(actionsUtil, "getRequiredInput")
      .withArgs("upload-database")
@@ -288,16 +301,16 @@ test.serial("Successfully uploading a database to github.com", async (t) => {

    await mockHttpRequests(201);

-    const loggedMessages: LoggedMessage[] = [];
+    const logger = new RecordingLogger();
    await cleanupAndUploadDatabases(
+      initAllState({ env, logger }),
      testRepoName,
      getCodeQL(),
      getTestConfig(tmpDir),
      testApiDetails,
-      createFeatures([]),
-      getRecordingLogger(loggedMessages),
+      "",
    );
-    checkExpectedLogMessages(t, loggedMessages, [
+    checkExpectedLogMessages(t, logger.messages, [
      "Successfully uploaded database for javascript",
    ]);
  });
@@ -305,7 +318,8 @@ test.serial("Successfully uploading a database to github.com", async (t) => {

 test.serial("Successfully uploading a database to GHEC-DR", async (t) => {
  await withTmpDir(async (tmpDir) => {
-    setupActionsVars(tmpDir, tmpDir);
+    const env = getTestEnv();
+    setupActionsVars(tmpDir, tmpDir, {}, env);
    sinon
      .stub(actionsUtil, "getRequiredInput")
      .withArgs("upload-database")
@@ -314,8 +328,9 @@ test.serial("Successfully uploading a database to GHEC-DR", async (t) => {

    const databaseUploadSpy = await mockHttpRequests(201);

-    const loggedMessages: LoggedMessage[] = [];
+    const logger = new RecordingLogger();
    await cleanupAndUploadDatabases(
+      initAllState({ env, logger }),
      testRepoName,
      getCodeQL(),
      getTestConfig(tmpDir),
@@ -324,10 +339,9 @@ test.serial("Successfully uploading a database to GHEC-DR", async (t) => {
        url: "https://tenant.ghe.com",
        apiURL: undefined,
      },
-      createFeatures([]),
-      getRecordingLogger(loggedMessages),
+      "",
    );
-    checkExpectedLogMessages(t, loggedMessages, [
+    checkExpectedLogMessages(t, logger.messages, [
      "Successfully uploaded database for javascript",
    ]);
    t.assert(
@@ -343,7 +357,8 @@ test.serial(
  "Records overlay and clear cleanup sizes when uploading an overlay-base database",
  async (t) => {
    await withTmpDir(async (tmpDir) => {
-      setupActionsVars(tmpDir, tmpDir);
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
      sinon
        .stub(actionsUtil, "getRequiredInput")
        .withArgs("upload-database")
@@ -375,14 +390,16 @@ test.serial(
      const config = getTestConfig(tmpDir);
      config.overlayDatabaseMode = OverlayDatabaseMode.OverlayBase;

-      const loggedMessages: LoggedMessage[] = [];
      const results = await cleanupAndUploadDatabases(
+        initAllState({
+          env,
+          features: createFeatures([Feature.UploadOverlayDbToApi]),
+        }),
        testRepoName,
        codeql,
        config,
        testApiDetails,
-        createFeatures([Feature.UploadOverlayDbToApi]),
-        getRecordingLogger(loggedMessages),
+        "",
      );

      // The database should be cleaned up at the `overlay` level for the upload
@@ -402,7 +419,8 @@ test.serial(
  "Does not measure clear cleanup size for a regular (non-overlay-base) upload",
  async (t) => {
    await withTmpDir(async (tmpDir) => {
-      setupActionsVars(tmpDir, tmpDir);
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
      sinon
        .stub(actionsUtil, "getRequiredInput")
        .withArgs("upload-database")
@@ -422,12 +440,15 @@ test.serial(
      });

      const results = await cleanupAndUploadDatabases(
+        initAllState({
+          env,
+          features: createFeatures([Feature.UploadOverlayDbToApi]),
+        }),
        testRepoName,
        codeql,
        getTestConfig(tmpDir),
        testApiDetails,
-        createFeatures([Feature.UploadOverlayDbToApi]),
-        getRecordingLogger([]),
+        "",
      );

      // A regular upload is cleaned only once, at the `clear` level.
@@ -441,7 +462,8 @@ test.serial(

 test.serial("Does not measure clear cleanup size in debug mode", async (t) => {
  await withTmpDir(async (tmpDir) => {
-    setupActionsVars(tmpDir, tmpDir);
+    const env = getTestEnv();
+    setupActionsVars(tmpDir, tmpDir, {}, env);
    sinon
      .stub(actionsUtil, "getRequiredInput")
      .withArgs("upload-database")
@@ -465,12 +487,15 @@ test.serial("Does not measure clear cleanup size in debug mode", async (t) => {
    config.debugMode = true;

    const results = await cleanupAndUploadDatabases(
+      initAllState({
+        env,
+        features: createFeatures([Feature.UploadOverlayDbToApi]),
+      }),
      testRepoName,
      codeql,
      config,
      testApiDetails,
-      createFeatures([Feature.UploadOverlayDbToApi]),
-      getRecordingLogger([]),
+      "",
    );

    // In debug mode we clean up at the `overlay` level for the upload but skip
@@ -486,7 +511,8 @@ test.serial(
  "Does not record a clear cleanup duration when the clear cleanup fails",
  async (t) => {
    await withTmpDir(async (tmpDir) => {
-      setupActionsVars(tmpDir, tmpDir);
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
      sinon
        .stub(actionsUtil, "getRequiredInput")
        .withArgs("upload-database")
@@ -510,12 +536,15 @@ test.serial(
      config.overlayDatabaseMode = OverlayDatabaseMode.OverlayBase;

      const results = await cleanupAndUploadDatabases(
+        initAllState({
+          env,
+          features: createFeatures([Feature.UploadOverlayDbToApi]),
+        }),
        testRepoName,
        codeql,
        config,
        testApiDetails,
-        createFeatures([Feature.UploadOverlayDbToApi]),
-        getRecordingLogger([]),
+        "",
      );

      // When the `clear` cleanup fails, no size is measured, so we should not
@@ -526,3 +555,86 @@ test.serial(
    });
  },
 );
+
+test.serial(
+  "uploadBundledDatabase provides expected request arguments",
+  async (t) =>
+    withTmpDir(async (tmpDir) => {
+      // Write some file that `uploadBundledDatabase` can use for its `fs.createReadStream(bundledDb)` call
+      // so we don't have to stub that or create a fake `ReadStream`.
+      const dbPath = path.join(tmpDir, "db");
+      const content = JSON.stringify({});
+      fs.writeFileSync(dbPath, content);
+
+      // A simple stub for `fetch` that satisfies Octokit when it inspects the response.
+      const fetchStub = sinon.stub().resolves({
+        status: 200,
+        headers: new Headers(),
+        text: async () => "",
+      });
+
+      // Construct a real `ApiClient`.
+      const client = apiClient.getApiClient(
+        getTestEnv(),
+        SAMPLE_DOTCOM_API_DETAILS,
+      );
+
+      // Then wrap the real `request` method in a stub that calls it with our stubbed `fetch`.
+      // This ensures that we have a real `ApiClient` with a mostly real `request`, but which
+      // does not perform any actual requests.
+      const request = client.request;
+      sinon.stub(client, "request").callsFake(async (route, options) =>
+        request(route, {
+          ...options,
+          request: { ...options?.request, fetch: fetchStub },
+        }),
+      );
+
+      // Stub `getApiClient` to return our modified `ApiClient`.
+      const getApiClient = sinon
+        .stub(apiClient, "getApiClient")
+        .returns(client);
+
+      // Calling `uploadBundledDatabase` shouldn't throw.
+      const nwo: RepositoryNwo = { owner: "test", repo: "foo" };
+      const language: BuiltInLanguage = BuiltInLanguage.java;
+
+      await t.notThrowsAsync(async () => {
+        await uploadBundledDatabase(
+          nwo,
+          language,
+          "123",
+          dbPath,
+          content.length,
+          SAMPLE_DOTCOM_API_DETAILS,
+        );
+      });
+
+      // Check that our stubs were called and that they received the expected arguments.
+      t.is(getApiClient.callCount, 1);
+      t.is(fetchStub.callCount, 1);
+
+      const args = fetchStub.args[0];
+      t.is(args.length, 2);
+
+      const url = args[0];
+      t.is(
+        url,
+        `https://uploads.github.com/repos/${nwo.owner}/${nwo.repo}/code-scanning/codeql/databases/${language}?name=${language}-database&commit_oid=123`,
+      );
+
+      const options = args[1];
+      t.like(options, {
+        // Going via `new Headers` and `Object.fromEntries` ensures we get the same cases
+        // for the header keys as we are given.
+        headers: Object.fromEntries(
+          new Headers({
+            authorization: `token ${SAMPLE_DOTCOM_API_DETAILS.auth}`,
+            "Content-Type": "application/zip",
+            "Content-Length": content.length.toString(),
+          }).entries(),
+        ),
+        method: "POST",
+      } satisfies RequestInit);
+    }),
+);
@@ -1,5 +1,6 @@
 import * as fs from "fs";

+import { ActionState } from "./action-common";
 import * as actionsUtil from "./actions-util";
 import { AnalysisKind } from "./analyses";
 import {
@@ -9,13 +10,14 @@ import {
 } from "./api-client";
 import { type CodeQL } from "./codeql";
 import { Config } from "./config-utils";
-import { Feature, FeatureEnablement } from "./feature-flags";
+import { Feature } from "./feature-flags";
 import * as gitUtils from "./git-utils";
+import { parseGitHubUrl } from "./github";
 import { Logger, withGroupAsync } from "./logging";
 import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import { RepositoryNwo } from "./repository";
 import * as util from "./util";
-import { asHTTPError, bundleDb, CleanupLevel, parseGitHubUrl } from "./util";
+import { asHTTPError, bundleDb, CleanupLevel } from "./util";

 /** Information about a database upload. */
 export interface DatabaseUploadResult {
@@ -45,13 +47,15 @@ export interface DatabaseUploadResult {
 }

 export async function cleanupAndUploadDatabases(
+  action: ActionState<["ReadOnlyEnv", "Logger", "FeatureFlags"]>,
  repositoryNwo: RepositoryNwo,
  codeql: CodeQL,
  config: Config,
  apiDetails: GitHubApiDetails,
-  features: FeatureEnablement,
-  logger: Logger,
+  checkoutPath: string,
 ): Promise<DatabaseUploadResult[]> {
+  const logger = action.logger;
+
  if (actionsUtil.getRequiredInput("upload-database") !== "true") {
    logger.debug("Database upload disabled in workflow. Skipping upload.");
    return [];
@@ -78,7 +82,7 @@ export async function cleanupAndUploadDatabases(
    return [];
  }

-  if (!(await gitUtils.isAnalyzingDefaultBranch())) {
+  if (!(await gitUtils.isAnalyzingDefaultBranch(action.env, checkoutPath))) {
    // We only want to upload a database if we are analyzing the default branch.
    logger.debug("Not analyzing default branch. Skipping upload.");
    return [];
@@ -87,7 +91,7 @@ export async function cleanupAndUploadDatabases(
  // If config.overlayDatabaseMode is OverlayBase, then we have overlay base databases for all languages.
  const shouldUploadOverlayBase =
    config.overlayDatabaseMode === OverlayDatabaseMode.OverlayBase &&
-    (await features.getValue(Feature.UploadOverlayDbToApi, codeql));
+    (await action.features.getValue(Feature.UploadOverlayDbToApi, codeql));
  const cleanupLevel = shouldUploadOverlayBase
    ? CleanupLevel.Overlay
    : CleanupLevel.Clear;
@@ -110,9 +114,7 @@ export async function cleanupAndUploadDatabases(
        includeDiagnostics: false,
      });
      bundledDbSize = fs.statSync(bundledDb).size;
-      const commitOid = await gitUtils.getCommitOid(
-        actionsUtil.getRequiredInput("checkout_path"),
-      );
+      const commitOid = await gitUtils.getCommitOid(action.env, checkoutPath);
      // Upload with manual retry logic. We disable Octokit's built-in retries
      // because the request body is a ReadStream, which can only be consumed
      // once.
@@ -257,7 +259,7 @@ async function recordClearCleanupSizes(
 *
 * @returns the duration of the upload in milliseconds
 */
-async function uploadBundledDatabase(
+export async function uploadBundledDatabase(
  repositoryNwo: RepositoryNwo,
  language: string,
  commitOid: string,
@@ -265,7 +267,10 @@ async function uploadBundledDatabase(
  bundledDbSize: number,
  apiDetails: GitHubApiDetails,
 ): Promise<number> {
-  const client = getApiClient();
+  // Ensure that the `apiDetails` that `getApiClient` uses match the ones we were given here,
+  // because we use `apiDetails.auth` below which must be used with the same instance that
+  // `apiDetails` refers to.
+  const client = getApiClient(util.getEnv(), apiDetails);

  const uploadsUrl = new URL(parseGitHubUrl(apiDetails.url));
  uploadsUrl.hostname = `uploads.${uploadsUrl.hostname}`;
@@ -291,7 +296,6 @@ async function uploadBundledDatabase(
        commit_oid: commitOid,
        data: bundledDbReadStream,
        headers: {
-          authorization: `token ${apiDetails.auth}`,
          "Content-Type": "application/zip",
          "Content-Length": bundledDbSize,
        },
@@ -55,25 +55,20 @@ test("getArtifactSuffix", (t) => {
  }
 });

-// These next tests check the correctness of the logic to determine whether or not
-// artifacts are uploaded in debug mode. Since it's not easy to mock the actual
-// call to upload an artifact, we just check that we get an "upload-failed" result,
-// instead of actually uploading the artifact.
-//
-// For tests where we expect artifact upload to be blocked, we check for a different
-// response from the function.
+// These next tests check whether `uploadArtifacts` attempts to upload an artifact. Since it's not
+// easy to mock the actual call to upload an artifact, we check that we get an "upload-failed"
+// result, instead of actually uploading the artifact.

-test("uploadDebugArtifacts when artifacts empty should emit 'no-artifacts-to-upload'", async (t) => {
+test("uploadArtifacts returns 'no-artifacts-to-upload' when there are no files to upload", async (t) => {
  // Test that no error is thrown if artifacts list is empty.
  const logger = getActionsLogger();
  await t.notThrowsAsync(async () => {
-    const uploaded = await debugArtifacts.uploadDebugArtifacts(
+    const uploaded = await debugArtifacts.uploadArtifacts(
      logger,
      [],
      "i-dont-exist",
      "artifactName",
      GitHubVariant.DOTCOM,
-      undefined,
    );
    t.is(
      uploaded,
@@ -83,17 +78,15 @@ test("uploadDebugArtifacts when artifacts empty should emit 'no-artifacts-to-upl
  });
 });

-test("uploadDebugArtifacts when no codeql version is used should invoke artifact upload", async (t) => {
-  // Test that the artifact is uploaded.
+test("uploadArtifacts attempts an upload when there are files to upload", async (t) => {
  const logger = getActionsLogger();
  await t.notThrowsAsync(async () => {
-    const uploaded = await debugArtifacts.uploadDebugArtifacts(
+    const uploaded = await debugArtifacts.uploadArtifacts(
      logger,
      ["hucairz"],
      "i-dont-exist",
      "artifactName",
      GitHubVariant.DOTCOM,
-      undefined,
    );
    t.is(
      uploaded,
@@ -103,44 +96,3 @@ test("uploadDebugArtifacts when no codeql version is used should invoke artifact
    );
  });
 });
-
-test("uploadDebugArtifacts when new codeql version is used should invoke artifact upload", async (t) => {
-  // Test that the artifact is uploaded.
-  const logger = getActionsLogger();
-  await t.notThrowsAsync(async () => {
-    const uploaded = await debugArtifacts.uploadDebugArtifacts(
-      logger,
-      ["hucairz"],
-      "i-dont-exist",
-      "artifactName",
-      GitHubVariant.DOTCOM,
-      "2.20.3",
-    );
-    t.is(
-      uploaded,
-      // The failure is expected since we don't want to actually upload any artifacts in unit tests.
-      "upload-failed",
-      "Expect failure to upload artifacts since root dir does not exist",
-    );
-  });
-});
-
-test("uploadDebugArtifacts when old codeql is used should avoid trying to upload artifacts", async (t) => {
-  // Test that the artifact is not uploaded.
-  const logger = getActionsLogger();
-  await t.notThrowsAsync(async () => {
-    const uploaded = await debugArtifacts.uploadDebugArtifacts(
-      logger,
-      ["hucairz"],
-      "i-dont-exist",
-      "artifactName",
-      GitHubVariant.DOTCOM,
-      "2.20.2",
-    );
-    t.is(
-      uploaded,
-      "upload-not-supported",
-      "Expected artifact upload to be blocked because of old CodeQL version",
-    );
-  });
-});
@@ -10,15 +10,11 @@ import { getOptionalInput, getTemporaryDirectory } from "./actions-util";
 import { dbIsFinalized } from "./analyze";
 import { scanArtifactsForTokens } from "./artifact-scanner";
 import { type CodeQL } from "./codeql";
-import { Config } from "./config-utils";
-import { EnvVar } from "./environment";
+import type { ActionConfig } from "./config/action-config";
+import { EnvVar, exportEnvVar } from "./environment";
 import * as json from "./json";
 import { Language } from "./languages";
 import { Logger, withGroup } from "./logging";
-import {
-  isSafeArtifactUpload,
-  SafeArtifactUploadVersion,
-} from "./tools-features";
 import {
  bundleDb,
  doesDirectoryExist,
@@ -40,7 +36,6 @@ export function sanitizeArtifactName(name: string): string {
 export async function uploadCombinedSarifArtifacts(
  logger: Logger,
  gitHubVariant: GitHubVariant,
-  codeQlVersion: string | undefined,
 ) {
  const tempDir = getTemporaryDirectory();

@@ -70,13 +65,12 @@ export async function uploadCombinedSarifArtifacts(
      }

      try {
-        await uploadDebugArtifacts(
+        await uploadArtifacts(
          logger,
          toUpload,
          baseTempDir,
          "combined-sarif-artifacts",
          gitHubVariant,
-          codeQlVersion,
        );
      } catch (e) {
        logger.warning(
@@ -95,7 +89,7 @@ export async function uploadCombinedSarifArtifacts(
 * @return The path to that debug artifact, or undefined if an error occurs.
 */
 function tryPrepareSarifDebugArtifact(
-  config: Config,
+  config: ActionConfig<"dbLocation">,
  language: Language,
  logger: Logger,
 ): string | undefined {
@@ -137,7 +131,7 @@ function tryPrepareSarifDebugArtifact(
 */
 async function tryBundleDatabase(
  codeql: CodeQL,
-  config: Config,
+  config: ActionConfig<"dbLocation">,
  language: Language,
  logger: Logger,
 ): Promise<string | undefined> {
@@ -163,6 +157,11 @@ async function tryBundleDatabase(
  }
 }

+/** The minimal configuration needed for `tryUploadAllAvailableDebugArtifacts`. */
+export type UploadDebugArtifactsConfig = ActionConfig<
+  "languages" | "gitHubVersion" | "dbLocation" | "debugArtifactName"
+>;
+
 /**
 * Attempt to upload all available debug artifacts.
 *
@@ -170,9 +169,8 @@ async function tryBundleDatabase(
 */
 export async function tryUploadAllAvailableDebugArtifacts(
  codeql: CodeQL,
-  config: Config,
+  config: UploadDebugArtifactsConfig,
  logger: Logger,
-  codeQlVersion: string | undefined,
 ) {
  const filesToUpload: string[] = [];
  try {
@@ -231,13 +229,12 @@ export async function tryUploadAllAvailableDebugArtifacts(

  try {
    await withGroup("Uploading debug artifacts", async () =>
-      uploadDebugArtifacts(
+      uploadArtifacts(
        logger,
        filesToUpload,
        config.dbLocation,
        config.debugArtifactName,
        config.gitHubVersion.type,
-        codeQlVersion,
      ),
    );
  } catch (e) {
@@ -283,26 +280,6 @@ export type UploadArtifactsResult =
  | "upload-successful"
  | "upload-failed";

-export async function uploadDebugArtifacts(
-  logger: Logger,
-  toUpload: string[],
-  rootDir: string,
-  artifactName: string,
-  ghVariant: GitHubVariant,
-  codeQlVersion: string | undefined,
-): Promise<UploadArtifactsResult | "upload-not-supported"> {
-  const uploadSupported = isSafeArtifactUpload(codeQlVersion);
-
-  if (!uploadSupported) {
-    core.info(
-      `Skipping debug artifact upload because the current CLI does not support safe upload. Please upgrade to CLI v${SafeArtifactUploadVersion} or later.`,
-    );
-    return "upload-not-supported";
-  }
-
-  return uploadArtifacts(logger, toUpload, rootDir, artifactName, ghVariant);
-}
-
 /**
 * Uploads the specified files as a single workflow artifact.
 *
@@ -330,7 +307,7 @@ export async function uploadArtifacts(
  // some issues early.
  if (isInTestMode()) {
    await scanArtifactsForTokens(toUpload, logger);
-    core.exportVariable("CODEQL_ACTION_ARTIFACT_SCAN_FINISHED", "true");
+    exportEnvVar("CODEQL_ACTION_ARTIFACT_SCAN_FINISHED", "true");
  }

  const suffix = getArtifactSuffix(getOptionalInput("matrix"));
@@ -381,7 +358,7 @@ export async function getArtifactUploaderClient(
 * all files in the database folder and return the path.
 */
 async function createPartialDatabaseBundle(
-  config: Config,
+  config: ActionConfig<"dbLocation">,
  language: Language,
 ): Promise<string> {
  const databasePath = getCodeQLDatabasePath(config, language);
@@ -422,7 +399,7 @@ async function createPartialDatabaseBundle(
 */
 async function createDatabaseBundleCli(
  codeql: CodeQL,
-  config: Config,
+  config: ActionConfig<"dbLocation">,
  language: Language,
 ): Promise<string> {
  const databaseBundlePath = await bundleDb(
@@ -1,6 +1,6 @@
 {
-  "bundleVersion": "codeql-bundle-v2.27.0",
-  "cliVersion": "2.27.0",
-  "priorBundleVersion": "codeql-bundle-v2.26.4",
-  "priorCliVersion": "2.26.4"
+  "bundleVersion": "codeql-bundle-v2.27.2",
+  "cliVersion": "2.27.2",
+  "priorBundleVersion": "codeql-bundle-v2.27.1",
+  "priorCliVersion": "2.27.1"
 }
@@ -313,6 +313,7 @@ export async function downloadDependencyCaches(

    const primaryKey = await cacheKey(codeql, features, language, patterns);
    const restoreKeys: string[] = [
+      primaryKey,
      await cachePrefix(codeql, features, language),
    ];

@@ -0,0 +1,12 @@
+import test from "ava";
+
+import { Env, ReadOnlyEnv } from "./environment";
+import { getTestEnv, setupTests } from "./testing-utils";
+
+setupTests(test);
+
+test("isTestingEnv() is true", (t) => {
+  t.true(new ReadOnlyEnv(process.env).isTestingEnv());
+  t.true(new Env(process.env).isTestingEnv());
+  t.true(getTestEnv().isTestingEnv());
+});
@@ -1,3 +1,10 @@
+import * as core from "@actions/core";
+
+/**
+ * This constant is set in `ava.setup.mjs` for tests.
+ */
+declare const __CODEQL_ACTION_TEST_ENV__: string | undefined;
+
 /**
 * Environment variables used by Default Setup to communicate the private registry proxy configuration.
 */
@@ -211,8 +218,20 @@ export enum ActionsEnvVars {
  RUNNER_TOOL_CACHE = "RUNNER_TOOL_CACHE",
 }

+/** Environment variables which are not specific to CodeQL. */
+export enum SystemEnvVar {
+  /**
+   * Used by Node and related tools to indicate what kind of environment we are running in.
+   */
+  NODE_ENV = "NODE_ENV",
+}
+
 /** A type representing all known environment variables. */
-export type KnownEnvVar = EnvVar | ActionsEnvVars | RegistryProxyVars;
+export type KnownEnvVar =
+  | EnvVar
+  | ActionsEnvVars
+  | RegistryProxyVars
+  | SystemEnvVar;

 /**
 * Gets an environment variable, but throws an error if it is not set.
@@ -289,6 +308,26 @@ export class ReadOnlyEnv<T extends string | undefined = string | undefined> {
  public entries(): Array<[string, T]> {
    return Object.entries(this.vars);
  }
+
+  /**
+   * Gets a value indicating whether we should skip uploads of
+   * all kinds (SARIF results, status reports, DBs, ...).
+   *
+   * This is not guaranteed to be set in all test environments.
+   */
+  public isSkippingUploadsInTests(): boolean {
+    return this.getOptional(EnvVar.TEST_MODE) === "true";
+  }
+
+  /**
+   * Gets a value indicative of whether we are in a testing environment
+   * by testing whether the value of the `NODE_ENV` variable is "test".
+   * This is expected to be the case if e.g. `ava` is running the tests
+   * or if this instance was constructed by `getTestEnv`.
+   */
+  public isTestingEnv(): boolean {
+    return __CODEQL_ACTION_TEST_ENV__ === "unit-test";
+  }
 }

 /**
@@ -307,6 +346,33 @@ export class Env<
    this.changed = true;
  }

+  /** Sets all environment variables given by `vars`. */
+  public setAll(vars: Record<string, T>): void {
+    for (const [key, val] of Object.entries(vars)) {
+      this.set(key, val);
+    }
+  }
+
+  /**
+   * Wrapper around `core.exportVariable` which does not call `core.exportVariable`
+   * when running unit tests. This is important, because otherwise `core.exportVariable`
+   * sets environment variables for other steps in a workflow when we run unit tests in CI.
+   *
+   * @param name The name of the environment variable to set and export.
+   * @param val The value to set and export for the environment variable.
+   */
+  public export(name: string, val: T): void {
+    // Setting the environment variable for this instance is always OK, including
+    // in tests, since we use fresh `Env` instances whenever needed. This allows
+    // tests to pass that rely on that part of the `core.exportVariable` behaviour.
+    this.set(name, val);
+
+    // Call `core.exportVariable` whenever we are not in a test environment.
+    if (!this.isTestingEnv()) {
+      core.exportVariable(name, val);
+    }
+  }
+
  /** Gets a value indicating whether `set` was called at least once. */
  public hasChanged(): boolean {
    return this.changed;
@@ -317,3 +383,34 @@ export class Env<
 export function getEnv(env: NodeJS.ProcessEnv = process.env): Env {
  return new Env(env);
 }
+
+/**
+ * Returns whether we are in test mode. This is used by CodeQL Action PR checks.
+ *
+ * In test mode, we skip several uploads (SARIF results, status reports, DBs, ...).
+ *
+ * @deprecated
+ *  The purpose of this function is ambiguous. Use `isSkippingUploadsInTests` on
+ *  a `ReadOnlyEnv` instance instead for equivalent behaviour. Use `isTestingEnv`
+ *  to determine if we are running in a unit test.
+ */
+export function isInTestMode(): boolean {
+  return getEnv().isSkippingUploadsInTests();
+}
+
+/**
+ * Wrapper around `core.exportVariable` which does not call `core.exportVariable`
+ * when running unit tests. This is important, because otherwise `core.exportVariable`
+ * sets environment variables for other steps in a workflow when we run unit tests in CI.
+ *
+ * @deprecated Use `export` on an `Env` instance instead.
+ */
+export function exportEnvVar(name: string, val: any): void {
+  const env = getEnv();
+
+  if (typeof val === "string") {
+    env.export(name, val);
+  } else {
+    env.export(name, JSON.stringify(val));
+  }
+}
@@ -168,7 +168,7 @@ export enum Feature {
   * Controls whether we may download a bundle containing only the single language being analysed,
   * rather than the combined bundle that contains every language.
   */
-  PerLanguageBundles = "per_language_bundles",
+  PerLanguageBundles = "per_language_bundles_v2",
  QaTelemetryEnabled = "qa_telemetry_enabled",
  /** Routes (some) API requests through the registry proxy. */
  ProxyApiRequests = "proxy_api_requests",
@@ -240,7 +240,7 @@ export const featureConfig = {
    defaultValue: false,
    envVar: "CODEQL_EXTRACTOR_CPP_AUTOINSTALL_DEPENDENCIES",
    legacyApi: true,
-    minimumVersion: "2.15.0",
+    minimumVersion: undefined,
  },
  [Feature.CsharpCacheBuildModeNone]: {
    defaultValue: false,
@@ -7,32 +7,42 @@ import test from "ava";
 import * as sinon from "sinon";

 import * as actionsUtil from "./actions-util";
+import { ActionsEnvVars, EnvVar } from "./environment";
 import * as gitUtils from "./git-utils";
-import { setupActionsVars, setupTests } from "./testing-utils";
+import { getTestEnv, setupActionsVars, setupTests } from "./testing-utils";
 import { withTmpDir } from "./util";

 setupTests(test);

-test.serial("getRef() throws on the empty string", async (t) => {
-  process.env["GITHUB_REF"] = "";
-  await t.throwsAsync(gitUtils.getRef);
+test("getRef() throws on the empty string", async (t) => {
+  const env = getTestEnv({ [ActionsEnvVars.GITHUB_REF]: "" });
+  await t.throwsAsync(() => gitUtils.getRef(env, ""));
 });

 test.serial(
  "getRef() returns merge PR ref if GITHUB_SHA still checked out",
  async (t) => {
    await withTmpDir(async (tmpDir: string) => {
-      setupActionsVars(tmpDir, tmpDir);
      const expectedRef = "refs/pull/1/merge";
      const currentSha = "a".repeat(40);
-      process.env["GITHUB_REF"] = expectedRef;
-      process.env["GITHUB_SHA"] = currentSha;
+
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
+      env.setAll({
+        [ActionsEnvVars.GITHUB_REF]: expectedRef,
+        [ActionsEnvVars.GITHUB_SHA]: currentSha,
+      });

      const callback = sinon.stub(gitUtils, "getCommitOid");
-      callback.withArgs("HEAD").resolves(currentSha);
+      callback
+        .withArgs(sinon.match.any, sinon.match.string, "HEAD")
+        .resolves(currentSha);

-      const actualRef = await gitUtils.getRef();
+      const actualRef = await gitUtils.getRef(env, tmpDir);
      t.deepEqual(actualRef, expectedRef);
+
+      t.is(callback.callCount, 1);
+      t.true(callback.calledOnceWith(env, tmpDir, "HEAD"));
    });
  },
 );
@@ -41,18 +51,33 @@ test.serial(
  "getRef() returns merge PR ref if GITHUB_REF still checked out but sha has changed (actions checkout@v1)",
  async (t) => {
    await withTmpDir(async (tmpDir: string) => {
-      setupActionsVars(tmpDir, tmpDir);
      const expectedRef = "refs/pull/1/merge";
-      process.env["GITHUB_REF"] = expectedRef;
-      process.env["GITHUB_SHA"] = "b".repeat(40);
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
+      env.setAll({
+        [ActionsEnvVars.GITHUB_REF]: expectedRef,
+        [ActionsEnvVars.GITHUB_SHA]: "b".repeat(40),
+      });
      const sha = "a".repeat(40);

      const callback = sinon.stub(gitUtils, "getCommitOid");
-      callback.withArgs("refs/remotes/pull/1/merge").resolves(sha);
-      callback.withArgs("HEAD").resolves(sha);
+      callback
+        .withArgs(
+          sinon.match.any,
+          sinon.match.string,
+          "refs/remotes/pull/1/merge",
+        )
+        .resolves(sha);
+      callback
+        .withArgs(sinon.match.any, sinon.match.string, "HEAD")
+        .resolves(sha);

-      const actualRef = await gitUtils.getRef();
+      const actualRef = await gitUtils.getRef(env, tmpDir);
      t.deepEqual(actualRef, expectedRef);
+
+      t.is(callback.callCount, 2);
+      t.true(callback.calledWith(env, tmpDir, "HEAD"));
+      t.true(callback.calledWith(env, tmpDir, "refs/remotes/pull/1/merge"));
    });
  },
 );
@@ -61,16 +86,28 @@ test.serial(
  "getRef() returns head PR ref if GITHUB_REF no longer checked out",
  async (t) => {
    await withTmpDir(async (tmpDir: string) => {
-      setupActionsVars(tmpDir, tmpDir);
-      process.env["GITHUB_REF"] = "refs/pull/1/merge";
-      process.env["GITHUB_SHA"] = "a".repeat(40);
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
+      env.setAll({
+        [ActionsEnvVars.GITHUB_REF]: "refs/pull/1/merge",
+        [ActionsEnvVars.GITHUB_SHA]: "a".repeat(40),
+      });

      const callback = sinon.stub(gitUtils, "getCommitOid");
-      callback.withArgs(tmpDir, "refs/pull/1/merge").resolves("a".repeat(40));
-      callback.withArgs(tmpDir, "HEAD").resolves("b".repeat(40));
+      callback
+        .withArgs(sinon.match.any, tmpDir, "refs/remotes/pull/1/merge")
+        .resolves("a".repeat(40));
+      callback
+        .withArgs(sinon.match.any, tmpDir, "HEAD")
+        .resolves("b".repeat(40));
+      callback.throws(new Error("Unexpected getCommitOid call in test."));

-      const actualRef = await gitUtils.getRef();
+      const actualRef = await gitUtils.getRef(env, tmpDir);
      t.deepEqual(actualRef, "refs/pull/1/head");
+
+      t.is(callback.callCount, 2);
+      t.true(callback.calledWith(env, tmpDir, "refs/remotes/pull/1/merge"));
+      t.true(callback.calledWith(env, tmpDir, "HEAD"));
    });
  },
 );
@@ -79,7 +116,6 @@ test.serial(
  "getRef() returns ref provided as an input and ignores current HEAD",
  async (t) => {
    await withTmpDir(async (tmpDir: string) => {
-      setupActionsVars(tmpDir, tmpDir);
      const getAdditionalInputStub = sinon.stub(
        actionsUtil,
        "getOptionalInput",
@@ -88,15 +124,26 @@ test.serial(
      getAdditionalInputStub.withArgs("sha").resolves("b".repeat(40));

      // These values are be ignored
-      process.env["GITHUB_REF"] = "refs/pull/1/merge";
-      process.env["GITHUB_SHA"] = "a".repeat(40);
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
+      env.setAll({
+        [ActionsEnvVars.GITHUB_REF]: "refs/pull/1/merge",
+        [ActionsEnvVars.GITHUB_SHA]: "a".repeat(40),
+      });

      const callback = sinon.stub(gitUtils, "getCommitOid");
-      callback.withArgs("refs/pull/1/merge").resolves("b".repeat(40));
-      callback.withArgs("HEAD").resolves("b".repeat(40));
+      callback
+        .withArgs(sinon.match.any, tmpDir, "refs/pull/1/merge")
+        .resolves("b".repeat(40));
+      callback
+        .withArgs(sinon.match.any, sinon.match.string, "HEAD")
+        .resolves("b".repeat(40));

-      const actualRef = await gitUtils.getRef();
+      const actualRef = await gitUtils.getRef(env, tmpDir);
      t.deepEqual(actualRef, "refs/pull/2/merge");
+
+      // getCommitOid shouldn't be called, because the ref should be taken from the input
+      t.is(callback.callCount, 0);
    });
  },
 );
@@ -105,14 +152,17 @@ test.serial(
  "getRef() returns CODE_SCANNING_REF as a fallback for GITHUB_REF",
  async (t) => {
    await withTmpDir(async (tmpDir: string) => {
-      setupActionsVars(tmpDir, tmpDir);
      const expectedRef = "refs/pull/1/HEAD";
      const currentSha = "a".repeat(40);
-      process.env["CODE_SCANNING_REF"] = expectedRef;
-      process.env["GITHUB_REF"] = "";
-      process.env["GITHUB_SHA"] = currentSha;
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
+      env.setAll({
+        [EnvVar.CODE_SCANNING_REF]: expectedRef,
+        [ActionsEnvVars.GITHUB_REF]: "",
+        [ActionsEnvVars.GITHUB_SHA]: currentSha,
+      });

-      const actualRef = await gitUtils.getRef();
+      const actualRef = await gitUtils.getRef(env, tmpDir);
      t.deepEqual(actualRef, expectedRef);
    });
  },
@@ -122,14 +172,17 @@ test.serial(
  "getRef() returns GITHUB_REF over CODE_SCANNING_REF if both are provided",
  async (t) => {
    await withTmpDir(async (tmpDir: string) => {
-      setupActionsVars(tmpDir, tmpDir);
      const expectedRef = "refs/pull/1/merge";
      const currentSha = "a".repeat(40);
-      process.env["CODE_SCANNING_REF"] = "refs/pull/1/HEAD";
-      process.env["GITHUB_REF"] = expectedRef;
-      process.env["GITHUB_SHA"] = currentSha;
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
+      env.setAll({
+        [EnvVar.CODE_SCANNING_REF]: "refs/pull/1/HEAD",
+        [ActionsEnvVars.GITHUB_REF]: expectedRef,
+        [ActionsEnvVars.GITHUB_SHA]: currentSha,
+      });

-      const actualRef = await gitUtils.getRef();
+      const actualRef = await gitUtils.getRef(env, tmpDir);
      t.deepEqual(actualRef, expectedRef);
    });
  },
@@ -139,7 +192,9 @@ test.serial(
  "getRef() throws an error if only `ref` is provided as an input",
  async (t) => {
    await withTmpDir(async (tmpDir: string) => {
-      setupActionsVars(tmpDir, tmpDir);
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
+
      const getAdditionalInputStub = sinon.stub(
        actionsUtil,
        "getOptionalInput",
@@ -148,7 +203,7 @@ test.serial(

      await t.throwsAsync(
        async () => {
-          await gitUtils.getRef();
+          await gitUtils.getRef(env, tmpDir);
        },
        {
          instanceOf: Error,
@@ -164,8 +219,12 @@ test.serial(
  "getRef() throws an error if only `sha` is provided as an input",
  async (t) => {
    await withTmpDir(async (tmpDir: string) => {
-      setupActionsVars(tmpDir, tmpDir);
-      process.env["GITHUB_WORKSPACE"] = "/tmp";
+      const env = getTestEnv();
+      setupActionsVars(tmpDir, tmpDir, {}, env);
+      env.setAll({
+        [ActionsEnvVars.GITHUB_WORKSPACE]: "/tmp",
+      });
+
      const getAdditionalInputStub = sinon.stub(
        actionsUtil,
        "getOptionalInput",
@@ -174,7 +233,7 @@ test.serial(

      await t.throwsAsync(
        async () => {
-          await gitUtils.getRef();
+          await gitUtils.getRef(env, tmpDir);
        },
        {
          instanceOf: Error,
@@ -187,13 +246,16 @@ test.serial(
 );

 test.serial("isAnalyzingDefaultBranch()", async (t) => {
-  process.env["GITHUB_EVENT_NAME"] = "push";
-  process.env["CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH"] = "true";
-  t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(), true);
-  process.env["CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH"] = "false";
+  const env = getTestEnv({
+    [ActionsEnvVars.GITHUB_EVENT_NAME]: "push",
+    CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH: "true",
+  });
+  t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(env, ""), true);
+
+  env.set("CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH", "false");

  await withTmpDir(async (tmpDir) => {
-    setupActionsVars(tmpDir, tmpDir);
+    setupActionsVars(tmpDir, tmpDir, {}, env);
    const envFile = path.join(tmpDir, "event.json");
    fs.writeFileSync(
      envFile,
@@ -203,17 +265,17 @@ test.serial("isAnalyzingDefaultBranch()", async (t) => {
        },
      }),
    );
-    process.env["GITHUB_EVENT_PATH"] = envFile;
+    env.set(ActionsEnvVars.GITHUB_EVENT_PATH, envFile);

-    process.env["GITHUB_REF"] = "main";
-    process.env["GITHUB_SHA"] = "1234";
-    t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(), true);
+    env.set(ActionsEnvVars.GITHUB_REF, "main");
+    env.set(ActionsEnvVars.GITHUB_SHA, "1234");
+    t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(env, tmpDir), true);

-    process.env["GITHUB_REF"] = "refs/heads/main";
-    t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(), true);
+    env.set(ActionsEnvVars.GITHUB_REF, "refs/heads/main");
+    t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(env, tmpDir), true);

-    process.env["GITHUB_REF"] = "feature";
-    t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(), false);
+    env.set(ActionsEnvVars.GITHUB_REF, "feature");
+    t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(env, tmpDir), false);

    fs.writeFileSync(
      envFile,
@@ -221,9 +283,9 @@ test.serial("isAnalyzingDefaultBranch()", async (t) => {
        schedule: "0 0 * * *",
      }),
    );
-    process.env["GITHUB_EVENT_NAME"] = "schedule";
-    process.env["GITHUB_REF"] = "refs/heads/main";
-    t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(), true);
+    env.set(ActionsEnvVars.GITHUB_EVENT_NAME, "schedule");
+    env.set(ActionsEnvVars.GITHUB_REF, "refs/heads/main");
+    t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(env, tmpDir), true);

    const getAdditionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
    getAdditionalInputStub
@@ -232,9 +294,9 @@ test.serial("isAnalyzingDefaultBranch()", async (t) => {
    getAdditionalInputStub
      .withArgs("sha")
      .resolves("0000000000000000000000000000000000000000");
-    process.env["GITHUB_EVENT_NAME"] = "schedule";
-    process.env["GITHUB_REF"] = "refs/heads/main";
-    t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(), false);
+    env.set(ActionsEnvVars.GITHUB_EVENT_NAME, "schedule");
+    env.set(ActionsEnvVars.GITHUB_REF, "refs/heads/main");
+    t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(env, tmpDir), false);
  });
 });

@@ -13,6 +13,7 @@ import {
  getWorkflowEvent,
  getWorkflowEventName,
 } from "./actions-util";
+import { ActionsEnvVars, EnvVar, type ReadOnlyEnv } from "./environment";
 import { ConfigurationError, getRequiredEnvParam } from "./util";

 /**
@@ -101,6 +102,7 @@ export const runGitCommand = async function (
 * Gets the SHA of the commit that is currently checked out.
 */
 export const getCommitOid = async function (
+  env: ReadOnlyEnv,
  checkoutPath: string,
  ref = "HEAD",
 ): Promise<string> {
@@ -119,7 +121,9 @@ export const getCommitOid = async function (
    );
    return stdout.trim();
  } catch {
-    return getOptionalInput("sha") || getRequiredEnvParam("GITHUB_SHA");
+    return (
+      getOptionalInput("sha") || env.getRequired(ActionsEnvVars.GITHUB_SHA)
+    );
  }
 };

@@ -241,7 +245,7 @@ export const getGitRoot = async function (
      ["rev-parse", "--show-toplevel"],
      `Cannot find Git repository root from the source root ${sourceRoot}.`,
    );
-    return stdout.trim();
+    return path.resolve(stdout.trim());
  } catch {
    // Errors are already logged by runGitCommand()
    return undefined;
@@ -314,18 +318,18 @@ export const getFileOidsUnderPath = async function (
  return fileOidMap;
 };

-function getRefFromEnv(): string {
+function getRefFromEnv(env: ReadOnlyEnv): string {
  // To workaround a limitation of Actions dynamic workflows not setting
  // the GITHUB_REF in some cases, we accept also the ref within the
  // CODE_SCANNING_REF variable. When possible, however, we prefer to use
  // the GITHUB_REF as that is a protected variable and cannot be overwritten.
  let refEnv: string;
  try {
-    refEnv = getRequiredEnvParam("GITHUB_REF");
+    refEnv = env.getRequired(ActionsEnvVars.GITHUB_REF);
  } catch (e) {
    // If the GITHUB_REF is not set, we try to rescue by getting the
    // CODE_SCANNING_REF.
-    const maybeRef = process.env["CODE_SCANNING_REF"];
+    const maybeRef = env.getOptional(EnvVar.CODE_SCANNING_REF);
    if (maybeRef === undefined || maybeRef.length === 0) {
      throw e;
    }
@@ -337,15 +341,16 @@ function getRefFromEnv(): string {
 /**
 * Get the ref currently being analyzed.
 */
-export async function getRef(): Promise<string> {
+export async function getRef(
+  env: ReadOnlyEnv,
+  checkoutPath: string | undefined,
+): Promise<string> {
  // Will be in the form "refs/heads/master" on a push event
  // or in the form "refs/pull/N/merge" on a pull_request event
  const refInput = getOptionalInput("ref");
  const shaInput = getOptionalInput("sha");
-  const checkoutPath =
-    getOptionalInput("checkout_path") ||
-    getOptionalInput("source-root") ||
-    getRequiredEnvParam("GITHUB_WORKSPACE");
+  checkoutPath =
+    checkoutPath ?? env.getRequired(ActionsEnvVars.GITHUB_WORKSPACE);

  const hasRefInput = !!refInput;
  const hasShaInput = !!shaInput;
@@ -356,8 +361,8 @@ export async function getRef(): Promise<string> {
    );
  }

-  const ref = refInput || getRefFromEnv();
-  const sha = shaInput || getRequiredEnvParam("GITHUB_SHA");
+  const ref = refInput || getRefFromEnv(env);
+  const sha = shaInput || env.getRequired(ActionsEnvVars.GITHUB_SHA);

  // If the ref is a user-provided input, we have to skip logic
  // and assume that it is really where they want to upload the results.
@@ -374,7 +379,7 @@ export async function getRef(): Promise<string> {
    return ref;
  }

-  const head = await getCommitOid(checkoutPath, "HEAD");
+  const head = await getCommitOid(env, checkoutPath, "HEAD");

  // in actions/checkout@v2+ we can check if git rev-parse HEAD == GITHUB_SHA
  // in actions/checkout@v1 this may not be true as it checks out the repository
@@ -384,6 +389,7 @@ export async function getRef(): Promise<string> {
  const hasChangedRef =
    sha !== head &&
    (await getCommitOid(
+      env,
      checkoutPath,
      ref.replace(/^refs\/pull\//, "refs/remotes/pull/"),
    )) !== head;
@@ -410,20 +416,23 @@ function removeRefsHeadsPrefix(ref: string): string {
 * environment variable can be set in cases where repository information might not be available, for
 * example dynamic workflows.
 */
-export async function isAnalyzingDefaultBranch(): Promise<boolean> {
-  if (process.env.CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH === "true") {
+export async function isAnalyzingDefaultBranch(
+  env: ReadOnlyEnv,
+  checkoutPath: string | undefined,
+): Promise<boolean> {
+  if (env.getOptional("CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH") === "true") {
    return true;
  }

  // Get the current ref and trim and refs/heads/ prefix
-  let currentRef = await getRef();
+  let currentRef = await getRef(env, checkoutPath);
  currentRef = removeRefsHeadsPrefix(currentRef);

-  const event = getWorkflowEvent();
+  const event = getWorkflowEvent(env);
  let defaultBranch = event?.repository?.default_branch;

-  if (getWorkflowEventName() === "schedule") {
-    defaultBranch = removeRefsHeadsPrefix(getRefFromEnv());
+  if (getWorkflowEventName(env) === "schedule") {
+    defaultBranch = removeRefsHeadsPrefix(getRefFromEnv(env));
  }

  return currentRef === defaultBranch;
@@ -0,0 +1,111 @@
+import test from "ava";
+
+import { ActionsEnvVars } from "./environment";
+import * as github from "./github";
+import { getTestEnv, setupTests } from "./testing-utils";
+
+setupTests(test);
+
+test("parseGitHubUrl", (t) => {
+  t.deepEqual(github.parseGitHubUrl("github.com"), "https://github.com");
+  t.deepEqual(
+    github.parseGitHubUrl("https://github.com"),
+    "https://github.com",
+  );
+  t.deepEqual(
+    github.parseGitHubUrl("https://api.github.com"),
+    "https://github.com",
+  );
+  t.deepEqual(
+    github.parseGitHubUrl("https://github.com/foo/bar"),
+    "https://github.com",
+  );
+
+  t.deepEqual(
+    github.parseGitHubUrl("github.example.com"),
+    "https://github.example.com/",
+  );
+  t.deepEqual(
+    github.parseGitHubUrl("https://github.example.com"),
+    "https://github.example.com/",
+  );
+  t.deepEqual(
+    github.parseGitHubUrl("https://api.github.example.com"),
+    "https://github.example.com/",
+  );
+  t.deepEqual(
+    github.parseGitHubUrl("https://github.example.com/api/v3"),
+    "https://github.example.com/",
+  );
+  t.deepEqual(
+    github.parseGitHubUrl("https://github.example.com:1234"),
+    "https://github.example.com:1234/",
+  );
+  t.deepEqual(
+    github.parseGitHubUrl("https://api.github.example.com:1234"),
+    "https://github.example.com:1234/",
+  );
+  t.deepEqual(
+    github.parseGitHubUrl("https://github.example.com:1234/api/v3"),
+    "https://github.example.com:1234/",
+  );
+  t.deepEqual(
+    github.parseGitHubUrl("https://github.example.com/base/path"),
+    "https://github.example.com/base/path/",
+  );
+  t.deepEqual(
+    github.parseGitHubUrl("https://github.example.com/base/path/api/v3"),
+    "https://github.example.com/base/path/",
+  );
+
+  t.throws(() => github.parseGitHubUrl(""), {
+    message: '"" is not a valid URL',
+  });
+  t.throws(() => github.parseGitHubUrl("ssh://github.com"), {
+    message: '"ssh://github.com" is not a http or https URL',
+  });
+  t.throws(() => github.parseGitHubUrl("http:///::::433"), {
+    message: '"http:///::::433" is not a valid URL',
+  });
+});
+
+test("getCurrentInstance throws if required env vars aren't set", (t) => {
+  t.throws(() => github.getCurrentInstance(getTestEnv()));
+  t.throws(() => {
+    const env = getTestEnv({
+      [ActionsEnvVars.GITHUB_SERVER_URL]: "https://localhost",
+    });
+    github.getCurrentInstance(env);
+  });
+  t.throws(() => {
+    const env = getTestEnv({
+      [ActionsEnvVars.GITHUB_API_URL]: "https://api.localhost",
+    });
+    github.getCurrentInstance(env);
+  });
+});
+
+test("getCurrentInstance constructs instance from environment", (t) => {
+  const url = "https://localhost";
+  const apiUrl = "https://api.localhost";
+
+  const env = getTestEnv({
+    [ActionsEnvVars.GITHUB_SERVER_URL]: url,
+    [ActionsEnvVars.GITHUB_API_URL]: apiUrl,
+  });
+  const instance = github.getCurrentInstance(env);
+
+  t.is(instance.url, url);
+  t.is(instance.apiURL, apiUrl);
+});
+
+test("getCurrentInstance constructs dotcom instance with dotcom env vars", (t) => {
+  const env = getTestEnv({
+    [ActionsEnvVars.GITHUB_SERVER_URL]: github.GITHUB_DOTCOM_URL,
+    [ActionsEnvVars.GITHUB_API_URL]: github.GITHUB_DOTCOM_API_URL,
+  });
+  const instance = github.getCurrentInstance(env);
+  const dotcomInstance = github.getDotcomInstance();
+
+  t.deepEqual(dotcomInstance, instance);
+});
@@ -0,0 +1,110 @@
+import { ActionsEnvVars, type ReadOnlyEnv } from "./environment";
+import { ConfigurationError } from "./util";
+
+/** A string representing a GitHub instance address. */
+export type InstanceURL = string;
+
+/**
+ * The URL for github.com.
+ */
+export const GITHUB_DOTCOM_URL: InstanceURL = "https://github.com";
+
+/** A string representing a GitHub API instance address. */
+export type InstanceApiURL = string;
+
+/**
+ * The URL for api.github.com.
+ */
+export const GITHUB_DOTCOM_API_URL: InstanceApiURL = "https://api.github.com";
+
+/**
+ * Represents information about a GitHub instance, how to authenticate to it,
+ * and how to authenticate to other repos on it.
+ */
+export type GitHubApiCombinedDetails = GitHubApiDetails &
+  GitHubApiExternalRepoDetails;
+
+/** Represents information about a GitHub instance. */
+export type GitHubInstance = {
+  /** The base URL of the GitHub instance, such as `https://github.com`. */
+  url: string;
+  /**
+   * The API base URL of the GitHub instance, such as `https://api.github.com`.
+   * Typically this is the `api.` subdomain of the `url` domain.
+   */
+  apiURL: string | undefined;
+};
+
+/** Represents a {@link GitHubInstance} with a token for accessing the API. */
+export type GitHubApiDetails = GitHubInstance & {
+  /** The token to use for accessing the API of the GitHub instance. */
+  auth?: string;
+};
+
+/**
+ * Represents information for accessing a repository on the same GitHub instance as the Action
+ * is currently running on.
+ */
+export type GitHubApiExternalRepoDetails = {
+  /** An optional token for accessing repo(s) on the same GitHub instance. */
+  externalRepoAuth?: string;
+};
+
+/**
+ * Parses user input of a github.com or GHES URL to a canonical form.
+ * Removes any API prefix or suffix if one is present.
+ */
+export function parseGitHubUrl(inputUrl: string): string {
+  const originalUrl = inputUrl;
+  if (inputUrl.indexOf("://") === -1) {
+    inputUrl = `https://${inputUrl}`;
+  }
+  if (!inputUrl.startsWith("http://") && !inputUrl.startsWith("https://")) {
+    throw new ConfigurationError(`"${originalUrl}" is not a http or https URL`);
+  }
+
+  let url: URL;
+  try {
+    url = new URL(inputUrl);
+  } catch {
+    throw new ConfigurationError(`"${originalUrl}" is not a valid URL`);
+  }
+
+  // If we detect this is trying to be to github.com
+  // then return with a fixed canonical URL.
+  if (url.hostname === "github.com" || url.hostname === "api.github.com") {
+    return GITHUB_DOTCOM_URL;
+  }
+
+  // Remove the API prefix if it's present
+  if (url.pathname.indexOf("/api/v3") !== -1) {
+    url.pathname = url.pathname.substring(0, url.pathname.indexOf("/api/v3"));
+  }
+  // Also consider subdomain isolation on GHES
+  if (url.hostname.startsWith("api.")) {
+    url.hostname = url.hostname.substring(4);
+  }
+
+  // Normalise path to having a trailing slash for consistency
+  if (!url.pathname.endsWith("/")) {
+    url.pathname = `${url.pathname}/`;
+  }
+
+  return url.toString();
+}
+
+/** Retrieves a {@link GitHubInstance} describing the instance we are running on. */
+export function getCurrentInstance(env: ReadOnlyEnv): GitHubInstance {
+  return {
+    url: env.getRequired(ActionsEnvVars.GITHUB_SERVER_URL),
+    apiURL: env.getRequired(ActionsEnvVars.GITHUB_API_URL),
+  };
+}
+
+/** Retrieves a {@link GitHubInstance} describing the GitHub.com instance. */
+export function getDotcomInstance(): GitHubInstance {
+  return {
+    url: GITHUB_DOTCOM_URL,
+    apiURL: GITHUB_DOTCOM_API_URL,
+  };
+}
@@ -7,6 +7,11 @@ import * as actionsUtil from "./actions-util";
 import { CodeScanning, RiskAssessment } from "./analyses";
 import { getApiClient, getGitHubVersion } from "./api-client";
 import { CodeQL, getCodeQL } from "./codeql";
+import {
+  hasConfigKey,
+  type AbortedInitConfig,
+  type ActionConfig,
+} from "./config/action-config";
 import {
  Config,
  isCodeScanningEnabled,
@@ -16,6 +21,7 @@ import {
  getArtifactSuffix,
  getArtifactUploaderClient,
  sanitizeArtifactName,
+  type UploadDebugArtifactsConfig,
 } from "./debug-artifacts";
 import * as dependencyCaching from "./dependency-caching";
 import { EnvVar, ReadOnlyEnv } from "./environment";
@@ -44,7 +50,7 @@ import {
 } from "./util";
 import {
  getCategoryInputOrThrow,
-  getCheckoutPathInputOrThrow,
+  getRepositoryRootOrThrow,
  getUploadInputOrThrow,
  getWorkflow,
 } from "./workflow";
@@ -86,6 +92,11 @@ interface FailedSarifInfo {
  checkoutPath: string;
 }

+/** The minimal Action configuration required to prepare and upload a failed SARIF. */
+export type FailedSarifConfig = ActionConfig<
+  "codeQLCmd" | "tempDir" | "analysisKinds" | "languages"
+>;
+
 /**
 * Tries to prepare a SARIF file that contains information about a failed analysis.
 *
@@ -94,7 +105,7 @@ interface FailedSarifInfo {
 async function prepareFailedSarif(
  logger: Logger,
  features: FeatureEnablement,
-  config: Config,
+  config: FailedSarifConfig,
 ): Promise<Result<FailedSarifInfo, UploadFailedSarifResult>> {
  if (!config.codeQLCmd) {
    return new Failure({
@@ -144,7 +155,15 @@ async function prepareFailedSarif(
      });
    }
    const category = getCategoryInputOrThrow(workflow, jobName, matrix);
-    const checkoutPath = getCheckoutPathInputOrThrow(workflow, jobName, matrix);
+
+    // Try to determine the path at which the repository that we failed to analyse is checked out at.
+    // We need this to relativise the paths in the SARIF.
+    const checkoutPath = getRepositoryRootOrThrow(
+      workflow,
+      jobName,
+      matrix,
+      config,
+    );

    const result = await generateFailedSarif(
      logger,
@@ -160,7 +179,7 @@ async function prepareFailedSarif(
 async function generateFailedSarif(
  logger: Logger,
  features: FeatureEnablement,
-  config: Config,
+  config: ActionConfig<"codeQLCmd" | "tempDir">,
  category: string | undefined,
  checkoutPath: string,
  sarifFile?: string,
@@ -192,7 +211,7 @@ async function generateFailedSarif(
 * category for the workflow.
 */
 async function maybeUploadFailedSarif(
-  config: Config,
+  config: FailedSarifConfig,
  repositoryNwo: RepositoryNwo,
  features: FeatureEnablement,
  logger: Logger,
@@ -227,7 +246,7 @@ async function maybeUploadFailedSarif(

 /** Uploads a failed SARIF file as workflow artifact, if it can be generated. */
 async function maybeUploadFailedSarifArtifact(
-  config: Config,
+  config: FailedSarifConfig,
  features: FeatureEnablement,
  logger: Logger,
 ): Promise<UploadFailedSarifResult> {
@@ -267,7 +286,7 @@ async function maybeUploadFailedSarifArtifact(
 * @returns The results of uploading the SARIF file for the failure.
 */
 export async function tryUploadSarifIfRunFailed(
-  config: Config,
+  config: FailedSarifConfig,
  repositoryNwo: RepositoryNwo,
  features: FeatureEnablement,
  logger: Logger,
@@ -324,13 +343,12 @@ export async function tryUploadSarifIfRunFailed(
 export async function uploadFailureInfo(
  uploadAllAvailableDebugArtifacts: (
    codeql: CodeQL,
-    config: Config,
+    config: UploadDebugArtifactsConfig,
    logger: Logger,
-    codeQlVersion: string,
  ) => Promise<void>,
-  printDebugLogs: (config: Config) => Promise<void>,
+  printDebugLogs: (logger: Logger, config: Partial<Config>) => Promise<void>,
  codeql: CodeQL,
-  config: Config,
+  config: Config | AbortedInitConfig,
  repositoryNwo: RepositoryNwo,
  features: FeatureEnablement,
  jobStatus: string | undefined,
@@ -377,21 +395,15 @@ export async function uploadFailureInfo(
  }

  // Upload appropriate Actions artifacts for debugging
-  if (config.debugMode) {
+  if (config.debugMode && hasConfigKey(config, "dbLocation")) {
    logger.info(
      "Debug mode is on. Uploading available database bundles and logs as Actions debugging artifacts...",
    );
-    const version = await codeql.getVersion();
-    await uploadAllAvailableDebugArtifacts(
-      codeql,
-      config,
-      logger,
-      version.version,
-    );
-    await printDebugLogs(config);
+    await uploadAllAvailableDebugArtifacts(codeql, config, logger);
+    await printDebugLogs(logger, config);
  }

-  if (actionsUtil.isSelfHostedRunner()) {
+  if (actionsUtil.isSelfHostedRunner() && config.dbLocation) {
    try {
      fs.rmSync(config.dbLocation, {
        recursive: true,
@@ -406,6 +418,10 @@ export async function uploadFailureInfo(
        `Failed to clean up database cluster directory ${config.dbLocation}. Details: ${e}`,
      );
    }
+  } else if (config.dbLocation === undefined) {
+    logger.debug(
+      "Skipping cleanup of database cluster directory since the configuration does not include a database path.",
+    );
  } else {
    logger.debug(
      "Skipping cleanup of database cluster directory since we are running on a GitHub-hosted " +
@@ -454,7 +470,7 @@ function isConclusiveJobStatus(jobStatus: string | undefined): boolean {
 */
 async function recordOverlayStatus(
  codeql: CodeQL,
-  config: Config,
+  config: Partial<Config>,
  features: FeatureEnablement,
  jobStatus: string | undefined,
  env: ReadOnlyEnv,
@@ -466,6 +482,11 @@ async function recordOverlayStatus(
    !(await features.getValue(Feature.OverlayAnalysisStatusSave))
  ) {
    return;
+  } else if (config.languages === undefined) {
+    logger.debug(
+      "Not recording overlay status, because the configuration contains no 'languages'.",
+    );
+    return;
  }

  // Only record a failure when the job outcome tells us something about the analysis. A cancelled
@@ -6,31 +6,35 @@

 import * as core from "@actions/core";

+import { runInActions, type Action, type ActionState } from "./action-common";
 import {
  restoreInputs,
  getOptionalInput,
  getTemporaryDirectory,
  printDebugLogs,
 } from "./actions-util";
-import { getGitHubVersion } from "./api-client";
+import { getGitHubVersion, wrapApiConfigurationError } from "./api-client";
 import { CachingKind } from "./caching-utils";
 import { getCodeQL } from "./codeql";
-import { type Config, getConfig } from "./config-utils";
+import {
+  hasConfigKey,
+  type AbortedInitConfig,
+  type Config,
+} from "./config/action-config";
+import { getAbortedInitConfig, getConfig } from "./config-utils";
 import * as debugArtifacts from "./debug-artifacts";
 import {
  DependencyCachingUsageReport,
  getDependencyCacheUsage,
 } from "./dependency-caching";
-import { EnvVar, getEnv } from "./environment";
+import { EnvVar, type ReadOnlyEnv } from "./environment";
 import { initFeatures } from "./feature-flags";
 import * as gitUtils from "./git-utils";
 import * as initActionPostHelper from "./init-action-post-helper";
-import { getActionsLogger } from "./logging";
 import { getRepositoryNwo } from "./repository";
 import {
  StatusReportBase,
  sendStatusReport,
-  sendUnhandledErrorStatusReport,
  createStatusReportBase,
  getActionsStatus,
  ActionName,
@@ -45,16 +49,17 @@ interface InitPostStatusReport
    initActionPostHelper.JobStatusReport,
    initActionPostHelper.DependencyCachingUsageReport {}

-async function run(startedAt: Date) {
+async function run(action: ActionState<["Base", "Logger", "Env"]>) {
  // To capture errors appropriately, keep as much code within the try-catch as
  // possible, and only use safe functions outside.
+  const logger = action.logger;

-  const logger = getActionsLogger();
-  let config: Config | undefined;
+  let config: Config | AbortedInitConfig | undefined;
  let uploadFailedSarifResult:
    | initActionPostHelper.UploadFailedSarifResult
    | undefined;
  let dependencyCachingUsage: DependencyCachingUsageReport | undefined;
+
  try {
    // Read the job status before restoring inputs, since it is provided by the Actions runtime
    // environment for this step and would otherwise be overwritten by the value that the `init`
@@ -62,9 +67,19 @@ async function run(startedAt: Date) {
    const jobStatus = getOptionalInput("job-status");

    // Restore inputs from `init` Action.
-    restoreInputs();
+    restoreInputs(logger);

-    const gitHubVersion = await getGitHubVersion();
+    const tmpDir = getTemporaryDirectory();
+    config = await getConfig(tmpDir, logger);
+
+    // If we weren't able to read the normal configuration file, the `init` step failed before it could write it.
+    // Try to load the "failed" configuration file instead which may have been written by the `init` step
+    // with a minimal configuration for this post-action.
+    if (config === undefined) {
+      config = getAbortedInitConfig(action, tmpDir);
+    }
+
+    const gitHubVersion = config?.gitHubVersion ?? (await getGitHubVersion());
    checkGitHubVersionInRange(gitHubVersion, logger);

    const repositoryNwo = getRepositoryNwo();
@@ -75,7 +90,6 @@ async function run(startedAt: Date) {
      logger,
    );

-    config = await getConfig(getTemporaryDirectory(), logger);
    if (config === undefined) {
      logger.warning(
        "Debugging artifacts are unavailable since the 'init' Action failed before it could produce any.",
@@ -91,7 +105,7 @@ async function run(startedAt: Date) {
        repositoryNwo,
        features,
        jobStatus,
-        getEnv(),
+        action.env,
        logger,
      );

@@ -100,20 +114,24 @@ async function run(startedAt: Date) {
      // do this under these circumstances to avoid slowing down analyses for PRs
      // and where caching may not be enabled.
      if (
-        (await gitUtils.isAnalyzingDefaultBranch()) &&
+        (await gitUtils.isAnalyzingDefaultBranch(
+          action.env,
+          config.repositoryRoot,
+        )) &&
+        hasConfigKey(config, "dependencyCachingEnabled") &&
        config.dependencyCachingEnabled !== CachingKind.None
      ) {
        dependencyCachingUsage = await getDependencyCacheUsage(logger);
      }
    }
  } catch (unwrappedError) {
-    const error = wrapError(unwrappedError);
+    const error = wrapApiConfigurationError(wrapError(unwrappedError));
    core.setFailed(error.message);

    const statusReportBase = await createStatusReportBase(
-      ActionName.InitPost,
+      action.name,
      getActionsStatus(error),
-      startedAt,
+      action.startedAt,
      config,
      await checkDiskUsage(logger),
      logger,
@@ -125,13 +143,13 @@ async function run(startedAt: Date) {
    }
    return;
  }
-  const jobStatus = getFinalJobStatus(config);
+  const jobStatus = getFinalJobStatus(action, config);
  logger.info(`CodeQL job status was ${getJobStatusDisplayName(jobStatus)}.`);

  const statusReportBase = await createStatusReportBase(
-    ActionName.InitPost,
+    action.name,
    "success",
-    startedAt,
+    action.startedAt,
    config,
    await checkDiskUsage(logger),
    logger,
@@ -156,16 +174,21 @@ async function run(startedAt: Date) {
 * Otherwise, we determine the job status based on whether the analyze step
 * completed successfully and whether we have a valid CodeQL config.
 */
-function getFinalJobStatus(config: Config | undefined): JobStatus {
-  const existingJobStatus = getJobStatusFromEnvironment();
+function getFinalJobStatus(
+  action: ActionState<["Env"]>,
+  config: Partial<Config> | undefined,
+): JobStatus {
+  const existingJobStatus = getJobStatusFromEnvironment(action.env);
  if (existingJobStatus !== undefined) {
    return existingJobStatus;
  }

  let jobStatus: JobStatus;

-  if (process.env[EnvVar.ANALYZE_DID_COMPLETE_SUCCESSFULLY] === "true") {
-    core.exportVariable(EnvVar.JOB_STATUS, JobStatus.SuccessStatus);
+  if (
+    action.env.getOptional(EnvVar.ANALYZE_DID_COMPLETE_SUCCESSFULLY) === "true"
+  ) {
+    action.env.export(EnvVar.JOB_STATUS, JobStatus.SuccessStatus);
    jobStatus = JobStatus.SuccessStatus;
  } else if (config !== undefined) {
    // - We have computed a CodeQL config
@@ -190,7 +213,7 @@ function getFinalJobStatus(config: Config | undefined): JobStatus {

  // This shouldn't be necessary, but in the odd case that we run more than one
  // `init` post step, ensure the job status is consistent between them.
-  core.exportVariable(EnvVar.JOB_STATUS, jobStatus);
+  action.env.export(EnvVar.JOB_STATUS, jobStatus);
  return jobStatus;
 }

@@ -199,8 +222,8 @@ function getFinalJobStatus(config: Config | undefined): JobStatus {
 *
 * If the job status is invalid, return `UnknownStatus`.
 */
-function getJobStatusFromEnvironment(): JobStatus | undefined {
-  const jobStatusFromEnvironment = process.env[EnvVar.JOB_STATUS];
+function getJobStatusFromEnvironment(env: ReadOnlyEnv): JobStatus | undefined {
+  const jobStatusFromEnvironment = env.getOptional(EnvVar.JOB_STATUS);

  if (jobStatusFromEnvironment !== undefined) {
    // Validate the job status from the environment. If it is invalid, return unknown.
@@ -215,18 +238,11 @@ function getJobStatusFromEnvironment(): JobStatus | undefined {
  return undefined;
 }

+const initPost: Action = {
+  name: ActionName.InitPost,
+  run,
+};
+
 export async function runWrapper() {
-  const startedAt = new Date();
-  const logger = getActionsLogger();
-  try {
-    await run(startedAt);
-  } catch (error) {
-    core.setFailed(`init post action failed: ${wrapError(error).message}`);
-    await sendUnhandledErrorStatusReport(
-      ActionName.InitPost,
-      startedAt,
-      error,
-      logger,
-    );
-  }
+  return await runInActions(initPost);
 }