Merge pull request #3447 from github/update-v4.32.1-f52cbc830

Merge main into releases/v4
2026-04-02 09:42:16 +00:00 · 2026-02-02 07:09:16 -08:00
parent b20883b0cd 42f00f2d33
commit 6bc82e05fd
47 changed files with 325350 additions and 129903 deletions
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -4,14 +4,15 @@ updates:
    directory: "/"
    schedule:
      interval: weekly
+    cooldown:
+      default-days: 7
+      exclude:
+        - "@actions/*"
    labels:
      - Rebuild
    # Ignore incompatible dependency updates
    ignore:
-      # There is a type incompatibility issue between v0.0.9 and our other dependencies.
-      - dependency-name: "@octokit/plugin-retry"
-        versions: ["~6.0.0"]
-      # This is broken due to the way configuration files have changed. 
+      # This is broken due to the way configuration files have changed.
      # This might be fixed when we move to eslint v9.
      - dependency-name: "eslint-plugin-import"
        versions: [">=2.30.0"]
@@ -28,6 +29,10 @@ updates:
      - "/.github/actions"
    schedule:
      interval: weekly
+    cooldown:
+      default-days: 7
+      exclude:
+        - "actions/*"
    labels:
      - Rebuild
    groups:
--- a/.github/workflows/__bundle-from-toolcache.yml
+++ b/.github/workflows/__bundle-from-toolcache.yml
@@ -56,7 +56,7 @@ jobs:
          use-all-platform-bundle: 'false'
          setup-kotlin: 'true'
      - name: Install @actions/tool-cache
-        run: npm install @actions/tool-cache
+        run: npm install @actions/tool-cache@3
      - name: Check toolcache contains CodeQL
        continue-on-error: true
        uses: actions/github-script@v8
--- a/.github/workflows/__bundle-toolcache.yml
+++ b/.github/workflows/__bundle-toolcache.yml
@@ -68,7 +68,7 @@ jobs:
            const codeqlPath = path.join(process.env['RUNNER_TOOL_CACHE'], 'CodeQL');
            fs.rmdirSync(codeqlPath, { recursive: true });
      - name: Install @actions/tool-cache
-        run: npm install @actions/tool-cache
+        run: npm install @actions/tool-cache@3
      - name: Check toolcache does not contain CodeQL
        uses: actions/github-script@v8
        with:
--- a/.github/workflows/__export-file-baseline-information.yml
+++ b/.github/workflows/__export-file-baseline-information.yml
@@ -125,5 +125,6 @@ jobs:
            fi
          done
    env:
+      CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS: false
      CODEQL_ACTION_SUBLANGUAGE_FILE_COVERAGE: true
      CODEQL_ACTION_TEST_MODE: true
--- a/.github/workflows/__global-proxy.yml
+++ b/.github/workflows/__global-proxy.yml
@@ -48,18 +48,6 @@ jobs:
    timeout-minutes: 45
    runs-on: ${{ matrix.os }}
    steps:
-  # These steps are required to initialise the `gh` cli in a container that doesn't
-  # come pre-installed with it. The reason for that is that this is later
-  # needed by the `prepare-test` workflow to find the latest release of CodeQL.
-      - name: Set up GitHub CLI
-        run: |
-          apt update
-          apt install -y curl libreadline8 gnupg2 software-properties-common zstd
-          curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg
-          apt-key add /usr/share/keyrings/githubcli-archive-keyring.gpg
-          apt-add-repository https://cli.github.com/packages
-          apt install -y gh
-        env: {}
      - name: Check out repository
        uses: actions/checkout@v6
      - name: Prepare test
--- a/.github/workflows/__rubocop-multi-language.yml
+++ b/.github/workflows/__rubocop-multi-language.yml
@@ -56,7 +56,7 @@ jobs:
          use-all-platform-bundle: 'false'
          setup-kotlin: 'true'
      - name: Set up Ruby
-        uses: ruby/setup-ruby@80740b3b13bf9857e28854481ca95a84e78a2bdf # v1.284.0
+        uses: ruby/setup-ruby@90be1154f987f4dc0fe0dd0feedac9e473aa4ba8 # v1.286.0
        with:
          ruby-version: 2.6
      - name: Install Code Scanning integration
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,11 @@

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

+## 4.32.1 - 02 Feb 2026
+
+- A warning is now shown in Default Setup workflow logs if a [private package registry is configured](https://docs.github.com/en/code-security/how-tos/secure-at-scale/configure-organization-security/manage-usage-and-access/giving-org-access-private-registries) using a GitHub Personal Access Token (PAT), but no username is configured. [#3422](https://github.com/github/codeql-action/pull/3422)
+- Fixed a bug which caused the CodeQL Action to fail when repository properties cannot successfully be retrieved. [#3421](https://github.com/github/codeql-action/pull/3421)
+
 ## 4.32.0 - 26 Jan 2026

 - Update default CodeQL bundle version to [2.24.0](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.24.0). [#3425](https://github.com/github/codeql-action/pull/3425)
--- a/lib/analyze-action-post.js
+++ b/lib/analyze-action-post.js
--- a/lib/analyze-action.js
+++ b/lib/analyze-action.js
--- a/lib/autobuild-action.js
+++ b/lib/autobuild-action.js
--- a/lib/init-action-post.js
+++ b/lib/init-action-post.js
--- a/lib/init-action.js
+++ b/lib/init-action.js
--- a/lib/resolve-environment-action.js
+++ b/lib/resolve-environment-action.js
--- a/lib/setup-codeql-action.js
+++ b/lib/setup-codeql-action.js
--- a/lib/start-proxy-action-post.js
+++ b/lib/start-proxy-action-post.js
--- a/lib/start-proxy-action.js
+++ b/lib/start-proxy-action.js
--- a/lib/upload-lib.js
+++ b/lib/upload-lib.js
--- a/lib/upload-sarif-action-post.js
+++ b/lib/upload-sarif-action-post.js
--- a/lib/upload-sarif-action.js
+++ b/lib/upload-sarif-action.js
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,25 +1,25 @@
 {
  "name": "codeql",
-  "version": "4.32.0",
+  "version": "4.32.1",
  "lockfileVersion": 3,
  "requires": true,
  "packages": {
    "": {
      "name": "codeql",
-      "version": "4.32.0",
+      "version": "4.32.1",
      "license": "MIT",
      "dependencies": {
-        "@actions/artifact": "^5.0.2",
+        "@actions/artifact": "^5.0.3",
        "@actions/artifact-legacy": "npm:@actions/artifact@^1.1.2",
-        "@actions/cache": "^5.0.3",
-        "@actions/core": "^2.0.2",
+        "@actions/cache": "^5.0.5",
+        "@actions/core": "^2.0.3",
        "@actions/exec": "^2.0.0",
-        "@actions/github": "^7.0.0",
+        "@actions/github": "^8.0.0",
        "@actions/glob": "^0.5.0",
        "@actions/http-client": "^3.0.0",
        "@actions/io": "^2.0.0",
-        "@actions/tool-cache": "^3.0.0",
-        "@octokit/plugin-retry": "^6.0.0",
+        "@actions/tool-cache": "^3.0.1",
+        "@octokit/plugin-retry": "^8.0.0",
        "@schemastore/package": "0.0.10",
        "archiver": "^7.0.1",
        "fast-deep-equal": "^3.1.3",
@@ -55,7 +55,7 @@
        "eslint-plugin-filenames": "^1.3.2",
        "eslint-plugin-github": "^5.1.8",
        "eslint-plugin-import": "2.29.1",
-        "eslint-plugin-jsdoc": "^62.2.0",
+        "eslint-plugin-jsdoc": "^62.3.0",
        "eslint-plugin-no-async-foreach": "^0.1.1",
        "glob": "^11.1.0",
        "nock": "^14.0.10",
@@ -72,14 +72,14 @@
      }
    },
    "node_modules/@actions/artifact": {
-      "version": "5.0.2",
-      "resolved": "https://registry.npmjs.org/@actions/artifact/-/artifact-5.0.2.tgz",
-      "integrity": "sha512-NmA+THO1s/Ubqf5y34EZofB1FRORcToa3T8Mb3/Z87TCCozTtvBUaxDn8OPPwgyYQ4ft0nd01Z4kFSu2DTWqGw==",
+      "version": "5.0.3",
+      "resolved": "https://registry.npmjs.org/@actions/artifact/-/artifact-5.0.3.tgz",
+      "integrity": "sha512-FIEG8Kum0wABZnktJvFi1xuVPc31xrunhZwLCvjrCGISQOm0ifyo7cjqf6PHiEeqoWMa5HIGOsB+lGM4aKCseA==",
      "license": "MIT",
      "dependencies": {
        "@actions/core": "^2.0.0",
        "@actions/github": "^6.0.1",
-        "@actions/http-client": "^3.0.1",
+        "@actions/http-client": "^3.0.2",
        "@azure/storage-blob": "^12.29.1",
        "@octokit/core": "^5.2.1",
        "@octokit/plugin-request-log": "^1.0.4",
@@ -164,6 +164,33 @@
        "undici": "^5.25.4"
      }
    },
+    "node_modules/@actions/artifact/node_modules/@octokit/auth-token": {
+      "version": "4.0.0",
+      "resolved": "https://registry.npmjs.org/@octokit/auth-token/-/auth-token-4.0.0.tgz",
+      "integrity": "sha512-tY/msAuJo6ARbK6SPIxZrPBms3xPbfwBrulZe0Wtr/DIY9lje2HeV1uoebShn6mx7SjCHif6EjMvoREj+gZ+SA==",
+      "license": "MIT",
+      "engines": {
+        "node": ">= 18"
+      }
+    },
+    "node_modules/@actions/artifact/node_modules/@octokit/core": {
+      "version": "5.2.2",
+      "resolved": "https://registry.npmjs.org/@octokit/core/-/core-5.2.2.tgz",
+      "integrity": "sha512-/g2d4sW9nUDJOMz3mabVQvOGhVa4e/BN/Um7yca9Bb2XTzPPnfTWHWQg+IsEYO7M3Vx+EXvaM/I2pJWIMun1bg==",
+      "license": "MIT",
+      "dependencies": {
+        "@octokit/auth-token": "^4.0.0",
+        "@octokit/graphql": "^7.1.0",
+        "@octokit/request": "^8.4.1",
+        "@octokit/request-error": "^5.1.1",
+        "@octokit/types": "^13.0.0",
+        "before-after-hook": "^2.2.0",
+        "universal-user-agent": "^6.0.0"
+      },
+      "engines": {
+        "node": ">= 18"
+      }
+    },
    "node_modules/@actions/artifact/node_modules/@octokit/endpoint": {
      "version": "9.0.6",
      "resolved": "https://registry.npmjs.org/@octokit/endpoint/-/endpoint-9.0.6.tgz",
@@ -177,12 +204,86 @@
        "node": ">= 18"
      }
    },
+    "node_modules/@actions/artifact/node_modules/@octokit/graphql": {
+      "version": "7.1.1",
+      "resolved": "https://registry.npmjs.org/@octokit/graphql/-/graphql-7.1.1.tgz",
+      "integrity": "sha512-3mkDltSfcDUoa176nlGoA32RGjeWjl3K7F/BwHwRMJUW/IteSa4bnSV8p2ThNkcIcZU2umkZWxwETSSCJf2Q7g==",
+      "license": "MIT",
+      "dependencies": {
+        "@octokit/request": "^8.4.1",
+        "@octokit/types": "^13.0.0",
+        "universal-user-agent": "^6.0.0"
+      },
+      "engines": {
+        "node": ">= 18"
+      }
+    },
    "node_modules/@actions/artifact/node_modules/@octokit/openapi-types": {
      "version": "12.11.0",
      "resolved": "https://registry.npmjs.org/@octokit/openapi-types/-/openapi-types-12.11.0.tgz",
      "integrity": "sha512-VsXyi8peyRq9PqIz/tpqiL2w3w80OgVMwBHltTml3LmVvXiphgeqmY9mvBw9Wu7e0QWk/fqD37ux8yP5uVekyQ==",
      "license": "MIT"
    },
+    "node_modules/@actions/artifact/node_modules/@octokit/plugin-paginate-rest": {
+      "version": "9.2.2",
+      "resolved": "https://registry.npmjs.org/@octokit/plugin-paginate-rest/-/plugin-paginate-rest-9.2.2.tgz",
+      "integrity": "sha512-u3KYkGF7GcZnSD/3UP0S7K5XUFT2FkOQdcfXZGZQPGv3lm4F2Xbf71lvjldr8c1H3nNbF+33cLEkWYbokGWqiQ==",
+      "license": "MIT",
+      "dependencies": {
+        "@octokit/types": "^12.6.0"
+      },
+      "engines": {
+        "node": ">= 18"
+      },
+      "peerDependencies": {
+        "@octokit/core": "5"
+      }
+    },
+    "node_modules/@actions/artifact/node_modules/@octokit/plugin-paginate-rest/node_modules/@octokit/openapi-types": {
+      "version": "20.0.0",
+      "resolved": "https://registry.npmjs.org/@octokit/openapi-types/-/openapi-types-20.0.0.tgz",
+      "integrity": "sha512-EtqRBEjp1dL/15V7WiX5LJMIxxkdiGJnabzYx5Apx4FkQIFgAfKumXeYAqqJCj1s+BMX4cPFIFC4OLCR6stlnA==",
+      "license": "MIT"
+    },
+    "node_modules/@actions/artifact/node_modules/@octokit/plugin-paginate-rest/node_modules/@octokit/types": {
+      "version": "12.6.0",
+      "resolved": "https://registry.npmjs.org/@octokit/types/-/types-12.6.0.tgz",
+      "integrity": "sha512-1rhSOfRa6H9w4YwK0yrf5faDaDTb+yLyBUKOCV4xtCDB5VmIPqd/v9yr9o6SAzOAlRxMiRiCic6JVM1/kunVkw==",
+      "license": "MIT",
+      "dependencies": {
+        "@octokit/openapi-types": "^20.0.0"
+      }
+    },
+    "node_modules/@actions/artifact/node_modules/@octokit/plugin-rest-endpoint-methods": {
+      "version": "10.4.1",
+      "resolved": "https://registry.npmjs.org/@octokit/plugin-rest-endpoint-methods/-/plugin-rest-endpoint-methods-10.4.1.tgz",
+      "integrity": "sha512-xV1b+ceKV9KytQe3zCVqjg+8GTGfDYwaT1ATU5isiUyVtlVAO3HNdzpS4sr4GBx4hxQ46s7ITtZrAsxG22+rVg==",
+      "license": "MIT",
+      "dependencies": {
+        "@octokit/types": "^12.6.0"
+      },
+      "engines": {
+        "node": ">= 18"
+      },
+      "peerDependencies": {
+        "@octokit/core": "5"
+      }
+    },
+    "node_modules/@actions/artifact/node_modules/@octokit/plugin-rest-endpoint-methods/node_modules/@octokit/openapi-types": {
+      "version": "20.0.0",
+      "resolved": "https://registry.npmjs.org/@octokit/openapi-types/-/openapi-types-20.0.0.tgz",
+      "integrity": "sha512-EtqRBEjp1dL/15V7WiX5LJMIxxkdiGJnabzYx5Apx4FkQIFgAfKumXeYAqqJCj1s+BMX4cPFIFC4OLCR6stlnA==",
+      "license": "MIT"
+    },
+    "node_modules/@actions/artifact/node_modules/@octokit/plugin-rest-endpoint-methods/node_modules/@octokit/types": {
+      "version": "12.6.0",
+      "resolved": "https://registry.npmjs.org/@octokit/types/-/types-12.6.0.tgz",
+      "integrity": "sha512-1rhSOfRa6H9w4YwK0yrf5faDaDTb+yLyBUKOCV4xtCDB5VmIPqd/v9yr9o6SAzOAlRxMiRiCic6JVM1/kunVkw==",
+      "license": "MIT",
+      "dependencies": {
+        "@octokit/openapi-types": "^20.0.0"
+      }
+    },
    "node_modules/@actions/artifact/node_modules/@octokit/plugin-retry": {
      "version": "3.0.9",
      "resolved": "https://registry.npmjs.org/@octokit/plugin-retry/-/plugin-retry-3.0.9.tgz",
@@ -243,16 +344,22 @@
      "resolved": "https://registry.npmjs.org/@octokit/openapi-types/-/openapi-types-24.2.0.tgz",
      "integrity": "sha512-9sIH3nSUttelJSXUrmGzl7QUBFul0/mB8HRYl3fOlgHbIWG+WnYDXU3v/2zMtAvuzZ/ed00Ei6on975FhBfzrg=="
    },
+    "node_modules/@actions/artifact/node_modules/before-after-hook": {
+      "version": "2.2.3",
+      "resolved": "https://registry.npmjs.org/before-after-hook/-/before-after-hook-2.2.3.tgz",
+      "integrity": "sha512-NzUnlZexiaH/46WDhANlyR2bXRopNg4F/zuSA3OpZnllCUgRaOF2znDioDWrmbNVsuZk6l9pMquQB38cfBZwkQ==",
+      "license": "Apache-2.0"
+    },
    "node_modules/@actions/cache": {
-      "version": "5.0.3",
-      "resolved": "https://registry.npmjs.org/@actions/cache/-/cache-5.0.3.tgz",
-      "integrity": "sha512-9joY8Oup+nIpksSBlkuf9/mltnhWx3lydk1tA2PVnXaxFLIIrKqrWDN2CZXlJ+PEErcBARKYn4mHiUCTyMh4Vg==",
+      "version": "5.0.5",
+      "resolved": "https://registry.npmjs.org/@actions/cache/-/cache-5.0.5.tgz",
+      "integrity": "sha512-jiQSg0gfd+C2KPgcmdCOq7dCuCIQQWQ4b1YfGIRaaA9w7PJbRwTOcCz4LiFEUnqZGf0ha/8OKL3BeNwetHzYsQ==",
      "license": "MIT",
      "dependencies": {
        "@actions/core": "^2.0.0",
        "@actions/exec": "^2.0.0",
-        "@actions/glob": "^0.5.0",
-        "@actions/http-client": "^3.0.1",
+        "@actions/glob": "^0.5.1",
+        "@actions/http-client": "^3.0.2",
        "@actions/io": "^2.0.0",
        "@azure/abort-controller": "^1.1.0",
        "@azure/core-rest-pipeline": "^1.22.0",
@@ -269,13 +376,13 @@
      }
    },
    "node_modules/@actions/core": {
-      "version": "2.0.2",
-      "resolved": "https://registry.npmjs.org/@actions/core/-/core-2.0.2.tgz",
-      "integrity": "sha512-Ast1V7yHbGAhplAsuVlnb/5J8Mtr/Zl6byPPL+Qjq3lmfIgWF1ak1iYfF/079cRERiuTALTXkSuEUdZeDCfGtA==",
+      "version": "2.0.3",
+      "resolved": "https://registry.npmjs.org/@actions/core/-/core-2.0.3.tgz",
+      "integrity": "sha512-Od9Thc3T1mQJYddvVPM4QGiLUewdh+3txmDYHHxoNdkqysR1MbCT+rFOtNUxYAz+7+6RIsqipVahY2GJqGPyxA==",
      "license": "MIT",
      "dependencies": {
        "@actions/exec": "^2.0.0",
-        "@actions/http-client": "^3.0.1"
+        "@actions/http-client": "^3.0.2"
      }
    },
    "node_modules/@actions/exec": {
@@ -288,129 +395,77 @@
      }
    },
    "node_modules/@actions/github": {
-      "version": "7.0.0",
-      "resolved": "https://registry.npmjs.org/@actions/github/-/github-7.0.0.tgz",
-      "integrity": "sha512-PyGODO938aoBTZd/IfN/+e+Pd5hUcVpyf+thm4CPESLeqhdSkq5QwMTGX9v84XHE1ifmHWBQ60KB8kIgm96opw==",
+      "version": "8.0.0",
+      "resolved": "https://registry.npmjs.org/@actions/github/-/github-8.0.0.tgz",
+      "integrity": "sha512-bBukvVRvIf7NshWEXFVnBaXs/ZyGzDvx+jbB5AdJij9CUG4VFEYJJD6T6y06dDkuULalQQUNvKXIH71yqw7SoQ==",
      "license": "MIT",
      "dependencies": {
        "@actions/http-client": "^3.0.1",
-        "@octokit/core": "^5.0.1",
-        "@octokit/plugin-paginate-rest": "^9.2.2",
-        "@octokit/plugin-rest-endpoint-methods": "^10.4.0",
-        "@octokit/request": "^8.4.1",
-        "@octokit/request-error": "^5.1.1",
+        "@octokit/core": "^7.0.6",
+        "@octokit/plugin-paginate-rest": "^14.0.0",
+        "@octokit/plugin-rest-endpoint-methods": "^17.0.0",
+        "@octokit/request": "^10.0.7",
+        "@octokit/request-error": "^7.1.0",
        "undici": "^5.28.5"
      }
    },
-    "node_modules/@actions/github/node_modules/@octokit/endpoint": {
-      "version": "9.0.6",
-      "resolved": "https://registry.npmjs.org/@octokit/endpoint/-/endpoint-9.0.6.tgz",
-      "integrity": "sha512-H1fNTMA57HbkFESSt3Y9+FBICv+0jFceJFPWDePYlR/iMGrwM5ph+Dd4XRQs+8X+PUFURLQgX9ChPfhJ/1uNQw==",
+    "node_modules/@actions/github/node_modules/@octokit/plugin-paginate-rest": {
+      "version": "14.0.0",
+      "resolved": "https://registry.npmjs.org/@octokit/plugin-paginate-rest/-/plugin-paginate-rest-14.0.0.tgz",
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      "license": "MIT",
      "dependencies": {
-        "@octokit/types": "^13.1.0",
-        "universal-user-agent": "^6.0.0"
+        "@octokit/types": "^16.0.0"
      },
      "engines": {
-        "node": ">= 18"
+        "node": ">= 20"
+      },
+      "peerDependencies": {
+        "@octokit/core": ">=6"
      }
    },
-    "node_modules/@actions/github/node_modules/@octokit/request": {
-      "version": "8.4.1",
-      "resolved": "https://registry.npmjs.org/@octokit/request/-/request-8.4.1.tgz",
-      "integrity": "sha512-qnB2+SY3hkCmBxZsR/MPCybNmbJe4KAlfWErXq+rBKkQJlbjdJeS85VI9r8UqeLYLvnAenU8Q1okM/0MBsAGXw==",
+    "node_modules/@actions/github/node_modules/@octokit/plugin-rest-endpoint-methods": {
+      "version": "17.0.0",
+      "resolved": "https://registry.npmjs.org/@octokit/plugin-rest-endpoint-methods/-/plugin-rest-endpoint-methods-17.0.0.tgz",
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      "license": "MIT",
      "dependencies": {
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-      "integrity": "sha512-u3KYkGF7GcZnSD/3UP0S7K5XUFT2FkOQdcfXZGZQPGv3lm4F2Xbf71lvjldr8c1H3nNbF+33cLEkWYbokGWqiQ==",
-      "license": "MIT",
-      "dependencies": {
-        "@octokit/types": "^12.6.0"
-      },
-      "engines": {
-        "node": ">= 18"
-      },
-      "peerDependencies": {
-        "@octokit/core": "5"
-      }
-    },
-    "node_modules/@octokit/plugin-paginate-rest/node_modules/@octokit/openapi-types": {
-      "version": "20.0.0",
-      "resolved": "https://registry.npmjs.org/@octokit/openapi-types/-/openapi-types-20.0.0.tgz",
-      "integrity": "sha512-EtqRBEjp1dL/15V7WiX5LJMIxxkdiGJnabzYx5Apx4FkQIFgAfKumXeYAqqJCj1s+BMX4cPFIFC4OLCR6stlnA==",
-      "license": "MIT"
-    },
-    "node_modules/@octokit/plugin-paginate-rest/node_modules/@octokit/types": {
-      "version": "12.6.0",
-      "resolved": "https://registry.npmjs.org/@octokit/types/-/types-12.6.0.tgz",
-      "integrity": "sha512-1rhSOfRa6H9w4YwK0yrf5faDaDTb+yLyBUKOCV4xtCDB5VmIPqd/v9yr9o6SAzOAlRxMiRiCic6JVM1/kunVkw==",
-      "license": "MIT",
-      "dependencies": {
-        "@octokit/openapi-types": "^20.0.0"
-      }
-    },
    "node_modules/@octokit/plugin-request-log": {
      "version": "1.0.4",
      "resolved": "https://registry.npmjs.org/@octokit/plugin-request-log/-/plugin-request-log-1.0.4.tgz",
@@ -1837,83 +1790,61 @@
        "@octokit/core": ">=3"
      }
    },
-    "node_modules/@octokit/plugin-rest-endpoint-methods": {
-      "version": "10.4.1",
-      "resolved": "https://registry.npmjs.org/@octokit/plugin-rest-endpoint-methods/-/plugin-rest-endpoint-methods-10.4.1.tgz",
-      "integrity": "sha512-xV1b+ceKV9KytQe3zCVqjg+8GTGfDYwaT1ATU5isiUyVtlVAO3HNdzpS4sr4GBx4hxQ46s7ITtZrAsxG22+rVg==",
-      "license": "MIT",
-      "dependencies": {
-        "@octokit/types": "^12.6.0"
-      },
-      "engines": {
-        "node": ">= 18"
-      },
-      "peerDependencies": {
-        "@octokit/core": "5"
-      }
-    },
-    "node_modules/@octokit/plugin-rest-endpoint-methods/node_modules/@octokit/openapi-types": {
-      "version": "20.0.0",
-      "resolved": "https://registry.npmjs.org/@octokit/openapi-types/-/openapi-types-20.0.0.tgz",
-      "integrity": "sha512-EtqRBEjp1dL/15V7WiX5LJMIxxkdiGJnabzYx5Apx4FkQIFgAfKumXeYAqqJCj1s+BMX4cPFIFC4OLCR6stlnA==",
-      "license": "MIT"
-    },
-    "node_modules/@octokit/plugin-rest-endpoint-methods/node_modules/@octokit/types": {
-      "version": "12.6.0",
-      "resolved": "https://registry.npmjs.org/@octokit/types/-/types-12.6.0.tgz",
-      "integrity": "sha512-1rhSOfRa6H9w4YwK0yrf5faDaDTb+yLyBUKOCV4xtCDB5VmIPqd/v9yr9o6SAzOAlRxMiRiCic6JVM1/kunVkw==",
-      "license": "MIT",
-      "dependencies": {
-        "@octokit/openapi-types": "^20.0.0"
-      }
-    },
    "node_modules/@octokit/plugin-retry": {
-      "version": "6.1.0",
-      "resolved": "https://registry.npmjs.org/@octokit/plugin-retry/-/plugin-retry-6.1.0.tgz",
-      "integrity": "sha512-WrO3bvq4E1Xh1r2mT9w6SDFg01gFmP81nIG77+p/MqW1JeXXgL++6umim3t6x0Zj5pZm3rXAN+0HEjmmdhIRig==",
+      "version": "8.0.3",
+      "resolved": "https://registry.npmjs.org/@octokit/plugin-retry/-/plugin-retry-8.0.3.tgz",
+      "integrity": "sha512-vKGx1i3MC0za53IzYBSBXcrhmd+daQDzuZfYDd52X5S0M2otf3kVZTVP8bLA3EkU0lTvd1WEC2OlNNa4G+dohA==",
+      "license": "MIT",
      "dependencies": {
-        "@octokit/request-error": "^5.0.0",
-        "@octokit/types": "^13.0.0",
+        "@octokit/request-error": "^7.0.2",
+        "@octokit/types": "^16.0.0",
        "bottleneck": "^2.15.3"
      },
      "engines": {
-        "node": ">= 18"
+        "node": ">= 20"
      },
      "peerDependencies": {
-        "@octokit/core": "5"
+        "@octokit/core": ">=7"
      }
    },
-    "node_modules/@octokit/plugin-retry/node_modules/@octokit/openapi-types": {
-      "version": "24.2.0",
-      "resolved": "https://registry.npmjs.org/@octokit/openapi-types/-/openapi-types-24.2.0.tgz",
-      "integrity": "sha512-9sIH3nSUttelJSXUrmGzl7QUBFul0/mB8HRYl3fOlgHbIWG+WnYDXU3v/2zMtAvuzZ/ed00Ei6on975FhBfzrg=="
-    },
-    "node_modules/@octokit/plugin-retry/node_modules/@octokit/request-error": {
-      "version": "5.1.1",
-      "resolved": "https://registry.npmjs.org/@octokit/request-error/-/request-error-5.1.1.tgz",
-      "integrity": "sha512-v9iyEQJH6ZntoENr9/yXxjuezh4My67CBSu9r6Ve/05Iu5gNgnisNWOsoJHTP6k0Rr0+HQIpnH+kyammu90q/g==",
+    "node_modules/@octokit/request": {
+      "version": "10.0.7",
+      "resolved": "https://registry.npmjs.org/@octokit/request/-/request-10.0.7.tgz",
+      "integrity": "sha512-v93h0i1yu4idj8qFPZwjehoJx4j3Ntn+JhXsdJrG9pYaX6j/XRz2RmasMUHtNgQD39nrv/VwTWSqK0RNXR8upA==",
+      "license": "MIT",
      "dependencies": {
-        "@octokit/types": "^13.1.0",
-        "deprecation": "^2.0.0",
-        "once": "^1.4.0"
+        "@octokit/endpoint": "^11.0.2",
+        "@octokit/request-error": "^7.0.2",
+        "@octokit/types": "^16.0.0",
+        "fast-content-type-parse": "^3.0.0",
+        "universal-user-agent": "^7.0.2"
      },
      "engines": {
-        "node": ">= 18"
+        "node": ">= 20"
      }
    },
-    "node_modules/@octokit/plugin-retry/node_modules/@octokit/types": {
-      "version": "13.10.0",
-      "resolved": "https://registry.npmjs.org/@octokit/types/-/types-13.10.0.tgz",
-      "integrity": "sha512-ifLaO34EbbPj0Xgro4G5lP5asESjwHracYJvVaPIyXMuiuXLlhic3S47cBdTb+jfODkTE5YtGCLt3Ay3+J97sA==",
+    "node_modules/@octokit/request-error": {
+      "version": "7.1.0",
+      "resolved": "https://registry.npmjs.org/@octokit/request-error/-/request-error-7.1.0.tgz",
+      "integrity": "sha512-KMQIfq5sOPpkQYajXHwnhjCC0slzCNScLHs9JafXc4RAJI+9f+jNDlBNaIMTvazOPLgb4BnlhGJOTbnN0wIjPw==",
+      "license": "MIT",
      "dependencies": {
-        "@octokit/openapi-types": "^24.2.0"
+        "@octokit/types": "^16.0.0"
+      },
+      "engines": {
+        "node": ">= 20"
      }
    },
+    "node_modules/@octokit/request/node_modules/universal-user-agent": {
+      "version": "7.0.3",
+      "resolved": "https://registry.npmjs.org/universal-user-agent/-/universal-user-agent-7.0.3.tgz",
+      "integrity": "sha512-TmnEAEAsBJVZM/AADELsK76llnwcf9vMKuPz8JflO1frO8Lchitr0fNaN9d+Ap0BjKtqWqd/J17qeDnXh8CL2A==",
+      "license": "ISC"
+    },
    "node_modules/@octokit/types": {
      "version": "16.0.0",
      "resolved": "https://registry.npmjs.org/@octokit/types/-/types-16.0.0.tgz",
      "integrity": "sha512-sKq+9r1Mm4efXW1FCk7hFSeJo4QKreL/tTbR0rz/qx/r1Oa2VV83LTA/H/MuCOX7uCIJmQVRKBcbmWoySjAnSg==",
-      "dev": true,
      "license": "MIT",
      "dependencies": {
        "@octokit/openapi-types": "^27.0.0"
@@ -3663,7 +3594,9 @@
      "license": "MIT"
    },
    "node_modules/before-after-hook": {
-      "version": "2.2.3",
+      "version": "4.0.0",
+      "resolved": "https://registry.npmjs.org/before-after-hook/-/before-after-hook-4.0.0.tgz",
+      "integrity": "sha512-q6tR3RPqIB1pMiTRMFcZwuG5T8vwp+vUvEG0vuI6B+Rikh5BfPp2fQ82c925FOs+b0lcFQ8CFrL+KbilfZFhOQ==",
      "license": "Apache-2.0"
    },
    "node_modules/binary": {
@@ -3834,9 +3767,9 @@
      }
    },
    "node_modules/caniuse-lite": {
-      "version": "1.0.30001727",
-      "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001727.tgz",
-      "integrity": "sha512-pB68nIHmbN6L/4C6MH1DokyR3bYqFwjaSs/sWDHGj4CTcFtQUQMuJftVwWkXq7mNWOybD3KhUv3oWHoGxgP14Q==",
+      "version": "1.0.30001766",
+      "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001766.tgz",
+      "integrity": "sha512-4C0lfJ0/YPjJQHagaE9x2Elb69CIqEPZeG0anQt9SIvIoOH4a4uaRl73IavyO+0qZh6MDLH//DrXThEYKHkmYA==",
      "dev": true,
      "funding": [
        {
@@ -3851,7 +3784,8 @@
          "type": "github",
          "url": "https://github.com/sponsors/ai"
        }
-      ]
+      ],
+      "license": "CC-BY-4.0"
    },
    "node_modules/cbor": {
      "version": "10.0.9",
@@ -4942,19 +4876,19 @@
      }
    },
    "node_modules/eslint-plugin-jsdoc": {
-      "version": "62.2.0",
-      "resolved": "https://registry.npmjs.org/eslint-plugin-jsdoc/-/eslint-plugin-jsdoc-62.2.0.tgz",
-      "integrity": "sha512-juIekE88Gy1FnjsQuwkrZ3OW4UCkQuhiBf9QqF9U1xgqtan4rQFCOUn4cKeHR1ObBqJ8/pG8a0lZlAuKlDLpdw==",
+      "version": "62.3.0",
+      "resolved": "https://registry.npmjs.org/eslint-plugin-jsdoc/-/eslint-plugin-jsdoc-62.3.0.tgz",
+      "integrity": "sha512-Gc5Ls5qQC6NwqtQTtJ2JE5BwvX348ZCZ+4+QiZ9RpoQ1TCcxFF8Z0E5jaLkTyYNqyhx+uKAvljNHE0B7PBw+iw==",
      "dev": true,
      "license": "BSD-3-Clause",
      "dependencies": {
-        "@es-joy/jsdoccomment": "~0.81.0",
+        "@es-joy/jsdoccomment": "~0.82.0",
        "@es-joy/resolve.exports": "1.2.0",
        "are-docs-informative": "^0.0.2",
        "comment-parser": "1.4.4",
        "debug": "^4.4.3",
        "escape-string-regexp": "^4.0.0",
-        "espree": "^11.0.0",
+        "espree": "^11.1.0",
        "esquery": "^1.7.0",
        "html-entities": "^2.6.0",
        "object-deep-merge": "^2.0.0",
@@ -5015,9 +4949,9 @@
      }
    },
    "node_modules/eslint-plugin-jsdoc/node_modules/espree": {
-      "version": "11.0.0",
-      "resolved": "https://registry.npmjs.org/espree/-/espree-11.0.0.tgz",
-      "integrity": "sha512-+gMeWRrIh/NsG+3NaLeWHuyeyk70p2tbvZIWBYcqQ4/7Xvars6GYTZNhF1sIeLcc6Wb11He5ffz3hsHyXFrw5A==",
+      "version": "11.1.0",
+      "resolved": "https://registry.npmjs.org/espree/-/espree-11.1.0.tgz",
+      "integrity": "sha512-WFWYhO1fV4iYkqOOvq8FbqIhr2pYfoDY0kCotMkDeNtGpiGGkZ1iov2u8ydjtgM8yF8rzK7oaTbw2NAzbAbehw==",
      "dev": true,
      "license": "BSD-2-Clause",
      "dependencies": {
@@ -5450,6 +5384,22 @@
        "url": "https://github.com/sindresorhus/execa?sponsor=1"
      }
    },
+    "node_modules/fast-content-type-parse": {
+      "version": "3.0.0",
+      "resolved": "https://registry.npmjs.org/fast-content-type-parse/-/fast-content-type-parse-3.0.0.tgz",
+      "integrity": "sha512-ZvLdcY8P+N8mGQJahJV5G4U88CSvT1rP8ApL6uETe88MBXrBHAkZlSEySdUlyztF7ccb+Znos3TFqaepHxdhBg==",
+      "funding": [
+        {
+          "type": "github",
+          "url": "https://github.com/sponsors/fastify"
+        },
+        {
+          "type": "opencollective",
+          "url": "https://opencollective.com/fastify"
+        }
+      ],
+      "license": "MIT"
+    },
    "node_modules/fast-deep-equal": {
      "version": "3.1.3",
      "license": "MIT"
@@ -5492,9 +5442,9 @@
      "license": "MIT"
    },
    "node_modules/fast-xml-parser": {
-      "version": "5.3.3",
-      "resolved": "https://registry.npmjs.org/fast-xml-parser/-/fast-xml-parser-5.3.3.tgz",
-      "integrity": "sha512-2O3dkPAAC6JavuMm8+4+pgTk+5hoAs+CjZ+sWcQLkX9+/tHRuTkQh/Oaifr8qDmZ8iEHb771Ea6G8CdwkrgvYA==",
+      "version": "5.3.4",
+      "resolved": "https://registry.npmjs.org/fast-xml-parser/-/fast-xml-parser-5.3.4.tgz",
+      "integrity": "sha512-EFd6afGmXlCx8H8WTZHhAoDaWaGyuIBoZJ2mknrNxug+aZKjkp0a0dlars9Izl+jF+7Gu1/5f/2h68cQpe0IiA==",
      "funding": [
        {
          "type": "github",
@@ -6536,9 +6486,9 @@
      }
    },
    "node_modules/jsdoc-type-pratt-parser": {
-      "version": "7.0.0",
-      "resolved": "https://registry.npmjs.org/jsdoc-type-pratt-parser/-/jsdoc-type-pratt-parser-7.0.0.tgz",
-      "integrity": "sha512-c7YbokssPOSHmqTbSAmTtnVgAVa/7lumWNYqomgd5KOMyPrRve2anx6lonfOsXEQacqF9FKVUj7bLg4vRSvdYA==",
+      "version": "7.1.0",
+      "resolved": "https://registry.npmjs.org/jsdoc-type-pratt-parser/-/jsdoc-type-pratt-parser-7.1.0.tgz",
+      "integrity": "sha512-SX7q7XyCwzM/MEDCYz0l8GgGbJAACGFII9+WfNYr5SLEKukHWRy2Jk3iWRe7P+lpYJNs7oQ+OSei4JtKGUjd7A==",
      "dev": true,
      "license": "MIT",
      "engines": {
@@ -8184,9 +8134,9 @@
      }
    },
    "node_modules/tar": {
-      "version": "7.5.6",
-      "resolved": "https://registry.npmjs.org/tar/-/tar-7.5.6.tgz",
-      "integrity": "sha512-xqUeu2JAIJpXyvskvU3uvQW8PAmHrtXp2KDuMJwQqW8Sqq0CaZBAQ+dKS3RBXVhU4wC5NjAdKrmh84241gO9cA==",
+      "version": "7.5.7",
+      "resolved": "https://registry.npmjs.org/tar/-/tar-7.5.7.tgz",
+      "integrity": "sha512-fov56fJiRuThVFXD6o6/Q354S7pnWMJIVlDBYijsTNx6jKSE4pvrDTs6lUnmGvNyfJwFQQwWy3owKz1ucIhveQ==",
      "dev": true,
      "license": "BlueOak-1.0.0",
      "dependencies": {
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
  "name": "codeql",
-  "version": "4.32.0",
+  "version": "4.32.1",
  "private": true,
  "description": "CodeQL action",
  "scripts": {
@@ -24,17 +24,17 @@
  },
  "license": "MIT",
  "dependencies": {
-    "@actions/artifact": "^5.0.2",
+    "@actions/artifact": "^5.0.3",
    "@actions/artifact-legacy": "npm:@actions/artifact@^1.1.2",
-    "@actions/cache": "^5.0.3",
-    "@actions/core": "^2.0.2",
+    "@actions/cache": "^5.0.5",
+    "@actions/core": "^2.0.3",
    "@actions/exec": "^2.0.0",
-    "@actions/github": "^7.0.0",
+    "@actions/github": "^8.0.0",
    "@actions/glob": "^0.5.0",
    "@actions/http-client": "^3.0.0",
    "@actions/io": "^2.0.0",
-    "@actions/tool-cache": "^3.0.0",
-    "@octokit/plugin-retry": "^6.0.0",
+    "@actions/tool-cache": "^3.0.1",
+    "@octokit/plugin-retry": "^8.0.0",
    "@schemastore/package": "0.0.10",
    "archiver": "^7.0.1",
    "fast-deep-equal": "^3.1.3",
@@ -70,7 +70,7 @@
    "eslint-plugin-filenames": "^1.3.2",
    "eslint-plugin-github": "^5.1.8",
    "eslint-plugin-import": "2.29.1",
-    "eslint-plugin-jsdoc": "^62.2.0",
+    "eslint-plugin-jsdoc": "^62.3.0",
    "eslint-plugin-no-async-foreach": "^0.1.1",
    "glob": "^11.1.0",
    "nock": "^14.0.10",
--- a/pr-checks/checks/bundle-from-toolcache.yml
+++ b/pr-checks/checks/bundle-from-toolcache.yml
@@ -4,7 +4,7 @@ versions:
  - toolcache
 steps:
  - name: Install @actions/tool-cache
-    run: npm install @actions/tool-cache
+    run: npm install @actions/tool-cache@3
  - name: Check toolcache contains CodeQL
    continue-on-error: true
    uses: actions/github-script@v8
--- a/pr-checks/checks/bundle-toolcache.yml
+++ b/pr-checks/checks/bundle-toolcache.yml
@@ -16,7 +16,7 @@ steps:
        const codeqlPath = path.join(process.env['RUNNER_TOOL_CACHE'], 'CodeQL');
        fs.rmdirSync(codeqlPath, { recursive: true });
  - name: Install @actions/tool-cache
-    run: npm install @actions/tool-cache
+    run: npm install @actions/tool-cache@3
  - name: Check toolcache does not contain CodeQL
    uses: actions/github-script@v8
    with:
--- a/pr-checks/checks/export-file-baseline-information.yml
+++ b/pr-checks/checks/export-file-baseline-information.yml
@@ -5,6 +5,7 @@ versions: ["nightly-latest"]
 installGo: true
 installDotNet: true
 env:
+  CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS: false
  CODEQL_ACTION_SUBLANGUAGE_FILE_COVERAGE: true
 steps:
  - uses: ./../action/init
--- a/pr-checks/checks/global-proxy.yml
+++ b/pr-checks/checks/global-proxy.yml
@@ -3,19 +3,6 @@ description: "Tests using a proxy specified by the https_proxy environment varia
 versions: ["linked", "nightly-latest"]
 container:
  image: ubuntu:22.04
-container-init-steps:
-  # These steps are required to initialise the `gh` cli in a container that doesn't
-  # come pre-installed with it. The reason for that is that this is later
-  # needed by the `prepare-test` workflow to find the latest release of CodeQL. 
-  name: Set up GitHub CLI
-  run: |
-    apt update
-    apt install -y curl libreadline8 gnupg2 software-properties-common zstd
-    curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg
-    apt-key add /usr/share/keyrings/githubcli-archive-keyring.gpg
-    apt-add-repository https://cli.github.com/packages
-    apt install -y gh
-  env: {}
 services:
  squid-proxy:
    image: ubuntu/squid:latest
--- a/pr-checks/checks/rubocop-multi-language.yml
+++ b/pr-checks/checks/rubocop-multi-language.yml
@@ -4,7 +4,7 @@ description: "Tests using RuboCop to analyze a multi-language repository and the
 versions: ["default"]
 steps:
  - name: Set up Ruby
-    uses: ruby/setup-ruby@80740b3b13bf9857e28854481ca95a84e78a2bdf # v1.284.0
+    uses: ruby/setup-ruby@90be1154f987f4dc0fe0dd0feedac9e473aa4ba8 # v1.286.0
    with:
      ruby-version: 2.6
  - name: Install Code Scanning integration
--- a/src/analyze.test.ts
+++ b/src/analyze.test.ts
@@ -87,7 +87,6 @@ test("status report fields", async (t) => {
          );
          return "";
        },
-        databasePrintBaseline: async () => "",
      });

      const config = createTestConfig({
--- a/src/analyze.ts
+++ b/src/analyze.ts
@@ -495,10 +495,18 @@ export async function runQueries(
        endTimeInterpretResults.getTime() - startTimeInterpretResults.getTime();
      logger.endGroup();

-      logger.info(analysisSummary);
-      if (qualityAnalysisSummary) {
+      if (analysisSummary.trim()) {
+        logger.info(analysisSummary);
+      }
+      if (qualityAnalysisSummary?.trim()) {
        logger.info(qualityAnalysisSummary);
      }
+      if (!config.enableFileCoverageInformation) {
+        logger.info(
+          "To speed up pull request analysis, file coverage information is only enabled when analyzing " +
+            "the default branch and protected branches.",
+        );
+      }

      if (await features.getValue(Feature.QaTelemetryEnabled)) {
        // Note: QA adds the `code-quality` query suite to the `queries` input,
--- a/src/artifact-scanner.test.ts
+++ b/src/artifact-scanner.test.ts
@@ -4,37 +4,122 @@ import * as path from "path";

 import test from "ava";

-import { scanArtifactsForTokens } from "./artifact-scanner";
+import {
+  GITHUB_PAT_CLASSIC_PATTERN,
+  isAuthToken,
+  scanArtifactsForTokens,
+  TokenType,
+} from "./artifact-scanner";
 import { getRunnerLogger } from "./logging";
-import { getRecordingLogger, LoggedMessage } from "./testing-utils";
+import {
+  checkExpectedLogMessages,
+  getRecordingLogger,
+  LoggedMessage,
+  makeTestToken,
+} from "./testing-utils";

-test("scanArtifactsForTokens detects GitHub tokens in files", async (t) => {
-  const logger = getRunnerLogger(true);
-  const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), "scanner-test-"));
-
-  try {
-    // Create a test file with a fake GitHub token
-    const testFile = path.join(tempDir, "test.txt");
-    fs.writeFileSync(
-      testFile,
-      "This is a test file with token ghp_1234567890123456789012345678901234AB",
-    );
-
-    const error = await t.throwsAsync(
-      async () => await scanArtifactsForTokens([testFile], logger),
-    );
-
-    t.regex(
-      error?.message || "",
-      /Found 1 potential GitHub token.*Personal Access Token/,
-    );
-    t.regex(error?.message || "", /test\.txt/);
-  } finally {
-    // Clean up
-    fs.rmSync(tempDir, { recursive: true, force: true });
-  }
+test("makeTestToken", (t) => {
+  t.is(makeTestToken().length, 36);
+  t.is(makeTestToken(255).length, 255);
 });

+test("isAuthToken", (t) => {
+  // Undefined for strings that aren't tokens
+  t.is(isAuthToken("some string"), undefined);
+  t.is(isAuthToken("ghp_"), undefined);
+  t.is(isAuthToken("ghp_123"), undefined);
+
+  // Token types for strings that are tokens.
+  t.is(isAuthToken(`ghp_${makeTestToken()}`), TokenType.PersonalAccessClassic);
+  t.is(isAuthToken(`ghp_${makeTestToken()}`), TokenType.PersonalAccessClassic);
+  t.is(
+    isAuthToken(`ghs_${makeTestToken(255)}`),
+    TokenType.AppInstallationAccess,
+  );
+  t.is(
+    isAuthToken(`github_pat_${makeTestToken(22)}_${makeTestToken(59)}`),
+    TokenType.PersonalAccessFineGrained,
+  );
+
+  // With a custom pattern set
+  t.is(
+    isAuthToken(`ghp_${makeTestToken()}`, [GITHUB_PAT_CLASSIC_PATTERN]),
+    TokenType.PersonalAccessClassic,
+  );
+  t.is(
+    isAuthToken(`github_pat_${makeTestToken(22)}_${makeTestToken(59)}`, [
+      GITHUB_PAT_CLASSIC_PATTERN,
+    ]),
+    undefined,
+  );
+});
+
+const testTokens = [
+  {
+    type: TokenType.PersonalAccessClassic,
+    value: `ghp_${makeTestToken()}`,
+    checkPattern: "Personal Access Token",
+  },
+  {
+    type: TokenType.PersonalAccessFineGrained,
+    value:
+      "github_pat_1234567890ABCDEFGHIJKL_MNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz1234567890ABCDEFGHI",
+    checkPattern: "Personal Access Token",
+  },
+  {
+    type: TokenType.OAuth,
+    value: `gho_${makeTestToken()}`,
+  },
+  {
+    type: TokenType.UserToServer,
+    value: `ghu_${makeTestToken()}`,
+  },
+  {
+    type: TokenType.ServerToServer,
+    value: `ghs_${makeTestToken()}`,
+  },
+  {
+    type: TokenType.Refresh,
+    value: `ghr_${makeTestToken()}`,
+  },
+  {
+    type: TokenType.AppInstallationAccess,
+    value: `ghs_${makeTestToken(255)}`,
+  },
+];
+
+for (const { type, value, checkPattern } of testTokens) {
+  test(`scanArtifactsForTokens detects GitHub ${type} tokens in files`, async (t) => {
+    const logMessages = [];
+    const logger = getRecordingLogger(logMessages, { logToConsole: false });
+    const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), "scanner-test-"));
+
+    try {
+      // Create a test file with a fake GitHub token
+      const testFile = path.join(tempDir, "test.txt");
+      fs.writeFileSync(testFile, `This is a test file with token ${value}`);
+
+      const error = await t.throwsAsync(
+        async () => await scanArtifactsForTokens([testFile], logger),
+      );
+
+      t.regex(
+        error?.message || "",
+        new RegExp(`Found 1 potential GitHub token.*${checkPattern || type}`),
+      );
+      t.regex(error?.message || "", /test\.txt/);
+
+      checkExpectedLogMessages(t, logMessages, [
+        "Starting best-effort check",
+        `Found 1 ${type}`,
+      ]);
+    } finally {
+      // Clean up
+      fs.rmSync(tempDir, { recursive: true, force: true });
+    }
+  });
+}
+
 test("scanArtifactsForTokens handles files without tokens", async (t) => {
  const logger = getRunnerLogger(true);
  const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), "scanner-test-"));
--- a/src/artifact-scanner.ts
+++ b/src/artifact-scanner.ts
@@ -7,33 +7,62 @@ import * as exec from "@actions/exec";
 import { Logger } from "./logging";
 import { getErrorMessage } from "./util";

+/**
+ * Enumerates known types of GitHub token formats.
+ */
+export enum TokenType {
+  PersonalAccessClassic = "Personal Access Token (Classic)",
+  PersonalAccessFineGrained = "Personal Access Token (Fine-grained)",
+  OAuth = "OAuth Access Token",
+  UserToServer = "User-to-Server Token",
+  ServerToServer = "Server-to-Server Token",
+  Refresh = "Refresh Token",
+  AppInstallationAccess = "App Installation Access Token",
+}
+
+/** A value of this type associates a token type with its pattern. */
+export interface TokenPattern {
+  type: TokenType;
+  pattern: RegExp;
+}
+
+/** The pattern for PATs (Classic) */
+export const GITHUB_PAT_CLASSIC_PATTERN: TokenPattern = {
+  type: TokenType.PersonalAccessClassic,
+  pattern: /\bghp_[a-zA-Z0-9]{36}\b/g,
+};
+
+/** The pattern for PATs (Fine-grained) */
+export const GITHUB_PAT_FINE_GRAINED_PATTERN: TokenPattern = {
+  type: TokenType.PersonalAccessFineGrained,
+  pattern: /\bgithub_pat_[a-zA-Z0-9_]+\b/g,
+};
+
 /**
 * GitHub token patterns to scan for.
 * These patterns match various GitHub token formats.
 */
-const GITHUB_TOKEN_PATTERNS = [
+const GITHUB_TOKEN_PATTERNS: TokenPattern[] = [
+  GITHUB_PAT_CLASSIC_PATTERN,
+  GITHUB_PAT_FINE_GRAINED_PATTERN,
  {
-    name: "Personal Access Token",
-    pattern: /\bghp_[a-zA-Z0-9]{36}\b/g,
-  },
-  {
-    name: "OAuth Access Token",
+    type: TokenType.OAuth,
    pattern: /\bgho_[a-zA-Z0-9]{36}\b/g,
  },
  {
-    name: "User-to-Server Token",
+    type: TokenType.UserToServer,
    pattern: /\bghu_[a-zA-Z0-9]{36}\b/g,
  },
  {
-    name: "Server-to-Server Token",
+    type: TokenType.ServerToServer,
    pattern: /\bghs_[a-zA-Z0-9]{36}\b/g,
  },
  {
-    name: "Refresh Token",
+    type: TokenType.Refresh,
    pattern: /\bghr_[a-zA-Z0-9]{36}\b/g,
  },
  {
-    name: "App Installation Access Token",
+    type: TokenType.AppInstallationAccess,
    pattern: /\bghs_[a-zA-Z0-9]{255}\b/g,
  },
 ];
@@ -48,6 +77,24 @@ interface ScanResult {
  findings: TokenFinding[];
 }

+/**
+ * Checks whether `value` matches any token `patterns`.
+ * @param value The value to match against.
+ * @param patterns The patterns to check.
+ * @returns The type of the first matching pattern, or `undefined` if none match.
+ */
+export function isAuthToken(
+  value: string,
+  patterns: TokenPattern[] = GITHUB_TOKEN_PATTERNS,
+) {
+  for (const { type, pattern } of patterns) {
+    if (value.match(pattern)) {
+      return type;
+    }
+  }
+  return undefined;
+}
+
 /**
 * Scans a file for GitHub tokens.
 *
@@ -65,13 +112,13 @@ function scanFileForTokens(
  try {
    const content = fs.readFileSync(filePath, "utf8");

-    for (const { name, pattern } of GITHUB_TOKEN_PATTERNS) {
+    for (const { type, pattern } of GITHUB_TOKEN_PATTERNS) {
      const matches = content.match(pattern);
      if (matches) {
        for (let i = 0; i < matches.length; i++) {
-          findings.push({ tokenType: name, filePath: relativePath });
+          findings.push({ tokenType: type, filePath: relativePath });
        }
-        logger.debug(`Found ${matches.length} ${name}(s) in ${relativePath}`);
+        logger.debug(`Found ${matches.length} ${type}(s) in ${relativePath}`);
      }
    }

--- a/src/codeql.ts
+++ b/src/codeql.ts
@@ -186,10 +186,6 @@ export interface CodeQL {
    config: Config,
    features: FeatureEnablement,
  ): Promise<string>;
-  /**
-   * Run 'codeql database print-baseline'.
-   */
-  databasePrintBaseline(databasePath: string): Promise<string>;
  /**
   * Run 'codeql database export-diagnostics'
   *
@@ -493,10 +489,6 @@ export function createStubCodeQL(partialCodeql: Partial<CodeQL>): CodeQL {
      partialCodeql,
      "databaseInterpretResults",
    ),
-    databasePrintBaseline: resolveFunction(
-      partialCodeql,
-      "databasePrintBaseline",
-    ),
    databaseExportDiagnostics: resolveFunction(
      partialCodeql,
      "databaseExportDiagnostics",
@@ -628,6 +620,13 @@ async function getCodeQLForCmd(
        extraArgs.push("--overlay-base");
      }

+      const baselineFilesOptions = config.enableFileCoverageInformation
+        ? [
+            "--calculate-language-specific-baseline",
+            "--sublanguage-file-coverage",
+          ]
+        : ["--no-calculate-baseline"];
+
      await runCli(
        cmd,
        [
@@ -639,12 +638,14 @@ async function getCodeQLForCmd(
          "--db-cluster",
          config.dbLocation,
          `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
          "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
          ...extraArgs,
          ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"],
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions],
          }),
        ],
        { stdin: externalRepositoryToken },
@@ -885,15 +886,6 @@ async function getCodeQLForCmd(
        noStreamStdout: true,
      });
    },
-    async databasePrintBaseline(databasePath: string): Promise<string> {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath,
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
    async databaseCleanupCluster(
      config: Config,
      cleanupLevel: CleanupLevel,
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -89,6 +89,7 @@ function createTestInitConfigInputs(
      },
      features: createFeatures([]),
      repositoryProperties: {},
+      enableFileCoverageInformation: true,
      logger: getRunnerLogger(true),
    } satisfies configUtils.InitConfigInputs,
    overrides,
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -26,7 +26,10 @@ import {
  parseUserConfig,
  UserConfig,
 } from "./config/db-config";
-import { addDiagnostic, makeTelemetryDiagnostic } from "./diagnostics";
+import {
+  addNoLanguageDiagnostic,
+  makeTelemetryDiagnostic,
+} from "./diagnostics";
 import { shouldPerformDiffInformedAnalysis } from "./diff-informed-analysis-utils";
 import { EnvVar } from "./environment";
 import * as errorMessages from "./error-messages";
@@ -214,6 +217,11 @@ export interface Config {
   * A partial mapping from repository properties that affect us to their values.
   */
  repositoryProperties: RepositoryProperties;
+
+  /**
+   * Whether to enable file coverage information.
+   */
+  enableFileCoverageInformation: boolean;
 }

 async function getSupportedLanguageMap(
@@ -433,6 +441,7 @@ export interface InitConfigInputs {
  apiDetails: api.GitHubApiCombinedDetails;
  features: FeatureEnablement;
  repositoryProperties: RepositoryProperties;
+  enableFileCoverageInformation: boolean;
  analysisKinds: AnalysisKind[];
  logger: Logger;
 }
@@ -462,6 +471,7 @@ export async function initActionState(
    repositoryProperties,
    analysisKinds,
    logger,
+    enableFileCoverageInformation,
  }: InitConfigInputs,
  userConfig: UserConfig,
 ): Promise<Config> {
@@ -542,6 +552,7 @@ export async function initActionState(
    overlayDatabaseMode: OverlayDatabaseMode.None,
    useOverlayDatabaseCaching: false,
    repositoryProperties,
+    enableFileCoverageInformation,
  };
 }

@@ -1408,11 +1419,8 @@ async function logGitVersionTelemetry(
  gitVersion: GitVersionInfo,
 ): Promise<void> {
  if (config.languages.length > 0) {
-    addDiagnostic(
+    addNoLanguageDiagnostic(
      config,
-      // Arbitrarily choose the first language. We could also choose all languages, but that
-      // increases the risk of misinterpreting the data.
-      config.languages[0],
      makeTelemetryDiagnostic(
        "codeql-action/git-version-telemetry",
        "Git version telemetry",
@@ -1438,11 +1446,8 @@ async function logGeneratedFilesTelemetry(
    return;
  }

-  addDiagnostic(
+  addNoLanguageDiagnostic(
    config,
-    // Arbitrarily choose the first language. We could also choose all languages, but that
-    // increases the risk of misinterpreting the data.
-    config.languages[0],
    makeTelemetryDiagnostic(
      "codeql-action/generated-files-telemetry",
      "Generated files telemetry",
--- a/src/diagnostics.ts
+++ b/src/diagnostics.ts
@@ -117,6 +117,20 @@ export function addDiagnostic(
  }
 }

+/** Adds a diagnostic that is not specific to any language. */
+export function addNoLanguageDiagnostic(
+  config: Config,
+  diagnostic: DiagnosticMessage,
+) {
+  addDiagnostic(
+    config,
+    // Arbitrarily choose the first language. We could also choose all languages, but that
+    // increases the risk of misinterpreting the data.
+    config.languages[0],
+    diagnostic,
+  );
+}
+
 /**
 * Writes the given diagnostic to the database.
 *
--- a/src/feature-flags.ts
+++ b/src/feature-flags.ts
@@ -70,6 +70,8 @@ export enum Feature {
  OverlayAnalysisSwift = "overlay_analysis_swift",
  PythonDefaultIsToNotExtractStdlib = "python_default_is_to_not_extract_stdlib",
  QaTelemetryEnabled = "qa_telemetry_enabled",
+  /** Note that this currently only disables baseline file coverage information. */
+  SkipFileCoverageOnPrs = "skip_file_coverage_on_prs",
  UploadOverlayDbToApi = "upload_overlay_db_to_api",
  UseRepositoryProperties = "use_repository_properties",
  ValidateDbConfig = "validate_db_config",
@@ -286,6 +288,15 @@ export const featureConfig = {
    legacyApi: true,
    minimumVersion: undefined,
  },
+  [Feature.SkipFileCoverageOnPrs]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: undefined,
+  },
  [Feature.UploadOverlayDbToApi]: {
    defaultValue: false,
    envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
--- a/src/feature-flags/properties.ts
+++ b/src/feature-flags/properties.ts
@@ -78,11 +78,17 @@ export async function loadPropertiesFromApi(
      }
    }

-    logger.debug("Loaded the following values for the repository properties:");
-    for (const [property, value] of Object.entries(properties).sort(
-      ([nameA], [nameB]) => nameA.localeCompare(nameB),
-    )) {
-      logger.debug(`  ${property}: ${value}`);
+    if (Object.keys(properties).length === 0) {
+      logger.debug("No known repository properties were found.");
+    } else {
+      logger.debug(
+        "Loaded the following values for the repository properties:",
+      );
+      for (const [property, value] of Object.entries(properties).sort(
+        ([nameA], [nameB]) => nameA.localeCompare(nameB),
+      )) {
+        logger.debug(`  ${property}: ${value}`);
+      }
    }

    return properties;
--- a/src/init-action-post-helper.ts
+++ b/src/init-action-post-helper.ts
@@ -1,6 +1,5 @@
 import * as fs from "fs";

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

 import * as actionsUtil from "./actions-util";
@@ -129,48 +128,31 @@ export async function tryUploadSarifIfRunFailed(
  features: FeatureEnablement,
  logger: Logger,
 ): Promise<UploadFailedSarifResult> {
-  if (process.env[EnvVar.ANALYZE_DID_COMPLETE_SUCCESSFULLY] !== "true") {
-    // If analyze didn't complete successfully and the job status hasn't
-    // already been set to Failure/ConfigurationError previously, this
-    // means that something along the way failed in a step that is not
-    // owned by the Action, for example a manual build step. We
-    // consider this a configuration error.
-    core.exportVariable(
-      EnvVar.JOB_STATUS,
-      process.env[EnvVar.JOB_STATUS] ?? JobStatus.ConfigErrorStatus,
-    );
-
-    // If the only enabled analysis kind is `code-quality`, then we shouldn't
-    // upload the failed SARIF to Code Scanning.
-    if (!isCodeScanningEnabled(config)) {
-      return {
-        upload_failed_run_skipped_because: "Code Scanning is not enabled.",
-      };
-    }
-
-    try {
-      return await maybeUploadFailedSarif(
-        config,
-        repositoryNwo,
-        features,
-        logger,
-      );
-    } catch (e) {
-      logger.debug(
-        `Failed to upload a SARIF file for this failed CodeQL code scanning run. ${e}`,
-      );
-      return createFailedUploadFailedSarifResult(e);
-    }
-  } else {
-    core.exportVariable(
-      EnvVar.JOB_STATUS,
-      process.env[EnvVar.JOB_STATUS] ?? JobStatus.SuccessStatus,
-    );
+  // Only upload the failed SARIF to Code scanning if Code scanning is enabled.
+  if (!isCodeScanningEnabled(config)) {
+    return {
+      upload_failed_run_skipped_because: "Code Scanning is not enabled.",
+    };
+  }
+  if (process.env[EnvVar.ANALYZE_DID_COMPLETE_SUCCESSFULLY] === "true") {
    return {
      upload_failed_run_skipped_because:
        "Analyze Action completed successfully",
    };
  }
+  try {
+    return await maybeUploadFailedSarif(
+      config,
+      repositoryNwo,
+      features,
+      logger,
+    );
+  } catch (e) {
+    logger.debug(
+      `Failed to upload a SARIF file for this failed CodeQL code scanning run. ${e}`,
+    );
+    return createFailedUploadFailedSarifResult(e);
+  }
 }

 export async function run(
@@ -335,20 +317,3 @@ async function removeUploadedSarif(
    );
  }
 }
-
-/**
- * Returns the final job status sent in the `init-post` Action, based on the
- * current value of the JOB_STATUS environment variable. If the variable is
- * unset, or if its value is not one of the JobStatus enum values, returns
- * Unknown. Otherwise it returns the status set in the environment variable.
- */
-export function getFinalJobStatus(): JobStatus {
-  const jobStatusFromEnvironment = process.env[EnvVar.JOB_STATUS];
-  if (
-    !jobStatusFromEnvironment ||
-    !Object.values(JobStatus).includes(jobStatusFromEnvironment as JobStatus)
-  ) {
-    return JobStatus.UnknownStatus;
-  }
-  return jobStatusFromEnvironment as JobStatus;
-}
--- a/src/init-action-post.ts
+++ b/src/init-action-post.ts
@@ -14,12 +14,13 @@ import {
 import { getGitHubVersion } from "./api-client";
 import { CachingKind } from "./caching-utils";
 import { getCodeQL } from "./codeql";
-import { Config, getConfig } from "./config-utils";
+import { type Config, getConfig } from "./config-utils";
 import * as debugArtifacts from "./debug-artifacts";
 import {
  DependencyCachingUsageReport,
  getDependencyCacheUsage,
 } from "./dependency-caching";
+import { EnvVar } from "./environment";
 import { Features } from "./feature-flags";
 import * as gitUtils from "./git-utils";
 import * as initActionPostHelper from "./init-action-post-helper";
@@ -33,6 +34,7 @@ import {
  getActionsStatus,
  ActionName,
  getJobStatusDisplayName,
+  JobStatus,
 } from "./status-report";
 import { checkDiskUsage, checkGitHubVersionInRange, wrapError } from "./util";

@@ -85,7 +87,7 @@ async function run(startedAt: Date) {
        logger,
      );

-      // If we are analysing the default branch and some kind of caching is enabled,
+      // If we are analyzing the default branch and some kind of caching is enabled,
      // then try to determine our overall cache usage for dependency caches. We only
      // do this under these circumstances to avoid slowing down analyses for PRs
      // and where caching may not be enabled.
@@ -115,7 +117,7 @@ async function run(startedAt: Date) {
    }
    return;
  }
-  const jobStatus = initActionPostHelper.getFinalJobStatus();
+  const jobStatus = getFinalJobStatus(config);
  logger.info(`CodeQL job status was ${getJobStatusDisplayName(jobStatus)}.`);

  const statusReportBase = await createStatusReportBase(
@@ -130,7 +132,7 @@ async function run(startedAt: Date) {
    const statusReport: InitPostStatusReport = {
      ...statusReportBase,
      ...uploadFailedSarifResult,
-      job_status: initActionPostHelper.getFinalJobStatus(),
+      job_status: jobStatus,
      dependency_caching_usage: dependencyCachingUsage,
    };
    logger.info("Sending status report for init-post step.");
@@ -139,6 +141,72 @@ async function run(startedAt: Date) {
  }
 }

+/**
+ * Determine the final job status to be reported in the status report.
+ *
+ * If the job status has already been set by another step, we use that.
+ * 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();
+  if (existingJobStatus !== undefined) {
+    return existingJobStatus;
+  }
+
+  let jobStatus: JobStatus;
+
+  if (process.env[EnvVar.ANALYZE_DID_COMPLETE_SUCCESSFULLY] === "true") {
+    core.exportVariable(EnvVar.JOB_STATUS, JobStatus.SuccessStatus);
+    jobStatus = JobStatus.SuccessStatus;
+  } else if (config !== undefined) {
+    // - We have computed a CodeQL config
+    // - Analyze didn't complete successfully
+    // - The job status hasn't already been set to Failure/ConfigurationError
+    //
+    // This means that something along the way failed in a step that is not
+    // owned by the Action, for example a manual build step. We consider this a
+    // configuration error.
+    jobStatus = JobStatus.ConfigErrorStatus;
+  } else {
+    // If we didn't manage to compute a CodeQL config, it is unclear at this
+    // point why the analyze Action didn't complete.
+    // - One possibility is that the workflow run was cancelled. We could
+    //   consider determining workflow cancellation using the GitHub API, but
+    //   for now we treat all these cases as unknown.
+    // - Another possibility is that we're running a workflow that only runs
+    //   `init`, for instance a workflow that was created before `setup-codeql`
+    //   was available and uses `init` just to set up the CodeQL tools.
+    jobStatus = JobStatus.UnknownStatus;
+  }
+
+  // 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);
+  return jobStatus;
+}
+
+/**
+ * Get the job status from the environment variable, if it has been set.
+ *
+ * If the job status is invalid, return `UnknownStatus`.
+ */
+function getJobStatusFromEnvironment(): JobStatus | undefined {
+  const jobStatusFromEnvironment = process.env[EnvVar.JOB_STATUS];
+
+  if (jobStatusFromEnvironment !== undefined) {
+    // Validate the job status from the environment. If it is invalid, return unknown.
+    if (
+      Object.values(JobStatus).includes(jobStatusFromEnvironment as JobStatus)
+    ) {
+      return jobStatusFromEnvironment as JobStatus;
+    }
+    return JobStatus.UnknownStatus;
+  }
+
+  return undefined;
+}
+
 async function runWrapper() {
  const startedAt = new Date();
  const logger = getActionsLogger();
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -2,6 +2,7 @@ import * as fs from "fs";
 import * as path from "path";

 import * as core from "@actions/core";
+import * as github from "@actions/github";
 import * as io from "@actions/io";
 import * as semver from "semver";
 import { v4 as uuidV4 } from "uuid";
@@ -30,18 +31,23 @@ import {
 } from "./dependency-caching";
 import {
  addDiagnostic,
+  addNoLanguageDiagnostic,
  flushDiagnostics,
  logUnwrittenDiagnostics,
  makeDiagnostic,
  makeTelemetryDiagnostic,
 } from "./diagnostics";
 import { EnvVar } from "./environment";
-import { Feature, Features } from "./feature-flags";
-import { loadPropertiesFromApi } from "./feature-flags/properties";
+import { Feature, FeatureEnablement, Features } from "./feature-flags";
+import {
+  loadPropertiesFromApi,
+  RepositoryProperties,
+} from "./feature-flags/properties";
 import {
  checkInstallPython311,
  checkPacksForOverlayCompatibility,
  cleanupDatabaseClusterDirectory,
+  getFileCoverageInformationEnabled,
  initCodeQL,
  initConfig,
  runDatabaseInitCluster,
@@ -53,7 +59,7 @@ import {
  OverlayBaseDatabaseDownloadStats,
  OverlayDatabaseMode,
 } from "./overlay-database-utils";
-import { getRepositoryNwo } from "./repository";
+import { getRepositoryNwo, RepositoryNwo } from "./repository";
 import { ToolsSource } from "./setup-codeql";
 import {
  ActionName,
@@ -87,6 +93,8 @@ import {
  checkActionVersion,
  getErrorMessage,
  BuildMode,
+  GitHubVersion,
+  Result,
 } from "./util";
 import { checkWorkflow } from "./workflow";

@@ -237,12 +245,12 @@ async function run(startedAt: Date) {
    );

    // Fetch the values of known repository properties that affect us.
-    const enableRepoProps = await features.getValue(
-      Feature.UseRepositoryProperties,
+    const repositoryPropertiesResult = await loadRepositoryProperties(
+      repositoryNwo,
+      gitHubVersion,
+      features,
+      logger,
    );
-    const repositoryProperties = enableRepoProps
-      ? await loadPropertiesFromApi(gitHubVersion, logger, repositoryNwo)
-      : {};

    // Create a unique identifier for this run.
    const jobRunUuid = uuidV4();
@@ -334,6 +342,7 @@ async function run(startedAt: Date) {
    }

    analysisKinds = await getAnalysisKinds(logger);
+    const debugMode = getOptionalInput("debug") === "true" || core.isDebug();
    config = await initConfig(features, {
      analysisKinds,
      languagesInput: getOptionalInput("languages"),
@@ -350,7 +359,7 @@ async function run(startedAt: Date) {
      // - The `init` Action is passed `debug: true`.
      // - Actions step debugging is enabled (e.g. by [enabling debug logging for a rerun](https://docs.github.com/en/actions/managing-workflow-runs/re-running-workflows-and-jobs#re-running-all-the-jobs-in-a-workflow),
      //   or by setting the `ACTIONS_STEP_DEBUG` secret to `true`).
-      debugMode: getOptionalInput("debug") === "true" || core.isDebug(),
+      debugMode,
      debugArtifactName:
        getOptionalInput("debug-artifact-name") || DEFAULT_DEBUG_ARTIFACT_NAME,
      debugDatabaseName:
@@ -363,10 +372,28 @@ async function run(startedAt: Date) {
      githubVersion: gitHubVersion,
      apiDetails,
      features,
-      repositoryProperties,
+      repositoryProperties: repositoryPropertiesResult.orElse({}),
+      enableFileCoverageInformation: await getFileCoverageInformationEnabled(
+        debugMode,
+        repositoryNwo,
+        features,
+      ),
      logger,
    });

+    if (repositoryPropertiesResult.isFailure()) {
+      addNoLanguageDiagnostic(
+        config,
+        makeTelemetryDiagnostic(
+          "codeql-action/repository-properties-load-failure",
+          "Failed to load repository properties",
+          {
+            error: getErrorMessage(repositoryPropertiesResult.value),
+          },
+        ),
+      );
+    }
+
    await checkInstallPython311(config.languages, codeql);
  } catch (unwrappedError) {
    const error = wrapError(unwrappedError);
@@ -429,11 +456,8 @@ async function run(startedAt: Date) {

    // Log CodeQL download telemetry, if appropriate
    if (toolsDownloadStatusReport) {
-      addDiagnostic(
+      addNoLanguageDiagnostic(
        config,
-        // Arbitrarily choose the first language. We could also choose all languages, but that
-        // increases the risk of misinterpreting the data.
-        config.languages[0],
        makeTelemetryDiagnostic(
          "codeql-action/bundle-download-telemetry",
          "CodeQL bundle download telemetry",
@@ -775,6 +799,49 @@ async function run(startedAt: Date) {
  );
 }

+/**
+ * Loads [repository properties](https://docs.github.com/en/organizations/managing-organization-settings/managing-custom-properties-for-repositories-in-your-organization) if applicable.
+ */
+async function loadRepositoryProperties(
+  repositoryNwo: RepositoryNwo,
+  gitHubVersion: GitHubVersion,
+  features: FeatureEnablement,
+  logger: Logger,
+): Promise<Result<RepositoryProperties, unknown>> {
+  // See if we can skip loading repository properties early. In particular,
+  // repositories owned by users cannot have repository properties, so we can
+  // skip the API call entirely in that case.
+  const repositoryOwnerType = github.context.payload.repository?.owner.type;
+  logger.debug(
+    `Repository owner type is '${repositoryOwnerType ?? "unknown"}'.`,
+  );
+  if (repositoryOwnerType === "User") {
+    logger.debug(
+      "Skipping loading repository properties because the repository is owned by a user and " +
+        "therefore cannot have repository properties.",
+    );
+    return Result.success({});
+  }
+
+  if (!(await features.getValue(Feature.UseRepositoryProperties))) {
+    logger.debug(
+      "Skipping loading repository properties because the UseRepositoryProperties feature flag is disabled.",
+    );
+    return Result.success({});
+  }
+
+  try {
+    return Result.success(
+      await loadPropertiesFromApi(gitHubVersion, logger, repositoryNwo),
+    );
+  } catch (error) {
+    logger.warning(
+      `Failed to load repository properties: ${getErrorMessage(error)}`,
+    );
+    return Result.failure(error);
+  }
+}
+
 function getTrapCachingEnabled(): boolean {
  // If the workflow specified something always respect that
  const trapCaching = getOptionalInput("trap-caching");
@@ -791,11 +858,8 @@ async function recordZstdAvailability(
  config: configUtils.Config,
  zstdAvailability: ZstdAvailability,
 ) {
-  addDiagnostic(
+  addNoLanguageDiagnostic(
    config,
-    // Arbitrarily choose the first language. We could also choose all languages, but that
-    // increases the risk of misinterpreting the data.
-    config.languages[0],
    makeTelemetryDiagnostic(
      "codeql-action/zstd-availability",
      "Zstandard availability",
--- a/src/init.test.ts
+++ b/src/init.test.ts
@@ -2,14 +2,20 @@ import * as fs from "fs";
 import path from "path";

 import test, { ExecutionContext } from "ava";
+import * as sinon from "sinon";

+import * as actionsUtil from "./actions-util";
 import { createStubCodeQL } from "./codeql";
+import { Feature } from "./feature-flags";
 import {
  checkPacksForOverlayCompatibility,
  cleanupDatabaseClusterDirectory,
+  getFileCoverageInformationEnabled,
 } from "./init";
 import { KnownLanguage } from "./languages";
+import { parseRepositoryNwo } from "./repository";
 import {
+  createFeatures,
  LoggedMessage,
  createTestConfig,
  getRecordingLogger,
@@ -442,3 +448,61 @@ test(
    expectedResult: true,
  },
 );
+
+test("file coverage information enabled when debugMode is true", async (t) => {
+  t.true(
+    await getFileCoverageInformationEnabled(
+      true, // debugMode
+      parseRepositoryNwo("github/codeql-action"),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+    ),
+  );
+});
+
+test("file coverage information enabled when not analyzing a pull request", async (t) => {
+  sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(false);
+
+  t.true(
+    await getFileCoverageInformationEnabled(
+      false, // debugMode
+      parseRepositoryNwo("github/codeql-action"),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+    ),
+  );
+});
+
+test("file coverage information enabled when owner is not 'github'", async (t) => {
+  sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
+
+  t.true(
+    await getFileCoverageInformationEnabled(
+      false, // debugMode
+      parseRepositoryNwo("other-org/some-repo"),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+    ),
+  );
+});
+
+test("file coverage information enabled when feature flag is not enabled", async (t) => {
+  sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
+
+  t.true(
+    await getFileCoverageInformationEnabled(
+      false, // debugMode
+      parseRepositoryNwo("github/codeql-action"),
+      createFeatures([]),
+    ),
+  );
+});
+
+test("file coverage information disabled when all conditions for skipping are met", async (t) => {
+  sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
+
+  t.false(
+    await getFileCoverageInformationEnabled(
+      false, // debugMode
+      parseRepositoryNwo("github/codeql-action"),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+    ),
+  );
+});
--- a/src/init.ts
+++ b/src/init.ts
@@ -5,13 +5,22 @@ import * as toolrunner from "@actions/exec/lib/toolrunner";
 import * as io from "@actions/io";
 import * as yaml from "js-yaml";

-import { getOptionalInput, isSelfHostedRunner } from "./actions-util";
+import {
+  getOptionalInput,
+  isAnalyzingPullRequest,
+  isSelfHostedRunner,
+} from "./actions-util";
 import { GitHubApiDetails } from "./api-client";
 import { CodeQL, setupCodeQL } from "./codeql";
 import * as configUtils from "./config-utils";
-import { CodeQLDefaultVersionInfo, FeatureEnablement } from "./feature-flags";
+import {
+  CodeQLDefaultVersionInfo,
+  Feature,
+  FeatureEnablement,
+} from "./feature-flags";
 import { KnownLanguage, Language } from "./languages";
 import { Logger, withGroupAsync } from "./logging";
+import { RepositoryNwo } from "./repository";
 import { ToolsSource } from "./setup-codeql";
 import { ZstdAvailability } from "./tar";
 import { ToolsDownloadStatusReport } from "./tools-download";
@@ -288,3 +297,21 @@ export function cleanupDatabaseClusterDirectory(
    }
  }
 }
+
+export async function getFileCoverageInformationEnabled(
+  debugMode: boolean,
+  repositoryNwo: RepositoryNwo,
+  features: FeatureEnablement,
+): Promise<boolean> {
+  return (
+    // Always enable file coverage information in debug mode
+    debugMode ||
+    // We're most interested in speeding up PRs, and we want to keep
+    // submitting file coverage information for the default branch since
+    // it is used to populate the status page.
+    !isAnalyzingPullRequest() ||
+    // For now, restrict this feature to the GitHub org
+    repositoryNwo.owner !== "github" ||
+    !(await features.getValue(Feature.SkipFileCoverageOnPrs))
+  );
+}
--- a/src/start-proxy.test.ts
+++ b/src/start-proxy.test.ts
@@ -7,7 +7,12 @@ import { KnownLanguage } from "./languages";
 import { getRunnerLogger } from "./logging";
 import * as startProxyExports from "./start-proxy";
 import { parseLanguage } from "./start-proxy";
-import { setupTests } from "./testing-utils";
+import {
+  checkExpectedLogMessages,
+  getRecordingLogger,
+  makeTestToken,
+  setupTests,
+} from "./testing-utils";

 setupTests(test);

@@ -174,6 +179,37 @@ test("getCredentials throws an error when non-printable characters are used", as
  }
 });

+test("getCredentials logs a warning when a PAT is used without a username", async (t) => {
+  const loggedMessages = [];
+  const logger = getRecordingLogger(loggedMessages);
+  const likelyWrongCredentials = toEncodedJSON([
+    {
+      type: "git_server",
+      host: "https://github.com/",
+      password: `ghp_${makeTestToken()}`,
+    },
+  ]);
+
+  const results = startProxyExports.getCredentials(
+    logger,
+    undefined,
+    likelyWrongCredentials,
+    undefined,
+  );
+
+  // The configuration should be accepted, despite the likely problem.
+  t.assert(results);
+  t.is(results.length, 1);
+  t.is(results[0].type, "git_server");
+  t.is(results[0].host, "https://github.com/");
+  t.assert(results[0].password?.startsWith("ghp_"));
+
+  // A warning should have been logged.
+  checkExpectedLogMessages(t, loggedMessages, [
+    "using a GitHub Personal Access Token (PAT), but no username was provided",
+  ]);
+});
+
 test("parseLanguage", async (t) => {
  // Exact matches
  t.deepEqual(parseLanguage("csharp"), KnownLanguage.csharp);
--- a/src/start-proxy.ts
+++ b/src/start-proxy.ts
@@ -1,6 +1,7 @@
 import * as core from "@actions/core";

 import { getApiClient } from "./api-client";
+import * as artifactScanner from "./artifact-scanner";
 import * as defaults from "./defaults.json";
 import { KnownLanguage } from "./languages";
 import { Logger } from "./logging";
@@ -62,6 +63,13 @@ export function parseLanguage(language: string): KnownLanguage | undefined {
  return undefined;
 }

+function isPAT(value: string) {
+  return artifactScanner.isAuthToken(value, [
+    artifactScanner.GITHUB_PAT_CLASSIC_PATTERN,
+    artifactScanner.GITHUB_PAT_FINE_GRAINED_PATTERN,
+  ]);
+}
+
 const LANGUAGE_TO_REGISTRY_TYPE: Partial<Record<KnownLanguage, string[]>> = {
  java: ["maven_repository"],
  csharp: ["nuget_feed"],
@@ -161,6 +169,19 @@ export function getCredentials(
      );
    }

+    // If the password or token looks like a GitHub PAT, warn if no username is configured.
+    if (
+      !isDefined(e.username) &&
+      ((isDefined(e.password) && isPAT(e.password)) ||
+        (isDefined(e.token) && isPAT(e.token)))
+    ) {
+      logger.warning(
+        `A ${e.type} private registry is configured for ${e.host || e.url} using a GitHub Personal Access Token (PAT), but no username was provided. ` +
+          `This may not work correctly. When configuring a private registry using a PAT, select "Username and password" and enter the username of the user ` +
+          `who generated the PAT.`,
+      );
+    }
+
    out.push({
      type: e.type,
      host: e.host,
--- a/src/testing-utils.ts
+++ b/src/testing-utils.ts
@@ -408,7 +408,14 @@ export function createTestConfig(overrides: Partial<Config>): Config {
      overlayDatabaseMode: OverlayDatabaseMode.None,
      useOverlayDatabaseCaching: false,
      repositoryProperties: {},
+      enableFileCoverageInformation: true,
    } satisfies Config,
    overrides,
  );
 }
+
+export function makeTestToken(length: number = 36) {
+  const chars =
+    "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789";
+  return chars.repeat(Math.ceil(length / chars.length)).slice(0, length);
+}
--- a/src/util.test.ts
+++ b/src/util.test.ts
@@ -563,3 +563,28 @@ test("joinAtMost - truncates list if array is > than limit", (t) => {
  t.assert(result.includes("test5"));
  t.false(result.includes("test6"));
 });
+
+test("Result.success creates a success result", (t) => {
+  const result = util.Result.success("test value");
+  t.true(result.isSuccess());
+  t.false(result.isFailure());
+  t.is(result.value, "test value");
+});
+
+test("Result.failure creates a failure result", (t) => {
+  const error = new Error("test error");
+  const result = util.Result.failure(error);
+  t.false(result.isSuccess());
+  t.true(result.isFailure());
+  t.is(result.value, error);
+});
+
+test("Result.orElse returns the value for a success result", (t) => {
+  const result = util.Result.success("success value");
+  t.is(result.orElse("default value"), "success value");
+});
+
+test("Result.orElse returns the default value for a failure result", (t) => {
+  const result = util.Result.failure(new Error("test error"));
+  t.is(result.orElse("default value"), "default value");
+});
--- a/src/util.ts
+++ b/src/util.ts
@@ -1292,3 +1292,43 @@ export function joinAtMost(

  return array.join(separator);
 }
+
+/** A success result. */
+type Success<T> = Result<T, never>;
+/** A failure result. */
+type Failure<E> = Result<never, E>;
+
+/**
+ * A simple result type representing either a success or a failure.
+ */
+export class Result<T, E> {
+  private constructor(
+    private readonly _ok: boolean,
+    public readonly value: T | E,
+  ) {}
+
+  /** Creates a success result. */
+  static success<T>(value: T): Success<T> {
+    return new Result(true, value) as Success<T>;
+  }
+
+  /** Creates a failure result. */
+  static failure<E>(value: E): Failure<E> {
+    return new Result(false, value) as Failure<E>;
+  }
+
+  /** Whether this result represents a success. */
+  isSuccess(): this is Success<T> {
+    return this._ok;
+  }
+
+  /** Whether this result represents a failure. */
+  isFailure(): this is Failure<E> {
+    return !this._ok;
+  }
+
+  /** Get the value if this is a success, or return the default value if this is a failure. */
+  orElse<U>(defaultValue: U): T | U {
+    return this.isSuccess() ? this.value : defaultValue;
+  }
+}
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -1,8 +1,8 @@
 {
  "compilerOptions": {
    /* Basic Options */
-    "lib": ["ES2021"],
-    "target": "ES2021",
+    "lib": ["ES2022"],
+    "target": "ES2022",
    "module": "commonjs",
    "outDir": "./build",
    "rootDir": "./src",