diff --git a/.github/workflows/__rubocop-multi-language.yml b/.github/workflows/__rubocop-multi-language.yml
index c405b44fed..96f2daccab 100644
--- a/.github/workflows/__rubocop-multi-language.yml
+++ b/.github/workflows/__rubocop-multi-language.yml
@@ -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@984c0c890880bbf811283d6f09c4607c62d210a4 # v1.323.0
         with:
           ruby-version: 2.6
       - name: Install Code Scanning integration
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 59a5385e86..34dff4a645 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 See the [releases page](https://github.com/github/codeql-action/releases) for the relevant changes to the CodeQL CLI and language packs.
 
+## 3.38.2 - 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)
+
 ## 3.38.1 - 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)
diff --git a/lib/defaults.json b/lib/defaults.json
index e4875a8a34..e201dfd79e 100644
--- a/lib/defaults.json
+++ b/lib/defaults.json
@@ -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-v2.27.1",
+  "cliVersion": "2.27.1",
+  "priorBundleVersion": "codeql-bundle-v2.27.0",
+  "priorCliVersion": "2.27.0"
 }
diff --git a/lib/entry-points.js b/lib/entry-points.js
index c83cbc5216..7b84b154a0 100644
--- a/lib/entry-points.js
+++ b/lib/entry-points.js
@@ -144779,6 +144779,7 @@ function doubleQuoteWhitespaceOnly(layout) {
 function applyForceQuotesOption(layout) {
   if (!layout.presenterOptions.forceQuotes) return;
   if (layout.isKey || layout.style !== SCALAR_STYLE.PLAIN) return;
+  if (layout.node.tag !== layout.presenterOptions.schema.defaultScalarTag.tagName) return;
   layout.style = layout.node.value.includes("\n") ? SCALAR_STYLE.DOUBLE_QUOTED : _preferredQuotedStyle(layout);
 }
 function tryLongOrMultilineAsBlock(layout) {
@@ -146167,7 +146168,7 @@ function getDiffRangesJsonFilePath(env = getEnv()) {
   return path2.join(getTemporaryDirectory(env), PR_DIFF_RANGE_JSON_FILENAME);
 }
 function getActionVersion() {
-  return "3.38.1";
+  return "3.38.2";
 }
 function getWorkflowEventName(env = getEnv()) {
   return env.getRequired("GITHUB_EVENT_NAME" /* GITHUB_EVENT_NAME */);
@@ -147732,8 +147733,8 @@ var path6 = __toESM(require("path"));
 var semver4 = __toESM(require_semver2());
 
 // src/defaults.json
-var bundleVersion = "codeql-bundle-v2.27.0";
-var cliVersion = "2.27.0";
+var bundleVersion = "codeql-bundle-v2.27.1";
+var cliVersion = "2.27.1";
 
 // src/overlay/index.ts
 var fs5 = __toESM(require("fs"));
@@ -151255,7 +151256,7 @@ async function checkOverlayBaseDatabase(codeql, config, logger, warningPrefix) {
   }
   return true;
 }
-async function cleanupAndUploadOverlayBaseDatabaseToCache(codeql, config, logger) {
+async function cleanupAndUploadOverlayBaseDatabaseToCache(codeql, config, logger, checkoutPath) {
   const overlayDatabaseMode = config.overlayDatabaseMode;
   if (overlayDatabaseMode !== "overlay-base" /* OverlayBase */) {
     logger.debug(
@@ -151303,7 +151304,6 @@ async function cleanupAndUploadOverlayBaseDatabaseToCache(codeql, config, logger
     return false;
   }
   const codeQlVersion = (await codeql.getVersion()).version;
-  const checkoutPath = getRequiredInput("checkout_path");
   const cacheSaveKey = await getCacheSaveKey(
     config,
     codeQlVersion,
@@ -153248,6 +153248,7 @@ async function getCodeQLForCmd(logger, cmd, checkVersion) {
           "--format=json",
           `--language=${language}`,
           "--extractor-include-aliases",
+          "-J-XX:-UsePerfData",
           ...getExtraOptionsFromEnv(["resolve", "extractor"])
         ],
         {
@@ -153887,7 +153888,7 @@ async function finalizeDatabaseCreation(codeql, features, config, threadsFlag, m
     trap_import_duration_ms: Math.round(trapImportTime)
   };
 }
-async function setupDiffInformedQueryRun(logger) {
+async function setupDiffInformedQueryRun(logger, checkoutPath) {
   return await withGroupAsync(
     "Generating diff range extension pack",
     async () => {
@@ -153898,7 +153899,6 @@ async function setupDiffInformedQueryRun(logger) {
         );
         return void 0;
       }
-      const checkoutPath = getRequiredInput("checkout_path");
       const packDir = writeDiffRangeDataExtensionPack(
         logger,
         diffRanges,
@@ -154174,7 +154174,8 @@ async function warnIfGoInstalledAfterInit(config, logger) {
 
 // src/database-upload.ts
 var fs18 = __toESM(require("fs"));
-async function cleanupAndUploadDatabases(repositoryNwo, codeql, config, apiDetails, features, logger) {
+async function cleanupAndUploadDatabases(action, repositoryNwo, codeql, config, apiDetails, checkoutPath) {
+  const logger = action.logger;
   if (getRequiredInput("upload-database") !== "true") {
     logger.debug("Database upload disabled in workflow. Skipping upload.");
     return [];
@@ -154197,7 +154198,7 @@ async function cleanupAndUploadDatabases(repositoryNwo, codeql, config, apiDetai
     logger.debug("Not analyzing default branch. Skipping upload.");
     return [];
   }
-  const shouldUploadOverlayBase = config.overlayDatabaseMode === "overlay-base" /* OverlayBase */ && await features.getValue("upload_overlay_db_to_api" /* UploadOverlayDbToApi */, codeql);
+  const shouldUploadOverlayBase = config.overlayDatabaseMode === "overlay-base" /* OverlayBase */ && await action.features.getValue("upload_overlay_db_to_api" /* UploadOverlayDbToApi */, codeql);
   const cleanupLevel = shouldUploadOverlayBase ? "overlay" /* Overlay */ : "clear" /* Clear */;
   await withGroupAsync("Cleaning up databases", async () => {
     await codeql.databaseCleanupCluster(config, cleanupLevel);
@@ -154210,9 +154211,7 @@ async function cleanupAndUploadDatabases(repositoryNwo, codeql, config, apiDetai
         includeDiagnostics: false
       });
       bundledDbSize = fs18.statSync(bundledDb).size;
-      const commitOid = await getCommitOid(
-        getRequiredInput("checkout_path")
-      );
+      const commitOid = await getCommitOid(checkoutPath);
       const maxAttempts = 4;
       let uploadDurationMs;
       for (let attempt = 1; attempt <= maxAttempts; attempt++) {
@@ -156547,7 +156546,11 @@ async function runAutobuildIfLegacyGoWorkflow(config, logger) {
   );
   await runAutobuild(config, "go" /* go */, logger);
 }
-async function run({ startedAt, logger }) {
+async function run({
+  startedAt,
+  logger,
+  actions
+}) {
   let uploadResults = void 0;
   let runStats = void 0;
   let config = void 0;
@@ -156613,7 +156616,11 @@ async function run({ startedAt, logger }) {
       getOptionalInput("ram") || process.env["CODEQL_RAM"],
       logger
     );
-    const diffRangePackDir = await setupDiffInformedQueryRun(logger);
+    const checkoutPath = actions.getRequiredInput("checkout_path");
+    const diffRangePackDir = await setupDiffInformedQueryRun(
+      logger,
+      checkoutPath
+    );
     await warnIfGoInstalledAfterInit(config, logger);
     await runAutobuildIfLegacyGoWorkflow(config, logger);
     dbCreationTimings = await runFinalize(
@@ -156653,7 +156660,6 @@ async function run({ startedAt, logger }) {
       getOptionalInput("upload")
     );
     if (runStats) {
-      const checkoutPath = getRequiredInput("checkout_path");
       const category = getOptionalInput("category");
       uploadResults = await postProcessAndUploadSarif(
         logger,
@@ -156679,14 +156685,19 @@ async function run({ startedAt, logger }) {
     } else {
       logger.info("Not uploading results");
     }
-    await cleanupAndUploadOverlayBaseDatabaseToCache(codeql, config, logger);
+    await cleanupAndUploadOverlayBaseDatabaseToCache(
+      codeql,
+      config,
+      logger,
+      checkoutPath
+    );
     databaseUploadResults = await cleanupAndUploadDatabases(
+      { logger, features },
       repositoryNwo,
       codeql,
       config,
       apiDetails,
-      features,
-      logger
+      checkoutPath
     );
     const trapCacheUploadStartTime = import_perf_hooks6.performance.now();
     didUploadTrapCaches = await uploadTrapCaches(codeql, config, logger);
@@ -162239,8 +162250,8 @@ async function run3(actionState) {
     apiDetails = {
       auth: getRequiredInput("token"),
       externalRepoAuth: getOptionalInput("external-repository-token"),
-      url: getRequiredEnvParam("GITHUB_SERVER_URL"),
-      apiURL: getRequiredEnvParam("GITHUB_API_URL")
+      url: actionState.env.getRequired("GITHUB_SERVER_URL" /* GITHUB_SERVER_URL */),
+      apiURL: actionState.env.getRequired("GITHUB_API_URL" /* GITHUB_API_URL */)
     };
     const gitHubVersion = await getGitHubVersion();
     checkGitHubVersionInRange(gitHubVersion, logger);
@@ -162259,7 +162270,7 @@ async function run3(actionState) {
     const repositoryProperties = repositoryPropertiesResult.orElse({});
     core22.exportVariable("CODEQL_ACTION_INIT_HAS_RUN" /* INIT_ACTION_HAS_RUN */, "true");
     sourceRoot = path25.resolve(
-      getRequiredEnvParam("GITHUB_WORKSPACE"),
+      actionState.env.getRequired("GITHUB_WORKSPACE" /* GITHUB_WORKSPACE */),
       getOptionalInput("source-root") || ""
     );
     let analysisKinds;
@@ -162355,7 +162366,9 @@ async function run3(actionState) {
       repository: repositoryNwo,
       tempDir: getTemporaryDirectory(),
       codeql,
-      workspacePath: getRequiredEnvParam("GITHUB_WORKSPACE"),
+      workspacePath: actionState.env.getRequired(
+        "GITHUB_WORKSPACE" /* GITHUB_WORKSPACE */
+      ),
       sourceRoot,
       githubVersion: gitHubVersion,
       apiDetails,
@@ -163254,8 +163267,8 @@ async function run6(actionState) {
     const apiDetails = {
       auth: getRequiredInput("token"),
       externalRepoAuth: getOptionalInput("external-repository-token"),
-      url: getRequiredEnvParam("GITHUB_SERVER_URL"),
-      apiURL: getRequiredEnvParam("GITHUB_API_URL")
+      url: actionState.env.getRequired("GITHUB_SERVER_URL" /* GITHUB_SERVER_URL */),
+      apiURL: actionState.env.getRequired("GITHUB_API_URL" /* GITHUB_API_URL */)
     };
     const gitHubVersion = await getGitHubVersion();
     checkGitHubVersionInRange(gitHubVersion, logger);
@@ -164473,7 +164486,7 @@ tmp/lib/tmp.js:
    *)
 
 js-yaml/dist/js-yaml.mjs:
-  (*! js-yaml 5.4.1 https://github.com/nodeca/js-yaml @license MIT *)
+  (*! js-yaml 5.4.2 https://github.com/nodeca/js-yaml @license MIT *)
 
 long/index.js:
   (**
diff --git a/package-lock.json b/package-lock.json
index 17a4eee8c3..955fcf6d93 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "codeql",
-  "version": "4.38.1",
+  "version": "4.38.2",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "codeql",
-      "version": "4.38.1",
+      "version": "4.38.2",
       "license": "MIT",
       "workspaces": [
         "pr-checks"
@@ -31,7 +31,7 @@
         "follow-redirects": "^1.16.0",
         "get-folder-size": "^5.0.0",
         "https-proxy-agent": "^7.0.6",
-        "js-yaml": "^5.4.1",
+        "js-yaml": "^5.4.2",
         "jsonschema": "1.5.0",
         "long": "^5.3.2",
         "node-forge": "^1.4.0",
@@ -58,7 +58,7 @@
         "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": "^64.5.2",
         "eslint-plugin-no-async-foreach": "^0.1.1",
         "glob": "^13.0.6",
         "globals": "^17.12.0",
@@ -5348,9 +5348,9 @@
       }
     },
     "node_modules/eslint-plugin-jsdoc": {
-      "version": "64.3.8",
-      "resolved": "https://registry.npmjs.org/eslint-plugin-jsdoc/-/eslint-plugin-jsdoc-64.3.8.tgz",
-      "integrity": "sha512-JXLYE2BVfmbqLrrslb9/vg3URg8okW5pMnppM+3EYwvPCbuOiSXGOJWaNK208wDx6xXawkIFGtRYgFgrW23dsg==",
+      "version": "64.5.2",
+      "resolved": "https://registry.npmjs.org/eslint-plugin-jsdoc/-/eslint-plugin-jsdoc-64.5.2.tgz",
+      "integrity": "sha512-GirLf/jpVQ/HSLVT98ztIrJ8GUlWWrrwExkofqzeIjjOxlqFtyqnpkRs30FLwEKh0xHEpgy35CU0qFn0I/Mh9w==",
       "dev": true,
       "license": "BSD-3-Clause",
       "dependencies": {
@@ -5374,7 +5374,13 @@
         "node": "^22.22.2 || >=24.15.0"
       },
       "peerDependencies": {
-        "eslint": "^7.0.0 || ^8.0.0 || ^9.0.0 || ^10.0.0"
+        "eslint": "^7.0.0 || ^8.0.0 || ^9.0.0 || ^10.0.0",
+        "typescript": "*"
+      },
+      "peerDependenciesMeta": {
+        "typescript": {
+          "optional": true
+        }
       }
     },
     "node_modules/eslint-plugin-jsdoc/node_modules/debug": {
@@ -7091,9 +7097,9 @@
       }
     },
     "node_modules/js-yaml": {
-      "version": "5.4.1",
-      "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-5.4.1.tgz",
-      "integrity": "sha512-28R/k+NAjeuf7+CKlTxWZVExJGwVVLwY06DgEnOMz2gEpfNkDcD7QvyiVPT0xy0XXhU8vHsd4Ot42OOPdJG7dQ==",
+      "version": "5.4.2",
+      "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-5.4.2.tgz",
+      "integrity": "sha512-m+aqu+LwO1O6sIopafj8HUVl5aawITwZQe/yHpMCKjaWBaA/d07B/QdMb3529REftiU+RMMHL3Vlsw3hON7vWg==",
       "funding": [
         {
           "type": "github",
@@ -10367,9 +10373,9 @@
       }
     },
     "node_modules/yaml": {
-      "version": "2.9.0",
-      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.9.0.tgz",
-      "integrity": "sha512-2AvhNX3mb8zd6Zy7INTtSpl1F15HW6Wnqj0srWlkKLcpYl/gMIMJiyuGq2KeI2YFxUPjdlB+3Lc10seMLtL4cA==",
+      "version": "2.9.1",
+      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.9.1.tgz",
+      "integrity": "sha512-3NxN8+78OdzbT7C/WjGsyfPAtJaN3FNDsWxv7Y7mcDsT/oOmgW8BpyQQFFBnvZE3j9Y2Sdz1ULFLezL7Eb2yFw==",
       "license": "ISC",
       "bin": {
         "yaml": "bin.mjs"
@@ -10460,7 +10466,7 @@
         "lite-matter": "^0.1.2",
         "mdast-util-from-markdown": "^2.0.3",
         "semver": "^7.8.5",
-        "yaml": "^2.9.0"
+        "yaml": "^2.9.1"
       },
       "devDependencies": {
         "@types/node": "^20.19.43",
diff --git a/package.json b/package.json
index 5596407dbd..c37bab23fe 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "codeql",
-  "version": "3.38.1",
+  "version": "3.38.2",
   "private": true,
   "description": "CodeQL action",
   "scripts": {
@@ -39,7 +39,7 @@
     "follow-redirects": "^1.16.0",
     "get-folder-size": "^5.0.0",
     "https-proxy-agent": "^7.0.6",
-    "js-yaml": "^5.4.1",
+    "js-yaml": "^5.4.2",
     "jsonschema": "1.5.0",
     "long": "^5.3.2",
     "node-forge": "^1.4.0",
@@ -66,7 +66,7 @@
     "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": "^64.5.2",
     "eslint-plugin-no-async-foreach": "^0.1.1",
     "glob": "^13.0.6",
     "globals": "^17.12.0",
diff --git a/pr-checks/bundle-changelog.test.ts b/pr-checks/bundle-changelog.test.ts
index 6cc4d096ba..fad06826a6 100644
--- a/pr-checks/bundle-changelog.test.ts
+++ b/pr-checks/bundle-changelog.test.ts
@@ -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 () => {
diff --git a/pr-checks/changelog.test.ts b/pr-checks/changelog.test.ts
index 817852e3e1..8132e65766 100755
--- a/pr-checks/changelog.test.ts
+++ b/pr-checks/changelog.test.ts
@@ -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),
+    );
+  });
+});
diff --git a/pr-checks/changelog.ts b/pr-checks/changelog.ts
index 4cf1e75494..496310d21f 100644
--- a/pr-checks/changelog.ts
+++ b/pr-checks/changelog.ts
@@ -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);
     }
   }
 
diff --git a/pr-checks/changelog/validate.mts b/pr-checks/changelog/validate.mts
index 2e28a4ab13..3c83276f38 100644
--- a/pr-checks/changelog/validate.mts
+++ b/pr-checks/changelog/validate.mts
@@ -119,14 +119,3 @@ 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);
-}
diff --git a/pr-checks/changelog/validate.test.mts b/pr-checks/changelog/validate.test.mts
index a38339d1c9..b8b1e33bb0 100644
--- a/pr-checks/changelog/validate.test.mts
+++ b/pr-checks/changelog/validate.test.mts
@@ -1,13 +1,10 @@
 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,
@@ -187,39 +184,3 @@ 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);
-    });
-  });
-});
diff --git a/pr-checks/changenotes.mts b/pr-checks/changenotes.mts
index 2fb86b0cac..980d103a28 100755
--- a/pr-checks/changenotes.mts
+++ b/pr-checks/changenotes.mts
@@ -3,21 +3,64 @@
 import * as fs from "node:fs";
 import { pathToFileURL } from "node:url";
 import { parseArgs } from "node:util";
+import path from "path";
 
-import { isValidAllChangenoteFiles } from "./changelog/validate.mjs";
+import { ExitCode } from "@actions/core";
+import { matter } from "lite-matter";
+
+import {
+  addBodyLinesToUnreleasedSection,
+  parseChangelog,
+  renderChangelog,
+  withChangelog,
+} from "./changelog";
+import { isValidChangenoteFile } from "./changelog/validate.mjs";
 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").
+ * */
+function listUnreleasedChangenoteDir(): string[] {
+  return fs
+    .readdirSync(CHANGENOTES_DIR)
+    .filter((name) => name !== ".gitkeep")
+    .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(1);
+    process.exit(ExitCode.Failure);
   }
 }
 
-function main(): number {
+function main(): ExitCode {
   const { positionals } = parseArgs({
     allowPositionals: true,
     strict: true,
@@ -27,24 +70,59 @@ function main(): number {
     case undefined:
     case "help":
       return usage();
+    case "assemble":
+      return assemble();
     case "validate":
       return validate();
     default:
       console.error(`Unknown command: ${command}`);
-      return 1;
+      return ExitCode.Failure;
   }
 }
 
-function usage(): number {
-  console.log(`Usage: changenotes.mts validate`);
-  return 0;
+function usage(): ExitCode {
+  const message =
+    "Usage: changenotes.mts assemble\n" +
+    "       changenotes.mts validate\n" +
+    "       changenotes.mts 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(): number {
+function validate(): ExitCode {
   try {
-    if (isValidAllChangenoteFiles(fs.readdirSync(CHANGENOTES_DIR))) {
+    const allChangenotesValid = getChangenotes().reduce(
+      (r, changenote) => r && isValidChangenoteFile(changenote.absolutePath),
+      true,
+    );
+    if (allChangenotesValid) {
       console.log(`All changenotes in '${CHANGENOTES_DIR}' are valid.`);
-      return 0;
+      return ExitCode.Success;
     }
   } catch (error) {
     console.error(
@@ -52,5 +130,5 @@ function validate(): number {
       error,
     );
   }
-  return 1;
+  return ExitCode.Failure;
 }
diff --git a/pr-checks/checks/rubocop-multi-language.yml b/pr-checks/checks/rubocop-multi-language.yml
index 37c5d36e90..550bdb6cc3 100644
--- a/pr-checks/checks/rubocop-multi-language.yml
+++ b/pr-checks/checks/rubocop-multi-language.yml
@@ -5,7 +5,7 @@ versions:
   - default
 steps:
   - name: Set up Ruby
-    uses: ruby/setup-ruby@95ef2b042f9d7a56d8268cba8559e2842e2ad01b # v1.321.0
+    uses: ruby/setup-ruby@984c0c890880bbf811283d6f09c4607c62d210a4 # v1.323.0
     with:
       ruby-version: 2.6
   - name: Install Code Scanning integration
diff --git a/pr-checks/package.json b/pr-checks/package.json
index 0c5091a793..58722bd0ea 100644
--- a/pr-checks/package.json
+++ b/pr-checks/package.json
@@ -10,7 +10,7 @@
     "lite-matter": "^0.1.2",
     "mdast-util-from-markdown": "^2.0.3",
     "semver": "^7.8.5",
-    "yaml": "^2.9.0"
+    "yaml": "^2.9.1"
   },
   "devDependencies": {
     "@types/node": "^20.19.43",
diff --git a/src/analyze-action.ts b/src/analyze-action.ts
index c3c2e40e7f..7963fa52bf 100644
--- a/src/analyze-action.ts
+++ b/src/analyze-action.ts
@@ -212,7 +212,11 @@ async function runAutobuildIfLegacyGoWorkflow(config: Config, logger: Logger) {
   await runAutobuild(config, BuiltInLanguage.go, logger);
 }
 
-async function run({ startedAt, logger }: ActionState<["Base", "Logger"]>) {
+async function run({
+  startedAt,
+  logger,
+  actions,
+}: ActionState<["Base", "Logger", "Actions"]>) {
   // To capture errors appropriately, keep as much code within the try-catch as
   // possible, and only use safe functions outside.
 
@@ -307,8 +311,13 @@ async function run({ startedAt, logger }: ActionState<["Base", "Logger"]>) {
       logger,
     );
 
+    const checkoutPath = actions.getRequiredInput("checkout_path");
+
     // 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 +363,6 @@ 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 +396,23 @@ 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,
+    );
 
     // 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(
+      { logger, features },
       repositoryNwo,
       codeql,
       config,
       apiDetails,
-      features,
-      logger,
+      checkoutPath,
     );
 
     // Possibly upload the TRAP caches for later re-use
diff --git a/src/analyze.ts b/src/analyze.ts
index 411477b597..8f90711682 100644
--- a/src/analyze.ts
+++ b/src/analyze.ts
@@ -5,7 +5,7 @@ import { performance } from "perf_hooks";
 import * as io from "@actions/io";
 import * as yaml from "js-yaml";
 
-import { getTemporaryDirectory, getRequiredInput } from "./actions-util";
+import { getTemporaryDirectory } from "./actions-util";
 import * as analyses from "./analyses";
 import { setupCppAutobuild } from "./autobuild";
 import { type CodeQL } from "./codeql";
@@ -233,6 +233,7 @@ async function finalizeDatabaseCreation(
  */
 export async function setupDiffInformedQueryRun(
   logger: Logger,
+  checkoutPath: string,
 ): Promise<string | undefined> {
   return await withGroupAsync(
     "Generating diff range extension pack",
@@ -245,7 +246,6 @@ export async function setupDiffInformedQueryRun(
         return undefined;
       }
 
-      const checkoutPath = getRequiredInput("checkout_path");
       const packDir = writeDiffRangeDataExtensionPack(
         logger,
         diffRanges,
diff --git a/src/codeql.ts b/src/codeql.ts
index 65e73d9451..fbc119a341 100644
--- a/src/codeql.ts
+++ b/src/codeql.ts
@@ -937,6 +937,7 @@ async function getCodeQLForCmd(
           "--format=json",
           `--language=${language}`,
           "--extractor-include-aliases",
+          "-J-XX:-UsePerfData",
           ...getExtraOptionsFromEnv(["resolve", "extractor"]),
         ],
         {
diff --git a/src/database-upload.test.ts b/src/database-upload.test.ts
index bcaf9f1c9e..b6ac5c8115 100644
--- a/src/database-upload.test.ts
+++ b/src/database-upload.test.ts
@@ -20,8 +20,9 @@ import {
   checkExpectedLogMessages,
   createFeatures,
   createTestConfig,
-  getRecordingLogger,
-  LoggedMessage,
+  getTestEnv,
+  initAllState,
+  RecordingLogger,
   setupActionsVars,
   setupTests,
 } from "./testing-utils";
@@ -90,23 +91,24 @@ 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 +119,8 @@ 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 +129,9 @@ test.serial(
 
       await mockHttpRequests(201);
 
-      const loggedMessages: LoggedMessage[] = [];
+      const logger = new RecordingLogger();
       await cleanupAndUploadDatabases(
+        initAllState({ env, logger }),
         testRepoName,
         getCodeQL(),
         {
@@ -135,10 +139,9 @@ 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 +150,8 @@ 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 +161,16 @@ 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 +180,24 @@ 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 +208,8 @@ 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 +218,17 @@ 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 +242,8 @@ 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 +258,17 @@ 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 +286,8 @@ 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 +296,16 @@ 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 +313,8 @@ 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 +323,9 @@ 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 +334,9 @@ 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 +352,8 @@ 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 +385,16 @@ 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 +414,8 @@ 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 +435,15 @@ 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 +457,8 @@ 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 +482,15 @@ 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 +506,8 @@ 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 +531,15 @@ 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
diff --git a/src/database-upload.ts b/src/database-upload.ts
index 0189bef1e6..9e4339fd47 100644
--- a/src/database-upload.ts
+++ b/src/database-upload.ts
@@ -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 {
@@ -9,7 +10,7 @@ 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 { Logger, withGroupAsync } from "./logging";
 import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
@@ -45,13 +46,15 @@ export interface DatabaseUploadResult {
 }
 
 export async function cleanupAndUploadDatabases(
+  action: ActionState<["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 [];
@@ -87,7 +90,7 @@ 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 +113,7 @@ 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(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.
diff --git a/src/defaults.json b/src/defaults.json
index e4875a8a34..e201dfd79e 100644
--- a/src/defaults.json
+++ b/src/defaults.json
@@ -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-v2.27.1",
+  "cliVersion": "2.27.1",
+  "priorBundleVersion": "codeql-bundle-v2.27.0",
+  "priorCliVersion": "2.27.0"
 }
diff --git a/src/git-utils.test.ts b/src/git-utils.test.ts
index b77d40a7ec..64b76590ae 100644
--- a/src/git-utils.test.ts
+++ b/src/git-utils.test.ts
@@ -29,10 +29,13 @@ test.serial(
       process.env["GITHUB_SHA"] = currentSha;
 
       const callback = sinon.stub(gitUtils, "getCommitOid");
-      callback.withArgs("HEAD").resolves(currentSha);
+      callback.withArgs(sinon.match.string, "HEAD").resolves(currentSha);
 
       const actualRef = await gitUtils.getRef();
       t.deepEqual(actualRef, expectedRef);
+
+      t.is(callback.callCount, 1);
+      t.true(callback.calledOnceWith(tmpDir, "HEAD"));
     });
   },
 );
@@ -48,11 +51,17 @@ test.serial(
       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.string, "refs/remotes/pull/1/merge")
+        .resolves(sha);
+      callback.withArgs(sinon.match.any, "HEAD").resolves(sha);
 
       const actualRef = await gitUtils.getRef();
       t.deepEqual(actualRef, expectedRef);
+
+      t.is(callback.callCount, 2);
+      t.true(callback.calledWith(tmpDir, "HEAD"));
+      t.true(callback.calledWith(tmpDir, "refs/remotes/pull/1/merge"));
     });
   },
 );
@@ -66,11 +75,18 @@ test.serial(
       process.env["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, "refs/remotes/pull/1/merge")
+        .resolves("a".repeat(40));
       callback.withArgs(tmpDir, "HEAD").resolves("b".repeat(40));
+      callback.throws(new Error("Unexpected getCommitOid call in test."));
 
       const actualRef = await gitUtils.getRef();
       t.deepEqual(actualRef, "refs/pull/1/head");
+
+      t.is(callback.callCount, 2);
+      t.true(callback.calledWith(tmpDir, "refs/remotes/pull/1/merge"));
+      t.true(callback.calledWith(tmpDir, "HEAD"));
     });
   },
 );
@@ -92,11 +108,14 @@ test.serial(
       process.env["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(tmpDir, "refs/pull/1/merge").resolves("b".repeat(40));
+      callback.withArgs(sinon.match.any, "HEAD").resolves("b".repeat(40));
 
       const actualRef = await gitUtils.getRef();
       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);
     });
   },
 );
diff --git a/src/init-action.ts b/src/init-action.ts
index 79c509a5be..e770fe9788 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -38,7 +38,7 @@ import {
   makeDiagnostic,
   makeTelemetryDiagnostic,
 } from "./diagnostics";
-import { EnvVar } from "./environment";
+import { ActionsEnvVars, EnvVar } from "./environment";
 import { Feature, FeatureEnablement, initFeatures } from "./feature-flags";
 import { loadRepositoryProperties } from "./feature-flags/properties";
 import {
@@ -81,7 +81,6 @@ import {
   DEFAULT_DEBUG_ARTIFACT_NAME,
   DEFAULT_DEBUG_DATABASE_NAME,
   getCodeQLMemoryLimit,
-  getRequiredEnvParam,
   getThreadsFlagValue,
   initializeEnvironment,
   ConfigurationError,
@@ -225,8 +224,8 @@ async function run(
     apiDetails = {
       auth: getRequiredInput("token"),
       externalRepoAuth: getOptionalInput("external-repository-token"),
-      url: getRequiredEnvParam("GITHUB_SERVER_URL"),
-      apiURL: getRequiredEnvParam("GITHUB_API_URL"),
+      url: actionState.env.getRequired(ActionsEnvVars.GITHUB_SERVER_URL),
+      apiURL: actionState.env.getRequired(ActionsEnvVars.GITHUB_API_URL),
     };
 
     const gitHubVersion = await getGitHubVersion();
@@ -255,7 +254,7 @@ async function run(
     // source-root is relative, it is relative to the GITHUB_WORKSPACE. If
     // source-root is absolute, it is used as given.
     sourceRoot = path.resolve(
-      getRequiredEnvParam("GITHUB_WORKSPACE"),
+      actionState.env.getRequired(ActionsEnvVars.GITHUB_WORKSPACE),
       getOptionalInput("source-root") || "",
     );
 
@@ -383,7 +382,9 @@ async function run(
       repository: repositoryNwo,
       tempDir: getTemporaryDirectory(),
       codeql,
-      workspacePath: getRequiredEnvParam("GITHUB_WORKSPACE"),
+      workspacePath: actionState.env.getRequired(
+        ActionsEnvVars.GITHUB_WORKSPACE,
+      ),
       sourceRoot,
       githubVersion: gitHubVersion,
       apiDetails,
diff --git a/src/overlay/caching.ts b/src/overlay/caching.ts
index c4557cd4ef..d246626780 100644
--- a/src/overlay/caching.ts
+++ b/src/overlay/caching.ts
@@ -3,11 +3,7 @@ import * as fs from "fs";
 import * as actionsCache from "@actions/cache";
 import * as semver from "semver";
 
-import {
-  getRequiredInput,
-  getWorkflowRunAttempt,
-  getWorkflowRunID,
-} from "../actions-util";
+import { getWorkflowRunAttempt, getWorkflowRunID } from "../actions-util";
 import { getAutomationID, listActionsCaches } from "../api-client";
 import { createCacheKeyHash } from "../caching-utils";
 import { type CodeQL } from "../codeql";
@@ -107,12 +103,13 @@ async function checkOverlayBaseDatabase(
  * Uploads the overlay-base database to the GitHub Actions cache. If conditions
  * for uploading are not met, the function does nothing and returns false.
  *
- * This function uses the `checkout_path` input to determine the repository path
+ * This function uses the `checkoutPath` to determine the repository path
  * and works only when called from `analyze` or `upload-sarif`.
  *
  * @param codeql The CodeQL instance
  * @param config The configuration object
  * @param logger The logger instance
+ * @param checkoutPath The path at which the repository is checked out at.
  * @returns A promise that resolves to true if the upload was performed and
  * successfully completed, or false otherwise
  */
@@ -120,6 +117,7 @@ export async function cleanupAndUploadOverlayBaseDatabaseToCache(
   codeql: CodeQL,
   config: Config,
   logger: Logger,
+  checkoutPath: string,
 ): Promise<boolean> {
   const overlayDatabaseMode = config.overlayDatabaseMode;
   if (overlayDatabaseMode !== OverlayDatabaseMode.OverlayBase) {
@@ -180,7 +178,6 @@ export async function cleanupAndUploadOverlayBaseDatabaseToCache(
   }
 
   const codeQlVersion = (await codeql.getVersion()).version;
-  const checkoutPath = getRequiredInput("checkout_path");
   const cacheSaveKey = await getCacheSaveKey(
     config,
     codeQlVersion,
diff --git a/src/per-language-bundles.test.ts b/src/per-language-bundles.test.ts
index b8f48512fe..0330b51a63 100644
--- a/src/per-language-bundles.test.ts
+++ b/src/per-language-bundles.test.ts
@@ -38,7 +38,6 @@ async function checkEligibility(
         [ActionsEnvVars.RUNNER_ENVIRONMENT]: "github-hosted",
       }),
       features: createFeatures([Feature.PerLanguageBundles]),
-      logger: getRecordingLogger([], { logToConsole: false }),
       ...stateOverrides,
     }),
     { ...ELIGIBLE_OPTIONS, ...overrides },
@@ -134,7 +133,6 @@ test("getPerLanguageBundleLanguage explains a disabled feature before checking e
   const messages: LoggedMessage[] = [];
   const language = await getPerLanguageBundleLanguage(
     initAllState({
-      env: getTestEnv(),
       features: createFeatures([]),
       logger: getRecordingLogger(messages, { logToConsole: false }),
     }),
diff --git a/src/per-language-bundles.ts b/src/per-language-bundles.ts
index f4e46403db..e4468d2f34 100644
--- a/src/per-language-bundles.ts
+++ b/src/per-language-bundles.ts
@@ -102,8 +102,11 @@ export async function getPerLanguageBundleLanguage(
     return explain("the job is not running on a GitHub-hosted runner");
   }
 
-  // Check whether per-language bundles are published for the requested CLI version.
-  // Latest-nightly selection skips this release-version check, but not the other eligibility checks.
+  // Nightly releases are identified by dates rather than versions. If
+  // `isLatestNightly` is `true`, the latest nightly is requested with
+  // `tools: nightly` and we don't yet have the corresponding tag at this point.
+  // Therefore, we skip the version check and don't have an equivalent.
+  // We can safely assume that the latest nightly will have per-language bundles.
   if (!isLatestNightly) {
     if (cliVersion === undefined) {
       return explain("the requested CLI version is unknown");
diff --git a/src/setup-codeql-action.ts b/src/setup-codeql-action.ts
index 4bd53e517f..91666f19cd 100644
--- a/src/setup-codeql-action.ts
+++ b/src/setup-codeql-action.ts
@@ -12,7 +12,7 @@ import { getGitHubVersion } from "./api-client";
 import { CodeQL } from "./codeql";
 import { ComputedInput, getToolsInput } from "./config/inputs";
 import { getRawLanguagesNoAutodetect } from "./config-utils";
-import { EnvVar } from "./environment";
+import { ActionsEnvVars, EnvVar } from "./environment";
 import { initFeatures } from "./feature-flags";
 import { loadRepositoryProperties } from "./feature-flags/properties";
 import { initCodeQL } from "./init";
@@ -32,7 +32,6 @@ import {
   checkDiskUsage,
   checkForTimeout,
   checkGitHubVersionInRange,
-  getRequiredEnvParam,
   initializeEnvironment,
   ConfigurationError,
   wrapError,
@@ -108,8 +107,8 @@ async function run(
     const apiDetails = {
       auth: getRequiredInput("token"),
       externalRepoAuth: getOptionalInput("external-repository-token"),
-      url: getRequiredEnvParam("GITHUB_SERVER_URL"),
-      apiURL: getRequiredEnvParam("GITHUB_API_URL"),
+      url: actionState.env.getRequired(ActionsEnvVars.GITHUB_SERVER_URL),
+      apiURL: actionState.env.getRequired(ActionsEnvVars.GITHUB_API_URL),
     };
 
     const gitHubVersion = await getGitHubVersion();
diff --git a/src/setup-codeql.test.ts b/src/setup-codeql.test.ts
index c35bdb8406..6ac5bebf18 100644
--- a/src/setup-codeql.test.ts
+++ b/src/setup-codeql.test.ts
@@ -69,25 +69,29 @@ function stubHostedNightly(tagName: string) {
     available: true,
     foundZstdBinary: true,
   });
-  const fetchRelease = sinon
-    .stub<Parameters<typeof fetch>, ReturnType<typeof fetch>>()
-    .rejects(new Error("Unexpected API request in nightly bundle test"));
-  fetchRelease
-    .withArgs(
-      "https://api.github.com/repos/dsp-testing/codeql-cli-nightlies/releases?per_page=1&page=1&prerelease=true",
-      sinon.match({ method: "GET" }),
-    )
-    .callsFake(
-      async () =>
-        new Response(JSON.stringify([{ tag_name: tagName }]), {
-          headers: { "content-type": "application/json" },
-        }),
-    );
   const client = github.getOctokit("123", {
-    request: { fetch: fetchRelease },
+    request: {
+      fetch: async () => {
+        throw new Error("Unexpected API request in nightly bundle test");
+      },
+    },
   });
+  const listReleases = sinon
+    .stub(client.rest.repos, "listReleases")
+    .rejects(new Error("Unexpected release request in nightly bundle test"));
+  listReleases
+    .withArgs({
+      owner: "dsp-testing",
+      repo: "codeql-cli-nightlies",
+      per_page: 1,
+      page: 1,
+      prerelease: true,
+    })
+    .resolves({
+      data: [{ tag_name: tagName }],
+    } as Awaited<ReturnType<typeof client.rest.repos.listReleases>>);
   sinon.stub(api, "getApiClient").value(() => client);
-  return fetchRelease;
+  return listReleases;
 }
 
 test.serial("parse codeql bundle url version", (t) => {
diff --git a/src/util.ts b/src/util.ts
index 456cd7c3d2..d74e07fa8d 100644
--- a/src/util.ts
+++ b/src/util.ts
@@ -682,7 +682,7 @@ export async function bundleDb(
   return databaseBundlePath;
 }
 
-/** Returns the elapsed milliseconds, rounded, since a `performance.now()` timestamp. */
+/** Returns the elapsed milliseconds, rounded, since `startTime` was recorded with `performance.now()`. */
 export function durationMsSince(startTime: number): number {
   return Math.round(performance.now() - startTime);
 }