diff --git a/.github/codeql/codeql-config.yml b/.github/codeql/codeql-config.yml
index 80657da5dd7..d2a6507d76b 100644
--- a/.github/codeql/codeql-config.yml
+++ b/.github/codeql/codeql-config.yml
@@ -8,6 +8,8 @@ queries:
     uses: ./.github/codeql/queries
 paths:
   - ./extensions/ql-vscode
+  - ./.github/workflows
+  - ./.github/actions
 paths-ignore:
   - '**/node_modules'
   - '**/build'
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index c2cc47f75e8..65fe95960a8 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -147,7 +147,7 @@ jobs:
           name: vscode-codeql-extension
 
       - name: Azure User-assigned managed identity login
-        uses: azure/login@v2
+        uses: azure/login@a457da9ea143d694b1b9c7c869ebb04ebe844ef5 # v2.3.0
         with:
           client-id: ${{ secrets.AZURE_CLIENT_ID }}
           tenant-id: ${{ secrets.AZURE_TENANT_ID }}
diff --git a/docs/test-plan.md b/docs/test-plan.md
index 904dda61b4c..90fe3cc2abf 100644
--- a/docs/test-plan.md
+++ b/docs/test-plan.md
@@ -45,7 +45,7 @@ choose to go through some of the Optional Test Cases.
 #### Test case 2: Running a problem query and viewing results
 
 1. Open the [javascript ReDoS query](https://github.com/github/codeql/blob/main/javascript/ql/src/Performance/ReDoS.ql).
-2. Select the `babel/babel` database (or download it if you don't have one already)
+2. Select the `angular-cn/ng-nice` database (or download it if you don't have one already)
 3. Run a local query.
 4. Once the query completes:
    - Check that the result messages are rendered
diff --git a/extensions/ql-vscode/.nvmrc b/extensions/ql-vscode/.nvmrc
index 3f35247103b..26600046d4b 100644
--- a/extensions/ql-vscode/.nvmrc
+++ b/extensions/ql-vscode/.nvmrc
@@ -1 +1 @@
-v20.18.2
+v22.15.1
diff --git a/extensions/ql-vscode/CHANGELOG.md b/extensions/ql-vscode/CHANGELOG.md
index 03054c92082..3ff85de5196 100644
--- a/extensions/ql-vscode/CHANGELOG.md
+++ b/extensions/ql-vscode/CHANGELOG.md
@@ -2,6 +2,16 @@
 
 ## [UNRELEASED]
 
+- Add new command "CodeQL: Trim Overlay Base Cache" that returns a database to the state prior to overlay evaluation, leaving only base predicates and types that may later be referenced during overlay evaluation. [#4082](https://github.com/github/vscode-codeql/pull/4082)
+
+## 1.17.4 - 10 July 2025
+
+- Fix variant analysis pack creation on some Windows systems [#4068](https://github.com/github/vscode-codeql/pull/4068)
+
+## 1.17.3 - 3 June 2025
+
+- Fix reporting of bad join orders in recursive predicates. [#4019](https://github.com/github/vscode-codeql/pull/4019)
+
 ## 1.17.2 - 27 March 2025
 
 - Always authenticate when downloading databases from GitHub, instead of only when in canary mode. [#3941](https://github.com/github/vscode-codeql/pull/3941)
diff --git a/extensions/ql-vscode/gulpfile.ts/deploy.ts b/extensions/ql-vscode/gulpfile.ts/deploy.ts
index da02b9fd494..7b98600815b 100644
--- a/extensions/ql-vscode/gulpfile.ts/deploy.ts
+++ b/extensions/ql-vscode/gulpfile.ts/deploy.ts
@@ -4,6 +4,7 @@ import {
   mkdirs,
   readdir,
   unlinkSync,
+  rename,
   remove,
   writeFile,
 } from "fs-extra";
@@ -45,6 +46,10 @@ async function copyPackage(
       copyDirectory(resolve(sourcePath, file), resolve(destPath, file)),
     ),
   );
+
+  // The koffi directory needs to be located at the root of the package to ensure
+  // that the koffi package can find its native modules.
+  await rename(resolve(destPath, "out", "koffi"), resolve(destPath, "koffi"));
 }
 
 export async function deployPackage(): Promise<DeployedPackage> {
diff --git a/extensions/ql-vscode/gulpfile.ts/index.ts b/extensions/ql-vscode/gulpfile.ts/index.ts
index d3084561cea..3c20b838c09 100644
--- a/extensions/ql-vscode/gulpfile.ts/index.ts
+++ b/extensions/ql-vscode/gulpfile.ts/index.ts
@@ -5,7 +5,7 @@ import {
   checkTypeScript,
   watchCheckTypeScript,
   cleanOutput,
-  copyWasmFiles,
+  copyModules,
 } from "./typescript";
 import { compileTextMateGrammar } from "./textmate";
 import { packageExtension } from "./package";
@@ -21,7 +21,7 @@ export const buildWithoutPackage = series(
   cleanOutput,
   parallel(
     compileEsbuild,
-    copyWasmFiles,
+    copyModules,
     checkTypeScript,
     compileTextMateGrammar,
     compileViewEsbuild,
@@ -46,7 +46,7 @@ export {
   watchCheckTypeScript,
   watchViewEsbuild,
   compileEsbuild,
-  copyWasmFiles,
+  copyModules,
   checkTypeScript,
   injectAppInsightsKey,
   compileViewEsbuild,
diff --git a/extensions/ql-vscode/gulpfile.ts/textmate.ts b/extensions/ql-vscode/gulpfile.ts/textmate.ts
index 0b7d2b88fac..8e061b440f9 100644
--- a/extensions/ql-vscode/gulpfile.ts/textmate.ts
+++ b/extensions/ql-vscode/gulpfile.ts/textmate.ts
@@ -9,6 +9,7 @@ import type {
   Pattern,
   TextmateGrammar,
 } from "./textmate-grammar";
+import { pipeline } from "stream/promises";
 
 /**
  * Replaces all rule references with the match pattern of the referenced rule.
@@ -276,7 +277,9 @@ export function transpileTextMateGrammar() {
 }
 
 export function compileTextMateGrammar() {
-  return src("syntaxes/*.tmLanguage.yml")
-    .pipe(transpileTextMateGrammar())
-    .pipe(dest("out/syntaxes"));
+  return pipeline(
+    src("syntaxes/*.tmLanguage.yml"),
+    transpileTextMateGrammar(),
+    dest("out/syntaxes"),
+  );
 }
diff --git a/extensions/ql-vscode/gulpfile.ts/typescript.ts b/extensions/ql-vscode/gulpfile.ts/typescript.ts
index c7f12785507..9d49b56821e 100644
--- a/extensions/ql-vscode/gulpfile.ts/typescript.ts
+++ b/extensions/ql-vscode/gulpfile.ts/typescript.ts
@@ -1,9 +1,10 @@
 import { gray, red } from "ansi-colors";
-import { dest, src, watch } from "gulp";
+import { dest, parallel, src, watch } from "gulp";
 import esbuild from "gulp-esbuild";
 import type { reporter } from "gulp-typescript";
 import { createProject } from "gulp-typescript";
 import del from "del";
+import { pipeline } from "stream/promises";
 
 export function goodReporter(): reporter.Reporter {
   return {
@@ -37,23 +38,23 @@ export function cleanOutput() {
 }
 
 export function compileEsbuild() {
-  return src("./src/extension.ts")
-    .pipe(
-      esbuild({
-        outfile: "extension.js",
-        bundle: true,
-        external: ["vscode", "fsevents"],
-        format: "cjs",
-        platform: "node",
-        target: "es2020",
-        sourcemap: "linked",
-        sourceRoot: "..",
-        loader: {
-          ".node": "copy",
-        },
-      }),
-    )
-    .pipe(dest("out"));
+  return pipeline(
+    src("./src/extension.ts"),
+    esbuild({
+      outfile: "extension.js",
+      bundle: true,
+      external: ["vscode", "fsevents"],
+      format: "cjs",
+      platform: "node",
+      target: "es2020",
+      sourcemap: "linked",
+      sourceRoot: "..",
+      loader: {
+        ".node": "copy",
+      },
+    }),
+    dest("out"),
+  );
 }
 
 export function watchEsbuild() {
@@ -70,7 +71,7 @@ export function watchCheckTypeScript() {
   watch(["src/**/*.ts", "!src/view/**/*.ts"], checkTypeScript);
 }
 
-export function copyWasmFiles() {
+function copyWasmFiles() {
   // We need to copy this file for the source-map package to work. Without this fie, the source-map
   // package is not able to load the WASM file because we are not including the full node_modules
   // directory. In version 0.7.4, it is not possible to call SourceMapConsumer.initialize in Node environments
@@ -82,3 +83,18 @@ export function copyWasmFiles() {
     encoding: false,
   }).pipe(dest("out"));
 }
+
+function copyNativeAddonFiles() {
+  // We need to copy these files manually because we only want to include Windows x64 to limit
+  // the size of the extension. Windows x64 is the most common platform that requires short path
+  // expansion, so we only include this platform.
+  // See src/common/short-paths.ts
+  return pipeline(
+    src("node_modules/koffi/build/koffi/win32_x64/*.node", {
+      encoding: false,
+    }),
+    dest("out/koffi/win32_x64"),
+  );
+}
+
+export const copyModules = parallel(copyWasmFiles, copyNativeAddonFiles);
diff --git a/extensions/ql-vscode/gulpfile.ts/view.ts b/extensions/ql-vscode/gulpfile.ts/view.ts
index fea09031d70..698f39c113e 100644
--- a/extensions/ql-vscode/gulpfile.ts/view.ts
+++ b/extensions/ql-vscode/gulpfile.ts/view.ts
@@ -3,28 +3,29 @@ import esbuild from "gulp-esbuild";
 import { createProject } from "gulp-typescript";
 import { goodReporter } from "./typescript";
 
+import { pipeline } from "stream/promises";
 import chromiumVersion from "./chromium-version.json";
 
 const tsProject = createProject("src/view/tsconfig.json");
 
 export function compileViewEsbuild() {
-  return src("./src/view/webview.tsx")
-    .pipe(
-      esbuild({
-        outfile: "webview.js",
-        bundle: true,
-        format: "iife",
-        platform: "browser",
-        target: `chrome${chromiumVersion.chromiumVersion}`,
-        jsx: "automatic",
-        sourcemap: "linked",
-        sourceRoot: "..",
-        loader: {
-          ".ttf": "file",
-        },
-      }),
-    )
-    .pipe(dest("out"));
+  return pipeline(
+    src("./src/view/webview.tsx"),
+    esbuild({
+      outfile: "webview.js",
+      bundle: true,
+      format: "iife",
+      platform: "browser",
+      target: `chrome${chromiumVersion.chromiumVersion}`,
+      jsx: "automatic",
+      sourcemap: "linked",
+      sourceRoot: "..",
+      loader: {
+        ".ttf": "file",
+      },
+    }),
+    dest("out"),
+  );
 }
 
 export function watchViewEsbuild() {
diff --git a/extensions/ql-vscode/package-lock.json b/extensions/ql-vscode/package-lock.json
index 76aaa93ff56..8d38cc4a32e 100644
--- a/extensions/ql-vscode/package-lock.json
+++ b/extensions/ql-vscode/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "vscode-codeql",
-  "version": "1.17.3",
+  "version": "1.17.5",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "vscode-codeql",
-      "version": "1.17.3",
+      "version": "1.17.5",
       "hasInstallScript": true,
       "license": "MIT",
       "dependencies": {
@@ -14,17 +14,18 @@
         "@octokit/plugin-retry": "^7.2.0",
         "@octokit/plugin-throttling": "^9.6.0",
         "@octokit/rest": "^21.1.1",
+        "@vscode-elements/react-elements": "^0.9.0",
         "@vscode/codicons": "^0.0.36",
         "@vscode/debugadapter": "^1.59.0",
         "@vscode/debugprotocol": "^1.68.0",
-        "@vscode/webview-ui-toolkit": "^1.0.1",
         "ajv": "^8.11.0",
         "chokidar": "^3.6.0",
         "d3": "^7.9.0",
         "d3-graphviz": "^5.0.2",
         "fs-extra": "^11.1.1",
         "js-yaml": "^4.1.0",
-        "msw": "^2.6.8",
+        "koffi": "^2.12.0",
+        "msw": "^2.7.4",
         "nanoid": "^5.0.7",
         "p-queue": "^8.0.1",
         "proper-lockfile": "^4.1.2",
@@ -56,23 +57,23 @@
         "@jest/environment-jsdom-abstract": "^30.0.0-alpha.7",
         "@microsoft/eslint-formatter-sarif": "^3.1.0",
         "@playwright/test": "^1.50.1",
-        "@storybook/addon-a11y": "^8.6.10",
-        "@storybook/addon-actions": "^8.6.10",
-        "@storybook/addon-essentials": "^8.6.10",
-        "@storybook/addon-interactions": "^8.6.10",
-        "@storybook/addon-links": "^8.6.10",
+        "@storybook/addon-a11y": "^8.6.14",
+        "@storybook/addon-actions": "^8.6.14",
+        "@storybook/addon-essentials": "^8.6.14",
+        "@storybook/addon-interactions": "^8.6.14",
+        "@storybook/addon-links": "^8.6.14",
         "@storybook/blocks": "^8.6.0",
-        "@storybook/components": "^8.6.10",
+        "@storybook/components": "^8.6.14",
         "@storybook/csf": "^0.1.13",
         "@storybook/icons": "^1.4.0",
-        "@storybook/manager-api": "^8.6.10",
-        "@storybook/react": "^8.6.10",
-        "@storybook/react-vite": "^8.6.10",
-        "@storybook/theming": "^8.6.10",
+        "@storybook/manager-api": "^8.6.14",
+        "@storybook/react": "^8.6.14",
+        "@storybook/react-vite": "^8.6.14",
+        "@storybook/theming": "^8.6.14",
         "@testing-library/dom": "^10.4.0",
         "@testing-library/jest-dom": "^6.6.3",
-        "@testing-library/react": "^16.1.0",
-        "@testing-library/user-event": "^14.5.2",
+        "@testing-library/react": "^16.3.0",
+        "@testing-library/user-event": "^14.6.1",
         "@types/cross-spawn": "^6.0.6",
         "@types/d3": "^7.4.0",
         "@types/d3-graphviz": "^2.6.6",
@@ -82,7 +83,7 @@
         "@types/gulp-replace": "^1.1.0",
         "@types/jest": "^29.5.12",
         "@types/js-yaml": "^4.0.6",
-        "@types/node": "20.17.*",
+        "@types/node": "22.15.*",
         "@types/proper-lockfile": "^4.1.4",
         "@types/react": "^18.3.12",
         "@types/react-dom": "^18.3.1",
@@ -95,8 +96,8 @@
         "@types/tmp": "^0.2.6",
         "@types/vscode": "1.90.0",
         "@types/yauzl": "^2.10.3",
-        "@typescript-eslint/eslint-plugin": "^8.28.0",
-        "@typescript-eslint/parser": "^8.28.0",
+        "@typescript-eslint/eslint-plugin": "^8.37.0",
+        "@typescript-eslint/parser": "^8.37.0",
         "@vscode/test-electron": "^2.3.9",
         "@vscode/vsce": "^3.2.1",
         "ansi-colors": "^4.1.1",
@@ -113,7 +114,7 @@
         "eslint-plugin-github": "^5.0.1",
         "eslint-plugin-import": "^2.31.0",
         "eslint-plugin-jest-dom": "^5.5.0",
-        "eslint-plugin-prettier": "^5.1.3",
+        "eslint-plugin-prettier": "^5.2.6",
         "eslint-plugin-react": "^7.37.2",
         "eslint-plugin-react-hooks": "^4.6.2",
         "eslint-plugin-storybook": "^0.8.0",
@@ -122,7 +123,7 @@
         "gulp-esbuild": "^0.14.0",
         "gulp-replace": "^1.1.3",
         "gulp-typescript": "^5.0.1",
-        "husky": "^9.1.5",
+        "husky": "^9.1.7",
         "jest": "^30.0.0-alpha.7",
         "jest-runner-vscode": "^3.0.1",
         "jsdom": "^26.0.0",
@@ -131,20 +132,21 @@
         "markdownlint-cli2-formatter-pretty": "^0.0.7",
         "npm-run-all": "^4.1.5",
         "patch-package": "^8.0.0",
-        "prettier": "^3.2.5",
-        "storybook": "^8.6.10",
+        "prettier": "^3.6.1",
+        "storybook": "^8.6.14",
         "tar-stream": "^3.1.7",
         "through2": "^4.0.2",
-        "ts-jest": "^29.2.5",
+        "ts-jest": "^29.3.2",
         "ts-json-schema-generator": "^2.3.0",
         "ts-node": "^10.9.2",
         "ts-unused-exports": "^10.1.0",
         "typescript": "^5.6.2",
-        "vite": "^6.2.4",
+        "typescript-plugin-css-modules": "^5.1.0",
+        "vite": "^6.3.4",
         "vite-node": "^3.0.7"
       },
       "engines": {
-        "node": "^20.18.2",
+        "node": "^22.15.1",
         "npm": ">=7.20.6",
         "vscode": "^1.90.0"
       }
@@ -159,17 +161,18 @@
       }
     },
     "node_modules/@achrinza/node-ipc": {
-      "version": "9.2.8",
-      "resolved": "https://registry.npmjs.org/@achrinza/node-ipc/-/node-ipc-9.2.8.tgz",
-      "integrity": "sha512-DSzEEkbMYbAUVlhy7fg+BzccoRuSQzqHbIPGxGv19OJ2WKwS3/9ChAnQcII4g+GujcHhyJ8BUuOVAx/S5uAfQg==",
+      "version": "9.2.9",
+      "resolved": "https://registry.npmjs.org/@achrinza/node-ipc/-/node-ipc-9.2.9.tgz",
+      "integrity": "sha512-7s0VcTwiK/0tNOVdSX9FWMeFdOEcsAOz9HesBldXxFMaGvIak7KC2z9tV9EgsQXn6KUsWsfIkViMNuIo0GoZDQ==",
       "dev": true,
+      "license": "MIT",
       "dependencies": {
         "@node-ipc/js-queue": "2.0.3",
         "event-pubsub": "4.3.0",
         "js-message": "1.0.7"
       },
       "engines": {
-        "node": "8 || 9 || 10 || 11 || 12 || 13 || 14 || 15 || 16 || 17 || 18 || 19 || 20 || 21"
+        "node": "8 || 9 || 10 || 11 || 12 || 13 || 14 || 15 || 16 || 17 || 18 || 19 || 20 || 21 || 22"
       }
     },
     "node_modules/@adobe/css-tools": {
@@ -473,16 +476,6 @@
         "node": ">= 14"
       }
     },
-    "node_modules/@azure/identity/node_modules/define-lazy-prop": {
-      "version": "2.0.0",
-      "resolved": "https://registry.npmjs.org/define-lazy-prop/-/define-lazy-prop-2.0.0.tgz",
-      "integrity": "sha512-Ds09qNh8yw3khSjiJjiUInaGX9xlqZDY7JVryGxdxV7NPeuqQfplOpQ66yJFZut3jLa5zOwkXw1g9EI2uKh4Og==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=8"
-      }
-    },
     "node_modules/@azure/identity/node_modules/http-proxy-agent": {
       "version": "7.0.2",
       "resolved": "https://registry.npmjs.org/http-proxy-agent/-/http-proxy-agent-7.0.2.tgz",
@@ -3085,16 +3078,20 @@
       }
     },
     "node_modules/@eslint-community/eslint-utils": {
-      "version": "4.4.0",
-      "resolved": "https://registry.npmjs.org/@eslint-community/eslint-utils/-/eslint-utils-4.4.0.tgz",
-      "integrity": "sha512-1/sA4dwrzBAyeUoQ6oxahHKmrZvsnLCg4RfxW3ZFGGmQkSNQPFNLV9CUEFQP1x9EYXHTo5p6xdhZM1Ne9p/AfA==",
+      "version": "4.7.0",
+      "resolved": "https://registry.npmjs.org/@eslint-community/eslint-utils/-/eslint-utils-4.7.0.tgz",
+      "integrity": "sha512-dyybb3AcajC7uha6CvhdVRJqaKyn7w2YKqKyAN37NKYgZT36w+iRb0Dymmc5qEJ549c/S31cMMSFd75bteCpCw==",
       "dev": true,
+      "license": "MIT",
       "dependencies": {
-        "eslint-visitor-keys": "^3.3.0"
+        "eslint-visitor-keys": "^3.4.3"
       },
       "engines": {
         "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
       },
+      "funding": {
+        "url": "https://opencollective.com/eslint"
+      },
       "peerDependencies": {
         "eslint": "^6.0.0 || ^7.0.0 || >=8.0.0"
       }
@@ -4904,9 +4901,9 @@
       }
     },
     "node_modules/@joshwooding/vite-plugin-react-docgen-typescript/node_modules/brace-expansion": {
-      "version": "2.0.1",
-      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.1.tgz",
-      "integrity": "sha512-XnAIvQ8eM+kC6aULx6wuQiwVsnzsi9d3WxzV3FpWTGA19F621kwdbsAcFKXgKUHZWsy+mY6iL1sHTxWEFCytDA==",
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.2.tgz",
+      "integrity": "sha512-Jt0vHyM+jmUBqojB7E1NIYadt0vI0Qxjxd2TErW94wDz+E2LAm5vKMXXwg6ZZBTHPuUlDgQHKXvjGBdfcF1ZDQ==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
@@ -5051,6 +5048,30 @@
         "@jridgewell/sourcemap-codec": "^1.4.14"
       }
     },
+    "node_modules/@lit-labs/ssr-dom-shim": {
+      "version": "1.3.0",
+      "resolved": "https://registry.npmjs.org/@lit-labs/ssr-dom-shim/-/ssr-dom-shim-1.3.0.tgz",
+      "integrity": "sha512-nQIWonJ6eFAvUUrSlwyHDm/aE8PBDu5kRpL0vHMg6K8fK3Diq1xdPjTnsJSwxABhaZ+5eBi1btQB5ShUTKo4nQ==",
+      "license": "BSD-3-Clause"
+    },
+    "node_modules/@lit/react": {
+      "version": "1.0.7",
+      "resolved": "https://registry.npmjs.org/@lit/react/-/react-1.0.7.tgz",
+      "integrity": "sha512-cencnwwLXQKiKxjfFzSgZRngcWJzUDZi/04E0fSaF86wZgchMdvTyu+lE36DrUfvuus3bH8+xLPrhM1cTjwpzw==",
+      "license": "BSD-3-Clause",
+      "peerDependencies": {
+        "@types/react": "17 || 18 || 19"
+      }
+    },
+    "node_modules/@lit/reactive-element": {
+      "version": "2.0.4",
+      "resolved": "https://registry.npmjs.org/@lit/reactive-element/-/reactive-element-2.0.4.tgz",
+      "integrity": "sha512-GFn91inaUa2oHLak8awSIigYz0cU0Payr1rcFsrkf5OJ5eSPxElyZfKh0f2p9FsTiZWXQdWGJeXZICEfXXYSXQ==",
+      "license": "BSD-3-Clause",
+      "dependencies": {
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+      }
+    },
     "node_modules/ts-json-schema-generator": {
       "version": "2.3.0",
       "resolved": "https://registry.npmjs.org/ts-json-schema-generator/-/ts-json-schema-generator-2.3.0.tgz",
@@ -25037,10 +25686,11 @@
       }
     },
     "node_modules/ts-json-schema-generator/node_modules/brace-expansion": {
-      "version": "2.0.1",
-      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.1.tgz",
-      "integrity": "sha512-XnAIvQ8eM+kC6aULx6wuQiwVsnzsi9d3WxzV3FpWTGA19F621kwdbsAcFKXgKUHZWsy+mY6iL1sHTxWEFCytDA==",
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.2.tgz",
+      "integrity": "sha512-Jt0vHyM+jmUBqojB7E1NIYadt0vI0Qxjxd2TErW94wDz+E2LAm5vKMXXwg6ZZBTHPuUlDgQHKXvjGBdfcF1ZDQ==",
       "dev": true,
+      "license": "MIT",
       "dependencies": {
         "balanced-match": "^1.0.0"
       }
@@ -25477,6 +26127,59 @@
         "node": ">=14.17"
       }
     },
+    "node_modules/typescript-plugin-css-modules": {
+      "version": "5.1.0",
+      "resolved": "https://registry.npmjs.org/typescript-plugin-css-modules/-/typescript-plugin-css-modules-5.1.0.tgz",
+      "integrity": "sha512-6h+sLBa4l+XYSTn/31vZHd/1c3SvAbLpobY6FxDiUOHJQG1eD9Gh3eCs12+Eqc+TCOAdxcO+zAPvUq0jBfdciw==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "@types/postcss-modules-local-by-default": "^4.0.2",
+        "@types/postcss-modules-scope": "^3.0.4",
+        "dotenv": "^16.4.2",
+        "icss-utils": "^5.1.0",
+        "less": "^4.2.0",
+        "lodash.camelcase": "^4.3.0",
+        "postcss": "^8.4.35",
+        "postcss-load-config": "^3.1.4",
+        "postcss-modules-extract-imports": "^3.0.0",
+        "postcss-modules-local-by-default": "^4.0.4",
+        "postcss-modules-scope": "^3.1.1",
+        "reserved-words": "^0.1.2",
+        "sass": "^1.70.0",
+        "source-map-js": "^1.0.2",
+        "stylus": "^0.62.0",
+        "tsconfig-paths": "^4.2.0"
+      },
+      "peerDependencies": {
+        "typescript": ">=4.0.0"
+      }
+    },
+    "node_modules/typescript-plugin-css-modules/node_modules/strip-bom": {
+      "version": "3.0.0",
+      "resolved": "https://registry.npmjs.org/strip-bom/-/strip-bom-3.0.0.tgz",
+      "integrity": "sha512-vavAMRXOgBVNF6nyEEmL3DBK19iRpDcoIwW+swQ+CbGiu7lju6t+JklA1MHweoWtadgt4ISVUsXLyDq34ddcwA==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=4"
+      }
+    },
+    "node_modules/typescript-plugin-css-modules/node_modules/tsconfig-paths": {
+      "version": "4.2.0",
+      "resolved": "https://registry.npmjs.org/tsconfig-paths/-/tsconfig-paths-4.2.0.tgz",
+      "integrity": "sha512-NoZ4roiN7LnbKn9QqE1amc9DJfzvZXxF4xDavcOWt1BPkdx+m+0gJuPM+S0vCe7zTJMYUP0R8pO2XMr+Y8oLIg==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "json5": "^2.2.2",
+        "minimist": "^1.2.6",
+        "strip-bom": "^3.0.0"
+      },
+      "engines": {
+        "node": ">=6"
+      }
+    },
     "node_modules/uc.micro": {
       "version": "2.1.0",
       "resolved": "https://registry.npmjs.org/uc.micro/-/uc.micro-2.1.0.tgz",
@@ -25549,10 +26252,11 @@
       }
     },
     "node_modules/undici-types": {
-      "version": "6.19.8",
-      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-6.19.8.tgz",
-      "integrity": "sha512-ve2KP6f/JnbPBFyobGHuerC9g1FYGn/F8n1LWTwNxCEzd6IfqTwUQcNXgEtmmQ6DlRrC1hrSrBnCZPokRrDHjw==",
-      "dev": true
+      "version": "6.21.0",
+      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-6.21.0.tgz",
+      "integrity": "sha512-iwDZqg0QAGrg9Rav5H4n0M64c3mkR59cJ6wQp+7C4nI0gsmExaedaYLNO44eT4AtBBwjbTiGPMlt2Md0T9H9JQ==",
+      "dev": true,
+      "license": "MIT"
     },
     "node_modules/unicode-canonical-property-names-ecmascript": {
       "version": "2.0.0",
@@ -25645,15 +26349,6 @@
         "node": ">=14.0.0"
       }
     },
-    "node_modules/untildify": {
-      "version": "4.0.0",
-      "resolved": "https://registry.npmjs.org/untildify/-/untildify-4.0.0.tgz",
-      "integrity": "sha512-KK8xQ1mkzZeg9inewmFVDNkg3l5LUhoq9kN6iWYB/CC9YMG8HA+c1Q8HwDe6dEX7kErrEVNVBO3fWsVq5iDgtw==",
-      "dev": true,
-      "engines": {
-        "node": ">=8"
-      }
-    },
     "node_modules/update-browserslist-db": {
       "version": "1.0.13",
       "resolved": "https://registry.npmjs.org/update-browserslist-db/-/update-browserslist-db-1.0.13.tgz",
@@ -25998,15 +26693,18 @@
       }
     },
     "node_modules/vite": {
-      "version": "6.2.4",
-      "resolved": "https://registry.npmjs.org/vite/-/vite-6.2.4.tgz",
-      "integrity": "sha512-veHMSew8CcRzhL5o8ONjy8gkfmFJAd5Ac16oxBUjlwgX3Gq2Wqr+qNC3TjPIpy7TPV/KporLga5GT9HqdrCizw==",
+      "version": "6.3.4",
+      "resolved": "https://registry.npmjs.org/vite/-/vite-6.3.4.tgz",
+      "integrity": "sha512-BiReIiMS2fyFqbqNT/Qqt4CVITDU9M9vE+DKcVAsB+ZV0wvTKd+3hMbkpxz1b+NmEDMegpVbisKiAZOnvO92Sw==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
         "esbuild": "^0.25.0",
+        "fdir": "^6.4.4",
+        "picomatch": "^4.0.2",
         "postcss": "^8.5.3",
-        "rollup": "^4.30.1"
+        "rollup": "^4.34.9",
+        "tinyglobby": "^0.2.13"
       },
       "bin": {
         "vite": "bin/vite.js"
@@ -26092,6 +26790,19 @@
         "url": "https://opencollective.com/vitest"
       }
     },
+    "node_modules/vite/node_modules/picomatch": {
+      "version": "4.0.2",
+      "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-4.0.2.tgz",
+      "integrity": "sha512-M7BAV6Rlcy5u+m6oPhAPFgJTzAioX/6B0DxyvDlo9l8+T3nLKbrczg2WLUyzd45L8RqfUMyGPzekbMvX2Ldkwg==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=12"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/jonschlinkert"
+      }
+    },
     "node_modules/vscode-extension-telemetry": {
       "version": "0.1.7",
       "resolved": "https://registry.npmjs.org/vscode-extension-telemetry/-/vscode-extension-telemetry-0.1.7.tgz",
@@ -26161,9 +26872,10 @@
       }
     },
     "node_modules/vscode-languageclient/node_modules/brace-expansion": {
-      "version": "2.0.1",
-      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.1.tgz",
-      "integrity": "sha512-XnAIvQ8eM+kC6aULx6wuQiwVsnzsi9d3WxzV3FpWTGA19F621kwdbsAcFKXgKUHZWsy+mY6iL1sHTxWEFCytDA==",
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.2.tgz",
+      "integrity": "sha512-Jt0vHyM+jmUBqojB7E1NIYadt0vI0Qxjxd2TErW94wDz+E2LAm5vKMXXwg6ZZBTHPuUlDgQHKXvjGBdfcF1ZDQ==",
+      "license": "MIT",
       "dependencies": {
         "balanced-match": "^1.0.0"
       }
@@ -26710,9 +27422,10 @@
       }
     },
     "node_modules/zip-a-folder/node_modules/brace-expansion": {
-      "version": "2.0.1",
-      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.1.tgz",
-      "integrity": "sha512-XnAIvQ8eM+kC6aULx6wuQiwVsnzsi9d3WxzV3FpWTGA19F621kwdbsAcFKXgKUHZWsy+mY6iL1sHTxWEFCytDA==",
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.2.tgz",
+      "integrity": "sha512-Jt0vHyM+jmUBqojB7E1NIYadt0vI0Qxjxd2TErW94wDz+E2LAm5vKMXXwg6ZZBTHPuUlDgQHKXvjGBdfcF1ZDQ==",
+      "license": "MIT",
       "dependencies": {
         "balanced-match": "^1.0.0"
       }
diff --git a/extensions/ql-vscode/package.json b/extensions/ql-vscode/package.json
index 3615e186750..8d5ee0dfc6b 100644
--- a/extensions/ql-vscode/package.json
+++ b/extensions/ql-vscode/package.json
@@ -4,7 +4,7 @@
   "description": "CodeQL for Visual Studio Code",
   "author": "GitHub",
   "private": true,
-  "version": "1.17.3",
+  "version": "1.17.5",
   "publisher": "GitHub",
   "license": "MIT",
   "icon": "media/VS-marketplace-CodeQL-icon.png",
@@ -14,7 +14,7 @@
   },
   "engines": {
     "vscode": "^1.90.0",
-    "node": "^20.18.2",
+    "node": "^22.15.1",
     "npm": ">=7.20.6"
   },
   "categories": [
@@ -571,6 +571,10 @@
         "command": "codeQL.runQueries",
         "title": "CodeQL: Run Queries in Selected Files"
       },
+      {
+        "command": "codeQL.runQuerySuite",
+        "title": "CodeQL: Run Selected Query Suite"
+      },
       {
         "command": "codeQL.quickEval",
         "title": "CodeQL: Quick Evaluation"
@@ -786,6 +790,10 @@
         "command": "codeQL.trimCache",
         "title": "CodeQL: Trim Cache"
       },
+      {
+        "command": "codeQL.trimOverlayBaseCache",
+        "title": "CodeQL: Trim Overlay Base Cache"
+      },
       {
         "command": "codeQL.installPackDependencies",
         "title": "CodeQL: Install Pack Dependencies"
@@ -954,6 +962,10 @@
         "command": "codeQLQueryHistory.copyRepoList",
         "title": "Copy Repository List"
       },
+      {
+        "command": "codeQLQueryHistory.viewAutofixes",
+        "title": "View Autofixes"
+      },
       {
         "command": "codeQLQueryResults.down",
         "title": "CodeQL: Navigate Down in Local Result Viewer"
@@ -1292,6 +1304,11 @@
           "group": "1_queryHistory@1",
           "when": "viewItem == remoteResultsItem"
         },
+        {
+          "command": "codeQLQueryHistory.viewAutofixes",
+          "group": "1_queryHistory@2",
+          "when": "viewItem == remoteResultsItem && config.codeQL.canary"
+        },
         {
           "command": "codeQLQueries.runLocalQueryFromQueriesPanel",
           "group": "inline",
@@ -1361,6 +1378,11 @@
           "group": "9_qlCommands",
           "when": "resourceScheme != codeql-zip-archive"
         },
+        {
+          "command": "codeQL.runQuerySuite",
+          "group": "9_qlCommands",
+          "when": "resourceScheme != codeql-zip-archive && resourceExtname == .qls && !explorerResourceIsFolder && !listMultiSelection && config.codeQL.canary"
+        },
         {
           "command": "codeQL.runVariantAnalysisContextExplorer",
           "group": "9_qlCommands",
@@ -1458,6 +1480,10 @@
           "command": "codeQL.runQueries",
           "when": "false"
         },
+        {
+          "command": "codeQL.runQuerySuite",
+          "when": "false"
+        },
         {
           "command": "codeQL.quickEval",
           "when": "editorLangId == ql"
@@ -1693,6 +1719,10 @@
           "command": "codeQLQueryHistory.copyRepoList",
           "when": "false"
         },
+        {
+          "command": "codeQLQueryHistory.viewAutofixes",
+          "when": "false"
+        },
         {
           "command": "codeQLQueryHistory.showQueryText",
           "when": "false"
@@ -1791,6 +1821,10 @@
         },
         {
           "command": "codeQL.trimCache"
+        },
+        {
+          "command": "codeQL.trimOverlayBaseCache",
+          "when": "codeQL.cliFeatures.queryServerTrimCacheWithMode"
         }
       ],
       "editor/context": [
@@ -1972,17 +2006,18 @@
     "@octokit/plugin-retry": "^7.2.0",
     "@octokit/plugin-throttling": "^9.6.0",
     "@octokit/rest": "^21.1.1",
+    "@vscode-elements/react-elements": "^0.9.0",
     "@vscode/codicons": "^0.0.36",
     "@vscode/debugadapter": "^1.59.0",
     "@vscode/debugprotocol": "^1.68.0",
-    "@vscode/webview-ui-toolkit": "^1.0.1",
     "ajv": "^8.11.0",
     "chokidar": "^3.6.0",
     "d3": "^7.9.0",
     "d3-graphviz": "^5.0.2",
     "fs-extra": "^11.1.1",
     "js-yaml": "^4.1.0",
-    "msw": "^2.6.8",
+    "koffi": "^2.12.0",
+    "msw": "^2.7.4",
     "nanoid": "^5.0.7",
     "p-queue": "^8.0.1",
     "proper-lockfile": "^4.1.2",
@@ -2014,23 +2049,23 @@
     "@jest/environment-jsdom-abstract": "^30.0.0-alpha.7",
     "@microsoft/eslint-formatter-sarif": "^3.1.0",
     "@playwright/test": "^1.50.1",
-    "@storybook/addon-a11y": "^8.6.10",
-    "@storybook/addon-actions": "^8.6.10",
-    "@storybook/addon-essentials": "^8.6.10",
-    "@storybook/addon-interactions": "^8.6.10",
-    "@storybook/addon-links": "^8.6.10",
+    "@storybook/addon-a11y": "^8.6.14",
+    "@storybook/addon-actions": "^8.6.14",
+    "@storybook/addon-essentials": "^8.6.14",
+    "@storybook/addon-interactions": "^8.6.14",
+    "@storybook/addon-links": "^8.6.14",
     "@storybook/blocks": "^8.6.0",
-    "@storybook/components": "^8.6.10",
+    "@storybook/components": "^8.6.14",
     "@storybook/csf": "^0.1.13",
     "@storybook/icons": "^1.4.0",
-    "@storybook/manager-api": "^8.6.10",
-    "@storybook/react": "^8.6.10",
-    "@storybook/react-vite": "^8.6.10",
-    "@storybook/theming": "^8.6.10",
+    "@storybook/manager-api": "^8.6.14",
+    "@storybook/react": "^8.6.14",
+    "@storybook/react-vite": "^8.6.14",
+    "@storybook/theming": "^8.6.14",
     "@testing-library/dom": "^10.4.0",
     "@testing-library/jest-dom": "^6.6.3",
-    "@testing-library/react": "^16.1.0",
-    "@testing-library/user-event": "^14.5.2",
+    "@testing-library/react": "^16.3.0",
+    "@testing-library/user-event": "^14.6.1",
     "@types/cross-spawn": "^6.0.6",
     "@types/d3": "^7.4.0",
     "@types/d3-graphviz": "^2.6.6",
@@ -2040,7 +2075,7 @@
     "@types/gulp-replace": "^1.1.0",
     "@types/jest": "^29.5.12",
     "@types/js-yaml": "^4.0.6",
-    "@types/node": "20.17.*",
+    "@types/node": "22.15.*",
     "@types/proper-lockfile": "^4.1.4",
     "@types/react": "^18.3.12",
     "@types/react-dom": "^18.3.1",
@@ -2053,8 +2088,8 @@
     "@types/tmp": "^0.2.6",
     "@types/vscode": "1.90.0",
     "@types/yauzl": "^2.10.3",
-    "@typescript-eslint/eslint-plugin": "^8.28.0",
-    "@typescript-eslint/parser": "^8.28.0",
+    "@typescript-eslint/eslint-plugin": "^8.37.0",
+    "@typescript-eslint/parser": "^8.37.0",
     "@vscode/test-electron": "^2.3.9",
     "@vscode/vsce": "^3.2.1",
     "ansi-colors": "^4.1.1",
@@ -2071,7 +2106,7 @@
     "eslint-plugin-github": "^5.0.1",
     "eslint-plugin-import": "^2.31.0",
     "eslint-plugin-jest-dom": "^5.5.0",
-    "eslint-plugin-prettier": "^5.1.3",
+    "eslint-plugin-prettier": "^5.2.6",
     "eslint-plugin-react": "^7.37.2",
     "eslint-plugin-react-hooks": "^4.6.2",
     "eslint-plugin-storybook": "^0.8.0",
@@ -2080,7 +2115,7 @@
     "gulp-esbuild": "^0.14.0",
     "gulp-replace": "^1.1.3",
     "gulp-typescript": "^5.0.1",
-    "husky": "^9.1.5",
+    "husky": "^9.1.7",
     "jest": "^30.0.0-alpha.7",
     "jest-runner-vscode": "^3.0.1",
     "jsdom": "^26.0.0",
@@ -2089,16 +2124,17 @@
     "markdownlint-cli2-formatter-pretty": "^0.0.7",
     "npm-run-all": "^4.1.5",
     "patch-package": "^8.0.0",
-    "prettier": "^3.2.5",
-    "storybook": "^8.6.10",
+    "prettier": "^3.6.1",
+    "storybook": "^8.6.14",
     "tar-stream": "^3.1.7",
     "through2": "^4.0.2",
-    "ts-jest": "^29.2.5",
+    "ts-jest": "^29.3.2",
     "ts-json-schema-generator": "^2.3.0",
     "ts-node": "^10.9.2",
     "ts-unused-exports": "^10.1.0",
     "typescript": "^5.6.2",
-    "vite": "^6.2.4",
+    "typescript-plugin-css-modules": "^5.1.0",
+    "vite": "^6.3.4",
     "vite-node": "^3.0.7"
   },
   "lint-staged": {
diff --git a/extensions/ql-vscode/scripts/source-map.ts b/extensions/ql-vscode/scripts/source-map.ts
index 551e4dc10a6..f0e6af88923 100644
--- a/extensions/ql-vscode/scripts/source-map.ts
+++ b/extensions/ql-vscode/scripts/source-map.ts
@@ -131,7 +131,7 @@ async function extractSourceMap() {
               resolve(sourceMapsDirectory, `${basename(file)}.map`),
             );
             rawSourceMaps.set(file, rawSourceMap);
-          } catch (e: unknown) {
+          } catch (e) {
             // If the file is not found, we will not decode it and not try reading this source map again
             if (e instanceof Error && "code" in e && e.code === "ENOENT") {
               rawSourceMaps.set(file, null);
diff --git a/extensions/ql-vscode/scripts/update-node-version.ts b/extensions/ql-vscode/scripts/update-node-version.ts
index a079356562a..8f412a3a683 100644
--- a/extensions/ql-vscode/scripts/update-node-version.ts
+++ b/extensions/ql-vscode/scripts/update-node-version.ts
@@ -93,7 +93,7 @@ async function updateNodeVersion() {
 
       // If it exists, we can break out of this loop
       break;
-    } catch (e: unknown) {
+    } catch (e) {
       if (!isExecError(e)) {
         throw e;
       }
diff --git a/extensions/ql-vscode/src/codeql-cli/cli-version.ts b/extensions/ql-vscode/src/codeql-cli/cli-version.ts
index 94f1169c30a..ebd30cbdb62 100644
--- a/extensions/ql-vscode/src/codeql-cli/cli-version.ts
+++ b/extensions/ql-vscode/src/codeql-cli/cli-version.ts
@@ -10,9 +10,7 @@ interface VersionResult {
 }
 
 export interface CliFeatures {
-  featuresInVersionResult?: boolean;
-  mrvaPackCreate?: boolean;
-  generateSummarySymbolMap?: boolean;
+  queryServerRunQueries?: boolean;
 }
 
 export interface VersionAndFeatures {
diff --git a/extensions/ql-vscode/src/codeql-cli/cli.ts b/extensions/ql-vscode/src/codeql-cli/cli.ts
index a34b6a351ea..f32c4a2555b 100644
--- a/extensions/ql-vscode/src/codeql-cli/cli.ts
+++ b/extensions/ql-vscode/src/codeql-cli/cli.ts
@@ -1191,15 +1191,12 @@ export class CodeQLCliServer implements Disposable {
     outputPath: string,
     endSummaryPath: string,
   ): Promise<string> {
-    const supportsGenerateSummarySymbolMap =
-      await this.cliConstraints.supportsGenerateSummarySymbolMap();
     const subcommandArgs = [
       "--format=text",
       `--end-summary=${endSummaryPath}`,
       "--sourcemap",
-      ...(supportsGenerateSummarySymbolMap
-        ? ["--summary-symbol-map", "--minify-output"]
-        : []),
+      "--summary-symbol-map",
+      "--minify-output",
       inputPath,
       outputPath,
     ];
@@ -1910,11 +1907,7 @@ export class CliVersionConstraint {
     /**/
   }
 
-  async supportsMrvaPackCreate(): Promise<boolean> {
-    return (await this.cli.getFeatures()).mrvaPackCreate === true;
-  }
-
-  async supportsGenerateSummarySymbolMap(): Promise<boolean> {
-    return (await this.cli.getFeatures()).generateSummarySymbolMap === true;
+  async supportsQueryServerRunQueries(): Promise<boolean> {
+    return (await this.cli.getFeatures()).queryServerRunQueries === true;
   }
 }
diff --git a/extensions/ql-vscode/src/codeql-cli/distribution.ts b/extensions/ql-vscode/src/codeql-cli/distribution.ts
index 0ec1bede7e4..75df3382e17 100644
--- a/extensions/ql-vscode/src/codeql-cli/distribution.ts
+++ b/extensions/ql-vscode/src/codeql-cli/distribution.ts
@@ -336,7 +336,7 @@ class ExtensionSpecificDistributionManager {
     const distributionStatePath = this.getDistributionStatePath();
     try {
       this.distributionState = await readJson(distributionStatePath);
-    } catch (e: unknown) {
+    } catch (e) {
       if (isIOError(e) && e.code === "ENOENT") {
         // If the file doesn't exist, that just means we need to create it
 
diff --git a/extensions/ql-vscode/src/common/commands.ts b/extensions/ql-vscode/src/common/commands.ts
index 2fd8a1995d4..64585a8c9e8 100644
--- a/extensions/ql-vscode/src/common/commands.ts
+++ b/extensions/ql-vscode/src/common/commands.ts
@@ -138,6 +138,7 @@ export type LocalQueryCommands = {
   "codeQLQueries.createQuery": () => Promise<void>;
   "codeQL.runLocalQueryFromFileTab": (uri: Uri) => Promise<void>;
   "codeQL.runQueries": ExplorerSelectionCommandFunction<Uri>;
+  "codeQL.runQuerySuite": ExplorerSelectionCommandFunction<Uri>;
   "codeQL.quickEval": (uri: Uri) => Promise<void>;
   "codeQL.quickEvalCount": (uri: Uri) => Promise<void>;
   "codeQL.quickEvalContextEditor": (uri: Uri) => Promise<void>;
@@ -196,6 +197,7 @@ export type QueryHistoryCommands = {
   "codeQLQueryHistory.itemClicked": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
   "codeQLQueryHistory.openOnGithub": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
   "codeQLQueryHistory.copyRepoList": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.viewAutofixes": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
 
   // Commands in the command palette
   "codeQL.exportSelectedVariantAnalysisResults": () => Promise<void>;
@@ -219,6 +221,7 @@ export type LocalDatabasesCommands = {
   "codeQL.upgradeCurrentDatabase": () => Promise<void>;
   "codeQL.clearCache": () => Promise<void>;
   "codeQL.trimCache": () => Promise<void>;
+  "codeQL.trimOverlayBaseCache": () => Promise<void>;
 
   // Explorer context menu
   "codeQL.setCurrentDatabase": (uri: Uri) => Promise<void>;
diff --git a/extensions/ql-vscode/src/common/helpers-pure.ts b/extensions/ql-vscode/src/common/helpers-pure.ts
index 20c1a780cb3..861e250b93f 100644
--- a/extensions/ql-vscode/src/common/helpers-pure.ts
+++ b/extensions/ql-vscode/src/common/helpers-pure.ts
@@ -69,7 +69,7 @@ export function getErrorMessage(e: unknown): string {
 }
 
 export function getErrorStack(e: unknown): string {
-  return e instanceof Error ? e.stack ?? "" : "";
+  return e instanceof Error ? (e.stack ?? "") : "";
 }
 
 export function asError(e: unknown): Error {
diff --git a/extensions/ql-vscode/src/common/interface-types.ts b/extensions/ql-vscode/src/common/interface-types.ts
index 2a0fb24c811..eca0779966a 100644
--- a/extensions/ql-vscode/src/common/interface-types.ts
+++ b/extensions/ql-vscode/src/common/interface-types.ts
@@ -163,6 +163,25 @@ interface SetUserSettingsMsg {
   userSettings: UserSettings;
 }
 
+export interface VariantAnalysisUserSettings {
+  /** Whether to display the "View Autofixes" button. */
+  shouldShowViewAutofixesButton: boolean;
+}
+
+export const DEFAULT_VARIANT_ANALYSIS_USER_SETTINGS: VariantAnalysisUserSettings =
+  {
+    shouldShowViewAutofixesButton: false,
+  };
+
+/**
+ * Message indicating that the user's variant analysis configuration
+ * settings have changed.
+ */
+interface SetVariantAnalysisUserSettingsMsg {
+  t: "setVariantAnalysisUserSettings";
+  variantAnalysisUserSettings: VariantAnalysisUserSettings;
+}
+
 /**
  * Message indicating that the results view should display interpreted
  * results.
@@ -527,6 +546,11 @@ interface OpenQueryTextMessage {
   t: "openQueryText";
 }
 
+interface ViewAutofixesMessage {
+  t: "viewAutofixes";
+  filterSort?: RepositoriesFilterSortStateWithIds;
+}
+
 interface CopyRepositoryListMessage {
   t: "copyRepositoryList";
   filterSort?: RepositoriesFilterSortStateWithIds;
@@ -554,13 +578,15 @@ export type ToVariantAnalysisMessage =
   | SetVariantAnalysisMessage
   | SetFilterSortStateMessage
   | SetRepoResultsMessage
-  | SetRepoStatesMessage;
+  | SetRepoStatesMessage
+  | SetVariantAnalysisUserSettingsMsg;
 
 export type FromVariantAnalysisMessage =
   | CommonFromViewMessages
   | RequestRepositoryResultsMessage
   | OpenQueryFileMessage
   | OpenQueryTextMessage
+  | ViewAutofixesMessage
   | CopyRepositoryListMessage
   | ExportResultsMessage
   | OpenLogsMessage
diff --git a/extensions/ql-vscode/src/common/query-language.ts b/extensions/ql-vscode/src/common/query-language.ts
index b28ebedad00..7e89e5a7139 100644
--- a/extensions/ql-vscode/src/common/query-language.ts
+++ b/extensions/ql-vscode/src/common/query-language.ts
@@ -1,4 +1,5 @@
 export enum QueryLanguage {
+  Actions = "actions",
   CSharp = "csharp",
   Cpp = "cpp",
   Go = "go",
@@ -12,6 +13,8 @@ export enum QueryLanguage {
 
 export function getLanguageDisplayName(language: string): string {
   switch (language) {
+    case QueryLanguage.Actions:
+      return "Actions";
     case QueryLanguage.CSharp:
       return "C#";
     case QueryLanguage.Cpp:
@@ -36,6 +39,7 @@ export function getLanguageDisplayName(language: string): string {
 }
 
 export const PACKS_BY_QUERY_LANGUAGE = {
+  [QueryLanguage.Actions]: ["codeql/actions-queries"],
   [QueryLanguage.Cpp]: ["codeql/cpp-queries"],
   [QueryLanguage.CSharp]: [
     "codeql/csharp-queries",
@@ -50,7 +54,7 @@ export const PACKS_BY_QUERY_LANGUAGE = {
 };
 
 export const dbSchemeToLanguage: Record<string, QueryLanguage> = {
-  "semmlecode.javascript.dbscheme": QueryLanguage.Javascript,
+  "semmlecode.javascript.dbscheme": QueryLanguage.Javascript, // This can also be QueryLanguage.Actions
   "semmlecode.cpp.dbscheme": QueryLanguage.Cpp,
   "semmlecode.dbscheme": QueryLanguage.Java,
   "semmlecode.python.dbscheme": QueryLanguage.Python,
@@ -61,6 +65,18 @@ export const dbSchemeToLanguage: Record<string, QueryLanguage> = {
   "swift.dbscheme": QueryLanguage.Swift,
 };
 
+export const languageToDbScheme = Object.entries(dbSchemeToLanguage).reduce(
+  (acc, [k, v]) => {
+    acc[v] = k;
+    return acc;
+  },
+  {} as { [k: string]: string },
+);
+
+// Actions dbscheme is the same as Javascript dbscheme
+languageToDbScheme[QueryLanguage.Actions] =
+  languageToDbScheme[QueryLanguage.Javascript];
+
 export function isQueryLanguage(language: string): language is QueryLanguage {
   return Object.values(QueryLanguage).includes(language as QueryLanguage);
 }
diff --git a/extensions/ql-vscode/src/common/short-paths.ts b/extensions/ql-vscode/src/common/short-paths.ts
index 838dac031e1..0025b96da05 100644
--- a/extensions/ql-vscode/src/common/short-paths.ts
+++ b/extensions/ql-vscode/src/common/short-paths.ts
@@ -1,7 +1,9 @@
-import { platform } from "os";
+import { arch, platform } from "os";
 import { basename, dirname, join, normalize, resolve } from "path";
 import { lstat, readdir } from "fs/promises";
 import type { BaseLogger } from "./logging";
+import type { KoffiFunction } from "koffi";
+import { getErrorMessage } from "./helpers-pure";
 
 /**
  * Expands a path that potentially contains 8.3 short names (e.g. "C:\PROGRA~1" instead of "C:\Program Files").
@@ -32,7 +34,23 @@ export async function expandShortPaths(
     return absoluteShortPath;
   }
 
-  return await expandShortPathRecursive(absoluteShortPath, logger);
+  const longPath = await expandShortPathRecursive(absoluteShortPath, logger);
+  if (longPath.indexOf("~") < 0) {
+    return longPath;
+  }
+
+  void logger.log(
+    "Short path was not resolved to long path, using native method",
+  );
+
+  try {
+    return await expandShortPathNative(absoluteShortPath, logger);
+  } catch (e) {
+    void logger.log(
+      `Failed to expand short path using native method: ${getErrorMessage(e)}`,
+    );
+    return longPath;
+  }
 }
 
 /**
@@ -115,3 +133,46 @@ async function expandShortPathRecursive(
   const longBase = await expandShortPathComponent(dir, shortBase, logger);
   return join(dir, longBase);
 }
+
+let GetLongPathNameW: KoffiFunction | undefined;
+
+async function expandShortPathNative(shortPath: string, logger: BaseLogger) {
+  if (platform() !== "win32") {
+    throw new Error("expandShortPathNative is only supported on Windows");
+  }
+
+  if (arch() !== "x64") {
+    throw new Error(
+      "expandShortPathNative is only supported on x64 architecture",
+    );
+  }
+
+  if (GetLongPathNameW === undefined) {
+    // We are using koffi/indirect here to avoid including the native addon for all
+    // platforms in the bundle since this is only used on Windows. Instead, the
+    // native addon is included in the Gulpfile.
+    const koffi = await import("koffi/indirect");
+
+    const lib = koffi.load("kernel32.dll");
+    GetLongPathNameW = lib.func("__stdcall", "GetLongPathNameW", "uint32", [
+      "str16",
+      "str16",
+      "uint32",
+    ]);
+  }
+
+  const MAX_PATH = 32767;
+  const buffer = Buffer.alloc(MAX_PATH * 2, 0);
+
+  const result = GetLongPathNameW(shortPath, buffer, MAX_PATH);
+
+  if (result === 0) {
+    throw new Error("Failed to get long path name");
+  }
+
+  const longPath = buffer.toString("utf16le", 0, (result - 1) * 2);
+
+  void logger.log(`Expanded short path ${shortPath} to ${longPath}`);
+
+  return longPath;
+}
diff --git a/extensions/ql-vscode/src/compare-performance/compare-performance-view.ts b/extensions/ql-vscode/src/compare-performance/compare-performance-view.ts
index c1633801ed6..a59367ea135 100644
--- a/extensions/ql-vscode/src/compare-performance/compare-performance-view.ts
+++ b/extensions/ql-vscode/src/compare-performance/compare-performance-view.ts
@@ -16,8 +16,9 @@ import { withProgress } from "../common/vscode/progress";
 import { telemetryListener } from "../common/vscode/telemetry";
 import type { HistoryItemLabelProvider } from "../query-history/history-item-label-provider";
 import { PerformanceOverviewScanner } from "../log-insights/performance-comparison";
-import { scanLog } from "../log-insights/log-scanner";
 import type { ResultsView } from "../local-queries";
+import { readJsonlFile } from "../common/jsonl-reader";
+import type { SummaryEvent } from "../log-insights/log-summary";
 
 export class ComparePerformanceView extends AbstractWebview<
   ToComparePerformanceViewMessage,
@@ -46,8 +47,20 @@ export class ComparePerformanceView extends AbstractWebview<
     function scanLogWithProgress(log: string, logDescription: string) {
       const bytes = statSync(log).size;
       return withProgress(
-        async (progress) =>
-          scanLog(log, new PerformanceOverviewScanner(), progress),
+        async (progress) => {
+          progress?.({
+            // all scans have step 1 - the backing progress tracker allows increments instead of
+            // steps - but for now we are happy with a tiny UI that says what is happening
+            message: `Scanning ...`,
+            step: 1,
+            maxStep: 2,
+          });
+          const scanner = new PerformanceOverviewScanner();
+          await readJsonlFile<SummaryEvent>(log, async (obj) => {
+            scanner.onEvent(obj);
+          });
+          return scanner;
+        },
 
         {
           title: `Scanning evaluator log ${logDescription} (${(bytes / 1024 / 1024).toFixed(1)} MB)`,
diff --git a/extensions/ql-vscode/src/compare/compare-view.ts b/extensions/ql-vscode/src/compare/compare-view.ts
index c4c25df546a..93538f52e6b 100644
--- a/extensions/ql-vscode/src/compare/compare-view.ts
+++ b/extensions/ql-vscode/src/compare/compare-view.ts
@@ -70,22 +70,20 @@ export class CompareView extends AbstractWebview<
     selectedResultSetName?: string,
   ) {
     const [fromSchemas, toSchemas] = await Promise.all([
-      this.cliServer.bqrsInfo(
-        from.completedQuery.query.resultsPaths.resultsPath,
-      ),
-      this.cliServer.bqrsInfo(to.completedQuery.query.resultsPaths.resultsPath),
+      this.cliServer.bqrsInfo(from.completedQuery.query.resultsPath),
+      this.cliServer.bqrsInfo(to.completedQuery.query.resultsPath),
     ]);
 
     const [fromSchemaNames, toSchemaNames] = await Promise.all([
       getResultSetNames(
         fromSchemas,
         from.completedQuery.query.metadata,
-        from.completedQuery.query.resultsPaths.interpretedResultsPath,
+        from.completedQuery.query.interpretedResultsPath,
       ),
       getResultSetNames(
         toSchemas,
         to.completedQuery.query.metadata,
-        to.completedQuery.query.resultsPaths.interpretedResultsPath,
+        to.completedQuery.query.interpretedResultsPath,
       ),
     ]);
 
@@ -101,15 +99,14 @@ export class CompareView extends AbstractWebview<
         schemaNames: fromSchemaNames,
         metadata: from.completedQuery.query.metadata,
         interpretedResultsPath:
-          from.completedQuery.query.resultsPaths.interpretedResultsPath,
+          from.completedQuery.query.interpretedResultsPath,
       },
       to,
       toInfo: {
         schemas: toSchemas,
         schemaNames: toSchemaNames,
         metadata: to.completedQuery.query.metadata,
-        interpretedResultsPath:
-          to.completedQuery.query.resultsPaths.interpretedResultsPath,
+        interpretedResultsPath: to.completedQuery.query.interpretedResultsPath,
       },
       commonResultSetNames,
     };
@@ -392,12 +389,12 @@ export class CompareView extends AbstractWebview<
       this.getResultSet(
         fromInfo.schemas,
         fromResultSetName,
-        from.completedQuery.query.resultsPaths.resultsPath,
+        from.completedQuery.query.resultsPath,
       ),
       this.getResultSet(
         toInfo.schemas,
         toResultSetName,
-        to.completedQuery.query.resultsPaths.resultsPath,
+        to.completedQuery.query.resultsPath,
       ),
     ]);
 
diff --git a/extensions/ql-vscode/src/compare/interpreted-results.ts b/extensions/ql-vscode/src/compare/interpreted-results.ts
index d5ca255ca4d..f98913a15e8 100644
--- a/extensions/ql-vscode/src/compare/interpreted-results.ts
+++ b/extensions/ql-vscode/src/compare/interpreted-results.ts
@@ -36,11 +36,9 @@ export async function compareInterpretedResults(
 
   const [fromResultSet, toResultSet, sourceLocationPrefix] = await Promise.all([
     getInterpretedResults(
-      fromQuery.completedQuery.query.resultsPaths.interpretedResultsPath,
-    ),
-    getInterpretedResults(
-      toQuery.completedQuery.query.resultsPaths.interpretedResultsPath,
+      fromQuery.completedQuery.query.interpretedResultsPath,
     ),
+    getInterpretedResults(toQuery.completedQuery.query.interpretedResultsPath),
     database.getSourceLocationPrefix(cliServer),
   ]);
 
diff --git a/extensions/ql-vscode/src/config.ts b/extensions/ql-vscode/src/config.ts
index 989e4931bcf..3cc4ec047e0 100644
--- a/extensions/ql-vscode/src/config.ts
+++ b/extensions/ql-vscode/src/config.ts
@@ -954,3 +954,17 @@ export class GitHubDatabaseConfigListener
     await GITHUB_DATABASE_UPDATE.updateValue(value, target);
   }
 }
+
+const AUTOFIX_SETTING = new Setting("autofix", ROOT_SETTING);
+
+export const AUTOFIX_PATH = new Setting("path", AUTOFIX_SETTING);
+
+export function getAutofixPath(): string | undefined {
+  return AUTOFIX_PATH.getValue<string>() || undefined;
+}
+
+export const AUTOFIX_MODEL = new Setting("model", AUTOFIX_SETTING);
+
+export function getAutofixModel(): string | undefined {
+  return AUTOFIX_MODEL.getValue<string>() || undefined;
+}
diff --git a/extensions/ql-vscode/src/databases/local-databases-ui.ts b/extensions/ql-vscode/src/databases/local-databases-ui.ts
index cfc53be40b6..d1ed2147fe7 100644
--- a/extensions/ql-vscode/src/databases/local-databases-ui.ts
+++ b/extensions/ql-vscode/src/databases/local-databases-ui.ts
@@ -284,6 +284,7 @@ export class DatabaseUI extends DisposableObject {
         this.handleUpgradeCurrentDatabase.bind(this),
       "codeQL.clearCache": this.handleClearCache.bind(this),
       "codeQL.trimCache": this.handleTrimCache.bind(this),
+      "codeQL.trimOverlayBaseCache": this.handleTrimOverlayBaseCache.bind(this),
       "codeQLDatabases.chooseDatabaseFolder":
         this.handleChooseDatabaseFolder.bind(this),
       "codeQLDatabases.chooseDatabaseArchive":
@@ -505,7 +506,7 @@ export class DatabaseUI extends DisposableObject {
   ): Promise<void> {
     try {
       await this.chooseAndSetDatabase(false, progress);
-    } catch (e: unknown) {
+    } catch (e) {
       void showAndLogExceptionWithTelemetry(
         this.app.logger,
         this.app.telemetry,
@@ -688,6 +689,25 @@ export class DatabaseUI extends DisposableObject {
     );
   }
 
+  private async handleTrimOverlayBaseCache(): Promise<void> {
+    return withProgress(
+      async () => {
+        if (
+          this.queryServer !== undefined &&
+          this.databaseManager.currentDatabaseItem !== undefined
+        ) {
+          await this.queryServer.trimCacheWithModeInDatabase(
+            this.databaseManager.currentDatabaseItem,
+            "overlay",
+          );
+        }
+      },
+      {
+        title: "Removing all overlay-dependent data from cache",
+      },
+    );
+  }
+
   private async handleGetCurrentDatabase(): Promise<string | undefined> {
     const dbItem = await this.getDatabaseItemInternal(undefined);
     return dbItem?.databaseUri.fsPath;
diff --git a/extensions/ql-vscode/src/databases/local-databases/database-manager.ts b/extensions/ql-vscode/src/databases/local-databases/database-manager.ts
index f820625a5d8..643c601cd3e 100644
--- a/extensions/ql-vscode/src/databases/local-databases/database-manager.ts
+++ b/extensions/ql-vscode/src/databases/local-databases/database-manager.ts
@@ -411,7 +411,7 @@ export class DatabaseManager extends DisposableObject {
         qlpackStoragePath,
       );
       await qlPackGenerator.generate();
-    } catch (e: unknown) {
+    } catch (e) {
       void this.logger.log(
         `Could not create skeleton QL pack: ${getErrorMessage(e)}`,
       );
diff --git a/extensions/ql-vscode/src/databases/ui/db-panel.ts b/extensions/ql-vscode/src/databases/ui/db-panel.ts
index 0605721d3ea..dbc61469d5a 100644
--- a/extensions/ql-vscode/src/databases/ui/db-panel.ts
+++ b/extensions/ql-vscode/src/databases/ui/db-panel.ts
@@ -432,7 +432,7 @@ export class DbPanel extends DisposableObject {
     try {
       // This will also validate that the controller repository is valid
       await getControllerRepo(this.app.credentials);
-    } catch (e: unknown) {
+    } catch (e) {
       if (e instanceof UserCancellationException) {
         return;
       }
diff --git a/extensions/ql-vscode/src/debugger/debug-protocol.ts b/extensions/ql-vscode/src/debugger/debug-protocol.ts
index 44e4fcf3b39..c24d72e412b 100644
--- a/extensions/ql-vscode/src/debugger/debug-protocol.ts
+++ b/extensions/ql-vscode/src/debugger/debug-protocol.ts
@@ -39,6 +39,7 @@ export interface EvaluationCompletedEvent extends Event {
     resultType: QueryResultType;
     message: string | undefined;
     evaluationTime: number;
+    outputBaseName: string;
   };
 }
 
diff --git a/extensions/ql-vscode/src/debugger/debug-session.ts b/extensions/ql-vscode/src/debugger/debug-session.ts
index 1a51df30a30..64100a7831f 100644
--- a/extensions/ql-vscode/src/debugger/debug-session.ts
+++ b/extensions/ql-vscode/src/debugger/debug-session.ts
@@ -16,7 +16,7 @@ import type { BaseLogger, LogOptions } from "../common/logging";
 import { queryServerLogger } from "../common/logging/vscode";
 import { QueryResultType } from "../query-server/messages";
 import type {
-  CoreQueryResults,
+  CoreQueryResult,
   CoreQueryRun,
   QueryRunner,
 } from "../query-server";
@@ -25,6 +25,7 @@ import type * as CodeQLProtocol from "./debug-protocol";
 import type { QuickEvalContext } from "../run-queries-shared";
 import { getErrorMessage } from "../common/helpers-pure";
 import { DisposableObject } from "../common/disposable-object";
+import { basename } from "path";
 
 // More complete implementations of `Event` for certain events, because the classes from
 // `@vscode/debugadapter` make it more difficult to provide some of the message values.
@@ -107,9 +108,9 @@ class EvaluationCompletedEvent
   public readonly event = "codeql-evaluation-completed";
   public readonly body: CodeQLProtocol.EvaluationCompletedEvent["body"];
 
-  constructor(results: CoreQueryResults) {
+  constructor(result: CoreQueryResult) {
     super("codeql-evaluation-completed");
-    this.body = results;
+    this.body = result;
   }
 }
 
@@ -143,6 +144,7 @@ const QUERY_THREAD_NAME = "Evaluation thread";
 class RunningQuery extends DisposableObject {
   private readonly tokenSource = this.push(new CancellationTokenSource());
   public readonly queryRun: CoreQueryRun;
+  private readonly queryPath: string;
 
   public constructor(
     queryRunner: QueryRunner,
@@ -154,21 +156,25 @@ class RunningQuery extends DisposableObject {
   ) {
     super();
 
+    this.queryPath = config.query;
     // Create the query run, which will give us some information about the query even before the
     // evaluation has completed.
     this.queryRun = queryRunner.createQueryRun(
       config.database,
-      {
-        queryPath: config.query,
-        quickEvalPosition: quickEvalContext?.quickEvalPosition,
-        quickEvalCountOnly: quickEvalContext?.quickEvalCount,
-      },
+      [
+        {
+          queryPath: this.queryPath,
+          outputBaseName: "results",
+          quickEvalPosition: quickEvalContext?.quickEvalPosition,
+          quickEvalCountOnly: quickEvalContext?.quickEvalCount,
+        },
+      ],
       true,
       config.additionalPacks,
       config.extensionPacks,
       config.additionalRunQueryArgs,
       queryStorageDir,
-      undefined,
+      basename(config.query),
       undefined,
     );
   }
@@ -208,7 +214,7 @@ class RunningQuery extends DisposableObject {
       progressStart.body.cancellable = true;
       this.sendEvent(progressStart);
       try {
-        return await this.queryRun.evaluate(
+        const completedQuery = await this.queryRun.evaluate(
           (p) => {
             const progressUpdate = new ProgressUpdateEvent(
               this.queryRun.id,
@@ -220,6 +226,14 @@ class RunningQuery extends DisposableObject {
           this.tokenSource.token,
           this.logger,
         );
+        return (
+          completedQuery.results.get(this.queryPath) ?? {
+            resultType: QueryResultType.OTHER_ERROR,
+            message: "Missing query results",
+            evaluationTime: 0,
+            outputBaseName: "unknown",
+          }
+        );
       } finally {
         this.sendEvent(new ProgressEndEvent(this.queryRun.id));
       }
@@ -229,6 +243,7 @@ class RunningQuery extends DisposableObject {
         resultType: QueryResultType.OTHER_ERROR,
         message,
         evaluationTime: 0,
+        outputBaseName: "unknown",
       };
     }
   }
diff --git a/extensions/ql-vscode/src/debugger/debugger-ui.ts b/extensions/ql-vscode/src/debugger/debugger-ui.ts
index 6eb9a2d9fc7..8d401897055 100644
--- a/extensions/ql-vscode/src/debugger/debugger-ui.ts
+++ b/extensions/ql-vscode/src/debugger/debugger-ui.ts
@@ -8,7 +8,7 @@ import { debug, Uri, CancellationTokenSource } from "vscode";
 import type { DebuggerCommands } from "../common/commands";
 import type { DatabaseManager } from "../databases/local-databases";
 import { DisposableObject } from "../common/disposable-object";
-import type { CoreQueryResults } from "../query-server";
+import type { CoreQueryResult } from "../query-server";
 import {
   getQuickEvalContext,
   saveBeforeStart,
@@ -134,8 +134,15 @@ class QLDebugAdapterTracker
     body: EvaluationCompletedEvent["body"],
   ): Promise<void> {
     if (this.localQueryRun !== undefined) {
-      const results: CoreQueryResults = body;
-      await this.localQueryRun.complete(results, (_) => {});
+      const results: CoreQueryResult = body;
+      await this.localQueryRun.complete(
+        {
+          results: new Map<string, CoreQueryResult>([
+            [this.configuration.query, results],
+          ]),
+        },
+        (_) => {},
+      );
       this.localQueryRun = undefined;
     }
   }
diff --git a/extensions/ql-vscode/src/extension.ts b/extensions/ql-vscode/src/extension.ts
index bf9e9be2b3d..b6766f3baff 100644
--- a/extensions/ql-vscode/src/extension.ts
+++ b/extensions/ql-vscode/src/extension.ts
@@ -28,7 +28,6 @@ import {
   CliConfigListener,
   DistributionConfigListener,
   GitHubDatabaseConfigListener,
-  joinOrderWarningThreshold,
   QueryHistoryConfigListener,
   QueryServerConfigListener,
   VariantAnalysisConfigListener,
@@ -102,7 +101,6 @@ import { getPackagingCommands } from "./packaging";
 import { HistoryItemLabelProvider } from "./query-history/history-item-label-provider";
 import { EvalLogViewer } from "./query-evaluation-logging";
 import { SummaryLanguageSupport } from "./log-insights/summary-language-support";
-import { JoinOrderScannerProvider } from "./log-insights/join-order";
 import { LogScannerService } from "./log-insights/log-scanner-service";
 import { VariantAnalysisView } from "./variant-analysis/variant-analysis-view";
 import { VariantAnalysisViewSerializer } from "./variant-analysis/variant-analysis-view-serializer";
@@ -465,6 +463,25 @@ export async function activate(
       );
       unsupportedWarningShown = true;
     });
+
+    // Expose the CodeQL CLI features to the extension context under `codeQL.cliFeatures.*`.
+    let cliFeatures: { [feature: string]: boolean | undefined } = {};
+    codeQlExtension.cliServer.addVersionChangedListener(async (ver) => {
+      for (const feat of Object.keys(cliFeatures)) {
+        cliFeatures[feat] = false;
+      }
+      cliFeatures = {
+        ...cliFeatures,
+        ...(ver?.features ?? {}),
+      };
+      for (const feat of Object.keys(cliFeatures)) {
+        await app.commands.execute(
+          "setContext",
+          `codeQL.cliFeatures.${feat}`,
+          cliFeatures[feat] ?? false,
+        );
+      }
+    });
   }
 
   return codeQlExtension;
@@ -669,7 +686,7 @@ async function installOrUpdateThenTryActivate(
 
   try {
     await prepareCodeTour(app.commands);
-  } catch (e: unknown) {
+  } catch (e) {
     void extLogger.log(
       `Could not open tutorial workspace automatically: ${getErrorMessage(e)}`,
     );
@@ -941,11 +958,6 @@ async function activateWithInstalledDistribution(
   void extLogger.log("Initializing evaluation log scanners.");
   const logScannerService = new LogScannerService(qhm);
   ctx.subscriptions.push(logScannerService);
-  ctx.subscriptions.push(
-    logScannerService.scanners.registerLogScannerProvider(
-      new JoinOrderScannerProvider(() => joinOrderWarningThreshold()),
-    ),
-  );
 
   void extLogger.log("Initializing compare view.");
   const compareView = new CompareView(
diff --git a/extensions/ql-vscode/src/koffi.d.ts b/extensions/ql-vscode/src/koffi.d.ts
new file mode 100644
index 00000000000..48cabce7265
--- /dev/null
+++ b/extensions/ql-vscode/src/koffi.d.ts
@@ -0,0 +1,4 @@
+// koffi/indirect is untyped in the upstream package, but it exports the same functions as koffi.
+declare module "koffi/indirect" {
+  export * from "koffi";
+}
diff --git a/extensions/ql-vscode/src/language-selection-panel/language-selection-data-provider.ts b/extensions/ql-vscode/src/language-selection-panel/language-selection-data-provider.ts
index a182e29595d..fe0fb4c072c 100644
--- a/extensions/ql-vscode/src/language-selection-panel/language-selection-data-provider.ts
+++ b/extensions/ql-vscode/src/language-selection-panel/language-selection-data-provider.ts
@@ -9,6 +9,7 @@ import {
 
 const ALL_LANGUAGE_SELECTION_OPTIONS = [
   undefined, // All languages
+  QueryLanguage.Actions,
   QueryLanguage.Cpp,
   QueryLanguage.CSharp,
   QueryLanguage.Go,
diff --git a/extensions/ql-vscode/src/language-support/ast-viewer/ast-builder.ts b/extensions/ql-vscode/src/language-support/ast-viewer/ast-builder.ts
index fd2203c0615..a8fd32a3276 100644
--- a/extensions/ql-vscode/src/language-support/ast-viewer/ast-builder.ts
+++ b/extensions/ql-vscode/src/language-support/ast-viewer/ast-builder.ts
@@ -7,7 +7,6 @@ import type {
 import type { DatabaseItem } from "../../databases/local-databases";
 import type { ChildAstItem, AstItem } from "./ast-viewer";
 import type { Uri } from "vscode";
-import type { QueryOutputDir } from "../../local-queries/query-output-dir";
 import { fileRangeFromURI } from "../contextual/file-range-from-uri";
 import { mapUrlValue } from "../../common/bqrs-raw-results-mapper";
 
@@ -17,15 +16,12 @@ import { mapUrlValue } from "../../common/bqrs-raw-results-mapper";
  */
 export class AstBuilder {
   private roots: AstItem[] | undefined;
-  private bqrsPath: string;
   constructor(
-    outputDir: QueryOutputDir,
+    private readonly bqrsPath: string,
     private cli: CodeQLCliServer,
     public db: DatabaseItem,
     public fileName: Uri,
-  ) {
-    this.bqrsPath = outputDir.bqrsPath;
-  }
+  ) {}
 
   async getRoots(): Promise<AstItem[]> {
     if (!this.roots) {
diff --git a/extensions/ql-vscode/src/language-support/contextual/location-finder.ts b/extensions/ql-vscode/src/language-support/contextual/location-finder.ts
index 01b8a5bbe76..0d3c25de93d 100644
--- a/extensions/ql-vscode/src/language-support/contextual/location-finder.ts
+++ b/extensions/ql-vscode/src/language-support/contextual/location-finder.ts
@@ -21,7 +21,6 @@ import {
 } from "./query-resolver";
 import type { CancellationToken, LocationLink } from "vscode";
 import { Uri } from "vscode";
-import type { QueryOutputDir } from "../../local-queries/query-output-dir";
 import type { QueryRunner } from "../../query-server";
 import { QueryResultType } from "../../query-server/messages";
 import { fileRangeFromURI } from "./file-range-from-uri";
@@ -84,9 +83,15 @@ export async function getLocationsForUriString(
       token,
       templates,
     );
-    if (results.resultType === QueryResultType.SUCCESS) {
+    const queryResult = results.results.get(query);
+    if (queryResult?.resultType === QueryResultType.SUCCESS) {
       links.push(
-        ...(await getLinksFromResults(results.outputDir, cli, db, filter)),
+        ...(await getLinksFromResults(
+          results.outputDir.getBqrsPath(queryResult.outputBaseName),
+          cli,
+          db,
+          filter,
+        )),
       );
     }
   }
@@ -94,13 +99,12 @@ export async function getLocationsForUriString(
 }
 
 async function getLinksFromResults(
-  outputDir: QueryOutputDir,
+  bqrsPath: string,
   cli: CodeQLCliServer,
   db: DatabaseItem,
   filter: (srcFile: string, destFile: string) => boolean,
 ): Promise<FullLocationLink[]> {
   const localLinks: FullLocationLink[] = [];
-  const bqrsPath = outputDir.bqrsPath;
   const info = await cli.bqrsInfo(bqrsPath);
   const selectInfo = info["result-sets"].find(
     (schema) => schema.name === SELECT_QUERY_NAME,
diff --git a/extensions/ql-vscode/src/language-support/contextual/query-resolver.ts b/extensions/ql-vscode/src/language-support/contextual/query-resolver.ts
index 4624fa6f383..0fe2a08d1fc 100644
--- a/extensions/ql-vscode/src/language-support/contextual/query-resolver.ts
+++ b/extensions/ql-vscode/src/language-support/contextual/query-resolver.ts
@@ -14,6 +14,7 @@ import type { CancellationToken } from "vscode";
 import type { ProgressCallback } from "../../common/vscode/progress";
 import type { CoreCompletedQuery, QueryRunner } from "../../query-server";
 import { createLockFileForStandardQuery } from "../../local-queries/standard-queries";
+import { basename } from "path";
 
 /**
  * This wil try to determine the qlpacks for a given database. If it can't find a matching
@@ -80,13 +81,19 @@ export async function runContextualQuery(
   const { cleanup } = await createLockFileForStandardQuery(cli, query);
   const queryRun = qs.createQueryRun(
     db.databaseUri.fsPath,
-    { queryPath: query, quickEvalPosition: undefined },
+    [
+      {
+        queryPath: query,
+        outputBaseName: "results",
+        quickEvalPosition: undefined,
+      },
+    ],
     false,
     getOnDiskWorkspaceFolders(),
     undefined,
     {},
     queryStorageDir,
-    undefined,
+    basename(query),
     templates,
   );
   void extLogger.log(
diff --git a/extensions/ql-vscode/src/language-support/contextual/template-provider.ts b/extensions/ql-vscode/src/language-support/contextual/template-provider.ts
index 19927bd8903..5fb75379001 100644
--- a/extensions/ql-vscode/src/language-support/contextual/template-provider.ts
+++ b/extensions/ql-vscode/src/language-support/contextual/template-provider.ts
@@ -209,8 +209,14 @@ export class TemplatePrintAstProvider {
       ? await this.cache.get(fileUri.toString(), progress, token)
       : await this.getAst(fileUri.toString(), progress, token);
 
+    const queryResults = Array.from(completedQuery.results.values());
+    if (queryResults.length !== 1) {
+      throw new Error(
+        `Expected exactly one query result, but found ${queryResults.length}.`,
+      );
+    }
     return new AstBuilder(
-      completedQuery.outputDir,
+      completedQuery.outputDir.getBqrsPath(queryResults[0].outputBaseName),
       this.cli,
       this.dbm.findDatabaseItem(Uri.file(completedQuery.dbPath))!,
       fileUri,
diff --git a/extensions/ql-vscode/src/local-queries/local-queries.ts b/extensions/ql-vscode/src/local-queries/local-queries.ts
index 2961586650b..4ada6cf5303 100644
--- a/extensions/ql-vscode/src/local-queries/local-queries.ts
+++ b/extensions/ql-vscode/src/local-queries/local-queries.ts
@@ -19,7 +19,11 @@ import { basename } from "path";
 import { showBinaryChoiceDialog } from "../common/vscode/dialog";
 import { getOnDiskWorkspaceFolders } from "../common/vscode/workspace-folders";
 import { displayQuickQuery } from "./quick-query";
-import type { CoreCompletedQuery, QueryRunner } from "../query-server";
+import type {
+  CoreCompletedQuery,
+  CoreQueryTarget,
+  QueryRunner,
+} from "../query-server";
 import type { QueryHistoryManager } from "../query-history/query-history-manager";
 import type {
   DatabaseQuickPickItem,
@@ -37,6 +41,7 @@ import {
   createTimestampFile,
   getQuickEvalContext,
   saveBeforeStart,
+  validateQuerySuiteUri,
   validateQueryUri,
 } from "../run-queries-shared";
 import type { CompletedLocalQueryInfo } from "../query-results";
@@ -107,6 +112,7 @@ export class LocalQueries extends DisposableObject {
       "codeQL.runQueries": createMultiSelectionCommand(
         this.runQueries.bind(this),
       ),
+      "codeQL.runQuerySuite": this.runQuerySuite.bind(this),
       "codeQL.quickEval": this.quickEval.bind(this),
       "codeQL.quickEvalCount": this.quickEvalCount.bind(this),
       "codeQL.quickEvalContextEditor": this.quickEval.bind(this),
@@ -239,6 +245,94 @@ export class LocalQueries extends DisposableObject {
     );
   }
 
+  private async runQuerySuite(fileUri: Uri): Promise<void> {
+    await withProgress(
+      async (progress, token) => {
+        const suitePath = validateQuerySuiteUri(fileUri);
+        const databaseItem = await this.databaseUI.getDatabaseItem(progress);
+        if (databaseItem === undefined) {
+          throw new Error("Can't run query suite without a selected database");
+        }
+        const selectedQuery: SelectedQuery = {
+          queryPath: suitePath,
+        };
+        const additionalPacks = getOnDiskWorkspaceFolders();
+        const extensionPacks =
+          await this.getDefaultExtensionPacks(additionalPacks);
+        const queries = await this.cliServer.resolveQueriesInSuite(
+          suitePath,
+          additionalPacks,
+        );
+        if (
+          !(await showBinaryChoiceDialog(
+            `You are about to run ${basename(suitePath)}, which contains ${queries.length} queries. Do you want to continue?`,
+          ))
+        ) {
+          return;
+        }
+        const queryTargets: CoreQueryTarget[] = [];
+        queries.forEach((query, index) => {
+          queryTargets.push({
+            queryPath: query,
+            outputBaseName: `${index.toString().padStart(3, "0")}-${basename(query)}`,
+            quickEvalPosition: undefined,
+            quickEvalCountOnly: false,
+          });
+        });
+        const coreQueryRun = this.queryRunner.createQueryRun(
+          databaseItem.databaseUri.fsPath,
+          queryTargets,
+          true,
+          additionalPacks,
+          extensionPacks,
+          {},
+          this.queryStorageDir,
+          basename(suitePath),
+          undefined,
+        );
+        // handle cancellation from the history view.
+        const source = new CancellationTokenSource();
+        try {
+          token.onCancellationRequested(() => source.cancel());
+
+          const localQueryRun = await this.createLocalQueryRun(
+            selectedQuery,
+            databaseItem,
+            coreQueryRun.outputDir,
+            source,
+          );
+
+          try {
+            const results = await coreQueryRun.evaluate(
+              progress,
+              source.token,
+              localQueryRun.logger,
+            );
+
+            await localQueryRun.complete(results, progress);
+
+            return results;
+          } catch (e) {
+            const err = asError(e);
+            await localQueryRun.fail(err);
+
+            if (token.isCancellationRequested) {
+              throw new UserCancellationException(err.message, true);
+            } else {
+              throw e;
+            }
+          }
+        } finally {
+          source.dispose();
+        }
+      },
+      {
+        title: "Running query suite",
+        cancellable: true,
+      },
+    );
+  }
+
   private async quickEval(uri: Uri): Promise<void> {
     await withProgress(
       async (progress, token) => {
@@ -452,17 +546,20 @@ export class LocalQueries extends DisposableObject {
 
     const coreQueryRun = this.queryRunner.createQueryRun(
       databaseItem.databaseUri.fsPath,
-      {
-        queryPath: selectedQuery.queryPath,
-        quickEvalPosition: selectedQuery.quickEval?.quickEvalPosition,
-        quickEvalCountOnly: selectedQuery.quickEval?.quickEvalCount,
-      },
+      [
+        {
+          queryPath: selectedQuery.queryPath,
+          outputBaseName: "results",
+          quickEvalPosition: selectedQuery.quickEval?.quickEvalPosition,
+          quickEvalCountOnly: selectedQuery.quickEval?.quickEvalCount,
+        },
+      ],
       true,
       additionalPacks,
       extensionPacks,
       {},
       this.queryStorageDir,
-      undefined,
+      basename(selectedQuery.queryPath),
       templates,
     );
 
diff --git a/extensions/ql-vscode/src/local-queries/local-query-run.ts b/extensions/ql-vscode/src/local-queries/local-query-run.ts
index 5ea2463caef..cbe151a6601 100644
--- a/extensions/ql-vscode/src/local-queries/local-query-run.ts
+++ b/extensions/ql-vscode/src/local-queries/local-query-run.ts
@@ -4,7 +4,7 @@ import {
   showAndLogExceptionWithTelemetry,
   showAndLogWarningMessage,
 } from "../common/logging";
-import type { CoreQueryResults } from "../query-server";
+import type { CoreQueryResult, CoreQueryResults } from "../query-server";
 import type { QueryHistoryManager } from "../query-history/query-history-manager";
 import type { DatabaseItem } from "../databases/local-databases";
 import type {
@@ -29,7 +29,7 @@ import type { Disposable } from "../common/disposable-object";
 import type { ProgressCallback } from "../common/vscode/progress";
 import { progressUpdate } from "../common/vscode/progress";
 
-function formatResultMessage(result: CoreQueryResults): string {
+function formatResultMessage(result: CoreQueryResult): string {
   switch (result.resultType) {
     case QueryResultType.CANCELLATION:
       return `cancelled after ${Math.round(
@@ -86,7 +86,9 @@ export class LocalQueryRun {
     progress: ProgressCallback,
   ): Promise<void> {
     const evalLogPaths = await this.summarizeEvalLog(
-      results.resultType,
+      Array.from(results.results.values()).every(
+        (result) => result.resultType === QueryResultType.SUCCESS,
+      ),
       this.outputDir,
       this.logger,
       progress,
@@ -95,9 +97,12 @@ export class LocalQueryRun {
       this.queryInfo.setEvaluatorLogPaths(evalLogPaths);
     }
     progress(progressUpdate(1, 4, "Getting completed query info"));
-    const queryWithResults = await this.getCompletedQueryInfo(results);
+    const queriesWithResults = await this.getCompletedQueryInfo(results);
     progress(progressUpdate(2, 4, "Updating query history"));
-    this.queryHistoryManager.completeQuery(this.queryInfo, queryWithResults);
+    this.queryHistoryManager.completeQueries(
+      this.queryInfo,
+      queriesWithResults,
+    );
     progress(progressUpdate(3, 4, "Showing results"));
     await this.localQueries.showResultsForCompletedQuery(
       this.queryInfo as CompletedLocalQueryInfo,
@@ -116,7 +121,7 @@ export class LocalQueryRun {
    */
   public async fail(err: Error): Promise<void> {
     const evalLogPaths = await this.summarizeEvalLog(
-      QueryResultType.OTHER_ERROR,
+      false,
       this.outputDir,
       this.logger,
       (_) => {},
@@ -136,7 +141,7 @@ export class LocalQueryRun {
    * Generate summaries of the structured evaluator log.
    */
   private async summarizeEvalLog(
-    resultType: QueryResultType,
+    runSuccessful: boolean,
     outputDir: QueryOutputDir,
     logger: BaseLogger,
     progress: ProgressCallback,
@@ -152,7 +157,7 @@ export class LocalQueryRun {
       }
     } else {
       // Raw evaluator log was not found. Notify the user, unless we know why it wasn't found.
-      if (resultType === QueryResultType.SUCCESS) {
+      if (runSuccessful) {
         void showAndLogWarningMessage(
           extLogger,
           `Failed to write structured evaluator log to ${outputDir.evalLogPath}.`,
@@ -168,41 +173,43 @@ export class LocalQueryRun {
   }
 
   /**
-   * Gets a `QueryWithResults` containing information about the evaluation of the query and its
+   * Gets a `QueryWithResults` containing information about the evaluation of the queries and their
    * result, in the form expected by the query history UI.
    */
   private async getCompletedQueryInfo(
     results: CoreQueryResults,
-  ): Promise<QueryWithResults> {
-    // Read the query metadata if possible, to use in the UI.
-    const metadata = await tryGetQueryMetadata(
-      this.cliServer,
-      this.queryInfo.initialInfo.queryPath,
-    );
-    const query = new QueryEvaluationInfo(
-      this.outputDir.querySaveDir,
-      this.dbItem.databaseUri.fsPath,
-      await this.dbItem.hasMetadataFile(),
-      this.queryInfo.initialInfo.quickEvalPosition,
-      metadata,
-    );
+  ): Promise<QueryWithResults[]> {
+    const infos: QueryWithResults[] = [];
+    for (const [queryPath, result] of results.results) {
+      // Read the query metadata if possible, to use in the UI.
+      const metadata = await tryGetQueryMetadata(this.cliServer, queryPath);
+      const query = new QueryEvaluationInfo(
+        this.outputDir.querySaveDir,
+        result.outputBaseName,
+        this.dbItem.databaseUri.fsPath,
+        await this.dbItem.hasMetadataFile(),
+        undefined,
+        metadata,
+      );
 
-    if (results.resultType !== QueryResultType.SUCCESS) {
-      const message = results.message
-        ? redactableError`Failed to run query: ${results.message}`
-        : redactableError`Failed to run query`;
-      void showAndLogExceptionWithTelemetry(
-        extLogger,
-        telemetryListener,
+      if (result.resultType !== QueryResultType.SUCCESS) {
+        const message = result.message
+          ? redactableError`Failed to run query: ${result.message}`
+          : redactableError`Failed to run query`;
+        void showAndLogExceptionWithTelemetry(
+          extLogger,
+          telemetryListener,
+          message,
+        );
+      }
+      const message = formatResultMessage(result);
+      const successful = result.resultType === QueryResultType.SUCCESS;
+      infos.push({
+        query,
         message,
-      );
+        successful,
+      });
     }
-    const message = formatResultMessage(results);
-    const successful = results.resultType === QueryResultType.SUCCESS;
-    return {
-      query,
-      message,
-      successful,
-    };
+    return infos;
   }
 }
diff --git a/extensions/ql-vscode/src/local-queries/query-output-dir.ts b/extensions/ql-vscode/src/local-queries/query-output-dir.ts
index a049849d54c..00be58078b7 100644
--- a/extensions/ql-vscode/src/local-queries/query-output-dir.ts
+++ b/extensions/ql-vscode/src/local-queries/query-output-dir.ts
@@ -30,10 +30,6 @@ function findQueryEvalLogEndSummaryFile(resultPath: string): string {
 export class QueryOutputDir {
   constructor(public readonly querySaveDir: string) {}
 
-  get dilPath() {
-    return join(this.querySaveDir, "results.dil");
-  }
-
   /**
    * Get the path that the compiled query is if it exists. Note that it only exists when using the legacy query server.
    */
@@ -41,10 +37,6 @@ export class QueryOutputDir {
     return join(this.querySaveDir, "compiledQuery.qlo");
   }
 
-  get csvPath() {
-    return join(this.querySaveDir, "results.csv");
-  }
-
   get logPath() {
     return findQueryLogFile(this.querySaveDir);
   }
@@ -69,7 +61,25 @@ export class QueryOutputDir {
     return findQueryEvalLogEndSummaryFile(this.querySaveDir);
   }
 
-  get bqrsPath() {
-    return join(this.querySaveDir, "results.bqrs");
+  getBqrsPath(outputBaseName: string): string {
+    return join(this.querySaveDir, `${outputBaseName}.bqrs`);
+  }
+
+  getInterpretedResultsPath(
+    metadataKind: string | undefined,
+    outputBaseName: string,
+  ): string {
+    return join(
+      this.querySaveDir,
+      `${outputBaseName}-${metadataKind === "graph" ? "graph" : `interpreted.sarif`}`,
+    );
+  }
+
+  getCsvPath(outputBaseName: string): string {
+    return join(this.querySaveDir, `${outputBaseName}.csv`);
+  }
+
+  getDilPath(outputBaseName: string): string {
+    return join(this.querySaveDir, `${outputBaseName}.dil`);
   }
 }
diff --git a/extensions/ql-vscode/src/local-queries/results-view.ts b/extensions/ql-vscode/src/local-queries/results-view.ts
index 4e28e9f9c73..00eae1138aa 100644
--- a/extensions/ql-vscode/src/local-queries/results-view.ts
+++ b/extensions/ql-vscode/src/local-queries/results-view.ts
@@ -556,10 +556,14 @@ export class ResultsView extends AbstractWebview<
     await this.postMessage({
       t: "setState",
       interpretation: interpretationPage,
-      origResultsPaths: fullQuery.completedQuery.query.resultsPaths,
+      origResultsPaths: {
+        resultsPath: fullQuery.completedQuery.query.resultsPath,
+        interpretedResultsPath:
+          fullQuery.completedQuery.query.interpretedResultsPath,
+      },
       resultsPath: this.convertPathToWebviewUri(
         panel,
-        fullQuery.completedQuery.query.resultsPaths.resultsPath,
+        fullQuery.completedQuery.query.resultsPath,
       ),
       parsedResultSets,
       sortedResultsMap,
@@ -704,10 +708,14 @@ export class ResultsView extends AbstractWebview<
     await this.postMessage({
       t: "setState",
       interpretation: this._interpretation,
-      origResultsPaths: results.completedQuery.query.resultsPaths,
+      origResultsPaths: {
+        resultsPath: results.completedQuery.query.resultsPath,
+        interpretedResultsPath:
+          results.completedQuery.query.interpretedResultsPath,
+      },
       resultsPath: this.convertPathToWebviewUri(
         panel,
-        results.completedQuery.query.resultsPaths.resultsPath,
+        results.completedQuery.query.resultsPath,
       ),
       parsedResultSets,
       sortedResultsMap,
@@ -842,7 +850,10 @@ export class ResultsView extends AbstractWebview<
               };
         await this._getInterpretedResults(
           query.metadata,
-          query.resultsPaths,
+          {
+            resultsPath: query.resultsPath,
+            interpretedResultsPath: query.interpretedResultsPath,
+          },
           sourceInfo,
           sourceLocationPrefix,
           sortState,
diff --git a/extensions/ql-vscode/src/local-queries/run-query.ts b/extensions/ql-vscode/src/local-queries/run-query.ts
index 1f06c656b56..06ed7037280 100644
--- a/extensions/ql-vscode/src/local-queries/run-query.ts
+++ b/extensions/ql-vscode/src/local-queries/run-query.ts
@@ -33,17 +33,20 @@ export async function runQuery({
   // Create a query run to execute
   const queryRun = queryRunner.createQueryRun(
     databaseItem.databaseUri.fsPath,
-    {
-      queryPath,
-      quickEvalPosition: undefined,
-      quickEvalCountOnly: false,
-    },
+    [
+      {
+        queryPath,
+        outputBaseName: "results",
+        quickEvalPosition: undefined,
+        quickEvalCountOnly: false,
+      },
+    ],
     false,
     additionalPacks,
     extensionPacks,
     {},
     queryStorageDir,
-    undefined,
+    basename(queryPath),
     undefined,
   );
 
@@ -54,13 +57,14 @@ export async function runQuery({
 
   try {
     const completedQuery = await queryRun.evaluate(progress, token, teeLogger);
+    const result = completedQuery.results.get(queryPath);
 
-    if (completedQuery.resultType !== QueryResultType.SUCCESS) {
+    if (result?.resultType !== QueryResultType.SUCCESS) {
       void showAndLogExceptionWithTelemetry(
         extLogger,
         telemetryListener,
         redactableError`Failed to run ${basename(queryPath)} query: ${
-          completedQuery.message ?? "No message"
+          result?.message ?? "No message"
         }`,
       );
       return;
diff --git a/extensions/ql-vscode/src/local-queries/skeleton-query-wizard.ts b/extensions/ql-vscode/src/local-queries/skeleton-query-wizard.ts
index 49d7bcaab11..f99eb8d2fda 100644
--- a/extensions/ql-vscode/src/local-queries/skeleton-query-wizard.ts
+++ b/extensions/ql-vscode/src/local-queries/skeleton-query-wizard.ts
@@ -38,6 +38,7 @@ import { getQlPackLanguage } from "../common/qlpack-language";
 type QueryLanguagesToDatabaseMap = Record<string, string>;
 
 export const QUERY_LANGUAGE_TO_DATABASE_REPO: QueryLanguagesToDatabaseMap = {
+  actions: "github/codeql",
   cpp: "google/brotli",
   csharp: "restsharp/RestSharp",
   go: "spf13/cobra",
@@ -131,7 +132,7 @@ export class SkeletonQueryWizard {
     // open the query file
     try {
       await this.openExampleFile();
-    } catch (e: unknown) {
+    } catch (e) {
       void this.app.logger.log(
         `Could not open example query file: ${getErrorMessage(e)}`,
       );
@@ -278,7 +279,7 @@ export class SkeletonQueryWizard {
       const qlPackGenerator = this.createQlPackGenerator();
 
       await qlPackGenerator.generate();
-    } catch (e: unknown) {
+    } catch (e) {
       void this.app.logger.log(
         `Could not create skeleton QL pack: ${getErrorMessage(e)}`,
       );
@@ -298,7 +299,7 @@ export class SkeletonQueryWizard {
 
       this.fileName = await this.determineNextFileName();
       await qlPackGenerator.createExampleQlFile(this.fileName);
-    } catch (e: unknown) {
+    } catch (e) {
       void this.app.logger.log(
         `Could not create query example file: ${getErrorMessage(e)}`,
       );
@@ -341,7 +342,7 @@ export class SkeletonQueryWizard {
       void withProgress(async (progress) => {
         try {
           await this.downloadDatabase(progress);
-        } catch (e: unknown) {
+        } catch (e) {
           if (e instanceof UserCancellationException) {
             return;
           }
diff --git a/extensions/ql-vscode/src/log-insights/join-order.ts b/extensions/ql-vscode/src/log-insights/join-order.ts
index 788da0a98e6..ce10487caf6 100644
--- a/extensions/ql-vscode/src/log-insights/join-order.ts
+++ b/extensions/ql-vscode/src/log-insights/join-order.ts
@@ -1,8 +1,5 @@
-import type {
-  EvaluationLogProblemReporter,
-  EvaluationLogScanner,
-  EvaluationLogScannerProvider,
-} from "./log-scanner";
+import { readJsonlFile } from "../common/jsonl-reader";
+import type { EvaluationLogProblemReporter } from "./log-scanner";
 import type {
   InLayer,
   ComputeRecursive,
@@ -19,23 +16,6 @@ function safeMax(it?: Iterable<number>) {
   return Number.isFinite(m) ? m : 0;
 }
 
-/**
- * Compute a key for the maps that that is sent to report generation.
- * Should only be used on events that are known to define queryCausingWork.
- */
-function makeKey(
-  queryCausingWork: string | undefined,
-  predicate: string,
-  suffix = "",
-): string {
-  if (queryCausingWork === undefined) {
-    throw new Error(
-      "queryCausingWork was not defined on an event we expected it to be defined for!",
-    );
-  }
-  return `${queryCausingWork}:${predicate}${suffix ? ` ${suffix}` : ""}`;
-}
-
 function getDependentPredicates(operations: string[]): string[] {
   const id = String.raw`[0-9a-zA-Z:#_\./]+`;
   const idWithAngleBrackets = String.raw`[0-9a-zA-Z:#_<>\./]+`;
@@ -128,14 +108,6 @@ function pointwiseSum(
   return result;
 }
 
-function pushValue<K, V>(m: Map<K, V[]>, k: K, v: V) {
-  if (!m.has(k)) {
-    m.set(k, []);
-  }
-  m.get(k)!.push(v);
-  return m;
-}
-
 function computeJoinOrderBadness(
   maxTupleCount: number,
   maxDependentPredicateSize: number,
@@ -154,41 +126,18 @@ interface Bucket {
   dependentPredicateSizes: Map<string, number>;
 }
 
-class JoinOrderScanner implements EvaluationLogScanner {
+class PredicateSizeScanner {
   // Map a predicate hash to its result size
-  private readonly predicateSizes = new Map<string, number>();
-  private readonly layerEvents = new Map<
-    string,
-    Array<ComputeRecursive | InLayer>
-  >();
-  // Map a key of the form 'query-with-demand : predicate name' to its badness input.
-  private readonly maxTupleCountMap = new Map<string, number[]>();
-  private readonly resultSizeMap = new Map<string, number[]>();
-  private readonly maxDependentPredicateSizeMap = new Map<string, number[]>();
-  private readonly joinOrderMetricMap = new Map<string, number>();
-
-  constructor(
-    private readonly problemReporter: EvaluationLogProblemReporter,
-    private readonly warningThreshold: number,
-  ) {}
+  readonly predicateSizes = new Map<string, number>();
+  readonly layerEvents = new Map<string, Array<ComputeRecursive | InLayer>>();
 
-  public onEvent(event: SummaryEvent): void {
+  onEvent(event: SummaryEvent): void {
     if (
       event.completionType !== undefined &&
       event.completionType !== "SUCCESS"
     ) {
       return; // Skip any evaluation that wasn't successful
     }
-
-    this.recordPredicateSizes(event);
-    this.computeBadnessMetric(event);
-  }
-
-  public onDone(): void {
-    void this;
-  }
-
-  private recordPredicateSizes(event: SummaryEvent): void {
     switch (event.evaluationStrategy) {
       case "EXTENSIONAL":
       case "COMPUTED_EXTENSIONAL":
@@ -215,29 +164,20 @@ class JoinOrderScanner implements EvaluationLogScanner {
       }
     }
   }
+}
 
-  private reportProblemIfNecessary(
-    event: SummaryEvent,
-    iteration: number,
-    metric: number,
-  ): void {
-    if (metric >= this.warningThreshold) {
-      this.problemReporter.reportProblem(
-        event.predicateName,
-        event.raHash,
-        iteration,
-        `Relation '${
-          event.predicateName
-        }' has an inefficient join order. Its join order metric is ${metric.toFixed(
-          2,
-        )}, which is larger than the threshold of ${this.warningThreshold.toFixed(
-          2,
-        )}.`,
-      );
-    }
-  }
+class JoinOrderScanner {
+  constructor(
+    private readonly predicateSizes: Map<string, number>,
+    private readonly layerEvents: Map<
+      string,
+      Array<ComputeRecursive | InLayer>
+    >,
+    private readonly problemReporter: EvaluationLogProblemReporter,
+    private readonly warningThreshold: number,
+  ) {}
 
-  private computeBadnessMetric(event: SummaryEvent): void {
+  public onEvent(event: SummaryEvent): void {
     if (
       event.completionType !== undefined &&
       event.completionType !== "SUCCESS"
@@ -252,7 +192,6 @@ class JoinOrderScanner implements EvaluationLogScanner {
         }
         // Compute the badness metric for a non-recursive predicate. The metric in this case is defined as:
         // badness = (max tuple count in the pipeline) / (largest predicate this pipeline depends on)
-        const key = makeKey(event.queryCausingWork, event.predicateName);
         const resultSize = event.resultSize;
 
         // There is only one entry in `pipelineRuns` if it's a non-recursive predicate.
@@ -260,20 +199,26 @@ class JoinOrderScanner implements EvaluationLogScanner {
           this.badnessInputsForNonRecursiveDelta(event.pipelineRuns[0], event);
 
         if (maxDependentPredicateSize > 0) {
-          pushValue(this.maxTupleCountMap, key, maxTupleCount);
-          pushValue(this.resultSizeMap, key, resultSize);
-          pushValue(
-            this.maxDependentPredicateSizeMap,
-            key,
-            maxDependentPredicateSize,
-          );
           const metric = computeJoinOrderBadness(
             maxTupleCount,
             maxDependentPredicateSize,
             resultSize!,
           );
-          this.joinOrderMetricMap.set(key, metric);
-          this.reportProblemIfNecessary(event, 0, metric);
+          if (metric >= this.warningThreshold) {
+            const message = `'${event.predicateName}@${event.raHash.substring(
+              0,
+              8,
+            )}' has an inefficient join order. Its join order metric is ${metric.toFixed(
+              2,
+            )}, which is larger than the threshold of ${this.warningThreshold.toFixed(
+              2,
+            )}.`;
+            this.problemReporter.reportProblemNonRecursive(
+              event.predicateName,
+              event.raHash,
+              message,
+            );
+          }
         }
         break;
       }
@@ -282,39 +227,40 @@ class JoinOrderScanner implements EvaluationLogScanner {
         // Compute the badness metric for a recursive predicate for each ordering.
         const sccMetricInput = this.badnessInputsForRecursiveDelta(event);
         // Loop through each predicate in the SCC
-        sccMetricInput.forEach((buckets, predicate) => {
-          // Loop through each ordering of the predicate
-          buckets.forEach((bucket, raReference) => {
-            // Format the key as demanding-query:name (ordering)
-            const key = makeKey(
-              event.queryCausingWork,
-              predicate,
-              `(${raReference})`,
-            );
-            const maxTupleCount = Math.max(...bucket.tupleCounts);
-            const resultSize = bucket.resultSize;
-            const maxDependentPredicateSize = Math.max(
-              ...bucket.dependentPredicateSizes.values(),
-            );
-
-            if (maxDependentPredicateSize > 0) {
-              pushValue(this.maxTupleCountMap, key, maxTupleCount);
-              pushValue(this.resultSizeMap, key, resultSize);
-              pushValue(
-                this.maxDependentPredicateSizeMap,
-                key,
-                maxDependentPredicateSize,
-              );
-              const metric = computeJoinOrderBadness(
-                maxTupleCount,
-                maxDependentPredicateSize,
-                resultSize,
+        sccMetricInput.forEach((hashToOrderToBucket, predicateName) => {
+          hashToOrderToBucket.forEach((orderToBucket, raHash) => {
+            // Loop through each ordering of the predicate.
+            orderToBucket.forEach((bucket, raReference) => {
+              const maxDependentPredicateSize = Math.max(
+                ...bucket.dependentPredicateSizes.values(),
               );
-              const oldMetric = this.joinOrderMetricMap.get(key);
-              if (oldMetric === undefined || metric > oldMetric) {
-                this.joinOrderMetricMap.set(key, metric);
+
+              if (maxDependentPredicateSize > 0) {
+                const maxTupleCount = Math.max(...bucket.tupleCounts);
+                const resultSize = bucket.resultSize;
+                const metric = computeJoinOrderBadness(
+                  maxTupleCount,
+                  maxDependentPredicateSize,
+                  resultSize,
+                );
+                if (metric >= this.warningThreshold) {
+                  const message = `The ${raReference} pipeline for '${predicateName}@${raHash.substring(
+                    0,
+                    8,
+                  )}' has an inefficient join order. Its join order metric is ${metric.toFixed(
+                    2,
+                  )}, which is larger than the threshold of ${this.warningThreshold.toFixed(
+                    2,
+                  )}.`;
+                  this.problemReporter.reportProblemForRecursionSummary(
+                    predicateName,
+                    raHash,
+                    raReference,
+                    message,
+                  );
+                }
               }
-            }
+            });
           });
         });
         break;
@@ -457,20 +403,28 @@ class JoinOrderScanner implements EvaluationLogScanner {
    */
   private badnessInputsForRecursiveDelta(
     event: ComputeRecursive,
-  ): Map<string, Map<string, Bucket>> {
-    // nameToOrderToBucket : predicate name -> ordering (i.e., standard, order_500000, etc.) -> bucket
-    const nameToOrderToBucket = new Map<string, Map<string, Bucket>>();
+  ): Map<string, Map<string, Map<string, Bucket>>> {
+    // nameToHashToOrderToBucket : predicate name -> RA hash -> ordering (i.e., standard, order_500000, etc.) -> bucket
+    const nameToHashToOrderToBucket = new Map<
+      string,
+      Map<string, Map<string, Bucket>>
+    >();
 
     // Iterate through the SCC and compute the metric inputs
     this.iterateSCC(event, (inLayerEvent, run, iteration) => {
       const raReference = run.raReference;
       const predicateName = inLayerEvent.predicateName;
-      if (!nameToOrderToBucket.has(predicateName)) {
-        nameToOrderToBucket.set(predicateName, new Map());
+      if (!nameToHashToOrderToBucket.has(predicateName)) {
+        nameToHashToOrderToBucket.set(predicateName, new Map());
       }
-      const orderTobucket = nameToOrderToBucket.get(predicateName)!;
-      if (!orderTobucket.has(raReference)) {
-        orderTobucket.set(raReference, {
+      const hashToOrderToBucket = nameToHashToOrderToBucket.get(predicateName)!;
+      const raHash = inLayerEvent.raHash;
+      if (!hashToOrderToBucket.has(raHash)) {
+        hashToOrderToBucket.set(raHash, new Map());
+      }
+      const orderToBucket = hashToOrderToBucket.get(raHash)!;
+      if (!orderToBucket.has(raReference)) {
+        orderToBucket.set(raReference, {
           tupleCounts: new Int32Array(0),
           resultSize: 0,
           dependentPredicateSizes: new Map(),
@@ -484,7 +438,7 @@ class JoinOrderScanner implements EvaluationLogScanner {
         iteration,
       );
 
-      const bucket = orderTobucket.get(raReference)!;
+      const bucket = orderToBucket.get(raReference)!;
       // Pointwise sum the tuple counts
       const newTupleCounts = pointwiseSum(
         bucket.tupleCounts,
@@ -504,23 +458,36 @@ class JoinOrderScanner implements EvaluationLogScanner {
         );
       }
 
-      orderTobucket.set(raReference, {
+      orderToBucket.set(raReference, {
         tupleCounts: newTupleCounts,
         resultSize,
         dependentPredicateSizes: newDependentPredicateSizes,
       });
     });
-    return nameToOrderToBucket;
+    return nameToHashToOrderToBucket;
   }
 }
 
-export class JoinOrderScannerProvider implements EvaluationLogScannerProvider {
-  constructor(private readonly getThreshdold: () => number) {}
+export async function scanAndReportJoinOrderProblems(
+  jsonSummaryLocation: string,
+  problemReporter: EvaluationLogProblemReporter,
+  warningThreshold: number,
+) {
+  // Do two passes over the summary JSON. The first pass collects the sizes of predicates, along
+  // with collecting layer events for each recursive SCC.
+  const predicateSizeScanner = new PredicateSizeScanner();
+  await readJsonlFile<SummaryEvent>(jsonSummaryLocation, async (obj) => {
+    predicateSizeScanner.onEvent(obj);
+  });
 
-  public createScanner(
-    problemReporter: EvaluationLogProblemReporter,
-  ): EvaluationLogScanner {
-    const threshold = this.getThreshdold();
-    return new JoinOrderScanner(problemReporter, threshold);
-  }
+  // The second pass takes the information from the first pass, computes join order scores, and reports those that exceed the threshold.
+  const joinOrderScanner = new JoinOrderScanner(
+    predicateSizeScanner.predicateSizes,
+    predicateSizeScanner.layerEvents,
+    problemReporter,
+    warningThreshold,
+  );
+  await readJsonlFile<SummaryEvent>(jsonSummaryLocation, async (obj) => {
+    joinOrderScanner.onEvent(obj);
+  });
 }
diff --git a/extensions/ql-vscode/src/log-insights/log-scanner-service.ts b/extensions/ql-vscode/src/log-insights/log-scanner-service.ts
index 3d78bb30aa8..e8e79d60bc5 100644
--- a/extensions/ql-vscode/src/log-insights/log-scanner-service.ts
+++ b/extensions/ql-vscode/src/log-insights/log-scanner-service.ts
@@ -2,11 +2,12 @@ import { Diagnostic, DiagnosticSeverity, languages, Range, Uri } from "vscode";
 import { DisposableObject } from "../common/disposable-object";
 import type { QueryHistoryInfo } from "../query-history/query-history-info";
 import type { EvaluationLogProblemReporter } from "./log-scanner";
-import { EvaluationLogScannerSet } from "./log-scanner";
 import type { PipelineInfo, SummarySymbols } from "./summary-parser";
 import { readFile } from "fs-extra";
 import { extLogger } from "../common/logging/vscode";
 import type { QueryHistoryManager } from "../query-history/query-history-manager";
+import { scanAndReportJoinOrderProblems } from "./join-order";
+import { joinOrderWarningThreshold } from "../config";
 
 /**
  * Compute the key used to find a predicate in the summary symbols.
@@ -28,17 +29,41 @@ class ProblemReporter implements EvaluationLogProblemReporter {
 
   constructor(private readonly symbols: SummarySymbols | undefined) {}
 
-  public reportProblem(
+  public reportProblemNonRecursive(
     predicateName: string,
     raHash: string,
-    iteration: number,
     message: string,
   ): void {
     const nameWithHash = predicateSymbolKey(predicateName, raHash);
     const predicateSymbol = this.symbols?.predicates[nameWithHash];
     let predicateInfo: PipelineInfo | undefined = undefined;
     if (predicateSymbol !== undefined) {
-      predicateInfo = predicateSymbol.iterations[iteration];
+      predicateInfo = predicateSymbol.iterations[0];
+    }
+    if (predicateInfo !== undefined) {
+      const range = new Range(
+        predicateInfo.raStartLine,
+        0,
+        predicateInfo.raEndLine + 1,
+        0,
+      );
+      this.diagnostics.push(
+        new Diagnostic(range, message, DiagnosticSeverity.Error),
+      );
+    }
+  }
+
+  public reportProblemForRecursionSummary(
+    predicateName: string,
+    raHash: string,
+    order: string,
+    message: string,
+  ): void {
+    const nameWithHash = predicateSymbolKey(predicateName, raHash);
+    const predicateSymbol = this.symbols?.predicates[nameWithHash];
+    let predicateInfo: PipelineInfo | undefined = undefined;
+    if (predicateSymbol !== undefined) {
+      predicateInfo = predicateSymbol.recursionSummaries[order];
     }
     if (predicateInfo !== undefined) {
       const range = new Range(
@@ -59,7 +84,6 @@ class ProblemReporter implements EvaluationLogProblemReporter {
 }
 
 export class LogScannerService extends DisposableObject {
-  public readonly scanners = new EvaluationLogScannerSet();
   private readonly diagnosticCollection = this.push(
     languages.createDiagnosticCollection("ql-eval-log"),
   );
@@ -127,9 +151,11 @@ export class LogScannerService extends DisposableObject {
       );
     }
     const problemReporter = new ProblemReporter(symbols);
-
-    await this.scanners.scanLog(jsonSummaryLocation, problemReporter);
-
+    await scanAndReportJoinOrderProblems(
+      jsonSummaryLocation,
+      problemReporter,
+      joinOrderWarningThreshold(),
+    );
     return problemReporter.diagnostics;
   }
 }
diff --git a/extensions/ql-vscode/src/log-insights/log-scanner.ts b/extensions/ql-vscode/src/log-insights/log-scanner.ts
index 0ad775e6ec1..22a9a5cdf78 100644
--- a/extensions/ql-vscode/src/log-insights/log-scanner.ts
+++ b/extensions/ql-vscode/src/log-insights/log-scanner.ts
@@ -1,139 +1,38 @@
-import type { Disposable } from "../common/disposable-object";
-import { readJsonlFile } from "../common/jsonl-reader";
-import type { ProgressCallback } from "../common/vscode/progress";
-import type { SummaryEvent } from "./log-summary";
-
 /**
  * Callback interface used to report diagnostics from a log scanner.
  */
 export interface EvaluationLogProblemReporter {
   /**
-   * Report a potential problem detected in the evaluation log.
+   * Report a potential problem detected in the evaluation log for a non-recursive predicate.
    *
    * @param predicateName The mangled name of the predicate with the problem.
    * @param raHash The RA hash of the predicate with the problem.
-   * @param iteration The iteration number with the problem. For a non-recursive predicate, this
-   * must be zero.
    * @param message The problem message.
    */
-  reportProblem(
+  reportProblemNonRecursive(
     predicateName: string,
     raHash: string,
-    iteration: number,
     message: string,
   ): void;
 
   /**
-   * Log a message about a problem in the implementation of the scanner. These will typically be
-   * displayed separate from any problems reported via `reportProblem()`.
-   */
-  log(message: string): void;
-}
-
-/**
- * Interface implemented by a log scanner. Instances are created via
- * `EvaluationLogScannerProvider.createScanner()`.
- */
-export interface EvaluationLogScanner {
-  /**
-   * Called for each event in the log summary, in order. The implementation can report problems via
-   * the `EvaluationLogProblemReporter` interface that was supplied to `createScanner()`.
-   * @param event The log summary event.
-   */
-  onEvent(event: SummaryEvent): void;
-  /**
-   * Called after all events in the log summary have been processed. The implementation can report
-   * problems via the `EvaluationLogProblemReporter` interface that was supplied to
-   * `createScanner()`.
-   */
-  onDone(): void;
-}
-
-/**
- * A factory for log scanners. When a log is to be scanned, all registered
- * `EvaluationLogScannerProviders` will be asked to create a new instance of `EvaluationLogScanner`
- * to do the scanning.
- */
-export interface EvaluationLogScannerProvider {
-  /**
-   * Create a new instance of `EvaluationLogScanner` to scan a single summary log.
-   * @param problemReporter Callback interface for reporting any problems discovered.
-   */
-  createScanner(
-    problemReporter: EvaluationLogProblemReporter,
-  ): EvaluationLogScanner;
-}
-
-export class EvaluationLogScannerSet {
-  private readonly scannerProviders = new Map<
-    number,
-    EvaluationLogScannerProvider
-  >();
-  private nextScannerProviderId = 0;
-
-  /**
-   * Register a provider that can create instances of `EvaluationLogScanner` to scan evaluation logs
-   * for problems.
-   * @param provider The provider.
-   * @returns A `Disposable` that, when disposed, will unregister the provider.
+   * Report a potential problem detected in the evaluation log for the summary of a recursive pipeline.
+   *
+   * @param predicateName The mangled name of the predicate with the problem.
+   * @param raHash The RA hash of the predicate with the problem.
+   * @param order The particular order (pipeline name) that had the problem.
+   * @param message The problem message.
    */
-  public registerLogScannerProvider(
-    provider: EvaluationLogScannerProvider,
-  ): Disposable {
-    const id = this.nextScannerProviderId;
-    this.nextScannerProviderId++;
-
-    this.scannerProviders.set(id, provider);
-    return {
-      dispose: () => {
-        this.scannerProviders.delete(id);
-      },
-    };
-  }
+  reportProblemForRecursionSummary(
+    predicateName: string,
+    raHash: string,
+    order: string,
+    message: string,
+  ): void;
 
   /**
-   * Scan the evaluator summary log for problems, using the scanners for all registered providers.
-   * @param jsonSummaryLocation The file path of the JSON summary log.
-   * @param problemReporter Callback interface for reporting any problems discovered.
+   * Log a message about a problem in the implementation of the scanner. These will typically be
+   * displayed separate from any problems reported via `reportProblem()`.
    */
-  public async scanLog(
-    jsonSummaryLocation: string,
-    problemReporter: EvaluationLogProblemReporter,
-  ): Promise<void> {
-    const scanners = [...this.scannerProviders.values()].map((p) =>
-      p.createScanner(problemReporter),
-    );
-
-    await readJsonlFile<SummaryEvent>(jsonSummaryLocation, async (obj) => {
-      scanners.forEach((scanner) => {
-        scanner.onEvent(obj);
-      });
-    });
-
-    scanners.forEach((scanner) => scanner.onDone());
-  }
-}
-
-/**
- * Scan the evaluator summary log using the given scanner. For convenience, returns the scanner.
- *
- * @param jsonSummaryLocation The file path of the JSON summary log.
- * @param scanner The scanner to process events from the log
- */
-export async function scanLog<T extends EvaluationLogScanner>(
-  jsonSummaryLocation: string,
-  scanner: T,
-  progress?: ProgressCallback,
-): Promise<T> {
-  progress?.({
-    // all scans have step 1 - the backing progress tracker allows increments instead of steps - but for now we are happy with a tiny UI that says what is happening
-    message: `Scanning ...`,
-    step: 1,
-    maxStep: 2,
-  });
-  await readJsonlFile<SummaryEvent>(jsonSummaryLocation, async (obj) => {
-    scanner.onEvent(obj);
-  });
-  scanner.onDone();
-  return scanner;
+  log(message: string): void;
 }
diff --git a/extensions/ql-vscode/src/log-insights/log-summary.ts b/extensions/ql-vscode/src/log-insights/log-summary.ts
index 5fa4bda58b8..6919210f98c 100644
--- a/extensions/ql-vscode/src/log-insights/log-summary.ts
+++ b/extensions/ql-vscode/src/log-insights/log-summary.ts
@@ -16,7 +16,8 @@ type EvaluationStrategy =
   | "EXTENSIONAL"
   | "SENTINEL_EMPTY"
   | "CACHACA"
-  | "CACHE_HIT";
+  | "CACHE_HIT"
+  | "NAMED_LOCAL";
 
 interface SummaryEventBase {
   evaluationStrategy: EvaluationStrategy;
@@ -28,6 +29,8 @@ interface SummaryEventBase {
 
 interface ResultEventBase extends SummaryEventBase {
   resultSize: number;
+  dependencies?: { [key: string]: string };
+  mainHash?: string;
 }
 
 export interface ComputeSimple extends ResultEventBase {
@@ -60,6 +63,15 @@ export interface InLayer extends ResultEventBase {
   predicateIterationMillis: number[];
 }
 
+interface NamedLocal extends ResultEventBase {
+  evaluationStrategy: "NAMED_LOCAL";
+  deltaSizes: number[];
+  ra: Ra;
+  pipelineRuns: PipelineRun[];
+  queryCausingWork?: string;
+  predicateIterationMillis: number[];
+}
+
 interface ComputedExtensional extends ResultEventBase {
   evaluationStrategy: "COMPUTED_EXTENSIONAL";
   queryCausingWork?: string;
@@ -92,4 +104,5 @@ export type SummaryEvent =
   | Extensional
   | SentinelEmpty
   | Cachaca
-  | CacheHit;
+  | CacheHit
+  | NamedLocal;
diff --git a/extensions/ql-vscode/src/log-insights/performance-comparison.ts b/extensions/ql-vscode/src/log-insights/performance-comparison.ts
index 46634cf8bf3..7dfb516b9c3 100644
--- a/extensions/ql-vscode/src/log-insights/performance-comparison.ts
+++ b/extensions/ql-vscode/src/log-insights/performance-comparison.ts
@@ -1,10 +1,11 @@
-import type { EvaluationLogScanner } from "./log-scanner";
+import { createHash } from "crypto";
 import type { SummaryEvent } from "./log-summary";
 
 export interface PipelineSummary {
   steps: string[];
   /** Total counts for each step in the RA array, across all iterations */
   counts: number[];
+  hash: string;
 }
 
 /**
@@ -27,6 +28,9 @@ export interface PerformanceComparisonDataFromLog {
    */
   names: string[];
 
+  /** RA hash of the `i`th predicate event */
+  raHashes: string[];
+
   /** Number of milliseconds spent evaluating the `i`th predicate from the `names` array. */
   timeCosts: number[];
 
@@ -53,12 +57,15 @@ export interface PerformanceComparisonDataFromLog {
    * All the pipeline runs seen for the `i`th predicate from the `names` array.
    */
   pipelineSummaryList: Array<Record<string, PipelineSummary>>;
+
+  /** All dependencies of the `i`th predicate from the `names` array, encoded as a list of indices in `names`. */
+  dependencyLists: number[][];
 }
 
-export class PerformanceOverviewScanner implements EvaluationLogScanner {
-  private readonly nameToIndex = new Map<string, number>();
+export class PerformanceOverviewScanner {
   private readonly data: PerformanceComparisonDataFromLog = {
     names: [],
+    raHashes: [],
     timeCosts: [],
     tupleCosts: [],
     cacheHitIndices: [],
@@ -66,28 +73,35 @@ export class PerformanceOverviewScanner implements EvaluationLogScanner {
     pipelineSummaryList: [],
     evaluationCounts: [],
     iterationCounts: [],
+    dependencyLists: [],
   };
+  private readonly raToIndex = new Map<string, number>();
+  private readonly mainHashToRepr = new Map<string, number>();
+  private readonly nameToIndex = new Map<string, number>();
 
-  private getPredicateIndex(name: string): number {
-    const { nameToIndex } = this;
-    let index = nameToIndex.get(name);
+  private getPredicateIndex(name: string, ra: string): number {
+    let index = this.raToIndex.get(ra);
     if (index === undefined) {
-      index = nameToIndex.size;
-      nameToIndex.set(name, index);
+      index = this.raToIndex.size;
+      this.raToIndex.set(ra, index);
       const {
         names,
+        raHashes,
         timeCosts,
         tupleCosts,
         iterationCounts,
         evaluationCounts,
         pipelineSummaryList,
+        dependencyLists,
       } = this.data;
       names.push(name);
+      raHashes.push(ra);
       timeCosts.push(0);
       tupleCosts.push(0);
       iterationCounts.push(0);
       evaluationCounts.push(0);
       pipelineSummaryList.push({});
+      dependencyLists.push([]);
     }
     return index;
   }
@@ -97,46 +111,63 @@ export class PerformanceOverviewScanner implements EvaluationLogScanner {
   }
 
   onEvent(event: SummaryEvent): void {
-    if (
-      event.completionType !== undefined &&
-      event.completionType !== "SUCCESS"
-    ) {
+    const { completionType, evaluationStrategy, predicateName, raHash } = event;
+    if (completionType !== undefined && completionType !== "SUCCESS") {
       return; // Skip any evaluation that wasn't successful
     }
 
-    switch (event.evaluationStrategy) {
-      case "EXTENSIONAL":
+    switch (evaluationStrategy) {
+      case "EXTENSIONAL": {
+        break;
+      }
       case "COMPUTED_EXTENSIONAL": {
+        if (predicateName.startsWith("cached_")) {
+          // Add a dependency from a cached COMPUTED_EXTENSIONAL to the predicate with the actual contents.
+          // The raHash of the this event may appear in a CACHE_HIT event in the other event log. The dependency
+          // we're adding here is needed in order to associate the original predicate with such a cache hit.
+          const originalName = predicateName.substring("cached_".length);
+          const originalIndex = this.nameToIndex.get(originalName);
+          if (originalIndex != null) {
+            const index = this.getPredicateIndex(predicateName, raHash);
+            this.data.dependencyLists[index].push(originalIndex);
+          }
+        }
         break;
       }
       case "CACHE_HIT":
       case "CACHACA": {
         // Record a cache hit, but only if the predicate has not been seen before.
         // We're mainly interested in the reuse of caches from an earlier query run as they can distort comparisons.
-        if (!this.nameToIndex.has(event.predicateName)) {
+        if (!this.raToIndex.has(raHash)) {
           this.data.cacheHitIndices.push(
-            this.getPredicateIndex(event.predicateName),
+            this.getPredicateIndex(predicateName, raHash),
           );
         }
         break;
       }
       case "SENTINEL_EMPTY": {
-        this.data.sentinelEmptyIndices.push(
-          this.getPredicateIndex(event.predicateName),
-        );
+        const index = this.getPredicateIndex(predicateName, raHash);
+        this.data.sentinelEmptyIndices.push(index);
+        const sentinelIndex = this.raToIndex.get(event.sentinelRaHash);
+        if (sentinelIndex != null) {
+          this.data.dependencyLists[index].push(sentinelIndex); // needed for matching up cache hits
+        }
         break;
       }
       case "COMPUTE_RECURSIVE":
       case "COMPUTE_SIMPLE":
+      case "NAMED_LOCAL":
       case "IN_LAYER": {
-        const index = this.getPredicateIndex(event.predicateName);
+        const index = this.getPredicateIndex(predicateName, raHash);
+        this.nameToIndex.set(predicateName, index);
         let totalTime = 0;
         let totalTuples = 0;
-        if (event.evaluationStrategy !== "IN_LAYER") {
+        if (evaluationStrategy === "COMPUTE_SIMPLE") {
           totalTime += event.millis;
         } else {
-          // IN_LAYER events do no record of their total time.
-          // Make a best-effort estimate by adding up the positive iteration times (they can be negative).
+          // Make a best-effort estimate of the total time by adding up the positive iteration times (they can be negative).
+          // Note that for COMPUTE_RECURSIVE the "millis" field contain the total time of the SCC, not just that predicate,
+          // but we don't have a good way to show that in the UI, so we rely on the accumulated iteration times.
           for (const millis of event.predicateIterationMillis ?? []) {
             if (millis > 0) {
               totalTime += millis;
@@ -149,13 +180,16 @@ export class PerformanceOverviewScanner implements EvaluationLogScanner {
           iterationCounts,
           evaluationCounts,
           pipelineSummaryList,
+          dependencyLists,
         } = this.data;
         const pipelineSummaries = pipelineSummaryList[index];
+        const dependencyList = dependencyLists[index];
         for (const { counts, raReference } of event.pipelineRuns ?? []) {
           // Get or create the pipeline summary for this RA
           const pipelineSummary = (pipelineSummaries[raReference] ??= {
             steps: event.ra[raReference],
             counts: counts.map(() => 0),
+            hash: getPipelineHash(event.ra[raReference]),
           });
           const { counts: totalTuplesPerStep } = pipelineSummary;
           for (let i = 0, length = counts.length; i < length; ++i) {
@@ -170,6 +204,25 @@ export class PerformanceOverviewScanner implements EvaluationLogScanner {
             totalTuplesPerStep[i] += count;
           }
         }
+        for (const dependencyHash of Object.values(event.dependencies ?? {})) {
+          const dependencyIndex = this.raToIndex.get(dependencyHash);
+          if (dependencyIndex != null) {
+            dependencyList.push(dependencyIndex);
+          }
+        }
+        // For predicates in the same SCC, add two-way dependencies with an arbitrary SCC member
+        const sccHash =
+          event.mainHash ??
+          (evaluationStrategy === "COMPUTE_RECURSIVE" ? raHash : null);
+        if (sccHash != null) {
+          const mainIndex = this.mainHashToRepr.get(sccHash);
+          if (mainIndex == null) {
+            this.mainHashToRepr.set(sccHash, index);
+          } else {
+            dependencyLists[index].push(mainIndex);
+            dependencyLists[mainIndex].push(index);
+          }
+        }
         timeCosts[index] += totalTime;
         tupleCosts[index] += totalTuples;
         iterationCounts[index] += event.pipelineRuns?.length ?? 0;
@@ -178,6 +231,12 @@ export class PerformanceOverviewScanner implements EvaluationLogScanner {
       }
     }
   }
+}
 
-  onDone(): void {}
+function getPipelineHash(steps: string[]) {
+  const md5 = createHash("md5");
+  for (const step of steps) {
+    md5.write(step);
+  }
+  return md5.digest("base64");
 }
diff --git a/extensions/ql-vscode/src/log-insights/summary-language-support.ts b/extensions/ql-vscode/src/log-insights/summary-language-support.ts
index 9919db114da..6546fd04ce2 100644
--- a/extensions/ql-vscode/src/log-insights/summary-language-support.ts
+++ b/extensions/ql-vscode/src/log-insights/summary-language-support.ts
@@ -113,7 +113,7 @@ export class SummaryLanguageSupport extends DisposableObject {
         const sourceMapText = await readFile(mapPath, "utf-8");
         const rawMap: RawSourceMap = JSON.parse(sourceMapText);
         this.sourceMap = await new SourceMapConsumer(rawMap);
-      } catch (e: unknown) {
+      } catch (e) {
         // Error reading sourcemap. Pretend there was no sourcemap.
         void extLogger.log(
           `Error reading sourcemap file '${mapPath}': ${getErrorMessage(e)}`,
diff --git a/extensions/ql-vscode/src/log-insights/summary-parser.ts b/extensions/ql-vscode/src/log-insights/summary-parser.ts
index 6a42efca187..61a3a8af250 100644
--- a/extensions/ql-vscode/src/log-insights/summary-parser.ts
+++ b/extensions/ql-vscode/src/log-insights/summary-parser.ts
@@ -1,6 +1,3 @@
-import { createReadStream, writeFile } from "fs-extra";
-import { LINE_ENDINGS, splitStreamAtSeparators } from "../common/split-stream";
-
 /**
  * Location information for a single pipeline invocation in the RA.
  */
@@ -18,6 +15,11 @@ interface PredicateSymbol {
    * `PipelineInfo` for each iteration. A non-recursive predicate will have a single iteration `0`.
    */
   iterations: Record<number, PipelineInfo>;
+
+  /**
+   * `PipelineInfo` for each order, summarised for all iterations that used that order. Empty for non-recursive predicates.
+   */
+  recursionSummaries: Record<string, PipelineInfo>;
 }
 
 /**
@@ -27,102 +29,3 @@ interface PredicateSymbol {
 export interface SummarySymbols {
   predicates: Record<string, PredicateSymbol>;
 }
-
-// Tuple counts for Expr::Expr::getParent#dispred#f0820431#ff@76d6745o:
-const NON_RECURSIVE_TUPLE_COUNT_REGEXP =
-  /^Evaluated relational algebra for predicate (?<predicateName>\S+) with tuple counts:$/;
-// Tuple counts for Expr::Expr::getEnclosingStmt#f0820431#bf@923ddwj9 on iteration 0 running pipeline base:
-const RECURSIVE_TUPLE_COUNT_REGEXP =
-  /^Evaluated relational algebra for predicate (?<predicateName>\S+) on iteration (?<iteration>\d+) running pipeline (?<pipeline>\S+) with tuple counts:$/;
-const RETURN_REGEXP = /^\s*return /;
-
-/**
- * Parse a human-readable evaluation log summary to find the location of the RA for each pipeline
- * run.
- *
- * TODO: Once we're more certain about the symbol format, we should have the CLI generate this as it
- * generates the human-readabe summary to avoid having to rely on regular expression matching of the
- * human-readable text.
- *
- * @param summaryPath The path to the summary file.
- * @param symbolsPath The path to the symbols file to generate.
- */
-export async function generateSummarySymbolsFile(
-  summaryPath: string,
-  symbolsPath: string,
-): Promise<void> {
-  const symbols = await generateSummarySymbols(summaryPath);
-  await writeFile(symbolsPath, JSON.stringify(symbols));
-}
-
-/**
- * Parse a human-readable evaluation log summary to find the location of the RA for each pipeline
- * run.
- *
- * @param fileLocation The path to the summary file.
- * @returns Symbol information for the summary file.
- */
-async function generateSummarySymbols(
-  summaryPath: string,
-): Promise<SummarySymbols> {
-  const stream = createReadStream(summaryPath, {
-    encoding: "utf-8",
-  });
-  try {
-    const lines = splitStreamAtSeparators(stream, LINE_ENDINGS);
-
-    const symbols: SummarySymbols = {
-      predicates: {},
-    };
-
-    let lineNumber = 0;
-    let raStartLine = 0;
-    let iteration = 0;
-    let predicateName: string | undefined = undefined;
-    let startLine = 0;
-    for await (const line of lines) {
-      if (predicateName === undefined) {
-        // Looking for the start of the predicate.
-        const nonRecursiveMatch = line.match(NON_RECURSIVE_TUPLE_COUNT_REGEXP);
-        if (nonRecursiveMatch) {
-          iteration = 0;
-          predicateName = nonRecursiveMatch.groups!.predicateName;
-        } else {
-          const recursiveMatch = line.match(RECURSIVE_TUPLE_COUNT_REGEXP);
-          if (recursiveMatch?.groups) {
-            predicateName = recursiveMatch.groups.predicateName;
-            iteration = parseInt(recursiveMatch.groups.iteration);
-          }
-        }
-        if (predicateName !== undefined) {
-          startLine = lineNumber;
-          raStartLine = lineNumber + 1;
-        }
-      } else {
-        const returnMatch = line.match(RETURN_REGEXP);
-        if (returnMatch) {
-          let symbol = symbols.predicates[predicateName];
-          if (symbol === undefined) {
-            symbol = {
-              iterations: {},
-            };
-            symbols.predicates[predicateName] = symbol;
-          }
-          symbol.iterations[iteration] = {
-            startLine,
-            raStartLine,
-            raEndLine: lineNumber,
-          };
-
-          predicateName = undefined;
-        }
-      }
-
-      lineNumber++;
-    }
-
-    return symbols;
-  } finally {
-    stream.close();
-  }
-}
diff --git a/extensions/ql-vscode/src/model-editor/extension-pack-picker.ts b/extensions/ql-vscode/src/model-editor/extension-pack-picker.ts
index 959a727e7e0..d5e8f0d78a5 100644
--- a/extensions/ql-vscode/src/model-editor/extension-pack-picker.ts
+++ b/extensions/ql-vscode/src/model-editor/extension-pack-picker.ts
@@ -115,7 +115,7 @@ export async function pickExtensionPack(
         existingExtensionPackPaths[0],
         databaseItem.language,
       );
-    } catch (e: unknown) {
+    } catch (e) {
       void showAndLogErrorMessage(
         logger,
         `Could not read extension pack ${formatPackName(packName)}`,
diff --git a/extensions/ql-vscode/src/model-editor/generate.ts b/extensions/ql-vscode/src/model-editor/generate.ts
index 9f4b20c13da..157ed78b78d 100644
--- a/extensions/ql-vscode/src/model-editor/generate.ts
+++ b/extensions/ql-vscode/src/model-editor/generate.ts
@@ -91,6 +91,14 @@ async function runSingleGenerateQuery(
   if (!completedQuery) {
     return undefined;
   }
+  const queryResults = Array.from(completedQuery.results.values());
+  if (queryResults.length !== 1) {
+    throw new Error(
+      `Expected exactly one query result, but got ${queryResults.length}`,
+    );
+  }
 
-  return cliServer.bqrsDecodeAll(completedQuery.outputDir.bqrsPath);
+  return cliServer.bqrsDecodeAll(
+    completedQuery.outputDir.getBqrsPath(queryResults[0].outputBaseName),
+  );
 }
diff --git a/extensions/ql-vscode/src/model-editor/model-editor-queries.ts b/extensions/ql-vscode/src/model-editor/model-editor-queries.ts
index 0e7ddd48c4e..f1e7429afbd 100644
--- a/extensions/ql-vscode/src/model-editor/model-editor-queries.ts
+++ b/extensions/ql-vscode/src/model-editor/model-editor-queries.ts
@@ -172,10 +172,19 @@ export async function runModelEditorQueries(
     maxStep: externalApiQueriesProgressMaxStep,
   });
 
+  const queryResults = Array.from(completedQuery.results.values());
+  if (queryResults.length !== 1) {
+    throw new Error(
+      `Expected exactly one query result, but got ${queryResults.length}`,
+    );
+  }
+
   const bqrsChunk = await readQueryResults({
     cliServer,
     logger,
-    bqrsPath: completedQuery.outputDir.bqrsPath,
+    bqrsPath: completedQuery.outputDir.getBqrsPath(
+      queryResults[0].outputBaseName,
+    ),
   });
   if (!bqrsChunk) {
     return;
diff --git a/extensions/ql-vscode/src/model-editor/model-editor-view.ts b/extensions/ql-vscode/src/model-editor/model-editor-view.ts
index 46422bf8b67..08202646b7e 100644
--- a/extensions/ql-vscode/src/model-editor/model-editor-view.ts
+++ b/extensions/ql-vscode/src/model-editor/model-editor-view.ts
@@ -455,7 +455,7 @@ export class ModelEditorView extends AbstractWebview<
         this.app.logger,
       );
       this.modelingStore.setModeledMethods(this.databaseItem, modeledMethods);
-    } catch (e: unknown) {
+    } catch (e) {
       void showAndLogErrorMessage(
         this.app.logger,
         `Unable to read data extension YAML: ${getErrorMessage(e)}`,
@@ -561,7 +561,7 @@ export class ModelEditorView extends AbstractWebview<
             t: "setAccessPathSuggestions",
             accessPathSuggestions: options,
           });
-        } catch (e: unknown) {
+        } catch (e) {
           void showAndLogExceptionWithTelemetry(
             this.app.logger,
             this.app.telemetry,
@@ -645,7 +645,7 @@ export class ModelEditorView extends AbstractWebview<
             progress,
             token: this.cancellationTokenSource.token,
           });
-        } catch (e: unknown) {
+        } catch (e) {
           void showAndLogExceptionWithTelemetry(
             this.app.logger,
             this.app.telemetry,
@@ -733,7 +733,7 @@ export class ModelEditorView extends AbstractWebview<
             progress,
             token: this.cancellationTokenSource.token,
           });
-        } catch (e: unknown) {
+        } catch (e) {
           void showAndLogExceptionWithTelemetry(
             this.app.logger,
             this.app.telemetry,
diff --git a/extensions/ql-vscode/src/model-editor/suggestion-queries.ts b/extensions/ql-vscode/src/model-editor/suggestion-queries.ts
index 37ce78fd3a5..f325fc2a4d5 100644
--- a/extensions/ql-vscode/src/model-editor/suggestion-queries.ts
+++ b/extensions/ql-vscode/src/model-editor/suggestion-queries.ts
@@ -109,7 +109,15 @@ export async function runSuggestionsQuery(
     maxStep,
   });
 
-  const bqrs = await cliServer.bqrsDecodeAll(completedQuery.outputDir.bqrsPath);
+  const queryResults = Array.from(completedQuery.results.values());
+  if (queryResults.length !== 1) {
+    throw new Error(
+      `Expected exactly one query result, but got ${queryResults.length}`,
+    );
+  }
+  const bqrs = await cliServer.bqrsDecodeAll(
+    completedQuery.outputDir.getBqrsPath(queryResults[0].outputBaseName),
+  );
 
   progress({
     message: "Finalizing results",
diff --git a/extensions/ql-vscode/src/query-history/history-item-label-provider.ts b/extensions/ql-vscode/src/query-history/history-item-label-provider.ts
index 89f0f89a027..8787e025daf 100644
--- a/extensions/ql-vscode/src/query-history/history-item-label-provider.ts
+++ b/extensions/ql-vscode/src/query-history/history-item-label-provider.ts
@@ -115,7 +115,7 @@ export class HistoryItemLabelProvider {
       startTime: item.startTime,
       queryName: item.getQueryName(),
       databaseName: item.databaseName,
-      resultCount: `(${resultCount} results)`,
+      resultCount: resultCount === -1 ? "" : `(${resultCount} results)`,
       status: message,
       queryFileBasename: item.getQueryFileName(),
       queryLanguage: this.getLanguageLabel(item),
diff --git a/extensions/ql-vscode/src/query-history/history-tree-data-provider.ts b/extensions/ql-vscode/src/query-history/history-tree-data-provider.ts
index 8f63d109eb5..7b355539a9a 100644
--- a/extensions/ql-vscode/src/query-history/history-tree-data-provider.ts
+++ b/extensions/ql-vscode/src/query-history/history-tree-data-provider.ts
@@ -138,12 +138,12 @@ export class HistoryTreeDataProvider
 
             const resultCount1 =
               h1.t === "local"
-                ? h1.completedQuery?.resultCount ?? -1
-                : h1.resultCount ?? -1;
+                ? (h1.completedQuery?.resultCount ?? -1)
+                : (h1.resultCount ?? -1);
             const resultCount2 =
               h2.t === "local"
-                ? h2.completedQuery?.resultCount ?? -1
-                : h2.resultCount ?? -1;
+                ? (h2.completedQuery?.resultCount ?? -1)
+                : (h2.resultCount ?? -1);
 
             switch (this.sortOrder) {
               case SortOrder.NameAsc:
diff --git a/extensions/ql-vscode/src/query-history/query-history-manager.ts b/extensions/ql-vscode/src/query-history/query-history-manager.ts
index 3074ceb3bb9..edf22f9b846 100644
--- a/extensions/ql-vscode/src/query-history/query-history-manager.ts
+++ b/extensions/ql-vscode/src/query-history/query-history-manager.ts
@@ -23,7 +23,8 @@ import { URLSearchParams } from "url";
 import { DisposableObject } from "../common/disposable-object";
 import { ONE_HOUR_IN_MS, TWO_HOURS_IN_MS } from "../common/time";
 import { assertNever, getErrorMessage } from "../common/helpers-pure";
-import type { CompletedLocalQueryInfo, LocalQueryInfo } from "../query-results";
+import type { CompletedLocalQueryInfo } from "../query-results";
+import { LocalQueryInfo } from "../query-results";
 import type { QueryHistoryInfo } from "./query-history-info";
 import {
   getActionsWorkflowRunUrl,
@@ -50,7 +51,10 @@ import type { QueryRunner } from "../query-server";
 import type { VariantAnalysisManager } from "../variant-analysis/variant-analysis-manager";
 import type { VariantAnalysisHistoryItem } from "./variant-analysis-history-item";
 import { getTotalResultCount } from "../variant-analysis/shared/variant-analysis";
-import { HistoryTreeDataProvider } from "./history-tree-data-provider";
+import {
+  HistoryTreeDataProvider,
+  SortOrder,
+} from "./history-tree-data-provider";
 import type { QueryHistoryDirs } from "./query-history-dirs";
 import type { QueryHistoryCommands } from "../common/commands";
 import type { App } from "../common/app";
@@ -97,15 +101,6 @@ const SHOW_QUERY_TEXT_QUICK_EVAL_MSG = `\
 
 `;
 
-enum SortOrder {
-  NameAsc = "NameAsc",
-  NameDesc = "NameDesc",
-  DateAsc = "DateAsc",
-  DateDesc = "DateDesc",
-  CountAsc = "CountAsc",
-  CountDesc = "CountDesc",
-}
-
 /**
  * Number of milliseconds two clicks have to arrive apart to be
  * considered a double-click.
@@ -337,6 +332,11 @@ export class QueryHistoryManager extends DisposableObject {
         this.handleOpenOnGithub.bind(this),
         "query",
       ),
+      "codeQLQueryHistory.viewAutofixes": createSingleSelectionCommand(
+        this.app.logger,
+        this.handleViewAutofixes.bind(this),
+        "query",
+      ),
       "codeQLQueryHistory.copyRepoList": createSingleSelectionCommand(
         this.app.logger,
         this.handleCopyRepoList.bind(this),
@@ -348,8 +348,37 @@ export class QueryHistoryManager extends DisposableObject {
     };
   }
 
-  public completeQuery(info: LocalQueryInfo, results: QueryWithResults): void {
-    info.completeThisQuery(results);
+  public completeQueries(
+    info: LocalQueryInfo,
+    results: QueryWithResults[],
+  ): void {
+    let first = true;
+    // Sorting results by the output/results basename should produce a deterministic order.
+    results.sort((a, b) => {
+      const aPath = a.query.outputBaseName;
+      const bPath = b.query.outputBaseName;
+      return aPath.localeCompare(bPath);
+    });
+    for (const result of results) {
+      if (first) {
+        // This is the first query, so we can just update the existing info.
+        info.completeThisQuery(result);
+        first = false;
+      } else {
+        // For other queries in the same run, we'll add new entries to the history pane. In the long
+        // term, it would be better if we could have a single entry containing sub-entries for each
+        // query.
+        const clonedInfo = new LocalQueryInfo(
+          info.initialInfo,
+          undefined,
+          info.failureReason,
+          undefined,
+          info.evaluatorLogPaths,
+        );
+        clonedInfo.completeThisQuery(result);
+        this.addQuery(clonedInfo);
+      }
+    }
     this._onDidCompleteQuery.fire(info);
   }
 
@@ -555,6 +584,23 @@ export class QueryHistoryManager extends DisposableObject {
       }),
     );
 
+    await Promise.all(
+      this.treeDataProvider.allHistory.map(async (item) => {
+        // Remove any local queries whose directories no longer exist. This can happen when running
+        // a query suite, which produces multiple queries in the history pane that all share the
+        // same underlying directory, which we may have just deleted above. (Ideally, there would be
+        // a first-class concept of a local multi-query run in this pane that would group them all
+        // together, but doing it this way at least avoids cluttering the history pane with entries
+        // that can no longer be viewed).
+        if (item.t === "local") {
+          const dir = item.completedQuery?.query.querySaveDir;
+          if (dir && !(await pathExists(dir))) {
+            this.treeDataProvider.remove(item);
+          }
+        }
+      }),
+    );
+
     await this.writeQueryHistory();
     const current = this.treeDataProvider.getCurrent();
     if (current !== undefined) {
@@ -942,7 +988,7 @@ export class QueryHistoryManager extends DisposableObject {
     if (hasInterpretedResults) {
       await tryOpenExternalFile(
         this.app.commands,
-        query.resultsPaths.interpretedResultsPath,
+        query.interpretedResultsPath,
       );
     } else {
       const label = this.labelProvider.getLabel(item);
@@ -1005,6 +1051,14 @@ export class QueryHistoryManager extends DisposableObject {
     );
   }
 
+  async handleViewAutofixes(item: QueryHistoryInfo) {
+    if (item.t !== "variant-analysis") {
+      return;
+    }
+
+    await this.variantAnalysisManager.viewAutofixes(item.variantAnalysis.id);
+  }
+
   async handleCopyRepoList(item: QueryHistoryInfo) {
     if (item.t !== "variant-analysis") {
       return;
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-dto.ts b/extensions/ql-vscode/src/query-history/store/query-history-dto.ts
index fd8bf01ccbc..78cb5b6064e 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-dto.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-dto.ts
@@ -14,6 +14,7 @@ export type QueryHistoryItemDto =
   | QueryHistoryVariantAnalysisDto;
 
 export enum QueryLanguageDto {
+  Actions = "actions",
   CSharp = "csharp",
   Cpp = "cpp",
   Go = "go",
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-language-domain-mapper.ts b/extensions/ql-vscode/src/query-history/store/query-history-language-domain-mapper.ts
index 615c820908b..1df15d41dd2 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-language-domain-mapper.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-language-domain-mapper.ts
@@ -6,6 +6,8 @@ export function mapQueryLanguageToDto(
   language: QueryLanguage,
 ): QueryLanguageDto {
   switch (language) {
+    case QueryLanguage.Actions:
+      return QueryLanguageDto.Actions;
     case QueryLanguage.CSharp:
       return QueryLanguageDto.CSharp;
     case QueryLanguage.Cpp:
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-language-dto-mapper.ts b/extensions/ql-vscode/src/query-history/store/query-history-language-dto-mapper.ts
index d4e0f03c1bf..1e3ea1c18a8 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-language-dto-mapper.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-language-dto-mapper.ts
@@ -6,6 +6,8 @@ export function mapQueryLanguageToDomainModel(
   language: QueryLanguageDto,
 ): QueryLanguage {
   switch (language) {
+    case QueryLanguageDto.Actions:
+      return QueryLanguage.Actions;
     case QueryLanguageDto.CSharp:
       return QueryLanguage.CSharp;
     case QueryLanguageDto.Cpp:
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-local-query-domain-mapper.ts b/extensions/ql-vscode/src/query-history/store/query-history-local-query-domain-mapper.ts
index 5f691e60785..61fe2e0bc4b 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-local-query-domain-mapper.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-local-query-domain-mapper.ts
@@ -118,6 +118,6 @@ function mapQueryEvaluationInfoToDto(
     databaseHasMetadataFile: queryEvaluationInfo.databaseHasMetadataFile,
     quickEvalPosition: queryEvaluationInfo.quickEvalPosition,
     metadata: queryEvaluationInfo.metadata,
-    resultsPaths: queryEvaluationInfo.resultsPaths,
+    outputBaseName: queryEvaluationInfo.outputBaseName,
   };
 }
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto-mapper.ts b/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto-mapper.ts
index 7afe4b907ad..aa42dd8c1a0 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto-mapper.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto-mapper.ts
@@ -104,6 +104,7 @@ function mapQueryEvaluationInfoToDomainModel(
 ): QueryEvaluationInfo {
   return new QueryEvaluationInfo(
     evaluationInfo.querySaveDir,
+    evaluationInfo.outputBaseName ?? "results",
     evaluationInfo.dbItemPath,
     evaluationInfo.databaseHasMetadataFile,
     evaluationInfo.quickEvalPosition,
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto.ts b/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto.ts
index b9a2f3448fa..2a6b3c78ea0 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto.ts
@@ -86,7 +86,10 @@ export interface QueryEvaluationInfoDto {
   databaseHasMetadataFile: boolean;
   quickEvalPosition?: PositionDto;
   metadata?: QueryMetadataDto;
-  resultsPaths: {
+  outputBaseName?: string;
+
+  // Superceded by outputBaseName
+  resultsPaths?: {
     resultsPath: string;
     interpretedResultsPath: string;
   };
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-store.ts b/extensions/ql-vscode/src/query-history/store/query-history-store.ts
index 279c17c4dc0..0b54908ceba 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-store.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-store.ts
@@ -61,7 +61,7 @@ export async function readQueryHistoryFromFile(
           // to see if they exist on disk.
           return true;
         }
-        const resultsPath = q.completedQuery?.query.resultsPaths.resultsPath;
+        const resultsPath = q.completedQuery?.query.resultsPath;
         return !!resultsPath && (await pathExists(resultsPath));
       },
     );
diff --git a/extensions/ql-vscode/src/query-results.ts b/extensions/ql-vscode/src/query-results.ts
index 69a99837b52..3e81762bc08 100644
--- a/extensions/ql-vscode/src/query-results.ts
+++ b/extensions/ql-vscode/src/query-results.ts
@@ -64,7 +64,7 @@ export class CompletedQueryInfo implements QueryWithResults {
      * sarif file.
      */
     public interpretedResultsSortState: InterpretedResultsSortState | undefined,
-    public resultCount: number = 0,
+    public resultCount: number = -1,
 
     /**
      * Map from result set name to SortedResultSetInfo.
@@ -78,11 +78,11 @@ export class CompletedQueryInfo implements QueryWithResults {
 
   getResultsPath(selectedTable: string, useSorted = true): string {
     if (!useSorted) {
-      return this.query.resultsPaths.resultsPath;
+      return this.query.resultsPath;
     }
     return (
       this.sortedResultsInfo[selectedTable]?.resultsPath ||
-      this.query.resultsPaths.resultsPath
+      this.query.resultsPath
     );
   }
 
@@ -102,7 +102,7 @@ export class CompletedQueryInfo implements QueryWithResults {
     };
 
     await server.sortBqrs(
-      this.query.resultsPaths.resultsPath,
+      this.query.resultsPath,
       sortedResultSetInfo.resultsPath,
       resultSetName,
       [sortState.columnIndex],
diff --git a/extensions/ql-vscode/src/query-server/messages.ts b/extensions/ql-vscode/src/query-server/messages.ts
index 44e0d515458..548e93ad32b 100644
--- a/extensions/ql-vscode/src/query-server/messages.ts
+++ b/extensions/ql-vscode/src/query-server/messages.ts
@@ -42,6 +42,22 @@ export interface TrimCacheParams {
   db: string;
 }
 
+/**
+ * Parameters for trimming the cache of a dataset with a specific mode.
+ */
+export interface TrimCacheWithModeParams {
+  /**
+   * The dataset that we want to trim the cache of.
+   */
+  db: string;
+  /**
+   * The cache cleanup mode to use.
+   */
+  mode: ClearCacheMode;
+}
+
+export type ClearCacheMode = "clear" | "trim" | "fit" | "overlay";
+
 /**
  * The result of trimming or clearing the cache.
  */
@@ -130,13 +146,29 @@ export interface RunQueryParams {
   extensionPacks?: string[];
 }
 
-interface RunQueryResult {
+export interface RunQueryResult {
   resultType: QueryResultType;
   message?: string;
   expectedDbschemeName?: string;
   evaluationTime: number;
 }
 
+export interface RunQueryInputOutput {
+  queryPath: string;
+  outputPath: string;
+  dilPath: string;
+}
+
+export interface RunQueriesParams {
+  inputOutputPaths: RunQueryInputOutput[];
+  db: string;
+  additionalPacks: string[];
+  externalInputs: Record<string, string>;
+  singletonExternalInputs: Record<string, string>;
+  logPath?: string;
+  extensionPacks?: string[];
+}
+
 interface UpgradeParams {
   db: string;
   additionalPacks: string[];
@@ -177,6 +209,14 @@ export const trimCache = new RequestType<
   ClearCacheResult,
   void
 >("evaluation/trimCache");
+/**
+ * Trim the cache of a dataset with a specific mode.
+ */
+export const trimCacheWithMode = new RequestType<
+  WithProgressId<TrimCacheWithModeParams>,
+  ClearCacheResult,
+  void
+>("evaluation/trimCacheWithMode");
 
 /**
  * Clear the pack cache
@@ -196,6 +236,12 @@ export const runQuery = new RequestType<
   void
 >("evaluation/runQuery");
 
+export const runQueries = new RequestType<
+  WithProgressId<RunQueriesParams>,
+  Record<string, RunQueryResult>,
+  void
+>("evaluation/runQueries");
+
 export const registerDatabases = new RequestType<
   WithProgressId<RegisterDatabasesParams>,
   RegisterDatabasesResult,
diff --git a/extensions/ql-vscode/src/query-server/query-runner.ts b/extensions/ql-vscode/src/query-server/query-runner.ts
index 7fbb3446575..5d42e6056d7 100644
--- a/extensions/ql-vscode/src/query-server/query-runner.ts
+++ b/extensions/ql-vscode/src/query-server/query-runner.ts
@@ -6,10 +6,12 @@ import { UserCancellationException } from "../common/vscode/progress";
 import type { DatabaseItem } from "../databases/local-databases/database-item";
 import { QueryOutputDir } from "../local-queries/query-output-dir";
 import type {
+  ClearCacheMode,
   ClearCacheParams,
   Position,
   QueryResultType,
   TrimCacheParams,
+  TrimCacheWithModeParams,
 } from "./messages";
 import {
   clearCache,
@@ -17,21 +19,29 @@ import {
   deregisterDatabases,
   registerDatabases,
   trimCache,
+  trimCacheWithMode,
   upgradeDatabase,
 } from "./messages";
 import type { BaseLogger, Logger } from "../common/logging";
-import { basename, join } from "path";
+import { join } from "path";
 import { nanoid } from "nanoid";
 import type { QueryServerClient } from "./query-server-client";
 import { getOnDiskWorkspaceFolders } from "../common/vscode/workspace-folders";
 import { compileAndRunQueryAgainstDatabaseCore } from "./run-queries";
 
 export interface CoreQueryTarget {
-  /** The full path to the query. */
+  /** Path to the query source file. */
   queryPath: string;
+
+  /**
+   * Base name to use for output files, without extension. For example, "foo" will result in the
+   * BQRS file being written to "<outputdir>/foo.bqrs".
+   */
+  outputBaseName: string;
+
   /**
    * Optional position of text to be used as QuickEval target. This need not be in the same file as
-   * `query`.
+   * `queryPath`.
    */
   quickEvalPosition?: Position;
   /**
@@ -40,14 +50,25 @@ export interface CoreQueryTarget {
   quickEvalCountOnly?: boolean;
 }
 
-export interface CoreQueryResults {
+export interface CoreQueryResult {
   readonly resultType: QueryResultType;
   readonly message: string | undefined;
   readonly evaluationTime: number;
+
+  /**
+   * The base name of the output file. Append '.bqrs' and join with the output directory to get the
+   * path to the BQRS.
+   */
+  readonly outputBaseName: string;
+}
+
+export interface CoreQueryResults {
+  /** A map from query path to its results. */
+  readonly results: Map<string, CoreQueryResult>;
 }
 
 export interface CoreQueryRun {
-  readonly queryTarget: CoreQueryTarget;
+  readonly queryTargets: CoreQueryTarget[];
   readonly dbPath: string;
   readonly id: string;
   readonly outputDir: QueryOutputDir;
@@ -124,9 +145,25 @@ export class QueryRunner {
     await this.qs.sendRequest(trimCache, params);
   }
 
+  async trimCacheWithModeInDatabase(
+    dbItem: DatabaseItem,
+    mode: ClearCacheMode,
+  ): Promise<void> {
+    if (dbItem.contents === undefined) {
+      throw new Error("Can't clean the cache in an invalid database.");
+    }
+
+    const db = dbItem.databaseUri.fsPath;
+    const params: TrimCacheWithModeParams = {
+      db,
+      mode,
+    };
+    await this.qs.sendRequest(trimCacheWithMode, params);
+  }
+
   public async compileAndRunQueryAgainstDatabaseCore(
     dbPath: string,
-    query: CoreQueryTarget,
+    queries: CoreQueryTarget[],
     additionalPacks: string[],
     extensionPacks: string[] | undefined,
     additionalRunQueryArgs: Record<string, unknown>,
@@ -142,7 +179,7 @@ export class QueryRunner {
     return await compileAndRunQueryAgainstDatabaseCore(
       this.qs,
       dbPath,
-      query,
+      queries,
       generateEvalLog,
       additionalPacks,
       extensionPacks,
@@ -213,19 +250,20 @@ export class QueryRunner {
    */
   public createQueryRun(
     dbPath: string,
-    query: CoreQueryTarget,
+    queries: CoreQueryTarget[],
     generateEvalLog: boolean,
     additionalPacks: string[],
     extensionPacks: string[] | undefined,
     additionalRunQueryArgs: Record<string, unknown>,
     queryStorageDir: string,
-    id = `${basename(query.queryPath)}-${nanoid()}`,
+    queryBasename: string,
     templates: Record<string, string> | undefined,
   ): CoreQueryRun {
+    const id = `${queryBasename}-${nanoid()}`;
     const outputDir = new QueryOutputDir(join(queryStorageDir, id));
 
     return {
-      queryTarget: query,
+      queryTargets: queries,
       dbPath,
       id,
       outputDir,
@@ -238,10 +276,10 @@ export class QueryRunner {
           id,
           outputDir,
           dbPath,
-          queryTarget: query,
+          queryTargets: queries,
           ...(await this.compileAndRunQueryAgainstDatabaseCore(
             dbPath,
-            query,
+            queries,
             additionalPacks,
             extensionPacks,
             additionalRunQueryArgs,
diff --git a/extensions/ql-vscode/src/query-server/query-server-client.ts b/extensions/ql-vscode/src/query-server/query-server-client.ts
index c342e3b4996..8087686992f 100644
--- a/extensions/ql-vscode/src/query-server/query-server-client.ts
+++ b/extensions/ql-vscode/src/query-server/query-server-client.ts
@@ -95,6 +95,14 @@ export class QueryServerClient extends DisposableObject {
     return this.opts.logger;
   }
 
+  /**
+   * Whether this query server supports the 'evaluation/runQueries' method for running multiple
+   * queries at once.
+   */
+  async supportsRunQueriesMethod(): Promise<boolean> {
+    return await this.cliServer.cliConstraints.supportsQueryServerRunQueries();
+  }
+
   /** Stops the query server by disposing of the current server process. */
   private stopQueryServer(): void {
     if (this.serverProcess !== undefined) {
diff --git a/extensions/ql-vscode/src/query-server/run-queries.ts b/extensions/ql-vscode/src/query-server/run-queries.ts
index 593979118e7..5a35144728f 100644
--- a/extensions/ql-vscode/src/query-server/run-queries.ts
+++ b/extensions/ql-vscode/src/query-server/run-queries.ts
@@ -1,10 +1,19 @@
 import type { CancellationToken } from "vscode";
 import type { ProgressCallback } from "../common/vscode/progress";
-import type { RunQueryParams } from "./messages";
-import { runQuery } from "./messages";
+import type {
+  RunQueryParams,
+  RunQueryResult,
+  RunQueriesParams,
+  RunQueryInputOutput,
+} from "./messages";
+import { runQueries, runQuery } from "./messages";
 import type { QueryOutputDir } from "../local-queries/query-output-dir";
 import type { QueryServerClient } from "./query-server-client";
-import type { CoreQueryResults, CoreQueryTarget } from "./query-runner";
+import type {
+  CoreQueryResult,
+  CoreQueryResults,
+  CoreQueryTarget,
+} from "./query-runner";
 import type { BaseLogger } from "../common/logging";
 
 /**
@@ -24,7 +33,7 @@ import type { BaseLogger } from "../common/logging";
 export async function compileAndRunQueryAgainstDatabaseCore(
   qs: QueryServerClient,
   dbPath: string,
-  query: CoreQueryTarget,
+  targets: CoreQueryTarget[],
   generateEvalLog: boolean,
   additionalPacks: string[],
   extensionPacks: string[] | undefined,
@@ -35,12 +44,36 @@ export async function compileAndRunQueryAgainstDatabaseCore(
   templates: Record<string, string> | undefined,
   logger: BaseLogger,
 ): Promise<CoreQueryResults> {
-  const target =
-    query.quickEvalPosition !== undefined
+  if (targets.length > 1) {
+    // We are running a batch of multiple queries; use the new query server API for that.
+    if (targets.some((target) => target.quickEvalPosition !== undefined)) {
+      throw new Error(
+        "Quick evaluation is not supported when running multiple queries.",
+      );
+    }
+    return compileAndRunQueriesAgainstDatabaseCore(
+      qs,
+      dbPath,
+      targets,
+      generateEvalLog,
+      additionalPacks,
+      extensionPacks,
+      additionalRunQueryArgs,
+      outputDir,
+      progress,
+      token,
+      templates,
+      logger,
+    );
+  }
+
+  const target = targets[0];
+  const compilationTarget =
+    target.quickEvalPosition !== undefined
       ? {
           quickEval: {
-            quickEvalPos: query.quickEvalPosition,
-            countOnly: query.quickEvalCountOnly,
+            quickEvalPos: target.quickEvalPosition,
+            countOnly: target.quickEvalCountOnly,
           },
         }
       : { query: {} };
@@ -51,11 +84,11 @@ export async function compileAndRunQueryAgainstDatabaseCore(
     additionalPacks,
     externalInputs: {},
     singletonExternalInputs: templates || {},
-    outputPath: outputDir.bqrsPath,
-    queryPath: query.queryPath,
-    dilPath: outputDir.dilPath,
+    queryPath: target.queryPath,
+    outputPath: outputDir.getBqrsPath(target.outputBaseName),
+    dilPath: outputDir.getDilPath(target.outputBaseName),
     logPath: evalLogPath,
-    target,
+    target: compilationTarget,
     extensionPacks,
     // Add any additional arguments without interpretation.
     ...additionalRunQueryArgs,
@@ -67,10 +100,83 @@ export async function compileAndRunQueryAgainstDatabaseCore(
   // properly will require a change in the query server.
   qs.activeQueryLogger = logger;
   const result = await qs.sendRequest(runQuery, queryToRun, token, progress);
+  return {
+    results: new Map<string, CoreQueryResult>([
+      [
+        target.queryPath,
+        {
+          resultType: result.resultType,
+          message: result.message,
+          evaluationTime: result.evaluationTime,
+          outputBaseName: target.outputBaseName,
+        },
+      ],
+    ]),
+  };
+}
+
+async function compileAndRunQueriesAgainstDatabaseCore(
+  qs: QueryServerClient,
+  dbPath: string,
+  targets: CoreQueryTarget[],
+  generateEvalLog: boolean,
+  additionalPacks: string[],
+  extensionPacks: string[] | undefined,
+  additionalRunQueryArgs: Record<string, unknown>,
+  outputDir: QueryOutputDir,
+  progress: ProgressCallback,
+  token: CancellationToken,
+  templates: Record<string, string> | undefined,
+  logger: BaseLogger,
+): Promise<CoreQueryResults> {
+  if (!(await qs.supportsRunQueriesMethod())) {
+    throw new Error(
+      "The CodeQL CLI does not support the 'evaluation/runQueries' query-server command. Please update to the latest version.",
+    );
+  }
+  const inputOutputPaths: RunQueryInputOutput[] = targets.map((target) => {
+    return {
+      queryPath: target.queryPath,
+      outputPath: outputDir.getBqrsPath(target.outputBaseName),
+      dilPath: outputDir.getDilPath(target.outputBaseName),
+    };
+  });
 
+  const evalLogPath = generateEvalLog ? outputDir.evalLogPath : undefined;
+  const queriesToRun: RunQueriesParams = {
+    db: dbPath,
+    additionalPacks,
+    externalInputs: {},
+    singletonExternalInputs: templates || {},
+    inputOutputPaths,
+    logPath: evalLogPath,
+    extensionPacks,
+    // Add any additional arguments without interpretation.
+    ...additionalRunQueryArgs,
+  };
+
+  // Update the active query logger every time there is a new request to compile.
+  // This isn't ideal because in situations where there are queries running
+  // in parallel, each query's log messages are interleaved. Fixing this
+  // properly will require a change in the query server.
+  qs.activeQueryLogger = logger;
+  const queryResults: Record<string, RunQueryResult> = await qs.sendRequest(
+    runQueries,
+    queriesToRun,
+    token,
+    progress,
+  );
+  const coreQueryResults = new Map<string, CoreQueryResult>();
+  targets.forEach((target) => {
+    const queryResult = queryResults[target.queryPath];
+    coreQueryResults.set(target.queryPath, {
+      resultType: queryResult.resultType,
+      message: queryResult.message,
+      evaluationTime: queryResult.evaluationTime,
+      outputBaseName: target.outputBaseName,
+    });
+  });
   return {
-    resultType: result.resultType,
-    message: result.message,
-    evaluationTime: result.evaluationTime,
+    results: coreQueryResults,
   };
 }
diff --git a/extensions/ql-vscode/src/run-queries-shared.ts b/extensions/ql-vscode/src/run-queries-shared.ts
index dac447ee20b..4e463812cb0 100644
--- a/extensions/ql-vscode/src/run-queries-shared.ts
+++ b/extensions/ql-vscode/src/run-queries-shared.ts
@@ -27,7 +27,6 @@ import type {
 import type { BaseLogger } from "./common/logging";
 import { showAndLogWarningMessage } from "./common/logging";
 import { extLogger } from "./common/logging/vscode";
-import { generateSummarySymbolsFile } from "./log-insights/summary-parser";
 import { getErrorMessage } from "./common/helpers-pure";
 import { createHash } from "crypto";
 import { QueryOutputDir } from "./local-queries/query-output-dir";
@@ -65,6 +64,7 @@ export class QueryEvaluationInfo extends QueryOutputDir {
    */
   constructor(
     querySaveDir: string,
+    public readonly outputBaseName: string,
     public readonly dbItemPath: string,
     public readonly databaseHasMetadataFile: boolean,
     public readonly quickEvalPosition?: Position,
@@ -73,23 +73,30 @@ export class QueryEvaluationInfo extends QueryOutputDir {
     super(querySaveDir);
   }
 
-  get resultsPaths() {
-    return {
-      resultsPath: this.bqrsPath,
-      interpretedResultsPath: join(
-        this.querySaveDir,
-        this.metadata?.kind === "graph"
-          ? "graphResults"
-          : "interpretedResults.sarif",
-      ),
-    };
+  get resultsPath() {
+    return this.getBqrsPath(this.outputBaseName);
   }
+
+  get interpretedResultsPath() {
+    return this.getInterpretedResultsPath(
+      this.metadata?.kind,
+      this.outputBaseName,
+    );
+  }
+
+  get csvPath() {
+    return this.getCsvPath(this.outputBaseName);
+  }
+
+  get dilPath() {
+    return this.getDilPath(this.outputBaseName);
+  }
+
   getSortedResultSetPath(resultSetName: string) {
     const hasher = createHash("sha256");
     hasher.update(resultSetName);
-    return join(
-      this.querySaveDir,
-      `sortedResults-${hasher.digest("hex")}.bqrs`,
+    return this.getBqrsPath(
+      `${this.outputBaseName}-sorted-${hasher.digest("hex")}`,
     );
   }
 
@@ -127,7 +134,7 @@ export class QueryEvaluationInfo extends QueryOutputDir {
    * Holds if this query actually has produced interpreted results.
    */
   async hasInterpretedResults(): Promise<boolean> {
-    return pathExists(this.resultsPaths.interpretedResultsPath);
+    return pathExists(this.interpretedResultsPath);
   }
 
   /**
@@ -205,7 +212,7 @@ export class QueryEvaluationInfo extends QueryOutputDir {
     let nextOffset: number | undefined = 0;
     do {
       const chunk: DecodedBqrsChunk = await cliServer.bqrsDecode(
-        this.resultsPaths.resultsPath,
+        this.resultsPath,
         resultSet,
         {
           pageSize: 100,
@@ -243,9 +250,9 @@ export class QueryEvaluationInfo extends QueryOutputDir {
    * If the query has no result sets, then return undefined.
    */
   async chooseResultSet(cliServer: CodeQLCliServer) {
-    const resultSets = (
-      await cliServer.bqrsInfo(this.resultsPaths.resultsPath)
-    )["result-sets"];
+    const resultSets = (await cliServer.bqrsInfo(this.resultsPath))[
+      "result-sets"
+    ];
     if (!resultSets.length) {
       return undefined;
     }
@@ -284,7 +291,7 @@ export class QueryEvaluationInfo extends QueryOutputDir {
     }
     await cliServer.generateResultsCsv(
       ensureMetadataIsComplete(this.metadata),
-      this.resultsPaths.resultsPath,
+      this.resultsPath,
       this.csvPath,
       sourceInfo,
     );
@@ -348,6 +355,23 @@ export function validateQueryPath(
   }
 }
 
+/**
+ * Validates that the specified URI represents a QL query suite (QLS), and returns the file system
+ * path to that suite.
+ */
+export function validateQuerySuiteUri(suiteUri: Uri): string {
+  if (suiteUri.scheme !== "file") {
+    throw new Error("Can only run queries that are on disk.");
+  }
+  const suitePath = suiteUri.fsPath;
+  if (!suitePath.endsWith(".qls")) {
+    throw new Error(
+      'The selected resource is not a CodeQL query suite; It should have the extension ".qls".',
+    );
+  }
+  return suitePath;
+}
+
 export interface QuickEvalContext {
   quickEvalPosition: Position;
   quickEvalText: string;
@@ -545,15 +569,6 @@ export async function generateEvalLogSummaries(
 
     if (humanReadableSummary !== undefined) {
       summarySymbols = outputDir.evalLogSummarySymbolsPath;
-      if (
-        !(await cliServer.cliConstraints.supportsGenerateSummarySymbolMap())
-      ) {
-        // We're using an old CLI that cannot generate the summary symbols file while generating the
-        // human-readable log summary. As a fallback, create it by parsing the human-readable
-        // summary.
-        progress(progressUpdate(3, 3, "Generating summary symbols file"));
-        await generateSummarySymbolsFile(humanReadableSummary, summarySymbols);
-      }
     }
   }
 
diff --git a/extensions/ql-vscode/src/stories/Overview.mdx b/extensions/ql-vscode/src/stories/Overview.mdx
index cc06ee5cfca..7d9939cb4d9 100644
--- a/extensions/ql-vscode/src/stories/Overview.mdx
+++ b/extensions/ql-vscode/src/stories/Overview.mdx
@@ -1,7 +1,5 @@
 import { Canvas, Meta, Story } from '@storybook/blocks';
 
-import { VSCodeButton } from '@vscode/webview-ui-toolkit/react';
-
 import iframeImage from './images/update-css-variables-iframe.png';
 import stylesImage from './images/update-css-variables-styles.png';
 import bodyImage from './images/update-css-variables-body.png';
diff --git a/extensions/ql-vscode/src/stories/common/Alert.stories.tsx b/extensions/ql-vscode/src/stories/common/Alert.stories.tsx
index 1a5db4f14f6..2267ccb2696 100644
--- a/extensions/ql-vscode/src/stories/common/Alert.stories.tsx
+++ b/extensions/ql-vscode/src/stories/common/Alert.stories.tsx
@@ -1,5 +1,5 @@
 import type { Meta, StoryFn } from "@storybook/react";
-import { VSCodeButton } from "@vscode/webview-ui-toolkit/react";
+import { VscodeButton } from "@vscode-elements/react-elements";
 
 import { VariantAnalysisContainer } from "../../view/variant-analysis/VariantAnalysisContainer";
 import { Alert } from "../../view/common";
@@ -84,8 +84,8 @@ ErrorWithButtons.args = {
     "Request to https://api.github.com/repos/octodemo/Hello-World/code-scanning/codeql/queries failed. Try running this query again.",
   actions: (
     <>
-      <VSCodeButton appearance="secondary">View actions logs</VSCodeButton>
-      <VSCodeButton>Retry</VSCodeButton>
+      <VscodeButton secondary>View actions logs</VscodeButton>
+      <VscodeButton>Retry</VscodeButton>
     </>
   ),
 };
diff --git a/extensions/ql-vscode/src/stories/model-editor/LibraryRow.stories.tsx b/extensions/ql-vscode/src/stories/model-editor/LibraryRow.stories.tsx
index 423a948cd0e..16cb303b786 100644
--- a/extensions/ql-vscode/src/stories/model-editor/LibraryRow.stories.tsx
+++ b/extensions/ql-vscode/src/stories/model-editor/LibraryRow.stories.tsx
@@ -220,6 +220,7 @@ LibraryRow.args = {
     ],
   },
   modifiedSignatures: new Set(["org.sql2o.Sql2o#Sql2o(String)"]),
+  selectedSignatures: new Set(["org.sql2o.Sql2o#Sql2o(String)"]),
   viewState: createMockModelEditorViewState({
     showGenerateButton: true,
   }),
diff --git a/extensions/ql-vscode/src/stories/model-editor/MethodRow.stories.tsx b/extensions/ql-vscode/src/stories/model-editor/MethodRow.stories.tsx
index 6b10353d0a9..f7bf0748b20 100644
--- a/extensions/ql-vscode/src/stories/model-editor/MethodRow.stories.tsx
+++ b/extensions/ql-vscode/src/stories/model-editor/MethodRow.stories.tsx
@@ -112,6 +112,7 @@ Source.args = {
   modeledMethods: [{ ...modeledMethod, type: "source" }],
   methodCanBeModeled: true,
   viewState,
+  onChange: () => {},
 };
 
 export const Sink = Template.bind({});
@@ -120,6 +121,7 @@ Sink.args = {
   modeledMethods: [{ ...modeledMethod, type: "sink" }],
   methodCanBeModeled: true,
   viewState,
+  onChange: () => {},
 };
 
 export const Summary = Template.bind({});
@@ -136,6 +138,7 @@ Neutral.args = {
   modeledMethods: [{ ...modeledMethod, type: "neutral" }],
   methodCanBeModeled: true,
   viewState,
+  onChange: () => {},
 };
 
 export const AlreadyModeled = Template.bind({});
@@ -155,6 +158,7 @@ MultipleModelings.args = {
   ],
   methodCanBeModeled: true,
   viewState,
+  onChange: () => {},
 };
 
 export const ValidationError = Template.bind({});
@@ -166,6 +170,7 @@ ValidationError.args = {
   ],
   methodCanBeModeled: true,
   viewState,
+  onChange: () => {},
 };
 
 export const MultipleValidationErrors = Template.bind({});
@@ -180,4 +185,5 @@ MultipleValidationErrors.args = {
   ],
   methodCanBeModeled: true,
   viewState,
+  onChange: () => {},
 };
diff --git a/extensions/ql-vscode/src/stories/results/AlertTable.stories.tsx b/extensions/ql-vscode/src/stories/results/AlertTable.stories.tsx
index bfb179a1fed..d2cc19f3916 100644
--- a/extensions/ql-vscode/src/stories/results/AlertTable.stories.tsx
+++ b/extensions/ql-vscode/src/stories/results/AlertTable.stories.tsx
@@ -431,4 +431,7 @@ WithCodeFlows.args = {
       showRawResults={() => action("show-raw-results")}
     />
   ),
+  userSettings: {
+    shouldShowProvenance: true,
+  },
 };
diff --git a/extensions/ql-vscode/src/stories/types.d.ts b/extensions/ql-vscode/src/stories/types.d.ts
new file mode 100644
index 00000000000..1eabbb4297e
--- /dev/null
+++ b/extensions/ql-vscode/src/stories/types.d.ts
@@ -0,0 +1 @@
+declare module "*.module.css";
diff --git a/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts b/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts
index c49d9d3f27e..5b29eed8fd0 100644
--- a/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts
+++ b/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts
@@ -1,10 +1,9 @@
 import type { CancellationToken } from "vscode";
-import { Uri, window } from "vscode";
-import { join, sep, basename, relative } from "path";
-import { dump, load } from "js-yaml";
-import { copy, writeFile, readFile, mkdirp } from "fs-extra";
-import type { DirectoryResult } from "tmp-promise";
-import { dir, tmpName } from "tmp-promise";
+import { window } from "vscode";
+import { join, basename, relative } from "path";
+import { dump } from "js-yaml";
+import { copy, writeFile, readFile, mkdirp, remove } from "fs-extra";
+import { nanoid } from "nanoid";
 import { tmpDir } from "../tmp-dir";
 import { getOnDiskWorkspaceFolders } from "../common/vscode/workspace-folders";
 import type { Credentials } from "../common/authentication";
@@ -28,13 +27,7 @@ import {
 } from "./repository-selection";
 import type { Repository } from "./shared/repository";
 import type { DbManager } from "../databases/db-manager";
-import {
-  getQlPackFilePath,
-  FALLBACK_QLPACK_FILENAME,
-  QLPACK_FILENAMES,
-  QLPACK_LOCK_FILENAMES,
-} from "../common/ql";
-import type { QlPackFile } from "../packaging/qlpack-file";
+import { FALLBACK_QLPACK_FILENAME } from "../common/ql";
 import { expandShortPaths } from "../common/short-paths";
 import type { QlPackDetails } from "./ql-pack-details";
 import type { ModelPackDetails } from "../common/model-pack-details";
@@ -69,8 +62,6 @@ async function generateQueryPack(
   );
 
   const mustSynthesizePack = qlPackDetails.qlPackFilePath === undefined;
-  const cliSupportsMrvaPackCreate =
-    await cliServer.cliConstraints.supportsMrvaPackCreate();
 
   let targetPackPath: string;
   let needsInstall: boolean;
@@ -88,15 +79,6 @@ async function generateQueryPack(
 
     // Install packs, since we just synthesized a dependency on the language's standard library.
     needsInstall = true;
-  } else if (!cliSupportsMrvaPackCreate) {
-    // We need to copy the query pack to a temporary directory and then fix it up to work with MRVA.
-    targetPackPath = tmpDir.queryPackDir;
-    await copyExistingQueryPack(cliServer, qlPackDetails, targetPackPath);
-
-    // We should already have all the dependencies available, but these older versions of the CLI
-    // have a bug where they will not search `--additional-packs` during validation in `codeql pack bundle`.
-    // Installing the packs will ensure that any extension packs get put in the right place.
-    needsInstall = true;
   } else {
     // The CLI supports creating a MRVA query pack directly from the source pack.
     targetPackPath = qlPackDetails.qlPackRootPath;
@@ -114,27 +96,18 @@ async function generateQueryPack(
     await cliServer.clearCache();
   }
 
-  let precompilationOpts: string[];
-  if (cliSupportsMrvaPackCreate) {
-    const queryOpts = qlPackDetails.queryFiles.flatMap((q) => [
-      "--query",
-      join(targetPackPath, relative(qlPackDetails.qlPackRootPath, q)),
-    ]);
-
-    precompilationOpts = [
-      "--mrva",
-      ...queryOpts,
-      // We need to specify the extension packs as dependencies so that they are included in the MRVA pack.
-      // The version range doesn't matter, since they'll always be found by source lookup.
-      ...extensionPacks.map((p) => `--extension-pack=${p.name}@*`),
-    ];
-  } else {
-    precompilationOpts = ["--qlx"];
-
-    if (extensionPacks.length > 0) {
-      await addExtensionPacksAsDependencies(targetPackPath, extensionPacks);
-    }
-  }
+  const queryOpts = qlPackDetails.queryFiles.flatMap((q) => [
+    "--query",
+    join(targetPackPath, relative(qlPackDetails.qlPackRootPath, q)),
+  ]);
+
+  const precompilationOpts = [
+    "--mrva",
+    ...queryOpts,
+    // We need to specify the extension packs as dependencies so that they are included in the MRVA pack.
+    // The version range doesn't matter, since they'll always be found by source lookup.
+    ...extensionPacks.map((p) => `--extension-pack=${p.name}@*`),
+  ];
 
   const bundlePath = tmpDir.bundleFile;
   void extLogger.log(
@@ -182,93 +155,29 @@ async function createNewQueryPack(
   );
 }
 
-async function copyExistingQueryPack(
-  cliServer: CodeQLCliServer,
-  qlPackDetails: QlPackDetails,
-  targetPackPath: string,
-) {
-  const toCopy = await cliServer.packPacklist(
-    qlPackDetails.qlPackRootPath,
-    false,
-  );
-
-  // Also include query files that contain extensible predicates. These query files are not
-  // needed for the query to run, but they are needed for the query pack to pass deep validation
-  // of data extensions.
-  const metadata = await cliServer.generateExtensiblePredicateMetadata(
-    qlPackDetails.qlPackRootPath,
-  );
-  metadata.extensible_predicates.forEach((predicate) => {
-    if (predicate.path.endsWith(".ql")) {
-      toCopy.push(join(qlPackDetails.qlPackRootPath, predicate.path));
-    }
-  });
-
-  [
-    // also copy the lock file (either new name or old name) and the query file itself. These are not included in the packlist.
-    ...QLPACK_LOCK_FILENAMES.map((f) => join(qlPackDetails.qlPackRootPath, f)),
-    ...qlPackDetails.queryFiles,
-  ].forEach((absolutePath) => {
-    if (absolutePath) {
-      toCopy.push(absolutePath);
-    }
-  });
-
-  let copiedCount = 0;
-  await copy(qlPackDetails.qlPackRootPath, targetPackPath, {
-    filter: (file: string) =>
-      // copy file if it is in the packlist, or it is a parent directory of a file in the packlist
-      !!toCopy.find((f) => {
-        // Normalized paths ensure that Windows drive letters are capitalized consistently.
-        const normalizedPath = Uri.file(f).fsPath;
-        const matches =
-          normalizedPath === file || normalizedPath.startsWith(file + sep);
-        if (matches) {
-          copiedCount++;
-        }
-        return matches;
-      }),
-  });
-
-  void extLogger.log(`Copied ${copiedCount} files to ${targetPackPath}`);
-
-  await fixPackFile(targetPackPath, qlPackDetails);
-}
-
 interface RemoteQueryTempDir {
-  remoteQueryDir: DirectoryResult;
+  remoteQueryDir: string;
   queryPackDir: string;
   compiledPackDir: string;
   bundleFile: string;
 }
 
 async function createRemoteQueriesTempDirectory(): Promise<RemoteQueryTempDir> {
-  const shortRemoteQueryDir = await dir({
-    dir: tmpDir.name,
-    unsafeCleanup: true,
-  });
   // Expand 8.3 filenames here to work around a CLI bug where `codeql pack bundle` produces an empty
   // archive if the pack path contains any 8.3 components.
-  const remoteQueryDir = {
-    ...shortRemoteQueryDir,
-    path: await expandShortPaths(shortRemoteQueryDir.path, extLogger),
-  };
-  const queryPackDir = join(remoteQueryDir.path, "query-pack");
+  const tmpDirPath = await expandShortPaths(tmpDir.name, extLogger);
+
+  const remoteQueryDir = join(tmpDirPath, `remote-query-${nanoid()}`);
+  await mkdirp(remoteQueryDir);
+
+  const queryPackDir = join(remoteQueryDir, "query-pack");
   await mkdirp(queryPackDir);
-  const compiledPackDir = join(remoteQueryDir.path, "compiled-pack");
-  const bundleFile = await expandShortPaths(
-    await getPackedBundlePath(tmpDir.name),
-    extLogger,
-  );
-  return { remoteQueryDir, queryPackDir, compiledPackDir, bundleFile };
-}
 
-async function getPackedBundlePath(remoteQueryDir: string): Promise<string> {
-  return tmpName({
-    dir: remoteQueryDir,
-    postfix: "generated.tgz",
-    prefix: "qlpack",
-  });
+  const compiledPackDir = join(remoteQueryDir, "compiled-pack");
+
+  const bundleFile = join(remoteQueryDir, `qlpack-${nanoid()}-generated.tgz`);
+
+  return { remoteQueryDir, queryPackDir, compiledPackDir, bundleFile };
 }
 
 interface PreparedRemoteQuery {
@@ -337,7 +246,7 @@ export async function prepareRemoteQueryRun(
       token,
     );
   } finally {
-    await tempDir.remoteQueryDir.cleanup();
+    await remove(tempDir.remoteQueryDir);
   }
 
   if (token.isCancellationRequested) {
@@ -363,42 +272,6 @@ export async function prepareRemoteQueryRun(
   };
 }
 
-/**
- * Fixes the qlpack.yml or codeql-pack.yml file to be correct in the context of the MRVA request.
- *
- * Performs the following fixes:
- *
- * - Updates the default suite of the query pack. This is used to ensure
- *   only the specified query is run.
- * - Ensures the query pack name is set to the name expected by the server.
- * - Removes any `${workspace}` version references from the qlpack.yml or codeql-pack.yml file. Converts them
- *   to `*` versions.
- *
- * @param targetPackPath The path to the directory containing the target pack
- * @param qlPackDetails The details of the original QL pack
- */
-async function fixPackFile(
-  targetPackPath: string,
-  qlPackDetails: QlPackDetails,
-): Promise<void> {
-  const packPath = await getQlPackFilePath(targetPackPath);
-
-  // This should not happen since we create the pack ourselves.
-  if (!packPath) {
-    throw new Error(
-      `Could not find ${QLPACK_FILENAMES.join(
-        " or ",
-      )} file in '${targetPackPath}'`,
-    );
-  }
-  const qlpack = load(await readFile(packPath, "utf8")) as QlPackFile;
-
-  updateDefaultSuite(qlpack, qlPackDetails);
-  removeWorkspaceRefs(qlpack);
-
-  await writeFile(packPath, dump(qlpack));
-}
-
 async function getExtensionPacksToInject(
   cliServer: CodeQLCliServer,
   workspaceFolders: string[],
@@ -427,41 +300,6 @@ async function getExtensionPacksToInject(
   return result;
 }
 
-async function addExtensionPacksAsDependencies(
-  queryPackDir: string,
-  extensionPacks: ModelPackDetails[],
-): Promise<void> {
-  const qlpackFile = await getQlPackFilePath(queryPackDir);
-  if (!qlpackFile) {
-    throw new Error(
-      `Could not find ${QLPACK_FILENAMES.join(
-        " or ",
-      )} file in '${queryPackDir}'`,
-    );
-  }
-
-  const syntheticQueryPack = load(
-    await readFile(qlpackFile, "utf8"),
-  ) as QlPackFile;
-
-  const dependencies = syntheticQueryPack.dependencies ?? {};
-  extensionPacks.forEach(({ name }) => {
-    // Add this extension pack as a dependency. It doesn't matter which
-    // version we specify, since we are guaranteed that the extension pack
-    // is resolved from source at the given path.
-    dependencies[name] = "*";
-  });
-
-  syntheticQueryPack.dependencies = dependencies;
-
-  await writeFile(qlpackFile, dump(syntheticQueryPack));
-}
-
-function updateDefaultSuite(qlpack: QlPackFile, qlPackDetails: QlPackDetails) {
-  delete qlpack.defaultSuiteFile;
-  qlpack.defaultSuite = generateDefaultSuite(qlPackDetails);
-}
-
 function generateDefaultSuite(qlPackDetails: QlPackDetails) {
   const queries = qlPackDetails.queryFiles.map((query) => {
     const relativePath = relative(qlPackDetails.qlPackRootPath, query);
@@ -562,15 +400,3 @@ async function getControllerRepoFromApi(
     }
   }
 }
-
-function removeWorkspaceRefs(qlpack: QlPackFile) {
-  if (!qlpack.dependencies) {
-    return;
-  }
-
-  for (const [key, value] of Object.entries(qlpack.dependencies)) {
-    if (value === "${workspace}") {
-      qlpack.dependencies[key] = "*";
-    }
-  }
-}
diff --git a/extensions/ql-vscode/src/variant-analysis/variant-analysis-manager.ts b/extensions/ql-vscode/src/variant-analysis/variant-analysis-manager.ts
index 4e56c3cea7f..9bb707a9775 100644
--- a/extensions/ql-vscode/src/variant-analysis/variant-analysis-manager.ts
+++ b/extensions/ql-vscode/src/variant-analysis/variant-analysis-manager.ts
@@ -73,6 +73,7 @@ import type {
   VariantAnalysisCommands,
 } from "../common/commands";
 import { exportVariantAnalysisResults } from "./export-results";
+import { viewAutofixesForVariantAnalysisResults } from "./view-autofixes";
 import {
   readRepoStates,
   REPO_STATES_FILENAME,
@@ -424,7 +425,7 @@ export class VariantAnalysisManager
         this.app.credentials,
         variantAnalysisSubmission,
       );
-    } catch (e: unknown) {
+    } catch (e) {
       // If the error is handled by the handleRequestError function, we don't need to throw
       if (
         e instanceof RequestError &&
@@ -967,6 +968,21 @@ export class VariantAnalysisManager
     );
   }
 
+  public async viewAutofixes(
+    variantAnalysisId: number,
+    filterSort: RepositoriesFilterSortStateWithIds = defaultFilterSortState,
+  ) {
+    await viewAutofixesForVariantAnalysisResults(
+      this,
+      this.variantAnalysisResultsManager,
+      variantAnalysisId,
+      filterSort,
+      this.app.credentials,
+      this.app,
+      this.cliServer,
+    );
+  }
+
   public async copyRepoListToClipboard(
     variantAnalysisId: number,
     filterSort: RepositoriesFilterSortStateWithIds = defaultFilterSortState,
diff --git a/extensions/ql-vscode/src/variant-analysis/variant-analysis-results-manager.ts b/extensions/ql-vscode/src/variant-analysis/variant-analysis-results-manager.ts
index 0f24e950325..01e27410ff0 100644
--- a/extensions/ql-vscode/src/variant-analysis/variant-analysis-results-manager.ts
+++ b/extensions/ql-vscode/src/variant-analysis/variant-analysis-results-manager.ts
@@ -44,6 +44,7 @@ export type LoadResultsOptions = {
 
 export class VariantAnalysisResultsManager extends DisposableObject {
   private static readonly RESULTS_DIRECTORY = "results";
+  private static readonly RESULTS_SARIF_FILENAME = "results.sarif";
 
   private readonly cachedResults: Map<
     CacheKey,
@@ -212,7 +213,10 @@ export class VariantAnalysisResultsManager extends DisposableObject {
       storageDirectory,
       VariantAnalysisResultsManager.RESULTS_DIRECTORY,
     );
-    const sarifPath = join(resultsDirectory, "results.sarif");
+    const sarifPath = join(
+      resultsDirectory,
+      VariantAnalysisResultsManager.RESULTS_SARIF_FILENAME,
+    );
     const bqrsPath = join(resultsDirectory, "results.bqrs");
 
     let interpretedResults: AnalysisAlert[] | undefined;
@@ -294,6 +298,17 @@ export class VariantAnalysisResultsManager extends DisposableObject {
     return join(variantAnalysisStoragePath, fullName);
   }
 
+  public getRepoResultsSarifStoragePath(
+    variantAnalysisStoragePath: string,
+    fullName: string,
+  ): string {
+    return join(
+      this.getRepoStorageDirectory(variantAnalysisStoragePath, fullName),
+      VariantAnalysisResultsManager.RESULTS_DIRECTORY,
+      VariantAnalysisResultsManager.RESULTS_SARIF_FILENAME,
+    );
+  }
+
   private createGitHubFileLinkPrefix(fullName: string, sha: string): string {
     return new URL(
       `/${fullName}/blob/${sha}`,
diff --git a/extensions/ql-vscode/src/variant-analysis/variant-analysis-view-manager.ts b/extensions/ql-vscode/src/variant-analysis/variant-analysis-view-manager.ts
index cc531c558e7..db591ac3d95 100644
--- a/extensions/ql-vscode/src/variant-analysis/variant-analysis-view-manager.ts
+++ b/extensions/ql-vscode/src/variant-analysis/variant-analysis-view-manager.ts
@@ -34,4 +34,8 @@ export interface VariantAnalysisViewManager<
     variantAnalysisId: number,
     filterSort?: RepositoriesFilterSortStateWithIds,
   ): Promise<void>;
+  viewAutofixes(
+    variantAnalysisId: number,
+    filterSort?: RepositoriesFilterSortStateWithIds,
+  ): Promise<void>;
 }
diff --git a/extensions/ql-vscode/src/variant-analysis/variant-analysis-view.ts b/extensions/ql-vscode/src/variant-analysis/variant-analysis-view.ts
index f8a87e47b87..555a3686e68 100644
--- a/extensions/ql-vscode/src/variant-analysis/variant-analysis-view.ts
+++ b/extensions/ql-vscode/src/variant-analysis/variant-analysis-view.ts
@@ -27,6 +27,7 @@ import type { App } from "../common/app";
 import {
   getVariantAnalysisDefaultResultsFilter,
   getVariantAnalysisDefaultResultsSort,
+  isCanary,
 } from "../config";
 
 export class VariantAnalysisView
@@ -53,6 +54,13 @@ export class VariantAnalysisView
     panel.reveal(undefined, true);
 
     await this.waitForPanelLoaded();
+
+    await this.postMessage({
+      t: "setVariantAnalysisUserSettings",
+      variantAnalysisUserSettings: {
+        shouldShowViewAutofixesButton: isCanary(),
+      },
+    });
   }
 
   public async updateView(variantAnalysis: VariantAnalysis): Promise<void> {
@@ -135,6 +143,12 @@ export class VariantAnalysisView
       case "openQueryText":
         await this.manager.openQueryText(this.variantAnalysisId);
         break;
+      case "viewAutofixes":
+        await this.manager.viewAutofixes(
+          this.variantAnalysisId,
+          msg.filterSort,
+        );
+        break;
       case "copyRepositoryList":
         await this.manager.copyRepoListToClipboard(
           this.variantAnalysisId,
diff --git a/extensions/ql-vscode/src/variant-analysis/view-autofixes.ts b/extensions/ql-vscode/src/variant-analysis/view-autofixes.ts
new file mode 100644
index 00000000000..de986bed080
--- /dev/null
+++ b/extensions/ql-vscode/src/variant-analysis/view-autofixes.ts
@@ -0,0 +1,912 @@
+import type { RepositoriesFilterSortStateWithIds } from "./shared/variant-analysis-filter-sort";
+import {
+  defaultFilterSortState,
+  filterAndSortRepositoriesWithResults,
+} from "./shared/variant-analysis-filter-sort";
+import type {
+  VariantAnalysis,
+  VariantAnalysisRepositoryTask,
+} from "./shared/variant-analysis";
+import type { Credentials } from "../common/authentication";
+import { extLogger } from "../common/logging/vscode";
+import type { App } from "../common/app";
+import type { CodeQLCliServer } from "../codeql-cli/cli";
+import {
+  pathExists,
+  ensureDir,
+  remove,
+  unlink,
+  readFile,
+  writeFile,
+  createWriteStream,
+} from "fs-extra";
+import {
+  withProgress,
+  progressUpdate,
+  reportStreamProgress,
+} from "../common/vscode/progress";
+import type { ProgressCallback } from "../common/vscode/progress";
+import { join, parse } from "path";
+import { pluralize } from "../common/word";
+import { readRepoTask } from "./repo-tasks-store";
+import { tmpDir } from "../tmp-dir";
+import { spawn } from "child_process";
+import type { execFileSync } from "child_process";
+import { tryOpenExternalFile } from "../common/vscode/external-files";
+import type { VariantAnalysisManager } from "./variant-analysis-manager";
+import type { VariantAnalysisResultsManager } from "./variant-analysis-results-manager";
+import {
+  getAutofixPath,
+  getAutofixModel,
+  downloadTimeout,
+  AUTOFIX_PATH,
+  AUTOFIX_MODEL,
+} from "../config";
+import { getErrorMessage } from "../common/helpers-pure";
+import { createTimeoutSignal } from "../common/fetch-stream";
+import { unzipToDirectoryConcurrently } from "../common/unzip-concurrently";
+import { reportUnzipProgress } from "../common/vscode/unzip-progress";
+import { getDirectoryNamesInsidePath } from "../common/files";
+import { Readable } from "stream";
+
+// Limit to three repos when generating autofixes so not sending
+// too many requests to autofix. Since we only need to validate
+// a handle of autofixes for each query, this should be sufficient.
+// Consider increasing this in the future if needed.
+const MAX_NUM_REPOS: number = 3;
+// Similarly, limit to three fixes per repo.
+const MAX_NUM_FIXES: number = 3;
+
+/**
+ * Generates autofixes for the results of a variant analysis.
+ */
+export async function viewAutofixesForVariantAnalysisResults(
+  variantAnalysisManager: VariantAnalysisManager,
+  variantAnalysisResultsManager: VariantAnalysisResultsManager,
+  variantAnalysisId: number,
+  filterSort: RepositoriesFilterSortStateWithIds = defaultFilterSortState,
+  credentials: Credentials,
+  app: App,
+  cliServer: CodeQLCliServer,
+): Promise<void> {
+  await withProgress(
+    async (progress: ProgressCallback) => {
+      // Get the path to the local autofix installation.
+      const localAutofixPath = await findLocalAutofix();
+
+      // Get the variant analysis with the given id.
+      const variantAnalysis =
+        variantAnalysisManager.tryGetVariantAnalysis(variantAnalysisId);
+      if (!variantAnalysis) {
+        throw new Error(`No variant analysis with id: ${variantAnalysisId}`);
+      }
+
+      // Generate the query help and output it to the override directory.
+      await overrideQueryHelp(variantAnalysis, cliServer, localAutofixPath);
+
+      // Get the full names (nwos) of the selected repositories.
+      const selectedRepoNames = getSelectedRepositoryNames(
+        variantAnalysis,
+        filterSort,
+      );
+
+      // Get storage paths for the autofix results.
+      const {
+        variantAnalysisIdStoragePath,
+        sourceRootsStoragePath,
+        autofixOutputStoragePath,
+      } = await getStoragePaths(variantAnalysisManager, variantAnalysisId);
+
+      // Process the selected repositories:
+      //  Get sarif
+      //  Download source root
+      //  Run autofix and output results
+      progress(
+        progressUpdate(
+          1,
+          2,
+          `Processing ${pluralize(selectedRepoNames.length, "repository", "repositories")}`,
+        ),
+      );
+      const outputTextFiles = await processSelectedRepositories(
+        variantAnalysisResultsManager,
+        selectedRepoNames,
+        variantAnalysisIdStoragePath,
+        sourceRootsStoragePath,
+        autofixOutputStoragePath,
+        localAutofixPath,
+        credentials,
+      );
+
+      // Output results from all repos to a combined markdown file.
+      progress(progressUpdate(2, 2, `Finalizing autofix results`));
+      const combinedOutputMarkdownFile = join(
+        autofixOutputStoragePath,
+        "autofix-output.md",
+      );
+      await mergeFiles(outputTextFiles, combinedOutputMarkdownFile, false);
+
+      // Open the combined markdown file.
+      await tryOpenExternalFile(app.commands, combinedOutputMarkdownFile);
+    },
+    {
+      title: "Generating Autofixes",
+      cancellable: false, // not cancellable for now
+    },
+  );
+}
+
+/**
+ * Finds the local autofix installation path from the `codeQL.autofix.path` setting.
+ * Throws an error if the path is not set or does not exist.
+ * @returns An object containing the local autofix path.
+ * @throws Error if the `codeQL.autofix.path` setting is not set or the path does not exist.
+ */
+async function findLocalAutofix(): Promise<string> {
+  const localAutofixPath = getAutofixPath();
+  if (!localAutofixPath) {
+    throw new Error(
+      `Path to local autofix installation not found. Make sure ${AUTOFIX_PATH.qualifiedName} is set correctly. Internal GitHub access required.`,
+    );
+  }
+  if (!(await pathExists(localAutofixPath))) {
+    throw new Error(`Local autofix path ${localAutofixPath} does not exist.`);
+  }
+  return localAutofixPath;
+}
+
+/**
+ * Overrides the query help from a given variant analysis
+ * at a location within the `localAutofixPath` directory .
+ */
+async function overrideQueryHelp(
+  variantAnalysis: VariantAnalysis,
+  cliServer: CodeQLCliServer,
+  localAutofixPath: string,
+): Promise<void> {
+  // Get path to the query used by the variant analysis.
+  const queryFilePath = variantAnalysis.query.filePath;
+  if (!(await pathExists(queryFilePath))) {
+    throw new Error(`Query file used by variant analysis not found.`);
+  }
+  const parsedQueryFilePath = parse(queryFilePath);
+  const queryFilePathNoExt = join(
+    parsedQueryFilePath.dir,
+    parsedQueryFilePath.name,
+  );
+
+  // Get the path to the query help, which may be either a `.qhelp` or a `.md` file.
+  // Note: we assume that the name of the query file is the same as the name of the query help file.
+  const queryHelpFilePathQhelp = `${queryFilePathNoExt}.qhelp`;
+  const queryHelpFilePathMarkdown = `${queryFilePathNoExt}.md`;
+
+  // Set `queryHelpFilePath` to the existing extension type.
+  let queryHelpFilePath: string;
+  if (await pathExists(queryHelpFilePathQhelp)) {
+    queryHelpFilePath = queryHelpFilePathQhelp;
+  } else if (await pathExists(queryHelpFilePathMarkdown)) {
+    queryHelpFilePath = queryHelpFilePathMarkdown;
+  } else {
+    throw new Error(
+      `Could not find query help file at either ${queryHelpFilePathQhelp} or ${queryHelpFilePathMarkdown}. Check that the query help file exists and is named correctly.`,
+    );
+  }
+
+  // Get the query metadata.
+  let metadata;
+  try {
+    metadata = await cliServer.resolveMetadata(queryFilePath);
+  } catch (e) {
+    throw new Error(
+      `Could not resolve query metadata for ${queryFilePath}. Reason: ${getErrorMessage(e)}`,
+    );
+  }
+  // Get the query ID (used for the overridden query help's filename).
+  const queryId = metadata.id;
+  if (!queryId) {
+    throw new Error(`Query metadata for ${queryFilePath} is missing an ID.`);
+  }
+  // Replace `/` with `-` for use with the overridden query help's filename.
+  // Use `replaceAll` since some query IDs have multiple slashes.
+  const queryIdWithDash = queryId.replaceAll("/", "-");
+
+  // Get the path to the output directory for overriding the query help.
+  // Note: the path to this directory may change in the future.
+  const queryHelpOverrideDirectory = join(
+    localAutofixPath,
+    "prompt-templates",
+    "qhelps",
+    `${queryIdWithDash}.md`,
+  );
+
+  await cliServer.generateQueryHelp(
+    queryHelpFilePath,
+    queryHelpOverrideDirectory,
+  );
+}
+
+/**
+ * Gets the full names (owner/repo) of the selected
+ * repositories from the given variant analysis while
+ * limiting the number of repositories to `MAX_NUM_REPOS`.
+ */
+function getSelectedRepositoryNames(
+  variantAnalysis: VariantAnalysis,
+  filterSort: RepositoriesFilterSortStateWithIds,
+): string[] {
+  // Get the repositories that were selected by the user.
+  const filteredRepositories = filterAndSortRepositoriesWithResults(
+    variantAnalysis.scannedRepos,
+    filterSort,
+  );
+
+  // Get the full names (owner/repo = nwo) of the selected repos.
+  let fullNames = filteredRepositories
+    ?.filter((a) => a.resultCount && a.resultCount > 0)
+    .map((a) => a.repository.fullName);
+  if (!fullNames || fullNames.length === 0) {
+    throw new Error("No repositories with results found.");
+  }
+
+  // Limit to MAX_NUM_REPOS by slicing the array.
+  if (fullNames.length > MAX_NUM_REPOS) {
+    fullNames = fullNames.slice(0, MAX_NUM_REPOS);
+    void extLogger.showWarningMessage(
+      `Only the first ${MAX_NUM_REPOS} repos (${fullNames.join(", ")}) will be included in the Autofix results.`,
+    );
+  }
+
+  return fullNames;
+}
+
+/**
+ * Gets the storage paths needed for the autofix results.
+ */
+async function getStoragePaths(
+  variantAnalysisManager: VariantAnalysisManager,
+  variantAnalysisId: number,
+): Promise<{
+  variantAnalysisIdStoragePath: string;
+  sourceRootsStoragePath: string;
+  autofixOutputStoragePath: string;
+}> {
+  // Confirm storage path for the variant analysis ID exists.
+  const variantAnalysisIdStoragePath =
+    variantAnalysisManager.getVariantAnalysisStorageLocation(variantAnalysisId);
+  if (!(await pathExists(variantAnalysisIdStoragePath))) {
+    throw new Error(
+      `Variant analysis storage location does not exist: ${variantAnalysisIdStoragePath}`,
+    );
+  }
+
+  // Storage path for all autofix info.
+  const autofixStoragePath = join(variantAnalysisIdStoragePath, "autofix");
+
+  // Storage path for the source roots used with autofix.
+  const sourceRootsStoragePath = join(autofixStoragePath, "source-roots");
+  await ensureDir(sourceRootsStoragePath);
+
+  // Storage path for the autofix output.
+  let autofixOutputStoragePath = join(autofixStoragePath, "output");
+  // If the path already exists, assume that it's a previous run
+  // and append "-n" to the end of the path where n is the next available number.
+  if (await pathExists(autofixOutputStoragePath)) {
+    let i = 1;
+    while (await pathExists(autofixOutputStoragePath + i.toString())) {
+      i++;
+    }
+    autofixOutputStoragePath = autofixOutputStoragePath += i.toString();
+  }
+  await ensureDir(autofixOutputStoragePath);
+
+  return {
+    variantAnalysisIdStoragePath,
+    sourceRootsStoragePath,
+    autofixOutputStoragePath,
+  };
+}
+
+/**
+ * Processes the selected repositories for autofix generation.
+ */
+async function processSelectedRepositories(
+  variantAnalysisResultsManager: VariantAnalysisResultsManager,
+  selectedRepoNames: string[],
+  variantAnalysisIdStoragePath: string,
+  sourceRootsStoragePath: string,
+  autofixOutputStoragePath: string,
+  localAutofixPath: string,
+  credentials: Credentials,
+): Promise<string[]> {
+  const outputTextFiles: string[] = [];
+  await Promise.all(
+    selectedRepoNames.map(async (nwo) =>
+      withProgress(
+        async (progressForRepo: ProgressCallback) => {
+          // Get the sarif file.
+          progressForRepo(progressUpdate(1, 3, `Getting sarif...`));
+          const sarifFile = await getRepoSarifFile(
+            variantAnalysisResultsManager,
+            variantAnalysisIdStoragePath,
+            nwo,
+          );
+
+          // Read the contents of the variant analysis' `repo_task.json` file,
+          // and confirm that the `databaseCommitSha` and `resultCount` exist.
+          const repoTask: VariantAnalysisRepositoryTask = await readRepoTask(
+            variantAnalysisResultsManager.getRepoStorageDirectory(
+              variantAnalysisIdStoragePath,
+              nwo,
+            ),
+          );
+          if (!repoTask.databaseCommitSha) {
+            throw new Error(`Missing database commit SHA for ${nwo}`);
+          }
+          if (!repoTask.resultCount) {
+            throw new Error(`Missing variant analysis result count for ${nwo}`);
+          }
+
+          // Download the source root.
+          // Using `0` as the progress step to force a dynamic vs static progress bar.
+          progressForRepo(progressUpdate(0, 3, `Fetching source root...`));
+          const srcRootPath = await downloadPublicCommitSource(
+            nwo,
+            repoTask.databaseCommitSha,
+            sourceRootsStoragePath,
+            credentials,
+            progressForRepo,
+          );
+
+          // Run autofix.
+          progressForRepo(progressUpdate(2, 3, `Running autofix...`));
+          await runAutofixForRepository(
+            nwo,
+            sarifFile,
+            srcRootPath,
+            localAutofixPath,
+            autofixOutputStoragePath,
+            repoTask.resultCount,
+            outputTextFiles,
+          );
+        },
+        {
+          title: `${nwo}`,
+          cancellable: false,
+        },
+      ),
+    ),
+  );
+
+  return outputTextFiles;
+}
+
+/**
+ * Gets the path to a SARIF file for a given `nwo`.
+ */
+async function getRepoSarifFile(
+  variantAnalysisResultsManager: VariantAnalysisResultsManager,
+  variantAnalysisIdStoragePath: string,
+  nwo: string,
+): Promise<string> {
+  if (
+    !(await variantAnalysisResultsManager.isVariantAnalysisRepoDownloaded(
+      variantAnalysisIdStoragePath,
+      nwo,
+    ))
+  ) {
+    throw new Error(`Variant analysis results not downloaded for ${nwo}`);
+  }
+  const sarifFile =
+    variantAnalysisResultsManager.getRepoResultsSarifStoragePath(
+      variantAnalysisIdStoragePath,
+      nwo,
+    );
+  if (!(await pathExists(sarifFile))) {
+    throw new Error(`SARIF file not found for ${nwo}`);
+  }
+  return sarifFile;
+}
+
+/**
+ * Downloads the source code of a public commit from a GitHub repository.
+ */
+async function downloadPublicCommitSource(
+  nwo: string,
+  sha: string,
+  outputPath: string,
+  credentials: Credentials,
+  progressCallback: ProgressCallback,
+): Promise<string> {
+  const [owner, repo] = nwo.split("/");
+  if (!owner || !repo) {
+    throw new Error(`Invalid repository name: ${nwo}`);
+  }
+
+  // Create output directory if it doesn't exist
+  await ensureDir(outputPath);
+
+  // Define the final checkout directory
+  const checkoutDir = join(
+    outputPath,
+    `${owner}-${repo}-${sha.substring(0, 7)}`,
+  );
+
+  // Check if directory already exists to avoid re-downloading
+  if (await pathExists(checkoutDir)) {
+    const dirNames = await getDirectoryNamesInsidePath(checkoutDir);
+    if (dirNames.length === 1) {
+      // The path to the source code should be a single directory inside `checkoutDir`.
+      const sourceRootDir = join(checkoutDir, dirNames[0]);
+      void extLogger.log(
+        `Source for ${nwo} at ${sha} already exists at ${sourceRootDir}.`,
+      );
+      return sourceRootDir;
+    } else {
+      // Remove `checkoutDir` to allow a re-download if the directory structure is unexpected.
+      void extLogger.log(
+        `Unexpected directory structure. Removing ${checkoutDir}`,
+      );
+      await remove(checkoutDir);
+    }
+  }
+
+  void extLogger.log(`Fetching source of repository ${nwo} at ${sha}...`);
+
+  try {
+    const octokit = await credentials.getOctokit();
+
+    // Get the zipball URL
+    const { url } = await octokit.rest.repos.downloadZipballArchive({
+      owner,
+      repo,
+      ref: sha,
+    });
+
+    // Create a temporary directory for downloading
+    const archivePath = join(
+      tmpDir.name,
+      `source-${owner}-${repo}-${Date.now()}.zip`,
+    );
+
+    // Set timeout
+    const {
+      signal,
+      onData,
+      dispose: disposeTimeout,
+    } = createTimeoutSignal(downloadTimeout());
+
+    // Fetch the url
+    let response: Response;
+    try {
+      response = await fetch(url, {
+        headers: {
+          Accept: "application/zip",
+        },
+        signal,
+      });
+    } catch (e) {
+      disposeTimeout();
+
+      if (e instanceof DOMException && e.name === "AbortError") {
+        const thrownError = new Error("The request timed out.");
+        thrownError.stack = e.stack;
+        throw thrownError;
+      }
+      throw new Error(
+        `Error fetching source root. Reason: ${getErrorMessage(e)}`,
+      );
+    }
+
+    // Download the source root from the response body
+    const body = response.body;
+    if (!body) {
+      throw new Error("No response body found");
+    }
+
+    const archiveFileStream = createWriteStream(archivePath);
+
+    const contentLength = response.headers.get("content-length");
+    const totalNumBytes = contentLength
+      ? parseInt(contentLength, 10)
+      : undefined;
+
+    const reportProgress = reportStreamProgress(
+      "Downloading source root...",
+      totalNumBytes,
+      progressCallback,
+    );
+
+    try {
+      const readable = Readable.fromWeb(body);
+      readable.on("data", (chunk) => {
+        onData();
+        reportProgress(chunk?.length ?? 0);
+      });
+      await new Promise((resolve, reject) => {
+        readable
+          .pipe(archiveFileStream)
+          .on("error", (err) => {
+            reject(err);
+          })
+          .on("finish", () => resolve(undefined));
+      });
+
+      await new Promise((resolve, reject) => {
+        archiveFileStream.close((err) => {
+          if (err) {
+            reject(err);
+          }
+          resolve(undefined);
+        });
+      });
+    } catch (e) {
+      // Close and remove the file if an error occurs
+      archiveFileStream.close(() => {
+        void remove(archivePath);
+      });
+
+      if (e instanceof DOMException && e.name === "AbortError") {
+        const thrownError = new Error("The download timed out.");
+        thrownError.stack = e.stack;
+        throw thrownError;
+      }
+
+      throw new Error(
+        `Error downloading source root. Reason: ${getErrorMessage(e)}`,
+      );
+    } finally {
+      disposeTimeout();
+    }
+
+    void extLogger.log(`Download complete, extracting source...`);
+
+    // Extract the downloaded zip file
+    await unzipToDirectoryConcurrently(
+      archivePath,
+      checkoutDir,
+      reportUnzipProgress(`Unzipping source root...`, progressCallback),
+    );
+    await remove(archivePath);
+
+    // Since `unzipToDirectoryConcurrently` extracts to a directory within
+    // `checkoutDir`, we need to return the path to that extracted directory.
+    const dirNames = await getDirectoryNamesInsidePath(checkoutDir);
+    if (dirNames.length === 1) {
+      return join(checkoutDir, dirNames[0]);
+    } else {
+      throw new Error(
+        `Expected exactly one unzipped source directory for ${nwo}, but found ${dirNames.length}.`,
+      );
+    }
+  } catch (error) {
+    await remove(checkoutDir);
+    throw new Error(
+      `Failed to download ${nwo} at ${sha}:. Reason: ${getErrorMessage(error)}`,
+    );
+  }
+}
+
+/**
+ * Runs autofix for a given repository (nwo).
+ */
+async function runAutofixForRepository(
+  nwo: string,
+  sarifFile: string,
+  srcRootPath: string,
+  localAutofixPath: string,
+  autofixOutputStoragePath: string,
+  resultCount: number,
+  outputTextFiles: string[],
+): Promise<void> {
+  // Get storage paths for the autofix results for this repository.
+  const {
+    repoAutofixOutputStoragePath,
+    outputTextFilePath,
+    transcriptFilePath,
+    fixDescriptionFilePath,
+  } = await getRepoStoragePaths(autofixOutputStoragePath, nwo);
+
+  // Get autofix binary.
+  // Switch to Go binary in the future and have user pass full path
+  // in an environment variable instead of hardcoding part here.
+  const cocofixBin = join(process.cwd(), localAutofixPath, "bin", "cocofix.js");
+
+  // Limit number of fixes generated.
+  const limitFixesBoolean: boolean = resultCount > MAX_NUM_FIXES;
+  if (limitFixesBoolean) {
+    void extLogger.log(
+      `Only generating autofixes for the first ${MAX_NUM_FIXES} alerts for ${nwo}.`,
+    );
+
+    // Run autofix in a loop for the first MAX_NUM_FIXES alerts.
+    // Not an ideal solution, but avoids modifying the input SARIF file.
+    const tempOutputTextFiles: string[] = [];
+    const fixDescriptionFiles: string[] = [];
+    const transcriptFiles: string[] = [];
+    for (let i = 0; i < MAX_NUM_FIXES; i++) {
+      const tempOutputTextFilePath = appendSuffixToFilePath(
+        outputTextFilePath,
+        i.toString(),
+      );
+      const tempFixDescriptionFilePath = appendSuffixToFilePath(
+        fixDescriptionFilePath,
+        i.toString(),
+      );
+      const tempTranscriptFilePath = appendSuffixToFilePath(
+        transcriptFilePath,
+        i.toString(),
+      );
+
+      tempOutputTextFiles.push(tempOutputTextFilePath);
+      fixDescriptionFiles.push(tempFixDescriptionFilePath);
+      transcriptFiles.push(tempTranscriptFilePath);
+
+      await runAutofixOnResults(
+        cocofixBin,
+        sarifFile,
+        srcRootPath,
+        tempOutputTextFilePath,
+        tempFixDescriptionFilePath,
+        tempTranscriptFilePath,
+        repoAutofixOutputStoragePath,
+        i,
+      );
+    }
+
+    // Merge the output files together.
+    // Caveat that autofix will call each alert "alert 0", which will look a bit odd in the merged output file.
+    await mergeFiles(tempOutputTextFiles, outputTextFilePath);
+    await mergeFiles(fixDescriptionFiles, fixDescriptionFilePath);
+    await mergeFiles(transcriptFiles, transcriptFilePath);
+  } else {
+    // Run autofix once for all alerts.
+    await runAutofixOnResults(
+      cocofixBin,
+      sarifFile,
+      srcRootPath,
+      outputTextFilePath,
+      fixDescriptionFilePath,
+      transcriptFilePath,
+      repoAutofixOutputStoragePath,
+    );
+  }
+
+  // Format the output text file with markdown.
+  await formatWithMarkdown(outputTextFilePath, `${nwo}`);
+
+  // Save output text files from each repo to later merge
+  // into a single markdown file containing all results.
+  outputTextFiles.push(outputTextFilePath);
+}
+
+/**
+ * Gets the storage paths for the autofix results for a given repository.
+ */
+async function getRepoStoragePaths(
+  autofixOutputStoragePath: string,
+  nwo: string,
+) {
+  // Create output directories for repo's autofix results.
+  const repoAutofixOutputStoragePath = join(
+    autofixOutputStoragePath,
+    nwo.replaceAll("/", "-"),
+  );
+  await ensureDir(repoAutofixOutputStoragePath);
+  return {
+    repoAutofixOutputStoragePath,
+    outputTextFilePath: join(repoAutofixOutputStoragePath, "output.txt"),
+    transcriptFilePath: join(repoAutofixOutputStoragePath, "transcript.md"),
+    fixDescriptionFilePath: join(
+      repoAutofixOutputStoragePath,
+      "fix-description.md",
+    ),
+  };
+}
+
+/**
+ * Runs autofix on the results in the given SARIF file.
+ */
+async function runAutofixOnResults(
+  cocofixBin: string,
+  sarifFile: string,
+  srcRootPath: string,
+  outputTextFilePath: string,
+  fixDescriptionFilePath: string,
+  transcriptFilePath: string,
+  workDir: string,
+  alertNumber?: number, // Optional parameter for specific alert
+): Promise<void> {
+  // Get autofix model from user settings.
+  const autofixModel = getAutofixModel();
+  if (!autofixModel) {
+    throw new Error(
+      `Autofix model not found. Make sure ${AUTOFIX_MODEL.qualifiedName} is set correctly.`,
+    );
+  }
+  // Set up args for autofix command.
+  const autofixArgs = [
+    "--sarif",
+    sarifFile,
+    "--source-root",
+    srcRootPath,
+    "--model",
+    autofixModel,
+    "--dev",
+    "--no-cache",
+    "--format",
+    "text",
+    "--diff-style",
+    "diff", // could do "text" instead if want line of "=" between fixes
+    "--output",
+    outputTextFilePath,
+    "--fix-description",
+    fixDescriptionFilePath,
+    "--transcript",
+    transcriptFilePath,
+  ];
+
+  // Add alert number argument if provided
+  if (alertNumber !== undefined) {
+    autofixArgs.push("--only-alert-number", alertNumber.toString());
+  }
+
+  await execAutofix(
+    cocofixBin,
+    autofixArgs,
+    {
+      cwd: workDir,
+      env: {
+        CAPI_DEV_KEY: process.env.CAPI_DEV_KEY,
+        PATH: process.env.PATH,
+      },
+    },
+    true,
+  );
+}
+
+/**
+ * Executes the autofix command.
+ */
+function execAutofix(
+  bin: string,
+  args: string[],
+  options: Parameters<typeof execFileSync>[2],
+  showCommand?: boolean,
+): Promise<void> {
+  return new Promise((resolve, reject) => {
+    try {
+      const cwd = options?.cwd || process.cwd();
+      if (showCommand) {
+        void extLogger.log(`Spawning '${bin} ${args.join(" ")}' in ${cwd}`);
+      }
+
+      let stdoutBuffer = "";
+      let stderrBuffer = "";
+
+      const p = spawn(bin, args, {
+        stdio: ["ignore", "pipe", "pipe"],
+        ...options,
+      });
+
+      // Listen for stdout
+      p.stdout?.on("data", (data) => {
+        stdoutBuffer += data.toString();
+      });
+
+      // Listen for stderr
+      p.stderr?.on("data", (data) => {
+        stderrBuffer += data.toString();
+      });
+
+      // Listen for errors
+      p.on("error", reject);
+
+      // Listen for process exit
+      p.on("exit", (code) => {
+        // Log collected output
+        if (stdoutBuffer.trim()) {
+          void extLogger.log(`Autofix stdout:\n${stdoutBuffer.trim()}`);
+        }
+
+        if (stderrBuffer.trim()) {
+          void extLogger.log(`Autofix stderr:\n${stderrBuffer.trim()}`);
+        }
+
+        if (code === 0) {
+          resolve();
+        } else {
+          reject(new Error(`Autofix process exited with code ${code}.`));
+        }
+      });
+    } catch (e) {
+      reject(e);
+    }
+  });
+}
+
+/**
+ * Creates a new file path by appending the given suffix.
+ * @param filePath The original file path.
+ * @param suffix The suffix to append to the file name (before the extension).
+ * @returns The new file path with the suffix appended.
+ */
+function appendSuffixToFilePath(filePath: string, suffix: string): string {
+  const { dir, name, ext } = parse(filePath);
+  return join(dir, `${name}-${suffix}${ext}`);
+}
+
+/**
+ * Merges the given `inputFiles` into a single `outputFile`.
+ * @param inputFiles - The list of input files to merge.
+ * @param outputFile - The output file path.
+ * @param deleteOriginalFiles - Whether to delete the original input files after merging.
+ */
+async function mergeFiles(
+  inputFiles: string[],
+  outputFile: string,
+  deleteOriginalFiles: boolean = true,
+): Promise<void> {
+  try {
+    // Check if any input files do not exist and return if so.
+    const pathChecks = await Promise.all(
+      inputFiles.map(async (path) => ({
+        exists: await pathExists(path),
+      })),
+    );
+    const anyPathMissing = pathChecks.some((check) => !check.exists);
+    if (inputFiles.length === 0 || anyPathMissing) {
+      return;
+    }
+
+    // Merge the files
+    const contents = await Promise.all(
+      inputFiles.map((file) => readFile(file, "utf8")),
+    );
+
+    // Write merged content
+    await writeFile(outputFile, contents.join("\n"));
+
+    // Delete original files
+    if (deleteOriginalFiles) {
+      await Promise.all(inputFiles.map((file) => unlink(file)));
+    }
+  } catch (error) {
+    throw new Error(`Error merging files. Reason: ${getErrorMessage(error)}`);
+  }
+}
+
+/**
+ * Formats the given input file with the specified header.
+ * @param inputFile The path to the input file to format.
+ * @param header The header to include in the formatted output.
+ */
+async function formatWithMarkdown(
+  inputFile: string,
+  header: string,
+): Promise<void> {
+  try {
+    // Check if the input file exists
+    const exists = await pathExists(inputFile);
+    if (!exists) {
+      return;
+    }
+
+    // Read the input file content
+    const content = await readFile(inputFile, "utf8");
+
+    const frontFormatting: string =
+      "<details><summary>Fix suggestion details</summary>\n\n```diff\n";
+
+    const backFormatting: string =
+      "```\n\n</details>\n\n ### Notes\n - notes placeholder\n\n";
+
+    // Format the content with Markdown
+    // Replace ``` in the content with \``` to avoid breaking the Markdown code block
+    const formattedContent = `## ${header}\n\n${frontFormatting}${content.replaceAll("```", "\\```")}${backFormatting}`;
+
+    // Write the formatted content back to the file
+    await writeFile(inputFile, formattedContent);
+  } catch (error) {
+    throw new Error(`Error formatting file. Reason: ${getErrorMessage(error)}`);
+  }
+}
diff --git a/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.module.css b/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.module.css
new file mode 100644
index 00000000000..70a8e8a1577
--- /dev/null
+++ b/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.module.css
@@ -0,0 +1,56 @@
+/* Styles have been copied from https://vscode-elements.github.io/elements-lite/components/action-button/configurator/ */
+.actionButton {
+  align-items: center;
+  background-color: transparent;
+  border-color: transparent;
+  border-style: solid;
+  border-width: 1px;
+  border-radius: 5px;
+  color: var(--vscode-foreground);
+  display: inline-flex;
+  cursor: pointer;
+  padding: 0;
+  user-select: none;
+}
+
+.actionButton:disabled {
+  color: var(--vscode-disabledForeground);
+  cursor: default;
+  pointer-events: none;
+}
+
+.actionButton :global(.codicon),
+.actionButton svg {
+  color: var(--vscode-icon-foreground);
+  display: block;
+  padding: 2px;
+}
+
+.actionButton svg {
+  box-sizing: content-box;
+  height: 16px;
+  width: 16px;
+}
+
+.actionButton:disabled :global(.codicon),
+.actionButton:disabled svg {
+  color: var(--vscode-disabledForeground);
+}
+
+.actionButton:hover {
+  background-color: var(--vscode-toolbar-hoverBackground);
+  outline: 1px dotted var(--vscode-contrastActiveBorder, transparent);
+  outline-offset: -1px;
+}
+
+.actionButton:active {
+  background-color: var(--vscode-toolbar-activeBackground);
+}
+
+.actionButton:focus {
+  outline: none;
+}
+
+.actionButton:focus-visible {
+  border-color: var(--vscode-focusBorder);
+}
diff --git a/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.tsx b/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.tsx
new file mode 100644
index 00000000000..f673fd56f96
--- /dev/null
+++ b/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.tsx
@@ -0,0 +1,9 @@
+import styles from "./ActionButton.module.css";
+
+// This is needed because vscode-elements/elements does not implement
+// the same styles for icon buttons as vscode/webview-ui-toolkit
+export const ActionButton = (props: React.ComponentProps<"button">) => (
+  <button type="button" {...props} className={styles.actionButton}>
+    {props.children}
+  </button>
+);
diff --git a/extensions/ql-vscode/src/view/common/Badge.tsx b/extensions/ql-vscode/src/view/common/Badge.tsx
new file mode 100644
index 00000000000..cb9826bcab8
--- /dev/null
+++ b/extensions/ql-vscode/src/view/common/Badge.tsx
@@ -0,0 +1,8 @@
+import { VscodeBadge } from "@vscode-elements/react-elements";
+
+// This applies the counter variant by default so the border-radius attribute is set
+export const Badge = (props: React.ComponentProps<typeof VscodeBadge>) => (
+  <VscodeBadge variant="counter" {...props}>
+    {props.children}
+  </VscodeBadge>
+);
diff --git a/extensions/ql-vscode/src/view/common/CodePaths/CodeFlowsDropdown.tsx b/extensions/ql-vscode/src/view/common/CodePaths/CodeFlowsDropdown.tsx
index 277013084f1..cc232060f0a 100644
--- a/extensions/ql-vscode/src/view/common/CodePaths/CodeFlowsDropdown.tsx
+++ b/extensions/ql-vscode/src/view/common/CodePaths/CodeFlowsDropdown.tsx
@@ -1,6 +1,9 @@
 import type { ChangeEvent, SetStateAction } from "react";
 import { useCallback } from "react";
-import { VSCodeDropdown, VSCodeOption } from "@vscode/webview-ui-toolkit/react";
+import {
+  VscodeOption,
+  VscodeSingleSelect,
+} from "@vscode-elements/react-elements";
 
 import type { CodeFlow } from "../../../variant-analysis/shared/analysis-result";
 
@@ -35,12 +38,12 @@ export const CodeFlowsDropdown = ({
     .toString();
 
   return (
-    <VSCodeDropdown value={value} onChange={handleChange}>
+    <VscodeSingleSelect value={value} onChange={handleChange}>
       {codeFlows.map((codeFlow, index) => (
-        <VSCodeOption key={index} value={index.toString()}>
+        <VscodeOption key={index} value={index.toString()}>
           {getCodeFlowName(codeFlow)}
-        </VSCodeOption>
+        </VscodeOption>
       ))}
-    </VSCodeDropdown>
+    </VscodeSingleSelect>
   );
 };
diff --git a/extensions/ql-vscode/src/view/common/Link.tsx b/extensions/ql-vscode/src/view/common/Link.tsx
index 9fa73906433..a0e37b92bcd 100644
--- a/extensions/ql-vscode/src/view/common/Link.tsx
+++ b/extensions/ql-vscode/src/view/common/Link.tsx
@@ -3,12 +3,12 @@ import { styled } from "styled-components";
 export const Link = styled.a`
   background: transparent;
   box-sizing: border-box;
-  color: var(--link-foreground);
+  color: var(--vscode-textLink-foreground);
   cursor: pointer;
   fill: currentcolor;
-  font-family: var(--font-family);
-  font-size: var(--type-ramp-base-font-size);
-  line-height: var(--type-ramp-base-line-height);
+  font-family: var(--vscode-font-family);
+  font-size: var(--vscode-font-size);
+  line-height: normal;
   outline: none;
 
   &:hover {
diff --git a/extensions/ql-vscode/src/view/common/SearchBox.tsx b/extensions/ql-vscode/src/view/common/SearchBox.tsx
index 464d303fa7e..7837c143e76 100644
--- a/extensions/ql-vscode/src/view/common/SearchBox.tsx
+++ b/extensions/ql-vscode/src/view/common/SearchBox.tsx
@@ -1,12 +1,16 @@
 import { useCallback } from "react";
 import { styled } from "styled-components";
-import { VSCodeTextField } from "@vscode/webview-ui-toolkit/react";
+import { VscodeTextfield } from "@vscode-elements/react-elements";
 import { Codicon } from "./icon";
 
-const TextField = styled(VSCodeTextField)`
+const TextField = styled(VscodeTextfield)`
   width: 100%;
 `;
 
+const SearchIcon = styled(Codicon)`
+  margin: 0 8px;
+`;
+
 type Props = {
   value: string;
   placeholder: string;
@@ -37,7 +41,7 @@ export const SearchBox = ({
       onInput={handleInput}
       className={className}
     >
-      <Codicon name="search" label="Search..." slot="start" />
+      <SearchIcon name="search" label="Search..." slot="content-before" />
     </TextField>
   );
 };
diff --git a/extensions/ql-vscode/src/view/common/SuggestBox/SuggestBox.tsx b/extensions/ql-vscode/src/view/common/SuggestBox/SuggestBox.tsx
index 32240fac67e..7e190a6d05a 100644
--- a/extensions/ql-vscode/src/view/common/SuggestBox/SuggestBox.tsx
+++ b/extensions/ql-vscode/src/view/common/SuggestBox/SuggestBox.tsx
@@ -14,15 +14,15 @@ import {
   useRole,
 } from "@floating-ui/react";
 import { css, styled } from "styled-components";
-import { VSCodeTextField } from "@vscode/webview-ui-toolkit/react";
 import type { Option } from "./options";
 import { findMatchingOptions } from "./options";
 import { SuggestBoxItem } from "./SuggestBoxItem";
 import { LabelText } from "./LabelText";
 import type { Diagnostic } from "./diagnostics";
 import { useOpenKey } from "./useOpenKey";
+import { VscodeTextfield } from "@vscode-elements/react-elements";
 
-const Input = styled(VSCodeTextField)<{ $error: boolean }>`
+const Input = styled(VscodeTextfield)<{ $error: boolean }>`
   width: 100%;
   font-family: var(--vscode-editor-font-family);
 
@@ -96,7 +96,7 @@ export type SuggestBoxProps<
 
   /**
    * Can be used to render a different component for the input. This is used
-   * in testing to use default HTML components rather than the VSCodeTextField
+   * in testing to use default HTML components rather than the VscodeTextfield
    * for easier testing.
    * @param props The props returned by `getReferenceProps` of {@link useInteractions}
    */
diff --git a/extensions/ql-vscode/src/view/compare-performance/ComparePerformance.tsx b/extensions/ql-vscode/src/view/compare-performance/ComparePerformance.tsx
index d072310ea9c..c9fac0a09dc 100644
--- a/extensions/ql-vscode/src/view/compare-performance/ComparePerformance.tsx
+++ b/extensions/ql-vscode/src/view/compare-performance/ComparePerformance.tsx
@@ -18,7 +18,7 @@ import type {
 } from "../../log-insights/performance-comparison";
 import { formatDecimal } from "../../common/number";
 import { styled } from "styled-components";
-import { Codicon, ViewTitle, WarningBox } from "../common";
+import { Codicon, ViewTitle } from "../common";
 import { abbreviateRANames, abbreviateRASteps } from "./RAPrettyPrinter";
 import { Renaming, RenamingInput } from "./RenamingInput";
 
@@ -35,6 +35,8 @@ function isPresent<T>(x: Optional<T>): x is T {
 }
 
 interface PredicateInfo {
+  name: string;
+  raHash: string;
   tuples: number;
   evaluationCount: number;
   iterationCount: number;
@@ -43,23 +45,37 @@ interface PredicateInfo {
 }
 
 class ComparisonDataset {
+  /**
+   * Predicates indexed by a key consisting of the name and its pipeline hash.
+   * Unlike the RA hash, the pipeline hash only depends on the predicate's own pipeline.
+   */
+  public keyToIndex = new Map<string, number>();
+  public raToIndex = new Map<string, number>();
   public nameToIndex = new Map<string, number>();
   public cacheHitIndices: Set<number>;
   public sentinelEmptyIndices: Set<number>;
 
-  constructor(public data: PerformanceComparisonDataFromLog) {
-    const { names } = data;
-    const { nameToIndex } = this;
+  constructor(private data: PerformanceComparisonDataFromLog) {
+    const { names, raHashes, pipelineSummaryList } = data;
+    const { keyToIndex, raToIndex, nameToIndex } = this;
     for (let i = 0; i < names.length; i++) {
-      nameToIndex.set(names[i], i);
+      const name = names[i];
+      const pipelineHash = getPipelineSummaryHash(pipelineSummaryList[i]);
+      keyToIndex.set(`${name}@${pipelineHash}`, i);
+      nameToIndex.set(name, i);
+      raToIndex.set(raHashes[i], i);
     }
     this.cacheHitIndices = new Set(data.cacheHitIndices);
     this.sentinelEmptyIndices = new Set(data.sentinelEmptyIndices);
   }
 
-  getTupleCountInfo(name: string): Optional<PredicateInfo> {
-    const { data, nameToIndex, cacheHitIndices, sentinelEmptyIndices } = this;
-    const index = nameToIndex.get(name);
+  keys() {
+    return Array.from(this.keyToIndex.keys());
+  }
+
+  getTupleCountInfo(key: string): Optional<PredicateInfo> {
+    const { data, keyToIndex, cacheHitIndices, sentinelEmptyIndices } = this;
+    const index = keyToIndex.get(key);
     if (index == null) {
       return AbsentReason.NotSeen;
     }
@@ -72,6 +88,8 @@ class ComparisonDataset {
       }
     }
     return {
+      name: data.names[index],
+      raHash: data.raHashes[index],
       evaluationCount: data.evaluationCounts[index],
       iterationCount: data.iterationCounts[index],
       timeCost: data.timeCosts[index],
@@ -79,9 +97,78 @@ class ComparisonDataset {
       pipelines: data.pipelineSummaryList[index],
     };
   }
+
+  /**
+   * Returns the RA hashes of all predicates that were evaluated in this data set, but not seen in `other`,
+   * because in `other` the dependency upon these predicates was cut off by a cache hit.
+   *
+   * For example, suppose predicate `A` depends on `B`, which depends on `C`, and the
+   * predicates were evaluated in the first log but not the second:
+   * ```
+   *                  first eval. log        second eval. log
+   * predicate A      seen evaluation        seen cache hit
+   *    |
+   *    V
+   * predicate B      seen evaluation        not seen
+   *    |
+   *    V
+   * predicate C      seen evaluation        not seen
+   * ```
+   *
+   * To ensure a meaningful comparison, we want to omit `predicate A` from the comparison view because of the cache hit.
+   *
+   * But predicates B and C did not have a recorded cache hit in the second log, because they were never scheduled for evaluation.
+   * Given the dependency graph, the most likely explanation is that they would have been evaluated if `A` had not been a cache hit.
+   * We therefore say that B and C are "shadowed" by the cache hit on A.
+   *
+   * The dependency graph is only visible in the first evaluation log, because `B` and `C` do not exist in the second log.
+   * So to compute this, we use the dependency graph from one log together with the set of cache hits in the other log.
+   */
+  getPredicatesShadowedByCacheHit(other: ComparisonDataset) {
+    const {
+      data: { dependencyLists, raHashes, names },
+      raToIndex,
+    } = this;
+    const cacheHits = new Set<string>();
+
+    function visit(index: number, raHash: string) {
+      if (cacheHits.has(raHash)) {
+        return;
+      }
+      cacheHits.add(raHash);
+      const dependencies = dependencyLists[index];
+      for (const dep of dependencies) {
+        const name = names[dep];
+        if (!other.nameToIndex.has(name)) {
+          visit(dep, raHashes[dep]);
+        }
+      }
+    }
+
+    for (const otherCacheHit of other.cacheHitIndices) {
+      {
+        // Look up by RA hash
+        const raHash = other.data.raHashes[otherCacheHit];
+        const ownIndex = raToIndex.get(raHash);
+        if (ownIndex != null) {
+          visit(ownIndex, raHash);
+        }
+      }
+      {
+        // Look up by name
+        const name = other.data.names[otherCacheHit];
+        const ownIndex = this.nameToIndex.get(name);
+        if (ownIndex != null) {
+          visit(ownIndex, raHashes[ownIndex]);
+        }
+      }
+    }
+
+    return cacheHits;
+  }
 }
 
-function renderOptionalValue(x: Optional<number>, unit?: string) {
+function renderOptionalValue(x: Optional<number>, unit: string | undefined) {
   switch (x) {
     case AbsentReason.NotSeen:
       return <AbsentNumberCell>n/a</AbsentNumberCell>;
@@ -336,6 +423,7 @@ function HighLevelStats(props: HighLevelStatsProps) {
 }
 
 interface Row {
+  key: string;
   name: string;
   before: Optional<PredicateInfo>;
   after: Optional<PredicateInfo>;
@@ -472,7 +560,7 @@ function ComparePerformanceWithData(props: {
 
   const comparison = data?.comparison;
 
-  const [hideCacheHits, setHideCacheHits] = useState(false);
+  const [hideCacheHits, setHideCacheHits] = useState(true);
 
   const [sortOrder, setSortOrder] = useState<"delta" | "absDelta">("absDelta");
 
@@ -480,19 +568,27 @@ function ComparePerformanceWithData(props: {
 
   const [isPerEvaluation, setPerEvaluation] = useState(false);
 
-  const nameSet = useMemo(
-    () => union(from.data.names, to.data.names),
-    [from, to],
-  );
+  const keySet = useMemo(() => union(from.keys(), to.keys()), [from, to]);
 
   const hasCacheHitMismatch = useRef(false);
 
+  const shadowedCacheHitsFrom = useMemo(
+    () =>
+      hideCacheHits ? from.getPredicatesShadowedByCacheHit(to) : new Set(),
+    [from, to, hideCacheHits],
+  );
+  const shadowedCacheHitsTo = useMemo(
+    () =>
+      hideCacheHits ? to.getPredicatesShadowedByCacheHit(from) : new Set(),
+    [from, to, hideCacheHits],
+  );
+
   const rows: Row[] = useMemo(() => {
     hasCacheHitMismatch.current = false;
-    return Array.from(nameSet)
-      .map((name) => {
-        const before = from.getTupleCountInfo(name);
-        const after = to.getTupleCountInfo(name);
+    return Array.from(keySet)
+      .map((key) => {
+        const before = from.getTupleCountInfo(key);
+        const after = to.getTupleCountInfo(key);
         const beforeValue = metricGetOptional(metric, before, isPerEvaluation);
         const afterValue = metricGetOptional(metric, after, isPerEvaluation);
         if (beforeValue === afterValue) {
@@ -507,14 +603,39 @@ function ComparePerformanceWithData(props: {
             return undefined!;
           }
         }
+        if (
+          (isPresent(before) &&
+            !isPresent(after) &&
+            shadowedCacheHitsFrom.has(before.raHash)) ||
+          (isPresent(after) &&
+            !isPresent(before) &&
+            shadowedCacheHitsTo.has(after.raHash))
+        ) {
+          return undefined!;
+        }
         const diff =
           (isPresent(afterValue) ? afterValue : 0) -
           (isPresent(beforeValue) ? beforeValue : 0);
-        return { name, before, after, diff } satisfies Row;
+        const name = isPresent(before)
+          ? before.name
+          : isPresent(after)
+            ? after.name
+            : key;
+        return { key, name, before, after, diff } satisfies Row;
       })
       .filter((x) => !!x)
       .sort(getSortOrder(sortOrder));
-  }, [nameSet, from, to, metric, hideCacheHits, sortOrder, isPerEvaluation]);
+  }, [
+    keySet,
+    from,
+    to,
+    metric,
+    hideCacheHits,
+    sortOrder,
+    isPerEvaluation,
+    shadowedCacheHitsFrom,
+    shadowedCacheHitsTo,
+  ]);
 
   const { totalBefore, totalAfter, totalDiff } = useMemo(() => {
     let totalBefore = 0;
@@ -575,23 +696,14 @@ function ComparePerformanceWithData(props: {
     <>
       <ViewTitle>Performance comparison</ViewTitle>
       {comparison && hasCacheHitMismatch.current && (
-        <WarningBox>
-          <strong>Inconsistent cache hits</strong>
-          <br />
-          Some predicates had a cache hit on one side but not the other. For
-          more accurate results, try running the{" "}
-          <strong>CodeQL: Clear Cache</strong> command before each query.
-          <br />
-          <br />
-          <label>
-            <input
-              type="checkbox"
-              checked={hideCacheHits}
-              onChange={() => setHideCacheHits(!hideCacheHits)}
-            />
-            Hide predicates with cache hits
-          </label>
-        </WarningBox>
+        <label>
+          <input
+            type="checkbox"
+            checked={hideCacheHits}
+            onChange={() => setHideCacheHits(!hideCacheHits)}
+          />
+          Hide differences due to cache hits
+        </label>
       )}
       <RenamingInput renamings={renamings} setRenamings={setRenamings} />
       Compare{" "}
@@ -712,8 +824,8 @@ function PredicateRowGroup(props: PredicateRowGroupProps) {
           <ChevronCell>
             <Chevron expanded={isExpanded} />
           </ChevronCell>
-          {comparison && renderOptionalValue(rowGroup.before)}
-          {renderOptionalValue(rowGroup.after)}
+          {comparison && renderOptionalValue(rowGroup.before, metric.unit)}
+          {renderOptionalValue(rowGroup.after, metric.unit)}
           {comparison && renderDelta(rowGroup.diff, metric.unit)}
           <NameCell>
             {renderedName} ({rowGroup.rows.length} predicates)
@@ -860,3 +972,14 @@ function collatePipelines(
 function samePipeline(a: string[], b: string[]) {
   return a.length === b.length && a.every((x, i) => x === b[i]);
 }
+
+function getPipelineSummaryHash(pipelines: Record<string, PipelineSummary>) {
+  // Note: we can't import "crypto" here because it is not available in the browser,
+  // so we just concatenate the hashes of the individual pipelines.
+  const keys = Object.keys(pipelines).sort();
+  let result = "";
+  for (const key of keys) {
+    result += `${pipelines[key].hash};`;
+  }
+  return result;
+}
diff --git a/extensions/ql-vscode/src/view/compare-performance/RenamingInput.tsx b/extensions/ql-vscode/src/view/compare-performance/RenamingInput.tsx
index 6d86c7e8182..c938cc6d1a4 100644
--- a/extensions/ql-vscode/src/view/compare-performance/RenamingInput.tsx
+++ b/extensions/ql-vscode/src/view/compare-performance/RenamingInput.tsx
@@ -1,9 +1,6 @@
 import type { ChangeEvent } from "react";
 import { styled } from "styled-components";
-import {
-  VSCodeButton,
-  VSCodeTextField,
-} from "@vscode/webview-ui-toolkit/react";
+import { VscodeButton, VscodeTextfield } from "@vscode-elements/react-elements";
 import { Codicon } from "../common";
 
 export class Renaming {
@@ -25,7 +22,7 @@ function tryCompilePattern(pattern: string): RegExp | undefined {
   }
 }
 
-const Input = styled(VSCodeTextField)`
+const Input = styled(VscodeTextfield)`
   width: 20em;
 `;
 
@@ -86,21 +83,21 @@ export function RenamingInput(props: RenamingInputProps) {
               setRenamings(newRenamings);
             }}
           ></Input>
-          <VSCodeButton
+          <VscodeButton
             onClick={() =>
               setRenamings(renamings.filter((_, i) => i !== index))
             }
           >
             <Codicon name="trash" />
-          </VSCodeButton>
+          </VscodeButton>
           <br />
         </Row>
       ))}
-      <VSCodeButton
+      <VscodeButton
         onClick={() => setRenamings([...renamings, new Renaming("", "")])}
       >
         Add renaming rule
-      </VSCodeButton>
+      </VscodeButton>
     </Details>
   );
 }
diff --git a/extensions/ql-vscode/src/view/jest.setup.ts b/extensions/ql-vscode/src/view/jest.setup.ts
index 23cb3e2f973..31dc6657d40 100644
--- a/extensions/ql-vscode/src/view/jest.setup.ts
+++ b/extensions/ql-vscode/src/view/jest.setup.ts
@@ -18,6 +18,20 @@ Object.defineProperty(window, "matchMedia", {
 // Used by Primer React
 window.CSS.supports = jest.fn().mockResolvedValue(false);
 
+// Functions that are not implemented in jsdom
+window.CSSStyleSheet.prototype.replaceSync = jest
+  .fn()
+  .mockReturnValue(undefined);
+window.ElementInternals.prototype.setFormValue = jest
+  .fn()
+  .mockReturnValue(undefined);
+window.ElementInternals.prototype.setValidity = jest
+  .fn()
+  .mockReturnValue(undefined);
+window.HTMLSlotElement.prototype.assignedElements = jest
+  .fn()
+  .mockReturnValue([]);
+
 // Store this on the window so we can mock it
 window.vsCodeApi = {
   postMessage: jest.fn(),
diff --git a/extensions/ql-vscode/src/view/method-modeling/MultipleModeledMethodsPanel.tsx b/extensions/ql-vscode/src/view/method-modeling/MultipleModeledMethodsPanel.tsx
index bb2fd6b2ab5..ed55c497d71 100644
--- a/extensions/ql-vscode/src/view/method-modeling/MultipleModeledMethodsPanel.tsx
+++ b/extensions/ql-vscode/src/view/method-modeling/MultipleModeledMethodsPanel.tsx
@@ -7,7 +7,6 @@ import {
 } from "../../model-editor/shared/multiple-modeled-methods";
 import { styled } from "styled-components";
 import { MethodModelingInputs } from "./MethodModelingInputs";
-import { VSCodeButton } from "@vscode/webview-ui-toolkit/react";
 import { Codicon } from "../common";
 import { validateModeledMethods } from "../../model-editor/shared/validation";
 import { ModeledMethodAlert } from "./ModeledMethodAlert";
@@ -15,6 +14,7 @@ import type { QueryLanguage } from "../../common/query-language";
 import { createEmptyModeledMethod } from "../../model-editor/modeled-method-empty";
 import { sendTelemetry } from "../common/telemetry";
 import type { ModelConfig } from "../../model-editor/languages";
+import { ActionButton } from "../common/ActionButton/ActionButton";
 
 export type MultipleModeledMethodsPanelProps = {
   language: QueryLanguage;
@@ -168,21 +168,19 @@ export const MultipleModeledMethodsPanel = ({
       )}
       <Footer>
         <PaginationActions>
-          <VSCodeButton
-            appearance="icon"
+          <ActionButton
             aria-label="Previous modeling"
             onClick={handlePreviousClick}
             disabled={modeledMethods.length < 2 || selectedIndex === 0}
           >
             <Codicon name="chevron-left" />
-          </VSCodeButton>
+          </ActionButton>
           {modeledMethods.length > 1 && (
             <div>
               {selectedIndex + 1}/{modeledMethods.length}
             </div>
           )}
-          <VSCodeButton
-            appearance="icon"
+          <ActionButton
             aria-label="Next modeling"
             onClick={handleNextClick}
             disabled={
@@ -191,25 +189,23 @@ export const MultipleModeledMethodsPanel = ({
             }
           >
             <Codicon name="chevron-right" />
-          </VSCodeButton>
+          </ActionButton>
         </PaginationActions>
         <ModificationActions>
-          <VSCodeButton
-            appearance="icon"
+          <ActionButton
             aria-label="Delete modeling"
             onClick={handleRemoveClick}
             disabled={!canRemoveModeledMethod(modeledMethods)}
           >
             <Codicon name="trash" />
-          </VSCodeButton>
-          <VSCodeButton
-            appearance="icon"
+          </ActionButton>
+          <ActionButton
             aria-label="Add modeling"
             onClick={handleAddClick}
             disabled={!canAddNewModeledMethod(modeledMethods)}
           >
             <Codicon name="add" />
-          </VSCodeButton>
+          </ActionButton>
         </ModificationActions>
       </Footer>
     </Container>
diff --git a/extensions/ql-vscode/src/view/method-modeling/__tests__/MultipleModeledMethodsPanel.spec.tsx b/extensions/ql-vscode/src/view/method-modeling/__tests__/MultipleModeledMethodsPanel.spec.tsx
index 9c0e0b464da..27372287bfc 100644
--- a/extensions/ql-vscode/src/view/method-modeling/__tests__/MultipleModeledMethodsPanel.spec.tsx
+++ b/extensions/ql-vscode/src/view/method-modeling/__tests__/MultipleModeledMethodsPanel.spec.tsx
@@ -52,32 +52,26 @@ describe(MultipleModeledMethodsPanel.name, () => {
       ).toHaveValue("none");
     });
 
-    it("disables all pagination", () => {
+    it("disables all pagination", async () => {
       render();
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeDisabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeDisabled();
+      const prevButton = await screen.findByLabelText("Previous modeling");
+      const nextButton = await screen.findByLabelText("Next modeling");
+
+      expect(prevButton).toBeDisabled();
+      expect(nextButton).toBeDisabled();
       expect(screen.queryByText("0/0")).not.toBeInTheDocument();
       expect(screen.queryByText("1/0")).not.toBeInTheDocument();
     });
 
-    it("cannot add or delete modeling", () => {
+    it("cannot add or delete modeling", async () => {
       render();
 
-      expect(
-        screen
-          .getByLabelText("Delete modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeDisabled();
-      expect(
-        screen.getByLabelText("Add modeling").getElementsByTagName("input")[0],
-      ).toBeDisabled();
+      const deleteButton = await screen.findByLabelText("Delete modeling");
+      const addButton = await screen.findByLabelText("Add modeling");
+
+      expect(deleteButton).toBeDisabled();
+      expect(addButton).toBeDisabled();
     });
   });
 
@@ -104,28 +98,22 @@ describe(MultipleModeledMethodsPanel.name, () => {
       ).toHaveValue("sink");
     });
 
-    it("disables all pagination", () => {
+    it("disables all pagination", async () => {
       render();
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeDisabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeDisabled();
+      const prevButton = await screen.findByLabelText("Previous modeling");
+      const nextButton = await screen.findByLabelText("Next modeling");
+
+      expect(prevButton).toBeDisabled();
+      expect(nextButton).toBeDisabled();
       expect(screen.queryByText("1/1")).not.toBeInTheDocument();
     });
 
-    it("cannot delete modeling", () => {
+    it("cannot delete modeling", async () => {
       render();
 
-      expect(
-        screen
-          .getByLabelText("Delete modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeDisabled();
+      const deleteButton = await screen.findByLabelText("Delete modeling");
+      expect(deleteButton).toBeDisabled();
     });
 
     it("can add modeling", async () => {
@@ -199,37 +187,26 @@ describe(MultipleModeledMethodsPanel.name, () => {
     it("disables the correct pagination", async () => {
       render();
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeDisabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      const prevButton = await screen.findByLabelText("Previous modeling");
+      const nextButton = await screen.findByLabelText("Next modeling");
+
+      expect(prevButton).toBeDisabled();
+      expect(nextButton).toBeEnabled();
     });
 
     it("can use the pagination", async () => {
       render();
 
-      await userEvent.click(screen.getByLabelText("Next modeling"));
+      const prevButton = await screen.findByLabelText("Previous modeling");
+      const nextButton = await screen.findByLabelText("Next modeling");
 
+      await userEvent.click(nextButton);
       await waitFor(() => {
-        expect(
-          screen
-            .getByLabelText("Previous modeling")
-            .getElementsByTagName("input")[0],
-        ).toBeEnabled();
+        expect(prevButton).toBeEnabled();
       });
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeEnabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeDisabled();
+      expect(prevButton).toBeEnabled();
+      expect(nextButton).toBeDisabled();
       expect(screen.getByText("2/2")).toBeInTheDocument();
 
       expect(
@@ -445,34 +422,20 @@ describe(MultipleModeledMethodsPanel.name, () => {
     it("can use the pagination", async () => {
       render();
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeDisabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      const prevButton = await screen.findByLabelText("Previous modeling");
+      const nextButton = await screen.findByLabelText("Next modeling");
+      expect(prevButton).toBeDisabled();
+      expect(nextButton).toBeEnabled();
       expect(screen.getByText("1/3")).toBeInTheDocument();
 
-      await userEvent.click(screen.getByLabelText("Next modeling"));
+      await userEvent.click(nextButton);
 
       await waitFor(() => {
-        expect(
-          screen
-            .getByLabelText("Previous modeling")
-            .getElementsByTagName("input")[0],
-        ).toBeEnabled();
+        expect(prevButton).toBeEnabled();
       });
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeEnabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      expect(prevButton).toBeEnabled();
+      expect(nextButton).toBeEnabled();
       expect(screen.getByText("2/3")).toBeInTheDocument();
 
       expect(
@@ -481,16 +444,10 @@ describe(MultipleModeledMethodsPanel.name, () => {
         }),
       ).toHaveValue("source");
 
-      await userEvent.click(screen.getByLabelText("Next modeling"));
+      await userEvent.click(nextButton);
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeEnabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeDisabled();
+      expect(prevButton).toBeEnabled();
+      expect(nextButton).toBeDisabled();
       expect(screen.getByText("3/3")).toBeInTheDocument();
 
       expect(
@@ -499,24 +456,14 @@ describe(MultipleModeledMethodsPanel.name, () => {
         }),
       ).toHaveValue("local");
 
-      await userEvent.click(screen.getByLabelText("Previous modeling"));
+      await userEvent.click(prevButton);
 
       await waitFor(() => {
-        expect(
-          screen
-            .getByLabelText("Next modeling")
-            .getElementsByTagName("input")[0],
-        ).toBeEnabled();
+        expect(nextButton).toBeEnabled();
       });
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeEnabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      expect(prevButton).toBeEnabled();
+      expect(nextButton).toBeEnabled();
       expect(screen.getByText("2/3")).toBeInTheDocument();
 
       expect(
@@ -574,12 +521,11 @@ describe(MultipleModeledMethodsPanel.name, () => {
 
     const render = createRender(modeledMethods);
 
-    it("can add modeling", () => {
+    it("can add modeling", async () => {
       render();
 
-      expect(
-        screen.getByLabelText("Add modeling").getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      const addButton = await screen.findByLabelText("Add modeling");
+      expect(addButton).toBeEnabled();
     });
 
     it("can delete first modeling", async () => {
diff --git a/extensions/ql-vscode/src/view/model-alerts/ModelAlertsActions.tsx b/extensions/ql-vscode/src/view/model-alerts/ModelAlertsActions.tsx
index e99689634d2..da73126d2fc 100644
--- a/extensions/ql-vscode/src/view/model-alerts/ModelAlertsActions.tsx
+++ b/extensions/ql-vscode/src/view/model-alerts/ModelAlertsActions.tsx
@@ -1,6 +1,6 @@
 import { styled } from "styled-components";
-import { VSCodeButton } from "@vscode/webview-ui-toolkit/react";
 import { VariantAnalysisStatus } from "../../variant-analysis/shared/variant-analysis";
+import { VscodeButton } from "@vscode-elements/react-elements";
 
 type ModelAlertsActionsProps = {
   variantAnalysisStatus: VariantAnalysisStatus;
@@ -14,7 +14,7 @@ const Container = styled.div`
   gap: 1em;
 `;
 
-const Button = styled(VSCodeButton)`
+const Button = styled(VscodeButton)`
   white-space: nowrap;
 `;
 
@@ -25,12 +25,12 @@ export const ModelAlertsActions = ({
   return (
     <Container>
       {variantAnalysisStatus === VariantAnalysisStatus.InProgress && (
-        <Button appearance="secondary" onClick={onStopRunClick}>
+        <Button secondary onClick={onStopRunClick}>
           Stop evaluation
         </Button>
       )}
       {variantAnalysisStatus === VariantAnalysisStatus.Canceling && (
-        <Button appearance="secondary" disabled={true}>
+        <Button secondary disabled={true}>
           Stopping evaluation
         </Button>
       )}
diff --git a/extensions/ql-vscode/src/view/model-alerts/ModelAlertsResults.tsx b/extensions/ql-vscode/src/view/model-alerts/ModelAlertsResults.tsx
index 8b27896d333..d10757e3748 100644
--- a/extensions/ql-vscode/src/view/model-alerts/ModelAlertsResults.tsx
+++ b/extensions/ql-vscode/src/view/model-alerts/ModelAlertsResults.tsx
@@ -1,7 +1,6 @@
 import { styled } from "styled-components";
 import type { ModelAlerts } from "../../model-editor/model-alerts/model-alerts";
 import { Codicon } from "../common";
-import { VSCodeBadge } from "@vscode/webview-ui-toolkit/react";
 import { useCallback, useEffect, useRef, useState } from "react";
 import { formatDecimal } from "../../common/number";
 import AnalysisAlertResult from "../variant-analysis/AnalysisAlertResult";
@@ -11,6 +10,7 @@ import { vscode } from "../vscode-api";
 import { createModeledMethodKey } from "../../model-editor/modeled-method";
 import type { ModeledMethod } from "../../model-editor/modeled-method";
 import { Link } from "../common/Link";
+import { Badge } from "../common/Badge";
 
 // This will ensure that these icons have a className which we can use in the TitleContainer
 const ExpandCollapseCodicon = styled(Codicon)``;
@@ -103,7 +103,7 @@ export const ModelAlertsResults = ({
         {!isExpanded && (
           <ExpandCollapseCodicon name="chevron-right" label="Expand" />
         )}
-        <VSCodeBadge>{formatDecimal(modelAlerts.alerts.length)}</VSCodeBadge>
+        <Badge>{formatDecimal(modelAlerts.alerts.length)}</Badge>
         <MethodName {...modelAlerts.model}></MethodName>
         <ModelTypeText>{modelAlerts.model.type}</ModelTypeText>
         <ViewLink
diff --git a/extensions/ql-vscode/src/view/model-alerts/ModelAlertsSort.tsx b/extensions/ql-vscode/src/view/model-alerts/ModelAlertsSort.tsx
index 043355a5782..e5d4e9f2eb6 100644
--- a/extensions/ql-vscode/src/view/model-alerts/ModelAlertsSort.tsx
+++ b/extensions/ql-vscode/src/view/model-alerts/ModelAlertsSort.tsx
@@ -1,10 +1,13 @@
 import { useCallback } from "react";
 import { styled } from "styled-components";
-import { VSCodeDropdown, VSCodeOption } from "@vscode/webview-ui-toolkit/react";
+import {
+  VscodeOption,
+  VscodeSingleSelect,
+} from "@vscode-elements/react-elements";
 import { SortKey } from "../../model-editor/shared/model-alerts-filter-sort";
 import { Codicon } from "../common";
 
-const Dropdown = styled(VSCodeDropdown)`
+const Dropdown = styled(VscodeSingleSelect)`
   width: 100%;
 `;
 
@@ -26,12 +29,12 @@ export const ModelAlertsSort = ({ value, onChange, className }: Props) => {
   );
 
   return (
-    <Dropdown value={value} onInput={handleInput} className={className}>
+    <Dropdown value={value} onChange={handleInput} className={className}>
       <Codicon name="sort-precedence" label="Sort..." slot="indicator" />
-      <VSCodeOption value={SortKey.Alphabetically}>Alphabetically</VSCodeOption>
-      <VSCodeOption value={SortKey.NumberOfResults}>
+      <VscodeOption value={SortKey.Alphabetically}>Alphabetically</VscodeOption>
+      <VscodeOption value={SortKey.NumberOfResults}>
         Number of results
-      </VSCodeOption>
+      </VscodeOption>
     </Dropdown>
   );
 };
diff --git a/extensions/ql-vscode/src/view/model-editor/LibraryRow.tsx b/extensions/ql-vscode/src/view/model-editor/LibraryRow.tsx
index 662d739ad7b..f2f1065b4d9 100644
--- a/extensions/ql-vscode/src/view/model-editor/LibraryRow.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/LibraryRow.tsx
@@ -7,11 +7,12 @@ import { calculateModeledPercentage } from "../../model-editor/shared/modeled-pe
 import { percentFormatter } from "./formatters";
 import { Codicon } from "../common";
 import { Mode } from "../../model-editor/shared/mode";
-import { VSCodeButton, VSCodeDivider } from "@vscode/webview-ui-toolkit/react";
+import { VscodeButton, VscodeDivider } from "@vscode-elements/react-elements";
 import type { ModelEditorViewState } from "../../model-editor/shared/view-state";
 import type { AccessPathSuggestionOptions } from "../../model-editor/suggestions";
 import type { ModelEvaluationRunState } from "../../model-editor/shared/model-evaluation-run-state";
 import { Tag } from "../common/Tag";
+import { ActionButton } from "../common/ActionButton/ActionButton";
 
 const LibraryContainer = styled.div`
   background-color: var(--vscode-peekViewResult-background);
@@ -34,9 +35,9 @@ const TitleContainer = styled.button`
   cursor: pointer;
 `;
 
-const SectionDivider = styled(VSCodeDivider)`
-  padding-top: 0.3rem;
-  padding-bottom: 0.3rem;
+const SectionDivider = styled(VscodeDivider)`
+  margin-top: 0.3rem;
+  margin-bottom: 0.8rem;
 `;
 
 const NameContainer = styled.div`
@@ -170,16 +171,16 @@ export const LibraryRow = ({
         </NameContainer>
         {viewState.showGenerateButton &&
           viewState.mode === Mode.Application && (
-            <VSCodeButton appearance="icon" onClick={handleModelFromSource}>
+            <ActionButton onClick={handleModelFromSource}>
               <Codicon name="code" label="Model from source" />
               &nbsp;Model from source
-            </VSCodeButton>
+            </ActionButton>
           )}
         {viewState.mode === Mode.Application && (
-          <VSCodeButton appearance="icon" onClick={handleModelDependency}>
+          <ActionButton onClick={handleModelDependency}>
             <Codicon name="references" label="Model dependency" />
             &nbsp;Model dependency
-          </VSCodeButton>
+          </ActionButton>
         )}
       </TitleContainer>
       {isExpanded && (
@@ -200,9 +201,9 @@ export const LibraryRow = ({
           />
           <SectionDivider />
           <ButtonsContainer>
-            <VSCodeButton onClick={handleSave} disabled={!hasUnsavedChanges}>
+            <VscodeButton onClick={handleSave} disabled={!hasUnsavedChanges}>
               {selectedSignatures.size === 0 ? "Save" : "Save selected"}
-            </VSCodeButton>
+            </VscodeButton>
           </ButtonsContainer>
         </>
       )}
diff --git a/extensions/ql-vscode/src/view/model-editor/MethodRow.tsx b/extensions/ql-vscode/src/view/model-editor/MethodRow.tsx
index 22dc54d2a48..6e753c3532d 100644
--- a/extensions/ql-vscode/src/view/model-editor/MethodRow.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/MethodRow.tsx
@@ -1,4 +1,3 @@
-import { VSCodeBadge, VSCodeButton } from "@vscode/webview-ui-toolkit/react";
 import {
   forwardRef,
   useCallback,
@@ -10,6 +9,7 @@ import {
 import { styled } from "styled-components";
 import { vscode } from "../vscode-api";
 import { Link } from "../common/Link";
+import { ActionButton } from "../common/ActionButton/ActionButton";
 
 import type { Method } from "../../model-editor/method";
 import type { ModeledMethod } from "../../model-editor/modeled-method";
@@ -35,6 +35,7 @@ import { ModelOutputSuggestBox } from "./ModelOutputSuggestBox";
 import { getModelsAsDataLanguage } from "../../model-editor/languages";
 import { ModelAlertsIndicator } from "./ModelAlertsIndicator";
 import type { ModelEvaluationRunState } from "../../model-editor/shared/model-evaluation-run-state";
+import { Badge } from "../common/Badge";
 
 const ApiOrMethodRow = styled.div`
   min-height: calc(var(--input-height) * 1px);
@@ -52,15 +53,16 @@ const ModelButtonsContainer = styled.div`
   gap: 1em;
 `;
 
-const UsagesButton = styled(VSCodeBadge)`
+const UsagesButton = styled(Badge)`
   cursor: pointer;
+  display: table;
 `;
 
 const ViewLink = styled(Link)`
   white-space: nowrap;
 `;
 
-const CodiconRow = styled(VSCodeButton)`
+const CodiconRow = styled(ActionButton)`
   min-height: calc(var(--input-height) * 1px);
   align-items: center;
 `;
@@ -318,7 +320,6 @@ const ModelableMethodRow = forwardRef<HTMLElement | undefined, MethodRowProps>(
                   ></ModelAlertsIndicator>
                   {index === 0 ? (
                     <CodiconRow
-                      appearance="icon"
                       aria-label="Add new model"
                       onClick={(event: React.MouseEvent) => {
                         event.stopPropagation();
@@ -330,7 +331,6 @@ const ModelableMethodRow = forwardRef<HTMLElement | undefined, MethodRowProps>(
                     </CodiconRow>
                   ) : (
                     <CodiconRow
-                      appearance="icon"
                       aria-label="Remove model"
                       onClick={(event: React.MouseEvent) => {
                         event.stopPropagation();
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelAlertsIndicator.tsx b/extensions/ql-vscode/src/view/model-editor/ModelAlertsIndicator.tsx
index 117d18903ca..a99bc815f1e 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelAlertsIndicator.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelAlertsIndicator.tsx
@@ -2,10 +2,10 @@ import { styled } from "styled-components";
 import type { ModeledMethod } from "../../model-editor/modeled-method";
 import type { ModelEvaluationRunState } from "../../model-editor/shared/model-evaluation-run-state";
 import type { ModelEditorViewState } from "../../model-editor/shared/view-state";
-import { VSCodeBadge } from "@vscode/webview-ui-toolkit/react";
 import { vscode } from "../vscode-api";
+import { Badge } from "../common/Badge";
 
-const ModelAlertsButton = styled(VSCodeBadge)`
+const ModelAlertsButton = styled(Badge)`
   cursor: pointer;
 `;
 
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelEditor.tsx b/extensions/ql-vscode/src/view/model-editor/ModelEditor.tsx
index 6d9628cf0db..344a0d32d98 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelEditor.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelEditor.tsx
@@ -1,6 +1,6 @@
 import { useCallback, useEffect, useMemo, useState } from "react";
 import type { ToModelEditorMessage } from "../../common/interface-types";
-import { VSCodeButton, VSCodeCheckbox } from "@vscode/webview-ui-toolkit/react";
+import { VscodeButton, VscodeCheckbox } from "@vscode-elements/react-elements";
 import { styled } from "styled-components";
 import type { Method } from "../../model-editor/method";
 import type { ModeledMethod } from "../../model-editor/modeled-method";
@@ -331,27 +331,27 @@ export function ModelEditor({
           </HeaderRow>
           <HeaderRow>
             <ButtonsContainer>
-              <VSCodeButton
+              <VscodeButton
                 onClick={onSaveAllClick}
                 disabled={modifiedSignatures.size === 0}
               >
                 {selectedSignatures.size === 0 ? "Save all" : "Save selected"}
-              </VSCodeButton>
-              <VSCodeButton
-                appearance="secondary"
+              </VscodeButton>
+              <VscodeButton
+                secondary
                 onClick={onDeselectAllClick}
                 disabled={selectedSignatures.size === 0}
               >
                 Deselect all
-              </VSCodeButton>
-              <VSCodeButton appearance="secondary" onClick={onRefreshClick}>
+              </VscodeButton>
+              <VscodeButton secondary onClick={onRefreshClick}>
                 Refresh
-              </VSCodeButton>
+              </VscodeButton>
               {viewState.showGenerateButton &&
                 viewState.mode === Mode.Framework && (
-                  <VSCodeButton onClick={onGenerateFromSourceClick}>
+                  <VscodeButton onClick={onGenerateFromSourceClick}>
                     Generate
-                  </VSCodeButton>
+                  </VscodeButton>
                 )}
               <ModelEvaluation
                 viewState={viewState}
@@ -367,12 +367,12 @@ export function ModelEditor({
         </HeaderColumn>
         <HeaderSpacer />
         <HeaderColumn>
-          <VSCodeCheckbox
+          <VscodeCheckbox
             checked={hideModeledMethods}
             onChange={onHideModeledMethods}
           >
             Hide modeled methods
-          </VSCodeCheckbox>
+          </VscodeCheckbox>
         </HeaderColumn>
       </HeaderContainer>
 
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelEditorProgressRing.tsx b/extensions/ql-vscode/src/view/model-editor/ModelEditorProgressRing.tsx
index 3994caddf82..523e8fd32c8 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelEditorProgressRing.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelEditorProgressRing.tsx
@@ -1,7 +1,7 @@
-import { VSCodeProgressRing } from "@vscode/webview-ui-toolkit/react";
+import { VscodeProgressRing } from "@vscode-elements/react-elements";
 import { styled } from "styled-components";
 
-export const ModelEditorProgressRing = styled(VSCodeProgressRing)`
+export const ModelEditorProgressRing = styled(VscodeProgressRing)`
   width: 16px;
   height: 16px;
   margin-right: 5px;
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelEvaluation.tsx b/extensions/ql-vscode/src/view/model-editor/ModelEvaluation.tsx
index 95b94aa5411..ba0266c083f 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelEvaluation.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelEvaluation.tsx
@@ -1,5 +1,4 @@
 import { styled } from "styled-components";
-import { VSCodeButton } from "@vscode/webview-ui-toolkit/react";
 import type { ModeledMethod } from "../../model-editor/modeled-method";
 import type { ModelEditorViewState } from "../../model-editor/shared/view-state";
 import type { ModelEvaluationRunState } from "../../model-editor/shared/model-evaluation-run-state";
@@ -7,6 +6,7 @@ import { modelEvaluationRunIsRunning } from "../../model-editor/shared/model-eva
 import { ModelEditorProgressRing } from "./ModelEditorProgressRing";
 import { LinkIconButton } from "../common/LinkIconButton";
 import { Link } from "../common/Link";
+import { VscodeButton } from "@vscode-elements/react-elements";
 
 export type Props = {
   viewState: ModelEditorViewState;
@@ -53,19 +53,19 @@ export const ModelEvaluation = ({
   return (
     <>
       {shouldShowEvaluateButton && (
-        <VSCodeButton
+        <VscodeButton
           onClick={onStartEvaluation}
-          appearance="secondary"
+          secondary
           disabled={!customModelsExist || unsavedChanges}
         >
           Evaluate
-        </VSCodeButton>
+        </VscodeButton>
       )}
       {shouldShowStopButton && (
-        <VSCodeButton onClick={onStopEvaluation} appearance="secondary">
+        <VscodeButton onClick={onStopEvaluation} secondary>
           <ModelEditorProgressRing />
           Stop evaluation
-        </VSCodeButton>
+        </VscodeButton>
       )}
       {shouldShowEvaluationRunLink && (
         <RunLink>
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelTypeTextbox.tsx b/extensions/ql-vscode/src/view/model-editor/ModelTypeTextbox.tsx
index d52ab1306bf..69f9a0829b9 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelTypeTextbox.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelTypeTextbox.tsx
@@ -4,8 +4,8 @@ import type {
   ModeledMethod,
   TypeModeledMethod,
 } from "../../model-editor/modeled-method";
-import { VSCodeTextField } from "@vscode/webview-ui-toolkit/react";
 import { useDebounceCallback } from "../common/useDebounceCallback";
+import { VscodeTextfield } from "@vscode-elements/react-elements";
 
 type Props = {
   modeledMethod: TypeModeledMethod;
@@ -53,7 +53,7 @@ export const ModelTypeTextbox = ({
   );
 
   return (
-    <VSCodeTextField
+    <VscodeTextfield
       value={value}
       onInput={handleChange}
       onClick={stopClickPropagation}
diff --git a/extensions/ql-vscode/src/view/model-editor/__tests__/MethodRow.spec.tsx b/extensions/ql-vscode/src/view/model-editor/__tests__/MethodRow.spec.tsx
index 3fac0dc0f99..6ce364b4393 100644
--- a/extensions/ql-vscode/src/view/model-editor/__tests__/MethodRow.spec.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/__tests__/MethodRow.spec.tsx
@@ -243,9 +243,9 @@ describe(MethodRow.name, () => {
       modeledMethods: [],
     });
 
-    const addButton = screen.queryByLabelText("Add new model");
+    const addButton = await screen.findByLabelText("Add new model");
     expect(addButton).toBeInTheDocument();
-    expect(addButton?.getElementsByTagName("input")[0]).toBeDisabled();
+    expect(addButton).toBeDisabled();
 
     expect(screen.queryByLabelText("Remove model")).not.toBeInTheDocument();
   });
@@ -255,9 +255,9 @@ describe(MethodRow.name, () => {
       modeledMethods: [{ ...modeledMethod, type: "none" }],
     });
 
-    const addButton = screen.queryByLabelText("Add new model");
+    const addButton = await screen.findByLabelText("Add new model");
     expect(addButton).toBeInTheDocument();
-    expect(addButton?.getElementsByTagName("input")[0]).toBeDisabled();
+    expect(addButton).toBeDisabled();
 
     expect(screen.queryByLabelText("Remove model")).not.toBeInTheDocument();
   });
@@ -267,9 +267,9 @@ describe(MethodRow.name, () => {
       modeledMethods: [modeledMethod],
     });
 
-    const addButton = screen.queryByLabelText("Add new model");
+    const addButton = await screen.findByLabelText("Add new model");
     expect(addButton).toBeInTheDocument();
-    expect(addButton?.getElementsByTagName("input")[0]).toBeEnabled();
+    expect(addButton).toBeEnabled();
 
     expect(screen.queryByLabelText("Remove model")).not.toBeInTheDocument();
   });
@@ -282,16 +282,16 @@ describe(MethodRow.name, () => {
       ],
     });
 
-    const addButton = screen.queryByLabelText("Add new model");
+    const addButton = await screen.findByLabelText("Add new model");
     expect(addButton).toBeInTheDocument();
-    expect(addButton?.getElementsByTagName("input")[0]).toBeEnabled();
+    expect(addButton).toBeEnabled();
 
-    const removeButton = screen.queryByLabelText("Remove model");
+    const removeButton = await screen.findByLabelText("Remove model");
     expect(removeButton).toBeInTheDocument();
-    expect(removeButton?.getElementsByTagName("input")[0]).toBeEnabled();
+    expect(removeButton).toBeEnabled();
   });
 
-  it("shows add model button on first row and remove model button on all other rows", async () => {
+  it("shows add model button on first row and remove model button on all other rows", () => {
     render({
       modeledMethods: [
         { ...modeledMethod, type: "source" },
@@ -303,12 +303,12 @@ describe(MethodRow.name, () => {
 
     const addButtons = screen.queryAllByLabelText("Add new model");
     expect(addButtons.length).toBe(1);
-    expect(addButtons[0]?.getElementsByTagName("input")[0]).toBeEnabled();
+    expect(addButtons[0]).toBeEnabled();
 
     const removeButtons = screen.queryAllByLabelText("Remove model");
     expect(removeButtons.length).toBe(3);
     for (const removeButton of removeButtons) {
-      expect(removeButton?.getElementsByTagName("input")[0]).toBeEnabled();
+      expect(removeButton).toBeEnabled();
     }
   });
 
diff --git a/extensions/ql-vscode/src/view/model-editor/__tests__/ModelEvaluation.spec.tsx b/extensions/ql-vscode/src/view/model-editor/__tests__/ModelEvaluation.spec.tsx
index 24897bfa098..150ace05b53 100644
--- a/extensions/ql-vscode/src/view/model-editor/__tests__/ModelEvaluation.spec.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/__tests__/ModelEvaluation.spec.tsx
@@ -1,4 +1,4 @@
-import { render as reactRender, screen } from "@testing-library/react";
+import { render as reactRender, screen, waitFor } from "@testing-library/react";
 import type { Props } from "../ModelEvaluation";
 import { ModelEvaluation } from "../ModelEvaluation";
 import { createMockModelEditorViewState } from "../../../../test/factories/model-editor/view-state";
@@ -39,47 +39,51 @@ describe(ModelEvaluation.name, () => {
   });
 
   describe("when showEvaluationUi is true", () => {
-    it("renders evaluation UI with 'Evaluate' button enabled", () => {
+    it("renders evaluation UI with 'Evaluate' button enabled", async () => {
       render();
 
-      const evaluateButton = screen.queryByText("Evaluate");
+      const evaluateButton = await screen.findByText("Evaluate");
       expect(evaluateButton).toBeInTheDocument();
-      expect(evaluateButton?.getElementsByTagName("input")[0]).toBeEnabled();
+      expect(evaluateButton).toBeEnabled();
 
       expect(screen.queryByText("Stop evaluation")).not.toBeInTheDocument();
 
       expect(screen.queryByText("Evaluation run")).not.toBeInTheDocument();
     });
 
-    it("disables 'Evaluate' button when there are no custom models", () => {
+    it("disables 'Evaluate' button when there are no custom models", async () => {
       render({
         modeledMethods: {},
       });
 
-      const evaluateButton = screen.queryByText("Evaluate");
+      const evaluateButton = await screen.findByText("Evaluate");
       expect(evaluateButton).toBeInTheDocument();
-      expect(evaluateButton?.getElementsByTagName("input")[0]).toBeDisabled();
+      await waitFor(() => {
+        expect(evaluateButton).toBeDisabled();
+      });
 
       expect(screen.queryByText("Stop evaluation")).not.toBeInTheDocument();
 
       expect(screen.queryByText("Evaluation run")).not.toBeInTheDocument();
     });
 
-    it("disables 'Evaluate' button when there are unsaved changes", () => {
+    it("disables 'Evaluate' button when there are unsaved changes", async () => {
       render({
         modifiedSignatures: new Set([method.signature]),
       });
 
-      const evaluateButton = screen.queryByText("Evaluate");
+      const evaluateButton = await screen.findByText("Evaluate");
       expect(evaluateButton).toBeInTheDocument();
-      expect(evaluateButton?.getElementsByTagName("input")[0]).toBeDisabled();
+      await waitFor(() => {
+        expect(evaluateButton).toBeDisabled();
+      });
 
       expect(screen.queryByText("Stop evaluation")).not.toBeInTheDocument();
 
       expect(screen.queryByText("Evaluation run")).not.toBeInTheDocument();
     });
 
-    it("renders 'Evaluate' button and 'Evaluation run' link when there is a completed evaluation", () => {
+    it("renders 'Evaluate' button and 'Evaluation run' link when there is a completed evaluation", async () => {
       render({
         evaluationRun: {
           isPreparing: false,
@@ -89,16 +93,16 @@ describe(ModelEvaluation.name, () => {
         },
       });
 
-      const evaluateButton = screen.queryByText("Evaluate");
+      const evaluateButton = await screen.findByText("Evaluate");
       expect(evaluateButton).toBeInTheDocument();
-      expect(evaluateButton?.getElementsByTagName("input")[0]).toBeEnabled();
+      expect(evaluateButton).toBeEnabled();
 
       expect(screen.queryByText("Evaluation run")).toBeInTheDocument();
 
       expect(screen.queryByText("Stop evaluation")).not.toBeInTheDocument();
     });
 
-    it("renders 'Stop evaluation' button when there is an in progress evaluation, but no variant analysis yet", () => {
+    it("renders 'Stop evaluation' button when there is an in progress evaluation, but no variant analysis yet", async () => {
       render({
         evaluationRun: {
           isPreparing: true,
@@ -106,18 +110,16 @@ describe(ModelEvaluation.name, () => {
         },
       });
 
-      const stopEvaluationButton = screen.queryByText("Stop evaluation");
+      const stopEvaluationButton = await screen.findByText("Stop evaluation");
       expect(stopEvaluationButton).toBeInTheDocument();
-      expect(
-        stopEvaluationButton?.getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      expect(stopEvaluationButton).toBeEnabled();
 
       expect(screen.queryByText("Evaluation run")).not.toBeInTheDocument();
 
       expect(screen.queryByText("Evaluate")).not.toBeInTheDocument();
     });
 
-    it("renders 'Stop evaluation' button and 'Evaluation run' link when there is an in progress evaluation with variant analysis", () => {
+    it("renders 'Stop evaluation' button and 'Evaluation run' link when there is an in progress evaluation with variant analysis", async () => {
       render({
         evaluationRun: {
           isPreparing: false,
@@ -127,11 +129,9 @@ describe(ModelEvaluation.name, () => {
         },
       });
 
-      const stopEvaluationButton = screen.queryByText("Stop evaluation");
+      const stopEvaluationButton = await screen.findByText("Stop evaluation");
       expect(stopEvaluationButton).toBeInTheDocument();
-      expect(
-        stopEvaluationButton?.getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      expect(stopEvaluationButton).toBeEnabled();
 
       expect(screen.queryByText("Evaluation run")).toBeInTheDocument();
 
diff --git a/extensions/ql-vscode/src/view/results/AlertTableResultRow.tsx b/extensions/ql-vscode/src/view/results/AlertTableResultRow.tsx
index 3ae0e5badac..3ab31ed3f7f 100644
--- a/extensions/ql-vscode/src/view/results/AlertTableResultRow.tsx
+++ b/extensions/ql-vscode/src/view/results/AlertTableResultRow.tsx
@@ -13,7 +13,7 @@ import { SarifLocation } from "./locations/SarifLocation";
 import { SarifMessageWithLocations } from "./locations/SarifMessageWithLocations";
 import { AlertTablePathRow } from "./AlertTablePathRow";
 import type { UserSettings } from "../../common/interface-types";
-import { VSCodeBadge } from "@vscode/webview-ui-toolkit/react";
+import { Badge } from "../common/Badge";
 
 export interface Props {
   result: Result;
@@ -109,7 +109,7 @@ export function AlertTableResultRow(props: Props) {
             />
             <td className="vscode-codeql__icon-cell">{listUnordered}</td>
             <td className="vscode-codeql__icon-cell">
-              <VSCodeBadge title="Shortest path">{shortestPath}</VSCodeBadge>
+              <Badge title="Shortest path">{shortestPath}</Badge>
             </td>
             <td colSpan={3}>{msg}</td>
           </>
diff --git a/extensions/ql-vscode/src/view/results/__tests__/AlertTablePathRow.spec.tsx b/extensions/ql-vscode/src/view/results/__tests__/AlertTablePathRow.spec.tsx
index ada710bee85..001fa322a34 100644
--- a/extensions/ql-vscode/src/view/results/__tests__/AlertTablePathRow.spec.tsx
+++ b/extensions/ql-vscode/src/view/results/__tests__/AlertTablePathRow.spec.tsx
@@ -22,7 +22,9 @@ describe(AlertTablePathRow.name, () => {
         currentPathExpanded={true}
         databaseUri={"dbUri"}
         sourceLocationPrefix="src"
-        userSettings={{ shouldShowProvenance: false }}
+        userSettings={{
+          shouldShowProvenance: false,
+        }}
         updateSelectionCallback={jest.fn()}
         toggleExpanded={jest.fn()}
         {...props}
diff --git a/extensions/ql-vscode/src/view/results/__tests__/AlertTableResultRow.spec.tsx b/extensions/ql-vscode/src/view/results/__tests__/AlertTableResultRow.spec.tsx
index 0aa7279ae72..9082384e9d2 100644
--- a/extensions/ql-vscode/src/view/results/__tests__/AlertTableResultRow.spec.tsx
+++ b/extensions/ql-vscode/src/view/results/__tests__/AlertTableResultRow.spec.tsx
@@ -17,7 +17,9 @@ describe(AlertTableResultRow.name, () => {
         selectedItemRef={mockRef}
         databaseUri={"dbUri"}
         sourceLocationPrefix="src"
-        userSettings={{ shouldShowProvenance: false }}
+        userSettings={{
+          shouldShowProvenance: false,
+        }}
         updateSelectionCallback={jest.fn()}
         toggleExpanded={jest.fn()}
         {...props}
diff --git a/extensions/ql-vscode/src/view/tsconfig.json b/extensions/ql-vscode/src/view/tsconfig.json
index 4abd2c7f8a9..d094c039d78 100644
--- a/extensions/ql-vscode/src/view/tsconfig.json
+++ b/extensions/ql-vscode/src/view/tsconfig.json
@@ -14,7 +14,12 @@
     "noImplicitReturns": true,
     "noFallthroughCasesInSwitch": true,
     "experimentalDecorators": true,
-    "skipLibCheck": true
+    "skipLibCheck": true,
+    "plugins": [
+      {
+        "name": "typescript-plugin-css-modules"
+      }
+    ]
   },
   "exclude": ["node_modules"]
 }
diff --git a/extensions/ql-vscode/src/view/types.d.ts b/extensions/ql-vscode/src/view/types.d.ts
new file mode 100644
index 00000000000..1eabbb4297e
--- /dev/null
+++ b/extensions/ql-vscode/src/view/types.d.ts
@@ -0,0 +1 @@
+declare module "*.module.css";
diff --git a/extensions/ql-vscode/src/view/variant-analysis/RepoRow.tsx b/extensions/ql-vscode/src/view/variant-analysis/RepoRow.tsx
index fc381fe016f..19edad08cc2 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/RepoRow.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/RepoRow.tsx
@@ -1,7 +1,7 @@
 import type { ChangeEvent } from "react";
 import { useCallback, useEffect, useState } from "react";
 import { styled } from "styled-components";
-import { VSCodeBadge, VSCodeCheckbox } from "@vscode/webview-ui-toolkit/react";
+import { VscodeCheckbox } from "@vscode-elements/react-elements";
 import type { VariantAnalysisScannedRepositoryState } from "../../variant-analysis/shared/variant-analysis";
 import {
   isCompletedAnalysisRepoStatus,
@@ -27,6 +27,7 @@ import StarCount from "../common/StarCount";
 import { useTelemetryOnChange } from "../common/telemetry";
 import { DeterminateProgressRing } from "../common/DeterminateProgressRing";
 import { ResultFormat } from "../../variant-analysis/shared/variant-analysis-result-format";
+import { Badge } from "../common/Badge";
 
 // This will ensure that these icons have a className which we can use in the TitleContainer
 const ExpandCollapseCodicon = styled(Codicon)``;
@@ -61,6 +62,10 @@ const MetadataContainer = styled.div`
   margin-left: auto;
 `;
 
+const Checkbox = styled(VscodeCheckbox)`
+  margin-right: -9px; // VscodeCheckbox has 9px margin on the right by default
+`;
+
 type VisibilityProps = {
   isPrivate?: boolean;
 };
@@ -254,7 +259,7 @@ export const RepoRow = ({
         disabled={disabled}
         aria-expanded={isExpanded}
       >
-        <VSCodeCheckbox
+        <Checkbox
           onChange={onChangeCheckbox}
           onClick={onClickCheckbox}
           checked={selected}
@@ -269,9 +274,9 @@ export const RepoRow = ({
           <ExpandCollapseCodicon name="chevron-right" label="Expand" />
         )}
         {resultsLoading && <LoadingIcon label="Results are loading" />}
-        <VSCodeBadge>
+        <Badge>
           {resultCount === undefined ? "-" : formatDecimal(resultCount)}
-        </VSCodeBadge>
+        </Badge>
         <span>{repository.fullName}</span>
         <Visibility isPrivate={repository.private} />
         <span>
diff --git a/extensions/ql-vscode/src/view/variant-analysis/RepositoriesFilter.tsx b/extensions/ql-vscode/src/view/variant-analysis/RepositoriesFilter.tsx
index 56596b2ecbf..206b33586fb 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/RepositoriesFilter.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/RepositoriesFilter.tsx
@@ -1,10 +1,13 @@
 import { useCallback } from "react";
 import { styled } from "styled-components";
-import { VSCodeDropdown, VSCodeOption } from "@vscode/webview-ui-toolkit/react";
+import {
+  VscodeOption,
+  VscodeSingleSelect,
+} from "@vscode-elements/react-elements";
 import { Codicon } from "../common";
 import { FilterKey } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 
-const Dropdown = styled(VSCodeDropdown)`
+const Dropdown = styled(VscodeSingleSelect)`
   width: 100%;
 `;
 
@@ -26,10 +29,10 @@ export const RepositoriesFilter = ({ value, onChange, className }: Props) => {
   );
 
   return (
-    <Dropdown value={value} onInput={handleInput} className={className}>
+    <Dropdown value={value} onChange={handleInput} className={className}>
       <Codicon name="list-filter" label="Filter..." slot="indicator" />
-      <VSCodeOption value={FilterKey.All}>All</VSCodeOption>
-      <VSCodeOption value={FilterKey.WithResults}>With results</VSCodeOption>
+      <VscodeOption value={FilterKey.All}>All</VscodeOption>
+      <VscodeOption value={FilterKey.WithResults}>With results</VscodeOption>
     </Dropdown>
   );
 };
diff --git a/extensions/ql-vscode/src/view/variant-analysis/RepositoriesResultFormat.tsx b/extensions/ql-vscode/src/view/variant-analysis/RepositoriesResultFormat.tsx
index 11ac814cc18..380599017eb 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/RepositoriesResultFormat.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/RepositoriesResultFormat.tsx
@@ -1,10 +1,13 @@
 import { useCallback } from "react";
 import { styled } from "styled-components";
-import { VSCodeDropdown, VSCodeOption } from "@vscode/webview-ui-toolkit/react";
+import {
+  VscodeOption,
+  VscodeSingleSelect,
+} from "@vscode-elements/react-elements";
 import { Codicon } from "../common";
 import { ResultFormat } from "../../variant-analysis/shared/variant-analysis-result-format";
 
-const Dropdown = styled(VSCodeDropdown)`
+const Dropdown = styled(VscodeSingleSelect)`
   width: 100%;
 `;
 
@@ -30,14 +33,14 @@ export const RepositoriesResultFormat = ({
   );
 
   return (
-    <Dropdown value={value} onInput={handleInput} className={className}>
+    <Dropdown value={value} onChange={handleInput} className={className}>
       <Codicon name="table" label="Result format..." slot="indicator" />
-      <VSCodeOption value={ResultFormat.Alerts}>
+      <VscodeOption value={ResultFormat.Alerts}>
         {ResultFormat.Alerts}
-      </VSCodeOption>
-      <VSCodeOption value={ResultFormat.RawResults}>
+      </VscodeOption>
+      <VscodeOption value={ResultFormat.RawResults}>
         {ResultFormat.RawResults}
-      </VSCodeOption>
+      </VscodeOption>
     </Dropdown>
   );
 };
diff --git a/extensions/ql-vscode/src/view/variant-analysis/RepositoriesSort.tsx b/extensions/ql-vscode/src/view/variant-analysis/RepositoriesSort.tsx
index d4383a3e1ea..96ec4c43dd4 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/RepositoriesSort.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/RepositoriesSort.tsx
@@ -1,10 +1,13 @@
 import { useCallback } from "react";
 import { styled } from "styled-components";
-import { VSCodeDropdown, VSCodeOption } from "@vscode/webview-ui-toolkit/react";
+import {
+  VscodeOption,
+  VscodeSingleSelect,
+} from "@vscode-elements/react-elements";
 import { SortKey } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 import { Codicon } from "../common";
 
-const Dropdown = styled(VSCodeDropdown)`
+const Dropdown = styled(VscodeSingleSelect)`
   width: 100%;
 `;
 
@@ -26,13 +29,13 @@ export const RepositoriesSort = ({ value, onChange, className }: Props) => {
   );
 
   return (
-    <Dropdown value={value} onInput={handleInput} className={className}>
+    <Dropdown value={value} onChange={handleInput} className={className}>
       <Codicon name="sort-precedence" label="Sort..." slot="indicator" />
-      <VSCodeOption value={SortKey.Alphabetically}>Alphabetically</VSCodeOption>
-      <VSCodeOption value={SortKey.NumberOfResults}>
+      <VscodeOption value={SortKey.Alphabetically}>Alphabetically</VscodeOption>
+      <VscodeOption value={SortKey.NumberOfResults}>
         Number of results
-      </VSCodeOption>
-      <VSCodeOption value={SortKey.Popularity}>Popularity</VSCodeOption>
+      </VscodeOption>
+      <VscodeOption value={SortKey.Popularity}>Popularity</VscodeOption>
     </Dropdown>
   );
 };
diff --git a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysis.tsx b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysis.tsx
index 5b68d114d6f..3ac0599ae6c 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysis.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysis.tsx
@@ -9,11 +9,15 @@ import { VariantAnalysisStatus } from "../../variant-analysis/shared/variant-ana
 import { VariantAnalysisHeader } from "./VariantAnalysisHeader";
 import { VariantAnalysisOutcomePanels } from "./VariantAnalysisOutcomePanels";
 import { VariantAnalysisLoading } from "./VariantAnalysisLoading";
-import type { ToVariantAnalysisMessage } from "../../common/interface-types";
+import type {
+  ToVariantAnalysisMessage,
+  VariantAnalysisUserSettings,
+} from "../../common/interface-types";
 import { vscode } from "../vscode-api";
 import { defaultFilterSortState } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 import { sendTelemetry, useTelemetryOnChange } from "../common/telemetry";
 import { useMessageFromExtension } from "../common/useMessageFromExtension";
+import { DEFAULT_VARIANT_ANALYSIS_USER_SETTINGS } from "../../common/interface-types";
 
 export type VariantAnalysisProps = {
   variantAnalysis?: VariantAnalysisDomainModel;
@@ -77,6 +81,10 @@ export function VariantAnalysis({
   useTelemetryOnChange(filterSortState, "variant-analysis-filter-sort-state", {
     debounceTimeoutMillis: 1000,
   });
+  const [variantAnalysisUserSettings, setVariantAnalysisUserSettings] =
+    useState<VariantAnalysisUserSettings>(
+      DEFAULT_VARIANT_ANALYSIS_USER_SETTINGS,
+    );
 
   useMessageFromExtension<ToVariantAnalysisMessage>((msg) => {
     if (msg.t === "setVariantAnalysis") {
@@ -102,9 +110,22 @@ export function VariantAnalysis({
           ...msg.repoStates,
         ];
       });
+    } else if (msg.t === "setVariantAnalysisUserSettings") {
+      setVariantAnalysisUserSettings(msg.variantAnalysisUserSettings);
     }
   }, []);
 
+  const viewAutofixes = useCallback(() => {
+    vscode.postMessage({
+      t: "viewAutofixes",
+      filterSort: {
+        ...filterSortState,
+        repositoryIds: selectedRepositoryIds,
+      },
+    });
+    sendTelemetry("variant-analysis-view-autofixes");
+  }, [filterSortState, selectedRepositoryIds]);
+
   const copyRepositoryList = useCallback(() => {
     vscode.postMessage({
       t: "copyRepositoryList",
@@ -148,9 +169,11 @@ export function VariantAnalysis({
         onOpenQueryFileClick={openQueryFile}
         onViewQueryTextClick={openQueryText}
         onStopQueryClick={stopQuery}
+        onViewAutofixesClick={viewAutofixes}
         onCopyRepositoryListClick={copyRepositoryList}
         onExportResultsClick={exportResults}
         onViewLogsClick={onViewLogsClick}
+        variantAnalysisUserSettings={variantAnalysisUserSettings}
       />
       <VariantAnalysisOutcomePanels
         variantAnalysis={variantAnalysis}
diff --git a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisActions.tsx b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisActions.tsx
index ed1b473c66a..abec9443946 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisActions.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisActions.tsx
@@ -1,6 +1,6 @@
 import { styled } from "styled-components";
-import { VSCodeButton } from "@vscode/webview-ui-toolkit/react";
 import { VariantAnalysisStatus } from "../../variant-analysis/shared/variant-analysis";
+import { VscodeButton } from "@vscode-elements/react-elements";
 
 export type VariantAnalysisActionsProps = {
   variantAnalysisStatus: VariantAnalysisStatus;
@@ -9,13 +9,17 @@ export type VariantAnalysisActionsProps = {
   stopQueryDisabled?: boolean;
 
   showResultActions?: boolean;
+  onViewAutofixesClick: () => void;
   onCopyRepositoryListClick: () => void;
   onExportResultsClick: () => void;
+  viewAutofixesDisabled?: boolean;
   copyRepositoryListDisabled?: boolean;
   exportResultsDisabled?: boolean;
 
   hasSelectedRepositories?: boolean;
   hasFilteredRepositories?: boolean;
+
+  showViewAutofixesButton: boolean;
 };
 
 const Container = styled.div`
@@ -24,7 +28,7 @@ const Container = styled.div`
   gap: 1em;
 `;
 
-const Button = styled(VSCodeButton)`
+const Button = styled(VscodeButton)`
   white-space: nowrap;
 `;
 
@@ -55,19 +59,37 @@ export const VariantAnalysisActions = ({
   onStopQueryClick,
   stopQueryDisabled,
   showResultActions,
+  onViewAutofixesClick,
   onCopyRepositoryListClick,
   onExportResultsClick,
+  viewAutofixesDisabled,
   copyRepositoryListDisabled,
   exportResultsDisabled,
   hasSelectedRepositories,
   hasFilteredRepositories,
+  showViewAutofixesButton,
 }: VariantAnalysisActionsProps) => {
   return (
     <Container>
       {showResultActions && (
         <>
+          {showViewAutofixesButton && (
+            <Button
+              secondary
+              onClick={onViewAutofixesClick}
+              disabled={viewAutofixesDisabled}
+            >
+              {chooseText({
+                hasSelectedRepositories,
+                hasFilteredRepositories,
+                normalText: "View Autofixes",
+                selectedText: "View Autofixes for selected results",
+                filteredText: "View Autofixes for filtered results",
+              })}
+            </Button>
+          )}
           <Button
-            appearance="secondary"
+            secondary
             onClick={onCopyRepositoryListClick}
             disabled={copyRepositoryListDisabled}
           >
@@ -96,7 +118,7 @@ export const VariantAnalysisActions = ({
       )}
       {variantAnalysisStatus === VariantAnalysisStatus.InProgress && (
         <Button
-          appearance="secondary"
+          secondary
           onClick={onStopQueryClick}
           disabled={stopQueryDisabled}
         >
@@ -104,7 +126,7 @@ export const VariantAnalysisActions = ({
         </Button>
       )}
       {variantAnalysisStatus === VariantAnalysisStatus.Canceling && (
-        <Button appearance="secondary" disabled={true}>
+        <Button secondary disabled={true}>
           Stopping query
         </Button>
       )}
diff --git a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisHeader.tsx b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisHeader.tsx
index bdd9b5e11be..6f9ad00ad33 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisHeader.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisHeader.tsx
@@ -22,6 +22,7 @@ import {
   filterAndSortRepositoriesWithResults,
 } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 import { ViewTitle } from "../common";
+import type { VariantAnalysisUserSettings } from "../../common/interface-types";
 
 type VariantAnalysisHeaderProps = {
   variantAnalysis: VariantAnalysis;
@@ -34,10 +35,13 @@ type VariantAnalysisHeaderProps = {
 
   onStopQueryClick: () => void;
 
+  onViewAutofixesClick: () => void;
   onCopyRepositoryListClick: () => void;
   onExportResultsClick: () => void;
 
   onViewLogsClick?: () => void;
+
+  variantAnalysisUserSettings: VariantAnalysisUserSettings;
 };
 
 const Container = styled.div`
@@ -82,9 +86,11 @@ export const VariantAnalysisHeader = ({
   onOpenQueryFileClick,
   onViewQueryTextClick,
   onStopQueryClick,
+  onViewAutofixesClick,
   onCopyRepositoryListClick,
   onExportResultsClick,
   onViewLogsClick,
+  variantAnalysisUserSettings,
 }: VariantAnalysisHeaderProps) => {
   const totalScannedRepositoryCount = useMemo(() => {
     return variantAnalysis.scannedRepos?.length ?? 0;
@@ -150,11 +156,13 @@ export const VariantAnalysisHeader = ({
           variantAnalysisStatus={variantAnalysis.status}
           showResultActions={(resultCount ?? 0) > 0}
           onStopQueryClick={onStopQueryClick}
+          onViewAutofixesClick={onViewAutofixesClick}
           onCopyRepositoryListClick={onCopyRepositoryListClick}
           onExportResultsClick={onExportResultsClick}
           stopQueryDisabled={!variantAnalysis.actionsWorkflowRunId}
           exportResultsDisabled={!hasDownloadedRepos}
           copyRepositoryListDisabled={!hasReposWithResults}
+          viewAutofixesDisabled={!hasReposWithResults}
           hasFilteredRepositories={
             variantAnalysis.scannedRepos?.length !==
             filteredRepositories?.length
@@ -162,6 +170,9 @@ export const VariantAnalysisHeader = ({
           hasSelectedRepositories={
             selectedRepositoryIds && selectedRepositoryIds.length > 0
           }
+          showViewAutofixesButton={
+            variantAnalysisUserSettings.shouldShowViewAutofixesButton
+          }
         />
       </Row>
       <VariantAnalysisStats
diff --git a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisOutcomePanels.tsx b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisOutcomePanels.tsx
index 469c7aa6d29..1f138ffd8cd 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisOutcomePanels.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisOutcomePanels.tsx
@@ -2,11 +2,10 @@ import type { Dispatch, SetStateAction } from "react";
 import { useState } from "react";
 import { styled } from "styled-components";
 import {
-  VSCodeBadge,
-  VSCodePanels,
-  VSCodePanelTab,
-  VSCodePanelView,
-} from "@vscode/webview-ui-toolkit/react";
+  VscodeTabHeader,
+  VscodeTabPanel,
+  VscodeTabs,
+} from "@vscode-elements/react-elements";
 import { formatDecimal } from "../../common/number";
 import type {
   VariantAnalysis,
@@ -21,6 +20,7 @@ import type { RepositoriesFilterSortState } from "../../variant-analysis/shared/
 import { RepositoriesSearchSortRow } from "./RepositoriesSearchSortRow";
 import { FailureReasonAlert } from "./FailureReasonAlert";
 import { ResultFormat } from "../../variant-analysis/shared/variant-analysis-result-format";
+import { Badge } from "../common/Badge";
 
 export type VariantAnalysisOutcomePanelProps = {
   variantAnalysis: VariantAnalysis;
@@ -34,8 +34,27 @@ export type VariantAnalysisOutcomePanelProps = {
   setFilterSortState: Dispatch<SetStateAction<RepositoriesFilterSortState>>;
 };
 
-const Tab = styled(VSCodePanelTab)`
+const Tabs = styled(VscodeTabs)`
+  column-gap: 32px;
+
+  > vscode-tab-header {
+    margin-right: 32px;
+  }
+`;
+
+const TabHeader = styled(VscodeTabHeader)`
   text-transform: uppercase;
+
+  > * {
+    // This copies the styles from @vscode/webview-ui-toolkit's VSCodePanelTab
+    &:last-child {
+      margin-left: 8px;
+    }
+  }
+`;
+
+const TabPanel = styled(VscodeTabPanel)`
+  padding: 10px 6px;
 `;
 
 const WarningsContainer = styled.div`
@@ -154,33 +173,31 @@ export const VariantAnalysisOutcomePanels = ({
         onResultFormatChange={setResultFormat}
         variantAnalysisQueryKind={variantAnalysis.query.kind}
       />
-      <VSCodePanels>
+      <Tabs>
         {scannedReposCount > 0 && (
-          <Tab>
+          <TabHeader>
             Analyzed
-            <VSCodeBadge appearance="secondary">
+            <Badge>
               {formatDecimal(variantAnalysis.scannedRepos?.length ?? 0)}
-            </VSCodeBadge>
-          </Tab>
-        )}
-        {notFoundRepos?.repositoryCount && (
-          <Tab>
-            No access
-            <VSCodeBadge appearance="secondary">
-              {formatDecimal(notFoundRepos.repositoryCount)}
-            </VSCodeBadge>
-          </Tab>
-        )}
-        {noCodeqlDbRepos?.repositoryCount && (
-          <Tab>
-            No database
-            <VSCodeBadge appearance="secondary">
-              {formatDecimal(noCodeqlDbRepos.repositoryCount)}
-            </VSCodeBadge>
-          </Tab>
+            </Badge>
+          </TabHeader>
         )}
+        {notFoundRepos?.repositoryCount !== undefined &&
+          notFoundRepos?.repositoryCount > 0 && (
+            <TabHeader>
+              No access
+              <Badge>{formatDecimal(notFoundRepos.repositoryCount)}</Badge>
+            </TabHeader>
+          )}
+        {noCodeqlDbRepos?.repositoryCount !== undefined &&
+          noCodeqlDbRepos?.repositoryCount > 0 && (
+            <TabHeader>
+              No database
+              <Badge>{formatDecimal(noCodeqlDbRepos.repositoryCount)}</Badge>
+            </TabHeader>
+          )}
         {scannedReposCount > 0 && (
-          <VSCodePanelView>
+          <TabPanel>
             <VariantAnalysisAnalyzedRepos
               variantAnalysis={variantAnalysis}
               repositoryStates={repositoryStates}
@@ -190,29 +207,31 @@ export const VariantAnalysisOutcomePanels = ({
               selectedRepositoryIds={selectedRepositoryIds}
               setSelectedRepositoryIds={setSelectedRepositoryIds}
             />
-          </VSCodePanelView>
-        )}
-        {notFoundRepos?.repositoryCount && (
-          <VSCodePanelView>
-            <VariantAnalysisSkippedRepositoriesTab
-              alertTitle="No access"
-              alertMessage="The following repositories can't be analyzed because they don’t exist or you don’t have access."
-              skippedRepositoryGroup={notFoundRepos}
-              filterSortState={filterSortState}
-            />
-          </VSCodePanelView>
-        )}
-        {noCodeqlDbRepos?.repositoryCount && (
-          <VSCodePanelView>
-            <VariantAnalysisSkippedRepositoriesTab
-              alertTitle="No CodeQL database"
-              alertMessage="The following repositories can't be analyzed because they don't currently have a CodeQL database available for the selected language."
-              skippedRepositoryGroup={noCodeqlDbRepos}
-              filterSortState={filterSortState}
-            />
-          </VSCodePanelView>
+          </TabPanel>
         )}
-      </VSCodePanels>
+        {notFoundRepos?.repositoryCount !== undefined &&
+          notFoundRepos?.repositoryCount > 0 && (
+            <TabPanel>
+              <VariantAnalysisSkippedRepositoriesTab
+                alertTitle="No access"
+                alertMessage="The following repositories can't be analyzed because they don’t exist or you don’t have access."
+                skippedRepositoryGroup={notFoundRepos}
+                filterSortState={filterSortState}
+              />
+            </TabPanel>
+          )}
+        {noCodeqlDbRepos?.repositoryCount !== undefined &&
+          noCodeqlDbRepos?.repositoryCount > 0 && (
+            <TabPanel>
+              <VariantAnalysisSkippedRepositoriesTab
+                alertTitle="No CodeQL database"
+                alertMessage="The following repositories can't be analyzed because they don't currently have a CodeQL database available for the selected language."
+                skippedRepositoryGroup={noCodeqlDbRepos}
+                filterSortState={filterSortState}
+              />
+            </TabPanel>
+          )}
+      </Tabs>
     </>
   );
 };
diff --git a/extensions/ql-vscode/src/view/variant-analysis/__tests__/RepoRow.spec.tsx b/extensions/ql-vscode/src/view/variant-analysis/__tests__/RepoRow.spec.tsx
index b1f4df59a71..1c89400615d 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/__tests__/RepoRow.spec.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/__tests__/RepoRow.spec.tsx
@@ -1,9 +1,4 @@
-import {
-  act,
-  render as reactRender,
-  screen,
-  waitFor,
-} from "@testing-library/react";
+import { act, render as reactRender, screen } from "@testing-library/react";
 import {
   VariantAnalysisRepoStatus,
   VariantAnalysisScannedRepositoryDownloadStatus,
@@ -403,7 +398,8 @@ describe(RepoRow.name, () => {
       status: VariantAnalysisRepoStatus.InProgress,
     });
 
-    expect(screen.getByRole("checkbox")).toBeDisabled();
+    const checkbox = await screen.findByRole("checkbox");
+    expect(checkbox).toBeDisabled();
   });
 
   it("does not allow selecting the item if the item has not been downloaded", async () => {
@@ -411,7 +407,8 @@ describe(RepoRow.name, () => {
       status: VariantAnalysisRepoStatus.Succeeded,
     });
 
-    expect(screen.getByRole("checkbox")).toBeDisabled();
+    const checkbox = await screen.findByRole("checkbox");
+    expect(checkbox).toBeDisabled();
   });
 
   it("does not allow selecting the item if the item has not been downloaded successfully", async () => {
@@ -423,11 +420,8 @@ describe(RepoRow.name, () => {
       },
     });
 
-    // It seems like sometimes the first render doesn't have the checkbox disabled
-    // Might be related to https://github.com/microsoft/vscode-webview-ui-toolkit/issues/404
-    await waitFor(() => {
-      expect(screen.getByRole("checkbox")).toBeDisabled();
-    });
+    const checkbox = await screen.findByRole("checkbox");
+    expect(checkbox).toBeDisabled();
   });
 
   it("allows selecting the item if the item has been downloaded", async () => {
@@ -440,6 +434,7 @@ describe(RepoRow.name, () => {
       },
     });
 
-    expect(screen.getByRole("checkbox")).toBeEnabled();
+    const checkbox = await screen.findByRole("checkbox");
+    expect(checkbox).toBeEnabled();
   });
 });
diff --git a/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysis.spec.tsx b/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysis.spec.tsx
index b8a7bfcd539..3279ed446d2 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysis.spec.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysis.spec.tsx
@@ -1,4 +1,4 @@
-import { render as reactRender, screen, waitFor } from "@testing-library/react";
+import { render as reactRender, screen } from "@testing-library/react";
 import {
   VariantAnalysisFailureReason,
   VariantAnalysisStatus,
@@ -57,9 +57,6 @@ describe(VariantAnalysis.name, () => {
     const variantAnalysis = createMockVariantAnalysis({});
     render({ variantAnalysis });
 
-    await waitFor(() => screen.getByDisplayValue("All"));
-    await waitFor(() => screen.getByDisplayValue("Number of results"));
-
     await postMessage<ToVariantAnalysisMessage>({
       t: "setFilterSortState",
       filterSortState: {
@@ -69,8 +66,11 @@ describe(VariantAnalysis.name, () => {
       },
     });
 
-    expect(screen.getByDisplayValue("With results")).toBeInTheDocument();
-    expect(screen.getByDisplayValue("Alphabetically")).toBeInTheDocument();
+    const withResults = await screen.findByText("With results");
+    expect(withResults).toBeInTheDocument();
+
+    const alphabetically = await screen.findByText("Alphabetically");
+    expect(alphabetically).toBeInTheDocument();
 
     expect(screen.queryByDisplayValue("All")).not.toBeInTheDocument();
     expect(
diff --git a/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysisActions.spec.tsx b/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysisActions.spec.tsx
index de19458646e..08d3fe84b54 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysisActions.spec.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysisActions.spec.tsx
@@ -6,11 +6,13 @@ import { VariantAnalysisActions } from "../VariantAnalysisActions";
 
 describe(VariantAnalysisActions.name, () => {
   const onStopQueryClick = jest.fn();
+  const onViewAutofixesClick = jest.fn();
   const onCopyRepositoryListClick = jest.fn();
   const onExportResultsClick = jest.fn();
 
   afterEach(() => {
     onStopQueryClick.mockReset();
+    onViewAutofixesClick.mockReset();
     onCopyRepositoryListClick.mockReset();
     onExportResultsClick.mockReset();
   });
@@ -22,8 +24,10 @@ describe(VariantAnalysisActions.name, () => {
     reactRender(
       <VariantAnalysisActions
         onStopQueryClick={onStopQueryClick}
+        onViewAutofixesClick={onViewAutofixesClick}
         onCopyRepositoryListClick={onCopyRepositoryListClick}
         onExportResultsClick={onExportResultsClick}
+        showViewAutofixesButton={false}
         {...props}
       />,
     );
@@ -50,9 +54,9 @@ describe(VariantAnalysisActions.name, () => {
       variantAnalysisStatus: VariantAnalysisStatus.Canceling,
     });
 
-    const button = screen.getByText("Stopping query");
+    const button = await screen.findByText("Stopping query");
     expect(button).toBeInTheDocument();
-    expect(button.getElementsByTagName("input")[0]).toBeDisabled();
+    expect(button).toBeDisabled();
   });
 
   it("does not render a stop query button when canceling", async () => {
diff --git a/extensions/ql-vscode/supported_cli_versions.json b/extensions/ql-vscode/supported_cli_versions.json
index 7c7d6b4cb12..57ccdc0c71d 100644
--- a/extensions/ql-vscode/supported_cli_versions.json
+++ b/extensions/ql-vscode/supported_cli_versions.json
@@ -1,4 +1,6 @@
 [
+  "v2.22.2",
+  "v2.21.4",
   "v2.20.7",
   "v2.19.4",
   "v2.18.4",
diff --git a/extensions/ql-vscode/test/data-extensions/pack-using-extensions/codeql-pack.lock.yml b/extensions/ql-vscode/test/data-extensions/pack-using-extensions/codeql-pack.lock.yml
new file mode 100644
index 00000000000..61121d6d0cf
--- /dev/null
+++ b/extensions/ql-vscode/test/data-extensions/pack-using-extensions/codeql-pack.lock.yml
@@ -0,0 +1,26 @@
+---
+lockVersion: 1.0.0
+dependencies:
+  codeql/dataflow:
+    version: 2.0.7
+  codeql/javascript-all:
+    version: 2.6.3
+  codeql/mad:
+    version: 1.0.23
+  codeql/regex:
+    version: 1.0.23
+  codeql/ssa:
+    version: 1.1.2
+  codeql/threat-models:
+    version: 1.0.23
+  codeql/tutorial:
+    version: 1.0.23
+  codeql/typetracking:
+    version: 2.0.7
+  codeql/util:
+    version: 2.0.10
+  codeql/xml:
+    version: 1.0.23
+  codeql/yaml:
+    version: 1.0.23
+compiled: false
diff --git a/extensions/ql-vscode/test/e2e/docker/Dockerfile b/extensions/ql-vscode/test/e2e/docker/Dockerfile
index 0f1e537538f..dbf0bad1899 100644
--- a/extensions/ql-vscode/test/e2e/docker/Dockerfile
+++ b/extensions/ql-vscode/test/e2e/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM codercom/code-server:4.98.2
+FROM codercom/code-server:4.102.0
 
 USER root
 
diff --git a/extensions/ql-vscode/test/jest-config.ts b/extensions/ql-vscode/test/jest-config.ts
index 5a6b6f64bef..3270067df7a 100644
--- a/extensions/ql-vscode/test/jest-config.ts
+++ b/extensions/ql-vscode/test/jest-config.ts
@@ -1,8 +1,13 @@
 // These are all the packages that DO need to be transformed. All other packages will be ignored.
 // These pacakges all use ES modules, so need to be transformed
-const transformScopes = ["@microsoft", "@octokit"];
+const transformScopes = [
+  "@microsoft",
+  "@octokit",
+  "@vscode-elements",
+  "@lit",
+  "@lit-labs",
+];
 const transformPackages = [
-  "@vscode/webview-ui-toolkit",
   "before-after-hook",
   "d3",
   "data-uri-to-buffer",
@@ -11,13 +16,14 @@ const transformPackages = [
   "fetch-blob",
   "formdata-polyfill",
   "internmap",
+  "lit",
   "nanoid",
   "p-queue",
   "p-timeout",
   "robust-predicates",
   "universal-user-agent",
 ];
-const transformWildcards = ["d3-(.*)"];
+const transformWildcards = ["d3-(.*)", "lit-(.*)"];
 const transformPatterns = [
   ...transformScopes.map((scope) => `${scope}/.+`),
   ...transformPackages,
diff --git a/extensions/ql-vscode/test/unit-tests/common/errors.test.ts b/extensions/ql-vscode/test/unit-tests/common/errors.test.ts
index ca9e01de37e..0f9cabf5c37 100644
--- a/extensions/ql-vscode/test/unit-tests/common/errors.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/common/errors.test.ts
@@ -37,7 +37,7 @@ describe("errorMessage", () => {
       myRealFunction();
 
       fail("Expected an error to be thrown");
-    } catch (e: unknown) {
+    } catch (e) {
       if (!(e instanceof Error)) {
         throw new Error("Expected an Error to be thrown");
       }
diff --git a/extensions/ql-vscode/test/unit-tests/data/evaluator-log-summaries/bad-join-order.jsonl b/extensions/ql-vscode/test/unit-tests/data/evaluator-log-summaries/bad-join-order.jsonl
index 8d366067387..59d6e67f64a 100644
--- a/extensions/ql-vscode/test/unit-tests/data/evaluator-log-summaries/bad-join-order.jsonl
+++ b/extensions/ql-vscode/test/unit-tests/data/evaluator-log-summaries/bad-join-order.jsonl
@@ -11458,7 +11458,7 @@
     "duplicationPercentages" : [ 0, -1, 1, 0, -1, 0, -1, 0, 0, -1, 1, 0, 1, -1, 1, 0 ]
   }, {
     "raReference" : "order_500000",
-    "counts" : [ 0, -1, 0, -1, 3138, -1, 3138, 3138, -1, 0, -1, 0, 0, -1, 0, -1, 133, 133, -1, 0, 0, -1, 133, 133, 3271, 3271, 3271 ],
+    "counts" : [ 0, -1, 0, -1, 31380000, -1, 3138, 3138, -1, 0, -1, 0, 0, -1, 0, -1, 133, 133, -1, 0, 0, -1, 133, 133, 3271, 3271, 3271 ],
     "duplicationPercentages" : [ 0, -1, 0, -1, 0, -1, 0, 0, -1, 0, -1, 0, 0, -1, 0, -1, 0, 0, -1, 0, 0, -1, 0, 0, 0, 0, 1 ]
   }, {
     "raReference" : "order_500000",
diff --git a/extensions/ql-vscode/test/unit-tests/log-scanner.test.ts b/extensions/ql-vscode/test/unit-tests/log-scanner.test.ts
index 3d49f3362a1..0012cecda23 100644
--- a/extensions/ql-vscode/test/unit-tests/log-scanner.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/log-scanner.test.ts
@@ -1,28 +1,39 @@
+import { scanAndReportJoinOrderProblems } from "../../src/log-insights/join-order";
 import type { EvaluationLogProblemReporter } from "../../src/log-insights/log-scanner";
-import { EvaluationLogScannerSet } from "../../src/log-insights/log-scanner";
-import { JoinOrderScannerProvider } from "../../src/log-insights/join-order";
 import { join } from "path";
 
 interface TestProblem {
   predicateName: string;
   raHash: string;
-  iteration: number;
+  order: string | undefined;
   message: string;
 }
 
 class TestProblemReporter implements EvaluationLogProblemReporter {
   public readonly problems: TestProblem[] = [];
 
-  public reportProblem(
+  public reportProblemNonRecursive(
     predicateName: string,
     raHash: string,
-    iteration: number,
     message: string,
   ): void {
     this.problems.push({
       predicateName,
       raHash,
-      iteration,
+      order: undefined,
+      message,
+    });
+  }
+  public reportProblemForRecursionSummary(
+    predicateName: string,
+    raHash: string,
+    order: string,
+    message: string,
+  ): void {
+    this.problems.push({
+      predicateName,
+      raHash,
+      order,
       message,
     });
   }
@@ -34,23 +45,33 @@ class TestProblemReporter implements EvaluationLogProblemReporter {
 
 describe("log scanners", () => {
   it("should detect bad join orders", async () => {
-    const scanners = new EvaluationLogScannerSet();
-    scanners.registerLogScannerProvider(new JoinOrderScannerProvider(() => 50));
     const summaryPath = join(
       __dirname,
       "data/evaluator-log-summaries/bad-join-order.jsonl",
     );
     const problemReporter = new TestProblemReporter();
-    await scanners.scanLog(summaryPath, problemReporter);
+    await scanAndReportJoinOrderProblems(summaryPath, problemReporter, 50);
+
+    expect(problemReporter.problems.length).toBe(2);
 
-    expect(problemReporter.problems.length).toBe(1);
-    expect(problemReporter.problems[0].predicateName).toBe("#select#ff");
+    expect(problemReporter.problems[0].predicateName).toBe(
+      "Enclosing::exprEnclosingElement#c50c5fbf#ff",
+    );
     expect(problemReporter.problems[0].raHash).toBe(
-      "1bb43c97jpmuh8r2v0f9hktim63",
+      "7cc60wtoigvl1lheqqa12d8fmi4",
     );
-    expect(problemReporter.problems[0].iteration).toBe(0);
+    expect(problemReporter.problems[0].order).toBe("order_500000");
     expect(problemReporter.problems[0].message).toBe(
-      "Relation '#select#ff' has an inefficient join order. Its join order metric is 4961.83, which is larger than the threshold of 50.00.",
+      "The order_500000 pipeline for 'Enclosing::exprEnclosingElement#c50c5fbf#ff@7cc60wto' has an inefficient join order. Its join order metric is 98.07, which is larger than the threshold of 50.00.",
+    );
+
+    expect(problemReporter.problems[1].predicateName).toBe("#select#ff");
+    expect(problemReporter.problems[1].raHash).toBe(
+      "1bb43c97jpmuh8r2v0f9hktim63",
+    );
+    expect(problemReporter.problems[1].order).toBeUndefined();
+    expect(problemReporter.problems[1].message).toBe(
+      "'#select#ff@1bb43c97' has an inefficient join order. Its join order metric is 4961.83, which is larger than the threshold of 50.00.",
     );
   });
 });
diff --git a/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-manager.test.ts b/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-manager.test.ts
index 598e3e159f9..850e221d84f 100644
--- a/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-manager.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-manager.test.ts
@@ -50,6 +50,7 @@ import { createMockVariantAnalysisConfig } from "../../../factories/config";
 import { setupServer } from "msw/node";
 import type { RequestHandler } from "msw";
 import { http } from "msw";
+import { getErrorMessage } from "../../../../src/common/helpers-pure";
 
 // up to 3 minutes per test
 jest.setTimeout(3 * 60 * 1000);
@@ -622,8 +623,8 @@ describe("Variant Analysis Manager", () => {
         await variantAnalysisManager.cancelVariantAnalysis(
           variantAnalysis.id + 100,
         );
-      } catch (error: any) {
-        expect(error.message).toBe(
+      } catch (error) {
+        expect(getErrorMessage(error)).toBe(
           `No variant analysis with id: ${variantAnalysis.id + 100}`,
         );
       }
@@ -637,8 +638,8 @@ describe("Variant Analysis Manager", () => {
 
       try {
         await variantAnalysisManager.cancelVariantAnalysis(variantAnalysis.id);
-      } catch (error: any) {
-        expect(error.message).toBe(
+      } catch (error) {
+        expect(getErrorMessage(error)).toBe(
           `No workflow run id for variant analysis with id: ${variantAnalysis.id}`,
         );
       }
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debug-controller.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debug-controller.ts
index 35435b1a797..1161282bedf 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debug-controller.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debug-controller.ts
@@ -83,14 +83,17 @@ class Tracker implements DebugAdapterTracker {
           kind: "evaluationCompleted",
           started: this.started!,
           results: {
-            ...this.started!,
-            ...this.completed!,
+            id: this.started!.id,
+            results: new Map([[this.queryPath!, this.completed!]]),
             outputDir: new QueryOutputDir(this.started!.outputDir),
-            queryTarget: {
-              queryPath: this.queryPath!,
-              quickEvalPosition:
-                this.started!.quickEvalContext?.quickEvalPosition,
-            },
+            queryTargets: [
+              {
+                queryPath: this.queryPath!,
+                outputBaseName: "results",
+                quickEvalPosition:
+                  this.started!.quickEvalContext?.quickEvalPosition,
+              },
+            ],
             dbPath: this.database!,
           },
         });
@@ -350,15 +353,19 @@ class DebugController
 
   public async expectSucceeded(): Promise<EvaluationCompletedEvent> {
     const event = await this.expectCompleted();
-    if (event.results.resultType !== QueryResultType.SUCCESS) {
-      expect(event.results.message).toBe("success");
+    const results = Array.from(event.results.results.values());
+    expect(results.length).toBe(1);
+    if (results[0].resultType !== QueryResultType.SUCCESS) {
+      expect(results[0].message).toBe("success");
     }
     return event;
   }
 
   public async expectFailed(): Promise<EvaluationCompletedEvent> {
     const event = await this.expectCompleted();
-    expect(event.results.resultType).not.toEqual(QueryResultType.SUCCESS);
+    const results = Array.from(event.results.results.values());
+    expect(results.length).toBe(1);
+    expect(results[0].resultType).not.toEqual(QueryResultType.SUCCESS);
     return event;
   }
 
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debugger.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debugger.test.ts
index d92a6a15cf5..76509030a4e 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debugger.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debugger.test.ts
@@ -10,10 +10,10 @@ import {
 import { describeWithCodeQL } from "../../cli";
 import { withDebugController } from "./debug-controller";
 import type { CodeQLCliServer } from "../../../../src/codeql-cli/cli";
-import type { QueryOutputDir } from "../../../../src/local-queries/query-output-dir";
 import { createVSCodeCommandManager } from "../../../../src/common/vscode/commands";
 import type { AllCommands } from "../../../../src/common/commands";
 import { getDataFolderFilePath } from "../utils";
+import type { CoreCompletedQuery } from "../../../../src/query-server";
 
 async function selectForQuickEval(
   path: string,
@@ -30,10 +30,15 @@ async function selectForQuickEval(
 }
 
 async function getResultCount(
-  outputDir: QueryOutputDir,
+  completedQuery: CoreCompletedQuery,
   cli: CodeQLCliServer,
 ): Promise<number> {
-  const info = await cli.bqrsInfo(outputDir.bqrsPath, 100);
+  const results = Array.from(completedQuery.results.values());
+  expect(results.length).toBe(1);
+  const info = await cli.bqrsInfo(
+    completedQuery.outputDir.getBqrsPath(results[0].outputBaseName),
+    100,
+  );
   const resultSet = info["result-sets"][0];
   return resultSet.rows;
 }
@@ -104,8 +109,9 @@ describeWithCodeQL()("Debugger", () => {
       expect(result.started.quickEvalContext!.quickEvalText).toBe(
         "InterestingNumber",
       );
-      expect(result.results.queryTarget.quickEvalPosition).toBeDefined();
-      expect(await getResultCount(result.results.outputDir, cli)).toBe(8);
+      expect(result.results.queryTargets.length).toBe(1);
+      expect(result.results.queryTargets[0].quickEvalPosition).toBeDefined();
+      expect(await getResultCount(result.results, cli)).toBe(8);
       await controller.expectStopped();
     });
   });
@@ -122,8 +128,9 @@ describeWithCodeQL()("Debugger", () => {
       expect(result.started.quickEvalContext!.quickEvalText).toBe(
         "InterestingNumber",
       );
-      expect(result.results.queryTarget.quickEvalPosition).toBeDefined();
-      expect(await getResultCount(result.results.outputDir, cli)).toBe(0);
+      expect(result.results.queryTargets.length).toBe(1);
+      expect(result.results.queryTargets[0].quickEvalPosition).toBeDefined();
+      expect(await getResultCount(result.results, cli)).toBe(0);
       await controller.expectStopped();
     });
   });
@@ -141,8 +148,9 @@ describeWithCodeQL()("Debugger", () => {
       expect(result.started.quickEvalContext!.quickEvalText).toBe(
         "InterestingNumber",
       );
-      expect(result.results.queryTarget.quickEvalPosition).toBeDefined();
-      expect(await getResultCount(result.results.outputDir, cli)).toBe(8);
+      expect(result.results.queryTargets.length).toBe(1);
+      expect(result.results.queryTargets[0].quickEvalPosition).toBeDefined();
+      expect(await getResultCount(result.results, cli)).toBe(8);
       await controller.expectStopped();
     });
   });
@@ -165,8 +173,9 @@ describeWithCodeQL()("Debugger", () => {
       expect(result.started.quickEvalContext!.quickEvalText).toBe(
         "getBigIntValue",
       );
-      expect(result.results.queryTarget.quickEvalPosition).toBeDefined();
-      expect(await getResultCount(result.results.outputDir, cli)).toBe(8);
+      expect(result.results.queryTargets.length).toBe(1);
+      expect(result.results.queryTargets[0].quickEvalPosition).toBeDefined();
+      expect(await getResultCount(result.results, cli)).toBe(8);
       await controller.expectStopped();
     });
   });
@@ -218,7 +227,7 @@ describeWithCodeQL()("Debugger", () => {
       await controller.expectSessionClosed();
 
       // Expect the number of results to be the same as if we had run the simple query, not the quick eval query.
-      expect(await getResultCount(result.results.outputDir, cli)).toBe(2);
+      expect(await getResultCount(result.results, cli)).toBe(2);
     });
   });
 });
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts
index cd5712382be..4e5c9489869 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts
@@ -78,6 +78,7 @@ describe("SkeletonQueryWizard", () => {
       getSupportedLanguages: jest
         .fn()
         .mockResolvedValue([
+          "actions",
           "ruby",
           "rust",
           "javascript",
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/queries.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/queries.test.ts
index 8f3f3216827..239b1ca0435 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/queries.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/queries.test.ts
@@ -162,7 +162,7 @@ describeWithCodeQL()("Queries", () => {
 
     async function runQueryWithExtensions() {
       console.log("Calling compileAndRunQuery");
-      const result = await compileAndRunQuery(
+      const completedQuery = await compileAndRunQuery(
         mode,
         appCommandManager,
         localQueries,
@@ -176,12 +176,14 @@ describeWithCodeQL()("Queries", () => {
       console.log("Completed compileAndRunQuery");
 
       // Check that query was successful
-      expect(result.resultType).toBe(QueryResultType.SUCCESS);
+      const results = Array.from(completedQuery.results.values());
+      expect(results.length).toBe(1);
+      expect(results[0].resultType).toBe(QueryResultType.SUCCESS);
 
       console.log("Loading query results");
       // Load query results
       const chunk = await qs.cliServer.bqrsDecode(
-        result.outputDir.bqrsPath,
+        completedQuery.outputDir.getBqrsPath(results[0].outputBaseName),
         SELECT_QUERY_NAME,
         {
           // there should only be one result
@@ -198,7 +200,7 @@ describeWithCodeQL()("Queries", () => {
 
   describe.each(MODES)("running queries (%s)", (mode) => {
     it("should run a query", async () => {
-      const result = await compileAndRunQuery(
+      const completedQuery = await compileAndRunQuery(
         mode,
         appCommandManager,
         localQueries,
@@ -211,13 +213,15 @@ describeWithCodeQL()("Queries", () => {
       );
 
       // just check that the query was successful
-      expect(result.resultType).toBe(QueryResultType.SUCCESS);
+      const results = Array.from(completedQuery.results.values());
+      expect(results.length).toBe(1);
+      expect(results[0].resultType).toBe(QueryResultType.SUCCESS);
     });
 
     // Asserts a fix for bug https://github.com/github/vscode-codeql/issues/733
     it("should restart the database and run a query", async () => {
       await appCommandManager.execute("codeQL.restartQueryServer");
-      const result = await compileAndRunQuery(
+      const completedQuery = await compileAndRunQuery(
         mode,
         appCommandManager,
         localQueries,
@@ -229,7 +233,9 @@ describeWithCodeQL()("Queries", () => {
         undefined,
       );
 
-      expect(result.resultType).toBe(QueryResultType.SUCCESS);
+      const results = Array.from(completedQuery.results.values());
+      expect(results.length).toBe(1);
+      expect(results[0].resultType).toBe(QueryResultType.SUCCESS);
     });
   });
 
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/query-server/query-server-client.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/query-server/query-server-client.test.ts
index c986e69ae62..874cefacc45 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/query-server/query-server-client.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/query-server/query-server-client.test.ts
@@ -3,9 +3,12 @@ import { dirSync } from "tmp";
 import { CancellationTokenSource } from "vscode-jsonrpc";
 import type { RunQueryParams } from "../../../../src/query-server/messages";
 import {
+  clearCache,
   QueryResultType,
   registerDatabases,
   runQuery,
+  trimCache,
+  trimCacheWithMode,
 } from "../../../../src/query-server/messages";
 import type { CodeQLCliServer } from "../../../../src/codeql-cli/cli";
 import type { BqrsCellValue } from "../../../../src/common/bqrs-cli-types";
@@ -198,5 +201,58 @@ describeWithCodeQL()("using the query server", () => {
         );
       }
     });
+
+    it("should invoke codeQL.trimOverlayBaseCache command when queryServerTrimCacheWithMode is enabled", async () => {
+      const features = (await cliServer.getFeatures()) as {
+        [feature: string]: boolean | undefined;
+      };
+
+      // Register the database first (if not already done)
+      await qs.sendRequest(registerDatabases, { databases: [db] });
+
+      try {
+        // Send the trimCacheWithMode request
+        const params = {
+          db,
+          mode: "overlay",
+        };
+        const result = await qs.sendRequest(
+          trimCacheWithMode,
+          params,
+          token,
+          () => {},
+        );
+
+        // The result should contain a deletionMessage string
+        expect(result).toHaveProperty("deletionMessage");
+        expect(typeof result.deletionMessage).toBe("string");
+        expect(features.queryServerTrimCacheWithMode).toBeTruthy();
+      } catch (e) {
+        expect(features.queryServerTrimCacheWithMode).toBeFalsy();
+        expect((e as Error).message).toContain(
+          "Unsupported request method: evaluation/trimCacheWithMode",
+        );
+      }
+    });
+
+    it("should invoke trimCache command and receive a deletionMessage", async () => {
+      // Register the database first (if not already done)
+      await qs.sendRequest(registerDatabases, { databases: [db] });
+
+      const params = { db };
+      const result = await qs.sendRequest(trimCache, params, token, () => {});
+      expect(result).toHaveProperty("deletionMessage");
+      expect(typeof result.deletionMessage).toBe("string");
+    });
+
+    it("should invoke clearCache command and receive a deletionMessage", async () => {
+      // Register the database first (if not already done)
+      await qs.sendRequest(registerDatabases, { databases: [db] });
+
+      const params = { db, dryRun: false };
+      const result = await qs.sendRequest(clearCache, params, token, () => {});
+      expect(result).toHaveProperty("deletionMessage");
+      expect(typeof result.deletionMessage).toBe("string");
+    });
   }
 });
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/run-cli.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/run-cli.test.ts
index ef92ee39e06..326cfdf4892 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/run-cli.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/run-cli.test.ts
@@ -16,7 +16,7 @@ import { faker } from "@faker-js/faker";
 import { getActivatedExtension } from "../global.helper";
 import type { BaseLogger } from "../../../src/common/logging";
 import { getQlPackForDbscheme } from "../../../src/databases/qlpack";
-import { dbSchemeToLanguage } from "../../../src/common/query-language";
+import { languageToDbScheme } from "../../../src/common/query-language";
 
 /**
  * Perform proper integration tests by running the CLI
@@ -27,14 +27,6 @@ describe("Use cli", () => {
 
   let logSpy: jest.SpiedFunction<BaseLogger["log"]>;
 
-  const languageToDbScheme = Object.entries(dbSchemeToLanguage).reduce(
-    (acc, [k, v]) => {
-      acc[v] = k;
-      return acc;
-    },
-    {} as { [k: string]: string },
-  );
-
   beforeEach(async () => {
     const extension = await getActivatedExtension();
     cli = extension.cliServer;
@@ -107,12 +99,17 @@ describe("Use cli", () => {
   itWithCodeQL()(
     "should resolve printAST queries for supported languages",
     async () => {
-      for (const lang of supportedLanguages) {
+      for (let lang of supportedLanguages) {
         if (lang === "go") {
           // The codeql-go submodule is not available in the integration tests.
           return;
         }
 
+        if (lang === "actions") {
+          // The actions queries use the javascript dbscheme.
+          lang = "javascript";
+        }
+
         console.log(`resolving printAST queries for ${lang}`);
         const pack = await getQlPackForDbscheme(cli, languageToDbScheme[lang]);
         expect(pack.dbschemePack).toContain(lang);
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/language-support/ast-viewer/ast-builder.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/language-support/ast-viewer/ast-builder.test.ts
index fd033de5f06..9fc96e98597 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/language-support/ast-viewer/ast-builder.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/language-support/ast-viewer/ast-builder.test.ts
@@ -2,7 +2,6 @@ import { readFileSync } from "fs-extra";
 
 import type { CodeQLCliServer } from "../../../../../src/codeql-cli/cli";
 import { Uri } from "vscode";
-import { QueryOutputDir } from "../../../../../src/local-queries/query-output-dir";
 import { mockDatabaseItem, mockedObject } from "../../../utils/mocking.helpers";
 import path from "path";
 import { AstBuilder } from "../../../../../src/language-support";
@@ -141,7 +140,7 @@ describe("AstBuilder", () => {
 
   function createAstBuilder() {
     return new AstBuilder(
-      new QueryOutputDir("/a/b/c"),
+      path.normalize("/a/b/c/results.bqrs"),
       mockCli,
       mockDatabaseItem({
         resolveSourceFile: undefined,
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/external-api-usage-query.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/external-api-usage-query.test.ts
index 7a4fcd6f531..bdc407502cb 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/external-api-usage-query.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/external-api-usage-query.test.ts
@@ -30,15 +30,13 @@ describe("runModelEditorQueries", () => {
     > = jest.spyOn(log, "showAndLogExceptionWithTelemetry");
 
     const outputDir = new QueryOutputDir(join((await file()).path, "1"));
-
+    const queryPath = "/a/b/c/ApplicationModeEndpoints.ql";
     const options = {
       cliServer: mockedObject<CodeQLCliServer>({
         resolveQlpacks: jest.fn().mockResolvedValue({
           "my/extensions": "/a/b/c/",
         }),
-        resolveQueriesInSuite: jest
-          .fn()
-          .mockResolvedValue(["/a/b/c/ApplicationModeEndpoints.ql"]),
+        resolveQueriesInSuite: jest.fn().mockResolvedValue([queryPath]),
         packPacklist: jest
           .fn()
           .mockResolvedValue([
@@ -50,7 +48,9 @@ describe("runModelEditorQueries", () => {
       queryRunner: mockedObject<QueryRunner>({
         createQueryRun: jest.fn().mockReturnValue({
           evaluate: jest.fn().mockResolvedValue({
-            resultType: QueryResultType.CANCELLATION,
+            results: new Map([
+              [queryPath, { resultType: QueryResultType.CANCELLATION }],
+            ]),
           }),
           outputDir,
         }),
@@ -88,15 +88,13 @@ describe("runModelEditorQueries", () => {
 
   it("should run query for random language", async () => {
     const outputDir = new QueryOutputDir(join((await file()).path, "1"));
-
+    const queryPath = "/a/b/c/ApplicationModeEndpoints.ql";
     const options = {
       cliServer: mockedObject<CodeQLCliServer>({
         resolveQlpacks: jest.fn().mockResolvedValue({
           "my/extensions": "/a/b/c/",
         }),
-        resolveQueriesInSuite: jest
-          .fn()
-          .mockResolvedValue(["/a/b/c/ApplicationModeEndpoints.ql"]),
+        resolveQueriesInSuite: jest.fn().mockResolvedValue([queryPath]),
         packPacklist: jest
           .fn()
           .mockResolvedValue([
@@ -122,6 +120,9 @@ describe("runModelEditorQueries", () => {
         createQueryRun: jest.fn().mockReturnValue({
           evaluate: jest.fn().mockResolvedValue({
             resultType: QueryResultType.SUCCESS,
+            results: new Map([
+              [queryPath, { resultType: QueryResultType.SUCCESS }],
+            ]),
             outputDir,
           }),
           outputDir,
@@ -156,17 +157,20 @@ describe("runModelEditorQueries", () => {
     expect(options.cliServer.resolveQlpacks).toHaveBeenCalledWith([], true);
     expect(options.queryRunner.createQueryRun).toHaveBeenCalledWith(
       "/a/b/c/src.zip",
-      {
-        queryPath: expect.stringMatching(/\S*ModeEndpoints\.ql/),
-        quickEvalPosition: undefined,
-        quickEvalCountOnly: false,
-      },
+      [
+        {
+          outputBaseName: "results",
+          queryPath: expect.stringMatching(/\S*ModeEndpoints\.ql/),
+          quickEvalPosition: undefined,
+          quickEvalCountOnly: false,
+        },
+      ],
       false,
       [],
       ["my/extensions"],
       {},
       "/tmp/queries",
-      undefined,
+      "ApplicationModeEndpoints.ql",
       undefined,
     );
   });
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/generate.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/generate.test.ts
index 173f901a7ee..7686e66d912 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/generate.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/generate.test.ts
@@ -28,12 +28,10 @@ describe("runGenerateQueries", () => {
     const outputDir = new QueryOutputDir(join(queryStorageDir, "1"));
 
     const onResults = jest.fn();
-
+    const queryPath = "/a/b/c/GenerateModel.ql";
     const options = {
       cliServer: mockedObject<CodeQLCliServer>({
-        resolveQueriesInSuite: jest
-          .fn()
-          .mockResolvedValue(["/a/b/c/GenerateModel.ql"]),
+        resolveQueriesInSuite: jest.fn().mockResolvedValue([queryPath]),
         bqrsDecodeAll: jest.fn().mockResolvedValue({
           sourceModel: {
             columns: [
@@ -101,7 +99,9 @@ describe("runGenerateQueries", () => {
       queryRunner: mockedObject<QueryRunner>({
         createQueryRun: jest.fn().mockReturnValue({
           evaluate: jest.fn().mockResolvedValue({
-            resultType: QueryResultType.SUCCESS,
+            results: new Map([
+              [queryPath, { resultType: QueryResultType.SUCCESS }],
+            ]),
             outputDir,
           }),
           outputDir,
@@ -221,17 +221,20 @@ describe("runGenerateQueries", () => {
     expect(options.queryRunner.createQueryRun).toHaveBeenCalledTimes(1);
     expect(options.queryRunner.createQueryRun).toHaveBeenCalledWith(
       "/a/b/c/src.zip",
-      {
-        queryPath: "/a/b/c/GenerateModel.ql",
-        quickEvalPosition: undefined,
-        quickEvalCountOnly: false,
-      },
+      [
+        {
+          outputBaseName: "results",
+          queryPath: "/a/b/c/GenerateModel.ql",
+          quickEvalPosition: undefined,
+          quickEvalCountOnly: false,
+        },
+      ],
       false,
       [],
       undefined,
       {},
       "/tmp/queries",
-      undefined,
+      "GenerateModel.ql",
       undefined,
     );
   });
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/suggestion-queries.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/suggestion-queries.test.ts
index e5c71658717..eeb41f869e1 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/suggestion-queries.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/suggestion-queries.test.ts
@@ -146,9 +146,8 @@ describe("runSuggestionsQuery", () => {
       .mockResolvedValueOnce(mockInputSuggestions)
       .mockResolvedValueOnce(mockOutputSuggestions);
 
-    const resolveQueriesInSuite = jest
-      .fn()
-      .mockResolvedValue(["/a/b/c/FrameworkModeAccessPathSuggestions.ql"]);
+    const queryPath = "/a/b/c/FrameworkModeAccessPathSuggestions.ql";
+    const resolveQueriesInSuite = jest.fn().mockResolvedValue([queryPath]);
 
     const options = {
       parseResults,
@@ -173,7 +172,9 @@ describe("runSuggestionsQuery", () => {
       queryRunner: mockedObject<QueryRunner>({
         createQueryRun: jest.fn().mockReturnValue({
           evaluate: jest.fn().mockResolvedValue({
-            resultType: QueryResultType.SUCCESS,
+            results: new Map([
+              [queryPath, { resultType: QueryResultType.SUCCESS }],
+            ]),
             outputDir,
           }),
           outputDir,
@@ -206,17 +207,20 @@ describe("runSuggestionsQuery", () => {
     expect(options.cliServer.resolveQlpacks).toHaveBeenCalledWith([], true);
     expect(options.queryRunner.createQueryRun).toHaveBeenCalledWith(
       "/a/b/c/src.zip",
-      {
-        queryPath: expect.stringMatching(/\S*AccessPathSuggestions\.ql/),
-        quickEvalPosition: undefined,
-        quickEvalCountOnly: false,
-      },
+      [
+        {
+          queryPath: expect.stringMatching(/\S*AccessPathSuggestions\.ql/),
+          outputBaseName: "results",
+          quickEvalPosition: undefined,
+          quickEvalCountOnly: false,
+        },
+      ],
       false,
       [],
       ["my/extensions"],
       {},
       "/tmp/queries",
-      undefined,
+      "FrameworkModeAccessPathSuggestions.ql",
       undefined,
     );
     expect(options.cliServer.resolveQueriesInSuite).toHaveBeenCalledTimes(1);
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts
index 34c092987cc..e8ae5a82975 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts
@@ -237,12 +237,12 @@ describe("write and read", () => {
     dbPath = "/a/b/c",
   ): QueryWithResults {
     // pretend that the results path exists
-    const resultsPath = join(queryPath, "results.bqrs");
     mkdirpSync(queryPath);
-    writeFileSync(resultsPath, "", "utf8");
+    writeFileSync(join(queryPath, "results.bqrs"), "", "utf8");
 
     const queryEvalInfo = new QueryEvaluationInfo(
       queryPath,
+      "results",
       Uri.file(dbPath).fsPath,
       true,
       undefined,
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-results.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-results.test.ts
index a2bc725849e..fc31fc909e3 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-results.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-results.test.ts
@@ -127,7 +127,7 @@ describe("query-results", () => {
       const expectedResultsPath = join(queryPath, "results.bqrs");
       const expectedSortedResultsPath = join(
         queryPath,
-        "sortedResults-cc8589f226adc134f87f2438e10075e0667571c72342068e2281e0b3b65e1092.bqrs",
+        "results-sorted-cc8589f226adc134f87f2438e10075e0667571c72342068e2281e0b3b65e1092.bqrs",
       );
       expect(spy).toHaveBeenCalledWith(
         expectedResultsPath,
@@ -419,12 +419,12 @@ describe("query-results", () => {
     dbPath = "/a/b/c",
   ): QueryWithResults {
     // pretend that the results path exists
-    const resultsPath = join(queryPath, "results.bqrs");
     mkdirpSync(queryPath);
-    writeFileSync(resultsPath, "", "utf8");
+    writeFileSync(join(queryPath, "results.bqrs"), "", "utf8");
 
     const queryEvalInfo = new QueryEvaluationInfo(
       queryPath,
+      "results",
       Uri.file(dbPath).fsPath,
       true,
       undefined,
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/run-queries.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/run-queries.test.ts
index 45e0063b1bb..8437249e815 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/run-queries.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/run-queries.test.ts
@@ -28,12 +28,10 @@ describe("run-queries", () => {
     const saveDir = "query-save-dir";
     const queryEvalInfo = createMockQueryEvaluationInfo(true, saveDir);
 
-    expect(queryEvalInfo.dilPath).toBe(join(saveDir, "results.dil"));
-    expect(queryEvalInfo.resultsPaths.resultsPath).toBe(
-      join(saveDir, "results.bqrs"),
-    );
-    expect(queryEvalInfo.resultsPaths.interpretedResultsPath).toBe(
-      join(saveDir, "interpretedResults.sarif"),
+    expect(queryEvalInfo.dilPath).toBe(join(saveDir, "foo.dil"));
+    expect(queryEvalInfo.resultsPath).toBe(join(saveDir, "foo.bqrs"));
+    expect(queryEvalInfo.interpretedResultsPath).toBe(
+      join(saveDir, "foo-interpreted.sarif"),
     );
     expect(queryEvalInfo.dbItemPath).toBe(Uri.file("/abc").fsPath);
   });
@@ -215,6 +213,7 @@ describe("run-queries", () => {
   ) {
     return new QueryEvaluationInfo(
       saveDir,
+      "foo",
       Uri.parse("file:///abc").fsPath,
       databaseHasMetadataFile,
       undefined,

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