diff --git a/.github/codeql/queries/unique-command-use.ql b/.github/codeql/queries/unique-command-use.ql
index 9602bf397..7c1d9e196 100644
--- a/.github/codeql/queries/unique-command-use.ql
+++ b/.github/codeql/queries/unique-command-use.ql
@@ -72,6 +72,20 @@
  
    override string getCommandName() { result = this.getArgument(0).(StringLiteral).getValue() }
  }
+
+ /**
+  * A usage of a command from the typescript code, by calling `CommandManager.execute`.
+  */
+ class CommandUsageCommandManagerMethodCallExpr extends CommandUsage, MethodCallExpr {
+   CommandUsageCommandManagerMethodCallExpr() {
+     this.getCalleeName() = "execute" and
+     this.getReceiver().getType().unfold().(TypeReference).getTypeName().getName() = "CommandManager" and
+     this.getArgument(0).(StringLiteral).getValue().matches("%codeQL%") and
+     not this.getFile().getRelativePath().matches("extensions/ql-vscode/test/%")
+   }
+
+   override string getCommandName() { result = this.getArgument(0).(StringLiteral).getValue() }
+ }
  
  /**
   * A usage of a command from any menu that isn't the command palette.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 8719e252a..01d89b1e4 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -2,7 +2,7 @@
 
 [fork]: https://github.com/github/vscode-codeql/fork
 [pr]: https://github.com/github/vscode-codeql/compare
-[style]: https://primer.style
+[style]: https://github.com/microsoft/vscode-webview-ui-toolkit
 [code-of-conduct]: CODE_OF_CONDUCT.md
 
 Hi there! We're thrilled that you'd like to contribute to this project. Your help is essential for keeping it great.
diff --git a/extensions/ql-vscode/CHANGELOG.md b/extensions/ql-vscode/CHANGELOG.md
index 83c4cd4c8..56dcf5fc9 100644
--- a/extensions/ql-vscode/CHANGELOG.md
+++ b/extensions/ql-vscode/CHANGELOG.md
@@ -2,6 +2,11 @@
 
 ## [UNRELEASED]
 
+## 1.8.1 - 23 March 2023
+
+- Show data flow paths of a variant analysis in a new tab. [#2172](https://github.com/github/vscode-codeql/pull/2172) & [#2182](https://github.com/github/vscode-codeql/pull/2182)
+- Show labels of entities in exported CSV results. [#2170](https://github.com/github/vscode-codeql/pull/2170)
+
 ## 1.8.0 - 9 March 2023
 
 - Send telemetry about unhandled errors happening within the extension. [#2125](https://github.com/github/vscode-codeql/pull/2125)
diff --git a/extensions/ql-vscode/package-lock.json b/extensions/ql-vscode/package-lock.json
index a39a7990d..3a2dee1bd 100644
--- a/extensions/ql-vscode/package-lock.json
+++ b/extensions/ql-vscode/package-lock.json
@@ -1,19 +1,17 @@
 {
   "name": "vscode-codeql",
-  "version": "1.8.1",
+  "version": "1.8.2",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
       "name": "vscode-codeql",
-      "version": "1.8.1",
+      "version": "1.8.2",
       "hasInstallScript": true,
       "license": "MIT",
       "dependencies": {
         "@octokit/plugin-retry": "^3.0.9",
         "@octokit/rest": "^19.0.4",
-        "@primer/octicons-react": "^17.6.0",
-        "@primer/react": "^35.0.0",
         "@vscode/codicons": "^0.0.31",
         "@vscode/webview-ui-toolkit": "^1.0.1",
         "ajv": "^8.11.0",
@@ -23,7 +21,7 @@
         "d3": "^7.6.1",
         "d3-graphviz": "^5.0.2",
         "fs-extra": "^10.0.1",
-        "glob-promise": "^4.2.2",
+        "glob-promise": "^6.0.2",
         "immutable": "^4.0.0",
         "js-yaml": "^4.1.0",
         "minimist": "~1.2.6",
@@ -56,7 +54,7 @@
         "@babel/core": "^7.18.13",
         "@babel/plugin-transform-modules-commonjs": "^7.18.6",
         "@faker-js/faker": "^7.5.0",
-        "@octokit/plugin-throttling": "^4.3.2",
+        "@octokit/plugin-throttling": "^5.0.1",
         "@storybook/addon-actions": "^6.5.10",
         "@storybook/addon-essentials": "^6.5.10",
         "@storybook/addon-interactions": "^6.5.10",
@@ -91,6 +89,7 @@
         "@types/semver": "~7.2.0",
         "@types/stream-chain": "~2.0.1",
         "@types/stream-json": "~1.7.1",
+        "@types/styled-components": "^5.1.11",
         "@types/tar-stream": "^2.2.2",
         "@types/through2": "^2.0.36",
         "@types/tmp": "^0.1.0",
@@ -105,7 +104,6 @@
         "@vscode/vsce": "^2.15.0",
         "ansi-colors": "^4.1.1",
         "applicationinsights": "^2.3.5",
-        "babel-loader": "^8.2.5",
         "cross-env": "^7.0.3",
         "css-loader": "~3.1.0",
         "del": "^6.0.0",
@@ -130,12 +128,12 @@
         "jest": "^29.0.3",
         "jest-environment-jsdom": "^29.0.3",
         "jest-runner-vscode": "^3.0.1",
-        "lint-staged": "~10.2.2",
+        "lint-staged": "~13.2.0",
         "mini-css-extract-plugin": "^2.6.1",
         "npm-run-all": "^4.1.5",
         "patch-package": "^6.5.0",
         "prettier": "^2.7.1",
-        "tar-stream": "^2.2.0",
+        "tar-stream": "^3.0.0",
         "through2": "^4.0.2",
         "ts-jest": "^29.0.1",
         "ts-json-schema-generator": "^1.1.2",
@@ -143,8 +141,8 @@
         "ts-node": "^10.7.0",
         "ts-protoc-gen": "^0.9.0",
         "typescript": "^4.5.5",
-        "webpack": "^5.62.2",
-        "webpack-cli": "^4.6.0"
+        "webpack": "^5.76.0",
+        "webpack-cli": "^5.0.1"
       },
       "engines": {
         "node": "^16.13.0",
@@ -2256,6 +2254,7 @@
       "version": "7.18.9",
       "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.18.9.tgz",
       "integrity": "sha512-lkqXDcvlFT5rvEjiu6+QYO+1GXrEHRo2LOtS7E4GtX5ESIZOgepqsZBVIj6Pv+a6zqsya9VCgiK1KAK4BvJDAw==",
+      "dev": true,
       "dependencies": {
         "regenerator-runtime": "^0.13.4"
       },
@@ -2526,17 +2525,17 @@
       }
     },
     "node_modules/@emotion/is-prop-valid": {
-      "version": "0.8.8",
-      "resolved": "https://registry.npmjs.org/@emotion/is-prop-valid/-/is-prop-valid-0.8.8.tgz",
-      "integrity": "sha512-u5WtneEAr5IDG2Wv65yhunPSMLIpuKsbuOktRojfrEiEvRyC85LgPMZI63cr7NUqT8ZIGdSVg8ZKGxIug4lXcA==",
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/@emotion/is-prop-valid/-/is-prop-valid-1.2.0.tgz",
+      "integrity": "sha512-3aDpDprjM0AwaxGE09bOPkNxHpBd+kA6jty3RnaEXdweX1DF1U3VQpPYb0g1IStAuK7SVQ1cy+bNBBKp4W3Fjg==",
       "dependencies": {
-        "@emotion/memoize": "0.7.4"
+        "@emotion/memoize": "^0.8.0"
       }
     },
     "node_modules/@emotion/memoize": {
-      "version": "0.7.4",
-      "resolved": "https://registry.npmjs.org/@emotion/memoize/-/memoize-0.7.4.tgz",
-      "integrity": "sha512-Ja/Vfqe3HpuzRsG1oBtWTHk2PGZ7GR+2Vz5iYGelAw8dx32K0y7PjVuxK6z1nMpZOqAFsRUPCkK1YjJ56qJlgw=="
+      "version": "0.8.0",
+      "resolved": "https://registry.npmjs.org/@emotion/memoize/-/memoize-0.8.0.tgz",
+      "integrity": "sha512-G/YwXTkv7Den9mXDO7AhLWkE3q+I92B+VqAE+dYG4NGPaHZGvt3G8Q0p9vmE+sq7rTGphUbAvmQ9YpbfMQGGlA=="
     },
     "node_modules/@emotion/stylis": {
       "version": "0.8.5",
@@ -2679,26 +2678,6 @@
       "integrity": "sha512-gIhjdJp/c2beaIWWIlsXdqXVRUz3r2BxBCpfz/F3JXHvSAQ1paMYjLH+maEATtENg+k5eLV7gA+9yPp762ieuw==",
       "dev": true
     },
-    "node_modules/@github/combobox-nav": {
-      "version": "2.1.7",
-      "resolved": "https://registry.npmjs.org/@github/combobox-nav/-/combobox-nav-2.1.7.tgz",
-      "integrity": "sha512-Webx0W5iTpkk5Chy9dB/1BEUORQ0qrwui8HaaVBiy75W2VOJg96WTuKj1rXENAJ3XTMhdEF53bn0LYfvP0EKvg=="
-    },
-    "node_modules/@github/markdown-toolbar-element": {
-      "version": "2.1.1",
-      "resolved": "https://registry.npmjs.org/@github/markdown-toolbar-element/-/markdown-toolbar-element-2.1.1.tgz",
-      "integrity": "sha512-J++rpd5H9baztabJQB82h26jtueOeBRSTqetk9Cri+Lj/s28ndu6Tovn0uHQaOKtBWDobFunk9b5pP5vcqt7cA=="
-    },
-    "node_modules/@github/paste-markdown": {
-      "version": "1.4.2",
-      "resolved": "https://registry.npmjs.org/@github/paste-markdown/-/paste-markdown-1.4.2.tgz",
-      "integrity": "sha512-ZwSgPyo9nA6TRngXV0QnFT4e5ujeOGxRDWN2aa6qfimz2o2VOsJ9bFGuGvB723nvzq5z9zKr6JWGtvK7MSJj3w=="
-    },
-    "node_modules/@github/relative-time-element": {
-      "version": "4.2.3",
-      "resolved": "https://registry.npmjs.org/@github/relative-time-element/-/relative-time-element-4.2.3.tgz",
-      "integrity": "sha512-M5NaacbpSmKUk6tYQ8r/LokSHeIb6D7rTTOqZ/htQX3b7KGKiDXI0t/WF7UDy58Go0NNfEahE9WzGEKcSjqfrA=="
-    },
     "node_modules/@gulp-sourcemaps/identity-map": {
       "version": "2.0.1",
       "resolved": "https://registry.npmjs.org/@gulp-sourcemaps/identity-map/-/identity-map-2.0.1.tgz",
@@ -5074,11 +5053,6 @@
         "@jridgewell/sourcemap-codec": "^1.4.10"
       }
     },
-    "node_modules/@lit-labs/react": {
-      "version": "1.1.1",
-      "resolved": "https://registry.npmjs.org/@lit-labs/react/-/react-1.1.1.tgz",
-      "integrity": "sha512-9TC+/ZWb6BJlWCyUr14FKFlaGnyKpeEDorufXozQgke/VoVrslUQNaL7nBmrAWdNrmzx5jWgi8lFmWwrxMjnlA=="
-    },
     "node_modules/@mdx-js/mdx": {
       "version": "1.6.22",
       "resolved": "https://registry.npmjs.org/@mdx-js/mdx/-/mdx-1.6.22.tgz",
@@ -5618,12 +5592,12 @@
       }
     },
     "node_modules/@octokit/plugin-throttling": {
-      "version": "4.3.2",
-      "resolved": "https://registry.npmjs.org/@octokit/plugin-throttling/-/plugin-throttling-4.3.2.tgz",
-      "integrity": "sha512-ZaCK599h3tzcoy0Jtdab95jgmD7X9iAk59E2E7hYKCAmnURaI4WpzwL9vckImilybUGrjY1JOWJapDs2N2D3vw==",
+      "version": "5.0.1",
+      "resolved": "https://registry.npmjs.org/@octokit/plugin-throttling/-/plugin-throttling-5.0.1.tgz",
+      "integrity": "sha512-I4qxs7wYvYlFuY3PAUGWAVPhFXG3RwnvTiSr5Fu/Auz7bYhDLnzS2MjwV8nGLq/FPrWwYiweeZrI5yjs1YG4tQ==",
       "dev": true,
       "dependencies": {
-        "@octokit/types": "^8.0.0",
+        "@octokit/types": "^9.0.0",
         "bottleneck": "^2.15.3"
       },
       "engines": {
@@ -5634,18 +5608,18 @@
       }
     },
     "node_modules/@octokit/plugin-throttling/node_modules/@octokit/openapi-types": {
-      "version": "14.0.0",
-      "resolved": "https://registry.npmjs.org/@octokit/openapi-types/-/openapi-types-14.0.0.tgz",
-      "integrity": "sha512-HNWisMYlR8VCnNurDU6os2ikx0s0VyEjDYHNS/h4cgb8DeOxQ0n72HyinUtdDVxJhFy3FWLGl0DJhfEWk3P5Iw==",
+      "version": "16.0.0",
+      "resolved": "https://registry.npmjs.org/@octokit/openapi-types/-/openapi-types-16.0.0.tgz",
+      "integrity": "sha512-JbFWOqTJVLHZSUUoF4FzAZKYtqdxWu9Z5m2QQnOyEa04fOFljvyh7D3GYKbfuaSWisqehImiVIMG4eyJeP5VEA==",
       "dev": true
     },
     "node_modules/@octokit/plugin-throttling/node_modules/@octokit/types": {
-      "version": "8.0.0",
-      "resolved": "https://registry.npmjs.org/@octokit/types/-/types-8.0.0.tgz",
-      "integrity": "sha512-65/TPpOJP1i3K4lBJMnWqPUJ6zuOtzhtagDvydAWbEXpbFYA0oMKKyLb95NFZZP0lSh/4b6K+DQlzvYQJQQePg==",
+      "version": "9.0.0",
+      "resolved": "https://registry.npmjs.org/@octokit/types/-/types-9.0.0.tgz",
+      "integrity": "sha512-LUewfj94xCMH2rbD5YJ+6AQ4AVjFYTgpp6rboWM5T7N3IsIF65SBEOVcYMGAEzO/kKNiNaW4LoWtoThOhH06gw==",
       "dev": true,
       "dependencies": {
-        "@octokit/openapi-types": "^14.0.0"
+        "@octokit/openapi-types": "^16.0.0"
       }
     },
     "node_modules/@octokit/request": {
@@ -6002,94 +5976,6 @@
         "url": "https://opencollective.com/webpack"
       }
     },
-    "node_modules/@primer/behaviors": {
-      "version": "1.3.3",
-      "resolved": "https://registry.npmjs.org/@primer/behaviors/-/behaviors-1.3.3.tgz",
-      "integrity": "sha512-iHMRuu8YWDJIdqCi1krx0cyFNeqszNKTOb0dXFu2wQ5BeIqxqPJLD7rjZ2Vjf/+YaPSbWuIQE1H6TaGMMsDfdA=="
-    },
-    "node_modules/@primer/octicons-react": {
-      "version": "17.12.0",
-      "resolved": "https://registry.npmjs.org/@primer/octicons-react/-/octicons-react-17.12.0.tgz",
-      "integrity": "sha512-GUjV6IT1Ck2lu2GVu1loR0e2dcX2e9aIVmX5rBdR7HJnRdYKY7XH+FnYj7y9sEmzUdNEDswxkefiQlfGrBXlzA==",
-      "engines": {
-        "node": ">=8"
-      },
-      "peerDependencies": {
-        "react": ">=15"
-      }
-    },
-    "node_modules/@primer/primitives": {
-      "version": "7.11.1",
-      "resolved": "https://registry.npmjs.org/@primer/primitives/-/primitives-7.11.1.tgz",
-      "integrity": "sha512-Sdss4XG96nqBqrTAyg+RuFOj+U5wkICK8n2hafcyT+lpSlZoIwcbmhyFjmDy9f88FkhHe2q0uCpQ8PjKd8ILTQ=="
-    },
-    "node_modules/@primer/react": {
-      "version": "35.21.0",
-      "resolved": "https://registry.npmjs.org/@primer/react/-/react-35.21.0.tgz",
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-        "@github/markdown-toolbar-element": "^2.1.0",
-        "@github/paste-markdown": "^1.4.0",
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-        "@primer/behaviors": "1.3.3",
-        "@primer/octicons-react": "^18.0.0",
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-        "@react-aria/ssr": "^3.1.0",
-        "@styled-system/css": "^5.1.5",
-        "@styled-system/props": "^5.1.5",
-        "@styled-system/theme-get": "^5.1.2",
-        "@types/styled-components": "^5.1.11",
-        "@types/styled-system": "^5.1.12",
-        "@types/styled-system__css": "^5.0.16",
-        "@types/styled-system__theme-get": "^5.0.1",
-        "classnames": "^2.3.1",
-        "color2k": "^2.0.0",
-        "deepmerge": "^4.2.2",
-        "focus-visible": "^5.2.0",
-        "fzy.js": "0.4.1",
-        "history": "^5.0.0",
-        "react-intersection-observer": "9.4.1",
-        "styled-system": "^5.1.5"
-      },
-      "engines": {
-        "node": ">=12",
-        "npm": ">=7"
-      },
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-        "styled-components": "4.x || 5.x"
-      }
-    },
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-      "resolved": "https://registry.npmjs.org/@primer/octicons-react/-/octicons-react-18.2.0.tgz",
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-      "engines": {
-        "node": ">=8"
-      },
-      "peerDependencies": {
-        "react": ">=15"
-      }
-    },
-    "node_modules/@primer/react/node_modules/classnames": {
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-      "resolved": "https://registry.npmjs.org/classnames/-/classnames-2.3.1.tgz",
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@@ -12560,124 +12446,6 @@
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-    "node_modules/@styled-system/border": {
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-      "resolved": "https://registry.npmjs.org/@styled-system/border/-/border-5.1.5.tgz",
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-            "onetime": "^5.1.2",
-            "signal-exit": "^3.0.3",
-            "strip-final-newline": "^2.0.0"
-          }
-        },
-        "get-stream": {
-          "version": "6.0.0",
-          "resolved": "https://registry.npmjs.org/get-stream/-/get-stream-6.0.0.tgz",
-          "integrity": "sha512-A1B3Bh1UmL0bidM/YX2NsCOTnGJePL9rO/M+Mw3m9f2gUpfokS0hi5Eah0WSUEWZdZhIZtMjkIYS7mDfOqNHbg==",
-          "dev": true
-        },
-        "human-signals": {
-          "version": "2.1.0",
-          "resolved": "https://registry.npmjs.org/human-signals/-/human-signals-2.1.0.tgz",
-          "integrity": "sha512-B4FFZ6q/T2jhhksgkbEW3HBvWIfDW85snkQgawt07S7J5QXTk6BkNV+0yAeZrM5QpMAdYlocGoljn0sJ/WQkFw==",
-          "dev": true
-        },
         "interpret": {
-          "version": "2.2.0",
-          "resolved": "https://registry.npmjs.org/interpret/-/interpret-2.2.0.tgz",
-          "integrity": "sha512-Ju0Bz/cEia55xDwUWEa8+olFpCiQoypjnQySseKtmjNrnps3P+xfpUmGr90T7yjlVJmOtybRvPXhKMbHr+fWnw==",
+          "version": "3.1.1",
+          "resolved": "https://registry.npmjs.org/interpret/-/interpret-3.1.1.tgz",
+          "integrity": "sha512-6xwYfHbajpoF0xLW+iwLkhwgvLoZDfjYfoFNu8ftMoXINzwuymNLd9u/KmwtdT2GbR+/Cz66otEGEVVUHX9QLQ==",
           "dev": true
         },
         "path-key": {
@@ -72611,12 +72212,12 @@
           "dev": true
         },
         "rechoir": {
-          "version": "0.7.0",
-          "resolved": "https://registry.npmjs.org/rechoir/-/rechoir-0.7.0.tgz",
-          "integrity": "sha512-ADsDEH2bvbjltXEP+hTIAmeFekTFK0V2BTxMkok6qILyAJEXV0AFfoWcAq4yfll5VdIMd/RVXq0lR+wQi5ZU3Q==",
+          "version": "0.8.0",
+          "resolved": "https://registry.npmjs.org/rechoir/-/rechoir-0.8.0.tgz",
+          "integrity": "sha512-/vxpCXddiX8NGfGO/mTafwjq4aFa/71pvamip0++IQk3zG8cbCj0fifNPrjjF1XMXUne91jL9OoxmdykoEtifQ==",
           "dev": true,
           "requires": {
-            "resolve": "^1.9.0"
+            "resolve": "^1.20.0"
           }
         },
         "shebang-command": {
diff --git a/extensions/ql-vscode/package.json b/extensions/ql-vscode/package.json
index 2ee9f8878..21863ca86 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": "1.8.1",
+  "version": "1.8.2",
   "publisher": "GitHub",
   "license": "MIT",
   "icon": "media/VS-marketplace-CodeQL-icon.png",
@@ -56,6 +56,7 @@
     "onCommand:codeQL.restartQueryServer",
     "onWebviewPanel:resultsView",
     "onWebviewPanel:codeQL.variantAnalysis",
+    "onWebviewPanel:codeQL.dataFlowPaths",
     "onFileSystem:codeql-zip-archive"
   ],
   "main": "./out/extension",
@@ -544,7 +545,12 @@
         "title": "CodeQL: Check for CLI Updates"
       },
       {
-        "command": "codeQLQueryHistory.openQuery",
+        "command": "codeQLQueryHistory.openQueryTitleMenu",
+        "title": "View Query",
+        "icon": "$(edit)"
+      },
+      {
+        "command": "codeQLQueryHistory.openQueryContextMenu",
         "title": "View Query",
         "icon": "$(edit)"
       },
@@ -554,7 +560,17 @@
         "icon": "$(preview)"
       },
       {
-        "command": "codeQLQueryHistory.removeHistoryItem",
+        "command": "codeQLQueryHistory.removeHistoryItemTitleMenu",
+        "title": "Delete",
+        "icon": "$(trash)"
+      },
+      {
+        "command": "codeQLQueryHistory.removeHistoryItemContextMenu",
+        "title": "Delete",
+        "icon": "$(trash)"
+      },
+      {
+        "command": "codeQLQueryHistory.removeHistoryItemContextInline",
         "title": "Delete",
         "icon": "$(trash)"
       },
@@ -741,7 +757,7 @@
           "group": "navigation"
         },
         {
-          "command": "codeQLQueryHistory.openQuery",
+          "command": "codeQLQueryHistory.openQueryTitleMenu",
           "when": "view == codeQLQueryHistory",
           "group": "navigation"
         },
@@ -751,7 +767,7 @@
           "group": "navigation"
         },
         {
-          "command": "codeQLQueryHistory.removeHistoryItem",
+          "command": "codeQLQueryHistory.removeHistoryItemTitleMenu",
           "when": "view == codeQLQueryHistory",
           "group": "navigation"
         },
@@ -848,17 +864,17 @@
           "group": "inline"
         },
         {
-          "command": "codeQLQueryHistory.openQuery",
+          "command": "codeQLQueryHistory.openQueryContextMenu",
           "group": "2_queryHistory@0",
           "when": "view == codeQLQueryHistory"
         },
         {
-          "command": "codeQLQueryHistory.removeHistoryItem",
+          "command": "codeQLQueryHistory.removeHistoryItemContextMenu",
           "group": "7_queryHistory@0",
           "when": "viewItem == interpretedResultsItem || viewItem == rawResultsItem || viewItem == remoteResultsItem || viewItem == cancelledRemoteResultsItemWithoutLogs || viewItem == cancelledResultsItem || viewItem == cancelledRemoteResultsItem"
         },
         {
-          "command": "codeQLQueryHistory.removeHistoryItem",
+          "command": "codeQLQueryHistory.removeHistoryItemContextInline",
           "group": "inline",
           "when": "viewItem == interpretedResultsItem || viewItem == rawResultsItem || viewItem == remoteResultsItem || viewItem == cancelledRemoteResultsItemWithoutLogs || viewItem == cancelledResultsItem || viewItem == cancelledRemoteResultsItem"
         },
@@ -1155,11 +1171,23 @@
           "when": "false"
         },
         {
-          "command": "codeQLQueryHistory.openQuery",
+          "command": "codeQLQueryHistory.openQueryTitleMenu",
           "when": "false"
         },
         {
-          "command": "codeQLQueryHistory.removeHistoryItem",
+          "command": "codeQLQueryHistory.openQueryContextMenu",
+          "when": "false"
+        },
+        {
+          "command": "codeQLQueryHistory.removeHistoryItemTitleMenu",
+          "when": "false"
+        },
+        {
+          "command": "codeQLQueryHistory.removeHistoryItemContextMenu",
+          "when": "false"
+        },
+        {
+          "command": "codeQLQueryHistory.removeHistoryItemContextInline",
           "when": "false"
         },
         {
@@ -1405,8 +1433,6 @@
   "dependencies": {
     "@octokit/plugin-retry": "^3.0.9",
     "@octokit/rest": "^19.0.4",
-    "@primer/octicons-react": "^17.6.0",
-    "@primer/react": "^35.0.0",
     "@vscode/codicons": "^0.0.31",
     "@vscode/webview-ui-toolkit": "^1.0.1",
     "ajv": "^8.11.0",
@@ -1416,7 +1442,7 @@
     "d3": "^7.6.1",
     "d3-graphviz": "^5.0.2",
     "fs-extra": "^10.0.1",
-    "glob-promise": "^4.2.2",
+    "glob-promise": "^6.0.2",
     "immutable": "^4.0.0",
     "js-yaml": "^4.1.0",
     "minimist": "~1.2.6",
@@ -1449,7 +1475,7 @@
     "@babel/core": "^7.18.13",
     "@babel/plugin-transform-modules-commonjs": "^7.18.6",
     "@faker-js/faker": "^7.5.0",
-    "@octokit/plugin-throttling": "^4.3.2",
+    "@octokit/plugin-throttling": "^5.0.1",
     "@storybook/addon-actions": "^6.5.10",
     "@storybook/addon-essentials": "^6.5.10",
     "@storybook/addon-interactions": "^6.5.10",
@@ -1484,6 +1510,7 @@
     "@types/semver": "~7.2.0",
     "@types/stream-chain": "~2.0.1",
     "@types/stream-json": "~1.7.1",
+    "@types/styled-components": "^5.1.11",
     "@types/tar-stream": "^2.2.2",
     "@types/through2": "^2.0.36",
     "@types/tmp": "^0.1.0",
@@ -1498,7 +1525,6 @@
     "@vscode/vsce": "^2.15.0",
     "ansi-colors": "^4.1.1",
     "applicationinsights": "^2.3.5",
-    "babel-loader": "^8.2.5",
     "cross-env": "^7.0.3",
     "css-loader": "~3.1.0",
     "del": "^6.0.0",
@@ -1523,12 +1549,12 @@
     "jest": "^29.0.3",
     "jest-environment-jsdom": "^29.0.3",
     "jest-runner-vscode": "^3.0.1",
-    "lint-staged": "~10.2.2",
+    "lint-staged": "~13.2.0",
     "mini-css-extract-plugin": "^2.6.1",
     "npm-run-all": "^4.1.5",
     "patch-package": "^6.5.0",
     "prettier": "^2.7.1",
-    "tar-stream": "^2.2.0",
+    "tar-stream": "^3.0.0",
     "through2": "^4.0.2",
     "ts-jest": "^29.0.1",
     "ts-json-schema-generator": "^1.1.2",
@@ -1536,8 +1562,8 @@
     "ts-node": "^10.7.0",
     "ts-protoc-gen": "^0.9.0",
     "typescript": "^4.5.5",
-    "webpack": "^5.62.2",
-    "webpack-cli": "^4.6.0"
+    "webpack": "^5.76.0",
+    "webpack-cli": "^5.0.1"
   },
   "lint-staged": {
     "./**/*.{json,css,scss}": [
diff --git a/extensions/ql-vscode/src/ast-cfg-commands.ts b/extensions/ql-vscode/src/ast-cfg-commands.ts
new file mode 100644
index 000000000..49749be22
--- /dev/null
+++ b/extensions/ql-vscode/src/ast-cfg-commands.ts
@@ -0,0 +1,90 @@
+import { Uri, window } from "vscode";
+import { withProgress } from "./progress";
+import { AstViewer } from "./astViewer";
+import {
+  TemplatePrintAstProvider,
+  TemplatePrintCfgProvider,
+} from "./contextual/templateProvider";
+import { compileAndRunQuery } from "./local-queries";
+import { QueryRunner } from "./queryRunner";
+import { QueryHistoryManager } from "./query-history/query-history-manager";
+import { DatabaseUI } from "./local-databases-ui";
+import { ResultsView } from "./interface";
+import { AstCfgCommands } from "./common/commands";
+
+type AstCfgOptions = {
+  queryRunner: QueryRunner;
+  queryHistoryManager: QueryHistoryManager;
+  databaseUI: DatabaseUI;
+  localQueryResultsView: ResultsView;
+  queryStorageDir: string;
+
+  astViewer: AstViewer;
+  astTemplateProvider: TemplatePrintAstProvider;
+  cfgTemplateProvider: TemplatePrintCfgProvider;
+};
+
+export function getAstCfgCommands({
+  queryRunner,
+  queryHistoryManager,
+  databaseUI,
+  localQueryResultsView,
+  queryStorageDir,
+  astViewer,
+  astTemplateProvider,
+  cfgTemplateProvider,
+}: AstCfgOptions): AstCfgCommands {
+  const viewAst = async (selectedFile: Uri) =>
+    withProgress(
+      async (progress, token) => {
+        const ast = await astTemplateProvider.provideAst(
+          progress,
+          token,
+          selectedFile ?? window.activeTextEditor?.document.uri,
+        );
+        if (ast) {
+          astViewer.updateRoots(await ast.getRoots(), ast.db, ast.fileName);
+        }
+      },
+      {
+        cancellable: true,
+        title: "Calculate AST",
+      },
+    );
+
+  const viewCfg = async () =>
+    withProgress(
+      async (progress, token) => {
+        const res = await cfgTemplateProvider.provideCfgUri(
+          window.activeTextEditor?.document,
+        );
+        if (res) {
+          await compileAndRunQuery(
+            queryRunner,
+            queryHistoryManager,
+            databaseUI,
+            localQueryResultsView,
+            queryStorageDir,
+            false,
+            res[0],
+            progress,
+            token,
+            undefined,
+          );
+        }
+      },
+      {
+        title: "Calculating Control Flow Graph",
+        cancellable: true,
+      },
+    );
+
+  return {
+    "codeQL.viewAst": viewAst,
+    "codeQL.viewAstContextExplorer": viewAst,
+    "codeQL.viewAstContextEditor": viewAst,
+    "codeQL.viewCfg": viewCfg,
+    "codeQL.viewCfgContextExplorer": viewCfg,
+    "codeQL.viewCfgContextEditor": viewCfg,
+  };
+}
diff --git a/extensions/ql-vscode/src/astViewer.ts b/extensions/ql-vscode/src/astViewer.ts
index 3c5d2bdf8..5105439f8 100644
--- a/extensions/ql-vscode/src/astViewer.ts
+++ b/extensions/ql-vscode/src/astViewer.ts
@@ -23,11 +23,11 @@ import {
   isWholeFileLoc,
   isLineColumnLoc,
 } from "./pure/bqrs-utils";
-import { commandRunner } from "./commandRunner";
 import { DisposableObject } from "./pure/disposable-object";
 import { showAndLogExceptionWithTelemetry } from "./helpers";
 import { asError, getErrorMessage } from "./pure/helpers-pure";
 import { redactableError } from "./pure/errors";
+import { AstViewerCommands } from "./common/commands";
 
 export interface AstItem {
   id: BqrsId;
@@ -55,15 +55,6 @@ class AstViewerDataProvider
   readonly onDidChangeTreeData: Event<AstItem | undefined> =
     this._onDidChangeTreeData.event;
 
-  constructor() {
-    super();
-    this.push(
-      commandRunner("codeQLAstViewer.gotoCode", async (item: AstItem) => {
-        await showLocation(item.fileLocation);
-      }),
-    );
-  }
-
   refresh(): void {
     this._onDidChangeTreeData.fire(undefined);
   }
@@ -126,16 +117,20 @@ export class AstViewer extends DisposableObject {
 
     this.push(this.treeView);
     this.push(this.treeDataProvider);
-    this.push(
-      commandRunner("codeQLAstViewer.clear", async () => {
-        this.clear();
-      }),
-    );
     this.push(
       window.onDidChangeTextEditorSelection(this.updateTreeSelection, this),
     );
   }
 
+  getCommands(): AstViewerCommands {
+    return {
+      "codeQLAstViewer.clear": async () => this.clear(),
+      "codeQLAstViewer.gotoCode": async (item: AstItem) => {
+        await showLocation(item.fileLocation);
+      },
+    };
+  }
+
   updateRoots(roots: AstItem[], db: DatabaseItem, fileUri: Uri) {
     this.treeDataProvider.roots = roots;
     this.treeDataProvider.db = db;
diff --git a/extensions/ql-vscode/src/cli.ts b/extensions/ql-vscode/src/cli.ts
index 321357da1..45c6a7f6c 100644
--- a/extensions/ql-vscode/src/cli.ts
+++ b/extensions/ql-vscode/src/cli.ts
@@ -9,7 +9,7 @@ import { Readable } from "stream";
 import { StringDecoder } from "string_decoder";
 import tk from "tree-kill";
 import { promisify } from "util";
-import { CancellationToken, commands, Disposable, Uri } from "vscode";
+import { CancellationToken, Disposable, Uri } from "vscode";
 
 import { BQRSInfo, DecodedBqrsChunk } from "./pure/bqrs-cli-types";
 import { allowCanaryQueryServer, CliConfig } from "./config";
@@ -1284,11 +1284,25 @@ export class CodeQLCliServer implements Disposable {
     );
   }
 
-  async packInstall(dir: string, forceUpdate = false) {
+  async packInstall(
+    dir: string,
+    { forceUpdate = false, workspaceFolders = [] as string[] } = {},
+  ) {
     const args = [dir];
     if (forceUpdate) {
       args.push("--mode", "update");
     }
+    if (workspaceFolders?.length > 0) {
+      if (await this.cliConstraints.supportsAdditionalPacksInstall()) {
+        args.push(
+          // Allow prerelease packs from the ql submodule.
+          "--allow-prerelease",
+          // Allow the use of --additional-packs argument without issueing a warning
+          "--no-strict-mode",
+          ...this.getAdditionalPacksArg(workspaceFolders),
+        );
+      }
+    }
     return this.runJsonCodeQlCliCommandWithAuthentication(
       ["pack", "install"],
       args,
@@ -1361,7 +1375,7 @@ export class CodeQLCliServer implements Disposable {
     if (!this._version) {
       this._version = this.refreshVersion();
       // this._version is only undefined upon config change, so we reset CLI-based context key only when necessary.
-      await commands.executeCommand(
+      await this.app.commands.execute(
         "setContext",
         "codeql.supportsEvalLog",
         await this.cliConstraints.supportsPerQueryEvalLog(),
@@ -1692,6 +1706,13 @@ export class CliVersionConstraint {
    */
   public static CLI_VERSION_WITH_QLPACKS_KIND = new SemVer("2.12.3");
 
+  /**
+   * CLI version that supports the `--additional-packs` option for the `pack install` command.
+   */
+  public static CLI_VERSION_WITH_ADDITIONAL_PACKS_INSTALL = new SemVer(
+    "2.12.4",
+  );
+
   constructor(private readonly cli: CodeQLCliServer) {
     /**/
   }
@@ -1755,4 +1776,10 @@ export class CliVersionConstraint {
       CliVersionConstraint.CLI_VERSION_WITH_QLPACKS_KIND,
     );
   }
+
+  async supportsAdditionalPacksInstall() {
+    return this.isVersionAtLeast(
+      CliVersionConstraint.CLI_VERSION_WITH_ADDITIONAL_PACKS_INSTALL,
+    );
+  }
 }
diff --git a/extensions/ql-vscode/src/commandRunner.ts b/extensions/ql-vscode/src/commandRunner.ts
deleted file mode 100644
index 4ff281c04..000000000
--- a/extensions/ql-vscode/src/commandRunner.ts
+++ /dev/null
@@ -1,268 +0,0 @@
-import {
-  CancellationToken,
-  ProgressOptions,
-  window as Window,
-  commands,
-  Disposable,
-  ProgressLocation,
-} from "vscode";
-import {
-  showAndLogExceptionWithTelemetry,
-  showAndLogWarningMessage,
-} from "./helpers";
-import { extLogger } from "./common";
-import { asError, getErrorMessage, getErrorStack } from "./pure/helpers-pure";
-import { telemetryListener } from "./telemetry";
-import { redactableError } from "./pure/errors";
-
-export class UserCancellationException extends Error {
-  /**
-   * @param message The error message
-   * @param silent If silent is true, then this exception will avoid showing a warning message to the user.
-   */
-  constructor(message?: string, public readonly silent = false) {
-    super(message);
-  }
-}
-
-export interface ProgressUpdate {
-  /**
-   * The current step
-   */
-  step: number;
-  /**
-   * The maximum step. This *should* be constant for a single job.
-   */
-  maxStep: number;
-  /**
-   * The current progress message
-   */
-  message: string;
-}
-
-export type ProgressCallback = (p: ProgressUpdate) => void;
-
-/**
- * A task that handles command invocations from `commandRunner`
- * and includes a progress monitor.
- *
- *
- * Arguments passed to the command handler are passed along,
- * untouched to this `ProgressTask` instance.
- *
- * @param progress a progress handler function. Call this
- * function with a `ProgressUpdate` instance in order to
- * denote some progress being achieved on this task.
- * @param token a cencellation token
- * @param args arguments passed to this task passed on from
- * `commands.registerCommand`.
- */
-export type ProgressTask<R> = (
-  progress: ProgressCallback,
-  token: CancellationToken,
-  ...args: any[]
-) => Thenable<R>;
-
-/**
- * A task that handles command invocations from `commandRunner`.
- * Arguments passed to the command handler are passed along,
- * untouched to this `NoProgressTask` instance.
- *
- * @param args arguments passed to this task passed on from
- * `commands.registerCommand`.
- */
-type NoProgressTask = (...args: any[]) => Promise<any>;
-
-/**
- * This mediates between the kind of progress callbacks we want to
- * write (where we *set* current progress position and give
- * `maxSteps`) and the kind vscode progress api expects us to write
- * (which increment progress by a certain amount out of 100%).
- *
- * Where possible, the `commandRunner` function below should be used
- * instead of this function. The commandRunner is meant for wrapping
- * top-level commands and provides error handling and other support
- * automatically.
- *
- * Only use this function if you need a progress monitor and the
- * control flow does not always come from a command (eg- during
- * extension activation, or from an internal language server
- * request).
- */
-export function withProgress<R>(
-  options: ProgressOptions,
-  task: ProgressTask<R>,
-  ...args: any[]
-): Thenable<R> {
-  let progressAchieved = 0;
-  return Window.withProgress(options, (progress, token) => {
-    return task(
-      (p) => {
-        const { message, step, maxStep } = p;
-        const increment = (100 * (step - progressAchieved)) / maxStep;
-        progressAchieved = step;
-        progress.report({ message, increment });
-      },
-      token,
-      ...args,
-    );
-  });
-}
-
-/**
- * A generic wrapper for command registration. This wrapper adds uniform error handling for commands.
- *
- * In this variant of the command runner, no progress monitor is used.
- *
- * @param commandId The ID of the command to register.
- * @param task The task to run. It is passed directly to `commands.registerCommand`. Any
- * arguments to the command handler are passed on to the task.
- */
-export function commandRunner(
-  commandId: string,
-  task: NoProgressTask,
-): Disposable {
-  return commands.registerCommand(commandId, async (...args: any[]) => {
-    const startTime = Date.now();
-    let error: Error | undefined;
-
-    try {
-      return await task(...args);
-    } catch (e) {
-      error = asError(e);
-      const errorMessage = redactableError(error)`${
-        getErrorMessage(e) || e
-      } (${commandId})`;
-      const errorStack = getErrorStack(e);
-      if (e instanceof UserCancellationException) {
-        // User has cancelled this action manually
-        if (e.silent) {
-          void extLogger.log(errorMessage.fullMessage);
-        } else {
-          void showAndLogWarningMessage(errorMessage.fullMessage);
-        }
-      } else {
-        // Include the full stack in the error log only.
-        const fullMessage = errorStack
-          ? `${errorMessage.fullMessage}\n${errorStack}`
-          : errorMessage.fullMessage;
-        void showAndLogExceptionWithTelemetry(errorMessage, {
-          fullMessage,
-          extraTelemetryProperties: {
-            command: commandId,
-          },
-        });
-      }
-      return undefined;
-    } finally {
-      const executionTime = Date.now() - startTime;
-      telemetryListener?.sendCommandUsage(commandId, executionTime, error);
-    }
-  });
-}
-
-/**
- * A generic wrapper for command registration.  This wrapper adds uniform error handling,
- * progress monitoring, and cancellation for commands.
- *
- * @param commandId The ID of the command to register.
- * @param task The task to run. It is passed directly to `commands.registerCommand`. Any
- * arguments to the command handler are passed on to the task after the progress callback
- * and cancellation token.
- * @param progressOptions Progress options to be sent to the progress monitor.
- */
-export function commandRunnerWithProgress<R>(
-  commandId: string,
-  task: ProgressTask<R>,
-  progressOptions: Partial<ProgressOptions>,
-  outputLogger = extLogger,
-): Disposable {
-  return commands.registerCommand(commandId, async (...args: any[]) => {
-    const startTime = Date.now();
-    let error: Error | undefined;
-    const progressOptionsWithDefaults = {
-      location: ProgressLocation.Notification,
-      ...progressOptions,
-    };
-    try {
-      return await withProgress(progressOptionsWithDefaults, task, ...args);
-    } catch (e) {
-      error = asError(e);
-      const errorMessage = redactableError`${
-        getErrorMessage(e) || e
-      } (${commandId})`;
-      const errorStack = getErrorStack(e);
-      if (e instanceof UserCancellationException) {
-        // User has cancelled this action manually
-        if (e.silent) {
-          void outputLogger.log(errorMessage.fullMessage);
-        } else {
-          void showAndLogWarningMessage(errorMessage.fullMessage, {
-            outputLogger,
-          });
-        }
-      } else {
-        // Include the full stack in the error log only.
-        const fullMessage = errorStack
-          ? `${errorMessage.fullMessage}\n${errorStack}`
-          : errorMessage.fullMessage;
-        void showAndLogExceptionWithTelemetry(errorMessage, {
-          outputLogger,
-          fullMessage,
-          extraTelemetryProperties: {
-            command: commandId,
-          },
-        });
-      }
-      return undefined;
-    } finally {
-      const executionTime = Date.now() - startTime;
-      telemetryListener?.sendCommandUsage(commandId, executionTime, error);
-    }
-  });
-}
-
-/**
- * Displays a progress monitor that indicates how much progess has been made
- * reading from a stream.
- *
- * @param readable The stream to read progress from
- * @param messagePrefix A prefix for displaying the message
- * @param totalNumBytes Total number of bytes in this stream
- * @param progress The progress callback used to set messages
- */
-export function reportStreamProgress(
-  readable: NodeJS.ReadableStream,
-  messagePrefix: string,
-  totalNumBytes?: number,
-  progress?: ProgressCallback,
-) {
-  if (progress && totalNumBytes) {
-    let numBytesDownloaded = 0;
-    const bytesToDisplayMB = (numBytes: number): string =>
-      `${(numBytes / (1024 * 1024)).toFixed(1)} MB`;
-    const updateProgress = () => {
-      progress({
-        step: numBytesDownloaded,
-        maxStep: totalNumBytes,
-        message: `${messagePrefix} [${bytesToDisplayMB(
-          numBytesDownloaded,
-        )} of ${bytesToDisplayMB(totalNumBytes)}]`,
-      });
-    };
-
-    // Display the progress straight away rather than waiting for the first chunk.
-    updateProgress();
-
-    readable.on("data", (data) => {
-      numBytesDownloaded += data.length;
-      updateProgress();
-    });
-  } else if (progress) {
-    progress({
-      step: 1,
-      maxStep: 2,
-      message: `${messagePrefix} (Size unknown)`,
-    });
-  }
-}
diff --git a/extensions/ql-vscode/src/common/app.ts b/extensions/ql-vscode/src/common/app.ts
index 67506a5fa..2e749c018 100644
--- a/extensions/ql-vscode/src/common/app.ts
+++ b/extensions/ql-vscode/src/common/app.ts
@@ -3,10 +3,10 @@ import { Disposable } from "../pure/disposable-object";
 import { AppEventEmitter } from "./events";
 import { Logger } from "./logging";
 import { Memento } from "./memento";
+import { AppCommandManager } from "./commands";
 
 export interface App {
   createEventEmitter<T>(): AppEventEmitter<T>;
-  executeCommand(command: string, ...args: any): Thenable<void>;
   readonly mode: AppMode;
   readonly logger: Logger;
   readonly subscriptions: Disposable[];
@@ -15,6 +15,7 @@ export interface App {
   readonly workspaceStoragePath?: string;
   readonly workspaceState: Memento;
   readonly credentials: Credentials;
+  readonly commands: AppCommandManager;
 }
 
 export enum AppMode {
diff --git a/extensions/ql-vscode/src/common/commands.ts b/extensions/ql-vscode/src/common/commands.ts
new file mode 100644
index 000000000..55e47f22b
--- /dev/null
+++ b/extensions/ql-vscode/src/common/commands.ts
@@ -0,0 +1,289 @@
+import type { CommandManager } from "../packages/commands";
+import type { Uri, Range, TextDocumentShowOptions } from "vscode";
+import type { AstItem } from "../astViewer";
+import type { DbTreeViewItem } from "../databases/ui/db-tree-view-item";
+import type { DatabaseItem } from "../local-databases";
+import type { QueryHistoryInfo } from "../query-history/query-history-info";
+import type { RepositoriesFilterSortStateWithIds } from "../pure/variant-analysis-filter-sort";
+import type { TestTreeNode } from "../test-tree-node";
+import type {
+  VariantAnalysis,
+  VariantAnalysisScannedRepository,
+  VariantAnalysisScannedRepositoryResult,
+} from "../variant-analysis/shared/variant-analysis";
+
+// A command function matching the signature that VS Code calls when
+// a command on a selection is invoked.
+export type SelectionCommandFunction<Item> = (
+  singleItem: Item,
+  multiSelect: Item[],
+) => Promise<void>;
+
+// A command function matching the signature that VS Code calls when
+// a command on a selection is invoked when canSelectMany is false.
+export type SingleSelectionCommandFunction<Item> = (
+  singleItem: Item,
+) => Promise<void>;
+
+/**
+ * Contains type definitions for all commands used by the extension.
+ *
+ * To add a new command first define its type here, then provide
+ * the implementation in the corresponding `getCommands` function.
+ */
+
+// Builtin commands where the implementation is provided by VS Code and not by this extension.
+// See https://code.visualstudio.com/api/references/commands
+export type BuiltInVsCodeCommands = {
+  // The codeQLDatabases.focus command is provided by VS Code because we've registered the custom view
+  "codeQLDatabases.focus": () => Promise<void>;
+  "markdown.showPreviewToSide": (uri: Uri) => Promise<void>;
+  revealFileInOS: (uri: Uri) => Promise<void>;
+  setContext: (
+    key: `${"codeql" | "codeQL"}${string}`,
+    value: unknown,
+  ) => Promise<void>;
+  "workbench.action.reloadWindow": () => Promise<void>;
+  "vscode.diff": (
+    leftSideResource: Uri,
+    rightSideResource: Uri,
+    title?: string,
+    columnOrOptions?: TextDocumentShowOptions,
+  ) => Promise<void>;
+  "vscode.open": (uri: Uri) => Promise<void>;
+  "vscode.openFolder": (uri: Uri) => Promise<void>;
+};
+
+// Commands that are available before the extension is fully activated.
+// These commands are *not* registered using the command manager, but can
+// be invoked using the command manager.
+export type PreActivationCommands = {
+  "codeQL.checkForUpdatesToCLI": () => Promise<void>;
+};
+
+// Base commands not tied directly to a module like e.g. variant analysis.
+export type BaseCommands = {
+  "codeQL.openDocumentation": () => Promise<void>;
+  "codeQL.showLogs": () => Promise<void>;
+  "codeQL.authenticateToGitHub": () => Promise<void>;
+
+  "codeQL.copyVersion": () => Promise<void>;
+  "codeQL.restartQueryServer": () => Promise<void>;
+};
+
+// Commands used when working with queries in the editor
+export type QueryEditorCommands = {
+  "codeQL.openReferencedFile": (selectedQuery: Uri) => Promise<void>;
+  "codeQL.openReferencedFileContextEditor": (
+    selectedQuery: Uri,
+  ) => Promise<void>;
+  "codeQL.openReferencedFileContextExplorer": (
+    selectedQuery: Uri,
+  ) => Promise<void>;
+  "codeQL.previewQueryHelp": (selectedQuery: Uri) => Promise<void>;
+};
+
+// Commands used for running local queries
+export type LocalQueryCommands = {
+  "codeQL.runQuery": (uri?: Uri) => Promise<void>;
+  "codeQL.runQueryContextEditor": (uri?: Uri) => Promise<void>;
+  "codeQL.runQueryOnMultipleDatabases": (uri?: Uri) => Promise<void>;
+  "codeQL.runQueryOnMultipleDatabasesContextEditor": (
+    uri?: Uri,
+  ) => Promise<void>;
+  "codeQL.runQueries": SelectionCommandFunction<Uri>;
+  "codeQL.quickEval": (uri: Uri) => Promise<void>;
+  "codeQL.quickEvalContextEditor": (uri: Uri) => Promise<void>;
+  "codeQL.codeLensQuickEval": (uri: Uri, range: Range) => Promise<void>;
+  "codeQL.quickQuery": () => Promise<void>;
+};
+
+export type ResultsViewCommands = {
+  "codeQLQueryResults.up": () => Promise<void>;
+  "codeQLQueryResults.down": () => Promise<void>;
+  "codeQLQueryResults.left": () => Promise<void>;
+  "codeQLQueryResults.right": () => Promise<void>;
+  "codeQLQueryResults.nextPathStep": () => Promise<void>;
+  "codeQLQueryResults.previousPathStep": () => Promise<void>;
+};
+
+// Commands used for the query history panel
+export type QueryHistoryCommands = {
+  // Commands in the "navigation" group
+  "codeQLQueryHistory.sortByName": () => Promise<void>;
+  "codeQLQueryHistory.sortByDate": () => Promise<void>;
+  "codeQLQueryHistory.sortByCount": () => Promise<void>;
+
+  // Commands in the context menu or in the hover menu
+  "codeQLQueryHistory.openQueryTitleMenu": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.openQueryContextMenu": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.removeHistoryItemTitleMenu": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.removeHistoryItemContextMenu": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.removeHistoryItemContextInline": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.renameItem": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.compareWith": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.showEvalLog": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.showEvalLogSummary": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.showEvalLogViewer": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.showQueryLog": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.showQueryText": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.openQueryDirectory": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.cancel": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.exportResults": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.viewCsvResults": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.viewCsvAlerts": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.viewSarifAlerts": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.viewDil": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.itemClicked": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.openOnGithub": SelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.copyRepoList": SelectionCommandFunction<QueryHistoryInfo>;
+
+  // Commands in the command palette
+  "codeQL.exportSelectedVariantAnalysisResults": () => Promise<void>;
+};
+
+// Commands used for the local databases panel
+export type LocalDatabasesCommands = {
+  // Command palette commands
+  "codeQL.chooseDatabaseFolder": () => Promise<void>;
+  "codeQL.chooseDatabaseArchive": () => Promise<void>;
+  "codeQL.chooseDatabaseInternet": () => Promise<void>;
+  "codeQL.chooseDatabaseGithub": () => Promise<void>;
+  "codeQL.upgradeCurrentDatabase": () => Promise<void>;
+  "codeQL.clearCache": () => Promise<void>;
+
+  // Explorer context menu
+  "codeQL.setCurrentDatabase": (uri: Uri) => Promise<void>;
+
+  // Database panel view title commands
+  "codeQLDatabases.chooseDatabaseFolder": () => Promise<void>;
+  "codeQLDatabases.chooseDatabaseArchive": () => Promise<void>;
+  "codeQLDatabases.chooseDatabaseInternet": () => Promise<void>;
+  "codeQLDatabases.chooseDatabaseGithub": () => Promise<void>;
+  "codeQLDatabases.sortByName": () => Promise<void>;
+  "codeQLDatabases.sortByDateAdded": () => Promise<void>;
+
+  // Database panel context menu
+  "codeQLDatabases.setCurrentDatabase": (
+    databaseItem: DatabaseItem,
+  ) => Promise<void>;
+
+  // Database panel selection commands
+  "codeQLDatabases.removeDatabase": SelectionCommandFunction<DatabaseItem>;
+  "codeQLDatabases.upgradeDatabase": SelectionCommandFunction<DatabaseItem>;
+  "codeQLDatabases.renameDatabase": SelectionCommandFunction<DatabaseItem>;
+  "codeQLDatabases.openDatabaseFolder": SelectionCommandFunction<DatabaseItem>;
+  "codeQLDatabases.addDatabaseSource": SelectionCommandFunction<DatabaseItem>;
+
+  // Codespace template commands
+  "codeQL.setDefaultTourDatabase": () => Promise<void>;
+
+  // Internal commands
+  "codeQLDatabases.removeOrphanedDatabases": () => Promise<void>;
+};
+
+// Commands tied to variant analysis
+export type VariantAnalysisCommands = {
+  "codeQL.autoDownloadVariantAnalysisResult": (
+    scannedRepo: VariantAnalysisScannedRepository,
+    variantAnalysisSummary: VariantAnalysis,
+  ) => Promise<void>;
+  "codeQL.copyVariantAnalysisRepoList": (
+    variantAnalysisId: number,
+    filterSort?: RepositoriesFilterSortStateWithIds,
+  ) => Promise<void>;
+  "codeQL.loadVariantAnalysisRepoResults": (
+    variantAnalysisId: number,
+    repositoryFullName: string,
+  ) => Promise<VariantAnalysisScannedRepositoryResult>;
+  "codeQL.monitorVariantAnalysis": (
+    variantAnalysis: VariantAnalysis,
+  ) => Promise<void>;
+  "codeQL.openVariantAnalysisLogs": (
+    variantAnalysisId: number,
+  ) => Promise<void>;
+  "codeQL.openVariantAnalysisView": (
+    variantAnalysisId: number,
+  ) => Promise<void>;
+  "codeQL.runVariantAnalysis": (uri?: Uri) => Promise<void>;
+  "codeQL.runVariantAnalysisContextEditor": (uri?: Uri) => Promise<void>;
+};
+
+export type DatabasePanelCommands = {
+  "codeQLVariantAnalysisRepositories.openConfigFile": () => Promise<void>;
+  "codeQLVariantAnalysisRepositories.addNewDatabase": () => Promise<void>;
+  "codeQLVariantAnalysisRepositories.addNewList": () => Promise<void>;
+  "codeQLVariantAnalysisRepositories.setupControllerRepository": () => Promise<void>;
+
+  "codeQLVariantAnalysisRepositories.setSelectedItem": SingleSelectionCommandFunction<DbTreeViewItem>;
+  "codeQLVariantAnalysisRepositories.setSelectedItemContextMenu": SingleSelectionCommandFunction<DbTreeViewItem>;
+  "codeQLVariantAnalysisRepositories.openOnGitHubContextMenu": SingleSelectionCommandFunction<DbTreeViewItem>;
+  "codeQLVariantAnalysisRepositories.renameItemContextMenu": SingleSelectionCommandFunction<DbTreeViewItem>;
+  "codeQLVariantAnalysisRepositories.removeItemContextMenu": SingleSelectionCommandFunction<DbTreeViewItem>;
+};
+
+export type AstCfgCommands = {
+  "codeQL.viewAst": (selectedFile: Uri) => Promise<void>;
+  "codeQL.viewAstContextExplorer": (selectedFile: Uri) => Promise<void>;
+  "codeQL.viewAstContextEditor": (selectedFile: Uri) => Promise<void>;
+  "codeQL.viewCfg": () => Promise<void>;
+  "codeQL.viewCfgContextExplorer": () => Promise<void>;
+  "codeQL.viewCfgContextEditor": () => Promise<void>;
+};
+
+export type AstViewerCommands = {
+  "codeQLAstViewer.clear": () => Promise<void>;
+  "codeQLAstViewer.gotoCode": (item: AstItem) => Promise<void>;
+};
+
+export type PackagingCommands = {
+  "codeQL.installPackDependencies": () => Promise<void>;
+  "codeQL.downloadPacks": () => Promise<void>;
+};
+
+export type EvalLogViewerCommands = {
+  "codeQLEvalLogViewer.clear": () => Promise<void>;
+};
+
+export type SummaryLanguageSupportCommands = {
+  "codeQL.gotoQL": () => Promise<void>;
+};
+
+export type TestUICommands = {
+  "codeQLTests.showOutputDifferences": (node: TestTreeNode) => Promise<void>;
+  "codeQLTests.acceptOutput": (node: TestTreeNode) => Promise<void>;
+};
+
+export type MockGitHubApiServerCommands = {
+  "codeQL.mockGitHubApiServer.startRecording": () => Promise<void>;
+  "codeQL.mockGitHubApiServer.saveScenario": () => Promise<void>;
+  "codeQL.mockGitHubApiServer.cancelRecording": () => Promise<void>;
+  "codeQL.mockGitHubApiServer.loadScenario": () => Promise<void>;
+  "codeQL.mockGitHubApiServer.unloadScenario": () => Promise<void>;
+};
+
+// All commands where the implementation is provided by this activated extension.
+export type AllExtensionCommands = BaseCommands &
+  QueryEditorCommands &
+  ResultsViewCommands &
+  QueryHistoryCommands &
+  LocalDatabasesCommands &
+  VariantAnalysisCommands &
+  DatabasePanelCommands &
+  AstCfgCommands &
+  AstViewerCommands &
+  PackagingCommands &
+  EvalLogViewerCommands &
+  SummaryLanguageSupportCommands &
+  Partial<TestUICommands> &
+  MockGitHubApiServerCommands;
+
+export type AllCommands = AllExtensionCommands &
+  PreActivationCommands &
+  BuiltInVsCodeCommands;
+
+export type AppCommandManager = CommandManager<AllCommands>;
+
+// Separate command manager because it uses a different logger
+export type QueryServerCommands = LocalQueryCommands;
+export type QueryServerCommandManager = CommandManager<QueryServerCommands>;
diff --git a/extensions/ql-vscode/src/common/logging/index.ts b/extensions/ql-vscode/src/common/logging/index.ts
index 35ed72fd7..7bc5d444b 100644
--- a/extensions/ql-vscode/src/common/logging/index.ts
+++ b/extensions/ql-vscode/src/common/logging/index.ts
@@ -1,3 +1,4 @@
 export * from "./logger";
+export * from "./tee-logger";
 export * from "./vscode/loggers";
 export * from "./vscode/output-channel-logger";
diff --git a/extensions/ql-vscode/src/common/logging/logger.ts b/extensions/ql-vscode/src/common/logging/logger.ts
index 89fc1e54b..61187585a 100644
--- a/extensions/ql-vscode/src/common/logging/logger.ts
+++ b/extensions/ql-vscode/src/common/logging/logger.ts
@@ -1,9 +1,6 @@
 export interface LogOptions {
   // If false, don't output a trailing newline for the log entry. Default true.
   trailingNewline?: boolean;
-
-  // If specified, add this log entry to the log file at the specified location.
-  additionalLogLocation?: string;
 }
 
 export interface Logger {
@@ -25,11 +22,4 @@ export interface Logger {
    * @param preserveFocus When `true` the channel will not take focus.
    */
   show(preserveFocus?: boolean): void;
-
-  /**
-   * Remove the log at the specified location.
-   *
-   * @param location log to remove
-   */
-  removeAdditionalLogLocation(location: string | undefined): void;
 }
diff --git a/extensions/ql-vscode/src/common/logging/tee-logger.ts b/extensions/ql-vscode/src/common/logging/tee-logger.ts
new file mode 100644
index 000000000..ddd6162eb
--- /dev/null
+++ b/extensions/ql-vscode/src/common/logging/tee-logger.ts
@@ -0,0 +1,68 @@
+import { appendFile, ensureFile } from "fs-extra";
+import { isAbsolute } from "path";
+import { getErrorMessage } from "../../pure/helpers-pure";
+import { Logger, LogOptions } from "./logger";
+
+/**
+ * An implementation of {@link Logger} that sends the output both to another {@link Logger}
+ * and to a file.
+ *
+ * The first time a message is written, an additional banner is written to the underlying logger
+ * pointing the user to the "side log" file.
+ */
+export class TeeLogger implements Logger {
+  private emittedRedirectMessage = false;
+  private error = false;
+
+  public constructor(
+    private readonly logger: Logger,
+    private readonly location: string,
+  ) {
+    if (!isAbsolute(location)) {
+      throw new Error(
+        `Additional Log Location must be an absolute path: ${location}`,
+      );
+    }
+  }
+
+  async log(message: string, options = {} as LogOptions): Promise<void> {
+    if (!this.emittedRedirectMessage) {
+      this.emittedRedirectMessage = true;
+      const msg = `| Log being saved to ${this.location} |`;
+      const separator = new Array(msg.length).fill("-").join("");
+      await this.logger.log(separator);
+      await this.logger.log(msg);
+      await this.logger.log(separator);
+    }
+
+    if (!this.error) {
+      try {
+        const trailingNewline = options.trailingNewline ?? true;
+        await ensureFile(this.location);
+
+        await appendFile(
+          this.location,
+          message + (trailingNewline ? "\n" : ""),
+          {
+            encoding: "utf8",
+          },
+        );
+      } catch (e) {
+        // Write an error message to the primary log, and stop trying to write to the side log.
+        this.error = true;
+        const errorMessage = getErrorMessage(e);
+        await this.logger.log(
+          `Error writing to additional log file: ${errorMessage}`,
+        );
+      }
+    }
+
+    if (!this.error) {
+      await this.logger.log(message, options);
+    }
+  }
+
+  show(preserveFocus?: boolean): void {
+    this.logger.show(preserveFocus);
+  }
+}
diff --git a/extensions/ql-vscode/src/common/logging/vscode/output-channel-logger.ts b/extensions/ql-vscode/src/common/logging/vscode/output-channel-logger.ts
index ed0baa0e2..4ea5db56d 100644
--- a/extensions/ql-vscode/src/common/logging/vscode/output-channel-logger.ts
+++ b/extensions/ql-vscode/src/common/logging/vscode/output-channel-logger.ts
@@ -1,6 +1,4 @@
 import { window as Window, OutputChannel, Progress } from "vscode";
-import { ensureFile, appendFile } from "fs-extra";
-import { isAbsolute } from "path";
 import { Logger, LogOptions } from "../logger";
 import { DisposableObject } from "../../../pure/disposable-object";
 
@@ -9,10 +7,6 @@ import { DisposableObject } from "../../../pure/disposable-object";
  */
 export class OutputChannelLogger extends DisposableObject implements Logger {
   public readonly outputChannel: OutputChannel;
-  private readonly additionalLocations = new Map<
-    string,
-    AdditionalLogLocation
-  >();
   isCustomLogDirectory: boolean;
 
   constructor(title: string) {
@@ -32,27 +26,6 @@ export class OutputChannelLogger extends DisposableObject implements Logger {
       } else {
         this.outputChannel.append(message);
       }
-
-      if (options.additionalLogLocation) {
-        if (!isAbsolute(options.additionalLogLocation)) {
-          throw new Error(
-            `Additional Log Location must be an absolute path: ${options.additionalLogLocation}`,
-          );
-        }
-        const logPath = options.additionalLogLocation;
-        let additional = this.additionalLocations.get(logPath);
-        if (!additional) {
-          const msg = `| Log being saved to ${logPath} |`;
-          const separator = new Array(msg.length).fill("-").join("");
-          this.outputChannel.appendLine(separator);
-          this.outputChannel.appendLine(msg);
-          this.outputChannel.appendLine(separator);
-          additional = new AdditionalLogLocation(logPath);
-          this.additionalLocations.set(logPath, additional);
-        }
-
-        await additional.log(message, options);
-      }
     } catch (e) {
       if (e instanceof Error && e.message === "Channel has been closed") {
         // Output channel is closed logging to console instead
@@ -69,31 +42,6 @@ export class OutputChannelLogger extends DisposableObject implements Logger {
   show(preserveFocus?: boolean): void {
     this.outputChannel.show(preserveFocus);
   }
-
-  removeAdditionalLogLocation(location: string | undefined): void {
-    if (location) {
-      this.additionalLocations.delete(location);
-    }
-  }
-}
-
-class AdditionalLogLocation {
-  constructor(private location: string) {}
-
-  async log(message: string, options = {} as LogOptions): Promise<void> {
-    if (options.trailingNewline === undefined) {
-      options.trailingNewline = true;
-    }
-    await ensureFile(this.location);
-
-    await appendFile(
-      this.location,
-      message + (options.trailingNewline ? "\n" : ""),
-      {
-        encoding: "utf8",
-      },
-    );
-  }
 }
 
 export type ProgressReporter = Progress<{ message: string }>;
diff --git a/extensions/ql-vscode/src/common/vscode/commands.ts b/extensions/ql-vscode/src/common/vscode/commands.ts
new file mode 100644
index 000000000..3d71ae004
--- /dev/null
+++ b/extensions/ql-vscode/src/common/vscode/commands.ts
@@ -0,0 +1,100 @@
+import { commands, Disposable } from "vscode";
+import { CommandFunction, CommandManager } from "../../packages/commands";
+import { extLogger, OutputChannelLogger } from "../logging";
+import {
+  asError,
+  getErrorMessage,
+  getErrorStack,
+} from "../../pure/helpers-pure";
+import { redactableError } from "../../pure/errors";
+import { UserCancellationException } from "../../progress";
+import {
+  showAndLogExceptionWithTelemetry,
+  showAndLogWarningMessage,
+} from "../../helpers";
+import { telemetryListener } from "../../telemetry";
+
+/**
+ * Create a command manager for VSCode, wrapping registerCommandWithErrorHandling
+ * and vscode.executeCommand.
+ */
+export function createVSCodeCommandManager<
+  Commands extends Record<string, CommandFunction>,
+>(outputLogger?: OutputChannelLogger): CommandManager<Commands> {
+  return new CommandManager((commandId, task) => {
+    return registerCommandWithErrorHandling(commandId, task, outputLogger);
+  }, wrapExecuteCommand);
+}
+
+/**
+ * A wrapper for command registration. This wrapper adds uniform error handling for commands.
+ *
+ * @param commandId The ID of the command to register.
+ * @param task The task to run. It is passed directly to `commands.registerCommand`. Any
+ * arguments to the command handler are passed on to the task.
+ */
+export function registerCommandWithErrorHandling(
+  commandId: string,
+  task: (...args: any[]) => Promise<any>,
+  outputLogger = extLogger,
+): Disposable {
+  return commands.registerCommand(commandId, async (...args: any[]) => {
+    const startTime = Date.now();
+    let error: Error | undefined;
+
+    try {
+      return await task(...args);
+    } catch (e) {
+      error = asError(e);
+      const errorMessage = redactableError(error)`${
+        getErrorMessage(e) || e
+      } (${commandId})`;
+      const errorStack = getErrorStack(e);
+      if (e instanceof UserCancellationException) {
+        // User has cancelled this action manually
+        if (e.silent) {
+          void outputLogger.log(errorMessage.fullMessage);
+        } else {
+          void showAndLogWarningMessage(errorMessage.fullMessage, {
+            outputLogger,
+          });
+        }
+      } else {
+        // Include the full stack in the error log only.
+        const fullMessage = errorStack
+          ? `${errorMessage.fullMessage}\n${errorStack}`
+          : errorMessage.fullMessage;
+        void showAndLogExceptionWithTelemetry(errorMessage, {
+          outputLogger,
+          fullMessage,
+          extraTelemetryProperties: {
+            command: commandId,
+          },
+        });
+      }
+      return undefined;
+    } finally {
+      const executionTime = Date.now() - startTime;
+      telemetryListener?.sendCommandUsage(commandId, executionTime, error);
+    }
+  });
+}
+
+/**
+ * wrapExecuteCommand wraps commands.executeCommand to satisfy that the
+ * type is a Promise. Type script does not seem to be smart enough
+ * to figure out that `ReturnType<Commands[CommandName]>` is actually
+ * a Promise, so we need to add a second layer of wrapping and unwrapping
+ * (The `Promise<Awaited<` part) to get the right types.
+ */
+async function wrapExecuteCommand<
+  Commands extends Record<string, CommandFunction>,
+  CommandName extends keyof Commands & string = keyof Commands & string,
+>(
+  commandName: CommandName,
+  ...args: Parameters<Commands[CommandName]>
+): Promise<Awaited<ReturnType<Commands[CommandName]>>> {
+  return await commands.executeCommand<
+    Awaited<ReturnType<Commands[CommandName]>>
+  >(commandName, ...args);
+}
diff --git a/extensions/ql-vscode/src/common/vscode/vscode-app.ts b/extensions/ql-vscode/src/common/vscode/vscode-app.ts
index 8f54341b6..a8f9da973 100644
--- a/extensions/ql-vscode/src/common/vscode/vscode-app.ts
+++ b/extensions/ql-vscode/src/common/vscode/vscode-app.ts
@@ -3,17 +3,24 @@ import { VSCodeCredentials } from "../../authentication";
 import { Disposable } from "../../pure/disposable-object";
 import { App, AppMode } from "../app";
 import { AppEventEmitter } from "../events";
-import { extLogger, Logger } from "../logging";
+import { extLogger, Logger, queryServerLogger } from "../logging";
 import { Memento } from "../memento";
 import { VSCodeAppEventEmitter } from "./events";
+import { AppCommandManager, QueryServerCommandManager } from "../commands";
+import { createVSCodeCommandManager } from "./commands";
 
 export class ExtensionApp implements App {
   public readonly credentials: VSCodeCredentials;
+  public readonly commands: AppCommandManager;
+  public readonly queryServerCommands: QueryServerCommandManager;
 
   public constructor(
     public readonly extensionContext: vscode.ExtensionContext,
   ) {
     this.credentials = new VSCodeCredentials();
+    this.commands = createVSCodeCommandManager();
+    this.queryServerCommands = createVSCodeCommandManager(queryServerLogger);
+    extensionContext.subscriptions.push(this.commands);
   }
 
   public get extensionPath(): string {
@@ -54,8 +61,4 @@ export class ExtensionApp implements App {
   public createEventEmitter<T>(): AppEventEmitter<T> {
     return new VSCodeAppEventEmitter<T>();
   }
-
-  public executeCommand(command: string, ...args: any): Thenable<void> {
-    return vscode.commands.executeCommand(command, ...args);
-  }
 }
diff --git a/extensions/ql-vscode/src/compare/compare-view.ts b/extensions/ql-vscode/src/compare/compare-view.ts
index 46c35562a..9ffa224a4 100644
--- a/extensions/ql-vscode/src/compare/compare-view.ts
+++ b/extensions/ql-vscode/src/compare/compare-view.ts
@@ -20,6 +20,8 @@ import { assertNever, getErrorMessage } from "../pure/helpers-pure";
 import { HistoryItemLabelProvider } from "../query-history/history-item-label-provider";
 import { AbstractWebview, WebviewPanelConfig } from "../abstract-webview";
 import { telemetryListener } from "../telemetry";
+import { redactableError } from "../pure/errors";
+import { showAndLogExceptionWithTelemetry } from "../helpers";
 
 interface ComparePair {
   from: CompletedLocalQueryInfo;
@@ -139,6 +141,14 @@ export class CompareView extends AbstractWebview<
         telemetryListener?.sendUIInteraction(msg.action);
         break;
 
+      case "unhandledError":
+        void showAndLogExceptionWithTelemetry(
+          redactableError(
+            msg.error,
+          )`Unhandled error in result comparison view: ${msg.error.message}`,
+        );
+        break;
+
       default:
         assertNever(msg);
     }
diff --git a/extensions/ql-vscode/src/contextual/locationFinder.ts b/extensions/ql-vscode/src/contextual/locationFinder.ts
index 86af86211..317861613 100644
--- a/extensions/ql-vscode/src/contextual/locationFinder.ts
+++ b/extensions/ql-vscode/src/contextual/locationFinder.ts
@@ -11,7 +11,7 @@ import {
 import { CodeQLCliServer } from "../cli";
 import { DatabaseManager, DatabaseItem } from "../local-databases";
 import fileRangeFromURI from "./fileRangeFromURI";
-import { ProgressCallback } from "../commandRunner";
+import { ProgressCallback } from "../progress";
 import { KeyType } from "./keyType";
 import {
   qlpackOfDatabase,
diff --git a/extensions/ql-vscode/src/contextual/queryResolver.ts b/extensions/ql-vscode/src/contextual/queryResolver.ts
index 550d1b6b4..40cf87cc6 100644
--- a/extensions/ql-vscode/src/contextual/queryResolver.ts
+++ b/extensions/ql-vscode/src/contextual/queryResolver.ts
@@ -16,7 +16,7 @@ import { DatabaseItem } from "../local-databases";
 import { extLogger } from "../common";
 import { createInitialQueryInfo } from "../run-queries-shared";
 import { CancellationToken, Uri } from "vscode";
-import { ProgressCallback } from "../commandRunner";
+import { ProgressCallback } from "../progress";
 import { QueryRunner } from "../queryRunner";
 import { redactableError } from "../pure/errors";
 import { QLPACK_FILENAMES } from "../pure/ql";
diff --git a/extensions/ql-vscode/src/contextual/templateProvider.ts b/extensions/ql-vscode/src/contextual/templateProvider.ts
index 448d36732..ddc23346c 100644
--- a/extensions/ql-vscode/src/contextual/templateProvider.ts
+++ b/extensions/ql-vscode/src/contextual/templateProvider.ts
@@ -4,7 +4,6 @@ import {
   Location,
   LocationLink,
   Position,
-  ProgressLocation,
   ReferenceContext,
   ReferenceProvider,
   TextDocument,
@@ -19,7 +18,7 @@ import {
 import { CodeQLCliServer } from "../cli";
 import { DatabaseManager } from "../local-databases";
 import { CachedOperation } from "../helpers";
-import { ProgressCallback, withProgress } from "../commandRunner";
+import { ProgressCallback, withProgress } from "../progress";
 import AstBuilder from "./astBuilder";
 import { KeyType } from "./keyType";
 import {
@@ -73,11 +72,6 @@ export class TemplateQueryDefinitionProvider implements DefinitionProvider {
 
   private async getDefinitions(uriString: string): Promise<LocationLink[]> {
     return withProgress(
-      {
-        location: ProgressLocation.Notification,
-        cancellable: true,
-        title: "Finding definitions",
-      },
       async (progress, token) => {
         return getLocationsForUriString(
           this.cli,
@@ -91,6 +85,10 @@ export class TemplateQueryDefinitionProvider implements DefinitionProvider {
           (src, _dest) => src === uriString,
         );
       },
+      {
+        cancellable: true,
+        title: "Finding definitions",
+      },
     );
   }
 }
@@ -136,11 +134,6 @@ export class TemplateQueryReferenceProvider implements ReferenceProvider {
 
   private async getReferences(uriString: string): Promise<FullLocationLink[]> {
     return withProgress(
-      {
-        location: ProgressLocation.Notification,
-        cancellable: true,
-        title: "Finding references",
-      },
       async (progress, token) => {
         return getLocationsForUriString(
           this.cli,
@@ -154,6 +147,10 @@ export class TemplateQueryReferenceProvider implements ReferenceProvider {
           (src, _dest) => src === uriString,
         );
       },
+      {
+        cancellable: true,
+        title: "Finding references",
+      },
     );
   }
 }
diff --git a/extensions/ql-vscode/src/databaseFetcher.ts b/extensions/ql-vscode/src/databaseFetcher.ts
index 1e31e7857..cd6c9acf9 100644
--- a/extensions/ql-vscode/src/databaseFetcher.ts
+++ b/extensions/ql-vscode/src/databaseFetcher.ts
@@ -1,7 +1,7 @@
 import fetch, { Response } from "node-fetch";
 import { zip } from "zip-a-folder";
 import { Open } from "unzipper";
-import { Uri, CancellationToken, commands, window } from "vscode";
+import { Uri, CancellationToken, window } from "vscode";
 import { CodeQLCliServer } from "./cli";
 import {
   ensureDir,
@@ -18,7 +18,7 @@ import { retry } from "@octokit/plugin-retry";
 
 import { DatabaseManager, DatabaseItem } from "./local-databases";
 import { showAndLogInformationMessage, tmpDir } from "./helpers";
-import { reportStreamProgress, ProgressCallback } from "./commandRunner";
+import { reportStreamProgress, ProgressCallback } from "./progress";
 import { extLogger } from "./common";
 import { getErrorMessage } from "./pure/helpers-pure";
 import {
@@ -26,6 +26,7 @@ import {
   isValidGitHubNwo,
 } from "./common/github-url-identifier-helper";
 import { Credentials } from "./common/authentication";
+import { AppCommandManager } from "./common/commands";
 
 /**
  * Prompts a user to fetch a database from a remote location. Database is assumed to be an archive file.
@@ -34,6 +35,7 @@ import { Credentials } from "./common/authentication";
  * @param storagePath where to store the unzipped database.
  */
 export async function promptImportInternetDatabase(
+  commandManager: AppCommandManager,
   databaseManager: DatabaseManager,
   storagePath: string,
   progress: ProgressCallback,
@@ -61,7 +63,7 @@ export async function promptImportInternetDatabase(
   );
 
   if (item) {
-    await commands.executeCommand("codeQLDatabases.focus");
+    await commandManager.execute("codeQLDatabases.focus");
     void showAndLogInformationMessage(
       "Database downloaded and imported successfully.",
     );
@@ -78,6 +80,7 @@ export async function promptImportInternetDatabase(
  * @param storagePath where to store the unzipped database.
  */
 export async function promptImportGithubDatabase(
+  commandManager: AppCommandManager,
   databaseManager: DatabaseManager,
   storagePath: string,
   credentials: Credentials | undefined,
@@ -141,7 +144,7 @@ export async function promptImportGithubDatabase(
     cli,
   );
   if (item) {
-    await commands.executeCommand("codeQLDatabases.focus");
+    await commandManager.execute("codeQLDatabases.focus");
     void showAndLogInformationMessage(
       "Database downloaded and imported successfully.",
     );
@@ -158,6 +161,7 @@ export async function promptImportGithubDatabase(
  * @param storagePath where to store the unzipped database.
  */
 export async function importArchiveDatabase(
+  commandManager: AppCommandManager,
   databaseUrl: string,
   databaseManager: DatabaseManager,
   storagePath: string,
@@ -177,7 +181,7 @@ export async function importArchiveDatabase(
       cli,
     );
     if (item) {
-      await commands.executeCommand("codeQLDatabases.focus");
+      await commandManager.execute("codeQLDatabases.focus");
       void showAndLogInformationMessage(
         "Database unzipped and imported successfully.",
       );
diff --git a/extensions/ql-vscode/src/databases/config/db-config-store.ts b/extensions/ql-vscode/src/databases/config/db-config-store.ts
index 54a3c549d..3013d164f 100644
--- a/extensions/ql-vscode/src/databases/config/db-config-store.ts
+++ b/extensions/ql-vscode/src/databases/config/db-config-store.ts
@@ -391,14 +391,14 @@ export class DbConfigStore extends DisposableObject {
 
     if (this.configErrors.length === 0) {
       this.config = newConfig;
-      await this.app.executeCommand(
+      await this.app.commands.execute(
         "setContext",
         "codeQLVariantAnalysisRepositories.configError",
         false,
       );
     } else {
       this.config = undefined;
-      await this.app.executeCommand(
+      await this.app.commands.execute(
         "setContext",
         "codeQLVariantAnalysisRepositories.configError",
         true,
@@ -426,14 +426,14 @@ export class DbConfigStore extends DisposableObject {
 
     if (this.configErrors.length === 0) {
       this.config = newConfig;
-      void this.app.executeCommand(
+      void this.app.commands.execute(
         "setContext",
         "codeQLVariantAnalysisRepositories.configError",
         false,
       );
     } else {
       this.config = undefined;
-      void this.app.executeCommand(
+      void this.app.commands.execute(
         "setContext",
         "codeQLVariantAnalysisRepositories.configError",
         true,
diff --git a/extensions/ql-vscode/src/databases/db-module.ts b/extensions/ql-vscode/src/databases/db-module.ts
index ceb46779a..8d47f75a8 100644
--- a/extensions/ql-vscode/src/databases/db-module.ts
+++ b/extensions/ql-vscode/src/databases/db-module.ts
@@ -6,10 +6,12 @@ import { DbConfigStore } from "./config/db-config-store";
 import { DbManager } from "./db-manager";
 import { DbPanel } from "./ui/db-panel";
 import { DbSelectionDecorationProvider } from "./ui/db-selection-decoration-provider";
+import { DatabasePanelCommands } from "../common/commands";
 
 export class DbModule extends DisposableObject {
   public readonly dbManager: DbManager;
   private readonly dbConfigStore: DbConfigStore;
+  private dbPanel: DbPanel | undefined;
 
   private constructor(app: App) {
     super();
@@ -26,15 +28,24 @@ export class DbModule extends DisposableObject {
     return dbModule;
   }
 
+  public getCommands(): DatabasePanelCommands {
+    if (!this.dbPanel) {
+      throw new Error("Database panel not initialized");
+    }
+
+    return {
+      ...this.dbPanel.getCommands(),
+    };
+  }
+
   private async initialize(app: App): Promise<void> {
     void extLogger.log("Initializing database module");
 
     await this.dbConfigStore.initialize();
 
-    const dbPanel = new DbPanel(this.dbManager, app.credentials);
-    await dbPanel.initialize();
+    this.dbPanel = new DbPanel(app, this.dbManager);
 
-    this.push(dbPanel);
+    this.push(this.dbPanel);
     this.push(this.dbConfigStore);
 
     const dbSelectionDecorationProvider = new DbSelectionDecorationProvider();
diff --git a/extensions/ql-vscode/src/databases/ui/db-panel.ts b/extensions/ql-vscode/src/databases/ui/db-panel.ts
index f9eccc5fc..80a0eec5b 100644
--- a/extensions/ql-vscode/src/databases/ui/db-panel.ts
+++ b/extensions/ql-vscode/src/databases/ui/db-panel.ts
@@ -1,5 +1,4 @@
 import {
-  commands,
   QuickPickItem,
   TreeView,
   TreeViewExpansionEvent,
@@ -7,7 +6,7 @@ import {
   window,
   workspace,
 } from "vscode";
-import { commandRunner, UserCancellationException } from "../../commandRunner";
+import { UserCancellationException } from "../../progress";
 import {
   getNwoFromGitHubUrl,
   isValidGitHubNwo,
@@ -31,7 +30,8 @@ import { DbTreeViewItem } from "./db-tree-view-item";
 import { getGitHubUrl } from "./db-tree-view-item-action";
 import { getControllerRepo } from "../../variant-analysis/run-remote-query";
 import { getErrorMessage } from "../../pure/helpers-pure";
-import { Credentials } from "../../common/authentication";
+import { DatabasePanelCommands } from "../../common/commands";
+import { App } from "../../common/app";
 
 export interface RemoteDatabaseQuickPickItem extends QuickPickItem {
   kind: string;
@@ -46,8 +46,8 @@ export class DbPanel extends DisposableObject {
   private readonly treeView: TreeView<DbTreeViewItem>;
 
   public constructor(
+    private readonly app: App,
     private readonly dbManager: DbManager,
-    private readonly credentials: Credentials,
   ) {
     super();
 
@@ -72,58 +72,28 @@ export class DbPanel extends DisposableObject {
     this.push(this.treeView);
   }
 
-  public async initialize(): Promise<void> {
-    this.push(
-      commandRunner("codeQLVariantAnalysisRepositories.openConfigFile", () =>
-        this.openConfigFile(),
-      ),
-    );
-    this.push(
-      commandRunner("codeQLVariantAnalysisRepositories.addNewDatabase", () =>
-        this.addNewRemoteDatabase(),
-      ),
-    );
-    this.push(
-      commandRunner("codeQLVariantAnalysisRepositories.addNewList", () =>
-        this.addNewList(),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLVariantAnalysisRepositories.setSelectedItem",
-        (treeViewItem: DbTreeViewItem) => this.setSelectedItem(treeViewItem),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLVariantAnalysisRepositories.setSelectedItemContextMenu",
-        (treeViewItem: DbTreeViewItem) => this.setSelectedItem(treeViewItem),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLVariantAnalysisRepositories.openOnGitHubContextMenu",
-        (treeViewItem: DbTreeViewItem) => this.openOnGitHub(treeViewItem),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLVariantAnalysisRepositories.renameItemContextMenu",
-        (treeViewItem: DbTreeViewItem) => this.renameItem(treeViewItem),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLVariantAnalysisRepositories.removeItemContextMenu",
-        (treeViewItem: DbTreeViewItem) => this.removeItem(treeViewItem),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLVariantAnalysisRepositories.setupControllerRepository",
-        () => this.setupControllerRepository(),
-      ),
-    );
+  public getCommands(): DatabasePanelCommands {
+    return {
+      "codeQLVariantAnalysisRepositories.openConfigFile":
+        this.openConfigFile.bind(this),
+      "codeQLVariantAnalysisRepositories.addNewDatabase":
+        this.addNewRemoteDatabase.bind(this),
+      "codeQLVariantAnalysisRepositories.addNewList":
+        this.addNewList.bind(this),
+      "codeQLVariantAnalysisRepositories.setupControllerRepository":
+        this.setupControllerRepository.bind(this),
+
+      "codeQLVariantAnalysisRepositories.setSelectedItem":
+        this.setSelectedItem.bind(this),
+      "codeQLVariantAnalysisRepositories.setSelectedItemContextMenu":
+        this.setSelectedItem.bind(this),
+      "codeQLVariantAnalysisRepositories.openOnGitHubContextMenu":
+        this.openOnGitHub.bind(this),
+      "codeQLVariantAnalysisRepositories.renameItemContextMenu":
+        this.renameItem.bind(this),
+      "codeQLVariantAnalysisRepositories.removeItemContextMenu":
+        this.removeItem.bind(this),
+    };
   }
 
   private async openConfigFile(): Promise<void> {
@@ -398,13 +368,13 @@ export class DbPanel extends DisposableObject {
       );
     }
 
-    await commands.executeCommand("vscode.open", Uri.parse(githubUrl));
+    await this.app.commands.execute("vscode.open", Uri.parse(githubUrl));
   }
 
   private async setupControllerRepository(): Promise<void> {
     try {
       // This will also validate that the controller repository is valid
-      await getControllerRepo(this.credentials);
+      await getControllerRepo(this.app.credentials);
     } catch (e: unknown) {
       if (e instanceof UserCancellationException) {
         return;
diff --git a/extensions/ql-vscode/src/distribution.ts b/extensions/ql-vscode/src/distribution.ts
index 119c82244..017da698d 100644
--- a/extensions/ql-vscode/src/distribution.ts
+++ b/extensions/ql-vscode/src/distribution.ts
@@ -14,7 +14,7 @@ import {
 } from "./helpers";
 import { extLogger } from "./common";
 import { getCodeQlCliVersion } from "./cli-version";
-import { ProgressCallback, reportStreamProgress } from "./commandRunner";
+import { ProgressCallback, reportStreamProgress } from "./progress";
 import {
   codeQlLauncherName,
   deprecatedCodeQlLauncherName,
diff --git a/extensions/ql-vscode/src/eval-log-viewer.ts b/extensions/ql-vscode/src/eval-log-viewer.ts
index c2f4b129b..b71d6c22f 100644
--- a/extensions/ql-vscode/src/eval-log-viewer.ts
+++ b/extensions/ql-vscode/src/eval-log-viewer.ts
@@ -8,11 +8,11 @@ import {
   EventEmitter,
   TreeItemCollapsibleState,
 } from "vscode";
-import { commandRunner } from "./commandRunner";
 import { DisposableObject } from "./pure/disposable-object";
 import { showAndLogExceptionWithTelemetry } from "./helpers";
 import { asError, getErrorMessage } from "./pure/helpers-pure";
 import { redactableError } from "./pure/errors";
+import { EvalLogViewerCommands } from "./common/commands";
 
 export interface EvalLogTreeItem {
   label?: string;
@@ -80,11 +80,12 @@ export class EvalLogViewer extends DisposableObject {
 
     this.push(this.treeView);
     this.push(this.treeDataProvider);
-    this.push(
-      commandRunner("codeQLEvalLogViewer.clear", async () => {
-        this.clear();
-      }),
-    );
+  }
+
+  public getCommands(): EvalLogViewerCommands {
+    return {
+      "codeQLEvalLogViewer.clear": async () => this.clear(),
+    };
   }
 
   private clear(): void {
diff --git a/extensions/ql-vscode/src/extension.ts b/extensions/ql-vscode/src/extension.ts
index e1ca5caef..a3fc19032 100644
--- a/extensions/ql-vscode/src/extension.ts
+++ b/extensions/ql-vscode/src/extension.ts
@@ -1,27 +1,21 @@
 import "source-map-support/register";
 import {
   CancellationToken,
-  CancellationTokenSource,
-  commands,
   Disposable,
   env,
   ExtensionContext,
   extensions,
   languages,
   ProgressLocation,
-  ProgressOptions,
-  QuickPickItem,
-  Range,
   Uri,
   version as vscodeVersion,
   window as Window,
-  window,
   workspace,
 } from "vscode";
 import { LanguageClient } from "vscode-languageclient/node";
 import { arch, platform } from "os";
 import { ensureDir } from "fs-extra";
-import { basename, join } from "path";
+import { join } from "path";
 import { dirSync } from "tmp-promise";
 import { testExplorerExtensionId, TestHub } from "vscode-test-adapter-api";
 import { lt, parse } from "semver";
@@ -36,14 +30,12 @@ import { CodeQLCliServer } from "./cli";
 import {
   CliConfigListener,
   DistributionConfigListener,
-  isCanary,
   joinOrderWarningThreshold,
-  MAX_QUERIES,
   QueryHistoryConfigListener,
   QueryServerConfigListener,
 } from "./config";
 import { install } from "./languageSupport";
-import { DatabaseItem, DatabaseManager } from "./local-databases";
+import { DatabaseManager } from "./local-databases";
 import { DatabaseUI } from "./local-databases-ui";
 import {
   TemplatePrintAstProvider,
@@ -62,7 +54,6 @@ import {
   GithubRateLimitedError,
 } from "./distribution";
 import {
-  findLanguage,
   showAndLogErrorMessage,
   showAndLogExceptionWithTelemetry,
   showAndLogInformationMessage,
@@ -71,6 +62,7 @@ import {
   showInformationMessageWithAction,
   tmpDir,
   tmpDirDisposal,
+  prepareCodeTour,
 } from "./helpers";
 import {
   asError,
@@ -88,55 +80,49 @@ import {
   queryServerLogger,
 } from "./common";
 import { QueryHistoryManager } from "./query-history/query-history-manager";
-import { CompletedLocalQueryInfo, LocalQueryInfo } from "./query-results";
+import { CompletedLocalQueryInfo } from "./query-results";
 import { QueryServerClient as LegacyQueryServerClient } from "./legacy-query-server/queryserver-client";
 import { QueryServerClient } from "./query-server/queryserver-client";
-import { displayQuickQuery } from "./quick-query";
 import { QLTestAdapterFactory } from "./test-adapter";
 import { TestUIService } from "./test-ui";
 import { CompareView } from "./compare/compare-view";
-import { gatherQlFiles } from "./pure/files";
 import { initializeTelemetry } from "./telemetry";
-import {
-  commandRunner,
-  commandRunnerWithProgress,
-  ProgressCallback,
-  ProgressUpdate,
-  withProgress,
-} from "./commandRunner";
+import { ProgressCallback, withProgress } from "./progress";
 import { CodeQlStatusBarHandler } from "./status-bar";
-import {
-  handleDownloadPacks,
-  handleInstallPackDependencies,
-} from "./packaging";
+import { getPackagingCommands } from "./packaging";
 import { HistoryItemLabelProvider } from "./query-history/history-item-label-provider";
-import {
-  exportSelectedVariantAnalysisResults,
-  exportVariantAnalysisResults,
-} from "./variant-analysis/export-results";
 import { EvalLogViewer } from "./eval-log-viewer";
 import { SummaryLanguageSupport } from "./log-insights/summary-language-support";
 import { JoinOrderScannerProvider } from "./log-insights/join-order";
 import { LogScannerService } from "./log-insights/log-scanner-service";
-import { createInitialQueryInfo } from "./run-queries-shared";
 import { LegacyQueryRunner } from "./legacy-query-server/legacyRunner";
 import { NewQueryRunner } from "./query-server/query-runner";
 import { QueryRunner } from "./queryRunner";
 import { VariantAnalysisView } from "./variant-analysis/variant-analysis-view";
 import { VariantAnalysisViewSerializer } from "./variant-analysis/variant-analysis-view-serializer";
-import {
-  VariantAnalysis,
-  VariantAnalysisScannedRepository,
-} from "./variant-analysis/shared/variant-analysis";
 import { VariantAnalysisManager } from "./variant-analysis/variant-analysis-manager";
 import { createVariantAnalysisContentProvider } from "./variant-analysis/variant-analysis-content-provider";
 import { VSCodeMockGitHubApiServer } from "./mocks/vscode-mock-gh-api-server";
 import { VariantAnalysisResultsManager } from "./variant-analysis/variant-analysis-results-manager";
 import { ExtensionApp } from "./common/vscode/vscode-app";
-import { RepositoriesFilterSortStateWithIds } from "./pure/variant-analysis-filter-sort";
 import { DbModule } from "./databases/db-module";
 import { redactableError } from "./pure/errors";
 import { QueryHistoryDirs } from "./query-history/query-history-dirs";
+import {
+  AllExtensionCommands,
+  BaseCommands,
+  PreActivationCommands,
+  QueryServerCommands,
+  TestUICommands,
+} from "./common/commands";
+import {
+  getLocalQueryCommands,
+  showResultsForCompletedQuery,
+} from "./local-queries";
+import { getAstCfgCommands } from "./ast-cfg-commands";
+import { getQueryEditorCommands } from "./query-editor";
+import { App } from "./common/app";
+import { registerCommandWithErrorHandling } from "./common/vscode/commands";
 
 /**
  * extension.ts
@@ -168,6 +154,64 @@ let isInstallingOrUpdatingDistribution = false;
 const extensionId = "GitHub.vscode-codeql";
 const extension = extensions.getExtension(extensionId);
 
+/**
+ * Return all commands that are not tied to the more specific managers.
+ */
+function getCommands(
+  app: App,
+  cliServer: CodeQLCliServer,
+  queryRunner: QueryRunner,
+): BaseCommands {
+  const getCliVersion = async () => {
+    try {
+      return await cliServer.getVersion();
+    } catch {
+      return "<missing>";
+    }
+  };
+
+  return {
+    "codeQL.openDocumentation": async () => {
+      await env.openExternal(Uri.parse("https://codeql.github.com/docs/"));
+    },
+    "codeQL.restartQueryServer": async () =>
+      withProgress(
+        async (progress: ProgressCallback, token: CancellationToken) => {
+          // We restart the CLI server too, to ensure they are the same version
+          cliServer.restartCliServer();
+          await queryRunner.restartQueryServer(progress, token);
+          void showAndLogInformationMessage("CodeQL Query Server restarted.", {
+            outputLogger: queryServerLogger,
+          });
+        },
+        {
+          title: "Restarting Query Server",
+        },
+      ),
+    "codeQL.copyVersion": async () => {
+      const text = `CodeQL extension version: ${
+        extension?.packageJSON.version
+      } \nCodeQL CLI version: ${await getCliVersion()} \nPlatform: ${platform()} ${arch()}`;
+      await env.clipboard.writeText(text);
+      void showAndLogInformationMessage(text);
+    },
+    "codeQL.authenticateToGitHub": async () => {
+      /**
+       * Credentials for authenticating to GitHub.
+       * These are used when making API calls.
+       */
+      const octokit = await app.credentials.getOctokit();
+      const userInfo = await octokit.users.getAuthenticated();
+      void showAndLogInformationMessage(
+        `Authenticated to GitHub as user: ${userInfo.data.login}`,
+      );
+    },
+    "codeQL.showLogs": async () => {
+      extLogger.show();
+    },
+  };
+}
+
 /**
  * If the user tries to execute vscode commands after extension activation is failed, give
  * a sensible error message.
@@ -192,7 +236,11 @@ function registerErrorStubs(
 
   stubbedCommands.forEach((command) => {
     if (excludedCommands.indexOf(command) === -1) {
-      errorStubs.push(commandRunner(command, stubGenerator(command)));
+      // This is purposefully using `registerCommandWithErrorHandling` instead of the command manager because these
+      // commands are untyped and registered pre-activation.
+      errorStubs.push(
+        registerCommandWithErrorHandling(command, stubGenerator(command)),
+      );
     }
   });
 }
@@ -212,6 +260,16 @@ export interface CodeQLExtensionInterface {
   readonly dispose: () => void;
 }
 
+interface DistributionUpdateConfig {
+  isUserInitiated: boolean;
+  shouldDisplayMessageWhenNoUpdates: boolean;
+  allowAutoUpdating: boolean;
+}
+
+const shouldUpdateOnNextActivationKey = "shouldUpdateOnNextActivation";
+
+const codeQlVersionRange = DEFAULT_DISTRIBUTION_VERSION_RANGE;
+
 // This is the minimum version of vscode that we _want_ to support. We want to update the language server library, but that
 // requires 1.67 or later. If we change the minimum version in the package.json, then anyone on an older version of vscode
 // silently be unable to upgrade. So, the solution is to first bump the minimum version here and release. Then
@@ -243,6 +301,8 @@ export async function activate(
   addUnhandledRejectionListener();
   install();
 
+  const app = new ExtensionApp(ctx);
+
   const codelensProvider = new QuickEvalCodeLensProvider();
   languages.registerCodeLensProvider(
     { scheme: "file", language: "ql" },
@@ -250,15 +310,12 @@ export async function activate(
   );
 
   ctx.subscriptions.push(distributionConfigListener);
-  const codeQlVersionRange = DEFAULT_DISTRIBUTION_VERSION_RANGE;
   const distributionManager = new DistributionManager(
     distributionConfigListener,
     codeQlVersionRange,
     ctx,
   );
 
-  const shouldUpdateOnNextActivationKey = "shouldUpdateOnNextActivation";
-
   registerErrorStubs([checkForUpdatesCommand], (command) => async () => {
     void showAndLogErrorMessage(
       `Can't execute ${command}: waiting to finish loading CodeQL CLI.`,
@@ -268,239 +325,36 @@ export async function activate(
   // Checking the vscode version should not block extension activation.
   void assertVSCodeVersionGreaterThan(MIN_VERSION, ctx);
 
-  interface DistributionUpdateConfig {
-    isUserInitiated: boolean;
-    shouldDisplayMessageWhenNoUpdates: boolean;
-    allowAutoUpdating: boolean;
-  }
-
-  async function installOrUpdateDistributionWithProgressTitle(
-    progressTitle: string,
-    config: DistributionUpdateConfig,
-  ): Promise<void> {
-    const minSecondsSinceLastUpdateCheck = config.isUserInitiated ? 0 : 86400;
-    const noUpdatesLoggingFunc = config.shouldDisplayMessageWhenNoUpdates
-      ? showAndLogInformationMessage
-      : async (message: string) => void extLogger.log(message);
-    const result =
-      await distributionManager.checkForUpdatesToExtensionManagedDistribution(
-        minSecondsSinceLastUpdateCheck,
-      );
-
-    // We do want to auto update if there is no distribution at all
-    const allowAutoUpdating =
-      config.allowAutoUpdating ||
-      !(await distributionManager.hasDistribution());
-
-    switch (result.kind) {
-      case DistributionUpdateCheckResultKind.AlreadyCheckedRecentlyResult:
-        void extLogger.log(
-          "Didn't perform CodeQL CLI update check since a check was already performed within the previous " +
-            `${minSecondsSinceLastUpdateCheck} seconds.`,
-        );
-        break;
-      case DistributionUpdateCheckResultKind.AlreadyUpToDate:
-        await noUpdatesLoggingFunc("CodeQL CLI already up to date.");
-        break;
-      case DistributionUpdateCheckResultKind.InvalidLocation:
-        await noUpdatesLoggingFunc(
-          "CodeQL CLI is installed externally so could not be updated.",
-        );
-        break;
-      case DistributionUpdateCheckResultKind.UpdateAvailable:
-        if (beganMainExtensionActivation || !allowAutoUpdating) {
-          const updateAvailableMessage =
-            `Version "${result.updatedRelease.name}" of the CodeQL CLI is now available. ` +
-            "Do you wish to upgrade?";
-          await ctx.globalState.update(shouldUpdateOnNextActivationKey, true);
-          if (
-            await showInformationMessageWithAction(
-              updateAvailableMessage,
-              "Restart and Upgrade",
-            )
-          ) {
-            await commands.executeCommand("workbench.action.reloadWindow");
-          }
-        } else {
-          const progressOptions: ProgressOptions = {
-            title: progressTitle,
-            location: ProgressLocation.Notification,
-          };
-
-          await withProgress(progressOptions, (progress) =>
-            distributionManager.installExtensionManagedDistributionRelease(
-              result.updatedRelease,
-              progress,
-            ),
-          );
-
-          await ctx.globalState.update(shouldUpdateOnNextActivationKey, false);
-          void showAndLogInformationMessage(
-            `CodeQL CLI updated to version "${result.updatedRelease.name}".`,
-          );
-        }
-        break;
-      default:
-        assertNever(result);
-    }
-  }
-
-  async function installOrUpdateDistribution(
-    config: DistributionUpdateConfig,
-  ): Promise<void> {
-    if (isInstallingOrUpdatingDistribution) {
-      throw new Error("Already installing or updating CodeQL CLI");
-    }
-    isInstallingOrUpdatingDistribution = true;
-    const codeQlInstalled =
-      (await distributionManager.getCodeQlPathWithoutVersionCheck()) !==
-      undefined;
-    const willUpdateCodeQl = ctx.globalState.get(
-      shouldUpdateOnNextActivationKey,
-    );
-    const messageText = willUpdateCodeQl
-      ? "Updating CodeQL CLI"
-      : codeQlInstalled
-      ? "Checking for updates to CodeQL CLI"
-      : "Installing CodeQL CLI";
-
-    try {
-      await installOrUpdateDistributionWithProgressTitle(messageText, config);
-    } catch (e) {
-      // Don't rethrow the exception, because if the config is changed, we want to be able to retry installing
-      // or updating the distribution.
-      const alertFunction =
-        codeQlInstalled && !config.isUserInitiated
-          ? showAndLogWarningMessage
-          : showAndLogErrorMessage;
-      const taskDescription = `${
-        willUpdateCodeQl
-          ? "update"
-          : codeQlInstalled
-          ? "check for updates to"
-          : "install"
-      } CodeQL CLI`;
-
-      if (e instanceof GithubRateLimitedError) {
-        void alertFunction(
-          `Rate limited while trying to ${taskDescription}. Please try again after ` +
-            `your rate limit window resets at ${e.rateLimitResetDate.toLocaleString(
-              env.language,
-            )}.`,
-        );
-      } else if (e instanceof GithubApiError) {
-        void alertFunction(
-          `Encountered GitHub API error while trying to ${taskDescription}. ${e}`,
-        );
-      }
-      void alertFunction(`Unable to ${taskDescription}. ${e}`);
-    } finally {
-      isInstallingOrUpdatingDistribution = false;
-    }
-  }
-
-  async function getDistributionDisplayingDistributionWarnings(): Promise<FindDistributionResult> {
-    const result = await distributionManager.getDistribution();
-    switch (result.kind) {
-      case FindDistributionResultKind.CompatibleDistribution:
-        void extLogger.log(
-          `Found compatible version of CodeQL CLI (version ${result.version.raw})`,
-        );
-        break;
-      case FindDistributionResultKind.IncompatibleDistribution: {
-        const fixGuidanceMessage = (() => {
-          switch (result.distribution.kind) {
-            case DistributionKind.ExtensionManaged:
-              return 'Please update the CodeQL CLI by running the "CodeQL: Check for CLI Updates" command.';
-            case DistributionKind.CustomPathConfig:
-              return `Please update the \"CodeQL CLI Executable Path\" setting to point to a CLI in the version range ${codeQlVersionRange}.`;
-            case DistributionKind.PathEnvironmentVariable:
-              return (
-                `Please update the CodeQL CLI on your PATH to a version compatible with ${codeQlVersionRange}, or ` +
-                `set the \"CodeQL CLI Executable Path\" setting to the path of a CLI version compatible with ${codeQlVersionRange}.`
-              );
-          }
-        })();
-
-        void showAndLogWarningMessage(
-          `The current version of the CodeQL CLI (${result.version.raw}) ` +
-            `is incompatible with this extension. ${fixGuidanceMessage}`,
-        );
-        break;
-      }
-      case FindDistributionResultKind.UnknownCompatibilityDistribution:
-        void showAndLogWarningMessage(
-          "Compatibility with the configured CodeQL CLI could not be determined. " +
-            "You may experience problems using the extension.",
-        );
-        break;
-      case FindDistributionResultKind.NoDistribution:
-        void showAndLogErrorMessage("The CodeQL CLI could not be found.");
-        break;
-      default:
-        assertNever(result);
-    }
-    return result;
-  }
-
-  async function installOrUpdateThenTryActivate(
-    config: DistributionUpdateConfig,
-  ): Promise<CodeQLExtensionInterface | Record<string, never>> {
-    await installOrUpdateDistribution(config);
-
-    // Display the warnings even if the extension has already activated.
-    const distributionResult =
-      await getDistributionDisplayingDistributionWarnings();
-    let extensionInterface: CodeQLExtensionInterface | Record<string, never> =
-      {};
-    if (
-      !beganMainExtensionActivation &&
-      distributionResult.kind !== FindDistributionResultKind.NoDistribution
-    ) {
-      extensionInterface = await activateWithInstalledDistribution(
-        ctx,
-        distributionManager,
-        distributionConfigListener,
-      );
-    } else if (
-      distributionResult.kind === FindDistributionResultKind.NoDistribution
-    ) {
-      registerErrorStubs([checkForUpdatesCommand], (command) => async () => {
-        const installActionName = "Install CodeQL CLI";
-        const chosenAction = await showAndLogErrorMessage(
-          `Can't execute ${command}: missing CodeQL CLI.`,
-          {
-            items: [installActionName],
-          },
-        );
-        if (chosenAction === installActionName) {
-          await installOrUpdateThenTryActivate({
-            isUserInitiated: true,
-            shouldDisplayMessageWhenNoUpdates: false,
-            allowAutoUpdating: true,
-          });
-        }
-      });
-    }
-    return extensionInterface;
-  }
-
   ctx.subscriptions.push(
     distributionConfigListener.onDidChangeConfiguration(() =>
-      installOrUpdateThenTryActivate({
-        isUserInitiated: true,
-        shouldDisplayMessageWhenNoUpdates: false,
-        allowAutoUpdating: true,
-      }),
+      installOrUpdateThenTryActivate(
+        ctx,
+        app,
+        distributionManager,
+        distributionConfigListener,
+        {
+          isUserInitiated: true,
+          shouldDisplayMessageWhenNoUpdates: false,
+          allowAutoUpdating: true,
+        },
+      ),
     ),
   );
   ctx.subscriptions.push(
-    commandRunner(checkForUpdatesCommand, () =>
-      installOrUpdateThenTryActivate({
-        isUserInitiated: true,
-        shouldDisplayMessageWhenNoUpdates: true,
-        allowAutoUpdating: true,
-      }),
+    // This is purposefully using `registerCommandWithErrorHandling` directly instead of the command manager
+    // because this command is registered pre-activation.
+    registerCommandWithErrorHandling(checkForUpdatesCommand, () =>
+      installOrUpdateThenTryActivate(
+        ctx,
+        app,
+        distributionManager,
+        distributionConfigListener,
+        {
+          isUserInitiated: true,
+          shouldDisplayMessageWhenNoUpdates: true,
+          allowAutoUpdating: true,
+        },
+      ),
     ),
   );
 
@@ -510,14 +364,20 @@ export async function activate(
     variantAnalysisViewSerializer,
   );
 
-  const codeQlExtension = await installOrUpdateThenTryActivate({
-    isUserInitiated: !!ctx.globalState.get(shouldUpdateOnNextActivationKey),
-    shouldDisplayMessageWhenNoUpdates: false,
+  const codeQlExtension = await installOrUpdateThenTryActivate(
+    ctx,
+    app,
+    distributionManager,
+    distributionConfigListener,
+    {
+      isUserInitiated: !!ctx.globalState.get(shouldUpdateOnNextActivationKey),
+      shouldDisplayMessageWhenNoUpdates: false,
 
-    // only auto update on startup if the user has previously requested an update
-    // otherwise, ask user to accept the update
-    allowAutoUpdating: !!ctx.globalState.get(shouldUpdateOnNextActivationKey),
-  });
+      // only auto update on startup if the user has previously requested an update
+      // otherwise, ask user to accept the update
+      allowAutoUpdating: !!ctx.globalState.get(shouldUpdateOnNextActivationKey),
+    },
+  );
 
   variantAnalysisViewSerializer.onExtensionLoaded(
     codeQlExtension.variantAnalysisManager,
@@ -526,6 +386,245 @@ export async function activate(
   return codeQlExtension;
 }
 
+async function installOrUpdateDistributionWithProgressTitle(
+  ctx: ExtensionContext,
+  app: ExtensionApp,
+  distributionManager: DistributionManager,
+  progressTitle: string,
+  config: DistributionUpdateConfig,
+): Promise<void> {
+  const minSecondsSinceLastUpdateCheck = config.isUserInitiated ? 0 : 86400;
+  const noUpdatesLoggingFunc = config.shouldDisplayMessageWhenNoUpdates
+    ? showAndLogInformationMessage
+    : async (message: string) => void extLogger.log(message);
+  const result =
+    await distributionManager.checkForUpdatesToExtensionManagedDistribution(
+      minSecondsSinceLastUpdateCheck,
+    );
+
+  // We do want to auto update if there is no distribution at all
+  const allowAutoUpdating =
+    config.allowAutoUpdating || !(await distributionManager.hasDistribution());
+
+  switch (result.kind) {
+    case DistributionUpdateCheckResultKind.AlreadyCheckedRecentlyResult:
+      void extLogger.log(
+        "Didn't perform CodeQL CLI update check since a check was already performed within the previous " +
+          `${minSecondsSinceLastUpdateCheck} seconds.`,
+      );
+      break;
+    case DistributionUpdateCheckResultKind.AlreadyUpToDate:
+      await noUpdatesLoggingFunc("CodeQL CLI already up to date.");
+      break;
+    case DistributionUpdateCheckResultKind.InvalidLocation:
+      await noUpdatesLoggingFunc(
+        "CodeQL CLI is installed externally so could not be updated.",
+      );
+      break;
+    case DistributionUpdateCheckResultKind.UpdateAvailable:
+      if (beganMainExtensionActivation || !allowAutoUpdating) {
+        const updateAvailableMessage =
+          `Version "${result.updatedRelease.name}" of the CodeQL CLI is now available. ` +
+          "Do you wish to upgrade?";
+        await ctx.globalState.update(shouldUpdateOnNextActivationKey, true);
+        if (
+          await showInformationMessageWithAction(
+            updateAvailableMessage,
+            "Restart and Upgrade",
+          )
+        ) {
+          await app.commands.execute("workbench.action.reloadWindow");
+        }
+      } else {
+        await withProgress(
+          (progress) =>
+            distributionManager.installExtensionManagedDistributionRelease(
+              result.updatedRelease,
+              progress,
+            ),
+          {
+            title: progressTitle,
+          },
+        );
+
+        await ctx.globalState.update(shouldUpdateOnNextActivationKey, false);
+        void showAndLogInformationMessage(
+          `CodeQL CLI updated to version "${result.updatedRelease.name}".`,
+        );
+      }
+      break;
+    default:
+      assertNever(result);
+  }
+}
+
+async function installOrUpdateDistribution(
+  ctx: ExtensionContext,
+  app: ExtensionApp,
+  distributionManager: DistributionManager,
+  config: DistributionUpdateConfig,
+): Promise<void> {
+  if (isInstallingOrUpdatingDistribution) {
+    throw new Error("Already installing or updating CodeQL CLI");
+  }
+  isInstallingOrUpdatingDistribution = true;
+  const codeQlInstalled =
+    (await distributionManager.getCodeQlPathWithoutVersionCheck()) !==
+    undefined;
+  const willUpdateCodeQl = ctx.globalState.get(shouldUpdateOnNextActivationKey);
+  const messageText = willUpdateCodeQl
+    ? "Updating CodeQL CLI"
+    : codeQlInstalled
+    ? "Checking for updates to CodeQL CLI"
+    : "Installing CodeQL CLI";
+
+  try {
+    await installOrUpdateDistributionWithProgressTitle(
+      ctx,
+      app,
+      distributionManager,
+      messageText,
+      config,
+    );
+  } catch (e) {
+    // Don't rethrow the exception, because if the config is changed, we want to be able to retry installing
+    // or updating the distribution.
+    const alertFunction =
+      codeQlInstalled && !config.isUserInitiated
+        ? showAndLogWarningMessage
+        : showAndLogErrorMessage;
+    const taskDescription = `${
+      willUpdateCodeQl
+        ? "update"
+        : codeQlInstalled
+        ? "check for updates to"
+        : "install"
+    } CodeQL CLI`;
+
+    if (e instanceof GithubRateLimitedError) {
+      void alertFunction(
+        `Rate limited while trying to ${taskDescription}. Please try again after ` +
+          `your rate limit window resets at ${e.rateLimitResetDate.toLocaleString(
+            env.language,
+          )}.`,
+      );
+    } else if (e instanceof GithubApiError) {
+      void alertFunction(
+        `Encountered GitHub API error while trying to ${taskDescription}. ${e}`,
+      );
+    }
+    void alertFunction(`Unable to ${taskDescription}. ${e}`);
+  } finally {
+    isInstallingOrUpdatingDistribution = false;
+  }
+}
+
+async function getDistributionDisplayingDistributionWarnings(
+  distributionManager: DistributionManager,
+): Promise<FindDistributionResult> {
+  const result = await distributionManager.getDistribution();
+  switch (result.kind) {
+    case FindDistributionResultKind.CompatibleDistribution:
+      void extLogger.log(
+        `Found compatible version of CodeQL CLI (version ${result.version.raw})`,
+      );
+      break;
+    case FindDistributionResultKind.IncompatibleDistribution: {
+      const fixGuidanceMessage = (() => {
+        switch (result.distribution.kind) {
+          case DistributionKind.ExtensionManaged:
+            return 'Please update the CodeQL CLI by running the "CodeQL: Check for CLI Updates" command.';
+          case DistributionKind.CustomPathConfig:
+            return `Please update the \"CodeQL CLI Executable Path\" setting to point to a CLI in the version range ${codeQlVersionRange}.`;
+          case DistributionKind.PathEnvironmentVariable:
+            return (
+              `Please update the CodeQL CLI on your PATH to a version compatible with ${codeQlVersionRange}, or ` +
+              `set the \"CodeQL CLI Executable Path\" setting to the path of a CLI version compatible with ${codeQlVersionRange}.`
+            );
+        }
+      })();
+
+      void showAndLogWarningMessage(
+        `The current version of the CodeQL CLI (${result.version.raw}) ` +
+          `is incompatible with this extension. ${fixGuidanceMessage}`,
+      );
+      break;
+    }
+    case FindDistributionResultKind.UnknownCompatibilityDistribution:
+      void showAndLogWarningMessage(
+        "Compatibility with the configured CodeQL CLI could not be determined. " +
+          "You may experience problems using the extension.",
+      );
+      break;
+    case FindDistributionResultKind.NoDistribution:
+      void showAndLogErrorMessage("The CodeQL CLI could not be found.");
+      break;
+    default:
+      assertNever(result);
+  }
+  return result;
+}
+
+async function installOrUpdateThenTryActivate(
+  ctx: ExtensionContext,
+  app: ExtensionApp,
+  distributionManager: DistributionManager,
+  distributionConfigListener: DistributionConfigListener,
+  config: DistributionUpdateConfig,
+): Promise<CodeQLExtensionInterface | Record<string, never>> {
+  await installOrUpdateDistribution(ctx, app, distributionManager, config);
+
+  try {
+    await prepareCodeTour(app.commands);
+  } catch (e: unknown) {
+    void extLogger.log(
+      `Could not open tutorial workspace automatically: ${getErrorMessage(e)}`,
+    );
+  }
+
+  // Display the warnings even if the extension has already activated.
+  const distributionResult =
+    await getDistributionDisplayingDistributionWarnings(distributionManager);
+  let extensionInterface: CodeQLExtensionInterface | Record<string, never> = {};
+  if (
+    !beganMainExtensionActivation &&
+    distributionResult.kind !== FindDistributionResultKind.NoDistribution
+  ) {
+    extensionInterface = await activateWithInstalledDistribution(
+      ctx,
+      app,
+      distributionManager,
+      distributionConfigListener,
+    );
+  } else if (
+    distributionResult.kind === FindDistributionResultKind.NoDistribution
+  ) {
+    registerErrorStubs([checkForUpdatesCommand], (command) => async () => {
+      const installActionName = "Install CodeQL CLI";
+      const chosenAction = await showAndLogErrorMessage(
+        `Can't execute ${command}: missing CodeQL CLI.`,
+        {
+          items: [installActionName],
+        },
+      );
+      if (chosenAction === installActionName) {
+        await installOrUpdateThenTryActivate(
+          ctx,
+          app,
+          distributionManager,
+          distributionConfigListener,
+          {
+            isUserInitiated: true,
+            shouldDisplayMessageWhenNoUpdates: false,
+            allowAutoUpdating: true,
+          },
+        );
+      }
+    });
+  }
+  return extensionInterface;
+}
+
 const PACK_GLOBS = [
   "**/codeql-pack.yml",
   "**/qlpack.yml",
@@ -538,6 +637,7 @@ const PACK_GLOBS = [
 
 async function activateWithInstalledDistribution(
   ctx: ExtensionContext,
+  app: ExtensionApp,
   distributionManager: DistributionManager,
   distributionConfigListener: DistributionConfigListener,
 ): Promise<CodeQLExtensionInterface> {
@@ -546,8 +646,6 @@ async function activateWithInstalledDistribution(
   // of activation.
   errorStubs.forEach((stub) => stub.dispose());
 
-  const app = new ExtensionApp(ctx);
-
   void extLogger.log("Initializing configuration listener...");
   const qlConfigurationListener =
     await QueryServerConfigListener.createQueryServerConfigListener(
@@ -571,7 +669,12 @@ async function activateWithInstalledDistribution(
   ctx.subscriptions.push(statusBar);
 
   void extLogger.log("Initializing query server client.");
-  const qs = await createQueryServer(qlConfigurationListener, cliServer, ctx);
+  const qs = await createQueryServer(
+    app,
+    qlConfigurationListener,
+    cliServer,
+    ctx,
+  );
 
   for (const glob of PACK_GLOBS) {
     const fsWatcher = workspace.createFileSystemWatcher(glob);
@@ -582,7 +685,7 @@ async function activateWithInstalledDistribution(
   }
 
   void extLogger.log("Initializing database manager.");
-  const dbm = new DatabaseManager(ctx, qs, cliServer, extLogger);
+  const dbm = new DatabaseManager(ctx, app, qs, cliServer, extLogger);
 
   // Let this run async.
   void dbm.loadPersistedState();
@@ -596,7 +699,6 @@ async function activateWithInstalledDistribution(
     getContextStoragePath(ctx),
     ctx.extensionPath,
   );
-  databaseUI.init();
   ctx.subscriptions.push(databaseUI);
 
   void extLogger.log("Initializing evaluator log viewer.");
@@ -607,9 +709,22 @@ async function activateWithInstalledDistribution(
   const queryHistoryConfigurationListener = new QueryHistoryConfigListener();
   ctx.subscriptions.push(queryHistoryConfigurationListener);
   const showResults = async (item: CompletedLocalQueryInfo) =>
-    showResultsForCompletedQuery(item, WebviewReveal.Forced);
+    showResultsForCompletedQuery(
+      localQueryResultsView,
+      item,
+      WebviewReveal.Forced,
+    );
   const queryStorageDir = join(ctx.globalStorageUri.fsPath, "queries");
   await ensureDir(queryStorageDir);
+
+  // Store contextual queries in a temporary folder so that they are removed
+  // when the application closes. There is no need for the user to interact with them.
+  const contextualQueryStorageDir = join(
+    tmpDir.name,
+    "contextual-query-storage",
+  );
+  await ensureDir(contextualQueryStorageDir);
+
   const labelProvider = new HistoryItemLabelProvider(
     queryHistoryConfigurationListener,
   );
@@ -662,6 +777,7 @@ async function activateWithInstalledDistribution(
   };
 
   const qhm = new QueryHistoryManager(
+    app,
     qs,
     dbm,
     localQueryResultsView,
@@ -672,7 +788,7 @@ async function activateWithInstalledDistribution(
     queryHistoryConfigurationListener,
     labelProvider,
     async (from: CompletedLocalQueryInfo, to: CompletedLocalQueryInfo) =>
-      showResultsForComparison(from, to),
+      showResultsForComparison(compareView, from, to),
   );
 
   ctx.subscriptions.push(qhm);
@@ -700,157 +816,6 @@ async function activateWithInstalledDistribution(
   void extLogger.log("Initializing source archive filesystem provider.");
   archiveFilesystemProvider_activate(ctx);
 
-  async function showResultsForComparison(
-    from: CompletedLocalQueryInfo,
-    to: CompletedLocalQueryInfo,
-  ): Promise<void> {
-    try {
-      await compareView.showResults(from, to);
-    } catch (e) {
-      void showAndLogExceptionWithTelemetry(
-        redactableError(asError(e))`Failed to show results: ${getErrorMessage(
-          e,
-        )}`,
-      );
-    }
-  }
-
-  async function showResultsForCompletedQuery(
-    query: CompletedLocalQueryInfo,
-    forceReveal: WebviewReveal,
-  ): Promise<void> {
-    await localQueryResultsView.showResults(query, forceReveal, false);
-  }
-
-  async function compileAndRunQuery(
-    quickEval: boolean,
-    selectedQuery: Uri | undefined,
-    progress: ProgressCallback,
-    token: CancellationToken,
-    databaseItem: DatabaseItem | undefined,
-    range?: Range,
-  ): Promise<void> {
-    if (qs !== undefined) {
-      // If no databaseItem is specified, use the database currently selected in the Databases UI
-      databaseItem =
-        databaseItem || (await databaseUI.getDatabaseItem(progress, token));
-      if (databaseItem === undefined) {
-        throw new Error("Can't run query without a selected database");
-      }
-      const databaseInfo = {
-        name: databaseItem.name,
-        databaseUri: databaseItem.databaseUri.toString(),
-      };
-
-      // handle cancellation from the history view.
-      const source = new CancellationTokenSource();
-      token.onCancellationRequested(() => source.cancel());
-
-      const initialInfo = await createInitialQueryInfo(
-        selectedQuery,
-        databaseInfo,
-        quickEval,
-        range,
-      );
-      const item = new LocalQueryInfo(initialInfo, source);
-      qhm.addQuery(item);
-      try {
-        const completedQueryInfo = await qs.compileAndRunQueryAgainstDatabase(
-          databaseItem,
-          initialInfo,
-          queryStorageDir,
-          progress,
-          source.token,
-          undefined,
-          item,
-        );
-        qhm.completeQuery(item, completedQueryInfo);
-        await showResultsForCompletedQuery(
-          item as CompletedLocalQueryInfo,
-          WebviewReveal.Forced,
-        );
-        // Note we must update the query history view after showing results as the
-        // display and sorting might depend on the number of results
-      } catch (e) {
-        const err = asError(e);
-        err.message = `Error running query: ${err.message}`;
-        item.failureReason = err.message;
-        throw e;
-      } finally {
-        await qhm.refreshTreeView();
-        source.dispose();
-      }
-    }
-  }
-
-  async function compileAndRunQueryOnMultipleDatabases(
-    progress: ProgressCallback,
-    token: CancellationToken,
-    uri: Uri | undefined,
-  ): Promise<void> {
-    let filteredDBs = dbm.databaseItems;
-    if (filteredDBs.length === 0) {
-      void showAndLogErrorMessage(
-        "No databases found. Please add a suitable database to your workspace.",
-      );
-      return;
-    }
-    // If possible, only show databases with the right language (otherwise show all databases).
-    const queryLanguage = await findLanguage(cliServer, uri);
-    if (queryLanguage) {
-      filteredDBs = dbm.databaseItems.filter(
-        (db) => db.language === queryLanguage,
-      );
-      if (filteredDBs.length === 0) {
-        void showAndLogErrorMessage(
-          `No databases found for language ${queryLanguage}. Please add a suitable database to your workspace.`,
-        );
-        return;
-      }
-    }
-    const quickPickItems = filteredDBs.map<DatabaseQuickPickItem>((dbItem) => ({
-      databaseItem: dbItem,
-      label: dbItem.name,
-      description: dbItem.language,
-    }));
-    /**
-     * Databases that were selected in the quick pick menu.
-     */
-    const quickpick = await window.showQuickPick<DatabaseQuickPickItem>(
-      quickPickItems,
-      { canPickMany: true, ignoreFocusOut: true },
-    );
-    if (quickpick !== undefined) {
-      // Collect all skipped databases and display them at the end (instead of popping up individual errors)
-      const skippedDatabases = [];
-      const errors = [];
-      for (const item of quickpick) {
-        try {
-          await compileAndRunQuery(
-            false,
-            uri,
-            progress,
-            token,
-            item.databaseItem,
-          );
-        } catch (e) {
-          skippedDatabases.push(item.label);
-          errors.push(getErrorMessage(e));
-        }
-      }
-      if (skippedDatabases.length > 0) {
-        void extLogger.log(`Errors:\n${errors.join("\n")}`);
-        void showAndLogWarningMessage(
-          `The following databases were skipped:\n${skippedDatabases.join(
-            "\n",
-          )}.\nFor details about the errors, see the logs.`,
-        );
-      }
-    } else {
-      void showAndLogErrorMessage("No databases selected.");
-    }
-  }
-
   const qhelpTmpDir = dirSync({
     prefix: "qhelp_",
     keep: false,
@@ -858,43 +823,6 @@ async function activateWithInstalledDistribution(
   });
   ctx.subscriptions.push({ dispose: qhelpTmpDir.removeCallback });
 
-  async function previewQueryHelp(selectedQuery: Uri): Promise<void> {
-    // selectedQuery is unpopulated when executing through the command palette
-    const pathToQhelp = selectedQuery
-      ? selectedQuery.fsPath
-      : window.activeTextEditor?.document.uri.fsPath;
-    if (pathToQhelp) {
-      // Create temporary directory
-      const relativePathToMd = `${basename(pathToQhelp, ".qhelp")}.md`;
-      const absolutePathToMd = join(qhelpTmpDir.name, relativePathToMd);
-      const uri = Uri.file(absolutePathToMd);
-      try {
-        await cliServer.generateQueryHelp(pathToQhelp, absolutePathToMd);
-        await commands.executeCommand("markdown.showPreviewToSide", uri);
-      } catch (e) {
-        const errorMessage = getErrorMessage(e).includes(
-          "Generating qhelp in markdown",
-        )
-          ? redactableError`Could not generate markdown from ${pathToQhelp}: Bad formatting in .qhelp file.`
-          : redactableError`Could not open a preview of the generated file (${absolutePathToMd}).`;
-        void showAndLogExceptionWithTelemetry(errorMessage, {
-          fullMessage: `${errorMessage}\n${getErrorMessage(e)}`,
-        });
-      }
-    }
-  }
-
-  async function openReferencedFile(selectedQuery: Uri): Promise<void> {
-    // If no file is selected, the path of the file in the editor is selected
-    const path =
-      selectedQuery?.fsPath || window.activeTextEditor?.document.uri.fsPath;
-    if (qs !== undefined && path) {
-      const resolved = await cliServer.resolveQlref(path);
-      const uri = Uri.file(resolved.resolvedPath);
-      await window.showTextDocument(uri, { preview: false });
-    }
-  }
-
   ctx.subscriptions.push(tmpDirDisposal);
 
   void extLogger.log("Initializing CodeQL language server.");
@@ -921,6 +849,7 @@ async function activateWithInstalledDistribution(
   const testExplorerExtension = extensions.getExtension<TestHub>(
     testExplorerExtensionId,
   );
+  let testUiCommands: Partial<TestUICommands> = {};
   if (testExplorerExtension) {
     const testHub = testExplorerExtension.exports;
     const testAdapterFactory = new QLTestAdapterFactory(
@@ -930,555 +859,87 @@ async function activateWithInstalledDistribution(
     );
     ctx.subscriptions.push(testAdapterFactory);
 
-    const testUIService = new TestUIService(testHub);
+    const testUIService = new TestUIService(app, testHub);
     ctx.subscriptions.push(testUIService);
+
+    testUiCommands = testUIService.getCommands();
   }
 
+  const astViewer = new AstViewer();
+  const astTemplateProvider = new TemplatePrintAstProvider(
+    cliServer,
+    qs,
+    dbm,
+    contextualQueryStorageDir,
+  );
+  const cfgTemplateProvider = new TemplatePrintCfgProvider(cliServer, dbm);
+
+  ctx.subscriptions.push(astViewer);
+
+  const summaryLanguageSupport = new SummaryLanguageSupport();
+  ctx.subscriptions.push(summaryLanguageSupport);
+
+  const mockServer = new VSCodeMockGitHubApiServer(ctx);
+  ctx.subscriptions.push(mockServer);
+
   void extLogger.log("Registering top-level command palette commands.");
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.runQuery",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        uri: Uri | undefined,
-      ) => await compileAndRunQuery(false, uri, progress, token, undefined),
-      {
-        title: "Running query",
-        cancellable: true,
-      },
 
-      // Open the query server logger on error since that's usually where the interesting errors appear.
-      queryServerLogger,
-    ),
-  );
-
-  // Since we are tracking extension usage through commands, this command mirrors the runQuery command
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.runQueryContextEditor",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        uri: Uri | undefined,
-      ) => await compileAndRunQuery(false, uri, progress, token, undefined),
-      {
-        title: "Running query",
-        cancellable: true,
-      },
-
-      // Open the query server logger on error since that's usually where the interesting errors appear.
-      queryServerLogger,
-    ),
-  );
-  interface DatabaseQuickPickItem extends QuickPickItem {
-    databaseItem: DatabaseItem;
-  }
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.runQueryOnMultipleDatabases",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        uri: Uri | undefined,
-      ) => await compileAndRunQueryOnMultipleDatabases(progress, token, uri),
-      {
-        title: "Running query on selected databases",
-        cancellable: true,
-      },
-    ),
-  );
-  // Since we are tracking extension usage through commands, this command mirrors the runQueryOnMultipleDatabases command
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.runQueryOnMultipleDatabasesContextEditor",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        uri: Uri | undefined,
-      ) => await compileAndRunQueryOnMultipleDatabases(progress, token, uri),
-      {
-        title: "Running query on selected databases",
-        cancellable: true,
-      },
-    ),
-  );
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.runQueries",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        _: Uri | undefined,
-        multi: Uri[],
-      ) => {
-        const maxQueryCount = MAX_QUERIES.getValue() as number;
-        const [files, dirFound] = await gatherQlFiles(
-          multi.map((uri) => uri.fsPath),
-        );
-        if (files.length > maxQueryCount) {
-          throw new Error(
-            `You tried to run ${files.length} queries, but the maximum is ${maxQueryCount}. Try selecting fewer queries or changing the 'codeQL.runningQueries.maxQueries' setting.`,
-          );
-        }
-        // warn user and display selected files when a directory is selected because some ql
-        // files may be hidden from the user.
-        if (dirFound) {
-          const fileString = files.map((file) => basename(file)).join(", ");
-          const res = await showBinaryChoiceDialog(
-            `You are about to run ${files.length} queries: ${fileString} Do you want to continue?`,
-          );
-          if (!res) {
-            return;
-          }
-        }
-        const queryUris = files.map((path) => Uri.parse(`file:${path}`, true));
-
-        // Use a wrapped progress so that messages appear with the queries remaining in it.
-        let queriesRemaining = queryUris.length;
-        function wrappedProgress(update: ProgressUpdate) {
-          const message =
-            queriesRemaining > 1
-              ? `${queriesRemaining} remaining. ${update.message}`
-              : update.message;
-          progress({
-            ...update,
-            message,
-          });
-        }
-
-        wrappedProgress({
-          maxStep: queryUris.length,
-          step: queryUris.length - queriesRemaining,
-          message: "",
-        });
-
-        await Promise.all(
-          queryUris.map(async (uri) =>
-            compileAndRunQuery(
-              false,
-              uri,
-              wrappedProgress,
-              token,
-              undefined,
-            ).then(() => queriesRemaining--),
-          ),
-        );
-      },
-      {
-        title: "Running queries",
-        cancellable: true,
-      },
-
-      // Open the query server logger on error since that's usually where the interesting errors appear.
-      queryServerLogger,
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.quickEval",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        uri: Uri | undefined,
-      ) => await compileAndRunQuery(true, uri, progress, token, undefined),
-      {
-        title: "Running query",
-        cancellable: true,
-      },
-      // Open the query server logger on error since that's usually where the interesting errors appear.
-      queryServerLogger,
-    ),
-  );
-
-  // Since we are tracking extension usage through commands, this command mirrors the "codeQL.quickEval" command
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.quickEvalContextEditor",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        uri: Uri | undefined,
-      ) => await compileAndRunQuery(true, uri, progress, token, undefined),
-      {
-        title: "Running query",
-        cancellable: true,
-      },
-      // Open the query server logger on error since that's usually where the interesting errors appear.
-      queryServerLogger,
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.codeLensQuickEval",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        uri: Uri,
-        range: Range,
-      ) =>
-        await compileAndRunQuery(true, uri, progress, token, undefined, range),
-      {
-        title: "Running query",
-        cancellable: true,
-      },
-
-      // Open the query server logger on error since that's usually where the interesting errors appear.
-      queryServerLogger,
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.quickQuery",
-      async (progress: ProgressCallback, token: CancellationToken) =>
-        displayQuickQuery(ctx, cliServer, databaseUI, progress, token),
-      {
-        title: "Run Quick Query",
-      },
-
-      // Open the query server logger on error since that's usually where the interesting errors appear.
-      queryServerLogger,
-    ),
-  );
-
-  async function runVariantAnalysis(
-    progress: ProgressCallback,
-    token: CancellationToken,
-    uri: Uri | undefined,
-  ): Promise<void> {
-    progress({
-      maxStep: 5,
-      step: 0,
-      message: "Getting credentials",
-    });
-
-    await variantAnalysisManager.runVariantAnalysis(
-      uri || window.activeTextEditor?.document.uri,
-      progress,
-      token,
-    );
-  }
-
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.runVariantAnalysis",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        uri: Uri | undefined,
-      ) => await runVariantAnalysis(progress, token, uri),
-      {
-        title: "Run Variant Analysis",
-        cancellable: true,
-      },
-    ),
-  );
-
-  // Since we are tracking extension usage through commands, this command mirrors the "codeQL.runVariantAnalysis" command
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.runVariantAnalysisContextEditor",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        uri: Uri | undefined,
-      ) => await runVariantAnalysis(progress, token, uri),
-      {
-        title: "Run Variant Analysis",
-        cancellable: true,
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.openVariantAnalysisLogs",
-      async (variantAnalysisId: number) => {
-        await variantAnalysisManager.openVariantAnalysisLogs(variantAnalysisId);
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.copyVariantAnalysisRepoList",
-      async (
-        variantAnalysisId: number,
-        filterSort?: RepositoriesFilterSortStateWithIds,
-      ) => {
-        await variantAnalysisManager.copyRepoListToClipboard(
-          variantAnalysisId,
-          filterSort,
-        );
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.monitorVariantAnalysis",
-      async (variantAnalysis: VariantAnalysis, token: CancellationToken) => {
-        await variantAnalysisManager.monitorVariantAnalysis(
-          variantAnalysis,
-          token,
-        );
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.autoDownloadVariantAnalysisResult",
-      async (
-        scannedRepo: VariantAnalysisScannedRepository,
-        variantAnalysisSummary: VariantAnalysis,
-        token: CancellationToken,
-      ) => {
-        await variantAnalysisManager.enqueueDownload(
-          scannedRepo,
-          variantAnalysisSummary,
-          token,
-        );
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.cancelVariantAnalysis",
-      async (variantAnalysisId: number) => {
-        await variantAnalysisManager.cancelVariantAnalysis(variantAnalysisId);
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner("codeQL.exportSelectedVariantAnalysisResults", async () => {
-      await exportSelectedVariantAnalysisResults(qhm);
+  const allCommands: AllExtensionCommands = {
+    ...getCommands(app, cliServer, qs),
+    ...getQueryEditorCommands({
+      commandManager: app.commands,
+      queryRunner: qs,
+      cliServer,
+      qhelpTmpDir: qhelpTmpDir.name,
     }),
-  );
-
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.exportVariantAnalysisResults",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        variantAnalysisId: number,
-        filterSort?: RepositoriesFilterSortStateWithIds,
-      ) => {
-        await exportVariantAnalysisResults(
-          variantAnalysisManager,
-          variantAnalysisId,
-          filterSort,
-          app.credentials,
-          progress,
-          token,
-        );
-      },
-      {
-        title: "Exporting variant analysis results",
-        cancellable: true,
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.loadVariantAnalysisRepoResults",
-      async (variantAnalysisId: number, repositoryFullName: string) => {
-        await variantAnalysisManager.loadResults(
-          variantAnalysisId,
-          repositoryFullName,
-        );
-      },
-    ),
-  );
-
-  // The "openVariantAnalysisView" command is internal-only.
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.openVariantAnalysisView",
-      async (variantAnalysisId: number) => {
-        await variantAnalysisManager.showView(variantAnalysisId);
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.openVariantAnalysisQueryText",
-      async (variantAnalysisId: number) => {
-        await variantAnalysisManager.openQueryText(variantAnalysisId);
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.openVariantAnalysisQueryFile",
-      async (variantAnalysisId: number) => {
-        await variantAnalysisManager.openQueryFile(variantAnalysisId);
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner("codeQL.openReferencedFile", openReferencedFile),
-  );
-
-  // Since we are tracking extension usage through commands, this command mirrors the "codeQL.openReferencedFile" command
-  ctx.subscriptions.push(
-    commandRunner("codeQL.openReferencedFileContextEditor", openReferencedFile),
-  );
-
-  // Since we are tracking extension usage through commands, this command mirrors the "codeQL.openReferencedFile" command
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.openReferencedFileContextExplorer",
-      openReferencedFile,
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner("codeQL.previewQueryHelp", previewQueryHelp),
-  );
-
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.restartQueryServer",
-      async (progress: ProgressCallback, token: CancellationToken) => {
-        // We restart the CLI server too, to ensure they are the same version
-        cliServer.restartCliServer();
-        await qs.restartQueryServer(progress, token);
-        void showAndLogInformationMessage("CodeQL Query Server restarted.", {
-          outputLogger: queryServerLogger,
-        });
-      },
-      {
-        title: "Restarting Query Server",
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.chooseDatabaseFolder",
-      (progress: ProgressCallback, token: CancellationToken) =>
-        databaseUI.handleChooseDatabaseFolder(progress, token),
-      {
-        title: "Choose a Database from a Folder",
-      },
-    ),
-  );
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.chooseDatabaseArchive",
-      (progress: ProgressCallback, token: CancellationToken) =>
-        databaseUI.handleChooseDatabaseArchive(progress, token),
-      {
-        title: "Choose a Database from an Archive",
-      },
-    ),
-  );
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.chooseDatabaseGithub",
-      async (progress: ProgressCallback, token: CancellationToken) => {
-        const credentials = isCanary() ? app.credentials : undefined;
-        await databaseUI.handleChooseDatabaseGithub(
-          credentials,
-          progress,
-          token,
-        );
-      },
-      {
-        title: "Adding database from GitHub",
-      },
-    ),
-  );
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.chooseDatabaseInternet",
-      (progress: ProgressCallback, token: CancellationToken) =>
-        databaseUI.handleChooseDatabaseInternet(progress, token),
-
-      {
-        title: "Adding database from URL",
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner("codeQL.openDocumentation", async () =>
-      env.openExternal(Uri.parse("https://codeql.github.com/docs/")),
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner("codeQL.copyVersion", async () => {
-      const text = `CodeQL extension version: ${
-        extension?.packageJSON.version
-      } \nCodeQL CLI version: ${await getCliVersion()} \nPlatform: ${platform()} ${arch()}`;
-      await env.clipboard.writeText(text);
-      void showAndLogInformationMessage(text);
+    ...localQueryResultsView.getCommands(),
+    ...qhm.getCommands(),
+    ...variantAnalysisManager.getCommands(),
+    ...databaseUI.getCommands(),
+    ...dbModule.getCommands(),
+    ...getAstCfgCommands({
+      queryRunner: qs,
+      queryHistoryManager: qhm,
+      databaseUI,
+      localQueryResultsView,
+      queryStorageDir,
+      astViewer,
+      astTemplateProvider,
+      cfgTemplateProvider,
     }),
-  );
-
-  const getCliVersion = async () => {
-    try {
-      return await cliServer.getVersion();
-    } catch {
-      return "<missing>";
-    }
+    ...astViewer.getCommands(),
+    ...getPackagingCommands({
+      cliServer,
+    }),
+    ...evalLogViewer.getCommands(),
+    ...summaryLanguageSupport.getCommands(),
+    ...testUiCommands,
+    ...mockServer.getCommands(),
   };
 
-  ctx.subscriptions.push(
-    commandRunner("codeQL.authenticateToGitHub", async () => {
-      /**
-       * Credentials for authenticating to GitHub.
-       * These are used when making API calls.
-       */
-      const octokit = await app.credentials.getOctokit();
-      const userInfo = await octokit.users.getAuthenticated();
-      void showAndLogInformationMessage(
-        `Authenticated to GitHub as user: ${userInfo.data.login}`,
-      );
+  for (const [commandName, command] of Object.entries(allCommands)) {
+    app.commands.register(commandName as keyof AllExtensionCommands, command);
+  }
+
+  const queryServerCommands: QueryServerCommands = {
+    ...getLocalQueryCommands({
+      app,
+      queryRunner: qs,
+      queryHistoryManager: qhm,
+      databaseManager: dbm,
+      cliServer,
+      databaseUI,
+      localQueryResultsView,
+      queryStorageDir,
     }),
-  );
+  };
 
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.installPackDependencies",
-      async (progress: ProgressCallback) =>
-        await handleInstallPackDependencies(cliServer, progress),
-      {
-        title: "Installing pack dependencies",
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.downloadPacks",
-      async (progress: ProgressCallback) =>
-        await handleDownloadPacks(cliServer, progress),
-      {
-        title: "Downloading packs",
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunner("codeQL.showLogs", async () => {
-      extLogger.show();
-    }),
-  );
-
-  ctx.subscriptions.push(new SummaryLanguageSupport());
+  for (const [commandName, command] of Object.entries(queryServerCommands)) {
+    app.queryServerCommands.register(
+      commandName as keyof QueryServerCommands,
+      command,
+    );
+  }
 
   void extLogger.log("Starting language server.");
   await client.start();
@@ -1490,13 +951,6 @@ async function activateWithInstalledDistribution(
   // Jump-to-definition and find-references
   void extLogger.log("Registering jump-to-definition handlers.");
 
-  // Store contextual queries in a temporary folder so that they are removed
-  // when the application closes. There is no need for the user to interact with them.
-  const contextualQueryStorageDir = join(
-    tmpDir.name,
-    "contextual-query-storage",
-  );
-  await ensureDir(contextualQueryStorageDir);
   languages.registerDefinitionProvider(
     { scheme: zipArchiveScheme },
     new TemplateQueryDefinitionProvider(
@@ -1517,169 +971,7 @@ async function activateWithInstalledDistribution(
     ),
   );
 
-  const astViewer = new AstViewer();
-  const printAstTemplateProvider = new TemplatePrintAstProvider(
-    cliServer,
-    qs,
-    dbm,
-    contextualQueryStorageDir,
-  );
-  const cfgTemplateProvider = new TemplatePrintCfgProvider(cliServer, dbm);
-
-  ctx.subscriptions.push(astViewer);
-
-  async function viewAst(
-    progress: ProgressCallback,
-    token: CancellationToken,
-    selectedFile: Uri,
-  ): Promise<void> {
-    const ast = await printAstTemplateProvider.provideAst(
-      progress,
-      token,
-      selectedFile ?? window.activeTextEditor?.document.uri,
-    );
-    if (ast) {
-      astViewer.updateRoots(await ast.getRoots(), ast.db, ast.fileName);
-    }
-  }
-
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.viewAst",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        selectedFile: Uri,
-      ) => await viewAst(progress, token, selectedFile),
-      {
-        cancellable: true,
-        title: "Calculate AST",
-      },
-    ),
-  );
-
-  // Since we are tracking extension usage through commands, this command mirrors the "codeQL.viewAst" command
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.viewAstContextExplorer",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        selectedFile: Uri,
-      ) => await viewAst(progress, token, selectedFile),
-      {
-        cancellable: true,
-        title: "Calculate AST",
-      },
-    ),
-  );
-
-  // Since we are tracking extension usage through commands, this command mirrors the "codeQL.viewAst" command
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.viewAstContextEditor",
-      async (
-        progress: ProgressCallback,
-        token: CancellationToken,
-        selectedFile: Uri,
-      ) => await viewAst(progress, token, selectedFile),
-      {
-        cancellable: true,
-        title: "Calculate AST",
-      },
-    ),
-  );
-
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.viewCfg",
-      async (progress: ProgressCallback, token: CancellationToken) => {
-        const res = await cfgTemplateProvider.provideCfgUri(
-          window.activeTextEditor?.document,
-        );
-        if (res) {
-          await compileAndRunQuery(false, res[0], progress, token, undefined);
-        }
-      },
-      {
-        title: "Calculating Control Flow Graph",
-        cancellable: true,
-      },
-    ),
-  );
-
-  // Since we are tracking extension usage through commands, this command mirrors the "codeQL.viewCfg" command
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.viewCfgContextExplorer",
-      async (progress: ProgressCallback, token: CancellationToken) => {
-        const res = await cfgTemplateProvider.provideCfgUri(
-          window.activeTextEditor?.document,
-        );
-        if (res) {
-          await compileAndRunQuery(false, res[0], progress, token, undefined);
-        }
-      },
-      {
-        title: "Calculating Control Flow Graph",
-        cancellable: true,
-      },
-    ),
-  );
-
-  // Since we are tracking extension usage through commands, this command mirrors the "codeQL.viewCfg" command
-  ctx.subscriptions.push(
-    commandRunnerWithProgress(
-      "codeQL.viewCfgContextEditor",
-      async (progress: ProgressCallback, token: CancellationToken) => {
-        const res = await cfgTemplateProvider.provideCfgUri(
-          window.activeTextEditor?.document,
-        );
-        if (res) {
-          await compileAndRunQuery(false, res[0], progress, token, undefined);
-        }
-      },
-      {
-        title: "Calculating Control Flow Graph",
-        cancellable: true,
-      },
-    ),
-  );
-
-  const mockServer = new VSCodeMockGitHubApiServer(ctx);
-  ctx.subscriptions.push(mockServer);
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.mockGitHubApiServer.startRecording",
-      async () => await mockServer.startRecording(),
-    ),
-  );
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.mockGitHubApiServer.saveScenario",
-      async () => await mockServer.saveScenario(),
-    ),
-  );
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.mockGitHubApiServer.cancelRecording",
-      async () => await mockServer.cancelRecording(),
-    ),
-  );
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.mockGitHubApiServer.loadScenario",
-      async () => await mockServer.loadScenario(),
-    ),
-  );
-  ctx.subscriptions.push(
-    commandRunner(
-      "codeQL.mockGitHubApiServer.unloadScenario",
-      async () => await mockServer.unloadScenario(),
-    ),
-  );
-
-  await commands.executeCommand("codeQLDatabases.removeOrphanedDatabases");
+  await app.commands.execute("codeQLDatabases.removeOrphanedDatabases");
 
   void extLogger.log("Reading query history");
   await qhm.readQueryHistory();
@@ -1700,6 +992,22 @@ async function activateWithInstalledDistribution(
   };
 }
 
+async function showResultsForComparison(
+  compareView: CompareView,
+  from: CompletedLocalQueryInfo,
+  to: CompletedLocalQueryInfo,
+): Promise<void> {
+  try {
+    await compareView.showResults(from, to);
+  } catch (e) {
+    void showAndLogExceptionWithTelemetry(
+      redactableError(asError(e))`Failed to show results: ${getErrorMessage(
+        e,
+      )}`,
+    );
+  }
+}
+
 function addUnhandledRejectionListener() {
   const handler = (error: unknown) => {
     // This listener will be triggered for errors from other extensions as
@@ -1734,7 +1042,8 @@ function addUnhandledRejectionListener() {
   // "uncaughtException" will trigger whenever an exception reaches the top level.
   // This covers extension initialization and any code within a `setTimeout`.
   // Notably this does not include exceptions thrown when executing commands,
-  // because `commandRunner` wraps the command body and handles errors.
+  // because `registerCommandWithErrorHandling` wraps the command body and
+  // handles errors.
   process.addListener("uncaughtException", handler);
 
   // "unhandledRejection" will trigger whenever any promise is rejected and it is
@@ -1744,6 +1053,7 @@ function addUnhandledRejectionListener() {
 }
 
 async function createQueryServer(
+  app: ExtensionApp,
   qlConfigurationListener: QueryServerConfigListener,
   cliServer: CodeQLCliServer,
   ctx: ExtensionContext,
@@ -1774,6 +1084,7 @@ async function createQueryServer(
     return new NewQueryRunner(qs);
   } else {
     const qs = new LegacyQueryServerClient(
+      app,
       qlConfigurationListener,
       cliServer,
       qsOpts,
@@ -1795,7 +1106,8 @@ async function initializeLogging(ctx: ExtensionContext): Promise<void> {
   ctx.subscriptions.push(ideServerLogger);
 }
 
-const checkForUpdatesCommand = "codeQL.checkForUpdatesToCLI";
+const checkForUpdatesCommand: keyof PreActivationCommands =
+  "codeQL.checkForUpdatesToCLI" as const;
 
 const avoidVersionCheck = "avoid-version-check-at-startup";
 const lastVersionChecked = "last-version-checked";
diff --git a/extensions/ql-vscode/src/helpers.ts b/extensions/ql-vscode/src/helpers.ts
index d3245a287..2576f6b48 100644
--- a/extensions/ql-vscode/src/helpers.ts
+++ b/extensions/ql-vscode/src/helpers.ts
@@ -18,13 +18,15 @@ import {
   env,
 } from "vscode";
 import { CodeQLCliServer, QlpacksInfo } from "./cli";
-import { UserCancellationException } from "./commandRunner";
+import { UserCancellationException } from "./progress";
 import { extLogger, OutputChannelLogger } from "./common";
 import { QueryMetadata } from "./pure/interface-types";
 import { telemetryListener } from "./telemetry";
 import { RedactableError } from "./pure/errors";
 import { getQlPackPath } from "./pure/ql";
 import { dbSchemeToLanguage } from "./common/query-language";
+import { isCodespacesTemplate } from "./config";
+import { AppCommandManager } from "./common/commands";
 
 // Shared temporary folder for the extension.
 export const tmpDir = dirSync({
@@ -266,6 +268,53 @@ export function isFolderAlreadyInWorkspace(folderName: string) {
   );
 }
 
+/** Check if the current workspace is the CodeTour and open the workspace folder.
+ * Without this, we can't run the code tour correctly.
+ **/
+export async function prepareCodeTour(
+  commandManager: AppCommandManager,
+): Promise<void> {
+  if (workspace.workspaceFolders?.length) {
+    const currentFolder = workspace.workspaceFolders[0].uri.fsPath;
+
+    const tutorialWorkspacePath = join(
+      currentFolder,
+      "tutorial.code-workspace",
+    );
+    const toursFolderPath = join(currentFolder, ".tours");
+
+    /** We're opening the tutorial workspace, if we detect it.
+     * This will only happen if the following three conditions are met:
+     * - the .tours folder exists
+     * - the tutorial.code-workspace file exists
+     * - the CODESPACES_TEMPLATE setting doesn't exist (it's only set if the user has already opened
+     * the tutorial workspace so it's a good indicator that the user is in the folder but has ignored
+     * the prompt to open the workspace)
+     */
+    if (
+      (await pathExists(tutorialWorkspacePath)) &&
+      (await pathExists(toursFolderPath)) &&
+      !isCodespacesTemplate()
+    ) {
+      const answer = await showBinaryChoiceDialog(
+        "We've detected you're in the CodeQL Tour repo. We will need to open the workspace file to continue. Reload?",
+      );
+
+      if (!answer) {
+        return;
+      }
+
+      const tutorialWorkspaceUri = Uri.parse(tutorialWorkspacePath);
+
+      void extLogger.log(
+        `In prepareCodeTour() method, going to open the tutorial workspace file: ${tutorialWorkspacePath}`,
+      );
+
+      await commandManager.execute("vscode.openFolder", tutorialWorkspaceUri);
+    }
+  }
+}
+
 /**
  * Provides a utility method to invoke a function only if a minimum time interval has elapsed since
  * the last invocation of that function.
diff --git a/extensions/ql-vscode/src/interface-utils.ts b/extensions/ql-vscode/src/interface-utils.ts
index da01c3135..68232dacd 100644
--- a/extensions/ql-vscode/src/interface-utils.ts
+++ b/extensions/ql-vscode/src/interface-utils.ts
@@ -109,7 +109,11 @@ export function tryResolveLocation(
   }
 }
 
-export type WebviewView = "results" | "compare" | "variant-analysis";
+export type WebviewView =
+  | "results"
+  | "compare"
+  | "variant-analysis"
+  | "data-flow-paths";
 
 export interface WebviewMessage {
   t: string;
diff --git a/extensions/ql-vscode/src/interface.ts b/extensions/ql-vscode/src/interface.ts
index 17655fa7c..a7d7dcff1 100644
--- a/extensions/ql-vscode/src/interface.ts
+++ b/extensions/ql-vscode/src/interface.ts
@@ -42,7 +42,6 @@ import {
   ParsedResultSets,
 } from "./pure/interface-types";
 import { Logger } from "./common";
-import { commandRunner } from "./commandRunner";
 import {
   CompletedQueryInfo,
   interpretResultsSarif,
@@ -72,6 +71,7 @@ import { isCanary, PAGE_SIZE } from "./config";
 import { HistoryItemLabelProvider } from "./query-history/history-item-label-provider";
 import { telemetryListener } from "./telemetry";
 import { redactableError } from "./pure/errors";
+import { ResultsViewCommands } from "./common/commands";
 
 /**
  * interface.ts
@@ -179,21 +179,6 @@ export class ResultsView extends AbstractWebview<
         this.handleSelectionChange.bind(this),
       ),
     );
-    const navigationCommands = {
-      "codeQLQueryResults.up": NavigationDirection.up,
-      "codeQLQueryResults.down": NavigationDirection.down,
-      "codeQLQueryResults.left": NavigationDirection.left,
-      "codeQLQueryResults.right": NavigationDirection.right,
-      // For backwards compatibility with keybindings set using an earlier version of the extension.
-      "codeQLQueryResults.nextPathStep": NavigationDirection.down,
-      "codeQLQueryResults.previousPathStep": NavigationDirection.up,
-    };
-    void logger.log("Registering result view navigation commands.");
-    for (const [commandId, direction] of Object.entries(navigationCommands)) {
-      this.push(
-        commandRunner(commandId, this.navigateResultView.bind(this, direction)),
-      );
-    }
 
     this.push(
       this.databaseManager.onDidChangeDatabaseItem(({ kind }) => {
@@ -209,6 +194,36 @@ export class ResultsView extends AbstractWebview<
     );
   }
 
+  public getCommands(): ResultsViewCommands {
+    return {
+      "codeQLQueryResults.up": this.navigateResultView.bind(
+        this,
+        NavigationDirection.up,
+      ),
+      "codeQLQueryResults.down": this.navigateResultView.bind(
+        this,
+        NavigationDirection.down,
+      ),
+      "codeQLQueryResults.left": this.navigateResultView.bind(
+        this,
+        NavigationDirection.left,
+      ),
+      "codeQLQueryResults.right": this.navigateResultView.bind(
+        this,
+        NavigationDirection.right,
+      ),
+      // For backwards compatibility with keybindings set using an earlier version of the extension.
+      "codeQLQueryResults.nextPathStep": this.navigateResultView.bind(
+        this,
+        NavigationDirection.down,
+      ),
+      "codeQLQueryResults.previousPathStep": this.navigateResultView.bind(
+        this,
+        NavigationDirection.up,
+      ),
+    };
+  }
+
   async navigateResultView(direction: NavigationDirection): Promise<void> {
     if (!this.panel?.visible) {
       return;
@@ -295,6 +310,13 @@ export class ResultsView extends AbstractWebview<
         case "telemetry":
           telemetryListener?.sendUIInteraction(msg.action);
           break;
+        case "unhandledError":
+          void showAndLogExceptionWithTelemetry(
+            redactableError(
+              msg.error,
+            )`Unhandled error in results view: ${msg.error.message}`,
+          );
+          break;
         default:
           assertNever(msg);
       }
diff --git a/extensions/ql-vscode/src/legacy-query-server/legacyRunner.ts b/extensions/ql-vscode/src/legacy-query-server/legacyRunner.ts
index 44eba17d9..f12434822 100644
--- a/extensions/ql-vscode/src/legacy-query-server/legacyRunner.ts
+++ b/extensions/ql-vscode/src/legacy-query-server/legacyRunner.ts
@@ -1,5 +1,5 @@
 import { CancellationToken } from "vscode";
-import { ProgressCallback } from "../commandRunner";
+import { ProgressCallback } from "../progress";
 import { DatabaseItem } from "../local-databases";
 import {
   Dataset,
diff --git a/extensions/ql-vscode/src/legacy-query-server/queryserver-client.ts b/extensions/ql-vscode/src/legacy-query-server/queryserver-client.ts
index 36146da31..50c0278db 100644
--- a/extensions/ql-vscode/src/legacy-query-server/queryserver-client.ts
+++ b/extensions/ql-vscode/src/legacy-query-server/queryserver-client.ts
@@ -1,8 +1,7 @@
-import { dirname } from "path";
 import { ensureFile } from "fs-extra";
 
 import { DisposableObject } from "../pure/disposable-object";
-import { CancellationToken, commands } from "vscode";
+import { CancellationToken } from "vscode";
 import { createMessageConnection, RequestType } from "vscode-jsonrpc/node";
 import * as cli from "../cli";
 import { QueryServerConfig } from "../config";
@@ -13,11 +12,10 @@ import {
   progress,
   ProgressMessage,
   WithProgressId,
-  compileQuery,
 } from "../pure/legacy-messages";
-import { ProgressCallback, ProgressTask } from "../commandRunner";
-import { findQueryLogFile } from "../run-queries-shared";
+import { ProgressCallback, ProgressTask } from "../progress";
 import { ServerProcess } from "../json-rpc-server";
+import { App } from "../common/app";
 
 type WithProgressReporting = (
   task: (
@@ -56,20 +54,24 @@ export class QueryServerClient extends DisposableObject {
     this.queryServerStartListeners.push(e);
   };
 
-  public activeQueryLogFile: string | undefined;
+  public activeQueryLogger: Logger;
 
   constructor(
+    app: App,
     readonly config: QueryServerConfig,
     readonly cliServer: cli.CodeQLCliServer,
     readonly opts: ServerOpts,
     withProgressReporting: WithProgressReporting,
   ) {
     super();
+    // Since no query is active when we initialize, just point the "active query logger" to the
+    // default logger.
+    this.activeQueryLogger = this.logger;
     // When the query server configuration changes, restart the query server.
     if (config.onDidChangeConfiguration !== undefined) {
       this.push(
         config.onDidChangeConfiguration(() =>
-          commands.executeCommand("codeQL.restartQueryServer"),
+          app.commands.execute("codeQL.restartQueryServer"),
         ),
       );
     }
@@ -177,9 +179,8 @@ export class QueryServerClient extends DisposableObject {
       args,
       this.logger,
       (data) =>
-        this.logger.log(data.toString(), {
+        this.activeQueryLogger.log(data.toString(), {
           trailingNewline: false,
-          additionalLogLocation: this.activeQueryLogFile,
         }),
       undefined, // no listener for stdout
       progressReporter,
@@ -240,8 +241,6 @@ export class QueryServerClient extends DisposableObject {
   ): Promise<R> {
     const id = this.nextProgress++;
     this.progressCallbacks[id] = progress;
-
-    this.updateActiveQuery(type.method, parameter);
     try {
       if (this.serverProcess === undefined) {
         throw new Error("No query server process found.");
@@ -255,18 +254,4 @@ export class QueryServerClient extends DisposableObject {
       delete this.progressCallbacks[id];
     }
   }
-
-  /**
-   * Updates the active query every time there is a new request to compile.
-   * The active query is used to specify the side log.
-   *
-   * 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.
-   */
-  private updateActiveQuery(method: string, parameter: any): void {
-    if (method === compileQuery.method) {
-      this.activeQueryLogFile = findQueryLogFile(dirname(parameter.resultPath));
-    }
-  }
 }
diff --git a/extensions/ql-vscode/src/legacy-query-server/run-queries.ts b/extensions/ql-vscode/src/legacy-query-server/run-queries.ts
index 0326d5c24..e2f3fb5f5 100644
--- a/extensions/ql-vscode/src/legacy-query-server/run-queries.ts
+++ b/extensions/ql-vscode/src/legacy-query-server/run-queries.ts
@@ -13,9 +13,9 @@ import {
   tryGetQueryMetadata,
   upgradesTmpDir,
 } from "../helpers";
-import { ProgressCallback } from "../commandRunner";
+import { ProgressCallback } from "../progress";
 import { QueryMetadata } from "../pure/interface-types";
-import { extLogger } from "../common";
+import { extLogger, Logger, TeeLogger } from "../common";
 import * as messages from "../pure/legacy-messages";
 import { InitialQueryInfo, LocalQueryInfo } from "../query-results";
 import * as qsClient from "./queryserver-client";
@@ -66,7 +66,8 @@ export class QueryInProgress {
     dbItem: DatabaseItem,
     progress: ProgressCallback,
     token: CancellationToken,
-    queryInfo?: LocalQueryInfo,
+    logger: Logger,
+    queryInfo: LocalQueryInfo | undefined,
   ): Promise<messages.EvaluationResult> {
     if (!dbItem.contents || dbItem.error) {
       throw new Error("Can't run query on invalid database.");
@@ -137,7 +138,7 @@ export class QueryInProgress {
           await this.queryEvalInfo.addQueryLogs(
             queryInfo,
             qs.cliServer,
-            qs.logger,
+            logger,
           );
         } else {
           void showAndLogWarningMessage(
@@ -162,6 +163,7 @@ export class QueryInProgress {
     program: messages.QlProgram,
     progress: ProgressCallback,
     token: CancellationToken,
+    logger: Logger,
   ): Promise<messages.CompilationMessage[]> {
     let compiled: messages.CheckQueryResult | undefined;
     try {
@@ -190,6 +192,11 @@ export class QueryInProgress {
         target,
       };
 
+      // 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;
       compiled = await qs.sendRequest(
         messages.compileQuery,
         params,
@@ -197,9 +204,7 @@ export class QueryInProgress {
         progress,
       );
     } finally {
-      void qs.logger.log(" - - - COMPILATION DONE - - - ", {
-        additionalLogLocation: this.queryEvalInfo.logPath,
-      });
+      void logger.log(" - - - COMPILATION DONE - - - ");
     }
     return (compiled?.messages || []).filter(
       (msg) => msg.severity === messages.Severity.ERROR,
@@ -386,6 +391,8 @@ export async function compileAndRunQueryAgainstDatabase(
     metadata,
     templates,
   );
+  const logger = new TeeLogger(qs.logger, query.queryEvalInfo.logPath);
+
   await query.queryEvalInfo.createTimestampFile();
 
   let upgradeDir: tmp.DirectoryResult | undefined;
@@ -402,7 +409,7 @@ export async function compileAndRunQueryAgainstDatabase(
     );
     let errors;
     try {
-      errors = await query.compile(qs, qlProgram, progress, token);
+      errors = await query.compile(qs, qlProgram, progress, token, logger);
     } catch (e) {
       if (
         e instanceof ResponseError &&
@@ -422,6 +429,7 @@ export async function compileAndRunQueryAgainstDatabase(
         dbItem,
         progress,
         token,
+        logger,
         queryInfo,
       );
       if (result.resultType !== messages.QueryResultType.SUCCESS) {
@@ -439,18 +447,14 @@ export async function compileAndRunQueryAgainstDatabase(
         result,
         successful: result.resultType === messages.QueryResultType.SUCCESS,
         logFileLocation: result.logFileLocation,
-        dispose: () => {
-          qs.logger.removeAdditionalLogLocation(result.logFileLocation);
-        },
       };
     } else {
       // Error dialogs are limited in size and scrollability,
       // so we include a general description of the problem,
       // and direct the user to the output window for the detailed compilation messages.
       // However we don't show quick eval errors there so we need to display them anyway.
-      void qs.logger.log(
+      void logger.log(
         `Failed to compile query ${initialInfo.queryPath} against database scheme ${qlProgram.dbschemePath}:`,
-        { additionalLogLocation: query.queryEvalInfo.logPath },
       );
 
       const formattedMessages: string[] = [];
@@ -459,9 +463,7 @@ export async function compileAndRunQueryAgainstDatabase(
         const message = error.message || "[no error message available]";
         const formatted = `ERROR: ${message} (${error.position.fileName}:${error.position.line}:${error.position.column}:${error.position.endLine}:${error.position.endColumn})`;
         formattedMessages.push(formatted);
-        void qs.logger.log(formatted, {
-          additionalLogLocation: query.queryEvalInfo.logPath,
-        });
+        void logger.log(formatted);
       }
       if (initialInfo.isQuickEval && formattedMessages.length <= 2) {
         // If there are more than 2 error messages, they will not be displayed well in a popup
@@ -484,9 +486,8 @@ export async function compileAndRunQueryAgainstDatabase(
     try {
       await upgradeDir?.cleanup();
     } catch (e) {
-      void qs.logger.log(
+      void logger.log(
         `Could not clean up the upgrades dir. Reason: ${getErrorMessage(e)}`,
-        { additionalLogLocation: query.queryEvalInfo.logPath },
       );
     }
   }
@@ -535,9 +536,6 @@ function createSyntheticResult(
       runId: 0,
     },
     successful: false,
-    dispose: () => {
-      /**/
-    },
   };
 }
 
diff --git a/extensions/ql-vscode/src/legacy-query-server/upgrades.ts b/extensions/ql-vscode/src/legacy-query-server/upgrades.ts
index 0ec182766..6b70bf58b 100644
--- a/extensions/ql-vscode/src/legacy-query-server/upgrades.ts
+++ b/extensions/ql-vscode/src/legacy-query-server/upgrades.ts
@@ -4,7 +4,7 @@ import {
   showAndLogExceptionWithTelemetry,
   tmpDir,
 } from "../helpers";
-import { ProgressCallback, UserCancellationException } from "../commandRunner";
+import { ProgressCallback, UserCancellationException } from "../progress";
 import { extLogger } from "../common";
 import * as messages from "../pure/legacy-messages";
 import * as qsClient from "./queryserver-client";
diff --git a/extensions/ql-vscode/src/local-databases-ui.ts b/extensions/ql-vscode/src/local-databases-ui.ts
index 5d6d8fcc0..f1d88edb6 100644
--- a/extensions/ql-vscode/src/local-databases-ui.ts
+++ b/extensions/ql-vscode/src/local-databases-ui.ts
@@ -21,11 +21,7 @@ import {
   DatabaseItem,
   DatabaseManager,
 } from "./local-databases";
-import {
-  commandRunner,
-  commandRunnerWithProgress,
-  ProgressCallback,
-} from "./commandRunner";
+import { ProgressCallback, withProgress } from "./progress";
 import {
   isLikelyDatabaseRoot,
   isLikelyDbLanguageFolder,
@@ -42,8 +38,8 @@ import { asError, asyncFilter, getErrorMessage } from "./pure/helpers-pure";
 import { QueryRunner } from "./queryRunner";
 import { isCanary } from "./config";
 import { App } from "./common/app";
-import { Credentials } from "./common/authentication";
 import { redactableError } from "./pure/errors";
+import { LocalDatabasesCommands } from "./common/commands";
 
 enum SortOrder {
   NameAsc = "NameAsc",
@@ -73,12 +69,12 @@ class DatabaseTreeDataProvider
 
     this.push(
       this.databaseManager.onDidChangeDatabaseItem(
-        this.handleDidChangeDatabaseItem,
+        this.handleDidChangeDatabaseItem.bind(this),
       ),
     );
     this.push(
       this.databaseManager.onDidChangeCurrentDatabaseItem(
-        this.handleDidChangeCurrentDatabaseItem,
+        this.handleDidChangeCurrentDatabaseItem.bind(this),
       ),
     );
   }
@@ -87,18 +83,18 @@ class DatabaseTreeDataProvider
     return this._onDidChangeTreeData.event;
   }
 
-  private handleDidChangeDatabaseItem = (event: DatabaseChangedEvent): void => {
+  private handleDidChangeDatabaseItem(event: DatabaseChangedEvent): void {
     // Note that events from the database manager are instances of DatabaseChangedEvent
     // and events fired by the UI are instances of DatabaseItem
 
     // When event.item is undefined, then the entire tree is refreshed.
     // When event.item is a db item, then only that item is refreshed.
     this._onDidChangeTreeData.fire(event.item);
-  };
+  }
 
-  private handleDidChangeCurrentDatabaseItem = (
+  private handleDidChangeCurrentDatabaseItem(
     event: DatabaseChangedEvent,
-  ): void => {
+  ): void {
     if (this.currentDatabaseItem) {
       this._onDidChangeTreeData.fire(this.currentDatabaseItem);
     }
@@ -106,7 +102,7 @@ class DatabaseTreeDataProvider
     if (this.currentDatabaseItem) {
       this._onDidChangeTreeData.fire(this.currentDatabaseItem);
     }
-  };
+  }
 
   public getTreeItem(element: DatabaseItem): TreeItem {
     const item = new TreeItem(element.name);
@@ -210,149 +206,53 @@ export class DatabaseUI extends DisposableObject {
     );
   }
 
-  init() {
-    void extLogger.log("Registering database panel commands.");
-    this.push(
-      commandRunnerWithProgress(
-        "codeQL.setCurrentDatabase",
-        this.handleSetCurrentDatabase,
-        {
-          title: "Importing database from archive",
-        },
-      ),
-    );
-    this.push(
-      commandRunnerWithProgress(
-        "codeQL.setDefaultTourDatabase",
-        this.handleSetDefaultTourDatabase,
-        {
-          title: "Set Default Database for Codespace CodeQL Tour",
-        },
-      ),
-    );
-    this.push(
-      commandRunnerWithProgress(
-        "codeQL.upgradeCurrentDatabase",
-        this.handleUpgradeCurrentDatabase,
-        {
-          title: "Upgrading current database",
-          cancellable: true,
-        },
-      ),
-    );
-    this.push(
-      commandRunnerWithProgress("codeQL.clearCache", this.handleClearCache, {
-        title: "Clearing Cache",
-      }),
-    );
-
-    this.push(
-      commandRunnerWithProgress(
-        "codeQLDatabases.chooseDatabaseFolder",
-        this.handleChooseDatabaseFolder,
-        {
-          title: "Adding database from folder",
-        },
-      ),
-    );
-    this.push(
-      commandRunnerWithProgress(
-        "codeQLDatabases.chooseDatabaseArchive",
-        this.handleChooseDatabaseArchive,
-        {
-          title: "Adding database from archive",
-        },
-      ),
-    );
-    this.push(
-      commandRunnerWithProgress(
-        "codeQLDatabases.chooseDatabaseInternet",
-        this.handleChooseDatabaseInternet,
-        {
-          title: "Adding database from URL",
-        },
-      ),
-    );
-    this.push(
-      commandRunnerWithProgress(
-        "codeQLDatabases.chooseDatabaseGithub",
-        async (progress: ProgressCallback, token: CancellationToken) => {
-          const credentials = isCanary() ? this.app.credentials : undefined;
-          await this.handleChooseDatabaseGithub(credentials, progress, token);
-        },
-        {
-          title: "Adding database from GitHub",
-        },
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLDatabases.setCurrentDatabase",
-        this.handleMakeCurrentDatabase,
-      ),
-    );
-    this.push(
-      commandRunner("codeQLDatabases.sortByName", this.handleSortByName),
-    );
-    this.push(
-      commandRunner(
-        "codeQLDatabases.sortByDateAdded",
-        this.handleSortByDateAdded,
-      ),
-    );
-    this.push(
-      commandRunnerWithProgress(
-        "codeQLDatabases.removeDatabase",
-        this.handleRemoveDatabase,
-        {
-          title: "Removing database",
-          cancellable: false,
-        },
-      ),
-    );
-    this.push(
-      commandRunnerWithProgress(
-        "codeQLDatabases.upgradeDatabase",
-        this.handleUpgradeDatabase,
-        {
-          title: "Upgrading database",
-          cancellable: true,
-        },
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLDatabases.renameDatabase",
-        this.handleRenameDatabase,
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLDatabases.openDatabaseFolder",
-        this.handleOpenFolder,
-      ),
-    );
-    this.push(
-      commandRunner("codeQLDatabases.addDatabaseSource", this.handleAddSource),
-    );
-    this.push(
-      commandRunner(
-        "codeQLDatabases.removeOrphanedDatabases",
-        this.handleRemoveOrphanedDatabases,
-      ),
-    );
+  public getCommands(): LocalDatabasesCommands {
+    return {
+      "codeQL.chooseDatabaseFolder":
+        this.handleChooseDatabaseFolderFromPalette.bind(this),
+      "codeQL.chooseDatabaseArchive":
+        this.handleChooseDatabaseArchiveFromPalette.bind(this),
+      "codeQL.chooseDatabaseInternet":
+        this.handleChooseDatabaseInternet.bind(this),
+      "codeQL.chooseDatabaseGithub": this.handleChooseDatabaseGithub.bind(this),
+      "codeQL.setCurrentDatabase": this.handleSetCurrentDatabase.bind(this),
+      "codeQL.setDefaultTourDatabase":
+        this.handleSetDefaultTourDatabase.bind(this),
+      "codeQL.upgradeCurrentDatabase":
+        this.handleUpgradeCurrentDatabase.bind(this),
+      "codeQL.clearCache": this.handleClearCache.bind(this),
+      "codeQLDatabases.chooseDatabaseFolder":
+        this.handleChooseDatabaseFolder.bind(this),
+      "codeQLDatabases.chooseDatabaseArchive":
+        this.handleChooseDatabaseArchive.bind(this),
+      "codeQLDatabases.chooseDatabaseInternet":
+        this.handleChooseDatabaseInternet.bind(this),
+      "codeQLDatabases.chooseDatabaseGithub":
+        this.handleChooseDatabaseGithub.bind(this),
+      "codeQLDatabases.setCurrentDatabase":
+        this.handleMakeCurrentDatabase.bind(this),
+      "codeQLDatabases.sortByName": this.handleSortByName.bind(this),
+      "codeQLDatabases.sortByDateAdded": this.handleSortByDateAdded.bind(this),
+      "codeQLDatabases.removeDatabase": this.handleRemoveDatabase.bind(this),
+      "codeQLDatabases.upgradeDatabase": this.handleUpgradeDatabase.bind(this),
+      "codeQLDatabases.renameDatabase": this.handleRenameDatabase.bind(this),
+      "codeQLDatabases.openDatabaseFolder": this.handleOpenFolder.bind(this),
+      "codeQLDatabases.addDatabaseSource": this.handleAddSource.bind(this),
+      "codeQLDatabases.removeOrphanedDatabases":
+        this.handleRemoveOrphanedDatabases.bind(this),
+    };
   }
 
-  private handleMakeCurrentDatabase = async (
+  private async handleMakeCurrentDatabase(
     databaseItem: DatabaseItem,
-  ): Promise<void> => {
+  ): Promise<void> {
     await this.databaseManager.setCurrentDatabaseItem(databaseItem);
-  };
+  }
 
-  handleChooseDatabaseFolder = async (
+  private async chooseDatabaseFolder(
     progress: ProgressCallback,
     token: CancellationToken,
-  ): Promise<void> => {
+  ): Promise<void> {
     try {
       await this.chooseAndSetDatabase(true, progress, token);
     } catch (e) {
@@ -362,47 +262,73 @@ export class DatabaseUI extends DisposableObject {
         )`Failed to choose and set database: ${getErrorMessage(e)}`,
       );
     }
-  };
+  }
 
-  private handleSetDefaultTourDatabase = async (
-    progress: ProgressCallback,
-    token: CancellationToken,
-  ): Promise<void> => {
-    try {
-      if (!workspace.workspaceFolders?.length) {
-        throw new Error("No workspace folder is open.");
-      } else {
-        // This specifically refers to the database folder in
-        // https://github.com/github/codespaces-codeql
-        const uri = Uri.parse(
-          `${workspace.workspaceFolders[0].uri}/.tours/codeql-tutorial-database`,
-        );
+  private async handleChooseDatabaseFolder(): Promise<void> {
+    return withProgress(
+      async (progress, token) => {
+        await this.chooseDatabaseFolder(progress, token);
+      },
+      {
+        title: "Adding database from folder",
+      },
+    );
+  }
 
-        let databaseItem = this.databaseManager.findDatabaseItem(uri);
-        const isTutorialDatabase = true;
-        if (databaseItem === undefined) {
-          databaseItem = await this.databaseManager.openDatabase(
-            progress,
-            token,
-            uri,
-            "CodeQL Tutorial Database",
-            isTutorialDatabase,
+  private async handleChooseDatabaseFolderFromPalette(): Promise<void> {
+    return withProgress(
+      async (progress, token) => {
+        await this.chooseDatabaseFolder(progress, token);
+      },
+      {
+        title: "Choose a Database from a Folder",
+      },
+    );
+  }
+
+  private async handleSetDefaultTourDatabase(): Promise<void> {
+    return withProgress(
+      async (progress, token) => {
+        try {
+          if (!workspace.workspaceFolders?.length) {
+            throw new Error("No workspace folder is open.");
+          } else {
+            // This specifically refers to the database folder in
+            // https://github.com/github/codespaces-codeql
+            const uri = Uri.parse(
+              `${workspace.workspaceFolders[0].uri}/.tours/codeql-tutorial-database`,
+            );
+
+            let databaseItem = this.databaseManager.findDatabaseItem(uri);
+            const isTutorialDatabase = true;
+            if (databaseItem === undefined) {
+              databaseItem = await this.databaseManager.openDatabase(
+                progress,
+                token,
+                uri,
+                "CodeQL Tutorial Database",
+                isTutorialDatabase,
+              );
+            }
+            await this.databaseManager.setCurrentDatabaseItem(databaseItem);
+            await this.handleTourDependencies();
+          }
+        } catch (e) {
+          // rethrow and let this be handled by default error handling.
+          throw new Error(
+            `Could not set the database for the Code Tour. Please make sure you are using the default workspace in your codespace: ${getErrorMessage(
+              e,
+            )}`,
           );
         }
-        await this.databaseManager.setCurrentDatabaseItem(databaseItem);
-        await this.handleTourDependencies();
-      }
-    } catch (e) {
-      // rethrow and let this be handled by default error handling.
-      throw new Error(
-        `Could not set the database for the Code Tour. Please make sure you are using the default workspace in your codespace: ${getErrorMessage(
-          e,
-        )}`,
-      );
-    }
-  };
+      },
+      {
+        title: "Set Default Database for Codespace CodeQL Tour",
+      },
+    );
+  }
 
-  private handleTourDependencies = async (): Promise<void> => {
+  private async handleTourDependencies(): Promise<void> {
     if (!workspace.workspaceFolders?.length) {
       throw new Error("No workspace folder is open.");
     } else {
@@ -416,9 +342,10 @@ export class DatabaseUI extends DisposableObject {
       }
       await cli.packInstall(tutorialQueriesPath);
     }
-  };
+  }
 
-  handleRemoveOrphanedDatabases = async (): Promise<void> => {
+  // Public because it's used in tests
+  public async handleRemoveOrphanedDatabases(): Promise<void> {
     void extLogger.log("Removing orphaned databases from workspace storage.");
     let dbDirs = undefined;
 
@@ -481,12 +408,12 @@ export class DatabaseUI extends DisposableObject {
         )}).\nTo delete unused databases, please remove them manually from the storage folder ${dirname}.`,
       );
     }
-  };
+  }
 
-  handleChooseDatabaseArchive = async (
+  private async chooseDatabaseArchive(
     progress: ProgressCallback,
     token: CancellationToken,
-  ): Promise<void> => {
+  ): Promise<void> {
     try {
       await this.chooseAndSetDatabase(false, progress, token);
     } catch (e: unknown) {
@@ -496,81 +423,132 @@ export class DatabaseUI extends DisposableObject {
         )`Failed to choose and set database: ${getErrorMessage(e)}`,
       );
     }
-  };
-
-  handleChooseDatabaseInternet = async (
-    progress: ProgressCallback,
-    token: CancellationToken,
-  ): Promise<DatabaseItem | undefined> => {
-    return await promptImportInternetDatabase(
-      this.databaseManager,
-      this.storagePath,
-      progress,
-      token,
-      this.queryServer?.cliServer,
-    );
-  };
-
-  handleChooseDatabaseGithub = async (
-    credentials: Credentials | undefined,
-    progress: ProgressCallback,
-    token: CancellationToken,
-  ): Promise<DatabaseItem | undefined> => {
-    return await promptImportGithubDatabase(
-      this.databaseManager,
-      this.storagePath,
-      credentials,
-      progress,
-      token,
-      this.queryServer?.cliServer,
-    );
-  };
-
-  async tryUpgradeCurrentDatabase(
-    progress: ProgressCallback,
-    token: CancellationToken,
-  ) {
-    await this.handleUpgradeCurrentDatabase(progress, token);
   }
 
-  private handleSortByName = async () => {
+  private async handleChooseDatabaseArchive(): Promise<void> {
+    return withProgress(
+      async (progress, token) => {
+        await this.chooseDatabaseArchive(progress, token);
+      },
+      {
+        title: "Adding database from archive",
+      },
+    );
+  }
+
+  private async handleChooseDatabaseArchiveFromPalette(): Promise<void> {
+    return withProgress(
+      async (progress, token) => {
+        await this.chooseDatabaseArchive(progress, token);
+      },
+      {
+        title: "Choose a Database from an Archive",
+      },
+    );
+  }
+
+  private async handleChooseDatabaseInternet(): Promise<void> {
+    return withProgress(
+      async (progress, token) => {
+        await promptImportInternetDatabase(
+          this.app.commands,
+          this.databaseManager,
+          this.storagePath,
+          progress,
+          token,
+          this.queryServer?.cliServer,
+        );
+      },
+      {
+        title: "Adding database from URL",
+      },
+    );
+  }
+
+  private async handleChooseDatabaseGithub(): Promise<void> {
+    return withProgress(
+      async (progress, token) => {
+        const credentials = isCanary() ? this.app.credentials : undefined;
+
+        await promptImportGithubDatabase(
+          this.app.commands,
+          this.databaseManager,
+          this.storagePath,
+          credentials,
+          progress,
+          token,
+          this.queryServer?.cliServer,
+        );
+      },
+      {
+        title: "Adding database from GitHub",
+      },
+    );
+  }
+
+  private async handleSortByName() {
     if (this.treeDataProvider.sortOrder === SortOrder.NameAsc) {
       this.treeDataProvider.sortOrder = SortOrder.NameDesc;
     } else {
       this.treeDataProvider.sortOrder = SortOrder.NameAsc;
     }
-  };
+  }
 
-  private handleSortByDateAdded = async () => {
+  private async handleSortByDateAdded() {
     if (this.treeDataProvider.sortOrder === SortOrder.DateAddedAsc) {
       this.treeDataProvider.sortOrder = SortOrder.DateAddedDesc;
     } else {
       this.treeDataProvider.sortOrder = SortOrder.DateAddedAsc;
     }
-  };
+  }
 
-  private handleUpgradeCurrentDatabase = async (
-    progress: ProgressCallback,
-    token: CancellationToken,
-  ): Promise<void> => {
-    await this.handleUpgradeDatabase(
-      progress,
-      token,
-      this.databaseManager.currentDatabaseItem,
-      [],
+  private async handleUpgradeCurrentDatabase(): Promise<void> {
+    return withProgress(
+      async (progress, token) => {
+        await this.handleUpgradeDatabaseInternal(
+          progress,
+          token,
+          this.databaseManager.currentDatabaseItem,
+          [],
+        );
+      },
+      {
+        title: "Upgrading current database",
+        cancellable: true,
+      },
     );
-  };
+  }
 
-  private handleUpgradeDatabase = async (
+  private async handleUpgradeDatabase(
+    databaseItem: DatabaseItem | undefined,
+    multiSelect: DatabaseItem[] | undefined,
+  ): Promise<void> {
+    return withProgress(
+      async (progress, token) => {
+        return await this.handleUpgradeDatabaseInternal(
+          progress,
+          token,
+          databaseItem,
+          multiSelect,
+        );
+      },
+      {
+        title: "Upgrading database",
+        cancellable: true,
+      },
+    );
+  }
+
+  private async handleUpgradeDatabaseInternal(
     progress: ProgressCallback,
     token: CancellationToken,
     databaseItem: DatabaseItem | undefined,
     multiSelect: DatabaseItem[] | undefined,
-  ): Promise<void> => {
+  ): Promise<void> {
     if (multiSelect?.length) {
       await Promise.all(
         multiSelect.map((dbItem) =>
-          this.handleUpgradeDatabase(progress, token, dbItem, []),
+          this.handleUpgradeDatabaseInternal(progress, token, dbItem, []),
         ),
       );
     }
@@ -602,78 +580,92 @@ export class DatabaseUI extends DisposableObject {
       progress,
       token,
     );
-  };
+  }
 
-  private handleClearCache = async (
-    progress: ProgressCallback,
-    token: CancellationToken,
-  ): Promise<void> => {
-    if (
-      this.queryServer !== undefined &&
-      this.databaseManager.currentDatabaseItem !== undefined
-    ) {
-      await this.queryServer.clearCacheInDatabase(
-        this.databaseManager.currentDatabaseItem,
-        progress,
-        token,
-      );
-    }
-  };
+  private async handleClearCache(): Promise<void> {
+    return withProgress(
+      async (progress, token) => {
+        if (
+          this.queryServer !== undefined &&
+          this.databaseManager.currentDatabaseItem !== undefined
+        ) {
+          await this.queryServer.clearCacheInDatabase(
+            this.databaseManager.currentDatabaseItem,
+            progress,
+            token,
+          );
+        }
+      },
+      {
+        title: "Clearing cache",
+      },
+    );
+  }
 
-  private handleSetCurrentDatabase = async (
-    progress: ProgressCallback,
-    token: CancellationToken,
-    uri: Uri,
-  ): Promise<void> => {
-    try {
-      // Assume user has selected an archive if the file has a .zip extension
-      if (uri.path.endsWith(".zip")) {
-        await importArchiveDatabase(
-          uri.toString(true),
-          this.databaseManager,
-          this.storagePath,
-          progress,
-          token,
-          this.queryServer?.cliServer,
-        );
-      } else {
-        await this.setCurrentDatabase(progress, token, uri);
-      }
-    } catch (e) {
-      // rethrow and let this be handled by default error handling.
-      throw new Error(
-        `Could not set database to ${basename(
-          uri.fsPath,
-        )}. Reason: ${getErrorMessage(e)}`,
-      );
-    }
-  };
+  private async handleSetCurrentDatabase(uri: Uri): Promise<void> {
+    return withProgress(
+      async (progress, token) => {
+        try {
+          // Assume user has selected an archive if the file has a .zip extension
+          if (uri.path.endsWith(".zip")) {
+            await importArchiveDatabase(
+              this.app.commands,
+              uri.toString(true),
+              this.databaseManager,
+              this.storagePath,
+              progress,
+              token,
+              this.queryServer?.cliServer,
+            );
+          } else {
+            await this.setCurrentDatabase(progress, token, uri);
+          }
+        } catch (e) {
+          // rethrow and let this be handled by default error handling.
+          throw new Error(
+            `Could not set database to ${basename(
+              uri.fsPath,
+            )}. Reason: ${getErrorMessage(e)}`,
+          );
+        }
+      },
+      {
+        title: "Importing database from archive",
+      },
+    );
+  }
 
-  private handleRemoveDatabase = async (
-    progress: ProgressCallback,
-    token: CancellationToken,
+  private async handleRemoveDatabase(
     databaseItem: DatabaseItem,
     multiSelect: DatabaseItem[] | undefined,
-  ): Promise<void> => {
-    if (multiSelect?.length) {
-      await Promise.all(
-        multiSelect.map((dbItem) =>
-          this.databaseManager.removeDatabaseItem(progress, token, dbItem),
-        ),
-      );
-    } else {
-      await this.databaseManager.removeDatabaseItem(
-        progress,
-        token,
-        databaseItem,
-      );
-    }
-  };
+  ): Promise<void> {
+    return withProgress(
+      async (progress, token) => {
+        if (multiSelect?.length) {
+          await Promise.all(
+            multiSelect.map((dbItem) =>
+              this.databaseManager.removeDatabaseItem(progress, token, dbItem),
+            ),
+          );
+        } else {
+          await this.databaseManager.removeDatabaseItem(
+            progress,
+            token,
+            databaseItem,
+          );
+        }
+      },
+      {
+        title: "Removing database",
+        cancellable: false,
+      },
+    );
+  }
 
-  private handleRenameDatabase = async (
+  private async handleRenameDatabase(
     databaseItem: DatabaseItem,
     multiSelect: DatabaseItem[] | undefined,
-  ): Promise<void> => {
+  ): Promise<void> {
     this.assertSingleDatabase(multiSelect);
 
     const newName = await window.showInputBox({
@@ -684,12 +676,12 @@ export class DatabaseUI extends DisposableObject {
     if (newName) {
       await this.databaseManager.renameDatabaseItem(databaseItem, newName);
     }
-  };
+  }
 
-  private handleOpenFolder = async (
+  private async handleOpenFolder(
     databaseItem: DatabaseItem,
     multiSelect: DatabaseItem[] | undefined,
-  ): Promise<void> => {
+  ): Promise<void> {
     if (multiSelect?.length) {
       await Promise.all(
         multiSelect.map((dbItem) => env.openExternal(dbItem.databaseUri)),
@@ -697,17 +689,17 @@ export class DatabaseUI extends DisposableObject {
     } else {
       await env.openExternal(databaseItem.databaseUri);
     }
-  };
+  }
 
   /**
    * Adds the source folder of a CodeQL database to the workspace.
    * When a database is first added in the "Databases" view, its source folder is added to the workspace.
    * If the source folder is removed from the workspace for some reason, we want to be able to re-add it if need be.
    */
-  private handleAddSource = async (
+  private async handleAddSource(
     databaseItem: DatabaseItem,
     multiSelect: DatabaseItem[] | undefined,
-  ): Promise<void> => {
+  ): Promise<void> {
     if (multiSelect?.length) {
       for (const dbItem of multiSelect) {
         await this.databaseManager.addDatabaseSourceArchiveFolder(dbItem);
@@ -715,7 +707,7 @@ export class DatabaseUI extends DisposableObject {
     } else {
       await this.databaseManager.addDatabaseSourceArchiveFolder(databaseItem);
     }
-  };
+  }
 
   /**
    * Return the current database directory. If we don't already have a
@@ -773,6 +765,7 @@ export class DatabaseUI extends DisposableObject {
       // we are selecting a database archive. Must unzip into a workspace-controlled area
       // before importing.
       return await importArchiveDatabase(
+        this.app.commands,
         uri.toString(true),
         this.databaseManager,
         this.storagePath,
diff --git a/extensions/ql-vscode/src/local-databases.ts b/extensions/ql-vscode/src/local-databases.ts
index 8ba756df7..918ddd5fc 100644
--- a/extensions/ql-vscode/src/local-databases.ts
+++ b/extensions/ql-vscode/src/local-databases.ts
@@ -12,7 +12,7 @@ import {
   isFolderAlreadyInWorkspace,
   showBinaryChoiceDialog,
 } from "./helpers";
-import { ProgressCallback, withProgress } from "./commandRunner";
+import { ProgressCallback, withProgress } from "./progress";
 import {
   zipArchiveScheme,
   encodeArchiveBasePath,
@@ -28,6 +28,7 @@ import { redactableError } from "./pure/errors";
 import { isCodespacesTemplate } from "./config";
 import { QlPackGenerator } from "./qlpack-generator";
 import { QueryLanguage } from "./common/query-language";
+import { App } from "./common/app";
 
 /**
  * databases.ts
@@ -593,6 +594,7 @@ export class DatabaseManager extends DisposableObject {
 
   constructor(
     private readonly ctx: ExtensionContext,
+    private readonly app: App,
     private readonly qs: QueryRunner,
     private readonly cli: cli.CodeQLCliServer,
     public logger: Logger,
@@ -794,74 +796,66 @@ export class DatabaseManager extends DisposableObject {
   }
 
   public async loadPersistedState(): Promise<void> {
-    return withProgress(
-      {
-        location: vscode.ProgressLocation.Notification,
-      },
-      async (progress, token) => {
-        const currentDatabaseUri =
-          this.ctx.workspaceState.get<string>(CURRENT_DB);
-        const databases = this.ctx.workspaceState.get<PersistedDatabaseItem[]>(
-          DB_LIST,
-          [],
+    return withProgress(async (progress, token) => {
+      const currentDatabaseUri =
+        this.ctx.workspaceState.get<string>(CURRENT_DB);
+      const databases = this.ctx.workspaceState.get<PersistedDatabaseItem[]>(
+        DB_LIST,
+        [],
+      );
+      let step = 0;
+      progress({
+        maxStep: databases.length,
+        message: "Loading persisted databases",
+        step,
+      });
+      try {
+        void this.logger.log(
+          `Found ${databases.length} persisted databases: ${databases
+            .map((db) => db.uri)
+            .join(", ")}`,
         );
-        let step = 0;
-        progress({
-          maxStep: databases.length,
-          message: "Loading persisted databases",
-          step,
-        });
-        try {
-          void this.logger.log(
-            `Found ${databases.length} persisted databases: ${databases
-              .map((db) => db.uri)
-              .join(", ")}`,
-          );
-          for (const database of databases) {
-            progress({
-              maxStep: databases.length,
-              message: `Loading ${
-                database.options?.displayName || "databases"
-              }`,
-              step: ++step,
-            });
+        for (const database of databases) {
+          progress({
+            maxStep: databases.length,
+            message: `Loading ${database.options?.displayName || "databases"}`,
+            step: ++step,
+          });
 
-            const databaseItem =
-              await this.createDatabaseItemFromPersistedState(
-                progress,
-                token,
-                database,
-              );
-            try {
-              await databaseItem.refresh();
-              await this.registerDatabase(progress, token, databaseItem);
-              if (currentDatabaseUri === database.uri) {
-                await this.setCurrentDatabaseItem(databaseItem, true);
-              }
-              void this.logger.log(
-                `Loaded database ${databaseItem.name} at URI ${database.uri}.`,
-              );
-            } catch (e) {
-              // When loading from persisted state, leave invalid databases in the list. They will be
-              // marked as invalid, and cannot be set as the current database.
-              void this.logger.log(
-                `Error loading database ${database.uri}: ${e}.`,
-              );
+          const databaseItem = await this.createDatabaseItemFromPersistedState(
+            progress,
+            token,
+            database,
+          );
+          try {
+            await databaseItem.refresh();
+            await this.registerDatabase(progress, token, databaseItem);
+            if (currentDatabaseUri === database.uri) {
+              await this.setCurrentDatabaseItem(databaseItem, true);
             }
+            void this.logger.log(
+              `Loaded database ${databaseItem.name} at URI ${database.uri}.`,
+            );
+          } catch (e) {
+            // When loading from persisted state, leave invalid databases in the list. They will be
+            // marked as invalid, and cannot be set as the current database.
+            void this.logger.log(
+              `Error loading database ${database.uri}: ${e}.`,
+            );
           }
-          await this.updatePersistedDatabaseList();
-        } catch (e) {
-          // database list had an unexpected type - nothing to be done?
-          void showAndLogExceptionWithTelemetry(
-            redactableError(
-              asError(e),
-            )`Database list loading failed: ${getErrorMessage(e)}`,
-          );
         }
+        await this.updatePersistedDatabaseList();
+      } catch (e) {
+        // database list had an unexpected type - nothing to be done?
+        void showAndLogExceptionWithTelemetry(
+          redactableError(
+            asError(e),
+          )`Database list loading failed: ${getErrorMessage(e)}`,
+        );
+      }
 
-        void this.logger.log("Finished loading persisted databases.");
-      },
-    );
+      void this.logger.log("Finished loading persisted databases.");
+    });
   }
 
   public get databaseItems(): readonly DatabaseItem[] {
@@ -883,7 +877,7 @@ export class DatabaseManager extends DisposableObject {
       this._currentDatabaseItem = item;
       this.updatePersistedCurrentDatabaseItem();
 
-      await vscode.commands.executeCommand(
+      await this.app.commands.execute(
         "setContext",
         "codeQL.currentDatabaseItem",
         item?.name,
diff --git a/extensions/ql-vscode/src/local-queries.ts b/extensions/ql-vscode/src/local-queries.ts
new file mode 100644
index 000000000..380c4d21d
--- /dev/null
+++ b/extensions/ql-vscode/src/local-queries.ts
@@ -0,0 +1,390 @@
+import { ProgressCallback, ProgressUpdate, withProgress } from "./progress";
+import {
+  CancellationToken,
+  CancellationTokenSource,
+  QuickPickItem,
+  Range,
+  Uri,
+  window,
+} from "vscode";
+import { extLogger } from "./common";
+import { MAX_QUERIES } from "./config";
+import { gatherQlFiles } from "./pure/files";
+import { basename } from "path";
+import {
+  findLanguage,
+  showAndLogErrorMessage,
+  showAndLogWarningMessage,
+  showBinaryChoiceDialog,
+} from "./helpers";
+import { displayQuickQuery } from "./quick-query";
+import { QueryRunner } from "./queryRunner";
+import { QueryHistoryManager } from "./query-history/query-history-manager";
+import { DatabaseUI } from "./local-databases-ui";
+import { ResultsView } from "./interface";
+import { DatabaseItem, DatabaseManager } from "./local-databases";
+import { createInitialQueryInfo } from "./run-queries-shared";
+import { CompletedLocalQueryInfo, LocalQueryInfo } from "./query-results";
+import { WebviewReveal } from "./interface-utils";
+import { asError, getErrorMessage } from "./pure/helpers-pure";
+import { CodeQLCliServer } from "./cli";
+import { LocalQueryCommands } from "./common/commands";
+import { App } from "./common/app";
+
+type LocalQueryOptions = {
+  app: App;
+  queryRunner: QueryRunner;
+  queryHistoryManager: QueryHistoryManager;
+  databaseManager: DatabaseManager;
+  cliServer: CodeQLCliServer;
+  databaseUI: DatabaseUI;
+  localQueryResultsView: ResultsView;
+  queryStorageDir: string;
+};
+
+export function getLocalQueryCommands({
+  app,
+  queryRunner,
+  queryHistoryManager,
+  databaseManager,
+  cliServer,
+  databaseUI,
+  localQueryResultsView,
+  queryStorageDir,
+}: LocalQueryOptions): LocalQueryCommands {
+  const runQuery = async (uri: Uri | undefined) =>
+    withProgress(
+      async (progress, token) => {
+        await compileAndRunQuery(
+          queryRunner,
+          queryHistoryManager,
+          databaseUI,
+          localQueryResultsView,
+          queryStorageDir,
+          false,
+          uri,
+          progress,
+          token,
+          undefined,
+        );
+      },
+      {
+        title: "Running query",
+        cancellable: true,
+      },
+    );
+
+  const runQueryOnMultipleDatabases = async (uri: Uri | undefined) =>
+    withProgress(
+      async (progress, token) =>
+        await compileAndRunQueryOnMultipleDatabases(
+          cliServer,
+          queryRunner,
+          queryHistoryManager,
+          databaseManager,
+          databaseUI,
+          localQueryResultsView,
+          queryStorageDir,
+          progress,
+          token,
+          uri,
+        ),
+      {
+        title: "Running query on selected databases",
+        cancellable: true,
+      },
+    );
+
+  const runQueries = async (_: Uri | undefined, multi: Uri[]) =>
+    withProgress(
+      async (progress, token) => {
+        const maxQueryCount = MAX_QUERIES.getValue() as number;
+        const [files, dirFound] = await gatherQlFiles(
+          multi.map((uri) => uri.fsPath),
+        );
+        if (files.length > maxQueryCount) {
+          throw new Error(
+            `You tried to run ${files.length} queries, but the maximum is ${maxQueryCount}. Try selecting fewer queries or changing the 'codeQL.runningQueries.maxQueries' setting.`,
+          );
+        }
+        // warn user and display selected files when a directory is selected because some ql
+        // files may be hidden from the user.
+        if (dirFound) {
+          const fileString = files.map((file) => basename(file)).join(", ");
+          const res = await showBinaryChoiceDialog(
+            `You are about to run ${files.length} queries: ${fileString} Do you want to continue?`,
+          );
+          if (!res) {
+            return;
+          }
+        }
+        const queryUris = files.map((path) => Uri.parse(`file:${path}`, true));
+
+        // Use a wrapped progress so that messages appear with the queries remaining in it.
+        let queriesRemaining = queryUris.length;
+
+        function wrappedProgress(update: ProgressUpdate) {
+          const message =
+            queriesRemaining > 1
+              ? `${queriesRemaining} remaining. ${update.message}`
+              : update.message;
+          progress({
+            ...update,
+            message,
+          });
+        }
+
+        wrappedProgress({
+          maxStep: queryUris.length,
+          step: queryUris.length - queriesRemaining,
+          message: "",
+        });
+
+        await Promise.all(
+          queryUris.map(async (uri) =>
+            compileAndRunQuery(
+              queryRunner,
+              queryHistoryManager,
+              databaseUI,
+              localQueryResultsView,
+              queryStorageDir,
+              false,
+              uri,
+              wrappedProgress,
+              token,
+              undefined,
+            ).then(() => queriesRemaining--),
+          ),
+        );
+      },
+      {
+        title: "Running queries",
+        cancellable: true,
+      },
+    );
+
+  const quickEval = async (uri: Uri) =>
+    withProgress(
+      async (progress, token) => {
+        await compileAndRunQuery(
+          queryRunner,
+          queryHistoryManager,
+          databaseUI,
+          localQueryResultsView,
+          queryStorageDir,
+          true,
+          uri,
+          progress,
+          token,
+          undefined,
+        );
+      },
+      {
+        title: "Running query",
+        cancellable: true,
+      },
+    );
+
+  const codeLensQuickEval = async (uri: Uri, range: Range) =>
+    withProgress(
+      async (progress, token) =>
+        await compileAndRunQuery(
+          queryRunner,
+          queryHistoryManager,
+          databaseUI,
+          localQueryResultsView,
+          queryStorageDir,
+          true,
+          uri,
+          progress,
+          token,
+          undefined,
+          range,
+        ),
+      {
+        title: "Running query",
+        cancellable: true,
+      },
+    );
+
+  const quickQuery = async () =>
+    withProgress(
+      async (progress, token) =>
+        displayQuickQuery(app, cliServer, databaseUI, progress, token),
+      {
+        title: "Run Quick Query",
+      },
+    );
+
+  return {
+    "codeQL.runQuery": runQuery,
+    "codeQL.runQueryContextEditor": runQuery,
+    "codeQL.runQueryOnMultipleDatabases": runQueryOnMultipleDatabases,
+    "codeQL.runQueryOnMultipleDatabasesContextEditor":
+      runQueryOnMultipleDatabases,
+    "codeQL.runQueries": runQueries,
+    "codeQL.quickEval": quickEval,
+    "codeQL.quickEvalContextEditor": quickEval,
+    "codeQL.codeLensQuickEval": codeLensQuickEval,
+    "codeQL.quickQuery": quickQuery,
+  };
+}
+
+export async function compileAndRunQuery(
+  qs: QueryRunner,
+  qhm: QueryHistoryManager,
+  databaseUI: DatabaseUI,
+  localQueryResultsView: ResultsView,
+  queryStorageDir: string,
+  quickEval: boolean,
+  selectedQuery: Uri | undefined,
+  progress: ProgressCallback,
+  token: CancellationToken,
+  databaseItem: DatabaseItem | undefined,
+  range?: Range,
+): Promise<void> {
+  if (qs !== undefined) {
+    // If no databaseItem is specified, use the database currently selected in the Databases UI
+    databaseItem =
+      databaseItem || (await databaseUI.getDatabaseItem(progress, token));
+    if (databaseItem === undefined) {
+      throw new Error("Can't run query without a selected database");
+    }
+    const databaseInfo = {
+      name: databaseItem.name,
+      databaseUri: databaseItem.databaseUri.toString(),
+    };
+
+    // handle cancellation from the history view.
+    const source = new CancellationTokenSource();
+    token.onCancellationRequested(() => source.cancel());
+
+    const initialInfo = await createInitialQueryInfo(
+      selectedQuery,
+      databaseInfo,
+      quickEval,
+      range,
+    );
+    const item = new LocalQueryInfo(initialInfo, source);
+    qhm.addQuery(item);
+    try {
+      const completedQueryInfo = await qs.compileAndRunQueryAgainstDatabase(
+        databaseItem,
+        initialInfo,
+        queryStorageDir,
+        progress,
+        source.token,
+        undefined,
+        item,
+      );
+      qhm.completeQuery(item, completedQueryInfo);
+      await showResultsForCompletedQuery(
+        localQueryResultsView,
+        item as CompletedLocalQueryInfo,
+        WebviewReveal.Forced,
+      );
+      // Note we must update the query history view after showing results as the
+      // display and sorting might depend on the number of results
+    } catch (e) {
+      const err = asError(e);
+      err.message = `Error running query: ${err.message}`;
+      item.failureReason = err.message;
+      throw e;
+    } finally {
+      await qhm.refreshTreeView();
+      source.dispose();
+    }
+  }
+}
+
+interface DatabaseQuickPickItem extends QuickPickItem {
+  databaseItem: DatabaseItem;
+}
+
+async function compileAndRunQueryOnMultipleDatabases(
+  cliServer: CodeQLCliServer,
+  qs: QueryRunner,
+  qhm: QueryHistoryManager,
+  dbm: DatabaseManager,
+  databaseUI: DatabaseUI,
+  localQueryResultsView: ResultsView,
+  queryStorageDir: string,
+  progress: ProgressCallback,
+  token: CancellationToken,
+  uri: Uri | undefined,
+): Promise<void> {
+  let filteredDBs = dbm.databaseItems;
+  if (filteredDBs.length === 0) {
+    void showAndLogErrorMessage(
+      "No databases found. Please add a suitable database to your workspace.",
+    );
+    return;
+  }
+  // If possible, only show databases with the right language (otherwise show all databases).
+  const queryLanguage = await findLanguage(cliServer, uri);
+  if (queryLanguage) {
+    filteredDBs = dbm.databaseItems.filter(
+      (db) => db.language === queryLanguage,
+    );
+    if (filteredDBs.length === 0) {
+      void showAndLogErrorMessage(
+        `No databases found for language ${queryLanguage}. Please add a suitable database to your workspace.`,
+      );
+      return;
+    }
+  }
+  const quickPickItems = filteredDBs.map<DatabaseQuickPickItem>((dbItem) => ({
+    databaseItem: dbItem,
+    label: dbItem.name,
+    description: dbItem.language,
+  }));
+  /**
+   * Databases that were selected in the quick pick menu.
+   */
+  const quickpick = await window.showQuickPick<DatabaseQuickPickItem>(
+    quickPickItems,
+    { canPickMany: true, ignoreFocusOut: true },
+  );
+  if (quickpick !== undefined) {
+    // Collect all skipped databases and display them at the end (instead of popping up individual errors)
+    const skippedDatabases = [];
+    const errors = [];
+    for (const item of quickpick) {
+      try {
+        await compileAndRunQuery(
+          qs,
+          qhm,
+          databaseUI,
+          localQueryResultsView,
+          queryStorageDir,
+          false,
+          uri,
+          progress,
+          token,
+          item.databaseItem,
+        );
+      } catch (e) {
+        skippedDatabases.push(item.label);
+        errors.push(getErrorMessage(e));
+      }
+    }
+    if (skippedDatabases.length > 0) {
+      void extLogger.log(`Errors:\n${errors.join("\n")}`);
+      void showAndLogWarningMessage(
+        `The following databases were skipped:\n${skippedDatabases.join(
+          "\n",
+        )}.\nFor details about the errors, see the logs.`,
+      );
+    }
+  } else {
+    void showAndLogErrorMessage("No databases selected.");
+  }
+}
+
+export async function showResultsForCompletedQuery(
+  localQueryResultsView: ResultsView,
+  query: CompletedLocalQueryInfo,
+  forceReveal: WebviewReveal,
+): Promise<void> {
+  await localQueryResultsView.showResults(query, forceReveal, false);
+}
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 c7968ba97..b6920fa30 100644
--- a/extensions/ql-vscode/src/log-insights/summary-language-support.ts
+++ b/extensions/ql-vscode/src/log-insights/summary-language-support.ts
@@ -13,9 +13,9 @@ import {
   workspace,
 } from "vscode";
 import { DisposableObject } from "../pure/disposable-object";
-import { commandRunner } from "../commandRunner";
 import { extLogger } from "../common";
 import { getErrorMessage } from "../pure/helpers-pure";
+import { SummaryLanguageSupportCommands } from "../common/commands";
 
 /** A `Position` within a specified file on disk. */
 interface PositionInFile {
@@ -73,8 +73,12 @@ export class SummaryLanguageSupport extends DisposableObject {
         this.handleDidCloseTextDocument.bind(this),
       ),
     );
+  }
 
-    this.push(commandRunner("codeQL.gotoQL", this.handleGotoQL.bind(this)));
+  public getCommands(): SummaryLanguageSupportCommands {
+    return {
+      "codeQL.gotoQL": this.handleGotoQL.bind(this),
+    };
   }
 
   /**
diff --git a/extensions/ql-vscode/src/mocks/vscode-mock-gh-api-server.ts b/extensions/ql-vscode/src/mocks/vscode-mock-gh-api-server.ts
index fbe43c2c9..50c821b56 100644
--- a/extensions/ql-vscode/src/mocks/vscode-mock-gh-api-server.ts
+++ b/extensions/ql-vscode/src/mocks/vscode-mock-gh-api-server.ts
@@ -15,6 +15,7 @@ import {
 } from "../config";
 import { DisposableObject } from "../pure/disposable-object";
 import { MockGitHubApiServer } from "./mock-gh-api-server";
+import { MockGitHubApiServerCommands } from "../common/commands";
 
 /**
  * "Interface" to the mock GitHub API server which implements VSCode interactions, such as
@@ -34,6 +35,19 @@ export class VSCodeMockGitHubApiServer extends DisposableObject {
     this.setupConfigListener();
   }
 
+  public getCommands(): MockGitHubApiServerCommands {
+    return {
+      "codeQL.mockGitHubApiServer.startRecording":
+        this.startRecording.bind(this),
+      "codeQL.mockGitHubApiServer.saveScenario": this.saveScenario.bind(this),
+      "codeQL.mockGitHubApiServer.cancelRecording":
+        this.cancelRecording.bind(this),
+      "codeQL.mockGitHubApiServer.loadScenario": this.loadScenario.bind(this),
+      "codeQL.mockGitHubApiServer.unloadScenario":
+        this.unloadScenario.bind(this),
+    };
+  }
+
   public async startServer(): Promise<void> {
     this.server.startServer();
   }
diff --git a/extensions/ql-vscode/src/packages/commands/CommandManager.ts b/extensions/ql-vscode/src/packages/commands/CommandManager.ts
index c0b1d38f2..6583840a7 100644
--- a/extensions/ql-vscode/src/packages/commands/CommandManager.ts
+++ b/extensions/ql-vscode/src/packages/commands/CommandManager.ts
@@ -1 +1,70 @@
-export class CommandManager {}
+/**
+ * Contains a generic implementation of typed commands.
+ *
+ * This allows different parts of the extension to register commands with a certain type,
+ * and then allow other parts to call those commands in a well-typed manner.
+ */
+
+import { Disposable } from "./Disposable";
+
+/**
+ * A command function is a completely untyped command.
+ */
+export type CommandFunction = (...args: any[]) => Promise<unknown>;
+
+/**
+ * The command manager basically takes a single input, the type
+ * of all the known commands. The second parameter is provided by
+ * default (and should not be needed by the caller) it is a
+ * technicality to allow the type system to look up commands.
+ */
+export class CommandManager<
+  Commands extends Record<string, CommandFunction>,
+  CommandName extends keyof Commands & string = keyof Commands & string,
+> implements Disposable
+{
+  // TODO: should this be a map?
+  // TODO: handle multiple command names
+  private commands: Disposable[] = [];
+
+  constructor(
+    private readonly commandRegister: <T extends CommandName>(
+      commandName: T,
+      fn: NonNullable<Commands[T]>,
+    ) => Disposable,
+    private readonly commandExecute: <T extends CommandName>(
+      commandName: T,
+      ...args: Parameters<Commands[T]>
+    ) => Promise<Awaited<ReturnType<Commands[T]>>>,
+  ) {}
+
+  /**
+   * Register a command with the specified name and implementation.
+   */
+  register<T extends CommandName>(
+    commandName: T,
+    definition: NonNullable<Commands[T]>,
+  ): void {
+    this.commands.push(this.commandRegister(commandName, definition));
+  }
+
+  /**
+   * Execute a command with the specified name and the provided arguments.
+   */
+  execute<T extends CommandName>(
+    commandName: T,
+    ...args: Parameters<Commands[T]>
+  ): Promise<Awaited<ReturnType<Commands[T]>>> {
+    return this.commandExecute(commandName, ...args);
+  }
+
+  /**
+   * Dispose the manager, disposing all the registered commands.
+   */
+  dispose(): void {
+    this.commands.forEach((cmd) => {
+      cmd.dispose();
+    });
+    this.commands = [];
+  }
+}
diff --git a/extensions/ql-vscode/src/packages/commands/Disposable.ts b/extensions/ql-vscode/src/packages/commands/Disposable.ts
new file mode 100644
index 000000000..3a6dd5c17
--- /dev/null
+++ b/extensions/ql-vscode/src/packages/commands/Disposable.ts
@@ -0,0 +1,7 @@
+/**
+ * This interface mirrors the vscode.Disaposable class, so that
+ * the command manager does not depend on vscode directly.
+ */
+export interface Disposable {
+  dispose(): void;
+}
diff --git a/extensions/ql-vscode/src/packaging.ts b/extensions/ql-vscode/src/packaging.ts
index c17621c09..64196d48c 100644
--- a/extensions/ql-vscode/src/packaging.ts
+++ b/extensions/ql-vscode/src/packaging.ts
@@ -5,11 +5,43 @@ import {
   showAndLogInformationMessage,
 } from "./helpers";
 import { QuickPickItem, window } from "vscode";
-import { ProgressCallback, UserCancellationException } from "./commandRunner";
+import {
+  ProgressCallback,
+  UserCancellationException,
+  withProgress,
+} from "./progress";
 import { extLogger } from "./common";
 import { asError, getErrorStack } from "./pure/helpers-pure";
 import { redactableError } from "./pure/errors";
 import { PACKS_BY_QUERY_LANGUAGE } from "./common/query-language";
+import { PackagingCommands } from "./common/commands";
+
+type PackagingOptions = {
+  cliServer: CodeQLCliServer;
+};
+
+export function getPackagingCommands({
+  cliServer,
+}: PackagingOptions): PackagingCommands {
+  return {
+    "codeQL.installPackDependencies": async () =>
+      withProgress(
+        async (progress: ProgressCallback) =>
+          await handleInstallPackDependencies(cliServer, progress),
+        {
+          title: "Installing pack dependencies",
+        },
+      ),
+    "codeQL.downloadPacks": async () =>
+      withProgress(
+        async (progress: ProgressCallback) =>
+          await handleDownloadPacks(cliServer, progress),
+        {
+          title: "Downloading packs",
+        },
+      ),
+  };
+}
 
 /**
  * Prompts user to choose packs to download, and downloads them.
diff --git a/extensions/ql-vscode/src/progress.ts b/extensions/ql-vscode/src/progress.ts
new file mode 100644
index 000000000..45758e39f
--- /dev/null
+++ b/extensions/ql-vscode/src/progress.ts
@@ -0,0 +1,128 @@
+import {
+  CancellationToken,
+  ProgressLocation,
+  ProgressOptions as VSCodeProgressOptions,
+  window as Window,
+} from "vscode";
+
+export class UserCancellationException extends Error {
+  /**
+   * @param message The error message
+   * @param silent If silent is true, then this exception will avoid showing a warning message to the user.
+   */
+  constructor(message?: string, public readonly silent = false) {
+    super(message);
+  }
+}
+
+export interface ProgressUpdate {
+  /**
+   * The current step
+   */
+  step: number;
+  /**
+   * The maximum step. This *should* be constant for a single job.
+   */
+  maxStep: number;
+  /**
+   * The current progress message
+   */
+  message: string;
+}
+
+export type ProgressCallback = (p: ProgressUpdate) => void;
+
+// Make certain properties within a type optional
+type Optional<T, K extends keyof T> = Pick<Partial<T>, K> & Omit<T, K>;
+
+export type ProgressOptions = Optional<VSCodeProgressOptions, "location">;
+
+/**
+ * A task that reports progress.
+ *
+ * @param progress a progress handler function. Call this
+ * function with a `ProgressUpdate` instance in order to
+ * denote some progress being achieved on this task.
+ * @param token a cancellation token
+ */
+export type ProgressTask<R> = (
+  progress: ProgressCallback,
+  token: CancellationToken,
+) => Thenable<R>;
+
+/**
+ * This mediates between the kind of progress callbacks we want to
+ * write (where we *set* current progress position and give
+ * `maxSteps`) and the kind vscode progress api expects us to write
+ * (which increment progress by a certain amount out of 100%).
+ */
+export function withProgress<R>(
+  task: ProgressTask<R>,
+  {
+    location = ProgressLocation.Notification,
+    title,
+    cancellable,
+  }: ProgressOptions = {},
+): Thenable<R> {
+  let progressAchieved = 0;
+  return Window.withProgress(
+    {
+      location,
+      title,
+      cancellable,
+    },
+    (progress, token) => {
+      return task((p) => {
+        const { message, step, maxStep } = p;
+        const increment = (100 * (step - progressAchieved)) / maxStep;
+        progressAchieved = step;
+        progress.report({ message, increment });
+      }, token);
+    },
+  );
+}
+
+/**
+ * Displays a progress monitor that indicates how much progess has been made
+ * reading from a stream.
+ *
+ * @param readable The stream to read progress from
+ * @param messagePrefix A prefix for displaying the message
+ * @param totalNumBytes Total number of bytes in this stream
+ * @param progress The progress callback used to set messages
+ */
+export function reportStreamProgress(
+  readable: NodeJS.ReadableStream,
+  messagePrefix: string,
+  totalNumBytes?: number,
+  progress?: ProgressCallback,
+) {
+  if (progress && totalNumBytes) {
+    let numBytesDownloaded = 0;
+    const bytesToDisplayMB = (numBytes: number): string =>
+      `${(numBytes / (1024 * 1024)).toFixed(1)} MB`;
+    const updateProgress = () => {
+      progress({
+        step: numBytesDownloaded,
+        maxStep: totalNumBytes,
+        message: `${messagePrefix} [${bytesToDisplayMB(
+          numBytesDownloaded,
+        )} of ${bytesToDisplayMB(totalNumBytes)}]`,
+      });
+    };
+
+    // Display the progress straight away rather than waiting for the first chunk.
+    updateProgress();
+
+    readable.on("data", (data) => {
+      numBytesDownloaded += data.length;
+      updateProgress();
+    });
+  } else if (progress) {
+    progress({
+      step: 1,
+      maxStep: 2,
+      message: `${messagePrefix} (Size unknown)`,
+    });
+  }
+}
diff --git a/extensions/ql-vscode/src/pure/errors.ts b/extensions/ql-vscode/src/pure/errors.ts
index dd42ebd74..28300d1fa 100644
--- a/extensions/ql-vscode/src/pure/errors.ts
+++ b/extensions/ql-vscode/src/pure/errors.ts
@@ -1,6 +1,6 @@
 export class RedactableError extends Error {
   constructor(
-    cause: Error | undefined,
+    cause: ErrorLike | undefined,
     private readonly strings: TemplateStringsArray,
     private readonly values: unknown[],
   ) {
@@ -54,19 +54,34 @@ export function redactableError(
   ...values: unknown[]
 ): RedactableError;
 export function redactableError(
-  error: Error,
+  error: ErrorLike,
 ): (strings: TemplateStringsArray, ...values: unknown[]) => RedactableError;
 
 export function redactableError(
-  errorOrStrings: Error | TemplateStringsArray,
+  errorOrStrings: ErrorLike | TemplateStringsArray,
   ...values: unknown[]
 ):
   | ((strings: TemplateStringsArray, ...values: unknown[]) => RedactableError)
   | RedactableError {
-  if (errorOrStrings instanceof Error) {
+  if (isErrorLike(errorOrStrings)) {
     return (strings: TemplateStringsArray, ...values: unknown[]) =>
       new RedactableError(errorOrStrings, strings, values);
   } else {
     return new RedactableError(undefined, errorOrStrings, values);
   }
 }
+
+export interface ErrorLike {
+  message: string;
+  stack?: string;
+}
+
+function isErrorLike(error: any): error is ErrorLike {
+  if (
+    typeof error.message === "string" &&
+    (error.stack === undefined || typeof error.stack === "string")
+  ) {
+    return true;
+  }
+  return false;
+}
diff --git a/extensions/ql-vscode/src/pure/interface-types.ts b/extensions/ql-vscode/src/pure/interface-types.ts
index bbc4b0903..2d68b39d2 100644
--- a/extensions/ql-vscode/src/pure/interface-types.ts
+++ b/extensions/ql-vscode/src/pure/interface-types.ts
@@ -12,6 +12,8 @@ import {
   VariantAnalysisScannedRepositoryState,
 } from "../variant-analysis/shared/variant-analysis";
 import { RepositoriesFilterSortStateWithIds } from "./variant-analysis-filter-sort";
+import { ErrorLike } from "./errors";
+import { DataFlowPaths } from "../variant-analysis/shared/data-flow-paths";
 
 /**
  * This module contains types and code that are shared between
@@ -182,14 +184,13 @@ export type IntoResultsViewMsg =
  * A message sent from the results view.
  */
 export type FromResultsViewMsg =
+  | CommonFromViewMessages
   | ViewSourceFileMsg
   | ToggleDiagnostics
   | ChangeRawResultsSortMsg
   | ChangeInterpretedResultsSortMsg
-  | ViewLoadedMsg
   | ChangePage
-  | OpenFileMsg
-  | TelemetryMessage;
+  | OpenFileMsg;
 
 /**
  * Message from the results view to open a database source
@@ -231,6 +232,21 @@ interface ViewLoadedMsg {
   viewName: string;
 }
 
+interface TelemetryMessage {
+  t: "telemetry";
+  action: string;
+}
+
+interface UnhandledErrorMessage {
+  t: "unhandledError";
+  error: ErrorLike;
+}
+
+type CommonFromViewMessages =
+  | ViewLoadedMsg
+  | TelemetryMessage
+  | UnhandledErrorMessage;
+
 /**
  * Message from the results view to signal a request to change the
  * page.
@@ -287,11 +303,10 @@ interface ChangeInterpretedResultsSortMsg {
  * Message from the compare view to the extension.
  */
 export type FromCompareViewMessage =
-  | ViewLoadedMsg
+  | CommonFromViewMessages
   | ChangeCompareMessage
   | ViewSourceFileMsg
-  | OpenQueryMessage
-  | TelemetryMessage;
+  | OpenQueryMessage;
 
 /**
  * Message from the compare view to request opening a query.
@@ -434,9 +449,9 @@ export interface CancelVariantAnalysisMessage {
   t: "cancelVariantAnalysis";
 }
 
-export interface TelemetryMessage {
-  t: "telemetry";
-  action: string;
+export interface ShowDataFlowPathsMessage {
+  t: "showDataFlowPaths";
+  dataFlowPaths: DataFlowPaths;
 }
 
 export type ToVariantAnalysisMessage =
@@ -445,7 +460,7 @@ export type ToVariantAnalysisMessage =
   | SetRepoStatesMessage;
 
 export type FromVariantAnalysisMessage =
-  | ViewLoadedMsg
+  | CommonFromViewMessages
   | RequestRepositoryResultsMessage
   | OpenQueryFileMessage
   | OpenQueryTextMessage
@@ -453,4 +468,13 @@ export type FromVariantAnalysisMessage =
   | ExportResultsMessage
   | OpenLogsMessage
   | CancelVariantAnalysisMessage
-  | TelemetryMessage;
+  | ShowDataFlowPathsMessage;
+
+export interface SetDataFlowPathsMessage {
+  t: "setDataFlowPaths";
+  dataFlowPaths: DataFlowPaths;
+}
+
+export type ToDataFlowPathsMessage = SetDataFlowPathsMessage;
+
+export type FromDataFlowPathsMessage = CommonFromViewMessages;
diff --git a/extensions/ql-vscode/src/pure/ql.ts b/extensions/ql-vscode/src/pure/ql.ts
index 62c2f006a..6bb08d674 100644
--- a/extensions/ql-vscode/src/pure/ql.ts
+++ b/extensions/ql-vscode/src/pure/ql.ts
@@ -2,6 +2,10 @@ import { join } from "path";
 import { pathExists } from "fs-extra";
 
 export const QLPACK_FILENAMES = ["qlpack.yml", "codeql-pack.yml"];
+export const QLPACK_LOCK_FILENAMES = [
+  "qlpack.lock.yml",
+  "codeql-pack.lock.yml",
+];
 export const FALLBACK_QLPACK_FILENAME = QLPACK_FILENAMES[0];
 
 export async function getQlPackPath(
diff --git a/extensions/ql-vscode/src/query-editor.ts b/extensions/ql-vscode/src/query-editor.ts
new file mode 100644
index 000000000..5821dc781
--- /dev/null
+++ b/extensions/ql-vscode/src/query-editor.ts
@@ -0,0 +1,88 @@
+import { Uri, window } from "vscode";
+import { CodeQLCliServer } from "./cli";
+import { QueryRunner } from "./queryRunner";
+import { basename, join } from "path";
+import { getErrorMessage } from "./pure/helpers-pure";
+import { redactableError } from "./pure/errors";
+import { showAndLogExceptionWithTelemetry } from "./helpers";
+import { AppCommandManager, QueryEditorCommands } from "./common/commands";
+
+type QueryEditorOptions = {
+  commandManager: AppCommandManager;
+
+  queryRunner: QueryRunner;
+  cliServer: CodeQLCliServer;
+
+  qhelpTmpDir: string;
+};
+
+export function getQueryEditorCommands({
+  commandManager,
+  queryRunner,
+  cliServer,
+  qhelpTmpDir,
+}: QueryEditorOptions): QueryEditorCommands {
+  const openReferencedFileCommand = async (selectedQuery: Uri) =>
+    await openReferencedFile(queryRunner, cliServer, selectedQuery);
+
+  return {
+    "codeQL.openReferencedFile": openReferencedFileCommand,
+    // Since we are tracking extension usage through commands, this command mirrors the "codeQL.openReferencedFile" command
+    "codeQL.openReferencedFileContextEditor": openReferencedFileCommand,
+    // Since we are tracking extension usage through commands, this command mirrors the "codeQL.openReferencedFile" command
+    "codeQL.openReferencedFileContextExplorer": openReferencedFileCommand,
+    "codeQL.previewQueryHelp": async (selectedQuery: Uri) =>
+      await previewQueryHelp(
+        commandManager,
+        cliServer,
+        qhelpTmpDir,
+        selectedQuery,
+      ),
+  };
+}
+
+async function previewQueryHelp(
+  commandManager: AppCommandManager,
+  cliServer: CodeQLCliServer,
+  qhelpTmpDir: string,
+  selectedQuery: Uri,
+): Promise<void> {
+  // selectedQuery is unpopulated when executing through the command palette
+  const pathToQhelp = selectedQuery
+    ? selectedQuery.fsPath
+    : window.activeTextEditor?.document.uri.fsPath;
+  if (pathToQhelp) {
+    // Create temporary directory
+    const relativePathToMd = `${basename(pathToQhelp, ".qhelp")}.md`;
+    const absolutePathToMd = join(qhelpTmpDir, relativePathToMd);
+    const uri = Uri.file(absolutePathToMd);
+    try {
+      await cliServer.generateQueryHelp(pathToQhelp, absolutePathToMd);
+      await commandManager.execute("markdown.showPreviewToSide", uri);
+    } catch (e) {
+      const errorMessage = getErrorMessage(e).includes(
+        "Generating qhelp in markdown",
+      )
+        ? redactableError`Could not generate markdown from ${pathToQhelp}: Bad formatting in .qhelp file.`
+        : redactableError`Could not open a preview of the generated file (${absolutePathToMd}).`;
+      void showAndLogExceptionWithTelemetry(errorMessage, {
+        fullMessage: `${errorMessage}\n${getErrorMessage(e)}`,
+      });
+    }
+  }
+}
+
+async function openReferencedFile(
+  qs: QueryRunner,
+  cliServer: CodeQLCliServer,
+  selectedQuery: Uri,
+): Promise<void> {
+  // If no file is selected, the path of the file in the editor is selected
+  const path =
+    selectedQuery?.fsPath || window.activeTextEditor?.document.uri.fsPath;
+  if (qs !== undefined && path) {
+    const resolved = await cliServer.resolveQlref(path);
+    const uri = Uri.file(resolved.resolvedPath);
+    await window.showTextDocument(uri, { preview: false });
+  }
+}
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 daffbb9d5..ca7ab3fd9 100644
--- a/extensions/ql-vscode/src/query-history/query-history-manager.ts
+++ b/extensions/ql-vscode/src/query-history/query-history-manager.ts
@@ -1,6 +1,5 @@
 import { join, dirname } from "path";
 import {
-  commands,
   Disposable,
   env,
   EventEmitter,
@@ -25,14 +24,8 @@ import {
 import { extLogger } from "../common";
 import { URLSearchParams } from "url";
 import { DisposableObject } from "../pure/disposable-object";
-import { commandRunner } from "../commandRunner";
 import { ONE_HOUR_IN_MS, TWO_HOURS_IN_MS } from "../pure/time";
-import {
-  asError,
-  assertNever,
-  getErrorMessage,
-  getErrorStack,
-} from "../pure/helpers-pure";
+import { asError, assertNever, getErrorMessage } from "../pure/helpers-pure";
 import { CompletedLocalQueryInfo, LocalQueryInfo } from "../query-results";
 import {
   getActionsWorkflowRunUrl,
@@ -49,7 +42,7 @@ import {
 import {
   deserializeQueryHistory,
   serializeQueryHistory,
-} from "../query-serialization";
+} from "./store/query-history-store";
 import { pathExists } from "fs-extra";
 import { CliVersionConstraint } from "../cli";
 import { HistoryItemLabelProvider } from "./history-item-label-provider";
@@ -66,6 +59,9 @@ import { getTotalResultCount } from "../variant-analysis/shared/variant-analysis
 import { HistoryTreeDataProvider } from "./history-tree-data-provider";
 import { redactableError } from "../pure/errors";
 import { QueryHistoryDirs } from "./query-history-dirs";
+import { QueryHistoryCommands } from "../common/commands";
+import { App } from "../common/app";
+import { tryOpenExternalFile } from "../vscode-utils/external-files";
 
 /**
  * query-history-manager.ts
@@ -135,6 +131,7 @@ export class QueryHistoryManager extends DisposableObject {
   readonly onDidCompleteQuery = this._onDidCompleteQuery.event;
 
   constructor(
+    private readonly app: App,
     private readonly qs: QueryRunner,
     private readonly dbm: DatabaseManager,
     private readonly localQueriesResultsView: ResultsView,
@@ -201,141 +198,6 @@ export class QueryHistoryManager extends DisposableObject {
       }),
     );
 
-    void extLogger.log("Registering query history panel commands.");
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.openQuery",
-        this.handleOpenQuery.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.removeHistoryItem",
-        this.handleRemoveHistoryItem.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.sortByName",
-        this.handleSortByName.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.sortByDate",
-        this.handleSortByDate.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.sortByCount",
-        this.handleSortByCount.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.renameItem",
-        this.handleRenameItem.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.compareWith",
-        this.handleCompareWith.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.showQueryLog",
-        this.handleShowQueryLog.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.openQueryDirectory",
-        this.handleOpenQueryDirectory.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.showEvalLog",
-        this.handleShowEvalLog.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.showEvalLogSummary",
-        this.handleShowEvalLogSummary.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.showEvalLogViewer",
-        this.handleShowEvalLogViewer.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner("codeQLQueryHistory.cancel", this.handleCancel.bind(this)),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.showQueryText",
-        this.handleShowQueryText.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.exportResults",
-        this.handleExportResults.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.viewCsvResults",
-        this.handleViewCsvResults.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.viewCsvAlerts",
-        this.handleViewCsvAlerts.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.viewSarifAlerts",
-        this.handleViewSarifAlerts.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.viewDil",
-        this.handleViewDil.bind(this),
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.itemClicked",
-        async (item: LocalQueryInfo) => {
-          return this.handleItemClicked(item, [item]);
-        },
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.openOnGithub",
-        async (item: LocalQueryInfo) => {
-          return this.handleOpenOnGithub(item, [item]);
-        },
-      ),
-    );
-    this.push(
-      commandRunner(
-        "codeQLQueryHistory.copyRepoList",
-        this.handleCopyRepoList.bind(this),
-      ),
-    );
-
     // There are two configuration items that affect the query history:
     // 1. The ttl for query history items.
     // 2. The default label for query history items.
@@ -370,6 +232,48 @@ export class QueryHistoryManager extends DisposableObject {
     this.registerToVariantAnalysisEvents();
   }
 
+  public getCommands(): QueryHistoryCommands {
+    return {
+      "codeQLQueryHistory.sortByName": this.handleSortByName.bind(this),
+      "codeQLQueryHistory.sortByDate": this.handleSortByDate.bind(this),
+      "codeQLQueryHistory.sortByCount": this.handleSortByCount.bind(this),
+
+      "codeQLQueryHistory.openQueryTitleMenu": this.handleOpenQuery.bind(this),
+      "codeQLQueryHistory.openQueryContextMenu":
+        this.handleOpenQuery.bind(this),
+      "codeQLQueryHistory.removeHistoryItemTitleMenu":
+        this.handleRemoveHistoryItem.bind(this),
+      "codeQLQueryHistory.removeHistoryItemContextMenu":
+        this.handleRemoveHistoryItem.bind(this),
+      "codeQLQueryHistory.removeHistoryItemContextInline":
+        this.handleRemoveHistoryItem.bind(this),
+      "codeQLQueryHistory.renameItem": this.handleRenameItem.bind(this),
+      "codeQLQueryHistory.compareWith": this.handleCompareWith.bind(this),
+      "codeQLQueryHistory.showEvalLog": this.handleShowEvalLog.bind(this),
+      "codeQLQueryHistory.showEvalLogSummary":
+        this.handleShowEvalLogSummary.bind(this),
+      "codeQLQueryHistory.showEvalLogViewer":
+        this.handleShowEvalLogViewer.bind(this),
+      "codeQLQueryHistory.showQueryLog": this.handleShowQueryLog.bind(this),
+      "codeQLQueryHistory.showQueryText": this.handleShowQueryText.bind(this),
+      "codeQLQueryHistory.openQueryDirectory":
+        this.handleOpenQueryDirectory.bind(this),
+      "codeQLQueryHistory.cancel": this.handleCancel.bind(this),
+      "codeQLQueryHistory.exportResults": this.handleExportResults.bind(this),
+      "codeQLQueryHistory.viewCsvResults": this.handleViewCsvResults.bind(this),
+      "codeQLQueryHistory.viewCsvAlerts": this.handleViewCsvAlerts.bind(this),
+      "codeQLQueryHistory.viewSarifAlerts":
+        this.handleViewSarifAlerts.bind(this),
+      "codeQLQueryHistory.viewDil": this.handleViewDil.bind(this),
+      "codeQLQueryHistory.itemClicked": this.handleItemClicked.bind(this),
+      "codeQLQueryHistory.openOnGithub": this.handleOpenOnGithub.bind(this),
+      "codeQLQueryHistory.copyRepoList": this.handleCopyRepoList.bind(this),
+
+      "codeQL.exportSelectedVariantAnalysisResults":
+        this.exportSelectedVariantAnalysisResults.bind(this),
+    };
+  }
+
   public completeQuery(info: LocalQueryInfo, results: QueryWithResults): void {
     info.completeThisQuery(results);
     this._onDidCompleteQuery.fire(info);
@@ -510,8 +414,7 @@ export class QueryHistoryManager extends DisposableObject {
     }
 
     if (finalSingleItem.t === "variant-analysis") {
-      await commands.executeCommand(
-        "codeQL.openVariantAnalysisQueryFile",
+      await this.variantAnalysisManager.openQueryFile(
         finalSingleItem.variantAnalysis.id,
       );
       return;
@@ -556,7 +459,6 @@ export class QueryHistoryManager extends DisposableObject {
           !(await pathExists(item.completedQuery?.query.querySaveDir))
         ) {
           this.treeDataProvider.remove(item);
-          item.completedQuery?.dispose();
         }
       }),
     );
@@ -577,7 +479,6 @@ export class QueryHistoryManager extends DisposableObject {
           // Removing in progress local queries is not supported. They must be cancelled first.
           if (item.status !== QueryStatus.InProgress) {
             this.treeDataProvider.remove(item);
-            item.completedQuery?.dispose();
 
             // User has explicitly asked for this query to be removed.
             // We need to delete it from disk as well.
@@ -779,7 +680,10 @@ export class QueryHistoryManager extends DisposableObject {
     }
 
     if (singleItem.completedQuery.logFileLocation) {
-      await this.tryOpenExternalFile(singleItem.completedQuery.logFileLocation);
+      await tryOpenExternalFile(
+        this.app.commands,
+        singleItem.completedQuery.logFileLocation,
+      );
     } else {
       void showAndLogWarningMessage("No log file available");
     }
@@ -847,7 +751,7 @@ export class QueryHistoryManager extends DisposableObject {
         }
       }
       try {
-        await commands.executeCommand(
+        await this.app.commands.execute(
           "revealFileInOS",
           Uri.file(externalFilePath),
         );
@@ -896,7 +800,10 @@ export class QueryHistoryManager extends DisposableObject {
     }
 
     if (finalSingleItem.evalLogLocation) {
-      await this.tryOpenExternalFile(finalSingleItem.evalLogLocation);
+      await tryOpenExternalFile(
+        this.app.commands,
+        finalSingleItem.evalLogLocation,
+      );
     } else {
       this.warnNoEvalLogs();
     }
@@ -921,7 +828,10 @@ export class QueryHistoryManager extends DisposableObject {
     }
 
     if (finalSingleItem.evalLogSummaryLocation) {
-      await this.tryOpenExternalFile(finalSingleItem.evalLogSummaryLocation);
+      await tryOpenExternalFile(
+        this.app.commands,
+        finalSingleItem.evalLogSummaryLocation,
+      );
       return;
     }
 
@@ -993,8 +903,7 @@ export class QueryHistoryManager extends DisposableObject {
         if (item.t === "local") {
           item.cancel();
         } else if (item.t === "variant-analysis") {
-          await commands.executeCommand(
-            "codeQL.cancelVariantAnalysis",
+          await this.variantAnalysisManager.cancelVariantAnalysis(
             item.variantAnalysis.id,
           );
         } else {
@@ -1020,8 +929,7 @@ export class QueryHistoryManager extends DisposableObject {
     }
 
     if (finalSingleItem.t === "variant-analysis") {
-      await commands.executeCommand(
-        "codeQL.openVariantAnalysisQueryText",
+      await this.variantAnalysisManager.openQueryText(
         finalSingleItem.variantAnalysis.id,
       );
       return;
@@ -1066,7 +974,10 @@ export class QueryHistoryManager extends DisposableObject {
     const query = finalSingleItem.completedQuery.query;
     const hasInterpretedResults = query.canHaveInterpretedResults();
     if (hasInterpretedResults) {
-      await this.tryOpenExternalFile(query.resultsPaths.interpretedResultsPath);
+      await tryOpenExternalFile(
+        this.app.commands,
+        query.resultsPaths.interpretedResultsPath,
+      );
     } else {
       const label = this.labelProvider.getLabel(finalSingleItem);
       void showAndLogInformationMessage(
@@ -1095,11 +1006,11 @@ export class QueryHistoryManager extends DisposableObject {
     }
     const query = finalSingleItem.completedQuery.query;
     if (await query.hasCsv()) {
-      void this.tryOpenExternalFile(query.csvPath);
+      void tryOpenExternalFile(this.app.commands, query.csvPath);
       return;
     }
     if (await query.exportCsvResults(this.qs.cliServer, query.csvPath)) {
-      void this.tryOpenExternalFile(query.csvPath);
+      void tryOpenExternalFile(this.app.commands, query.csvPath);
     }
   }
 
@@ -1122,7 +1033,8 @@ export class QueryHistoryManager extends DisposableObject {
       return;
     }
 
-    await this.tryOpenExternalFile(
+    await tryOpenExternalFile(
+      this.app.commands,
       await finalSingleItem.completedQuery.query.ensureCsvAlerts(
         this.qs.cliServer,
         this.dbm,
@@ -1149,7 +1061,8 @@ export class QueryHistoryManager extends DisposableObject {
       return;
     }
 
-    await this.tryOpenExternalFile(
+    await tryOpenExternalFile(
+      this.app.commands,
       await finalSingleItem.completedQuery.query.ensureDilPath(
         this.qs.cliServer,
       ),
@@ -1175,7 +1088,7 @@ export class QueryHistoryManager extends DisposableObject {
 
     const actionsWorkflowRunUrl = getActionsWorkflowRunUrl(finalSingleItem);
 
-    await commands.executeCommand(
+    await this.app.commands.execute(
       "vscode.open",
       Uri.parse(actionsWorkflowRunUrl),
     );
@@ -1199,7 +1112,7 @@ export class QueryHistoryManager extends DisposableObject {
       return;
     }
 
-    await commands.executeCommand(
+    await this.app.commands.execute(
       "codeQL.copyVariantAnalysisRepoList",
       finalSingleItem.variantAnalysis.id,
     );
@@ -1223,12 +1136,27 @@ export class QueryHistoryManager extends DisposableObject {
       return;
     }
 
-    await commands.executeCommand(
-      "codeQL.exportVariantAnalysisResults",
+    await this.variantAnalysisManager.exportResults(
       finalSingleItem.variantAnalysis.id,
     );
   }
 
+  /**
+   * Exports the results of the currently-selected variant analysis.
+   */
+  async exportSelectedVariantAnalysisResults(): Promise<void> {
+    const queryHistoryItem = this.getCurrentQueryHistoryItem();
+    if (!queryHistoryItem || queryHistoryItem.t !== "variant-analysis") {
+      throw new Error(
+        "No variant analysis results currently open. To open results, click an item in the query history view.",
+      );
+    }
+
+    await this.variantAnalysisManager.exportResults(
+      queryHistoryItem.variantAnalysis.id,
+    );
+  }
+
   addQuery(item: QueryHistoryInfo) {
     this.treeDataProvider.pushQuery(item);
     this.updateTreeViewSelectionIfVisible();
@@ -1254,47 +1182,6 @@ export class QueryHistoryManager extends DisposableObject {
     }
   }
 
-  private async tryOpenExternalFile(fileLocation: string) {
-    const uri = Uri.file(fileLocation);
-    try {
-      await window.showTextDocument(uri, { preview: false });
-    } catch (e) {
-      const msg = getErrorMessage(e);
-      if (
-        msg.includes(
-          "Files above 50MB cannot be synchronized with extensions",
-        ) ||
-        msg.includes("too large to open")
-      ) {
-        const res = await showBinaryChoiceDialog(
-          `VS Code does not allow extensions to open files >50MB. This file
-exceeds that limit. Do you want to open it outside of VS Code?
-
-You can also try manually opening it inside VS Code by selecting
-the file in the file explorer and dragging it into the workspace.`,
-        );
-        if (res) {
-          try {
-            await commands.executeCommand("revealFileInOS", uri);
-          } catch (e) {
-            void showAndLogExceptionWithTelemetry(
-              redactableError(
-                asError(e),
-              )`Failed to reveal file in OS: ${getErrorMessage(e)}`,
-            );
-          }
-        }
-      } else {
-        void showAndLogExceptionWithTelemetry(
-          redactableError(asError(e))`Could not open file ${fileLocation}`,
-          {
-            fullMessage: `${getErrorMessage(e)}\n${getErrorStack(e)}`,
-          },
-        );
-      }
-    }
-  }
-
   private async findOtherQueryToCompare(
     singleItem: QueryHistoryInfo,
     multiSelect: QueryHistoryInfo[],
diff --git a/extensions/ql-vscode/src/query-serialization.ts b/extensions/ql-vscode/src/query-history/store/query-history-store.ts
similarity index 89%
rename from extensions/ql-vscode/src/query-serialization.ts
rename to extensions/ql-vscode/src/query-history/store/query-history-store.ts
index c2611a06b..bad4a4677 100644
--- a/extensions/ql-vscode/src/query-serialization.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-store.ts
@@ -1,18 +1,18 @@
 import { pathExists, readFile, remove, mkdir, writeFile } from "fs-extra";
 import { dirname } from "path";
 
-import { showAndLogExceptionWithTelemetry } from "./helpers";
+import { showAndLogExceptionWithTelemetry } from "../../helpers";
 import {
   asError,
   asyncFilter,
   getErrorMessage,
   getErrorStack,
-} from "./pure/helpers-pure";
-import { CompletedQueryInfo, LocalQueryInfo } from "./query-results";
-import { QueryHistoryInfo } from "./query-history/query-history-info";
-import { QueryEvaluationInfo } from "./run-queries-shared";
-import { QueryResultType } from "./pure/legacy-messages";
-import { redactableError } from "./pure/errors";
+} from "../../pure/helpers-pure";
+import { CompletedQueryInfo, LocalQueryInfo } from "../../query-results";
+import { QueryHistoryInfo } from "../query-history-info";
+import { QueryEvaluationInfo } from "../../run-queries-shared";
+import { QueryResultType } from "../../pure/legacy-messages";
+import { redactableError } from "../../pure/errors";
 
 export async function deserializeQueryHistory(
   fsPath: string,
@@ -55,10 +55,6 @@ export async function deserializeQueryHistory(
               q.completedQuery.query,
               QueryEvaluationInfo.prototype,
             );
-            // deserialized queries do not need to be disposed
-            q.completedQuery.dispose = () => {
-              /**/
-            };
 
             // Previously, there was a typo in the completedQuery type. There was a field
             // `sucessful` and it was renamed to `successful`. We need to handle this case.
diff --git a/extensions/ql-vscode/src/query-results.ts b/extensions/ql-vscode/src/query-results.ts
index c9f3f2d93..33100bde8 100644
--- a/extensions/ql-vscode/src/query-results.ts
+++ b/extensions/ql-vscode/src/query-results.ts
@@ -55,11 +55,6 @@ export class CompletedQueryInfo implements QueryWithResults {
   readonly logFileLocation?: string;
   resultCount: number;
 
-  /**
-   * This dispose method is called when the query is removed from the history view.
-   */
-  dispose: () => void;
-
   /**
    * Map from result set name to SortedResultSetInfo.
    */
@@ -85,10 +80,6 @@ export class CompletedQueryInfo implements QueryWithResults {
 
     this.message = evaluation.message;
     this.successful = evaluation.successful;
-    // Use the dispose method from the evaluation.
-    // The dispose will clean up any additional log locations that this
-    // query may have created.
-    this.dispose = evaluation.dispose;
 
     this.sortedResultsInfo = {};
     this.resultCount = 0;
diff --git a/extensions/ql-vscode/src/query-server/query-runner.ts b/extensions/ql-vscode/src/query-server/query-runner.ts
index d80a07cbc..ebb90907b 100644
--- a/extensions/ql-vscode/src/query-server/query-runner.ts
+++ b/extensions/ql-vscode/src/query-server/query-runner.ts
@@ -1,5 +1,5 @@
 import { CancellationToken } from "vscode";
-import { ProgressCallback, UserCancellationException } from "../commandRunner";
+import { ProgressCallback, UserCancellationException } from "../progress";
 import { DatabaseItem } from "../local-databases";
 import {
   clearCache,
diff --git a/extensions/ql-vscode/src/query-server/queryserver-client.ts b/extensions/ql-vscode/src/query-server/queryserver-client.ts
index 824e3bae8..428526299 100644
--- a/extensions/ql-vscode/src/query-server/queryserver-client.ts
+++ b/extensions/ql-vscode/src/query-server/queryserver-client.ts
@@ -1,4 +1,3 @@
-import { dirname } from "path";
 import { ensureFile } from "fs-extra";
 
 import { DisposableObject } from "../pure/disposable-object";
@@ -12,9 +11,7 @@ import {
   ProgressMessage,
   WithProgressId,
 } from "../pure/new-messages";
-import * as messages from "../pure/new-messages";
-import { ProgressCallback, ProgressTask } from "../commandRunner";
-import { findQueryLogFile } from "../run-queries-shared";
+import { ProgressCallback, ProgressTask } from "../progress";
 import { ServerProcess } from "../json-rpc-server";
 
 type ServerOpts = {
@@ -53,7 +50,7 @@ export class QueryServerClient extends DisposableObject {
     this.queryServerStartListeners.push(e);
   };
 
-  public activeQueryLogFile: string | undefined;
+  public activeQueryLogger: Logger;
 
   constructor(
     readonly config: QueryServerConfig,
@@ -62,6 +59,9 @@ export class QueryServerClient extends DisposableObject {
     withProgressReporting: WithProgressReporting,
   ) {
     super();
+    // Since no query is active when we initialize, just point the "active query logger" to the
+    // default logger.
+    this.activeQueryLogger = this.logger;
     // When the query server configuration changes, restart the query server.
     if (config.onDidChangeConfiguration !== undefined) {
       this.push(
@@ -167,9 +167,8 @@ export class QueryServerClient extends DisposableObject {
       args,
       this.logger,
       (data) =>
-        this.logger.log(data.toString(), {
+        this.activeQueryLogger.log(data.toString(), {
           trailingNewline: false,
-          additionalLogLocation: this.activeQueryLogFile,
         }),
       undefined, // no listener for stdout
       progressReporter,
@@ -210,7 +209,6 @@ export class QueryServerClient extends DisposableObject {
     const id = this.nextProgress++;
     this.progressCallbacks[id] = progress;
 
-    this.updateActiveQuery(type.method, parameter);
     try {
       if (this.serverProcess === undefined) {
         throw new Error("No query server process found.");
@@ -224,20 +222,4 @@ export class QueryServerClient extends DisposableObject {
       delete this.progressCallbacks[id];
     }
   }
-
-  /**
-   * Updates the active query every time there is a new request to compile.
-   * The active query is used to specify the side log.
-   *
-   * 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.
-   */
-  private updateActiveQuery(method: string, parameter: any): void {
-    if (method === messages.runQuery.method) {
-      this.activeQueryLogFile = findQueryLogFile(
-        dirname(dirname((parameter as messages.RunQueryParams).outputPath)),
-      );
-    }
-  }
 }
diff --git a/extensions/ql-vscode/src/query-server/run-queries.ts b/extensions/ql-vscode/src/query-server/run-queries.ts
index f9ee0a6d7..a08680cc4 100644
--- a/extensions/ql-vscode/src/query-server/run-queries.ts
+++ b/extensions/ql-vscode/src/query-server/run-queries.ts
@@ -1,7 +1,7 @@
 import { join } from "path";
 import { CancellationToken } from "vscode";
 import * as cli from "../cli";
-import { ProgressCallback } from "../commandRunner";
+import { ProgressCallback } from "../progress";
 import { DatabaseItem } from "../local-databases";
 import {
   getOnDiskWorkspaceFolders,
@@ -9,7 +9,7 @@ import {
   showAndLogWarningMessage,
   tryGetQueryMetadata,
 } from "../helpers";
-import { extLogger } from "../common";
+import { extLogger, TeeLogger } from "../common";
 import * as messages from "../pure/new-messages";
 import { QueryResultType } from "../pure/legacy-messages";
 import { InitialQueryInfo, LocalQueryInfo } from "../query-results";
@@ -88,9 +88,15 @@ export async function compileAndRunQueryAgainstDatabase(
     target,
     extensionPacks,
   };
+  const logger = new TeeLogger(qs.logger, query.logPath);
   await query.createTimestampFile();
   let result: messages.RunQueryResult | undefined;
   try {
+    // 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;
     result = await qs.sendRequest(
       messages.runQuery,
       queryToRun,
@@ -105,7 +111,7 @@ export async function compileAndRunQueryAgainstDatabase(
   } finally {
     if (queryInfo) {
       if (await query.hasEvalLog()) {
-        await query.addQueryLogs(queryInfo, qs.cliServer, qs.logger);
+        await query.addQueryLogs(queryInfo, qs.cliServer, logger);
       } else {
         void showAndLogWarningMessage(
           `Failed to write structured evaluator log to ${query.evalLogPath}.`,
@@ -160,8 +166,5 @@ export async function compileAndRunQueryAgainstDatabase(
     },
     message,
     successful,
-    dispose: () => {
-      qs.logger.removeAdditionalLogLocation(undefined);
-    },
   };
 }
diff --git a/extensions/ql-vscode/src/queryRunner.ts b/extensions/ql-vscode/src/queryRunner.ts
index a2e92ee66..0ef8058e5 100644
--- a/extensions/ql-vscode/src/queryRunner.ts
+++ b/extensions/ql-vscode/src/queryRunner.ts
@@ -1,6 +1,6 @@
 import { CancellationToken } from "vscode";
 import { CodeQLCliServer } from "./cli";
-import { ProgressCallback } from "./commandRunner";
+import { ProgressCallback } from "./progress";
 import { DatabaseItem } from "./local-databases";
 import { InitialQueryInfo, LocalQueryInfo } from "./query-results";
 import { QueryWithResults } from "./run-queries-shared";
diff --git a/extensions/ql-vscode/src/quick-query.ts b/extensions/ql-vscode/src/quick-query.ts
index 7829896d7..47c3ca3a9 100644
--- a/extensions/ql-vscode/src/quick-query.ts
+++ b/extensions/ql-vscode/src/quick-query.ts
@@ -1,13 +1,7 @@
 import { ensureDir, writeFile, pathExists, readFile } from "fs-extra";
 import { dump, load } from "js-yaml";
 import { basename, join } from "path";
-import {
-  CancellationToken,
-  ExtensionContext,
-  window as Window,
-  workspace,
-  Uri,
-} from "vscode";
+import { CancellationToken, window as Window, workspace, Uri } from "vscode";
 import { LSPErrorCodes, ResponseError } from "vscode-languageclient";
 import { CodeQLCliServer } from "./cli";
 import { DatabaseUI } from "./local-databases-ui";
@@ -17,9 +11,10 @@ import {
   getQlPackForDbscheme,
   showBinaryChoiceDialog,
 } from "./helpers";
-import { ProgressCallback, UserCancellationException } from "./commandRunner";
+import { ProgressCallback, UserCancellationException } from "./progress";
 import { getErrorMessage } from "./pure/helpers-pure";
 import { FALLBACK_QLPACK_FILENAME, getQlPackPath } from "./pure/ql";
+import { App } from "./common/app";
 
 const QUICK_QUERIES_DIR_NAME = "quick-queries";
 const QUICK_QUERY_QUERY_NAME = "quick-query.ql";
@@ -30,8 +25,8 @@ export function isQuickQueryPath(queryPath: string): boolean {
   return basename(queryPath) === QUICK_QUERY_QUERY_NAME;
 }
 
-async function getQuickQueriesDir(ctx: ExtensionContext): Promise<string> {
-  const storagePath = ctx.storagePath;
+async function getQuickQueriesDir(app: App): Promise<string> {
+  const storagePath = app.workspaceStoragePath;
   if (storagePath === undefined) {
     throw new Error("Workspace storage path is undefined");
   }
@@ -57,7 +52,7 @@ function findExistingQuickQueryEditor() {
  * Show a buffer the user can enter a simple query into.
  */
 export async function displayQuickQuery(
-  ctx: ExtensionContext,
+  app: App,
   cliServer: CodeQLCliServer,
   databaseUI: DatabaseUI,
   progress: ProgressCallback,
@@ -73,7 +68,7 @@ export async function displayQuickQuery(
     }
 
     const workspaceFolders = workspace.workspaceFolders || [];
-    const queriesDir = await getQuickQueriesDir(ctx);
+    const queriesDir = await getQuickQueriesDir(app);
 
     // We need to have a multi-root workspace to make quick query work
     // at all. Changing the workspace from single-root to multi-root
@@ -143,7 +138,7 @@ export async function displayQuickQuery(
 
     if (shouldRewrite) {
       await cliServer.clearCache();
-      await cliServer.packInstall(queriesDir, true);
+      await cliServer.packInstall(queriesDir, { forceUpdate: true });
     }
 
     await Window.showTextDocument(await workspace.openTextDocument(qlFile));
diff --git a/extensions/ql-vscode/src/run-queries-shared.ts b/extensions/ql-vscode/src/run-queries-shared.ts
index 66f85e7e1..da4b7e86c 100644
--- a/extensions/ql-vscode/src/run-queries-shared.ts
+++ b/extensions/ql-vscode/src/run-queries-shared.ts
@@ -12,7 +12,7 @@ import {
   window,
 } from "vscode";
 import { isCanary, AUTOSAVE_SETTING } from "./config";
-import { UserCancellationException } from "./commandRunner";
+import { UserCancellationException } from "./progress";
 import {
   pathExists,
   readFile,
@@ -30,7 +30,7 @@ import { nanoid } from "nanoid";
 import { CodeQLCliServer } from "./cli";
 import { SELECT_QUERY_NAME } from "./contextual/locationFinder";
 import { DatabaseManager } from "./local-databases";
-import { DecodedBqrsChunk } from "./pure/bqrs-cli-types";
+import { DecodedBqrsChunk, EntityValue } from "./pure/bqrs-cli-types";
 import { extLogger, Logger } from "./common";
 import { generateSummarySymbolsFile } from "./log-insights/summary-parser";
 import { getErrorMessage } from "./pure/helpers-pure";
@@ -298,12 +298,8 @@ export class QueryEvaluationInfo {
         this.evalLogEndSummaryPath,
         "utf-8",
       );
-      void logger.log(" --- Evaluator Log Summary --- ", {
-        additionalLogLocation: this.logPath,
-      });
-      void logger.log(endSummaryContent, {
-        additionalLogLocation: this.logPath,
-      });
+      void logger.log(" --- Evaluator Log Summary --- ");
+      void logger.log(endSummaryContent);
     } catch (e) {
       void showAndLogWarningMessage(
         `Could not read structured evaluator log end of summary file at ${this.evalLogEndSummaryPath}.`,
@@ -355,11 +351,17 @@ export class QueryEvaluationInfo {
       chunk.tuples.forEach((tuple) => {
         out.write(
           `${tuple
-            .map((v, i) =>
-              chunk.columns[i].kind === "String"
-                ? `"${typeof v === "string" ? v.replaceAll('"', '""') : v}"`
-                : v,
-            )
+            .map((v, i) => {
+              if (chunk.columns[i].kind === "String") {
+                return `"${
+                  typeof v === "string" ? v.replaceAll('"', '""') : v
+                }"`;
+              } else if (chunk.columns[i].kind === "Entity") {
+                return (v as EntityValue).label;
+              } else {
+                return v;
+              }
+            })
             .join(",")}\n`,
         );
       });
@@ -436,7 +438,6 @@ export class QueryEvaluationInfo {
 export interface QueryWithResults {
   readonly query: QueryEvaluationInfo;
   readonly logFileLocation?: string;
-  readonly dispose: () => void;
   readonly successful?: boolean;
   readonly message?: string;
   readonly result: legacyMessages.EvaluationResult;
diff --git a/extensions/ql-vscode/src/stories/common/CodePaths.stories.tsx b/extensions/ql-vscode/src/stories/common/CodePaths.stories.tsx
index 5b68f1c2d..793c66099 100644
--- a/extensions/ql-vscode/src/stories/common/CodePaths.stories.tsx
+++ b/extensions/ql-vscode/src/stories/common/CodePaths.stories.tsx
@@ -1,7 +1,6 @@
 import * as React from "react";
 
 import { ComponentStory, ComponentMeta } from "@storybook/react";
-import { ThemeProvider } from "@primer/react";
 
 import { CodePaths } from "../../view/common";
 import type { CodeFlow } from "../../variant-analysis/shared/analysis-result";
@@ -9,13 +8,7 @@ import type { CodeFlow } from "../../variant-analysis/shared/analysis-result";
 export default {
   title: "Code Paths",
   component: CodePaths,
-  decorators: [
-    (Story) => (
-      <ThemeProvider colorMode="auto">
-        <Story />
-      </ThemeProvider>
-    ),
-  ],
+  decorators: [(Story) => <Story />],
 } as ComponentMeta<typeof CodePaths>;
 
 const Template: ComponentStory<typeof CodePaths> = (args) => (
diff --git a/extensions/ql-vscode/src/stories/data-flow-paths/DataFlowPaths.stories.tsx b/extensions/ql-vscode/src/stories/data-flow-paths/DataFlowPaths.stories.tsx
new file mode 100644
index 000000000..dd1598360
--- /dev/null
+++ b/extensions/ql-vscode/src/stories/data-flow-paths/DataFlowPaths.stories.tsx
@@ -0,0 +1,19 @@
+import * as React from "react";
+
+import { ComponentMeta, ComponentStory } from "@storybook/react";
+
+import { DataFlowPaths as DataFlowPathsComponent } from "../../view/data-flow-paths/DataFlowPaths";
+import { createMockDataFlowPaths } from "../../../test/factories/variant-analysis/shared/data-flow-paths";
+export default {
+  title: "Data Flow Paths/Data Flow Paths",
+  component: DataFlowPathsComponent,
+} as ComponentMeta<typeof DataFlowPathsComponent>;
+
+const Template: ComponentStory<typeof DataFlowPathsComponent> = (args) => (
+  <DataFlowPathsComponent {...args} />
+);
+
+export const PowerShell = Template.bind({});
+PowerShell.args = {
+  dataFlowPaths: createMockDataFlowPaths(),
+};
diff --git a/extensions/ql-vscode/src/telemetry.ts b/extensions/ql-vscode/src/telemetry.ts
index 4c4cd79d2..6062cb345 100644
--- a/extensions/ql-vscode/src/telemetry.ts
+++ b/extensions/ql-vscode/src/telemetry.ts
@@ -16,7 +16,7 @@ import {
 } from "./config";
 import * as appInsights from "applicationinsights";
 import { extLogger } from "./common";
-import { UserCancellationException } from "./commandRunner";
+import { UserCancellationException } from "./progress";
 import { showBinaryChoiceWithUrlDialog } from "./helpers";
 import { RedactableError } from "./pure/errors";
 
diff --git a/extensions/ql-vscode/src/test-ui.ts b/extensions/ql-vscode/src/test-ui.ts
index f0a642576..45b8f41a7 100644
--- a/extensions/ql-vscode/src/test-ui.ts
+++ b/extensions/ql-vscode/src/test-ui.ts
@@ -1,6 +1,6 @@
 import { lstat, copy, pathExists, createFile } from "fs-extra";
 import { basename } from "path";
-import { Uri, TextDocumentShowOptions, commands, window } from "vscode";
+import { Uri, TextDocumentShowOptions, window } from "vscode";
 import {
   TestHub,
   TestController,
@@ -14,9 +14,9 @@ import {
 import { showAndLogWarningMessage } from "./helpers";
 import { TestTreeNode } from "./test-tree-node";
 import { DisposableObject } from "./pure/disposable-object";
-import { UIService } from "./vscode-utils/ui-service";
 import { QLTestAdapter, getExpectedFile, getActualFile } from "./test-adapter";
-import { extLogger } from "./common";
+import { TestUICommands } from "./common/commands";
+import { App } from "./common/app";
 
 type VSCodeTestEvent =
   | TestRunStartedEvent
@@ -42,22 +42,23 @@ class QLTestListener extends DisposableObject {
 /**
  * Service that implements all UI and commands for QL tests.
  */
-export class TestUIService extends UIService implements TestController {
+export class TestUIService extends DisposableObject implements TestController {
   private readonly listeners: Map<TestAdapter, QLTestListener> = new Map();
 
-  constructor(private readonly testHub: TestHub) {
+  constructor(private readonly app: App, private readonly testHub: TestHub) {
     super();
 
-    void extLogger.log("Registering CodeQL test panel commands.");
-    this.registerCommand(
-      "codeQLTests.showOutputDifferences",
-      this.showOutputDifferences,
-    );
-    this.registerCommand("codeQLTests.acceptOutput", this.acceptOutput);
-
     testHub.registerTestController(this);
   }
 
+  public getCommands(): TestUICommands {
+    return {
+      "codeQLTests.showOutputDifferences":
+        this.showOutputDifferences.bind(this),
+      "codeQLTests.acceptOutput": this.acceptOutput.bind(this),
+    };
+  }
+
   public dispose(): void {
     this.testHub.unregisterTestController(this);
 
@@ -105,7 +106,7 @@ export class TestUIService extends UIService implements TestController {
 
       if (await pathExists(actualPath)) {
         const actualUri = Uri.file(actualPath);
-        await commands.executeCommand<void>(
+        await this.app.commands.execute(
           "vscode.diff",
           expectedUri,
           actualUri,
diff --git a/extensions/ql-vscode/src/variant-analysis/data-flow-paths-view.ts b/extensions/ql-vscode/src/variant-analysis/data-flow-paths-view.ts
new file mode 100644
index 000000000..cfaf568db
--- /dev/null
+++ b/extensions/ql-vscode/src/variant-analysis/data-flow-paths-view.ts
@@ -0,0 +1,68 @@
+import { ExtensionContext, ViewColumn } from "vscode";
+import { AbstractWebview, WebviewPanelConfig } from "../abstract-webview";
+import { assertNever } from "../pure/helpers-pure";
+import { telemetryListener } from "../telemetry";
+import {
+  FromDataFlowPathsMessage,
+  ToDataFlowPathsMessage,
+} from "../pure/interface-types";
+import { DataFlowPaths } from "./shared/data-flow-paths";
+import { showAndLogExceptionWithTelemetry } from "../helpers";
+import { redactableError } from "../pure/errors";
+
+export class DataFlowPathsView extends AbstractWebview<
+  ToDataFlowPathsMessage,
+  FromDataFlowPathsMessage
+> {
+  public static readonly viewType = "codeQL.dataFlowPaths";
+
+  public constructor(ctx: ExtensionContext) {
+    super(ctx);
+  }
+
+  public async showDataFlows(dataFlowPaths: DataFlowPaths) {
+    const panel = await this.getPanel();
+    panel.reveal(undefined, true);
+
+    await this.waitForPanelLoaded();
+
+    await this.postMessage({
+      t: "setDataFlowPaths",
+      dataFlowPaths,
+    });
+  }
+
+  protected async getPanelConfig(): Promise<WebviewPanelConfig> {
+    return {
+      viewId: DataFlowPathsView.viewType,
+      title: "Data Flow Paths",
+      viewColumn: ViewColumn.Active,
+      preserveFocus: true,
+      view: "data-flow-paths",
+    };
+  }
+
+  protected onPanelDispose(): void {
+    // Nothing to dispose
+  }
+
+  protected async onMessage(msg: FromDataFlowPathsMessage): Promise<void> {
+    switch (msg.t) {
+      case "viewLoaded":
+        this.onWebViewLoaded();
+        break;
+      case "telemetry":
+        telemetryListener?.sendUIInteraction(msg.action);
+        break;
+      case "unhandledError":
+        void showAndLogExceptionWithTelemetry(
+          redactableError(
+            msg.error,
+          )`Unhandled error in data flow paths view: ${msg.error.message}`,
+        );
+        break;
+      default:
+        assertNever(msg);
+    }
+  }
+}
diff --git a/extensions/ql-vscode/src/variant-analysis/export-results.ts b/extensions/ql-vscode/src/variant-analysis/export-results.ts
index faf3f0ee5..a866436b7 100644
--- a/extensions/ql-vscode/src/variant-analysis/export-results.ts
+++ b/extensions/ql-vscode/src/variant-analysis/export-results.ts
@@ -9,10 +9,13 @@ import {
   window,
   workspace,
 } from "vscode";
-import { ProgressCallback, UserCancellationException } from "../commandRunner";
+import {
+  ProgressCallback,
+  UserCancellationException,
+  withProgress,
+} from "../progress";
 import { showInformationMessageWithAction } from "../helpers";
 import { extLogger } from "../common";
-import { QueryHistoryManager } from "../query-history/query-history-manager";
 import { createGist } from "./gh-api/gh-api-client";
 import {
   generateVariantAnalysisMarkdown,
@@ -33,25 +36,6 @@ import {
 } from "../pure/variant-analysis-filter-sort";
 import { Credentials } from "../common/authentication";
 
-/**
- * Exports the results of the currently-selected variant analysis.
- */
-export async function exportSelectedVariantAnalysisResults(
-  queryHistoryManager: QueryHistoryManager,
-): Promise<void> {
-  const queryHistoryItem = queryHistoryManager.getCurrentQueryHistoryItem();
-  if (!queryHistoryItem || queryHistoryItem.t !== "variant-analysis") {
-    throw new Error(
-      "No variant analysis results currently open. To open results, click an item in the query history view.",
-    );
-  }
-
-  return commands.executeCommand(
-    "codeQL.exportVariantAnalysisResults",
-    queryHistoryItem.variantAnalysis.id,
-  );
-}
-
 const MAX_VARIANT_ANALYSIS_EXPORT_PROGRESS_STEPS = 2;
 
 /**
@@ -63,108 +47,117 @@ export async function exportVariantAnalysisResults(
   variantAnalysisId: number,
   filterSort: RepositoriesFilterSortStateWithIds | undefined,
   credentials: Credentials,
-  progress: ProgressCallback,
-  token: CancellationToken,
 ): Promise<void> {
-  const variantAnalysis = await variantAnalysisManager.getVariantAnalysis(
-    variantAnalysisId,
-  );
-  if (!variantAnalysis) {
-    void extLogger.log(
-      `Could not find variant analysis with id ${variantAnalysisId}`,
-    );
-    throw new Error(
-      "There was an error when trying to retrieve variant analysis information",
-    );
-  }
+  await withProgress(
+    async (progress: ProgressCallback, token: CancellationToken) => {
+      const variantAnalysis = await variantAnalysisManager.getVariantAnalysis(
+        variantAnalysisId,
+      );
+      if (!variantAnalysis) {
+        void extLogger.log(
+          `Could not find variant analysis with id ${variantAnalysisId}`,
+        );
+        throw new Error(
+          "There was an error when trying to retrieve variant analysis information",
+        );
+      }
 
-  if (token.isCancellationRequested) {
-    throw new UserCancellationException("Cancelled");
-  }
+      if (token.isCancellationRequested) {
+        throw new UserCancellationException("Cancelled");
+      }
 
-  const repoStates = await variantAnalysisManager.getRepoStates(
-    variantAnalysisId,
-  );
-
-  void extLogger.log(
-    `Exporting variant analysis results for variant analysis with id ${variantAnalysis.id}`,
-  );
-
-  progress({
-    maxStep: MAX_VARIANT_ANALYSIS_EXPORT_PROGRESS_STEPS,
-    step: 0,
-    message: "Determining export format",
-  });
-
-  const exportFormat = await determineExportFormat();
-  if (!exportFormat) {
-    return;
-  }
-
-  if (token.isCancellationRequested) {
-    throw new UserCancellationException("Cancelled");
-  }
-
-  const repositories = filterAndSortRepositoriesWithResults(
-    variantAnalysis.scannedRepos,
-    filterSort,
-  )?.filter(
-    (repo) =>
-      repo.resultCount &&
-      repoStates.find((r) => r.repositoryId === repo.repository.id)
-        ?.downloadStatus ===
-        VariantAnalysisScannedRepositoryDownloadStatus.Succeeded,
-  );
-
-  async function* getAnalysesResults(): AsyncGenerator<
-    [VariantAnalysisScannedRepository, VariantAnalysisScannedRepositoryResult]
-  > {
-    if (!variantAnalysis) {
-      return;
-    }
-
-    if (!repositories) {
-      return;
-    }
-
-    for (const repo of repositories) {
-      const result = await variantAnalysisManager.loadResults(
-        variantAnalysis.id,
-        repo.repository.fullName,
-        {
-          skipCacheStore: true,
-        },
+      const repoStates = await variantAnalysisManager.getRepoStates(
+        variantAnalysisId,
       );
 
-      yield [repo, result];
-    }
-  }
+      void extLogger.log(
+        `Exporting variant analysis results for variant analysis with id ${variantAnalysis.id}`,
+      );
 
-  const exportDirectory =
-    variantAnalysisManager.getVariantAnalysisStorageLocation(
-      variantAnalysis.id,
-    );
+      progress({
+        maxStep: MAX_VARIANT_ANALYSIS_EXPORT_PROGRESS_STEPS,
+        step: 0,
+        message: "Determining export format",
+      });
 
-  // The date will be formatted like the following: 20221115T123456Z. The time is in UTC.
-  const formattedDate = new Date()
-    .toISOString()
-    .replace(/[-:]/g, "")
-    .replace(/\.\d+Z$/, "Z");
-  const exportedResultsDirectory = join(
-    exportDirectory,
-    "exported-results",
-    `results_${formattedDate}`,
-  );
+      const exportFormat = await determineExportFormat();
+      if (!exportFormat) {
+        return;
+      }
 
-  await exportVariantAnalysisAnalysisResults(
-    exportedResultsDirectory,
-    variantAnalysis,
-    getAnalysesResults(),
-    repositories?.length ?? 0,
-    exportFormat,
-    credentials,
-    progress,
-    token,
+      if (token.isCancellationRequested) {
+        throw new UserCancellationException("Cancelled");
+      }
+
+      const repositories = filterAndSortRepositoriesWithResults(
+        variantAnalysis.scannedRepos,
+        filterSort,
+      )?.filter(
+        (repo) =>
+          repo.resultCount &&
+          repoStates.find((r) => r.repositoryId === repo.repository.id)
+            ?.downloadStatus ===
+            VariantAnalysisScannedRepositoryDownloadStatus.Succeeded,
+      );
+
+      async function* getAnalysesResults(): AsyncGenerator<
+        [
+          VariantAnalysisScannedRepository,
+          VariantAnalysisScannedRepositoryResult,
+        ]
+      > {
+        if (!variantAnalysis) {
+          return;
+        }
+
+        if (!repositories) {
+          return;
+        }
+
+        for (const repo of repositories) {
+          const result = await variantAnalysisManager.loadResults(
+            variantAnalysis.id,
+            repo.repository.fullName,
+            {
+              skipCacheStore: true,
+            },
+          );
+
+          yield [repo, result];
+        }
+      }
+
+      const exportDirectory =
+        variantAnalysisManager.getVariantAnalysisStorageLocation(
+          variantAnalysis.id,
+        );
+
+      // The date will be formatted like the following: 20221115T123456Z. The time is in UTC.
+      const formattedDate = new Date()
+        .toISOString()
+        .replace(/[-:]/g, "")
+        .replace(/\.\d+Z$/, "Z");
+      const exportedResultsDirectory = join(
+        exportDirectory,
+        "exported-results",
+        `results_${formattedDate}`,
+      );
+
+      await exportVariantAnalysisAnalysisResults(
+        exportedResultsDirectory,
+        variantAnalysis,
+        getAnalysesResults(),
+        repositories?.length ?? 0,
+        exportFormat,
+        credentials,
+        progress,
+        token,
+      );
+    },
+    {
+      title: "Exporting variant analysis results",
+      cancellable: true,
+    },
   );
 }
 
diff --git a/extensions/ql-vscode/src/variant-analysis/repository-selection.ts b/extensions/ql-vscode/src/variant-analysis/repository-selection.ts
index 59f0b7b7b..b8ddcdb51 100644
--- a/extensions/ql-vscode/src/variant-analysis/repository-selection.ts
+++ b/extensions/ql-vscode/src/variant-analysis/repository-selection.ts
@@ -1,4 +1,4 @@
-import { UserCancellationException } from "../commandRunner";
+import { UserCancellationException } from "../progress";
 import { DbManager } from "../databases/db-manager";
 import { DbItemKind } from "../databases/db-item";
 
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 8b64aa8c7..6b9565a99 100644
--- a/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts
+++ b/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts
@@ -18,7 +18,7 @@ import {
   getRemoteControllerRepo,
   setRemoteControllerRepo,
 } from "../config";
-import { ProgressCallback, UserCancellationException } from "../commandRunner";
+import { ProgressCallback, UserCancellationException } from "../progress";
 import { RequestError } from "@octokit/types/dist-types";
 import { QueryMetadata } from "../pure/interface-types";
 import { getErrorMessage, REPO_REGEX } from "../pure/helpers-pure";
@@ -34,6 +34,7 @@ import {
   getQlPackPath,
   FALLBACK_QLPACK_FILENAME,
   QLPACK_FILENAMES,
+  QLPACK_LOCK_FILENAMES,
 } from "../pure/ql";
 
 export interface QlPack {
@@ -70,42 +71,23 @@ async function generateQueryPack(
   const originalPackRoot = await findPackRoot(queryFile);
   const packRelativePath = relative(originalPackRoot, queryFile);
   const targetQueryFileName = join(queryPackDir, packRelativePath);
+  const workspaceFolders = getOnDiskWorkspaceFolders();
 
   let language: string | undefined;
+
+  // Check if the query is already in a query pack.
+  // If so, copy the entire query pack to the temporary directory.
+  // Otherwise, copy only the query file to the temporary directory
+  // and generate a synthetic query pack.
   if (await getQlPackPath(originalPackRoot)) {
     // don't include ql files. We only want the queryFile to be copied.
-    const toCopy = await cliServer.packPacklist(originalPackRoot, false);
-
-    // also copy the lock file (either new name or old name) and the query file itself. These are not included in the packlist.
-    [
-      join(originalPackRoot, "qlpack.lock.yml"),
-      join(originalPackRoot, "codeql-pack.lock.yml"),
+    await copyExistingQueryPack(
+      cliServer,
+      originalPackRoot,
       queryFile,
-    ].forEach((absolutePath) => {
-      if (absolutePath) {
-        toCopy.push(absolutePath);
-      }
-    });
-
-    let copiedCount = 0;
-    await copy(originalPackRoot, queryPackDir, {
-      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 ${queryPackDir}`);
-
-    await fixPackFile(queryPackDir, packRelativePath);
+      queryPackDir,
+      packRelativePath,
+    );
 
     language = await findLanguage(cliServer, Uri.file(targetQueryFileName));
   } else {
@@ -114,20 +96,12 @@ async function generateQueryPack(
 
     // copy only the query file to the query pack directory
     // and generate a synthetic query pack
-    void extLogger.log(`Copying ${queryFile} to ${queryPackDir}`);
-    await copy(queryFile, targetQueryFileName);
-    void extLogger.log("Generating synthetic query pack");
-    const syntheticQueryPack = {
-      name: QUERY_PACK_NAME,
-      version: "0.0.0",
-      dependencies: {
-        [`codeql/${language}-all`]: "*",
-      },
-      defaultSuite: generateDefaultSuite(packRelativePath),
-    };
-    await writeFile(
-      join(queryPackDir, FALLBACK_QLPACK_FILENAME),
-      dump(syntheticQueryPack),
+    await createNewQueryPack(
+      queryFile,
+      queryPackDir,
+      targetQueryFileName,
+      language,
+      packRelativePath,
     );
   }
   if (!language) {
@@ -149,12 +123,21 @@ async function generateQueryPack(
     precompilationOpts = ["--no-precompile"];
   }
 
+  if (await cliServer.useExtensionPacks()) {
+    await injectExtensionPacks(cliServer, queryPackDir, workspaceFolders);
+  }
+
+  await cliServer.packInstall(queryPackDir, {
+    workspaceFolders,
+  });
+
+  // Clear the CLI cache so that the most recent qlpack lock file is used.
+  await cliServer.clearCache();
+
   const bundlePath = await getPackedBundlePath(queryPackDir);
   void extLogger.log(
     `Compiling and bundling query pack from ${queryPackDir} to ${bundlePath}. (This may take a while.)`,
   );
-  await cliServer.packInstall(queryPackDir);
-  const workspaceFolders = getOnDiskWorkspaceFolders();
   await cliServer.packBundle(
     queryPackDir,
     workspaceFolders,
@@ -168,6 +151,70 @@ async function generateQueryPack(
   };
 }
 
+async function createNewQueryPack(
+  queryFile: string,
+  queryPackDir: string,
+  targetQueryFileName: string,
+  language: string | undefined,
+  packRelativePath: string,
+) {
+  void extLogger.log(`Copying ${queryFile} to ${queryPackDir}`);
+  await copy(queryFile, targetQueryFileName);
+  void extLogger.log("Generating synthetic query pack");
+  const syntheticQueryPack = {
+    name: QUERY_PACK_NAME,
+    version: "0.0.0",
+    dependencies: {
+      [`codeql/${language}-all`]: "*",
+    },
+    defaultSuite: generateDefaultSuite(packRelativePath),
+  };
+  await writeFile(
+    join(queryPackDir, FALLBACK_QLPACK_FILENAME),
+    dump(syntheticQueryPack),
+  );
+}
+
+async function copyExistingQueryPack(
+  cliServer: cli.CodeQLCliServer,
+  originalPackRoot: string,
+  queryFile: string,
+  queryPackDir: string,
+  packRelativePath: string,
+) {
+  const toCopy = await cliServer.packPacklist(originalPackRoot, false);
+
+  [
+    // 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(originalPackRoot, f)),
+    queryFile,
+  ].forEach((absolutePath) => {
+    if (absolutePath) {
+      toCopy.push(absolutePath);
+    }
+  });
+
+  let copiedCount = 0;
+  await copy(originalPackRoot, queryPackDir, {
+    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 ${queryPackDir}`);
+
+  await fixPackFile(queryPackDir, packRelativePath);
+}
+
 async function findPackRoot(queryFile: string): Promise<string> {
   // recursively find the directory containing qlpack.yml or codeql-pack.yml
   let dir = dirname(queryFile);
@@ -329,19 +376,54 @@ async function fixPackFile(
   }
   const qlpack = load(await readFile(packPath, "utf8")) as QlPack;
 
-  // update pack name
   qlpack.name = QUERY_PACK_NAME;
-
-  // update default suite
-  delete qlpack.defaultSuiteFile;
-  qlpack.defaultSuite = generateDefaultSuite(packRelativePath);
-
-  // remove any ${workspace} version references
+  updateDefaultSuite(qlpack, packRelativePath);
   removeWorkspaceRefs(qlpack);
 
   await writeFile(packPath, dump(qlpack));
 }
 
+async function injectExtensionPacks(
+  cliServer: cli.CodeQLCliServer,
+  queryPackDir: string,
+  workspaceFolders: string[],
+) {
+  const qlpackFile = await getQlPackPath(queryPackDir);
+  if (!qlpackFile) {
+    throw new Error(
+      `Could not find ${QLPACK_FILENAMES.join(
+        " or ",
+      )} file in '${queryPackDir}'`,
+    );
+  }
+  const syntheticQueryPack = load(await readFile(qlpackFile, "utf8")) as QlPack;
+
+  const extensionPacks = await cliServer.resolveQlpacks(workspaceFolders, true);
+  Object.entries(extensionPacks).forEach(([name, paths]) => {
+    // We are guaranteed that there is at least one path found for each extension pack.
+    // If there are multiple paths, then we have a problem. This means that there is
+    // ambiguity in which path to use. This is an error.
+    if (paths.length > 1) {
+      throw new Error(
+        `Multiple versions of extension pack '${name}' found: ${paths.join(
+          ", ",
+        )}`,
+      );
+    }
+    // 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.
+    syntheticQueryPack.dependencies[name] = "*";
+  });
+  await writeFile(qlpackFile, dump(syntheticQueryPack));
+  await cliServer.clearCache();
+}
+
+function updateDefaultSuite(qlpack: QlPack, packRelativePath: string) {
+  delete qlpack.defaultSuiteFile;
+  qlpack.defaultSuite = generateDefaultSuite(packRelativePath);
+}
+
 function generateDefaultSuite(packRelativePath: string) {
   return [
     {
diff --git a/extensions/ql-vscode/src/variant-analysis/shared/data-flow-paths.ts b/extensions/ql-vscode/src/variant-analysis/shared/data-flow-paths.ts
new file mode 100644
index 000000000..7ed20b69f
--- /dev/null
+++ b/extensions/ql-vscode/src/variant-analysis/shared/data-flow-paths.ts
@@ -0,0 +1,8 @@
+import { AnalysisMessage, CodeFlow, ResultSeverity } from "./analysis-result";
+
+export interface DataFlowPaths {
+  codeFlows: CodeFlow[];
+  ruleDescription: string;
+  message: AnalysisMessage;
+  severity: ResultSeverity;
+}
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 af42da85c..276a3af36 100644
--- a/extensions/ql-vscode/src/variant-analysis/variant-analysis-manager.ts
+++ b/extensions/ql-vscode/src/variant-analysis/variant-analysis-manager.ts
@@ -51,7 +51,11 @@ import {
 import { readFile, readJson, remove, pathExists, outputJson } from "fs-extra";
 import { EOL } from "os";
 import { cancelVariantAnalysis } from "./gh-api/gh-actions-api-client";
-import { ProgressCallback, UserCancellationException } from "../commandRunner";
+import {
+  ProgressCallback,
+  UserCancellationException,
+  withProgress,
+} from "../progress";
 import { CodeQLCliServer } from "../cli";
 import {
   defaultFilterSortState,
@@ -62,6 +66,8 @@ import { URLSearchParams } from "url";
 import { DbManager } from "../databases/db-manager";
 import { App } from "../common/app";
 import { redactableError } from "../pure/errors";
+import { AppCommandManager, VariantAnalysisCommands } from "../common/commands";
+import { exportVariantAnalysisResults } from "./export-results";
 
 export class VariantAnalysisManager
   extends DisposableObject
@@ -123,11 +129,54 @@ export class VariantAnalysisManager
     );
   }
 
+  getCommands(): VariantAnalysisCommands {
+    return {
+      "codeQL.autoDownloadVariantAnalysisResult":
+        this.enqueueDownload.bind(this),
+      "codeQL.copyVariantAnalysisRepoList":
+        this.copyRepoListToClipboard.bind(this),
+      "codeQL.loadVariantAnalysisRepoResults": this.loadResults.bind(this),
+      "codeQL.monitorVariantAnalysis": this.monitorVariantAnalysis.bind(this),
+      "codeQL.openVariantAnalysisLogs": this.openVariantAnalysisLogs.bind(this),
+      "codeQL.openVariantAnalysisView": this.showView.bind(this),
+      "codeQL.runVariantAnalysis":
+        this.runVariantAnalysisFromCommand.bind(this),
+      // Since we are tracking extension usage through commands, this command mirrors the "codeQL.runVariantAnalysis" command
+      "codeQL.runVariantAnalysisContextEditor":
+        this.runVariantAnalysisFromCommand.bind(this),
+    };
+  }
+
+  get commandManager(): AppCommandManager {
+    return this.app.commands;
+  }
+
+  private async runVariantAnalysisFromCommand(uri?: Uri) {
+    return withProgress(
+      async (progress, token) =>
+        this.runVariantAnalysis(
+          uri || Window.activeTextEditor?.document.uri,
+          progress,
+          token,
+        ),
+      {
+        title: "Run Variant Analysis",
+        cancellable: true,
+      },
+    );
+  }
+
   public async runVariantAnalysis(
     uri: Uri | undefined,
     progress: ProgressCallback,
     token: CancellationToken,
   ): Promise<void> {
+    progress({
+      maxStep: 5,
+      step: 0,
+      message: "Getting credentials",
+    });
+
     const {
       actionBranch,
       base64Pack,
@@ -452,19 +501,16 @@ export class VariantAnalysisManager
 
   public async monitorVariantAnalysis(
     variantAnalysis: VariantAnalysis,
-    cancellationToken: CancellationToken,
   ): Promise<void> {
     await this.variantAnalysisMonitor.monitorVariantAnalysis(
       variantAnalysis,
       this.app.credentials,
-      cancellationToken,
     );
   }
 
   public async autoDownloadVariantAnalysisResult(
     scannedRepo: VariantAnalysisScannedRepository,
     variantAnalysis: VariantAnalysis,
-    cancellationToken: CancellationToken,
   ): Promise<void> {
     if (
       this.repoStates.get(variantAnalysis.id)?.[scannedRepo.repository.id]
@@ -481,13 +527,6 @@ export class VariantAnalysisManager
 
     await this.onRepoStateUpdated(variantAnalysis.id, repoState);
 
-    if (cancellationToken && cancellationToken.isCancellationRequested) {
-      repoState.downloadStatus =
-        VariantAnalysisScannedRepositoryDownloadStatus.Failed;
-      await this.onRepoStateUpdated(variantAnalysis.id, repoState);
-      return;
-    }
-
     let repoTask: VariantAnalysisRepositoryTask;
     try {
       const repoTaskResponse = await getVariantAnalysisRepo(
@@ -562,14 +601,9 @@ export class VariantAnalysisManager
   public async enqueueDownload(
     scannedRepo: VariantAnalysisScannedRepository,
     variantAnalysis: VariantAnalysis,
-    token: CancellationToken,
   ): Promise<void> {
     await this.queue.add(() =>
-      this.autoDownloadVariantAnalysisResult(
-        scannedRepo,
-        variantAnalysis,
-        token,
-      ),
+      this.autoDownloadVariantAnalysisResult(scannedRepo, variantAnalysis),
     );
   }
 
@@ -647,6 +681,18 @@ export class VariantAnalysisManager
     await env.clipboard.writeText(text.join(EOL));
   }
 
+  public async exportResults(
+    variantAnalysisId: number,
+    filterSort?: RepositoriesFilterSortStateWithIds,
+  ) {
+    await exportVariantAnalysisResults(
+      this,
+      variantAnalysisId,
+      filterSort,
+      this.app.credentials,
+    );
+  }
+
   private getRepoStatesStoragePath(variantAnalysisId: number): string {
     return join(
       this.getVariantAnalysisStorageLocation(variantAnalysisId),
diff --git a/extensions/ql-vscode/src/variant-analysis/variant-analysis-monitor.ts b/extensions/ql-vscode/src/variant-analysis/variant-analysis-monitor.ts
index f7683fb4b..7fa8f3b14 100644
--- a/extensions/ql-vscode/src/variant-analysis/variant-analysis-monitor.ts
+++ b/extensions/ql-vscode/src/variant-analysis/variant-analysis-monitor.ts
@@ -1,4 +1,4 @@
-import { CancellationToken, commands, EventEmitter } from "vscode";
+import { commands, EventEmitter } from "vscode";
 import { getVariantAnalysis } from "./gh-api/gh-api-client";
 
 import {
@@ -37,7 +37,6 @@ export class VariantAnalysisMonitor extends DisposableObject {
   public async monitorVariantAnalysis(
     variantAnalysis: VariantAnalysis,
     credentials: Credentials,
-    cancellationToken: CancellationToken,
   ): Promise<void> {
     let attemptCount = 0;
     const scannedReposDownloaded: number[] = [];
@@ -45,10 +44,6 @@ export class VariantAnalysisMonitor extends DisposableObject {
     while (attemptCount <= VariantAnalysisMonitor.maxAttemptCount) {
       await sleep(VariantAnalysisMonitor.sleepTime);
 
-      if (cancellationToken && cancellationToken.isCancellationRequested) {
-        return;
-      }
-
       if (await this.shouldCancelMonitor(variantAnalysis.id)) {
         return;
       }
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 7f307c42d..4db740683 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
@@ -2,6 +2,8 @@ import {
   VariantAnalysis,
   VariantAnalysisScannedRepositoryState,
 } from "./shared/variant-analysis";
+import { AppCommandManager } from "../common/commands";
+import { RepositoriesFilterSortStateWithIds } from "../pure/variant-analysis-filter-sort";
 
 export interface VariantAnalysisViewInterface {
   variantAnalysisId: number;
@@ -11,6 +13,8 @@ export interface VariantAnalysisViewInterface {
 export interface VariantAnalysisViewManager<
   T extends VariantAnalysisViewInterface,
 > {
+  commandManager: AppCommandManager;
+
   registerView(view: T): void;
   unregisterView(view: T): void;
   getView(variantAnalysisId: number): T | undefined;
@@ -21,4 +25,11 @@ export interface VariantAnalysisViewManager<
   getRepoStates(
     variantAnalysisId: number,
   ): Promise<VariantAnalysisScannedRepositoryState[]>;
+  openQueryFile(variantAnalysisId: number): Promise<void>;
+  openQueryText(variantAnalysisId: number): Promise<void>;
+  cancelVariantAnalysis(variantAnalysisId: number): Promise<void>;
+  exportResults(
+    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 e41a85205..ffd07c146 100644
--- a/extensions/ql-vscode/src/variant-analysis/variant-analysis-view.ts
+++ b/extensions/ql-vscode/src/variant-analysis/variant-analysis-view.ts
@@ -15,14 +15,21 @@ import {
   VariantAnalysisViewInterface,
   VariantAnalysisViewManager,
 } from "./variant-analysis-view-manager";
-import { showAndLogWarningMessage } from "../helpers";
+import {
+  showAndLogExceptionWithTelemetry,
+  showAndLogWarningMessage,
+} from "../helpers";
 import { telemetryListener } from "../telemetry";
+import { redactableError } from "../pure/errors";
+import { DataFlowPathsView } from "./data-flow-paths-view";
+import { DataFlowPaths } from "./shared/data-flow-paths";
 
 export class VariantAnalysisView
   extends AbstractWebview<ToVariantAnalysisMessage, FromVariantAnalysisMessage>
   implements VariantAnalysisViewInterface
 {
   public static readonly viewType = "codeQL.variantAnalysis";
+  private readonly dataFlowPathsView: DataFlowPathsView;
 
   public constructor(
     ctx: ExtensionContext,
@@ -32,6 +39,8 @@ export class VariantAnalysisView
     super(ctx);
 
     manager.registerView(this);
+
+    this.dataFlowPathsView = new DataFlowPathsView(ctx);
   }
 
   public async openView() {
@@ -106,10 +115,7 @@ export class VariantAnalysisView
 
         break;
       case "cancelVariantAnalysis":
-        void commands.executeCommand(
-          "codeQL.cancelVariantAnalysis",
-          this.variantAnalysisId,
-        );
+        await this.manager.cancelVariantAnalysis(this.variantAnalysisId);
         break;
       case "requestRepositoryResults":
         void commands.executeCommand(
@@ -119,16 +125,10 @@ export class VariantAnalysisView
         );
         break;
       case "openQueryFile":
-        void commands.executeCommand(
-          "codeQL.openVariantAnalysisQueryFile",
-          this.variantAnalysisId,
-        );
+        await this.manager.openQueryFile(this.variantAnalysisId);
         break;
       case "openQueryText":
-        void commands.executeCommand(
-          "codeQL.openVariantAnalysisQueryText",
-          this.variantAnalysisId,
-        );
+        await this.manager.openQueryText(this.variantAnalysisId);
         break;
       case "copyRepositoryList":
         void commands.executeCommand(
@@ -138,21 +138,30 @@ export class VariantAnalysisView
         );
         break;
       case "exportResults":
-        void commands.executeCommand(
-          "codeQL.exportVariantAnalysisResults",
+        await this.manager.exportResults(
           this.variantAnalysisId,
           msg.filterSort,
         );
         break;
       case "openLogs":
-        await commands.executeCommand(
+        await this.manager.commandManager.execute(
           "codeQL.openVariantAnalysisLogs",
           this.variantAnalysisId,
         );
         break;
+      case "showDataFlowPaths":
+        await this.showDataFlows(msg.dataFlowPaths);
+        break;
       case "telemetry":
         telemetryListener?.sendUIInteraction(msg.action);
         break;
+      case "unhandledError":
+        void showAndLogExceptionWithTelemetry(
+          redactableError(
+            msg.error,
+          )`Unhandled error in variant analysis results view: ${msg.error.message}`,
+        );
+        break;
       default:
         assertNever(msg);
     }
@@ -193,4 +202,8 @@ export class VariantAnalysisView
       ? `${variantAnalysis.query.name} - Variant Analysis Results`
       : `Variant Analysis ${this.variantAnalysisId} - Results`;
   }
+
+  private async showDataFlows(dataFlows: DataFlowPaths): Promise<void> {
+    await this.dataFlowPathsView.showDataFlows(dataFlows);
+  }
 }
diff --git a/extensions/ql-vscode/src/view/common/CodePaths/CodePaths.tsx b/extensions/ql-vscode/src/view/common/CodePaths/CodePaths.tsx
index 90bd3b44e..e7bb09f5b 100644
--- a/extensions/ql-vscode/src/view/common/CodePaths/CodePaths.tsx
+++ b/extensions/ql-vscode/src/view/common/CodePaths/CodePaths.tsx
@@ -1,17 +1,13 @@
 import * as React from "react";
-import { useRef, useState } from "react";
 import styled from "styled-components";
 import { VSCodeLink } from "@vscode/webview-ui-toolkit/react";
 
-import { Overlay, ThemeProvider } from "@primer/react";
-
 import {
   AnalysisMessage,
   CodeFlow,
   ResultSeverity,
 } from "../../../variant-analysis/shared/analysis-result";
-import { CodePathsOverlay } from "./CodePathsOverlay";
-import { useTelemetryOnChange } from "../telemetry";
+import { vscode } from "../../vscode-api";
 
 const ShowPathsLink = styled(VSCodeLink)`
   cursor: pointer;
@@ -24,46 +20,27 @@ export type CodePathsProps = {
   severity: ResultSeverity;
 };
 
-const filterIsOpenTelemetry = (v: boolean) => v;
-
 export const CodePaths = ({
   codeFlows,
   ruleDescription,
   message,
   severity,
 }: CodePathsProps) => {
-  const [isOpen, setIsOpen] = useState(false);
-  useTelemetryOnChange(isOpen, "code-path-is-open", {
-    filterTelemetryOnValue: filterIsOpenTelemetry,
-  });
-
-  const linkRef = useRef<HTMLAnchorElement>(null);
-
-  const closeOverlay = () => setIsOpen(false);
+  const onShowPathsClick = () => {
+    vscode.postMessage({
+      t: "showDataFlowPaths",
+      dataFlowPaths: {
+        codeFlows,
+        ruleDescription,
+        message,
+        severity,
+      },
+    });
+  };
 
   return (
     <>
-      <ShowPathsLink onClick={() => setIsOpen(true)} ref={linkRef}>
-        Show paths
-      </ShowPathsLink>
-      {isOpen && (
-        <ThemeProvider colorMode="auto">
-          <Overlay
-            returnFocusRef={linkRef}
-            onEscape={closeOverlay}
-            onClickOutside={closeOverlay}
-            anchorSide="outside-top"
-          >
-            <CodePathsOverlay
-              codeFlows={codeFlows}
-              ruleDescription={ruleDescription}
-              message={message}
-              severity={severity}
-              onClose={closeOverlay}
-            />
-          </Overlay>
-        </ThemeProvider>
-      )}
+      <ShowPathsLink onClick={onShowPathsClick}>Show paths</ShowPathsLink>
     </>
   );
 };
diff --git a/extensions/ql-vscode/src/view/common/CodePaths/CodePathsOverlay.tsx b/extensions/ql-vscode/src/view/common/CodePaths/CodePathsOverlay.tsx
deleted file mode 100644
index 7ba11898a..000000000
--- a/extensions/ql-vscode/src/view/common/CodePaths/CodePathsOverlay.tsx
+++ /dev/null
@@ -1,112 +0,0 @@
-import * as React from "react";
-import { useState } from "react";
-import styled from "styled-components";
-
-import {
-  AnalysisMessage,
-  CodeFlow,
-  ResultSeverity,
-} from "../../../variant-analysis/shared/analysis-result";
-import { useTelemetryOnChange } from "../telemetry";
-import { SectionTitle } from "../SectionTitle";
-import { VerticalSpace } from "../VerticalSpace";
-import { CodeFlowsDropdown } from "./CodeFlowsDropdown";
-import { CodePath } from "./CodePath";
-
-const StyledCloseButton = styled.button`
-  position: absolute;
-  top: 1em;
-  right: 4em;
-  background-color: var(--vscode-editor-background);
-  color: var(--vscode-editor-foreground);
-  border: none;
-  cursor: pointer;
-
-  &:focus-visible {
-    outline: none;
-  }
-`;
-
-const OverlayContainer = styled.div`
-  height: 100%;
-  width: 100%;
-  padding: 2em;
-  position: fixed;
-  top: 0;
-  left: 0;
-  background-color: var(--vscode-editor-background);
-  color: var(--vscode-editor-foreground);
-  overflow-y: scroll;
-`;
-
-const CloseButton = ({ onClick }: { onClick: () => void }) => (
-  <StyledCloseButton onClick={onClick} tabIndex={-1}>
-    <span className="codicon codicon-chrome-close" />
-  </StyledCloseButton>
-);
-
-const PathsContainer = styled.div`
-  display: flex;
-  justify-content: center;
-  align-items: center;
-`;
-
-const PathDetailsContainer = styled.div`
-  padding: 0;
-  border: 0;
-`;
-
-const PathDropdownContainer = styled.div`
-  flex-grow: 1;
-  padding: 0 0 0 0.2em;
-  border: none;
-`;
-
-type CodePathsOverlayProps = {
-  codeFlows: CodeFlow[];
-  ruleDescription: string;
-  message: AnalysisMessage;
-  severity: ResultSeverity;
-  onClose: () => void;
-};
-
-export const CodePathsOverlay = ({
-  codeFlows,
-  ruleDescription,
-  message,
-  severity,
-  onClose,
-}: CodePathsOverlayProps) => {
-  const [selectedCodeFlow, setSelectedCodeFlow] = useState(codeFlows[0]);
-  useTelemetryOnChange(selectedCodeFlow, "code-flow-selected");
-
-  return (
-    <OverlayContainer>
-      <CloseButton onClick={onClose} />
-
-      <SectionTitle>{ruleDescription}</SectionTitle>
-      <VerticalSpace size={2} />
-
-      <PathsContainer>
-        <PathDetailsContainer>
-          {codeFlows.length} paths available:{" "}
-          {selectedCodeFlow.threadFlows.length} steps in
-        </PathDetailsContainer>
-        <PathDropdownContainer>
-          <CodeFlowsDropdown
-            codeFlows={codeFlows}
-            setSelectedCodeFlow={setSelectedCodeFlow}
-          />
-        </PathDropdownContainer>
-      </PathsContainer>
-
-      <VerticalSpace size={2} />
-      <CodePath
-        codeFlow={selectedCodeFlow}
-        severity={severity}
-        message={message}
-      />
-      <VerticalSpace size={3} />
-    </OverlayContainer>
-  );
-};
diff --git a/extensions/ql-vscode/src/view/common/CodePaths/__tests__/CodePaths.spec.tsx b/extensions/ql-vscode/src/view/common/CodePaths/__tests__/CodePaths.spec.tsx
index a45ed417b..1ff6135e1 100644
--- a/extensions/ql-vscode/src/view/common/CodePaths/__tests__/CodePaths.spec.tsx
+++ b/extensions/ql-vscode/src/view/common/CodePaths/__tests__/CodePaths.spec.tsx
@@ -18,20 +18,25 @@ describe(CodePaths.name, () => {
       />,
     );
 
-  it("renders correctly when unexpanded", () => {
+  it("renders 'show paths' link", () => {
     render();
 
     expect(screen.getByText("Show paths")).toBeInTheDocument();
-    expect(screen.queryByText("Code snippet text")).not.toBeInTheDocument();
-    expect(screen.queryByText("Rule description")).not.toBeInTheDocument();
   });
 
-  it("renders correctly when expanded", async () => {
+  it("posts extension message when 'show paths' link clicked", async () => {
     render();
 
     await userEvent.click(screen.getByText("Show paths"));
 
-    expect(screen.getByText("Code snippet text")).toBeInTheDocument();
-    expect(screen.getByText("Rule description")).toBeInTheDocument();
+    expect((window as any).vsCodeApi.postMessage).toHaveBeenCalledWith({
+      t: "showDataFlowPaths",
+      dataFlowPaths: {
+        codeFlows: createMockCodeFlows(),
+        ruleDescription: "Rule description",
+        message: createMockAnalysisMessage(),
+        severity: "Recommendation",
+      },
+    });
   });
 });
diff --git a/extensions/ql-vscode/src/view/common/errors.ts b/extensions/ql-vscode/src/view/common/errors.ts
new file mode 100644
index 000000000..e6a443de1
--- /dev/null
+++ b/extensions/ql-vscode/src/view/common/errors.ts
@@ -0,0 +1,54 @@
+import { getErrorMessage, getErrorStack } from "../../pure/helpers-pure";
+import { vscode } from "../vscode-api";
+
+// Keep track of previous errors that have happened.
+// The listeners for uncaught errors and rejections can get triggered
+// twice for each error. This is believed to be an effect caused
+// by React's error boundaries. Adding an error boundary stops
+// this duplicate reporting for errors that happen during component
+// rendering, but unfortunately errors from event handlers and
+// timeouts are still duplicated and there does not appear to be
+// a way around this.
+const previousErrors: Set<Error> = new Set();
+
+function shouldReportError(error: Error): boolean {
+  const seenBefore = previousErrors.has(error);
+  previousErrors.add(error);
+  setTimeout(() => {
+    previousErrors.delete(error);
+  }, 1000);
+  return !seenBefore;
+}
+
+const unhandledErrorListener = (event: ErrorEvent) => {
+  if (shouldReportError(event.error)) {
+    vscode.postMessage({
+      t: "unhandledError",
+      error: {
+        message: getErrorMessage(event.error),
+        stack: getErrorStack(event.error),
+      },
+    });
+  }
+};
+
+const unhandledRejectionListener = (event: PromiseRejectionEvent) => {
+  if (shouldReportError(event.reason)) {
+    vscode.postMessage({
+      t: "unhandledError",
+      error: {
+        message: getErrorMessage(event.reason),
+        stack: getErrorStack(event.reason),
+      },
+    });
+  }
+};
+
+/**
+ * Adds listeners for unhandled errors / rejected promises.
+ * When an error is detected a "unhandledError" message is posted to the view.
+ */
+export function registerUnhandledErrorListener() {
+  window.addEventListener("error", unhandledErrorListener);
+  window.addEventListener("unhandledrejection", unhandledRejectionListener);
+}
diff --git a/extensions/ql-vscode/src/view/data-flow-paths/DataFlowPaths.tsx b/extensions/ql-vscode/src/view/data-flow-paths/DataFlowPaths.tsx
new file mode 100644
index 000000000..7bccc0bed
--- /dev/null
+++ b/extensions/ql-vscode/src/view/data-flow-paths/DataFlowPaths.tsx
@@ -0,0 +1,71 @@
+import * as React from "react";
+import styled from "styled-components";
+import { useState } from "react";
+
+import { useTelemetryOnChange } from "../common/telemetry";
+import { CodeFlowsDropdown } from "../common/CodePaths/CodeFlowsDropdown";
+import { SectionTitle, VerticalSpace } from "../common";
+import { CodePath } from "../common/CodePaths/CodePath";
+import { DataFlowPaths as DataFlowPathsDomainModel } from "../../variant-analysis/shared/data-flow-paths";
+
+const PathsContainer = styled.div`
+  display: flex;
+  justify-content: center;
+  align-items: center;
+`;
+
+const PathDetailsContainer = styled.div`
+  padding: 0;
+  border: 0;
+`;
+
+const PathDropdownContainer = styled.div`
+  flex-grow: 1;
+  padding: 0 0 0 0.2em;
+  border: none;
+`;
+
+export type DataFlowPathsProps = {
+  dataFlowPaths: DataFlowPathsDomainModel;
+};
+
+export const DataFlowPaths = ({
+  dataFlowPaths,
+}: {
+  dataFlowPaths: DataFlowPathsDomainModel;
+}): JSX.Element => {
+  const [selectedCodeFlow, setSelectedCodeFlow] = useState(
+    dataFlowPaths.codeFlows[0],
+  );
+  useTelemetryOnChange(selectedCodeFlow, "code-flow-selected");
+
+  const { codeFlows, ruleDescription, message, severity } = dataFlowPaths;
+
+  return (
+    <>
+      <VerticalSpace size={2} />
+      <SectionTitle>{ruleDescription}</SectionTitle>
+      <VerticalSpace size={2} />
+
+      <PathsContainer>
+        <PathDetailsContainer>
+          {codeFlows.length} paths available:{" "}
+          {selectedCodeFlow?.threadFlows.length} steps in
+        </PathDetailsContainer>
+        <PathDropdownContainer>
+          <CodeFlowsDropdown
+            codeFlows={codeFlows}
+            setSelectedCodeFlow={setSelectedCodeFlow}
+          />
+        </PathDropdownContainer>
+      </PathsContainer>
+
+      <VerticalSpace size={2} />
+      <CodePath
+        codeFlow={selectedCodeFlow}
+        severity={severity}
+        message={message}
+      />
+    </>
+  );
+};
diff --git a/extensions/ql-vscode/src/view/data-flow-paths/DataFlowPathsView.tsx b/extensions/ql-vscode/src/view/data-flow-paths/DataFlowPathsView.tsx
new file mode 100644
index 000000000..de3d490a7
--- /dev/null
+++ b/extensions/ql-vscode/src/view/data-flow-paths/DataFlowPathsView.tsx
@@ -0,0 +1,47 @@
+import * as React from "react";
+import { useEffect, useState } from "react";
+import { ToDataFlowPathsMessage } from "../../pure/interface-types";
+import { DataFlowPaths as DataFlowPathsDomainModel } from "../../variant-analysis/shared/data-flow-paths";
+import { DataFlowPaths } from "./DataFlowPaths";
+
+export type DataFlowPathsViewProps = {
+  dataFlowPaths?: DataFlowPathsDomainModel;
+};
+
+export function DataFlowPathsView({
+  dataFlowPaths: initialDataFlowPaths,
+}: DataFlowPathsViewProps): JSX.Element {
+  const [dataFlowPaths, setDataFlowPaths] = useState<
+    DataFlowPathsDomainModel | undefined
+  >(initialDataFlowPaths);
+
+  useEffect(() => {
+    const listener = (evt: MessageEvent) => {
+      if (evt.origin === window.origin) {
+        const msg: ToDataFlowPathsMessage = evt.data;
+        if (msg.t === "setDataFlowPaths") {
+          setDataFlowPaths(msg.dataFlowPaths);
+
+          // Scroll to the top of the page when we're rendering
+          // new data flow paths.
+          window.scrollTo(0, 0);
+        }
+      } else {
+        // sanitize origin
+        const origin = evt.origin.replace(/\n|\r/g, "");
+        console.error(`Invalid event origin ${origin}`);
+      }
+    };
+    window.addEventListener("message", listener);
+
+    return () => {
+      window.removeEventListener("message", listener);
+    };
+  }, []);
+
+  if (!dataFlowPaths) {
+    return <>Loading data flow paths</>;
+  }
+
+  return <DataFlowPaths dataFlowPaths={dataFlowPaths} />;
+}
diff --git a/extensions/ql-vscode/src/view/data-flow-paths/__tests__/DataFlowPaths.spec.tsx b/extensions/ql-vscode/src/view/data-flow-paths/__tests__/DataFlowPaths.spec.tsx
new file mode 100644
index 000000000..02efd2105
--- /dev/null
+++ b/extensions/ql-vscode/src/view/data-flow-paths/__tests__/DataFlowPaths.spec.tsx
@@ -0,0 +1,31 @@
+import * as React from "react";
+import { render as reactRender, screen } from "@testing-library/react";
+import { DataFlowPaths, DataFlowPathsProps } from "../DataFlowPaths";
+import { createMockDataFlowPaths } from "../../../../test/factories/variant-analysis/shared/data-flow-paths";
+
+describe(DataFlowPaths.name, () => {
+  const render = (props: DataFlowPathsProps) =>
+    reactRender(<DataFlowPaths {...props} />);
+
+  it("renders data flow paths", () => {
+    const dataFlowPaths = createMockDataFlowPaths();
+
+    render({ dataFlowPaths });
+
+    expect(screen.getByText(dataFlowPaths.ruleDescription)).toBeInTheDocument();
+    expect(
+      screen.getByText("1 paths available", { exact: false }),
+    ).toBeInTheDocument();
+    expect(
+      screen.getByText("3 steps in", {
+        exact: false,
+      }),
+    ).toBeInTheDocument();
+
+    expect(
+      screen.getByText("This zip file may have a dangerous path", {
+        exact: false,
+      }),
+    ).toBeInTheDocument();
+  });
+});
diff --git a/extensions/ql-vscode/src/view/data-flow-paths/__tests__/DataFlowPathsView.spec.tsx b/extensions/ql-vscode/src/view/data-flow-paths/__tests__/DataFlowPathsView.spec.tsx
new file mode 100644
index 000000000..7baefc06c
--- /dev/null
+++ b/extensions/ql-vscode/src/view/data-flow-paths/__tests__/DataFlowPathsView.spec.tsx
@@ -0,0 +1,31 @@
+import * as React from "react";
+import { render as reactRender, screen } from "@testing-library/react";
+import {
+  DataFlowPathsView,
+  DataFlowPathsViewProps,
+} from "../DataFlowPathsView";
+import { createMockCodeFlows } from "../../../../test/factories/variant-analysis/shared/CodeFlow";
+import { createMockDataFlowPaths } from "../../../../test/factories/variant-analysis/shared/data-flow-paths";
+
+describe(DataFlowPathsView.name, () => {
+  const render = (props: Partial<DataFlowPathsViewProps>) =>
+    reactRender(<DataFlowPathsView {...props} />);
+
+  it("renders a loading data flow paths view", () => {
+    render({});
+
+    expect(screen.getByText("Loading data flow paths")).toBeInTheDocument();
+  });
+
+  it("renders a data flow paths view", () => {
+    const dataFlowPaths = createMockDataFlowPaths({
+      ruleDescription: "Rule description",
+      codeFlows: createMockCodeFlows(),
+    });
+
+    render({ dataFlowPaths });
+
+    expect(screen.queryByText("Code snippet text")).toBeInTheDocument();
+    expect(screen.getByText("Rule description")).toBeInTheDocument();
+  });
+});
diff --git a/extensions/ql-vscode/src/view/data-flow-paths/index.tsx b/extensions/ql-vscode/src/view/data-flow-paths/index.tsx
new file mode 100644
index 000000000..5fd13430b
--- /dev/null
+++ b/extensions/ql-vscode/src/view/data-flow-paths/index.tsx
@@ -0,0 +1,9 @@
+import * as React from "react";
+import { WebviewDefinition } from "../webview-definition";
+import { DataFlowPathsView } from "./DataFlowPathsView";
+
+const definition: WebviewDefinition = {
+  component: <DataFlowPathsView />,
+};
+
+export default definition;
diff --git a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysis.tsx b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysis.tsx
index cf4a0df25..83d473563 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysis.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysis.tsx
@@ -13,7 +13,7 @@ import { VariantAnalysisLoading } from "./VariantAnalysisLoading";
 import { ToVariantAnalysisMessage } from "../../pure/interface-types";
 import { vscode } from "../vscode-api";
 import { defaultFilterSortState } from "../../pure/variant-analysis-filter-sort";
-import { useTelemetryOnChange } from "../common/telemetry";
+import { sendTelemetry, useTelemetryOnChange } from "../common/telemetry";
 
 export type VariantAnalysisProps = {
   variantAnalysis?: VariantAnalysisDomainModel;
@@ -25,18 +25,21 @@ const openQueryFile = () => {
   vscode.postMessage({
     t: "openQueryFile",
   });
+  sendTelemetry("variant-analysis-open-query-file");
 };
 
 const openQueryText = () => {
   vscode.postMessage({
     t: "openQueryText",
   });
+  sendTelemetry("variant-analysis-open-query-text");
 };
 
 const stopQuery = () => {
   vscode.postMessage({
     t: "cancelVariantAnalysis",
   });
+  sendTelemetry("variant-analysis-cancel");
 };
 
 const openLogs = () => {
@@ -136,6 +139,7 @@ export function VariantAnalysis({
         repositoryIds: selectedRepositoryIds,
       },
     });
+    sendTelemetry("variant-analysis-export-results");
   }, [filterSortState, selectedRepositoryIds]);
 
   if (
diff --git a/extensions/ql-vscode/src/view/webview.tsx b/extensions/ql-vscode/src/view/webview.tsx
index 4698a33d8..9207975d9 100644
--- a/extensions/ql-vscode/src/view/webview.tsx
+++ b/extensions/ql-vscode/src/view/webview.tsx
@@ -7,8 +7,11 @@ import { WebviewDefinition } from "./webview-definition";
 
 // Allow all views to use Codicons
 import "@vscode/codicons/dist/codicon.css";
+import { registerUnhandledErrorListener } from "./common/errors";
 
 const render = () => {
+  registerUnhandledErrorListener();
+
   const element = document.getElementById("root");
 
   if (!element) {
@@ -27,9 +30,9 @@ const render = () => {
   // eslint-disable-next-line @typescript-eslint/no-var-requires
   const view: WebviewDefinition = require(`./${viewName}/index.tsx`).default;
 
-  createRoot(element).render(
+  const root = createRoot(element);
+  root.render(
     <StrictMode>
-      {/* Post a message to the extension when fully loaded. See https://github.com/reactwg/react-18/discussions/5 ("What about the render callback?")*/}
       <div ref={() => vscode.postMessage({ t: "viewLoaded", viewName })}>
         {view.component}
       </div>
diff --git a/extensions/ql-vscode/src/vscode-utils/external-files.ts b/extensions/ql-vscode/src/vscode-utils/external-files.ts
new file mode 100644
index 000000000..b355199ef
--- /dev/null
+++ b/extensions/ql-vscode/src/vscode-utils/external-files.ts
@@ -0,0 +1,50 @@
+import { Uri, window } from "vscode";
+import { AppCommandManager } from "../common/commands";
+import {
+  showAndLogExceptionWithTelemetry,
+  showBinaryChoiceDialog,
+} from "../helpers";
+import { redactableError } from "../pure/errors";
+import { asError, getErrorMessage, getErrorStack } from "../pure/helpers-pure";
+
+export async function tryOpenExternalFile(
+  commandManager: AppCommandManager,
+  fileLocation: string,
+) {
+  const uri = Uri.file(fileLocation);
+  try {
+    await window.showTextDocument(uri, { preview: false });
+  } catch (e) {
+    const msg = getErrorMessage(e);
+    if (
+      msg.includes("Files above 50MB cannot be synchronized with extensions") ||
+      msg.includes("too large to open")
+    ) {
+      const res = await showBinaryChoiceDialog(
+        `VS Code does not allow extensions to open files >50MB. This file
+exceeds that limit. Do you want to open it outside of VS Code?
+
+You can also try manually opening it inside VS Code by selecting
+the file in the file explorer and dragging it into the workspace.`,
+      );
+      if (res) {
+        try {
+          await commandManager.execute("revealFileInOS", uri);
+        } catch (e) {
+          void showAndLogExceptionWithTelemetry(
+            redactableError(
+              asError(e),
+            )`Failed to reveal file in OS: ${getErrorMessage(e)}`,
+          );
+        }
+      }
+    } else {
+      void showAndLogExceptionWithTelemetry(
+        redactableError(asError(e))`Could not open file ${fileLocation}`,
+        {
+          fullMessage: `${getErrorMessage(e)}\n${getErrorStack(e)}`,
+        },
+      );
+    }
+  }
+}
diff --git a/extensions/ql-vscode/src/vscode-utils/ui-service.ts b/extensions/ql-vscode/src/vscode-utils/ui-service.ts
deleted file mode 100644
index c2ffef0c8..000000000
--- a/extensions/ql-vscode/src/vscode-utils/ui-service.ts
+++ /dev/null
@@ -1,32 +0,0 @@
-import { TreeDataProvider, window } from "vscode";
-import { DisposableObject } from "../pure/disposable-object";
-import { commandRunner } from "../commandRunner";
-
-/**
- * A VS Code service that interacts with the UI, including handling commands.
- */
-export class UIService extends DisposableObject {
-  protected constructor() {
-    super();
-  }
-
-  /**
-   * Registers a command handler with Visual Studio Code.
-   * @param command The ID of the command to register.
-   * @param callback Callback function to implement the command.
-   * @remarks The command handler is automatically unregistered when the service is disposed.
-   */
-  protected registerCommand(
-    command: string,
-    callback: (...args: any[]) => any,
-  ): void {
-    this.push(commandRunner(command, callback.bind(this)));
-  }
-
-  protected registerTreeDataProvider<T>(
-    viewId: string,
-    treeDataProvider: TreeDataProvider<T>,
-  ): void {
-    this.push(window.registerTreeDataProvider<T>(viewId, treeDataProvider));
-  }
-}
diff --git a/extensions/ql-vscode/supported_cli_versions.json b/extensions/ql-vscode/supported_cli_versions.json
index 58b5b931d..124e33c2b 100644
--- a/extensions/ql-vscode/supported_cli_versions.json
+++ b/extensions/ql-vscode/supported_cli_versions.json
@@ -1,5 +1,5 @@
 [
-  "v2.12.4",
+  "v2.12.5",
   "v2.11.6",
   "v2.7.6",
   "v2.8.5",
diff --git a/extensions/ql-vscode/test/__mocks__/appMock.ts b/extensions/ql-vscode/test/__mocks__/appMock.ts
index e5f74be29..1b6d9da9d 100644
--- a/extensions/ql-vscode/test/__mocks__/appMock.ts
+++ b/extensions/ql-vscode/test/__mocks__/appMock.ts
@@ -6,23 +6,25 @@ import { createMockLogger } from "./loggerMock";
 import { createMockMemento } from "../mock-memento";
 import { testCredentialsWithStub } from "../factories/authentication";
 import { Credentials } from "../../src/common/authentication";
+import { AppCommandManager } from "../../src/common/commands";
+import { createMockCommandManager } from "./commandsMock";
 
 export function createMockApp({
   extensionPath = "/mock/extension/path",
   workspaceStoragePath = "/mock/workspace/storage/path",
   globalStoragePath = "/mock/global/storage/path",
   createEventEmitter = <T>() => new MockAppEventEmitter<T>(),
-  executeCommand = jest.fn(() => Promise.resolve()),
   workspaceState = createMockMemento(),
   credentials = testCredentialsWithStub(),
+  commands = createMockCommandManager(),
 }: {
   extensionPath?: string;
   workspaceStoragePath?: string;
   globalStoragePath?: string;
   createEventEmitter?: <T>() => AppEventEmitter<T>;
-  executeCommand?: () => Promise<void>;
   workspaceState?: Memento;
   credentials?: Credentials;
+  commands?: AppCommandManager;
 }): App {
   return {
     mode: AppMode.Test,
@@ -33,8 +35,8 @@ export function createMockApp({
     globalStoragePath,
     workspaceState,
     createEventEmitter,
-    executeCommand,
     credentials,
+    commands,
   };
 }
 
diff --git a/extensions/ql-vscode/test/__mocks__/commandsMock.ts b/extensions/ql-vscode/test/__mocks__/commandsMock.ts
new file mode 100644
index 000000000..16e92606b
--- /dev/null
+++ b/extensions/ql-vscode/test/__mocks__/commandsMock.ts
@@ -0,0 +1,13 @@
+import { AppCommandManager } from "../../src/common/commands";
+import { CommandFunction, CommandManager } from "../../src/packages/commands";
+import { Disposable } from "../../src/packages/commands/Disposable";
+
+export function createMockCommandManager({
+  registerCommand = jest.fn(),
+  executeCommand = jest.fn(),
+}: {
+  registerCommand?: (commandName: string, fn: CommandFunction) => Disposable;
+  executeCommand?: (commandName: string, ...args: any[]) => Promise<any>;
+} = {}): AppCommandManager {
+  return new CommandManager(registerCommand, executeCommand);
+}
diff --git a/extensions/ql-vscode/test/__mocks__/loggerMock.ts b/extensions/ql-vscode/test/__mocks__/loggerMock.ts
index 665720357..ff69b0f6e 100644
--- a/extensions/ql-vscode/test/__mocks__/loggerMock.ts
+++ b/extensions/ql-vscode/test/__mocks__/loggerMock.ts
@@ -4,6 +4,5 @@ export function createMockLogger(): Logger {
   return {
     log: jest.fn(() => Promise.resolve()),
     show: jest.fn(),
-    removeAdditionalLogLocation: jest.fn(),
   };
 }
diff --git a/extensions/ql-vscode/test/common/logging/output-channel-logger.test.ts b/extensions/ql-vscode/test/common/logging/output-channel-logger.test.ts
index a15bea5aa..b05ebdb17 100644
--- a/extensions/ql-vscode/test/common/logging/output-channel-logger.test.ts
+++ b/extensions/ql-vscode/test/common/logging/output-channel-logger.test.ts
@@ -1,7 +1,7 @@
 import { readdirSync, readFileSync } from "fs-extra";
 import { join } from "path";
 import * as tmp from "tmp";
-import { OutputChannelLogger } from "../../../src/common";
+import { Logger, OutputChannelLogger, TeeLogger } from "../../../src/common";
 
 jest.setTimeout(999999);
 
@@ -58,16 +58,19 @@ describe("OutputChannelLogger tests", function () {
     expect(mockOutputChannel.appendLine).not.toBeCalledWith("yyy");
     expect(mockOutputChannel.append).toBeCalledWith("yyy");
 
-    await logger.log("zzz", createLogOptions("hucairz"));
+    const hucairz = createSideLogger(logger, "hucairz");
+    await hucairz.log("zzz");
 
     // should have created 1 side log
     expect(readdirSync(tempFolders.storagePath.name)).toEqual(["hucairz"]);
   });
 
   it("should create a side log", async () => {
-    await logger.log("xxx", createLogOptions("first"));
-    await logger.log("yyy", createLogOptions("second"));
-    await logger.log("zzz", createLogOptions("first", false));
+    const first = createSideLogger(logger, "first");
+    await first.log("xxx");
+    const second = createSideLogger(logger, "second");
+    await second.log("yyy");
+    await first.log("zzz", { trailingNewline: false });
     await logger.log("aaa");
 
     // expect 2 side logs
@@ -82,16 +85,13 @@ describe("OutputChannelLogger tests", function () {
     ).toBe("yyy\n");
   });
 
-  function createLogOptions(
+  function createSideLogger(
+    logger: Logger,
     additionalLogLocation: string,
-    trailingNewline?: boolean,
-  ) {
-    return {
-      additionalLogLocation: join(
-        tempFolders.storagePath.name,
-        additionalLogLocation,
-      ),
-      trailingNewline,
-    };
+  ): Logger {
+    return new TeeLogger(
+      logger,
+      join(tempFolders.storagePath.name, additionalLogLocation),
+    );
   }
 });
diff --git a/extensions/ql-vscode/test/factories/extension-context.ts b/extensions/ql-vscode/test/factories/extension-context.ts
index d871e77d6..8c90b330c 100644
--- a/extensions/ql-vscode/test/factories/extension-context.ts
+++ b/extensions/ql-vscode/test/factories/extension-context.ts
@@ -19,5 +19,6 @@ export function createMockExtensionContext({
     globalStorageUri: vscode.Uri.file(globalStoragePath),
     storageUri: vscode.Uri.file(workspaceStoragePath),
     workspaceState: createMockMemento(),
+    subscriptions: [],
   } as any as vscode.ExtensionContext;
 }
diff --git a/extensions/ql-vscode/test/factories/query-history/local-query-history-item.ts b/extensions/ql-vscode/test/factories/query-history/local-query-history-item.ts
index 157f60f3b..a67de64b0 100644
--- a/extensions/ql-vscode/test/factories/query-history/local-query-history-item.ts
+++ b/extensions/ql-vscode/test/factories/query-history/local-query-history-item.ts
@@ -74,7 +74,6 @@ export function createMockQueryWithResults({
   hasInterpretedResults?: boolean;
   hasMetadata?: boolean;
 }): QueryWithResults {
-  const dispose = jest.fn();
   const deleteQuery = jest.fn();
   const metadata = hasMetadata
     ? ({ name: "query-name" } as QueryMetadata)
@@ -87,7 +86,6 @@ export function createMockQueryWithResults({
       metadata,
     } as unknown as QueryEvaluationInfo,
     successful: didRunSuccessfully,
-    dispose,
     result: {
       evaluationTime: 1,
       queryId: 0,
diff --git a/extensions/ql-vscode/test/factories/variant-analysis/shared/data-flow-paths.ts b/extensions/ql-vscode/test/factories/variant-analysis/shared/data-flow-paths.ts
new file mode 100644
index 000000000..9f0ae98ac
--- /dev/null
+++ b/extensions/ql-vscode/test/factories/variant-analysis/shared/data-flow-paths.ts
@@ -0,0 +1,122 @@
+import {
+  AnalysisMessage,
+  CodeFlow,
+  ResultSeverity,
+} from "../../../../src/variant-analysis/shared/analysis-result";
+import { DataFlowPaths } from "../../../../src/variant-analysis/shared/data-flow-paths";
+
+const defaultCodeFlows: CodeFlow[] = [
+  {
+    threadFlows: [
+      {
+        fileLink: {
+          fileLinkPrefix:
+            "https://github.com/PowerShell/PowerShell/blob/450d884668ca477c6581ce597958f021fac30bff",
+          filePath:
+            "src/System.Management.Automation/help/UpdatableHelpSystem.cs",
+        },
+        codeSnippet: {
+          startLine: 1260,
+          endLine: 1260,
+          text: "                        string extractPath = Path.Combine(destination, entry.FullName);",
+        },
+        highlightedRegion: {
+          startLine: 1260,
+          startColumn: 72,
+          endLine: 1260,
+          endColumn: 86,
+        },
+        message: {
+          tokens: [
+            {
+              t: "text",
+              text: "access to property FullName : String",
+            },
+          ],
+        },
+      },
+      {
+        fileLink: {
+          fileLinkPrefix:
+            "https://github.com/PowerShell/PowerShell/blob/450d884668ca477c6581ce597958f021fac30bff",
+          filePath:
+            "src/System.Management.Automation/help/UpdatableHelpSystem.cs",
+        },
+        codeSnippet: {
+          startLine: 1260,
+          endLine: 1260,
+          text: "                        string extractPath = Path.Combine(destination, entry.FullName);",
+        },
+        highlightedRegion: {
+          startLine: 1260,
+          startColumn: 46,
+          endLine: 1260,
+          endColumn: 87,
+        },
+        message: {
+          tokens: [
+            {
+              t: "text",
+              text: "call to method Combine : String",
+            },
+          ],
+        },
+      },
+      {
+        fileLink: {
+          fileLinkPrefix:
+            "https://github.com/PowerShell/PowerShell/blob/450d884668ca477c6581ce597958f021fac30bff",
+          filePath:
+            "src/System.Management.Automation/help/UpdatableHelpSystem.cs",
+        },
+        codeSnippet: {
+          startLine: 1261,
+          endLine: 1261,
+          text: "                        entry.ExtractToFile(extractPath);",
+        },
+        highlightedRegion: {
+          startLine: 1261,
+          startColumn: 45,
+          endLine: 1261,
+          endColumn: 56,
+        },
+        message: {
+          tokens: [
+            {
+              t: "text",
+              text: "access to local variable extractPath",
+            },
+          ],
+        },
+      },
+    ],
+  },
+];
+
+const defaultMessage: AnalysisMessage = {
+  tokens: [
+    {
+      t: "text",
+      text: "This zip file may have a dangerous path",
+    },
+  ],
+};
+
+export function createMockDataFlowPaths({
+  codeFlows = defaultCodeFlows,
+  ruleDescription = "ZipSlip vulnerability",
+  message = defaultMessage,
+  severity = "Warning",
+}: {
+  codeFlows?: CodeFlow[];
+  ruleDescription?: string;
+  message?: AnalysisMessage;
+  severity?: ResultSeverity;
+} = {}): DataFlowPaths {
+  return {
+    codeFlows,
+    ruleDescription,
+    message,
+    severity,
+  };
+}
diff --git a/extensions/ql-vscode/test/unit-tests/databases/config/db-config-store.test.ts b/extensions/ql-vscode/test/unit-tests/databases/config/db-config-store.test.ts
index 7e0af0d86..ca4b7ead6 100644
--- a/extensions/ql-vscode/test/unit-tests/databases/config/db-config-store.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/databases/config/db-config-store.test.ts
@@ -19,6 +19,7 @@ import {
   createRemoteUserDefinedListDbItem,
 } from "../../../factories/db-item-factories";
 import { createMockApp } from "../../../__mocks__/appMock";
+import { createMockCommandManager } from "../../../__mocks__/commandsMock";
 
 describe("db config store", () => {
   const extensionPath = join(__dirname, "../../../..");
@@ -136,14 +137,16 @@ describe("db config store", () => {
     it("should set codeQLVariantAnalysisRepositories.configError to true when config has error", async () => {
       const testDataStoragePathInvalid = join(__dirname, "data", "invalid");
 
+      const executeCommand = jest.fn();
       const app = createMockApp({
         extensionPath,
         workspaceStoragePath: testDataStoragePathInvalid,
+        commands: createMockCommandManager({ executeCommand }),
       });
       const configStore = new DbConfigStore(app, false);
       await configStore.initialize();
 
-      expect(app.executeCommand).toBeCalledWith(
+      expect(executeCommand).toBeCalledWith(
         "setContext",
         "codeQLVariantAnalysisRepositories.configError",
         true,
@@ -152,14 +155,16 @@ describe("db config store", () => {
     });
 
     it("should set codeQLVariantAnalysisRepositories.configError to false when config is valid", async () => {
+      const executeCommand = jest.fn();
       const app = createMockApp({
         extensionPath,
         workspaceStoragePath: testDataStoragePath,
+        commands: createMockCommandManager({ executeCommand }),
       });
       const configStore = new DbConfigStore(app, false);
       await configStore.initialize();
 
-      expect(app.executeCommand).toBeCalledWith(
+      expect(executeCommand).toBeCalledWith(
         "setContext",
         "codeQLVariantAnalysisRepositories.configError",
         false,
diff --git a/extensions/ql-vscode/test/unit-tests/packages/commands/CommandManager.test.ts b/extensions/ql-vscode/test/unit-tests/packages/commands/CommandManager.test.ts
index 40b78d932..96bede0b6 100644
--- a/extensions/ql-vscode/test/unit-tests/packages/commands/CommandManager.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/packages/commands/CommandManager.test.ts
@@ -1,8 +1,111 @@
-import { CommandManager } from "../../../../src/packages/commands";
+import {
+  CommandFunction,
+  CommandManager,
+} from "../../../../src/packages/commands";
 
-describe(CommandManager.name, () => {
-  it("can create a command manager", () => {
-    const commandManager = new CommandManager();
-    expect(commandManager).not.toBeUndefined();
+describe("CommandManager", () => {
+  it("can register a command", () => {
+    const commandRegister = jest.fn();
+    const commandManager = new CommandManager<Record<string, CommandFunction>>(
+      commandRegister,
+      jest.fn(),
+    );
+    const myCommand = jest.fn();
+    commandManager.register("abc", myCommand);
+    expect(commandRegister).toHaveBeenCalledTimes(1);
+    expect(commandRegister).toHaveBeenCalledWith("abc", myCommand);
+  });
+
+  it("can register typed commands", async () => {
+    const commands = {
+      "codeQL.openVariantAnalysisLogs": async (variantAnalysisId: number) => {
+        return variantAnalysisId * 10;
+      },
+    };
+    const commandManager = new CommandManager<typeof commands>(
+      jest.fn(),
+      jest.fn(),
+    );
+
+    // @ts-expect-error wrong command name should give a type error
+    commandManager.register("abc", jest.fn());
+
+    commandManager.register(
+      "codeQL.openVariantAnalysisLogs",
+      // @ts-expect-error wrong function parameter type should give a type error
+      async (variantAnalysisId: string): Promise<number> => 10,
+    );
+
+    commandManager.register(
+      "codeQL.openVariantAnalysisLogs",
+      // @ts-expect-error wrong function return type should give a type error
+      async (variantAnalysisId: number): Promise<string> => "hello",
+    );
+
+    // Working types
+    commandManager.register(
+      "codeQL.openVariantAnalysisLogs",
+      async (variantAnalysisId: number): Promise<number> =>
+        variantAnalysisId * 10,
+    );
+  });
+
+  it("can dispose of its commands", () => {
+    const dispose1 = jest.fn();
+    const dispose2 = jest.fn();
+    const commandRegister = jest
+      .fn()
+      .mockReturnValueOnce({ dispose: dispose1 })
+      .mockReturnValueOnce({ dispose: dispose2 });
+    const commandManager = new CommandManager<Record<string, CommandFunction>>(
+      commandRegister,
+      jest.fn(),
+    );
+    commandManager.register("abc", jest.fn());
+    commandManager.register("def", jest.fn());
+    expect(dispose1).not.toHaveBeenCalled();
+    expect(dispose2).not.toHaveBeenCalled();
+    commandManager.dispose();
+    expect(dispose1).toHaveBeenCalledTimes(1);
+    expect(dispose2).toHaveBeenCalledTimes(1);
+  });
+
+  it("can execute a command", async () => {
+    const commandExecute = jest.fn().mockReturnValue(7);
+    const commandManager = new CommandManager<Record<string, CommandFunction>>(
+      jest.fn(),
+      commandExecute,
+    );
+    const result = await commandManager.execute("abc", "hello", true);
+    expect(result).toEqual(7);
+    expect(commandExecute).toHaveBeenCalledTimes(1);
+    expect(commandExecute).toHaveBeenCalledWith("abc", "hello", true);
+  });
+
+  it("can execute typed commands", async () => {
+    const commands = {
+      "codeQL.openVariantAnalysisLogs": async (variantAnalysisId: number) => {
+        return variantAnalysisId * 10;
+      },
+    };
+    const commandManager = new CommandManager<typeof commands>(
+      jest.fn(),
+      jest.fn(),
+    );
+
+    // @ts-expect-error wrong command name should give a type error
+    await commandManager.execute("abc", 4);
+
+    await commandManager.execute(
+      "codeQL.openVariantAnalysisLogs",
+      // @ts-expect-error wrong argument type should give a type error
+      "xyz",
+    );
+
+    // @ts-expect-error wrong number of arguments should give a type error
+    await commandManager.execute("codeQL.openVariantAnalysisLogs", 2, 3);
+
+    // Working types
+    await commandManager.execute("codeQL.openVariantAnalysisLogs", 7);
   });
 });
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 024a1bc82..05e9b5ed6 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
@@ -1,5 +1,4 @@
 import {
-  CancellationTokenSource,
   commands,
   env,
   extensions,
@@ -54,7 +53,6 @@ jest.setTimeout(3 * 60 * 1000);
 
 describe("Variant Analysis Manager", () => {
   let app: App;
-  let cancellationTokenSource: CancellationTokenSource;
   let variantAnalysisManager: VariantAnalysisManager;
   let variantAnalysisResultsManager: VariantAnalysisResultsManager;
   let variantAnalysis: VariantAnalysis;
@@ -63,8 +61,6 @@ describe("Variant Analysis Manager", () => {
   beforeEach(async () => {
     jest.spyOn(extLogger, "log").mockResolvedValue(undefined);
 
-    cancellationTokenSource = new CancellationTokenSource();
-
     scannedRepos = createMockScannedRepos();
     variantAnalysis = createMockVariantAnalysis({
       status: VariantAnalysisStatus.InProgress,
@@ -203,7 +199,6 @@ describe("Variant Analysis Manager", () => {
         await variantAnalysisManager.autoDownloadVariantAnalysisResult(
           scannedRepos[0],
           variantAnalysis,
-          cancellationTokenSource.token,
         );
 
         expect(getVariantAnalysisRepoResultStub).not.toHaveBeenCalled();
@@ -228,23 +223,10 @@ describe("Variant Analysis Manager", () => {
         getVariantAnalysisRepoResultStub.mockResolvedValue(response);
       });
 
-      it("should return early if variant analysis is cancelled", async () => {
-        cancellationTokenSource.cancel();
-
-        await variantAnalysisManager.autoDownloadVariantAnalysisResult(
-          scannedRepos[0],
-          variantAnalysis,
-          cancellationTokenSource.token,
-        );
-
-        expect(getVariantAnalysisRepoStub).not.toHaveBeenCalled();
-      });
-
       it("should fetch a repo task", async () => {
         await variantAnalysisManager.autoDownloadVariantAnalysisResult(
           scannedRepos[0],
           variantAnalysis,
-          cancellationTokenSource.token,
         );
 
         expect(getVariantAnalysisRepoStub).toHaveBeenCalled();
@@ -254,7 +236,6 @@ describe("Variant Analysis Manager", () => {
         await variantAnalysisManager.autoDownloadVariantAnalysisResult(
           scannedRepos[0],
           variantAnalysis,
-          cancellationTokenSource.token,
         );
 
         expect(getVariantAnalysisRepoResultStub).toHaveBeenCalled();
@@ -265,7 +246,6 @@ describe("Variant Analysis Manager", () => {
         await variantAnalysisManager.autoDownloadVariantAnalysisResult(
           scannedRepos[0],
           variantAnalysis,
-          cancellationTokenSource.token,
         );
 
         getVariantAnalysisRepoStub.mockClear();
@@ -273,7 +253,6 @@ describe("Variant Analysis Manager", () => {
         await variantAnalysisManager.autoDownloadVariantAnalysisResult(
           scannedRepos[0],
           variantAnalysis,
-          cancellationTokenSource.token,
         );
 
         expect(getVariantAnalysisRepoStub).not.toHaveBeenCalled();
@@ -283,7 +262,6 @@ describe("Variant Analysis Manager", () => {
         await variantAnalysisManager.autoDownloadVariantAnalysisResult(
           scannedRepos[0],
           variantAnalysis,
-          cancellationTokenSource.token,
         );
 
         await expect(fs.readJson(repoStatesPath)).resolves.toEqual({
@@ -304,7 +282,6 @@ describe("Variant Analysis Manager", () => {
           variantAnalysisManager.autoDownloadVariantAnalysisResult(
             scannedRepos[0],
             variantAnalysis,
-            cancellationTokenSource.token,
           ),
         ).rejects.toThrow();
 
@@ -320,7 +297,6 @@ describe("Variant Analysis Manager", () => {
           variantAnalysisManager.autoDownloadVariantAnalysisResult(
             scannedRepos[0],
             variantAnalysis,
-            cancellationTokenSource.token,
           ),
         ).rejects.toThrow();
 
@@ -329,7 +305,6 @@ describe("Variant Analysis Manager", () => {
         await variantAnalysisManager.autoDownloadVariantAnalysisResult(
           scannedRepos[1],
           variantAnalysis,
-          cancellationTokenSource.token,
         );
 
         await expect(fs.readJson(repoStatesPath)).resolves.toEqual({
@@ -355,7 +330,6 @@ describe("Variant Analysis Manager", () => {
           variantAnalysisManager.autoDownloadVariantAnalysisResult(
             scannedRepos[0],
             variantAnalysis,
-            cancellationTokenSource.token,
           ),
         ).rejects.toThrow();
 
@@ -364,7 +338,6 @@ describe("Variant Analysis Manager", () => {
         await variantAnalysisManager.autoDownloadVariantAnalysisResult(
           scannedRepos[1],
           variantAnalysis,
-          cancellationTokenSource.token,
         );
 
         await expect(fs.readJson(repoStatesPath)).resolves.toEqual({
@@ -400,7 +373,6 @@ describe("Variant Analysis Manager", () => {
         await variantAnalysisManager.autoDownloadVariantAnalysisResult(
           scannedRepos[0],
           variantAnalysis,
-          cancellationTokenSource.token,
         );
 
         await expect(fs.readJson(repoStatesPath)).resolves.toEqual({
@@ -439,17 +411,14 @@ describe("Variant Analysis Manager", () => {
       await variantAnalysisManager.enqueueDownload(
         scannedRepos[0],
         variantAnalysis,
-        cancellationTokenSource.token,
       );
       await variantAnalysisManager.enqueueDownload(
         scannedRepos[1],
         variantAnalysis,
-        cancellationTokenSource.token,
       );
       await variantAnalysisManager.enqueueDownload(
         scannedRepos[2],
         variantAnalysis,
-        cancellationTokenSource.token,
       );
 
       expect(variantAnalysisManager.downloadsQueueSize()).toBe(0);
diff --git a/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-monitor.test.ts b/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-monitor.test.ts
index 0c9082c91..329e85685 100644
--- a/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-monitor.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-monitor.test.ts
@@ -1,4 +1,4 @@
-import { CancellationTokenSource, commands, extensions } from "vscode";
+import { commands, extensions } from "vscode";
 import { CodeQLExtensionInterface } from "../../../../src/extension";
 
 import * as ghApiClient from "../../../../src/variant-analysis/gh-api/gh-api-client";
@@ -33,7 +33,6 @@ describe("Variant Analysis Monitor", () => {
   let mockGetVariantAnalysis: jest.SpiedFunction<
     typeof ghApiClient.getVariantAnalysis
   >;
-  let cancellationTokenSource: CancellationTokenSource;
   let variantAnalysisMonitor: VariantAnalysisMonitor;
   let shouldCancelMonitor: jest.Mock<Promise<boolean>, [number]>;
   let variantAnalysis: VariantAnalysis;
@@ -45,8 +44,6 @@ describe("Variant Analysis Monitor", () => {
   const onVariantAnalysisChangeSpy = jest.fn();
 
   beforeEach(async () => {
-    cancellationTokenSource = new CancellationTokenSource();
-
     variantAnalysis = createMockVariantAnalysis({});
 
     shouldCancelMonitor = jest.fn();
@@ -71,25 +68,12 @@ describe("Variant Analysis Monitor", () => {
     limitNumberOfAttemptsToMonitor();
   });
 
-  it("should return early if variant analysis is cancelled", async () => {
-    cancellationTokenSource.cancel();
-
-    await variantAnalysisMonitor.monitorVariantAnalysis(
-      variantAnalysis,
-      testCredentialsWithStub(),
-      cancellationTokenSource.token,
-    );
-
-    expect(onVariantAnalysisChangeSpy).not.toHaveBeenCalled();
-  });
-
   it("should return early if variant analysis should be cancelled", async () => {
     shouldCancelMonitor.mockResolvedValue(true);
 
     await variantAnalysisMonitor.monitorVariantAnalysis(
       variantAnalysis,
       testCredentialsWithStub(),
-      cancellationTokenSource.token,
     );
 
     expect(onVariantAnalysisChangeSpy).not.toHaveBeenCalled();
@@ -107,7 +91,6 @@ describe("Variant Analysis Monitor", () => {
       await variantAnalysisMonitor.monitorVariantAnalysis(
         variantAnalysis,
         testCredentialsWithStub(),
-        cancellationTokenSource.token,
       );
 
       expect(mockGetVariantAnalysis).toHaveBeenCalledTimes(1);
@@ -157,7 +140,6 @@ describe("Variant Analysis Monitor", () => {
         await variantAnalysisMonitor.monitorVariantAnalysis(
           variantAnalysis,
           testCredentialsWithStub(),
-          cancellationTokenSource.token,
         );
 
         expect(commandSpy).toBeCalledTimes(succeededRepos.length);
@@ -176,7 +158,6 @@ describe("Variant Analysis Monitor", () => {
         await variantAnalysisMonitor.monitorVariantAnalysis(
           variantAnalysis,
           testCredentialsWithStub(),
-          cancellationTokenSource.token,
         );
 
         expect(mockGetDownloadResult).toBeCalledTimes(succeededRepos.length);
@@ -186,7 +167,6 @@ describe("Variant Analysis Monitor", () => {
             index + 1,
             processScannedRepository(succeededRepo),
             processUpdatedVariantAnalysis(variantAnalysis, mockApiResponse),
-            undefined,
           );
         });
       });
@@ -209,7 +189,6 @@ describe("Variant Analysis Monitor", () => {
         await variantAnalysisMonitor.monitorVariantAnalysis(
           variantAnalysis,
           testCredentialsWithStub(),
-          cancellationTokenSource.token,
         );
 
         expect(commandSpy).not.toHaveBeenCalled();
@@ -219,7 +198,6 @@ describe("Variant Analysis Monitor", () => {
         await variantAnalysisMonitor.monitorVariantAnalysis(
           variantAnalysis,
           testCredentialsWithStub(),
-          cancellationTokenSource.token,
         );
 
         expect(mockGetDownloadResult).not.toBeCalled();
@@ -278,7 +256,6 @@ describe("Variant Analysis Monitor", () => {
         await variantAnalysisMonitor.monitorVariantAnalysis(
           variantAnalysis,
           testCredentialsWithStub(),
-          cancellationTokenSource.token,
         );
 
         expect(mockGetVariantAnalysis).toBeCalledTimes(4);
@@ -297,7 +274,6 @@ describe("Variant Analysis Monitor", () => {
         await variantAnalysisMonitor.monitorVariantAnalysis(
           variantAnalysis,
           testCredentialsWithStub(),
-          cancellationTokenSource.token,
         );
 
         expect(mockGetDownloadResult).not.toBeCalled();
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/data-extension-pack/extension-file.yml b/extensions/ql-vscode/test/vscode-tests/cli-integration/data-extension-pack/extension-file.yml
new file mode 100644
index 000000000..e2c26ddff
--- /dev/null
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/data-extension-pack/extension-file.yml
@@ -0,0 +1,12 @@
+extensions:
+  - addsTo:
+      pack: codeql/javascript-all
+      extensible: sourceModel
+    data:
+      - [ "@example/read-write-user-data", "Member[readUserData].ReturnValue.Awaited", "remote" ]
+
+  - addsTo:
+      pack: codeql/javascript-all
+      extensible: sinkModel
+    data:
+      - [ "@example/read-write-user-data", "Member[writeUserData].Argument[0]", "command-line-injection" ]
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/data-extension-pack/qlpack.yml b/extensions/ql-vscode/test/vscode-tests/cli-integration/data-extension-pack/qlpack.yml
new file mode 100644
index 000000000..b834c739b
--- /dev/null
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/data-extension-pack/qlpack.yml
@@ -0,0 +1,8 @@
+name: github/extension-pack-for-testing
+version: 0.0.0
+library: true
+extensionTargets:
+  github/remote-query-pack: "*"
+
+dataExtensions:
+  - extension-file.yml
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/databaseFetcher.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/databaseFetcher.test.ts
index 407c22176..3ba6d5806 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/databaseFetcher.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/databaseFetcher.test.ts
@@ -9,6 +9,7 @@ import {
   promptImportInternetDatabase,
 } from "../../../src/databaseFetcher";
 import { cleanDatabases, dbLoc, DB_URL, storagePath } from "../global.helper";
+import { createMockCommandManager } from "../../__mocks__/commandsMock";
 
 jest.setTimeout(60_000);
 
@@ -53,6 +54,7 @@ describe("DatabaseFetcher", () => {
     it("should add a database from a folder", async () => {
       const uri = Uri.file(dbLoc);
       let dbItem = await importArchiveDatabase(
+        createMockCommandManager(),
         uri.toString(true),
         databaseManager,
         storagePath,
@@ -75,6 +77,7 @@ describe("DatabaseFetcher", () => {
       inputBoxStub.mockResolvedValue(DB_URL);
 
       let dbItem = await promptImportInternetDatabase(
+        createMockCommandManager(),
         databaseManager,
         storagePath,
         progressCallback,
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/legacy-query.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/legacy-query.test.ts
index 6c014b609..faacb6db2 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/legacy-query.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/legacy-query.test.ts
@@ -12,6 +12,7 @@ import { CodeQLExtensionInterface } from "../../../src/extension";
 import { describeWithCodeQL } from "../cli";
 import { QueryServerClient } from "../../../src/legacy-query-server/queryserver-client";
 import { extLogger, ProgressReporter } from "../../../src/common";
+import { createMockApp } from "../../__mocks__/appMock";
 
 const baseDir = join(__dirname, "../../../test/data");
 
@@ -121,6 +122,7 @@ describeWithCodeQL()("using the legacy query server", () => {
       cliServer.quiet = true;
 
       qs = new QueryServerClient(
+        createMockApp({}),
         {
           codeQlPath:
             (await extension.distributionManager.getCodeQlPathWithoutVersionCheck()) ||
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/new-query.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/new-query.test.ts
index a7d8f9d4b..4d47f3b02 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/new-query.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/new-query.test.ts
@@ -13,6 +13,7 @@ import { extLogger, ProgressReporter } from "../../../src/common";
 import { QueryResultType } from "../../../src/pure/new-messages";
 import { cleanDatabases, dbLoc, storagePath } from "../global.helper";
 import { importArchiveDatabase } from "../../../src/databaseFetcher";
+import { createMockCommandManager } from "../../__mocks__/commandsMock";
 
 const baseDir = join(__dirname, "../../../test/data");
 
@@ -147,6 +148,7 @@ describeWithCodeQL()("using the new query server", () => {
       await cleanDatabases(extension.databaseManager);
       const uri = Uri.file(dbLoc);
       const maybeDbItem = await importArchiveDatabase(
+        createMockCommandManager(),
         uri.toString(true),
         extension.databaseManager,
         storagePath,
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 65b304235..b750bbae9 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
@@ -26,6 +26,7 @@ import { createInitialQueryInfo } from "../../../src/run-queries-shared";
 import { QueryRunner } from "../../../src/queryRunner";
 import { CompletedQueryInfo } from "../../../src/query-results";
 import { SELECT_QUERY_NAME } from "../../../src/contextual/locationFinder";
+import { createMockCommandManager } from "../../__mocks__/commandsMock";
 
 jest.setTimeout(20_000);
 
@@ -78,6 +79,7 @@ describeWithCodeQL()("Queries", () => {
     await cleanDatabases(databaseManager);
     const uri = Uri.file(dbLoc);
     const maybeDbItem = await importArchiveDatabase(
+      createMockCommandManager(),
       uri.toString(true),
       databaseManager,
       storagePath,
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/variant-analysis/variant-analysis-manager.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/variant-analysis/variant-analysis-manager.test.ts
index e0a81a209..dd02364a4 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/variant-analysis/variant-analysis-manager.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/variant-analysis/variant-analysis-manager.test.ts
@@ -12,7 +12,7 @@ import * as ghApiClient from "../../../../src/variant-analysis/gh-api/gh-api-cli
 import { join } from "path";
 
 import { VariantAnalysisManager } from "../../../../src/variant-analysis/variant-analysis-manager";
-import { CodeQLCliServer } from "../../../../src/cli";
+import { CliVersionConstraint, CodeQLCliServer } from "../../../../src/cli";
 import {
   fixWorkspaceReferences,
   restoreWorkspaceReferences,
@@ -25,7 +25,7 @@ import {
 } from "../../../../src/variant-analysis/shared/variant-analysis";
 import { VariantAnalysis as VariantAnalysisApiResponse } from "../../../../src/variant-analysis/gh-api/variant-analysis";
 import { createMockApiResponse } from "../../../factories/variant-analysis/gh-api/variant-analysis-api-response";
-import { UserCancellationException } from "../../../../src/commandRunner";
+import { UserCancellationException } from "../../../../src/progress";
 import { Repository } from "../../../../src/variant-analysis/gh-api/repository";
 import { DbManager } from "../../../../src/databases/db-manager";
 import { ExtensionApp } from "../../../../src/common/vscode/vscode-app";
@@ -255,6 +255,30 @@ describe("Variant Analysis Manager", () => {
           qlxFilesThatExist: ["subfolder/in-pack.qlx"],
         });
       });
+
+      it("should run a remote query with extension packs inside a qlpack", async () => {
+        if (!(await cli.cliConstraints.supportsQlpacksKind())) {
+          console.log(
+            `Skipping test because qlpacks kind is only suppported in CLI version ${CliVersionConstraint.CLI_VERSION_WITH_QLPACKS_KIND} or later.`,
+          );
+          return;
+        }
+        await cli.setUseExtensionPacks(true);
+        await doVariantAnalysisTest({
+          queryPath: "data-remote-qlpack-nested/subfolder/in-pack.ql",
+          filesThatExist: [
+            "subfolder/in-pack.ql",
+            "otherfolder/lib.qll",
+            ".codeql/libraries/semmle/targets-extension/0.0.0/ext/extension.yml",
+          ],
+          filesThatDoNotExist: ["subfolder/not-in-pack.ql"],
+          qlxFilesThatExist: ["subfolder/in-pack.qlx"],
+          dependenciesToCheck: [
+            "codeql/javascript-all",
+            "semmle/targets-extension",
+          ],
+        });
+      });
     });
 
     async function doVariantAnalysisTest({
@@ -262,11 +286,13 @@ describe("Variant Analysis Manager", () => {
       filesThatExist,
       qlxFilesThatExist,
       filesThatDoNotExist,
+      dependenciesToCheck = ["codeql/javascript-all"],
     }: {
       queryPath: string;
       filesThatExist: string[];
       qlxFilesThatExist: string[];
       filesThatDoNotExist: string[];
+      dependenciesToCheck?: string[];
     }) {
       const fileUri = getFile(queryPath);
       await variantAnalysisManager.runVariantAnalysis(
@@ -328,8 +354,10 @@ describe("Variant Analysis Manager", () => {
 
       const actualLockKeys = Object.keys(qlpackLockContents.dependencies);
 
-      // The lock file should contain at least codeql/javascript-all.
-      expect(actualLockKeys).toContain("codeql/javascript-all");
+      // The lock file should contain at least the specified dependencies.
+      dependenciesToCheck.forEach((dep) =>
+        expect(actualLockKeys).toContain(dep),
+      );
     }
 
     function getFile(file: string): Uri {
diff --git a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-databases.test.ts b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-databases.test.ts
index 61c68b9c2..c106110e8 100644
--- a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-databases.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-databases.test.ts
@@ -13,7 +13,7 @@ import {
   FullDatabaseOptions,
 } from "../../../src/local-databases";
 import { Logger } from "../../../src/common";
-import { ProgressCallback } from "../../../src/commandRunner";
+import { ProgressCallback } from "../../../src/progress";
 import { CodeQLCliServer, DbInfo } from "../../../src/cli";
 import {
   encodeArchiveBasePath,
@@ -25,6 +25,7 @@ import * as helpers from "../../../src/helpers";
 import { Setting } from "../../../src/config";
 import { QlPackGenerator } from "../../../src/qlpack-generator";
 import { mockedObject } from "../utils/mocking.helpers";
+import { createMockApp } from "../../__mocks__/appMock";
 
 describe("local databases", () => {
   const MOCK_DB_OPTIONS: FullDatabaseOptions = {
@@ -87,6 +88,7 @@ describe("local databases", () => {
 
     databaseManager = new DatabaseManager(
       extensionContext,
+      createMockApp({}),
       mockedObject<QueryRunner>({
         registerDatabase: registerSpy,
         deregisterDatabase: deregisterSpy,
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/helpers.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/helpers.test.ts
index cf2a022c2..49bb5117d 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/helpers.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/helpers.test.ts
@@ -15,7 +15,14 @@ import {
 import { dump } from "js-yaml";
 import * as tmp from "tmp";
 import { join } from "path";
-import { writeFileSync, mkdirSync, ensureDirSync, symlinkSync } from "fs-extra";
+import {
+  writeFileSync,
+  mkdirSync,
+  ensureDirSync,
+  symlinkSync,
+  writeFile,
+  mkdir,
+} from "fs-extra";
 import { DirResult } from "tmp";
 
 import {
@@ -24,13 +31,16 @@ import {
   isFolderAlreadyInWorkspace,
   isLikelyDatabaseRoot,
   isLikelyDbLanguageFolder,
+  prepareCodeTour,
   showBinaryChoiceDialog,
   showBinaryChoiceWithUrlDialog,
   showInformationMessageWithAction,
   walkDirectory,
 } from "../../../src/helpers";
-import { reportStreamProgress } from "../../../src/commandRunner";
+import { reportStreamProgress } from "../../../src/progress";
 import { QueryLanguage } from "../../../src/common/query-language";
+import { Setting } from "../../../src/config";
+import { createMockCommandManager } from "../../__mocks__/commandsMock";
 
 describe("helpers", () => {
   describe("Invocation rate limiter", () => {
@@ -559,3 +569,105 @@ describe("isFolderAlreadyInWorkspace", () => {
     expect(isFolderAlreadyInWorkspace("/third/path")).toBe(false);
   });
 });
+
+describe("prepareCodeTour", () => {
+  let dir: tmp.DirResult;
+  let showInformationMessageSpy: jest.SpiedFunction<
+    typeof window.showInformationMessage
+  >;
+
+  beforeEach(() => {
+    dir = tmp.dirSync();
+
+    const mockWorkspaceFolders = [
+      {
+        uri: Uri.file(dir.name),
+        name: "test",
+        index: 0,
+      },
+    ] as WorkspaceFolder[];
+
+    jest
+      .spyOn(workspace, "workspaceFolders", "get")
+      .mockReturnValue(mockWorkspaceFolders);
+
+    showInformationMessageSpy = jest
+      .spyOn(window, "showInformationMessage")
+      .mockResolvedValue({ title: "Yes" });
+  });
+
+  afterEach(() => {
+    dir.removeCallback();
+  });
+
+  describe("if we're in the tour repo", () => {
+    describe("if the workspace is not already open", () => {
+      it("should open the tutorial workspace", async () => {
+        // set up directory to have a 'tutorial.code-workspace' file
+        const tutorialWorkspacePath = join(dir.name, "tutorial.code-workspace");
+        await writeFile(tutorialWorkspacePath, "{}");
+
+        // set up a .tours directory to indicate we're in the tour codespace
+        const tourDirPath = join(dir.name, ".tours");
+        await mkdir(tourDirPath);
+
+        // spy that we open the workspace file by calling the 'vscode.openFolder' command
+        const executeCommand = jest.fn();
+        await prepareCodeTour(createMockCommandManager({ executeCommand }));
+
+        expect(showInformationMessageSpy).toHaveBeenCalled();
+        expect(executeCommand).toHaveBeenCalledWith(
+          "vscode.openFolder",
+          expect.objectContaining({
+            path: Uri.parse(tutorialWorkspacePath).fsPath,
+          }),
+        );
+      });
+    });
+
+    describe("if the workspace is already open", () => {
+      it("should not open the tutorial workspace", async () => {
+        // Set isCodespaceTemplate to true to indicate the workspace has already been opened
+        jest.spyOn(Setting.prototype, "getValue").mockReturnValue(true);
+
+        // set up directory to have a 'tutorial.code-workspace' file
+        const tutorialWorkspacePath = join(dir.name, "tutorial.code-workspace");
+        await writeFile(tutorialWorkspacePath, "{}");
+
+        // set up a .tours directory to indicate we're in the tour codespace
+        const tourDirPath = join(dir.name, ".tours");
+        await mkdir(tourDirPath);
+
+        // spy that we open the workspace file by calling the 'vscode.openFolder' command
+        const executeCommand = jest.fn();
+        await prepareCodeTour(createMockCommandManager({ executeCommand }));
+
+        expect(executeCommand).not.toHaveBeenCalled();
+      });
+    });
+  });
+
+  describe("if we're in a different tour repo", () => {
+    it("should not open the tutorial workspace", async () => {
+      // set up a .tours directory
+      const tourDirPath = join(dir.name, ".tours");
+      await mkdir(tourDirPath);
+
+      // spy that we open the workspace file by calling the 'vscode.openFolder' command
+      const executeCommand = jest.fn();
+      await prepareCodeTour(createMockCommandManager({ executeCommand }));
+
+      expect(executeCommand).not.toHaveBeenCalled();
+    });
+  });
+
+  describe("if we're in a different repo with no tour", () => {
+    it("should not open the tutorial workspace", async () => {
+      // spy that we open the workspace file by calling the 'vscode.openFolder' command
+      const executeCommand = jest.fn();
+      await prepareCodeTour(createMockCommandManager({ executeCommand }));
+
+      expect(executeCommand).not.toHaveBeenCalled();
+    });
+  });
+});
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/history-tree-data-provider.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/history-tree-data-provider.test.ts
index b63448a40..ca0b0add8 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/history-tree-data-provider.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/history-tree-data-provider.test.ts
@@ -27,6 +27,7 @@ import {
 } from "../../../../src/query-history/history-tree-data-provider";
 import { QueryHistoryManager } from "../../../../src/query-history/query-history-manager";
 import { createMockQueryHistoryDirs } from "../../../factories/query-history/query-history-dirs";
+import { createMockApp } from "../../../__mocks__/appMock";
 
 describe("HistoryTreeDataProvider", () => {
   const mockExtensionLocation = join(tmpDir.name, "mock-extension-location");
@@ -421,6 +422,7 @@ describe("HistoryTreeDataProvider", () => {
 
   async function createMockQueryHistory(allHistory: QueryHistoryInfo[]) {
     const qhm = new QueryHistoryManager(
+      createMockApp({}),
       {} as QueryRunner,
       {} as DatabaseManager,
       localQueriesResultsViewStub,
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/query-history-manager.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/query-history-manager.test.ts
index 07dfbe51d..2ca728c6b 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/query-history-manager.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/query-history-manager.test.ts
@@ -22,56 +22,49 @@ import { createMockVariantAnalysisHistoryItem } from "../../../factories/query-h
 import { VariantAnalysisHistoryItem } from "../../../../src/query-history/variant-analysis-history-item";
 import { QueryStatus } from "../../../../src/query-status";
 import { VariantAnalysisStatus } from "../../../../src/variant-analysis/shared/variant-analysis";
-import { TextEditor } from "vscode";
 import { WebviewReveal } from "../../../../src/interface-utils";
 import * as helpers from "../../../../src/helpers";
-import { mockedObject, mockedQuickPickItem } from "../../utils/mocking.helpers";
+import { mockedQuickPickItem } from "../../utils/mocking.helpers";
 import { createMockQueryHistoryDirs } from "../../../factories/query-history/query-history-dirs";
+import { createMockApp } from "../../../__mocks__/appMock";
+import { App } from "../../../../src/common/app";
+import { createMockCommandManager } from "../../../__mocks__/commandsMock";
 
 describe("QueryHistoryManager", () => {
   const mockExtensionLocation = join(tmpDir.name, "mock-extension-location");
   let configListener: QueryHistoryConfigListener;
-  let showTextDocumentSpy: jest.SpiedFunction<
-    typeof vscode.window.showTextDocument
-  >;
-  let showInformationMessageSpy: jest.SpiedFunction<
-    typeof vscode.window.showInformationMessage
-  >;
   let showQuickPickSpy: jest.SpiedFunction<typeof vscode.window.showQuickPick>;
-  let executeCommandSpy: jest.SpiedFunction<
-    typeof vscode.commands.executeCommand
+  let cancelVariantAnalysisSpy: jest.SpiedFunction<
+    typeof variantAnalysisManagerStub.cancelVariantAnalysis
   >;
   const doCompareCallback = jest.fn();
 
+  let executeCommand: jest.MockedFn<
+    (commandName: string, ...args: any[]) => Promise<any>
+  >;
+  let mockApp: App;
+
   let queryHistoryManager: QueryHistoryManager;
 
   let localQueriesResultsViewStub: ResultsView;
   let variantAnalysisManagerStub: VariantAnalysisManager;
 
-  let tryOpenExternalFile: Function;
-
   let allHistory: QueryHistoryInfo[];
   let localQueryHistory: LocalQueryInfo[];
   let variantAnalysisHistory: VariantAnalysisHistoryItem[];
 
   beforeEach(() => {
-    showTextDocumentSpy = jest
-      .spyOn(vscode.window, "showTextDocument")
-      .mockResolvedValue(mockedObject<TextEditor>({}));
-    showInformationMessageSpy = jest
-      .spyOn(vscode.window, "showInformationMessage")
-      .mockResolvedValue(undefined);
     showQuickPickSpy = jest
       .spyOn(vscode.window, "showQuickPick")
       .mockResolvedValue(undefined);
-    executeCommandSpy = jest
-      .spyOn(vscode.commands, "executeCommand")
-      .mockResolvedValue(undefined);
+
+    executeCommand = jest.fn();
+    mockApp = createMockApp({
+      commands: createMockCommandManager({ executeCommand }),
+    });
 
     jest.spyOn(extLogger, "log").mockResolvedValue(undefined);
 
-    tryOpenExternalFile = (QueryHistoryManager.prototype as any)
-      .tryOpenExternalFile;
     configListener = new QueryHistoryConfigListener();
     localQueriesResultsViewStub = {
       showResults: jest.fn(),
@@ -82,9 +75,15 @@ describe("QueryHistoryManager", () => {
       onVariantAnalysisStatusUpdated: jest.fn(),
       onVariantAnalysisRemoved: jest.fn(),
       removeVariantAnalysis: jest.fn(),
+      cancelVariantAnalysis: jest.fn(),
+      exportResults: jest.fn(),
       showView: jest.fn(),
     } as any as VariantAnalysisManager;
 
+    cancelVariantAnalysisSpy = jest
+      .spyOn(variantAnalysisManagerStub, "cancelVariantAnalysis")
+      .mockResolvedValue(undefined);
+
     localQueryHistory = [
       // completed
       createMockLocalQueryInfo({
@@ -148,51 +147,6 @@ describe("QueryHistoryManager", () => {
       queryHistoryManager.dispose();
     }
   });
-  describe("tryOpenExternalFile", () => {
-    it("should open an external file", async () => {
-      await tryOpenExternalFile("xxx");
-      expect(showTextDocumentSpy).toHaveBeenCalledTimes(1);
-      expect(showTextDocumentSpy).toHaveBeenCalledWith(
-        vscode.Uri.file("xxx"),
-        expect.anything(),
-      );
-      expect(executeCommandSpy).not.toBeCalled();
-    });
-
-    [
-      "too large to open",
-      "Files above 50MB cannot be synchronized with extensions",
-    ].forEach((msg) => {
-      it(`should fail to open a file because "${msg}" and open externally`, async () => {
-        showTextDocumentSpy.mockRejectedValue(new Error(msg));
-        showInformationMessageSpy.mockResolvedValue({ title: "Yes" });
-
-        await tryOpenExternalFile("xxx");
-        const uri = vscode.Uri.file("xxx");
-        expect(showTextDocumentSpy).toHaveBeenCalledTimes(1);
-        expect(showTextDocumentSpy).toHaveBeenCalledWith(
-          uri,
-          expect.anything(),
-        );
-        expect(executeCommandSpy).toHaveBeenCalledWith("revealFileInOS", uri);
-      });
-
-      it(`should fail to open a file because "${msg}" and NOT open externally`, async () => {
-        showTextDocumentSpy.mockRejectedValue(new Error(msg));
-        showInformationMessageSpy.mockResolvedValue({ title: "No" });
-
-        await tryOpenExternalFile("xxx");
-        const uri = vscode.Uri.file("xxx");
-        expect(showTextDocumentSpy).toHaveBeenCalledTimes(1);
-        expect(showTextDocumentSpy).toHaveBeenCalledWith(
-          uri,
-          expect.anything(),
-        );
-        expect(showInformationMessageSpy).toBeCalled();
-        expect(executeCommandSpy).not.toBeCalled();
-      });
-    });
-  });
 
   describe("handleItemClicked", () => {
     describe("single click", () => {
@@ -344,7 +298,6 @@ describe("QueryHistoryManager", () => {
         });
 
         it("should remove the item", () => {
-          expect(toDelete.completedQuery!.dispose).toBeCalledTimes(1);
           expect(queryHistoryManager.treeDataProvider.allHistory).toEqual(
             expect.not.arrayContaining([toDelete]),
           );
@@ -387,7 +340,6 @@ describe("QueryHistoryManager", () => {
         });
 
         it("should remove the item", () => {
-          expect(toDelete.completedQuery!.dispose).toBeCalledTimes(1);
           expect(queryHistoryManager.treeDataProvider.allHistory).toEqual(
             expect.not.arrayContaining([toDelete]),
           );
@@ -731,8 +683,7 @@ describe("QueryHistoryManager", () => {
         const inProgress1 = variantAnalysisHistory[1];
 
         await queryHistoryManager.handleCancel(inProgress1, [inProgress1]);
-        expect(executeCommandSpy).toBeCalledWith(
-          "codeQL.cancelVariantAnalysis",
+        expect(cancelVariantAnalysisSpy).toBeCalledWith(
           inProgress1.variantAnalysis.id,
         );
       });
@@ -748,12 +699,10 @@ describe("QueryHistoryManager", () => {
           inProgress1,
           inProgress2,
         ]);
-        expect(executeCommandSpy).toBeCalledWith(
-          "codeQL.cancelVariantAnalysis",
+        expect(cancelVariantAnalysisSpy).toBeCalledWith(
           inProgress1.variantAnalysis.id,
         );
-        expect(executeCommandSpy).toBeCalledWith(
-          "codeQL.cancelVariantAnalysis",
+        expect(cancelVariantAnalysisSpy).toBeCalledWith(
           inProgress2.variantAnalysis.id,
         );
       });
@@ -795,8 +744,7 @@ describe("QueryHistoryManager", () => {
         await queryHistoryManager.handleCancel(completedVariantAnalysis, [
           completedVariantAnalysis,
         ]);
-        expect(executeCommandSpy).not.toBeCalledWith(
-          "codeQL.cancelVariantAnalysis",
+        expect(cancelVariantAnalysisSpy).not.toBeCalledWith(
           completedVariantAnalysis.variantAnalysis,
         );
       });
@@ -812,12 +760,10 @@ describe("QueryHistoryManager", () => {
           completedVariantAnalysis,
           failedVariantAnalysis,
         ]);
-        expect(executeCommandSpy).not.toBeCalledWith(
-          "codeQL.cancelVariantAnalysis",
+        expect(cancelVariantAnalysisSpy).not.toBeCalledWith(
           completedVariantAnalysis.variantAnalysis.id,
         );
-        expect(executeCommandSpy).not.toBeCalledWith(
-          "codeQL.cancelVariantAnalysis",
+        expect(cancelVariantAnalysisSpy).not.toBeCalledWith(
           failedVariantAnalysis.variantAnalysis.id,
         );
       });
@@ -831,7 +777,7 @@ describe("QueryHistoryManager", () => {
       const item = localQueryHistory[4];
       await queryHistoryManager.handleCopyRepoList(item, [item]);
 
-      expect(executeCommandSpy).not.toBeCalled();
+      expect(executeCommand).not.toBeCalled();
     });
 
     it("should copy repo list for a single variant analysis", async () => {
@@ -839,7 +785,7 @@ describe("QueryHistoryManager", () => {
 
       const item = variantAnalysisHistory[1];
       await queryHistoryManager.handleCopyRepoList(item, [item]);
-      expect(executeCommandSpy).toBeCalledWith(
+      expect(executeCommand).toBeCalledWith(
         "codeQL.copyVariantAnalysisRepoList",
         item.variantAnalysis.id,
       );
@@ -851,7 +797,7 @@ describe("QueryHistoryManager", () => {
       const item1 = variantAnalysisHistory[1];
       const item2 = variantAnalysisHistory[3];
       await queryHistoryManager.handleCopyRepoList(item1, [item1, item2]);
-      expect(executeCommandSpy).not.toBeCalled();
+      expect(executeCommand).not.toBeCalled();
     });
   });
 
@@ -862,7 +808,7 @@ describe("QueryHistoryManager", () => {
       const item = localQueryHistory[4];
       await queryHistoryManager.handleExportResults(item, [item]);
 
-      expect(executeCommandSpy).not.toBeCalled();
+      expect(variantAnalysisManagerStub.exportResults).not.toBeCalled();
     });
 
     it("should export results for a single variant analysis", async () => {
@@ -870,8 +816,7 @@ describe("QueryHistoryManager", () => {
 
       const item = variantAnalysisHistory[1];
       await queryHistoryManager.handleExportResults(item, [item]);
-      expect(executeCommandSpy).toBeCalledWith(
-        "codeQL.exportVariantAnalysisResults",
+      expect(variantAnalysisManagerStub.exportResults).toBeCalledWith(
         item.variantAnalysis.id,
       );
     });
@@ -882,7 +827,7 @@ describe("QueryHistoryManager", () => {
       const item1 = variantAnalysisHistory[1];
       const item2 = variantAnalysisHistory[3];
       await queryHistoryManager.handleExportResults(item1, [item1, item2]);
-      expect(executeCommandSpy).not.toBeCalled();
+      expect(variantAnalysisManagerStub.exportResults).not.toBeCalled();
     });
   });
 
@@ -1149,6 +1094,7 @@ describe("QueryHistoryManager", () => {
 
   async function createMockQueryHistory(allHistory: QueryHistoryInfo[]) {
     const qhm = new QueryHistoryManager(
+      mockApp,
       {} as QueryRunner,
       {} as DatabaseManager,
       localQueriesResultsViewStub,
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-serialization.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts
similarity index 89%
rename from extensions/ql-vscode/test/vscode-tests/no-workspace/query-serialization.test.ts
rename to extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts
index 5b22b9aef..9adb3d550 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-serialization.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts
@@ -1,19 +1,22 @@
 import {
   deserializeQueryHistory,
   serializeQueryHistory,
-} from "../../../src/query-serialization";
+} from "../../../../../src/query-history/store/query-history-store";
 import { join } from "path";
 import { writeFileSync, mkdirpSync, writeFile } from "fs-extra";
-import { LocalQueryInfo, InitialQueryInfo } from "../../../src/query-results";
-import { QueryWithResults } from "../../../src/run-queries-shared";
-import { DatabaseInfo } from "../../../src/pure/interface-types";
+import {
+  LocalQueryInfo,
+  InitialQueryInfo,
+} from "../../../../../src/query-results";
+import { QueryWithResults } from "../../../../../src/run-queries-shared";
+import { DatabaseInfo } from "../../../../../src/pure/interface-types";
 import { CancellationTokenSource, Uri } from "vscode";
-import { tmpDir } from "../../../src/helpers";
-import { QueryResultType } from "../../../src/pure/legacy-messages";
-import { QueryInProgress } from "../../../src/legacy-query-server/run-queries";
-import { VariantAnalysisHistoryItem } from "../../../src/query-history/variant-analysis-history-item";
-import { QueryHistoryInfo } from "../../../src/query-history/query-history-info";
-import { createMockVariantAnalysisHistoryItem } from "../../factories/query-history/variant-analysis-history-item";
+import { tmpDir } from "../../../../../src/helpers";
+import { QueryResultType } from "../../../../../src/pure/legacy-messages";
+import { QueryInProgress } from "../../../../../src/legacy-query-server/run-queries";
+import { VariantAnalysisHistoryItem } from "../../../../../src/query-history/variant-analysis-history-item";
+import { QueryHistoryInfo } from "../../../../../src/query-history/query-history-info";
+import { createMockVariantAnalysisHistoryItem } from "../../../../factories/query-history/variant-analysis-history-item";
 import { nanoid } from "nanoid";
 
 describe("serialize and deserialize", () => {
@@ -259,7 +262,6 @@ describe("serialize and deserialize", () => {
       query: query.queryEvalInfo,
       successful: didRunSuccessfully,
       message: "foo",
-      dispose: jest.fn(),
       result: {
         evaluationTime: 1,
         queryId: 0,
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/variant-analysis-history.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/variant-analysis-history.test.ts
index 6441d2fea..f6115af31 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/variant-analysis-history.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/variant-analysis-history.test.ts
@@ -8,7 +8,7 @@ import {
 } from "fs-extra";
 import { join } from "path";
 
-import { commands, ExtensionContext, Uri } from "vscode";
+import { ExtensionContext, Uri } from "vscode";
 import { DatabaseManager } from "../../../../src/local-databases";
 import { tmpDir, walkDirectory } from "../../../../src/helpers";
 import { DisposableBucket } from "../../disposable-bucket";
@@ -21,6 +21,7 @@ import { VariantAnalysisManager } from "../../../../src/variant-analysis/variant
 import { QueryHistoryManager } from "../../../../src/query-history/query-history-manager";
 import { mockedObject } from "../../utils/mocking.helpers";
 import { createMockQueryHistoryDirs } from "../../../factories/query-history/query-history-dirs";
+import { createMockApp } from "../../../__mocks__/appMock";
 
 // set a higher timeout since recursive delete may take a while, expecially on Windows.
 jest.setTimeout(120000);
@@ -54,9 +55,12 @@ describe("Variant Analyses and QueryHistoryManager", () => {
     rehydrateVariantAnalysis: rehydrateVariantAnalysisStub,
     onVariantAnalysisStatusUpdated: jest.fn(),
     showView: showViewStub,
+    openQueryText: jest.fn(),
   } as any as VariantAnalysisManager;
 
-  let executeCommandSpy: jest.SpiedFunction<typeof commands.executeCommand>;
+  let openQueryTextSpy: jest.SpiedFunction<
+    typeof variantAnalysisManagerStub.openQueryText
+  >;
 
   beforeEach(async () => {
     // Since these tests change the state of the query history manager, we need to copy the original
@@ -70,6 +74,7 @@ describe("Variant Analyses and QueryHistoryManager", () => {
     ).queries;
 
     qhm = new QueryHistoryManager(
+      createMockApp({}),
       {} as QueryRunner,
       {} as DatabaseManager,
       localQueriesResultsViewStub,
@@ -95,8 +100,8 @@ describe("Variant Analyses and QueryHistoryManager", () => {
     );
     disposables.push(qhm);
 
-    executeCommandSpy = jest
-      .spyOn(commands, "executeCommand")
+    openQueryTextSpy = jest
+      .spyOn(variantAnalysisManagerStub, "openQueryText")
       .mockResolvedValue(undefined);
   });
 
@@ -180,8 +185,7 @@ describe("Variant Analyses and QueryHistoryManager", () => {
     await qhm.readQueryHistory();
     await qhm.handleShowQueryText(qhm.treeDataProvider.allHistory[0], []);
 
-    expect(executeCommandSpy).toHaveBeenCalledWith(
-      "codeQL.openVariantAnalysisQueryText",
+    expect(openQueryTextSpy).toHaveBeenCalledWith(
       rawQueryHistory[0].variantAnalysis.id,
     );
   });
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/vscode-utils/external-files.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/vscode-utils/external-files.test.ts
new file mode 100644
index 000000000..b87ee3fe6
--- /dev/null
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/vscode-utils/external-files.test.ts
@@ -0,0 +1,69 @@
+import * as vscode from "vscode";
+import { tryOpenExternalFile } from "../../../../../src/vscode-utils/external-files";
+import { createMockCommandManager } from "../../../../__mocks__/commandsMock";
+import { mockedObject } from "../../../utils/mocking.helpers";
+
+describe("tryOpenExternalFile", () => {
+  let showTextDocumentSpy: jest.SpiedFunction<
+    typeof vscode.window.showTextDocument
+  >;
+  let showInformationMessageSpy: jest.SpiedFunction<
+    typeof vscode.window.showInformationMessage
+  >;
+
+  beforeEach(() => {
+    showTextDocumentSpy = jest
+      .spyOn(vscode.window, "showTextDocument")
+      .mockResolvedValue(mockedObject<vscode.TextEditor>({}));
+    showInformationMessageSpy = jest
+      .spyOn(vscode.window, "showInformationMessage")
+      .mockResolvedValue(undefined);
+  });
+
+  it("should open an external file", async () => {
+    const executeCommand = jest.fn();
+    const commandManager = createMockCommandManager({ executeCommand });
+
+    await tryOpenExternalFile(commandManager, "xxx");
+    expect(showTextDocumentSpy).toHaveBeenCalledTimes(1);
+    expect(showTextDocumentSpy).toHaveBeenCalledWith(
+      vscode.Uri.file("xxx"),
+      expect.anything(),
+    );
+    expect(executeCommand).not.toBeCalled();
+  });
+
+  [
+    "too large to open",
+    "Files above 50MB cannot be synchronized with extensions",
+  ].forEach((msg) => {
+    it(`should fail to open a file because "${msg}" and open externally`, async () => {
+      const executeCommand = jest.fn();
+      const commandManager = createMockCommandManager({ executeCommand });
+
+      showTextDocumentSpy.mockRejectedValue(new Error(msg));
+      showInformationMessageSpy.mockResolvedValue({ title: "Yes" });
+
+      await tryOpenExternalFile(commandManager, "xxx");
+      const uri = vscode.Uri.file("xxx");
+      expect(showTextDocumentSpy).toHaveBeenCalledTimes(1);
+      expect(showTextDocumentSpy).toHaveBeenCalledWith(uri, expect.anything());
+      expect(executeCommand).toHaveBeenCalledWith("revealFileInOS", uri);
+    });
+
+    it(`should fail to open a file because "${msg}" and NOT open externally`, async () => {
+      const executeCommand = jest.fn();
+      const commandManager = createMockCommandManager({ executeCommand });
+
+      showTextDocumentSpy.mockRejectedValue(new Error(msg));
+      showInformationMessageSpy.mockResolvedValue({ title: "No" });
+
+      await tryOpenExternalFile(commandManager, "xxx");
+      const uri = vscode.Uri.file("xxx");
+      expect(showTextDocumentSpy).toHaveBeenCalledTimes(1);
+      expect(showTextDocumentSpy).toHaveBeenCalledWith(uri, expect.anything());
+      expect(showInformationMessageSpy).toBeCalled();
+      expect(executeCommand).not.toBeCalled();
+    });
+  });
+});
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 14992fee2..e32078ccc 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
@@ -470,7 +470,6 @@ describe("query-results", () => {
       query: query.queryEvalInfo,
       successful: didRunSuccessfully,
       message: "foo",
-      dispose: jest.fn(),
       result: {
         evaluationTime: 1,
         queryId: 0,
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 f7f74c5e3..d576b1004 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
@@ -190,6 +190,7 @@ describe("run-queries", () => {
         mockQlProgram,
         mockProgress as any,
         mockCancel as any,
+        qs.logger,
       );
 
       expect(results).toEqual([{ message: "err", severity: Severity.ERROR }]);
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/telemetry.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/telemetry.test.ts
index 4517837cf..47738ba85 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/telemetry.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/telemetry.test.ts
@@ -9,7 +9,7 @@ import {
   TelemetryListener,
   telemetryListener as globalTelemetryListener,
 } from "../../../src/telemetry";
-import { UserCancellationException } from "../../../src/commandRunner";
+import { UserCancellationException } from "../../../src/progress";
 import { ENABLE_TELEMETRY } from "../../../src/config";
 import { createMockExtensionContext } from "./index";
 import { vscodeGetConfigurationMock } from "../test-config";