diff --git a/extensions/ql-vscode/src/common/commands.ts b/extensions/ql-vscode/src/common/commands.ts
index ff52f56a9..8e9c4bb9c 100644
--- a/extensions/ql-vscode/src/common/commands.ts
+++ b/extensions/ql-vscode/src/common/commands.ts
@@ -30,6 +30,12 @@ export type SingleSelectionCommandFunction<Item> = (
  * the implementation in the corresponding `getCommands` function.
  */
 
+// Builtin commands where the implementation is provided by VS Code and not by this extension.
+export type VSCodeCommands = {
+  "markdown.showPreviewToSide": (uri: Uri) => Promise<void>;
+  "workbench.action.reloadWindow": () => Promise<void>;
+};
+
 // Base commands not tied directly to a module like e.g. variant analysis.
 export type BaseCommands = {
   "codeQL.openDocumentation": () => Promise<void>;
@@ -185,7 +191,8 @@ export type EvalLogViewerCommands = {
   "codeQLEvalLogViewer.clear": () => Promise<void>;
 };
 
-export type AllCommands = BaseCommands &
+// All commands where the implementation is provided by this extension.
+export type AllCodeQLCommands = BaseCommands &
   QueryHistoryCommands &
   LocalDatabasesCommands &
   VariantAnalysisCommands &
@@ -194,6 +201,8 @@ export type AllCommands = BaseCommands &
   PackagingCommands &
   EvalLogViewerCommands;
 
+export type AllCommands = AllCodeQLCommands & VSCodeCommands;
+
 export type AppCommandManager = CommandManager<AllCommands>;
 
 // Separate command manager because it uses a different logger
diff --git a/extensions/ql-vscode/src/extension.ts b/extensions/ql-vscode/src/extension.ts
index 7d3653296..49d5fe674 100644
--- a/extensions/ql-vscode/src/extension.ts
+++ b/extensions/ql-vscode/src/extension.ts
@@ -1,7 +1,6 @@
 import "source-map-support/register";
 import {
   CancellationToken,
-  commands,
   Disposable,
   env,
   ExtensionContext,
@@ -112,7 +111,7 @@ import { redactableError } from "./pure/errors";
 import { QueryHistoryDirs } from "./query-history/query-history-dirs";
 import { DirResult } from "tmp";
 import {
-  AllCommands,
+  AllCodeQLCommands,
   BaseCommands,
   QueryServerCommands,
 } from "./common/commands";
@@ -265,6 +264,8 @@ export async function activate(
   addUnhandledRejectionListener();
   install();
 
+  const app = new ExtensionApp(ctx);
+
   const codelensProvider = new QuickEvalCodeLensProvider();
   languages.registerCodeLensProvider(
     { scheme: "file", language: "ql" },
@@ -291,6 +292,7 @@ export async function activate(
     distributionConfigListener.onDidChangeConfiguration(() =>
       installOrUpdateThenTryActivate(
         ctx,
+        app,
         distributionManager,
         distributionConfigListener,
         {
@@ -305,6 +307,7 @@ export async function activate(
     commandRunner(checkForUpdatesCommand, () =>
       installOrUpdateThenTryActivate(
         ctx,
+        app,
         distributionManager,
         distributionConfigListener,
         {
@@ -324,6 +327,7 @@ export async function activate(
 
   const codeQlExtension = await installOrUpdateThenTryActivate(
     ctx,
+    app,
     distributionManager,
     distributionConfigListener,
     {
@@ -345,6 +349,7 @@ export async function activate(
 
 async function installOrUpdateDistributionWithProgressTitle(
   ctx: ExtensionContext,
+  app: ExtensionApp,
   distributionManager: DistributionManager,
   progressTitle: string,
   config: DistributionUpdateConfig,
@@ -389,7 +394,7 @@ async function installOrUpdateDistributionWithProgressTitle(
             "Restart and Upgrade",
           )
         ) {
-          await commands.executeCommand("workbench.action.reloadWindow");
+          await app.commands.execute("workbench.action.reloadWindow");
         }
       } else {
         await withProgress(
@@ -416,6 +421,7 @@ async function installOrUpdateDistributionWithProgressTitle(
 
 async function installOrUpdateDistribution(
   ctx: ExtensionContext,
+  app: ExtensionApp,
   distributionManager: DistributionManager,
   config: DistributionUpdateConfig,
 ): Promise<void> {
@@ -436,6 +442,7 @@ async function installOrUpdateDistribution(
   try {
     await installOrUpdateDistributionWithProgressTitle(
       ctx,
+      app,
       distributionManager,
       messageText,
       config,
@@ -521,11 +528,12 @@ async function getDistributionDisplayingDistributionWarnings(
 
 async function installOrUpdateThenTryActivate(
   ctx: ExtensionContext,
+  app: ExtensionApp,
   distributionManager: DistributionManager,
   distributionConfigListener: DistributionConfigListener,
   config: DistributionUpdateConfig,
 ): Promise<CodeQLExtensionInterface | Record<string, never>> {
-  await installOrUpdateDistribution(ctx, distributionManager, config);
+  await installOrUpdateDistribution(ctx, app, distributionManager, config);
 
   try {
     await prepareCodeTour();
@@ -545,6 +553,7 @@ async function installOrUpdateThenTryActivate(
   ) {
     extensionInterface = await activateWithInstalledDistribution(
       ctx,
+      app,
       distributionManager,
       distributionConfigListener,
     );
@@ -562,6 +571,7 @@ async function installOrUpdateThenTryActivate(
       if (chosenAction === installActionName) {
         await installOrUpdateThenTryActivate(
           ctx,
+          app,
           distributionManager,
           distributionConfigListener,
           {
@@ -588,6 +598,7 @@ const PACK_GLOBS = [
 
 async function activateWithInstalledDistribution(
   ctx: ExtensionContext,
+  app: ExtensionApp,
   distributionManager: DistributionManager,
   distributionConfigListener: DistributionConfigListener,
 ): Promise<CodeQLExtensionInterface> {
@@ -596,8 +607,6 @@ 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(
@@ -821,7 +830,7 @@ async function activateWithInstalledDistribution(
 
   void extLogger.log("Registering top-level command palette commands.");
 
-  const allCommands: AllCommands = {
+  const allCommands: AllCodeQLCommands = {
     ...getCommands(cliServer, qs),
     ...qhm.getCommands(),
     ...variantAnalysisManager.getCommands(),
@@ -844,7 +853,7 @@ async function activateWithInstalledDistribution(
   };
 
   for (const [commandName, command] of Object.entries(allCommands)) {
-    app.commands.register(commandName as keyof AllCommands, command);
+    app.commands.register(commandName as keyof AllCodeQLCommands, command);
   }
 
   const queryServerCommands: QueryServerCommands = {
@@ -895,7 +904,7 @@ async function activateWithInstalledDistribution(
 
   ctx.subscriptions.push(
     commandRunner("codeQL.previewQueryHelp", async (selectedQuery: Uri) => {
-      await previewQueryHelp(cliServer, qhelpTmpDir, selectedQuery);
+      await previewQueryHelp(app, cliServer, qhelpTmpDir, selectedQuery);
     }),
   );
 
@@ -1002,7 +1011,7 @@ async function activateWithInstalledDistribution(
     ),
   );
 
-  await commands.executeCommand("codeQLDatabases.removeOrphanedDatabases");
+  await app.commands.execute("codeQLDatabases.removeOrphanedDatabases");
 
   void extLogger.log("Reading query history");
   await qhm.readQueryHistory();
@@ -1040,6 +1049,7 @@ async function showResultsForComparison(
 }
 
 async function previewQueryHelp(
+  app: ExtensionApp,
   cliServer: CodeQLCliServer,
   qhelpTmpDir: DirResult,
   selectedQuery: Uri,
@@ -1055,7 +1065,7 @@ async function previewQueryHelp(
     const uri = Uri.file(absolutePathToMd);
     try {
       await cliServer.generateQueryHelp(pathToQhelp, absolutePathToMd);
-      await commands.executeCommand("markdown.showPreviewToSide", uri);
+      await app.commands.execute("markdown.showPreviewToSide", uri);
     } catch (e) {
       const errorMessage = getErrorMessage(e).includes(
         "Generating qhelp in markdown",