Extension integration testing improvements

- Include vscode-codeql workspace storage in CODEQL_DATABASES_BASE_DIRS
  alongside global storage (picks up databases from current workspace)
- Add settings: additionalDatabaseDirs, additionalQueryRunResultsDirs,
  additionalMrvaRunResultsDirs for user-appended discovery directories
- Add .gitignore for extension build artifacts (dist/, server/, *.vsix)
- Update clean script to remove server/ and *.vsix
- Fix launch.json: use npx for vitest (hoisted node_modules), add
  5 debug configs (run ext, host tests, unit tests, current file, server)
- Export environmentBuilder and serverManager from extension API
- Add Extension Host integration tests: bridge env var path validation,
  MCP server definition tests
- Add unit tests: storage paths workspace methods, env var multi-path
  assembly, user-configured dir appending, discovery var passthrough
- Add extension host integration tests for common workspace states:
  - empty (no folders) vscode workspace;
  - single-root folder vscode workspace;
  - multi-root folder vscode workspace.

Author: data-douser

.vscode/launch.json

@@ -2,33 +2,98 @@
   "version": "0.2.0",
   "configurations": [
     {
-      "name": "Run Extension",
+      "name": "Run Extension (vscode-codeql-development-mcp-server)",
       "type": "extensionHost",
       "request": "launch",
       "args": [
-        "--extensionDevelopmentPath=${workspaceFolder}/extensions/vscode"
+        "--extensionDevelopmentPath=${workspaceFolder:codeql-development-mcp-server}/extensions/vscode"
       ],
       "outFiles": [
-        "${workspaceFolder}/extensions/vscode/dist/**/*.js",
-        "${workspaceFolder}/extensions/vscode/dist/**/*.cjs"
+        "${workspaceFolder:codeql-development-mcp-server}/extensions/vscode/dist/**/*.js",
+        "${workspaceFolder:codeql-development-mcp-server}/extensions/vscode/dist/**/*.cjs"
       ],
       "preLaunchTask": "npm: bundle - extensions/vscode",
       "sourceMaps": true
     },
     {
-      "name": "Extension Tests",
+      "name": "Extension Host Tests - No Workspace (vscode-codeql-development-mcp-server)",
       "type": "extensionHost",
       "request": "launch",
       "args": [
-        "--extensionDevelopmentPath=${workspaceFolder}/extensions/vscode",
-        "--extensionTestsPath=${workspaceFolder}/extensions/vscode/dist/test/suite/index.cjs"
+        "--extensionDevelopmentPath=${workspaceFolder:codeql-development-mcp-server}/extensions/vscode",
+        "--extensionTestsPath=${workspaceFolder:codeql-development-mcp-server}/extensions/vscode/dist/test/suite/index.cjs"
       ],
       "outFiles": [
-        "${workspaceFolder}/extensions/vscode/dist/**/*.js",
-        "${workspaceFolder}/extensions/vscode/dist/**/*.cjs"
+        "${workspaceFolder:codeql-development-mcp-server}/extensions/vscode/dist/**/*.js",
+        "${workspaceFolder:codeql-development-mcp-server}/extensions/vscode/dist/**/*.cjs"
       ],
       "preLaunchTask": "npm: bundle - extensions/vscode",
       "sourceMaps": true
+    },
+    {
+      "name": "Extension Host Tests - Single Folder (vscode-codeql-development-mcp-server)",
+      "type": "extensionHost",
+      "request": "launch",
+      "args": [
+        "--extensionDevelopmentPath=${workspaceFolder:codeql-development-mcp-server}/extensions/vscode",
+        "--extensionTestsPath=${workspaceFolder:codeql-development-mcp-server}/extensions/vscode/dist/test/suite/index.cjs",
+        "${workspaceFolder:codeql-development-mcp-server}/extensions/vscode/test/fixtures/single-folder-workspace"
+      ],
+      "outFiles": [
+        "${workspaceFolder:codeql-development-mcp-server}/extensions/vscode/dist/**/*.js",
+        "${workspaceFolder:codeql-development-mcp-server}/extensions/vscode/dist/**/*.cjs"
+      ],
+      "preLaunchTask": "npm: bundle - extensions/vscode",
+      "sourceMaps": true
+    },
+    {
+      "name": "Extension Host Tests - Multi-Root (vscode-codeql-development-mcp-server)",
+      "type": "extensionHost",
+      "request": "launch",
+      "args": [
+        "--extensionDevelopmentPath=${workspaceFolder:codeql-development-mcp-server}/extensions/vscode",
+        "--extensionTestsPath=${workspaceFolder:codeql-development-mcp-server}/extensions/vscode/dist/test/suite/index.cjs",
+        "${workspaceFolder:codeql-development-mcp-server}/extensions/vscode/test/fixtures/multi-root-workspace/test.code-workspace"
+      ],
+      "outFiles": [
+        "${workspaceFolder:codeql-development-mcp-server}/extensions/vscode/dist/**/*.js",
+        "${workspaceFolder:codeql-development-mcp-server}/extensions/vscode/dist/**/*.cjs"
+      ],
+      "preLaunchTask": "npm: bundle - extensions/vscode",
+      "sourceMaps": true
+    },
+    {
+      "name": "Unit Tests (vscode-codeql-development-mcp-server)",
+      "type": "node",
+      "request": "launch",
+      "runtimeExecutable": "npx",
+      "runtimeArgs": ["vitest", "--run"],
+      "cwd": "${workspaceFolder:codeql-development-mcp-server}/extensions/vscode",
+      "sourceMaps": true,
+      "console": "integratedTerminal",
+      "internalConsoleOptions": "neverOpen"
+    },
+    {
+      "name": "Unit Test - Current File (vscode-codeql-development-mcp-server)",
+      "type": "node",
+      "request": "launch",
+      "runtimeExecutable": "npx",
+      "runtimeArgs": ["vitest", "--run", "${relativeFile}"],
+      "cwd": "${workspaceFolder:codeql-development-mcp-server}/extensions/vscode",
+      "sourceMaps": true,
+      "console": "integratedTerminal",
+      "internalConsoleOptions": "neverOpen"
+    },
+    {
+      "name": "Server Unit Tests (vscode-codeql-development-mcp-server)",
+      "type": "node",
+      "request": "launch",
+      "runtimeExecutable": "npx",
+      "runtimeArgs": ["vitest", "--run"],
+      "cwd": "${workspaceFolder:codeql-development-mcp-server}/server",
+      "sourceMaps": true,
+      "console": "integratedTerminal",
+      "internalConsoleOptions": "neverOpen"
     }
   ]
 }

extensions/vscode/.gitignore

@@ -0,0 +1,5 @@
+# Build artifacts
+dist/
+server/
+coverage/
+*.vsix

extensions/vscode/.vscodeignore

@@ -4,7 +4,6 @@ src/**
 test/**
 scripts/**
 node_modules/**
-.gitignore
 tsconfig.json
 test/tsconfig.json
 vitest.config.ts

extensions/vscode/esbuild.config.js

@@ -34,7 +34,11 @@ const testSuiteConfig = {
   ...shared,
   entryPoints: [
     'test/suite/index.ts',
+    'test/suite/bridge.integration.test.ts',
     'test/suite/extension.integration.test.ts',
+    'test/suite/mcp-server.integration.test.ts',
+    'test/suite/mcp-tool-e2e.integration.test.ts',
+    'test/suite/workspace-scenario.integration.test.ts',
   ],
   outdir: 'dist/test/suite',
   outfile: undefined, // outdir and outfile are mutually exclusive

extensions/vscode/package.json

@@ -81,6 +81,24 @@
           "additionalProperties": {
             "type": "string"
           }
+        },
+        "codeql-mcp.additionalDatabaseDirs": {
+          "type": "array",
+          "items": { "type": "string" },
+          "default": [],
+          "description": "Additional directories to search for CodeQL databases. Appended to CODEQL_DATABASES_BASE_DIRS alongside the vscode-codeql storage paths."
+        },
+        "codeql-mcp.additionalMrvaRunResultsDirs": {
+          "type": "array",
+          "items": { "type": "string" },
+          "default": [],
+          "description": "Additional directories containing MRVA run result subdirectories. Appended to CODEQL_MRVA_RUN_RESULTS_DIRS alongside the vscode-codeql variant analysis storage path."
+        },
+        "codeql-mcp.additionalQueryRunResultsDirs": {
+          "type": "array",
+          "items": { "type": "string" },
+          "default": [],
+          "description": "Additional directories containing query run result subdirectories. Appended to CODEQL_QUERY_RUN_RESULTS_DIRS alongside the vscode-codeql query storage path."
         }
       }
     },
@@ -111,7 +129,7 @@
     "build": "npm run clean && npm run lint && npm run bundle",
     "bundle": "node esbuild.config.js",
     "bundle:server": "node scripts/bundle-server.js",
-    "clean": "rm -rf dist",
+    "clean": "rm -rf dist server *.vsix",
     "lint": "eslint src/ test/",
     "lint:fix": "eslint src/ test/ --fix",
     "package": "vsce package --out codeql-development-mcp-server.vsix",

extensions/vscode/src/bridge/environment-builder.ts

@@ -42,6 +42,9 @@ export class EnvironmentBuilder extends DisposableObject {
 
     const env: Record<string, string> = {};
 
+    // User configuration
+    const config = vscode.workspace.getConfiguration('codeql-mcp');
+
     // Transport mode is always stdio when launched from VS Code
     env.TRANSPORT_MODE = 'stdio';
 
@@ -78,17 +81,26 @@ export class EnvironmentBuilder extends DisposableObject {
 
     env.CODEQL_ADDITIONAL_PACKS = additionalPaths.join(':');
 
-    // Database discovery directory for list_codeql_databases
-    env.CODEQL_DATABASES_BASE_DIRS = this.storagePaths.getDatabaseStoragePath();
+    // Database discovery directories for list_codeql_databases
+    // Includes: global storage, workspace storage, and user-configured dirs
+    const dbDirs = [...this.storagePaths.getAllDatabaseStoragePaths()];
+    const userDbDirs = config.get<string[]>('additionalDatabaseDirs', []);
+    dbDirs.push(...userDbDirs);
+    env.CODEQL_DATABASES_BASE_DIRS = dbDirs.join(':');
 
     // MRVA run results directory for variant analysis discovery
-    env.CODEQL_MRVA_RUN_RESULTS_DIRS = this.storagePaths.getVariantAnalysisStoragePath();
+    const mrvaDirs = [this.storagePaths.getVariantAnalysisStoragePath()];
+    const userMrvaDirs = config.get<string[]>('additionalMrvaRunResultsDirs', []);
+    mrvaDirs.push(...userMrvaDirs);
+    env.CODEQL_MRVA_RUN_RESULTS_DIRS = mrvaDirs.join(':');
 
     // Query run results directory for query history discovery
-    env.CODEQL_QUERY_RUN_RESULTS_DIRS = this.storagePaths.getQueryStoragePath();
+    const queryDirs = [this.storagePaths.getQueryStoragePath()];
+    const userQueryDirs = config.get<string[]>('additionalQueryRunResultsDirs', []);
+    queryDirs.push(...userQueryDirs);
+    env.CODEQL_QUERY_RUN_RESULTS_DIRS = queryDirs.join(':');
 
     // User-configured additional environment variables
-    const config = vscode.workspace.getConfiguration('codeql-mcp');
     const additionalEnv = config.get<Record<string, string>>('additionalEnv', {});
     for (const [key, value] of Object.entries(additionalEnv)) {
       env[key] = value;

extensions/vscode/src/bridge/storage-paths.ts

@@ -19,13 +19,21 @@ const VSCODE_CODEQL_EXTENSION_ID = 'GitHub.vscode-codeql';
  */
 export class StoragePaths extends DisposableObject {
   private readonly vsCodeGlobalStorageRoot: string;
+  private readonly vsCodeWorkspaceStorageRoot: string | undefined;
 
   constructor(private readonly context: vscode.ExtensionContext) {
     super();
     // Our extension's globalStorageUri is something like:
     //   .../<vscode-global-storage>/advanced-security.vscode-codeql-development-mcp-server/
     // The parent directory is the vscode global storage root.
     this.vsCodeGlobalStorageRoot = dirname(context.globalStorageUri.fsPath);
+
+    // Our extension's storageUri (workspace-scoped) is something like:
+    //   .../<vscode-workspace-storage>/<workspace-id>/advanced-security.vscode-codeql-development-mcp-server/
+    // The parent directory is this workspace's storage root.
+    if (context.storageUri) {
+      this.vsCodeWorkspaceStorageRoot = dirname(context.storageUri.fsPath);
+    }
   }
 
   /** Global storage directory for the vscode-codeql extension. */
@@ -34,13 +42,36 @@ export class StoragePaths extends DisposableObject {
   }
 
   /**
-   * Directory where vscode-codeql stores downloaded/managed databases.
-   * Databases are stored directly under the global storage path.
+   * Directory where vscode-codeql stores downloaded/managed databases
+   * at the global level (e.g. databases added from GitHub).
    */
   getDatabaseStoragePath(): string {
     return this.getCodeqlGlobalStoragePath();
   }
 
+  /**
+   * Directory where vscode-codeql stores workspace-scoped databases
+   * (e.g. databases created from repos in the current workspace).
+   * Returns `undefined` if no workspace is open.
+   */
+  getWorkspaceDatabaseStoragePath(): string | undefined {
+    if (!this.vsCodeWorkspaceStorageRoot) return undefined;
+    return join(this.vsCodeWorkspaceStorageRoot, VSCODE_CODEQL_EXTENSION_ID);
+  }
+
+  /**
+   * All database storage paths: global + workspace-scoped.
+   * Suitable for colon-joining into `CODEQL_DATABASES_BASE_DIRS`.
+   */
+  getAllDatabaseStoragePaths(): string[] {
+    const paths = [this.getDatabaseStoragePath()];
+    const workspacePath = this.getWorkspaceDatabaseStoragePath();
+    if (workspacePath) {
+      paths.push(workspacePath);
+    }
+    return paths;
+  }
+
   /**
    * Directory where vscode-codeql stores query results.
    * Path: `<globalStorageUri>/queries/<queryBasename>-<nanoid>/`

extensions/vscode/src/extension.ts

@@ -187,7 +187,7 @@ export async function activate(
   }
 
   logger.info('CodeQL Development MCP Server extension activated.');
-  return { mcpProvider };
+  return { environmentBuilder: envBuilder, mcpProvider, serverManager };
 }
 
 export function deactivate(): void {

extensions/vscode/src/server/server-manager.ts

@@ -129,16 +129,33 @@ export class ServerManager extends DisposableObject {
   // ---------------------------------------------------------------------------
 
   /**
-   * Absolute path to the bundled MCP server entry point inside the extension.
-   * Returns `undefined` if the bundled server is not present (e.g. dev build
-   * that hasn't run `vscode:prepublish` yet).
+   * Absolute path to the MCP server entry point.
+   *
+   * Checks two locations:
+   * 1. **VSIX layout**: `<extensionRoot>/server/dist/codeql-development-mcp-server.js`
+   *    (created by `bundle:server` during `vscode:prepublish`)
+   * 2. **Monorepo dev layout**: `<extensionRoot>/../../server/dist/codeql-development-mcp-server.js`
+   *    (the adjacent server build when running from Extension Development Host)
+   *
+   * Returns `undefined` if neither location exists.
    */
   getBundledServerPath(): string | undefined {
     const extensionRoot = this.context.extensionUri.fsPath;
-    const candidate = join(extensionRoot, BUNDLED_SERVER_ENTRY);
+
+    // VSIX layout: server files bundled inside the extension
+    const vsixCandidate = join(extensionRoot, BUNDLED_SERVER_ENTRY);
+    try {
+      accessSync(vsixCandidate, constants.R_OK);
+      return vsixCandidate;
+    } catch {
+      // Not in VSIX layout — try monorepo
+    }
+
+    // Monorepo dev layout: extensions/vscode/../../server/dist/...
+    const monorepoCandidate = join(extensionRoot, '..', '..', BUNDLED_SERVER_ENTRY);
     try {
-      accessSync(candidate, constants.R_OK);
-      return candidate;
+      accessSync(monorepoCandidate, constants.R_OK);
+      return monorepoCandidate;
     } catch {
       return undefined;
     }