Pass whole extensions rather than just context files (#10910)

Co-authored-by: Jake Macdonald <jakemac@google.com>

packages/cli/src/config/config.integration.test.ts

@@ -243,38 +243,6 @@ describe('Configuration Integration Tests', () => {
     });
   });
 
-  describe('Extension Context Files', () => {
-    it('should have an empty array for extension context files by default', () => {
-      const configParams: ConfigParameters = {
-        sessionId: 'test-session',
-        cwd: '/tmp',
-        model: 'test-model',
-        embeddingModel: 'test-embedding-model',
-        sandbox: undefined,
-        targetDir: tempDir,
-        debugMode: false,
-      };
-      const config = new Config(configParams);
-      expect(config.getExtensionContextFilePaths()).toEqual([]);
-    });
-
-    it('should correctly store and return extension context file paths', () => {
-      const contextFiles = ['/path/to/file1.txt', '/path/to/file2.js'];
-      const configParams: ConfigParameters = {
-        sessionId: 'test-session',
-        cwd: '/tmp',
-        model: 'test-model',
-        embeddingModel: 'test-embedding-model',
-        sandbox: undefined,
-        targetDir: tempDir,
-        debugMode: false,
-        extensionContextFilePaths: contextFiles,
-      };
-      const config = new Config(configParams);
-      expect(config.getExtensionContextFilePaths()).toEqual(contextFiles);
-    });
-  });
-
   describe('Approval Mode Integration Tests', () => {
     let parseArguments: typeof import('./config.js').parseArguments;
 

packages/cli/src/config/config.ts

@@ -40,7 +40,6 @@ import {
 } from '@google/gemini-cli-core';
 import type { Settings } from './settings.js';
 
-import { annotateActiveExtensions } from './extension.js';
 import { getCliVersion } from '../utils/version.js';
 import { loadSandboxConfig } from './sandboxConfig.js';
 import { resolvePath } from '../utils/resolvePath.js';
@@ -48,7 +47,6 @@ import { appEvents } from '../utils/events.js';
 
 import { isWorkspaceTrusted } from './trustedFolders.js';
 import { createPolicyEngineConfig } from './policy.js';
-import type { ExtensionEnablementManager } from './extensions/extensionEnablement.js';
 
 export interface CliArgs {
   query: string | undefined;
@@ -289,7 +287,7 @@ export async function loadHierarchicalGeminiMemory(
   debugMode: boolean,
   fileService: FileDiscoveryService,
   settings: Settings,
-  extensionContextFilePaths: string[] = [],
+  extensions: GeminiCLIExtension[],
   folderTrust: boolean,
   memoryImportFormat: 'flat' | 'tree' = 'tree',
   fileFilteringOptions?: FileFilteringOptions,
@@ -315,7 +313,7 @@ export async function loadHierarchicalGeminiMemory(
     includeDirectoriesToReadGemini,
     debugMode,
     fileService,
-    extensionContextFilePaths,
+    extensions,
     folderTrust,
     memoryImportFormat,
     fileFilteringOptions,
@@ -364,8 +362,7 @@ export function isDebugMode(argv: CliArgs): boolean {
 
 export async function loadCliConfig(
   settings: Settings,
-  extensions: GeminiCLIExtension[],
-  extensionEnablementManager: ExtensionEnablementManager,
+  allExtensions: GeminiCLIExtension[],
   sessionId: string,
   argv: CliArgs,
   cwd: string = process.cwd(),
@@ -379,16 +376,6 @@ export async function loadCliConfig(
   const folderTrust = settings.security?.folderTrust?.enabled ?? false;
   const trustedFolder = isWorkspaceTrusted(settings)?.isTrusted ?? true;
 
-  const allExtensions = annotateActiveExtensions(
-    extensions,
-    cwd,
-    extensionEnablementManager,
-  );
-
-  const activeExtensions = extensions.filter(
-    (_, i) => allExtensions[i].isActive,
-  );
-
   // Set the context filename in the server's memoryTool module BEFORE loading memory
   // TODO(b/343434939): This is a bit of a hack. The contextFileName should ideally be passed
   // directly to the Config constructor in core, and have core handle setGeminiMdFilename.
@@ -400,10 +387,6 @@ export async function loadCliConfig(
     setServerGeminiMdFilename(getCurrentGeminiMdFilename());
   }
 
-  const extensionContextFilePaths = activeExtensions.flatMap(
-    (e) => e.contextFiles,
-  );
-
   const fileService = new FileDiscoveryService(cwd);
 
   const fileFiltering = {
@@ -425,13 +408,13 @@ export async function loadCliConfig(
       debugMode,
       fileService,
       settings,
-      extensionContextFilePaths,
+      allExtensions,
       trustedFolder,
       memoryImportFormat,
       fileFiltering,
     );
 
-  let mcpServers = mergeMcpServers(settings, activeExtensions);
+  let mcpServers = mergeMcpServers(settings, allExtensions);
   const question = argv.promptInteractive || argv.prompt || '';
 
   // Determine approval mode with backward compatibility
@@ -527,7 +510,7 @@ export async function loadCliConfig(
 
   const excludeTools = mergeExcludeTools(
     settings,
-    activeExtensions,
+    allExtensions,
     extraExcludes.length > 0 ? extraExcludes : undefined,
   );
   const blockedMcpServers: Array<{ name: string; extensionName: string }> = [];
@@ -618,10 +601,10 @@ export async function loadCliConfig(
     fileDiscoveryService: fileService,
     bugCommand: settings.advanced?.bugCommand,
     model: resolvedModel,
-    extensionContextFilePaths,
     maxSessionTurns: settings.model?.maxSessionTurns ?? -1,
     experimentalZedIntegration: argv.experimentalAcp || false,
     listExtensions: argv.listExtensions || false,
+    enabledExtensions: argv.extensions,
     extensions: allExtensions,
     blockedMcpServers,
     noBrowser: !!process.env['NO_BROWSER'],
@@ -668,7 +651,7 @@ function allowedMcpServers(
         if (!isAllowed) {
           blockedMcpServers.push({
             name: key,
-            extensionName: server.extensionName || '',
+            extensionName: server.extension?.name || '',
           });
         }
         return isAllowed;
@@ -678,7 +661,7 @@ function allowedMcpServers(
     blockedMcpServers.push(
       ...Object.entries(mcpServers).map(([key, server]) => ({
         name: key,
-        extensionName: server.extensionName || '',
+        extensionName: server.extension?.name || '',
       })),
     );
     mcpServers = {};
@@ -689,6 +672,9 @@ function allowedMcpServers(
 function mergeMcpServers(settings: Settings, extensions: GeminiCLIExtension[]) {
   const mcpServers = { ...(settings.mcpServers || {}) };
   for (const extension of extensions) {
+    if (!extension.isActive) {
+      continue;
+    }
     Object.entries(extension.mcpServers || {}).forEach(([key, server]) => {
       if (mcpServers[key]) {
         debugLogger.warn(
@@ -698,7 +684,7 @@ function mergeMcpServers(settings: Settings, extensions: GeminiCLIExtension[]) {
       }
       mcpServers[key] = {
         ...server,
-        extensionName: extension.name,
+        extension,
       };
     });
   }
@@ -715,6 +701,9 @@ function mergeExcludeTools(
     ...(extraExcludes || []),
   ]);
   for (const extension of extensions) {
+    if (!extension.isActive) {
+      continue;
+    }
     for (const tool of extension.excludeTools || []) {
       allExcludeTools.add(tool);
     }

packages/cli/src/config/extension.test.ts

@@ -14,7 +14,6 @@ import {
   ExtensionStorage,
   INSTALL_METADATA_FILENAME,
   INSTALL_WARNING_MESSAGE,
-  annotateActiveExtensions,
   disableExtension,
   enableExtension,
   installOrUpdateExtension,
@@ -202,7 +201,7 @@ describe('extension tests', () => {
       ]);
     });
 
-    it('should filter out disabled extensions', () => {
+    it('should annotate disabled extensions', () => {
       createExtension({
         extensionsDir: userExtensionsDir,
         name: 'disabled-extension',
@@ -213,20 +212,19 @@ describe('extension tests', () => {
         name: 'enabled-extension',
         version: '2.0.0',
       });
+      const manager = new ExtensionEnablementManager();
       disableExtension(
         'disabled-extension',
         SettingScope.User,
+        manager,
         tempWorkspaceDir,
       );
-      const manager = new ExtensionEnablementManager();
       const extensions = loadExtensions(manager);
-      const activeExtensions = annotateActiveExtensions(
-        extensions,
-        tempWorkspaceDir,
-        manager,
-      ).filter((e) => e.isActive);
-      expect(activeExtensions).toHaveLength(1);
-      expect(activeExtensions[0].name).toBe('enabled-extension');
+      expect(extensions).toHaveLength(2);
+      expect(extensions[0].name).toBe('disabled-extension');
+      expect(extensions[0].isActive).toBe(false);
+      expect(extensions[1].name).toBe('enabled-extension');
+      expect(extensions[1].isActive).toBe(true);
     });
 
     it('should hydrate variables', () => {
@@ -477,6 +475,7 @@ describe('extension tests', () => {
       const extension = loadExtension({
         extensionDir: badExtDir,
         workspaceDir: tempWorkspaceDir,
+        extensionEnablementManager: new ExtensionEnablementManager(),
       });
 
       expect(extension).toBeNull();
@@ -501,6 +500,7 @@ describe('extension tests', () => {
         const extension = loadExtension({
           extensionDir,
           workspaceDir: tempWorkspaceDir,
+          extensionEnablementManager: new ExtensionEnablementManager(),
         });
 
         const expectedHash = createHash('sha256')
@@ -523,6 +523,7 @@ describe('extension tests', () => {
         const extension = loadExtension({
           extensionDir,
           workspaceDir: tempWorkspaceDir,
+          extensionEnablementManager: new ExtensionEnablementManager(),
         });
 
         const expectedHash = createHash('sha256')
@@ -545,6 +546,7 @@ describe('extension tests', () => {
         const extension = loadExtension({
           extensionDir,
           workspaceDir: tempWorkspaceDir,
+          extensionEnablementManager: new ExtensionEnablementManager(),
         });
 
         const expectedHash = createHash('sha256')
@@ -567,6 +569,7 @@ describe('extension tests', () => {
         const extension = loadExtension({
           extensionDir,
           workspaceDir: tempWorkspaceDir,
+          extensionEnablementManager: new ExtensionEnablementManager(),
         });
 
         const expectedHash = createHash('sha256')
@@ -589,6 +592,7 @@ describe('extension tests', () => {
         const extension = loadExtension({
           extensionDir,
           workspaceDir: tempWorkspaceDir,
+          extensionEnablementManager: new ExtensionEnablementManager(),
         });
 
         const expectedHash = createHash('sha256')
@@ -616,6 +620,7 @@ describe('extension tests', () => {
         const extension = loadExtension({
           extensionDir: new ExtensionStorage(extensionName).getExtensionDir(),
           workspaceDir: tempWorkspaceDir,
+          extensionEnablementManager: new ExtensionEnablementManager(),
         });
 
         const expectedHash = createHash('sha256')
@@ -634,6 +639,7 @@ describe('extension tests', () => {
         const extension = loadExtension({
           extensionDir,
           workspaceDir: tempWorkspaceDir,
+          extensionEnablementManager: new ExtensionEnablementManager(),
         });
 
         const expectedHash = createHash('sha256')
@@ -644,182 +650,6 @@ describe('extension tests', () => {
     });
   });
 
-  describe('annotateActiveExtensions', () => {
-    const extensions: GeminiCLIExtension[] = [
-      {
-        path: '/path/to/ext1',
-        name: 'ext1',
-        version: '1.0.0',
-        contextFiles: [],
-        isActive: true,
-      },
-      {
-        path: '/path/to/ext2',
-        name: 'ext2',
-        version: '1.0.0',
-        contextFiles: [],
-        isActive: true,
-      },
-      {
-        path: '/path/to/ext3',
-        name: 'ext3',
-        version: '1.0.0',
-        contextFiles: [],
-        isActive: true,
-      },
-    ];
-
-    it('should mark all extensions as active if no enabled extensions are provided', () => {
-      const activeExtensions = annotateActiveExtensions(
-        extensions,
-        '/path/to/workspace',
-        new ExtensionEnablementManager(),
-      );
-      expect(activeExtensions).toHaveLength(3);
-      expect(activeExtensions.every((e) => e.isActive)).toBe(true);
-    });
-
-    it('should mark only the enabled extensions as active', () => {
-      const activeExtensions = annotateActiveExtensions(
-        extensions,
-        '/path/to/workspace',
-        new ExtensionEnablementManager(['ext1', 'ext3']),
-      );
-      expect(activeExtensions).toHaveLength(3);
-      expect(activeExtensions.find((e) => e.name === 'ext1')?.isActive).toBe(
-        true,
-      );
-      expect(activeExtensions.find((e) => e.name === 'ext2')?.isActive).toBe(
-        false,
-      );
-      expect(activeExtensions.find((e) => e.name === 'ext3')?.isActive).toBe(
-        true,
-      );
-    });
-
-    it('should mark all extensions as inactive when "none" is provided', () => {
-      const activeExtensions = annotateActiveExtensions(
-        extensions,
-        '/path/to/workspace',
-        new ExtensionEnablementManager(['none']),
-      );
-      expect(activeExtensions).toHaveLength(3);
-      expect(activeExtensions.every((e) => !e.isActive)).toBe(true);
-    });
-
-    it('should handle case-insensitivity', () => {
-      const activeExtensions = annotateActiveExtensions(
-        extensions,
-        '/path/to/workspace',
-        new ExtensionEnablementManager(['EXT1']),
-      );
-      expect(activeExtensions.find((e) => e.name === 'ext1')?.isActive).toBe(
-        true,
-      );
-    });
-
-    it('should log an error for unknown extensions', () => {
-      const consoleSpy = vi
-        .spyOn(console, 'error')
-        .mockImplementation(() => {});
-      annotateActiveExtensions(
-        extensions,
-        '/path/to/workspace',
-        new ExtensionEnablementManager(['ext4']),
-      );
-      expect(consoleSpy).toHaveBeenCalledWith('Extension not found: ext4');
-      consoleSpy.mockRestore();
-    });
-
-    describe('autoUpdate', () => {
-      it('should be false if autoUpdate is not set in install metadata', () => {
-        const activeExtensions = annotateActiveExtensions(
-          extensions,
-          tempHomeDir,
-          new ExtensionEnablementManager(),
-        );
-        expect(
-          activeExtensions.every(
-            (e) => e.installMetadata?.autoUpdate === false,
-          ),
-        ).toBe(false);
-      });
-
-      it('should be true if autoUpdate is true in install metadata', () => {
-        const extensionsWithAutoUpdate: GeminiCLIExtension[] = extensions.map(
-          (e) => ({
-            ...e,
-            installMetadata: {
-              ...e.installMetadata!,
-              autoUpdate: true,
-            },
-          }),
-        );
-        const activeExtensions = annotateActiveExtensions(
-          extensionsWithAutoUpdate,
-          tempHomeDir,
-          new ExtensionEnablementManager(),
-        );
-        expect(
-          activeExtensions.every((e) => e.installMetadata?.autoUpdate === true),
-        ).toBe(true);
-      });
-
-      it('should respect the per-extension settings from install metadata', () => {
-        const extensionsWithAutoUpdate: GeminiCLIExtension[] = [
-          {
-            path: '/path/to/ext1',
-            name: 'ext1',
-            version: '1.0.0',
-            contextFiles: [],
-            installMetadata: {
-              source: 'test',
-              type: 'local',
-              autoUpdate: true,
-            },
-            isActive: true,
-          },
-          {
-            path: '/path/to/ext2',
-            name: 'ext2',
-            version: '1.0.0',
-            contextFiles: [],
-            installMetadata: {
-              source: 'test',
-              type: 'local',
-              autoUpdate: false,
-            },
-            isActive: true,
-          },
-          {
-            path: '/path/to/ext3',
-            name: 'ext3',
-            version: '1.0.0',
-            contextFiles: [],
-            isActive: true,
-          },
-        ];
-        const activeExtensions = annotateActiveExtensions(
-          extensionsWithAutoUpdate,
-          tempHomeDir,
-          new ExtensionEnablementManager(),
-        );
-        expect(
-          activeExtensions.find((e) => e.name === 'ext1')?.installMetadata
-            ?.autoUpdate,
-        ).toBe(true);
-        expect(
-          activeExtensions.find((e) => e.name === 'ext2')?.installMetadata
-            ?.autoUpdate,
-        ).toBe(false);
-        expect(
-          activeExtensions.find((e) => e.name === 'ext3')?.installMetadata
-            ?.autoUpdate,
-        ).toBe(undefined);
-      });
-    });
-  });
-
   describe('installExtension', () => {
     it('should install an extension from a local path', async () => {
       const sourceExtDir = createExtension({
@@ -1194,6 +1024,7 @@ This extension will run the following MCP servers:
           await loadExtensionConfig({
             extensionDir: sourceExtDir,
             workspaceDir: process.cwd(),
+            extensionEnablementManager: new ExtensionEnablementManager(),
           }),
         ),
       ).resolves.toBe('my-local-extension');
@@ -1512,7 +1343,11 @@ This extension will run the following MCP servers:
         version: '1.0.0',
       });
 
-      disableExtension('my-extension', SettingScope.User);
+      disableExtension(
+        'my-extension',
+        SettingScope.User,
+        new ExtensionEnablementManager(),
+      );
       expect(
         isEnabled({
           name: 'my-extension',
@@ -1531,6 +1366,7 @@ This extension will run the following MCP servers:
       disableExtension(
         'my-extension',
         SettingScope.Workspace,
+        new ExtensionEnablementManager(),
         tempWorkspaceDir,
       );
       expect(
@@ -1554,8 +1390,16 @@ This extension will run the following MCP servers:
         version: '1.0.0',
       });
 
-      disableExtension('my-extension', SettingScope.User);
-      disableExtension('my-extension', SettingScope.User);
+      disableExtension(
+        'my-extension',
+        SettingScope.User,
+        new ExtensionEnablementManager(),
+      );
+      disableExtension(
+        'my-extension',
+        SettingScope.User,
+        new ExtensionEnablementManager(),
+      );
       expect(
         isEnabled({
           name: 'my-extension',
@@ -1566,7 +1410,11 @@ This extension will run the following MCP servers:
 
     it('should throw an error if you request system scope', () => {
       expect(() =>
-        disableExtension('my-extension', SettingScope.System),
+        disableExtension(
+          'my-extension',
+          SettingScope.System,
+          new ExtensionEnablementManager(),
+        ),
       ).toThrow('System and SystemDefaults scopes are not supported.');
     });
 
@@ -1577,7 +1425,11 @@ This extension will run the following MCP servers:
         version: '1.0.0',
       });
 
-      disableExtension('ext1', SettingScope.Workspace);
+      disableExtension(
+        'ext1',
+        SettingScope.Workspace,
+        new ExtensionEnablementManager(),
+      );
 
       expect(mockLogExtensionDisable).toHaveBeenCalled();
       expect(ExtensionDisableEvent).toHaveBeenCalledWith(
@@ -1595,12 +1447,7 @@ This extension will run the following MCP servers:
     const getActiveExtensions = (): GeminiCLIExtension[] => {
       const manager = new ExtensionEnablementManager();
       const extensions = loadExtensions(manager);
-      const activeExtensions = annotateActiveExtensions(
-        extensions,
-        tempWorkspaceDir,
-        manager,
-      );
-      return activeExtensions.filter((e) => e.isActive);
+      return extensions.filter((e) => e.isActive);
     };
 
     it('should enable an extension at the user scope', () => {
@@ -1609,11 +1456,12 @@ This extension will run the following MCP servers:
         name: 'ext1',
         version: '1.0.0',
       });
-      disableExtension('ext1', SettingScope.User);
+      const extensionEnablementManager = new ExtensionEnablementManager();
+      disableExtension('ext1', SettingScope.User, extensionEnablementManager);
       let activeExtensions = getActiveExtensions();
       expect(activeExtensions).toHaveLength(0);
 
-      enableExtension('ext1', SettingScope.User);
+      enableExtension('ext1', SettingScope.User, extensionEnablementManager);
       activeExtensions = getActiveExtensions();
       expect(activeExtensions).toHaveLength(1);
       expect(activeExtensions[0].name).toBe('ext1');
@@ -1625,11 +1473,20 @@ This extension will run the following MCP servers:
         name: 'ext1',
         version: '1.0.0',
       });
-      disableExtension('ext1', SettingScope.Workspace);
+      const extensionEnablementManager = new ExtensionEnablementManager();
+      disableExtension(
+        'ext1',
+        SettingScope.Workspace,
+        extensionEnablementManager,
+      );
       let activeExtensions = getActiveExtensions();
       expect(activeExtensions).toHaveLength(0);
 
-      enableExtension('ext1', SettingScope.Workspace);
+      enableExtension(
+        'ext1',
+        SettingScope.Workspace,
+        extensionEnablementManager,
+      );
       activeExtensions = getActiveExtensions();
       expect(activeExtensions).toHaveLength(1);
       expect(activeExtensions[0].name).toBe('ext1');
@@ -1641,8 +1498,17 @@ This extension will run the following MCP servers:
         name: 'ext1',
         version: '1.0.0',
       });
-      disableExtension('ext1', SettingScope.Workspace);
-      enableExtension('ext1', SettingScope.Workspace);
+      const extensionEnablementManager = new ExtensionEnablementManager();
+      disableExtension(
+        'ext1',
+        SettingScope.Workspace,
+        extensionEnablementManager,
+      );
+      enableExtension(
+        'ext1',
+        SettingScope.Workspace,
+        extensionEnablementManager,
+      );
 
       expect(mockLogExtensionEnable).toHaveBeenCalled();
       expect(ExtensionEnableEvent).toHaveBeenCalledWith(

packages/cli/src/config/extension.ts

@@ -142,6 +142,7 @@ export function loadExtensions(
     const extension = loadExtension({
       extensionDir,
       workspaceDir,
+      extensionEnablementManager,
     });
     if (extension != null) {
       extensions.push(extension);
@@ -151,10 +152,7 @@ export function loadExtensions(
   const uniqueExtensions = new Map<string, GeminiCLIExtension>();
 
   for (const extension of extensions) {
-    if (
-      !uniqueExtensions.has(extension.name) &&
-      extensionEnablementManager.isEnabled(extension.name, workspaceDir)
-    ) {
+    if (!uniqueExtensions.has(extension.name)) {
       uniqueExtensions.set(extension.name, extension);
     }
   }
@@ -165,7 +163,7 @@ export function loadExtensions(
 export function loadExtension(
   context: LoadExtensionContext,
 ): GeminiCLIExtension | null {
-  const { extensionDir, workspaceDir } = context;
+  const { extensionDir, workspaceDir, extensionEnablementManager } = context;
   if (!fs.statSync(extensionDir).isDirectory()) {
     return null;
   }
@@ -181,6 +179,7 @@ export function loadExtension(
     let config = loadExtensionConfig({
       extensionDir: effectiveExtensionPath,
       workspaceDir,
+      extensionEnablementManager,
     });
 
     config = resolveEnvVarsInObject(config);
@@ -230,7 +229,7 @@ export function loadExtension(
       installMetadata,
       mcpServers: config.mcpServers,
       excludeTools: config.excludeTools,
-      isActive: true, // Barring any other signals extensions should be considered Active.
+      isActive: extensionEnablementManager.isEnabled(config.name, workspaceDir),
       id,
     };
   } catch (e) {
@@ -245,6 +244,7 @@ export function loadExtension(
 
 export function loadExtensionByName(
   name: string,
+  extensionEnablementManager: ExtensionEnablementManager,
   workspaceDir: string = process.cwd(),
 ): GeminiCLIExtension | null {
   const userExtensionsDir = ExtensionStorage.getUserExtensionsDir();
@@ -257,7 +257,11 @@ export function loadExtensionByName(
     if (!fs.statSync(extensionDir).isDirectory()) {
       continue;
     }
-    const extension = loadExtension({ extensionDir, workspaceDir });
+    const extension = loadExtension({
+      extensionDir,
+      workspaceDir,
+      extensionEnablementManager,
+    });
     if (extension && extension.name.toLowerCase() === name.toLowerCase()) {
       return extension;
     }
@@ -294,25 +298,6 @@ function getContextFileNames(config: ExtensionConfig): string[] {
   return config.contextFileName;
 }
 
-/**
- * Returns an annotated list of extensions. If an extension is listed in enabledExtensionNames, it will be active.
- * If enabledExtensionNames is empty, an extension is active unless it is disabled.
- * @param extensions The base list of extensions.
- * @param enabledExtensionNames The names of explicitly enabled extensions.
- * @param workspaceDir The current workspace directory.
- */
-export function annotateActiveExtensions(
-  extensions: GeminiCLIExtension[],
-  workspaceDir: string,
-  manager: ExtensionEnablementManager,
-): GeminiCLIExtension[] {
-  manager.validateExtensionOverrides(extensions);
-  return extensions.map((extension) => ({
-    ...extension,
-    isActive: manager.isEnabled(extension.name, workspaceDir),
-  }));
-}
-
 /**
  * Requests consent from the user to perform an action, by reading a Y/n
  * character from stdin.
@@ -409,6 +394,7 @@ export async function installOrUpdateExtension(
   const telemetryConfig = getTelemetryConfig(cwd);
   let newExtensionConfig: ExtensionConfig | null = null;
   let localSourcePath: string | undefined;
+  const extensionEnablementManager = new ExtensionEnablementManager();
 
   try {
     const settings = loadSettings(cwd).merged;
@@ -480,6 +466,7 @@ export async function installOrUpdateExtension(
       newExtensionConfig = loadExtensionConfig({
         extensionDir: localSourcePath,
         workspaceDir: cwd,
+        extensionEnablementManager,
       });
 
       const newExtensionName = newExtensionConfig.name;
@@ -555,7 +542,11 @@ export async function installOrUpdateExtension(
           'success',
         ),
       );
-      enableExtension(newExtensionConfig.name, SettingScope.User);
+      enableExtension(
+        newExtensionConfig.name,
+        SettingScope.User,
+        extensionEnablementManager,
+      );
     }
 
     return newExtensionConfig!.name;
@@ -567,6 +558,7 @@ export async function installOrUpdateExtension(
         newExtensionConfig = loadExtensionConfig({
           extensionDir: localSourcePath,
           workspaceDir: cwd,
+          extensionEnablementManager,
         });
       } catch {
         // Ignore error, this is just for logging.
@@ -791,38 +783,38 @@ export function toOutputString(
 export function disableExtension(
   name: string,
   scope: SettingScope,
+  extensionEnablementManager: ExtensionEnablementManager,
   cwd: string = process.cwd(),
 ) {
   const config = getTelemetryConfig(cwd);
   if (scope === SettingScope.System || scope === SettingScope.SystemDefaults) {
     throw new Error('System and SystemDefaults scopes are not supported.');
   }
-  const extension = loadExtensionByName(name, cwd);
+  const extension = loadExtensionByName(name, extensionEnablementManager, cwd);
   if (!extension) {
     throw new Error(`Extension with name ${name} does not exist.`);
   }
 
-  const manager = new ExtensionEnablementManager([name]);
   const scopePath = scope === SettingScope.Workspace ? cwd : os.homedir();
-  manager.disable(name, true, scopePath);
+  extensionEnablementManager.disable(name, true, scopePath);
   logExtensionDisable(config, new ExtensionDisableEvent(name, scope));
 }
 
 export function enableExtension(
   name: string,
   scope: SettingScope,
+  extensionEnablementManager: ExtensionEnablementManager,
   cwd: string = process.cwd(),
 ) {
   if (scope === SettingScope.System || scope === SettingScope.SystemDefaults) {
     throw new Error('System and SystemDefaults scopes are not supported.');
   }
-  const extension = loadExtensionByName(name, cwd);
+  const extension = loadExtensionByName(name, extensionEnablementManager, cwd);
   if (!extension) {
     throw new Error(`Extension with name ${name} does not exist.`);
   }
-  const manager = new ExtensionEnablementManager();
   const scopePath = scope === SettingScope.Workspace ? cwd : os.homedir();
-  manager.enable(name, true, scopePath);
+  extensionEnablementManager.enable(name, true, scopePath);
   const config = getTelemetryConfig(cwd);
   logExtensionEnable(config, new ExtensionEnableEvent(name, scope));
 }

packages/cli/src/config/extensions/github.test.ts

@@ -22,6 +22,7 @@ import * as path from 'node:path';
 import * as tar from 'tar';
 import * as archiver from 'archiver';
 import type { GeminiCLIExtension } from '@google/gemini-cli-core';
+import { ExtensionEnablementManager } from './extensionEnablement.js';
 
 const mockPlatform = vi.hoisted(() => vi.fn());
 const mockArch = vi.hoisted(() => vi.fn());
@@ -149,7 +150,10 @@ describe('git extension helpers', () => {
         },
         contextFiles: [],
       };
-      const result = await checkForExtensionUpdate(extension);
+      const result = await checkForExtensionUpdate(
+        extension,
+        new ExtensionEnablementManager(),
+      );
       expect(result).toBe(ExtensionUpdateState.NOT_UPDATABLE);
     });
 
@@ -166,7 +170,10 @@ describe('git extension helpers', () => {
         contextFiles: [],
       };
       mockGit.getRemotes.mockResolvedValue([]);
-      const result = await checkForExtensionUpdate(extension);
+      const result = await checkForExtensionUpdate(
+        extension,
+        new ExtensionEnablementManager(),
+      );
       expect(result).toBe(ExtensionUpdateState.ERROR);
     });
 
@@ -188,7 +195,10 @@ describe('git extension helpers', () => {
       mockGit.listRemote.mockResolvedValue('remote-hash\tHEAD');
       mockGit.revparse.mockResolvedValue('local-hash');
 
-      const result = await checkForExtensionUpdate(extension);
+      const result = await checkForExtensionUpdate(
+        extension,
+        new ExtensionEnablementManager(),
+      );
       expect(result).toBe(ExtensionUpdateState.UPDATE_AVAILABLE);
     });
 
@@ -210,7 +220,10 @@ describe('git extension helpers', () => {
       mockGit.listRemote.mockResolvedValue('same-hash\tHEAD');
       mockGit.revparse.mockResolvedValue('same-hash');
 
-      const result = await checkForExtensionUpdate(extension);
+      const result = await checkForExtensionUpdate(
+        extension,
+        new ExtensionEnablementManager(),
+      );
       expect(result).toBe(ExtensionUpdateState.UP_TO_DATE);
     });
 
@@ -228,7 +241,10 @@ describe('git extension helpers', () => {
       };
       mockGit.getRemotes.mockRejectedValue(new Error('git error'));
 
-      const result = await checkForExtensionUpdate(extension);
+      const result = await checkForExtensionUpdate(
+        extension,
+        new ExtensionEnablementManager(),
+      );
       expect(result).toBe(ExtensionUpdateState.ERROR);
     });
   });

packages/cli/src/config/extensions/github.ts

@@ -20,6 +20,7 @@ import { EXTENSIONS_CONFIG_FILENAME, loadExtension } from '../extension.js';
 import * as tar from 'tar';
 import extract from 'extract-zip';
 import { fetchJson, getGitHubToken } from './github_fetch.js';
+import { type ExtensionEnablementManager } from './extensionEnablement.js';
 
 /**
  * Clones a Git repository to a specified local path.
@@ -152,6 +153,7 @@ export async function fetchReleaseFromGithub(
 
 export async function checkForExtensionUpdate(
   extension: GeminiCLIExtension,
+  extensionEnablementManager: ExtensionEnablementManager,
   cwd: string = process.cwd(),
 ): Promise<ExtensionUpdateState> {
   const installMetadata = extension.installMetadata;
@@ -159,6 +161,7 @@ export async function checkForExtensionUpdate(
     const newExtension = loadExtension({
       extensionDir: installMetadata.source,
       workspaceDir: cwd,
+      extensionEnablementManager,
     });
     if (!newExtension) {
       debugLogger.error(

packages/cli/src/config/extensions/update.test.ts

@@ -11,7 +11,6 @@ import * as path from 'node:path';
 import {
   EXTENSIONS_CONFIG_FILENAME,
   INSTALL_METADATA_FILENAME,
-  annotateActiveExtensions,
   loadExtension,
 } from '../extension.js';
 import { checkForAllExtensionUpdates, updateExtension } from './update.js';
@@ -128,18 +127,15 @@ describe('update tests', () => {
         );
       });
       mockGit.getRemotes.mockResolvedValue([{ name: 'origin' }]);
-      const extension = annotateActiveExtensions(
-        [
-          loadExtension({
-            extensionDir: targetExtDir,
-            workspaceDir: tempWorkspaceDir,
-          })!,
-        ],
-        process.cwd(),
-        new ExtensionEnablementManager(),
-      )[0];
+      const extensionEnablementManager = new ExtensionEnablementManager();
+      const extension = loadExtension({
+        extensionDir: targetExtDir,
+        workspaceDir: tempWorkspaceDir,
+        extensionEnablementManager,
+      })!;
       const updateInfo = await updateExtension(
         extension,
+        extensionEnablementManager,
         tempHomeDir,
         async (_) => true,
         ExtensionUpdateState.UPDATE_AVAILABLE,
@@ -185,18 +181,15 @@ describe('update tests', () => {
       mockGit.getRemotes.mockResolvedValue([{ name: 'origin' }]);
 
       const dispatch = vi.fn();
-      const extension = annotateActiveExtensions(
-        [
-          loadExtension({
-            extensionDir,
-            workspaceDir: tempWorkspaceDir,
-          })!,
-        ],
-        process.cwd(),
-        new ExtensionEnablementManager(),
-      )[0];
+      const extensionEnablementManager = new ExtensionEnablementManager();
+      const extension = loadExtension({
+        extensionDir,
+        workspaceDir: tempWorkspaceDir,
+        extensionEnablementManager,
+      })!;
       await updateExtension(
         extension,
+        extensionEnablementManager,
         tempHomeDir,
         async (_) => true,
         ExtensionUpdateState.UPDATE_AVAILABLE,
@@ -235,19 +228,16 @@ describe('update tests', () => {
       mockGit.getRemotes.mockResolvedValue([{ name: 'origin' }]);
 
       const dispatch = vi.fn();
-      const extension = annotateActiveExtensions(
-        [
-          loadExtension({
-            extensionDir,
-            workspaceDir: tempWorkspaceDir,
-          })!,
-        ],
-        process.cwd(),
-        new ExtensionEnablementManager(),
-      )[0];
+      const extensionEnablementManager = new ExtensionEnablementManager();
+      const extension = loadExtension({
+        extensionDir,
+        workspaceDir: tempWorkspaceDir,
+        extensionEnablementManager,
+      })!;
       await expect(
         updateExtension(
           extension,
+          extensionEnablementManager,
           tempHomeDir,
           async (_) => true,
           ExtensionUpdateState.UPDATE_AVAILABLE,
@@ -283,16 +273,12 @@ describe('update tests', () => {
           type: 'git',
         },
       });
-      const extension = annotateActiveExtensions(
-        [
-          loadExtension({
-            extensionDir,
-            workspaceDir: tempWorkspaceDir,
-          })!,
-        ],
-        process.cwd(),
-        new ExtensionEnablementManager(),
-      )[0];
+      const extensionEnablementManager = new ExtensionEnablementManager();
+      const extension = loadExtension({
+        extensionDir,
+        workspaceDir: tempWorkspaceDir,
+        extensionEnablementManager,
+      })!;
 
       mockGit.getRemotes.mockResolvedValue([
         { name: 'origin', refs: { fetch: 'https://some.git/repo' } },
@@ -303,6 +289,7 @@ describe('update tests', () => {
       const dispatch = vi.fn();
       await checkForAllExtensionUpdates(
         [extension],
+        extensionEnablementManager,
         dispatch,
         tempWorkspaceDir,
       );
@@ -325,16 +312,12 @@ describe('update tests', () => {
           type: 'git',
         },
       });
-      const extension = annotateActiveExtensions(
-        [
-          loadExtension({
-            extensionDir,
-            workspaceDir: tempWorkspaceDir,
-          })!,
-        ],
-        process.cwd(),
-        new ExtensionEnablementManager(),
-      )[0];
+      const extensionEnablementManager = new ExtensionEnablementManager();
+      const extension = loadExtension({
+        extensionDir,
+        workspaceDir: tempWorkspaceDir,
+        extensionEnablementManager,
+      })!;
 
       mockGit.getRemotes.mockResolvedValue([
         { name: 'origin', refs: { fetch: 'https://some.git/repo' } },
@@ -345,6 +328,7 @@ describe('update tests', () => {
       const dispatch = vi.fn();
       await checkForAllExtensionUpdates(
         [extension],
+        extensionEnablementManager,
         dispatch,
         tempWorkspaceDir,
       );
@@ -371,19 +355,16 @@ describe('update tests', () => {
         version: '1.0.0',
         installMetadata: { source: sourceExtensionDir, type: 'local' },
       });
-      const extension = annotateActiveExtensions(
-        [
-          loadExtension({
-            extensionDir: installedExtensionDir,
-            workspaceDir: tempWorkspaceDir,
-          })!,
-        ],
-        process.cwd(),
-        new ExtensionEnablementManager(),
-      )[0];
+      const extensionEnablementManager = new ExtensionEnablementManager();
+      const extension = loadExtension({
+        extensionDir: installedExtensionDir,
+        workspaceDir: tempWorkspaceDir,
+        extensionEnablementManager,
+      })!;
       const dispatch = vi.fn();
       await checkForAllExtensionUpdates(
         [extension],
+        extensionEnablementManager,
         dispatch,
         tempWorkspaceDir,
       );
@@ -410,19 +391,16 @@ describe('update tests', () => {
         version: '1.0.0',
         installMetadata: { source: sourceExtensionDir, type: 'local' },
       });
-      const extension = annotateActiveExtensions(
-        [
-          loadExtension({
-            extensionDir: installedExtensionDir,
-            workspaceDir: tempWorkspaceDir,
-          })!,
-        ],
-        process.cwd(),
-        new ExtensionEnablementManager(),
-      )[0];
+      const extensionEnablementManager = new ExtensionEnablementManager();
+      const extension = loadExtension({
+        extensionDir: installedExtensionDir,
+        workspaceDir: tempWorkspaceDir,
+        extensionEnablementManager,
+      })!;
       const dispatch = vi.fn();
       await checkForAllExtensionUpdates(
         [extension],
+        extensionEnablementManager,
         dispatch,
         tempWorkspaceDir,
       );
@@ -445,22 +423,19 @@ describe('update tests', () => {
           type: 'git',
         },
       });
-      const extension = annotateActiveExtensions(
-        [
-          loadExtension({
-            extensionDir,
-            workspaceDir: tempWorkspaceDir,
-          })!,
-        ],
-        process.cwd(),
-        new ExtensionEnablementManager(),
-      )[0];
+      const extensionEnablementManager = new ExtensionEnablementManager();
+      const extension = loadExtension({
+        extensionDir,
+        workspaceDir: tempWorkspaceDir,
+        extensionEnablementManager,
+      })!;
 
       mockGit.getRemotes.mockRejectedValue(new Error('Git error'));
 
       const dispatch = vi.fn();
       await checkForAllExtensionUpdates(
         [extension],
+        extensionEnablementManager,
         dispatch,
         tempWorkspaceDir,
       );

packages/cli/src/config/extensions/update.ts

@@ -21,6 +21,7 @@ import { checkForExtensionUpdate } from './github.js';
 import { debugLogger, type GeminiCLIExtension } from '@google/gemini-cli-core';
 import * as fs from 'node:fs';
 import { getErrorMessage } from '../../utils/errors.js';
+import { type ExtensionEnablementManager } from './extensionEnablement.js';
 
 export interface ExtensionUpdateInfo {
   name: string;
@@ -30,6 +31,7 @@ export interface ExtensionUpdateInfo {
 
 export async function updateExtension(
   extension: GeminiCLIExtension,
+  extensionEnablementManager: ExtensionEnablementManager,
   cwd: string = process.cwd(),
   requestConsent: (consent: string) => Promise<boolean>,
   currentState: ExtensionUpdateState,
@@ -67,6 +69,7 @@ export async function updateExtension(
     const previousExtensionConfig = await loadExtensionConfig({
       extensionDir: extension.path,
       workspaceDir: cwd,
+      extensionEnablementManager,
     });
     await installOrUpdateExtension(
       installMetadata,
@@ -79,6 +82,7 @@ export async function updateExtension(
     const updatedExtension = loadExtension({
       extensionDir: updatedExtensionStorage.getExtensionDir(),
       workspaceDir: cwd,
+      extensionEnablementManager,
     });
     if (!updatedExtension) {
       dispatchExtensionStateUpdate({
@@ -120,6 +124,7 @@ export async function updateAllUpdatableExtensions(
   requestConsent: (consent: string) => Promise<boolean>,
   extensions: GeminiCLIExtension[],
   extensionsState: Map<string, ExtensionUpdateStatus>,
+  extensionEnablementManager: ExtensionEnablementManager,
   dispatch: (action: ExtensionUpdateAction) => void,
 ): Promise<ExtensionUpdateInfo[]> {
   return (
@@ -133,6 +138,7 @@ export async function updateAllUpdatableExtensions(
         .map((extension) =>
           updateExtension(
             extension,
+            extensionEnablementManager,
             cwd,
             requestConsent,
             extensionsState.get(extension.name)!.status,
@@ -150,6 +156,7 @@ export interface ExtensionUpdateCheckResult {
 
 export async function checkForAllExtensionUpdates(
   extensions: GeminiCLIExtension[],
+  extensionEnablementManager: ExtensionEnablementManager,
   dispatch: (action: ExtensionUpdateAction) => void,
   cwd: string = process.cwd(),
 ): Promise<void> {
@@ -174,11 +181,12 @@ export async function checkForAllExtensionUpdates(
       },
     });
     promises.push(
-      checkForExtensionUpdate(extension, cwd).then((state) =>
-        dispatch({
-          type: 'SET_STATE',
-          payload: { name: extension.name, state },
-        }),
+      checkForExtensionUpdate(extension, extensionEnablementManager, cwd).then(
+        (state) =>
+          dispatch({
+            type: 'SET_STATE',
+            payload: { name: extension.name, state },
+          }),
       ),
     );
   }

packages/cli/src/config/extensions/variableSchema.ts

@@ -4,6 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
+import type { ExtensionEnablementManager } from './extensionEnablement.js';
+
 export interface VariableDefinition {
   type: 'string';
   description: string;
@@ -18,6 +20,7 @@ export interface VariableSchema {
 export interface LoadExtensionContext {
   extensionDir: string;
   workspaceDir: string;
+  extensionEnablementManager: ExtensionEnablementManager;
 }
 
 const PATH_SEPARATOR_DEFINITION = {

packages/cli/src/config/settings.test.ts

@@ -50,7 +50,7 @@ import {
 import * as fs from 'node:fs'; // fs will be mocked separately
 import stripJsonComments from 'strip-json-comments'; // Will be mocked separately
 import { isWorkspaceTrusted } from './trustedFolders.js';
-import { disableExtension } from './extension.js';
+import { disableExtension, ExtensionStorage } from './extension.js';
 
 // These imports will get the versions from the vi.mock('./settings.js', ...) factory.
 import {
@@ -65,7 +65,8 @@ import {
   migrateDeprecatedSettings,
   SettingScope,
 } from './settings.js';
-import { FatalConfigError, GEMINI_DIR } from '@google/gemini-cli-core';
+import { FatalConfigError, GEMINI_DIR, Storage } from '@google/gemini-cli-core';
+import { ExtensionEnablementManager } from './extensions/extensionEnablement.js';
 
 const MOCK_WORKSPACE_DIR = '/mock/workspace';
 // Use the (mocked) GEMINI_DIR for consistency
@@ -93,9 +94,7 @@ vi.mock('fs', async (importOriginal) => {
   };
 });
 
-vi.mock('./extension.js', () => ({
-  disableExtension: vi.fn(),
-}));
+vi.mock('./extension.js');
 
 vi.mock('strip-json-comments', () => ({
   default: vi.fn((content) => content),
@@ -2349,7 +2348,9 @@ describe('Settings Loading and Merging', () => {
       mockFsExistsSync = vi.mocked(fs.existsSync);
       mockFsReadFileSync = vi.mocked(fs.readFileSync);
       mockDisableExtension = vi.mocked(disableExtension);
-
+      vi.mocked(ExtensionStorage.getUserExtensionsDir).mockReturnValue(
+        new Storage(osActual.homedir()).getExtensionsDir(),
+      );
       (mockFsExistsSync as Mock).mockReturnValue(true);
       vi.mocked(isWorkspaceTrusted).mockReturnValue({
         isTrusted: true,
@@ -2392,11 +2393,13 @@ describe('Settings Loading and Merging', () => {
       expect(mockDisableExtension).toHaveBeenCalledWith(
         'user-ext-1',
         SettingScope.User,
+        expect.any(ExtensionEnablementManager),
         MOCK_WORKSPACE_DIR,
       );
       expect(mockDisableExtension).toHaveBeenCalledWith(
         'shared-ext',
         SettingScope.User,
+        expect.any(ExtensionEnablementManager),
         MOCK_WORKSPACE_DIR,
       );
 
@@ -2404,11 +2407,13 @@ describe('Settings Loading and Merging', () => {
       expect(mockDisableExtension).toHaveBeenCalledWith(
         'workspace-ext-1',
         SettingScope.Workspace,
+        expect.any(ExtensionEnablementManager),
         MOCK_WORKSPACE_DIR,
       );
       expect(mockDisableExtension).toHaveBeenCalledWith(
         'shared-ext',
         SettingScope.Workspace,
+        expect.any(ExtensionEnablementManager),
         MOCK_WORKSPACE_DIR,
       );
 

packages/cli/src/config/settings.ts

@@ -31,6 +31,7 @@ import { resolveEnvVarsInObject } from '../utils/envVarResolver.js';
 import { customDeepMerge, type MergeableObject } from '../utils/deepMerge.js';
 import { updateSettingsFilePreservingFormat } from '../utils/commentJson.js';
 import { disableExtension } from './extension.js';
+import { ExtensionEnablementManager } from './extensions/extensionEnablement.js';
 
 function getMergeStrategyForPath(path: string[]): MergeStrategy | undefined {
   let current: SettingDefinition | undefined = undefined;
@@ -755,8 +756,14 @@ export function migrateDeprecatedSettings(
       console.log(
         `Migrating deprecated extensions.disabled settings from ${scope} settings...`,
       );
+      const extensionEnablementManager = new ExtensionEnablementManager();
       for (const extension of settings.extensions.disabled ?? []) {
-        disableExtension(extension, scope, workspaceDir);
+        disableExtension(
+          extension,
+          scope,
+          extensionEnablementManager,
+          workspaceDir,
+        );
       }
 
       const newExtensionsValue = { ...settings.extensions };