Fix -e <extension> for disabled extensions (#9994)

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

@@ -8,6 +8,7 @@ import type { CommandModule } from 'yargs';
 import {
   loadExtensions,
   annotateActiveExtensions,
+  ExtensionStorage,
   requestConsentNonInteractive,
 } from '../../config/extension.js';
 import {
@@ -19,6 +20,7 @@ import {
 import { checkForExtensionUpdate } from '../../config/extensions/github.js';
 import { getErrorMessage } from '../../utils/errors.js';
 import { ExtensionUpdateState } from '../../ui/state/extensions.js';
+import { ExtensionEnablementManager } from '../../config/extensions/extensionEnablement.js';
 
 interface UpdateArgs {
   name?: string;
@@ -30,11 +32,17 @@ const updateOutput = (info: ExtensionUpdateInfo) =>
 
 export async function handleUpdate(args: UpdateArgs) {
   const workingDir = process.cwd();
-  const allExtensions = loadExtensions();
+  const extensionEnablementManager = new ExtensionEnablementManager(
+    ExtensionStorage.getUserExtensionsDir(),
+    // Force enable named extensions, otherwise we will only update the enabled
+    // ones.
+    args.name ? [args.name] : [],
+  );
+  const allExtensions = loadExtensions(extensionEnablementManager);
   const extensions = annotateActiveExtensions(
     allExtensions,
-    allExtensions.map((e) => e.config.name),
     workingDir,
+    extensionEnablementManager,
   );
   if (args.name) {
     try {

packages/cli/src/commands/mcp/list.test.ts

@@ -7,7 +7,7 @@
 import { vi, describe, it, expect, beforeEach, afterEach } from 'vitest';
 import { listMcpServers } from './list.js';
 import { loadSettings } from '../../config/settings.js';
-import { loadExtensions } from '../../config/extension.js';
+import { ExtensionStorage, loadExtensions } from '../../config/extension.js';
 import { createTransport } from '@google/gemini-cli-core';
 import { Client } from '@modelcontextprotocol/sdk/client/index.js';
 
@@ -16,6 +16,9 @@ vi.mock('../../config/settings.js', () => ({
 }));
 vi.mock('../../config/extension.js', () => ({
   loadExtensions: vi.fn(),
+  ExtensionStorage: {
+    getUserExtensionsDir: vi.fn(),
+  },
 }));
 vi.mock('@google/gemini-cli-core', () => ({
   createTransport: vi.fn(),
@@ -34,6 +37,7 @@ vi.mock('@google/gemini-cli-core', () => ({
 }));
 vi.mock('@modelcontextprotocol/sdk/client/index.js');
 
+const mockedExtensionStorage = ExtensionStorage as vi.Mock;
 const mockedLoadSettings = loadSettings as vi.Mock;
 const mockedLoadExtensions = loadExtensions as vi.Mock;
 const mockedCreateTransport = createTransport as vi.Mock;
@@ -69,6 +73,9 @@ describe('mcp list command', () => {
     MockedClient.mockImplementation(() => mockClient);
     mockedCreateTransport.mockResolvedValue(mockTransport);
     mockedLoadExtensions.mockReturnValue([]);
+    mockedExtensionStorage.getUserExtensionsDir.mockReturnValue(
+      '/mocked/extensions/dir',
+    );
   });
 
   afterEach(() => {

packages/cli/src/commands/mcp/list.ts

@@ -10,7 +10,8 @@ import { loadSettings } from '../../config/settings.js';
 import type { MCPServerConfig } from '@google/gemini-cli-core';
 import { MCPServerStatus, createTransport } from '@google/gemini-cli-core';
 import { Client } from '@modelcontextprotocol/sdk/client/index.js';
-import { loadExtensions } from '../../config/extension.js';
+import { ExtensionStorage, loadExtensions } from '../../config/extension.js';
+import { ExtensionEnablementManager } from '../../config/extensions/extensionEnablement.js';
 
 const COLOR_GREEN = '\u001b[32m';
 const COLOR_YELLOW = '\u001b[33m';
@@ -21,7 +22,9 @@ async function getMcpServersFromConfig(): Promise<
   Record<string, MCPServerConfig>
 > {
   const settings = loadSettings();
-  const extensions = loadExtensions();
+  const extensions = loadExtensions(
+    new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
+  );
   const mcpServers = { ...(settings.merged.mcpServers || {}) };
   for (const extension of extensions) {
     Object.entries(extension.config.mcpServers || {}).forEach(

packages/cli/src/config/config.ts

@@ -45,6 +45,7 @@ import { appEvents } from '../utils/events.js';
 
 import { isWorkspaceTrusted } from './trustedFolders.js';
 import { createPolicyEngineConfig } from './policy.js';
+import type { ExtensionEnablementManager } from './extensions/extensionEnablement.js';
 
 // Simple console logger for now - replace with actual logger if available
 const logger = {
@@ -408,6 +409,7 @@ export function isDebugMode(argv: CliArgs): boolean {
 export async function loadCliConfig(
   settings: Settings,
   extensions: Extension[],
+  extensionEnablementManager: ExtensionEnablementManager,
   sessionId: string,
   argv: CliArgs,
   cwd: string = process.cwd(),
@@ -423,8 +425,8 @@ export async function loadCliConfig(
 
   const allExtensions = annotateActiveExtensions(
     extensions,
-    argv.extensions || [],
     cwd,
+    extensionEnablementManager,
   );
 
   const activeExtensions = extensions.filter(

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

@@ -10,6 +10,7 @@ import * as os from 'node:os';
 import * as path from 'node:path';
 import {
   EXTENSIONS_CONFIG_FILENAME,
+  ExtensionStorage,
   INSTALL_METADATA_FILENAME,
   annotateActiveExtensions,
   disableExtension,
@@ -152,7 +153,9 @@ describe('extension tests', () => {
         version: '1.0.0',
       });
 
-      const extensions = loadExtensions();
+      const extensions = loadExtensions(
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
+      );
       expect(extensions).toHaveLength(1);
       expect(extensions[0].path).toBe(extensionDir);
       expect(extensions[0].config.name).toBe('test-extension');
@@ -171,7 +174,9 @@ describe('extension tests', () => {
         version: '2.0.0',
       });
 
-      const extensions = loadExtensions();
+      const extensions = loadExtensions(
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
+      );
 
       expect(extensions).toHaveLength(2);
       const ext1 = extensions.find((e) => e.config.name === 'ext1');
@@ -191,7 +196,9 @@ describe('extension tests', () => {
         contextFileName: 'my-context-file.md',
       });
 
-      const extensions = loadExtensions();
+      const extensions = loadExtensions(
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
+      );
 
       expect(extensions).toHaveLength(1);
       const ext1 = extensions.find((e) => e.config.name === 'ext1');
@@ -216,11 +223,14 @@ describe('extension tests', () => {
         SettingScope.User,
         tempWorkspaceDir,
       );
-      const extensions = loadExtensions();
+      const manager = new ExtensionEnablementManager(
+        ExtensionStorage.getUserExtensionsDir(),
+      );
+      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');
@@ -240,7 +250,9 @@ describe('extension tests', () => {
         },
       });
 
-      const extensions = loadExtensions();
+      const extensions = loadExtensions(
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
+      );
       expect(extensions).toHaveLength(1);
       const loadedConfig = extensions[0].config;
       const expectedCwd = path.join(
@@ -269,7 +281,9 @@ describe('extension tests', () => {
       );
 
       expect(extensionName).toEqual('my-linked-extension');
-      const extensions = loadExtensions();
+      const extensions = loadExtensions(
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
+      );
       expect(extensions).toHaveLength(1);
 
       const linkedExt = extensions[0];
@@ -318,7 +332,11 @@ describe('extension tests', () => {
         };
         fs.writeFileSync(configPath, JSON.stringify(extensionConfig));
 
-        const extensions = loadExtensions();
+        const extensions = loadExtensions(
+          new ExtensionEnablementManager(
+            ExtensionStorage.getUserExtensionsDir(),
+          ),
+        );
 
         expect(extensions).toHaveLength(1);
         const extension = extensions[0];
@@ -369,7 +387,9 @@ describe('extension tests', () => {
         JSON.stringify(extensionConfig),
       );
 
-      const extensions = loadExtensions();
+      const extensions = loadExtensions(
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
+      );
 
       expect(extensions).toHaveLength(1);
       const extension = extensions[0];
@@ -397,7 +417,9 @@ describe('extension tests', () => {
       const badConfigPath = path.join(badExtDir, EXTENSIONS_CONFIG_FILENAME);
       fs.writeFileSync(badConfigPath, '{ "name": "bad-ext"'); // Malformed
 
-      const extensions = loadExtensions();
+      const extensions = loadExtensions(
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
+      );
 
       expect(extensions).toHaveLength(1);
       expect(extensions[0].config.name).toBe('good-ext');
@@ -429,7 +451,9 @@ describe('extension tests', () => {
       const badConfigPath = path.join(badExtDir, EXTENSIONS_CONFIG_FILENAME);
       fs.writeFileSync(badConfigPath, JSON.stringify({ version: '1.0.0' }));
 
-      const extensions = loadExtensions();
+      const extensions = loadExtensions(
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
+      );
 
       expect(extensions).toHaveLength(1);
       expect(extensions[0].config.name).toBe('good-ext');
@@ -457,7 +481,9 @@ describe('extension tests', () => {
         },
       });
 
-      const extensions = loadExtensions();
+      const extensions = loadExtensions(
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
+      );
       expect(extensions).toHaveLength(1);
       const loadedConfig = extensions[0].config;
       expect(loadedConfig.mcpServers?.['test-server'].trust).toBeUndefined();
@@ -508,8 +534,8 @@ describe('extension tests', () => {
     it('should mark all extensions as active if no enabled extensions are provided', () => {
       const activeExtensions = annotateActiveExtensions(
         extensions,
-        [],
         '/path/to/workspace',
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
       );
       expect(activeExtensions).toHaveLength(3);
       expect(activeExtensions.every((e) => e.isActive)).toBe(true);
@@ -518,8 +544,11 @@ describe('extension tests', () => {
     it('should mark only the enabled extensions as active', () => {
       const activeExtensions = annotateActiveExtensions(
         extensions,
-        ['ext1', 'ext3'],
         '/path/to/workspace',
+        new ExtensionEnablementManager(
+          ExtensionStorage.getUserExtensionsDir(),
+          ['ext1', 'ext3'],
+        ),
       );
       expect(activeExtensions).toHaveLength(3);
       expect(activeExtensions.find((e) => e.name === 'ext1')?.isActive).toBe(
@@ -536,8 +565,11 @@ describe('extension tests', () => {
     it('should mark all extensions as inactive when "none" is provided', () => {
       const activeExtensions = annotateActiveExtensions(
         extensions,
-        ['none'],
         '/path/to/workspace',
+        new ExtensionEnablementManager(
+          ExtensionStorage.getUserExtensionsDir(),
+          ['none'],
+        ),
       );
       expect(activeExtensions).toHaveLength(3);
       expect(activeExtensions.every((e) => !e.isActive)).toBe(true);
@@ -546,8 +578,11 @@ describe('extension tests', () => {
     it('should handle case-insensitivity', () => {
       const activeExtensions = annotateActiveExtensions(
         extensions,
-        ['EXT1'],
         '/path/to/workspace',
+        new ExtensionEnablementManager(
+          ExtensionStorage.getUserExtensionsDir(),
+          ['EXT1'],
+        ),
       );
       expect(activeExtensions.find((e) => e.name === 'ext1')?.isActive).toBe(
         true,
@@ -558,7 +593,14 @@ describe('extension tests', () => {
       const consoleSpy = vi
         .spyOn(console, 'error')
         .mockImplementation(() => {});
-      annotateActiveExtensions(extensions, ['ext4'], '/path/to/workspace');
+      annotateActiveExtensions(
+        extensions,
+        '/path/to/workspace',
+        new ExtensionEnablementManager(
+          ExtensionStorage.getUserExtensionsDir(),
+          ['ext4'],
+        ),
+      );
       expect(consoleSpy).toHaveBeenCalledWith('Extension not found: ext4');
       consoleSpy.mockRestore();
     });
@@ -567,8 +609,10 @@ describe('extension tests', () => {
       it('should be false if autoUpdate is not set in install metadata', () => {
         const activeExtensions = annotateActiveExtensions(
           extensions,
-          [],
           tempHomeDir,
+          new ExtensionEnablementManager(
+            ExtensionStorage.getUserExtensionsDir(),
+          ),
         );
         expect(
           activeExtensions.every(
@@ -587,8 +631,10 @@ describe('extension tests', () => {
         }));
         const activeExtensions = annotateActiveExtensions(
           extensionsWithAutoUpdate,
-          [],
           tempHomeDir,
+          new ExtensionEnablementManager(
+            ExtensionStorage.getUserExtensionsDir(),
+          ),
         );
         expect(
           activeExtensions.every((e) => e.installMetadata?.autoUpdate === true),
@@ -625,8 +671,10 @@ describe('extension tests', () => {
         ];
         const activeExtensions = annotateActiveExtensions(
           extensionsWithAutoUpdate,
-          [],
           tempHomeDir,
+          new ExtensionEnablementManager(
+            ExtensionStorage.getUserExtensionsDir(),
+          ),
         );
         expect(
           activeExtensions.find((e) => e.name === 'ext1')?.installMetadata
@@ -1015,7 +1063,13 @@ This extension will run the following MCP servers:
       await uninstallExtension('my-local-extension');
 
       expect(fs.existsSync(sourceExtDir)).toBe(false);
-      expect(loadExtensions()).toHaveLength(1);
+      expect(
+        loadExtensions(
+          new ExtensionEnablementManager(
+            ExtensionStorage.getUserExtensionsDir(),
+          ),
+        ),
+      ).toHaveLength(1);
       expect(fs.existsSync(otherExtDir)).toBe(true);
     });
 
@@ -1154,7 +1208,11 @@ This extension will run the following MCP servers:
           ],
           async (_) => true,
         );
-        const extensions = loadExtensions();
+        const extensions = loadExtensions(
+          new ExtensionEnablementManager(
+            ExtensionStorage.getUserExtensionsDir(),
+          ),
+        );
 
         expect(extensions).toEqual([]);
       });
@@ -1194,7 +1252,9 @@ This extension will run the following MCP servers:
         'extensions',
       );
       const userExt1Path = path.join(userExtensionsDir, 'ext1');
-      const extensions = loadExtensions();
+      const extensions = loadExtensions(
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
+      );
 
       expect(extensions).toHaveLength(2);
       const metadataPath = path.join(userExt1Path, INSTALL_METADATA_FILENAME);
@@ -1326,11 +1386,14 @@ This extension will run the following MCP servers:
     });
 
     const getActiveExtensions = (): GeminiCLIExtension[] => {
-      const extensions = loadExtensions();
+      const manager = new ExtensionEnablementManager(
+        ExtensionStorage.getUserExtensionsDir(),
+      );
+      const extensions = loadExtensions(manager);
       const activeExtensions = annotateActiveExtensions(
         extensions,
-        [],
         tempWorkspaceDir,
+        manager,
       );
       return activeExtensions.filter((e) => e.isActive);
     };

packages/cli/src/config/extension.ts

@@ -146,6 +146,7 @@ function getTelemetryConfig(cwd: string) {
 }
 
 export function loadExtensions(
+  extensionEnablementManager: ExtensionEnablementManager,
   workspaceDir: string = process.cwd(),
 ): Extension[] {
   const settings = loadSettings(workspaceDir).merged;
@@ -160,14 +161,11 @@ export function loadExtensions(
   }
 
   const uniqueExtensions = new Map<string, Extension>();
-  const manager = new ExtensionEnablementManager(
-    ExtensionStorage.getUserExtensionsDir(),
-  );
 
   for (const extension of allExtensions) {
     if (
       !uniqueExtensions.has(extension.config.name) &&
-      manager.isEnabled(extension.config.name, workspaceDir)
+      extensionEnablementManager.isEnabled(extension.config.name, workspaceDir)
     ) {
       uniqueExtensions.set(extension.config.name, extension);
     }
@@ -323,64 +321,17 @@ function getContextFileNames(config: ExtensionConfig): string[] {
  */
 export function annotateActiveExtensions(
   extensions: Extension[],
-  enabledExtensionNames: string[],
   workspaceDir: string,
+  manager: ExtensionEnablementManager,
 ): GeminiCLIExtension[] {
-  const manager = new ExtensionEnablementManager(
-    ExtensionStorage.getUserExtensionsDir(),
-  );
-  const annotatedExtensions: GeminiCLIExtension[] = [];
-  if (enabledExtensionNames.length === 0) {
-    return extensions.map((extension) => ({
-      name: extension.config.name,
-      version: extension.config.version,
-      isActive: manager.isEnabled(extension.config.name, workspaceDir),
-      path: extension.path,
-      installMetadata: extension.installMetadata,
-    }));
-  }
-
-  const lowerCaseEnabledExtensions = new Set(
-    enabledExtensionNames.map((e) => e.trim().toLowerCase()),
-  );
-
-  if (
-    lowerCaseEnabledExtensions.size === 1 &&
-    lowerCaseEnabledExtensions.has('none')
-  ) {
-    return extensions.map((extension) => ({
-      name: extension.config.name,
-      version: extension.config.version,
-      isActive: false,
-      path: extension.path,
-      installMetadata: extension.installMetadata,
-    }));
-  }
-
-  const notFoundNames = new Set(lowerCaseEnabledExtensions);
-
-  for (const extension of extensions) {
-    const lowerCaseName = extension.config.name.toLowerCase();
-    const isActive = lowerCaseEnabledExtensions.has(lowerCaseName);
-
-    if (isActive) {
-      notFoundNames.delete(lowerCaseName);
-    }
-
-    annotatedExtensions.push({
-      name: extension.config.name,
-      version: extension.config.version,
-      isActive,
-      path: extension.path,
-      installMetadata: extension.installMetadata,
-    });
-  }
-
-  for (const requestedName of notFoundNames) {
-    console.error(`Extension not found: ${requestedName}`);
-  }
-
-  return annotatedExtensions;
+  manager.validateExtensionOverrides(extensions);
+  return extensions.map((extension) => ({
+    name: extension.config.name,
+    version: extension.config.version,
+    isActive: manager.isEnabled(extension.config.name, workspaceDir),
+    path: extension.path,
+    installMetadata: extension.installMetadata,
+  }));
 }
 
 /**
@@ -711,6 +662,7 @@ export async function uninstallExtension(
   }
   const manager = new ExtensionEnablementManager(
     ExtensionStorage.getUserExtensionsDir(),
+    [extensionName],
   );
   manager.remove(extensionName);
   const storage = new ExtensionStorage(extensionName);
@@ -789,6 +741,7 @@ export function disableExtension(
 
   const manager = new ExtensionEnablementManager(
     ExtensionStorage.getUserExtensionsDir(),
+    [name],
   );
   const scopePath = scope === SettingScope.Workspace ? cwd : os.homedir();
   manager.disable(name, true, scopePath);

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

@@ -6,6 +6,7 @@
 
 import fs from 'node:fs';
 import path from 'node:path';
+import { type Extension } from '../extension.js';
 
 export interface ExtensionEnablementConfig {
   overrides: string[];
@@ -104,24 +105,56 @@ function globToRegex(glob: string): RegExp {
   return new RegExp(`^${regexString}$`);
 }
 
-/**
- * Determines if an extension is enabled based on the configuration and current path.
- * The last matching rule in the overrides list wins.
- *
- * @param config The enablement configuration for a single extension.
- * @param currentPath The absolute path of the current working directory.
- * @returns True if the extension is enabled, false otherwise.
- */
 export class ExtensionEnablementManager {
   private configFilePath: string;
   private configDir: string;
+  // If non-empty, this overrides all other extension configuration and enables
+  // only the ones in this list.
+  private enabledExtensionNamesOverride: string[];
 
-  constructor(configDir: string) {
+  constructor(configDir: string, enabledExtensionNames?: string[]) {
     this.configDir = configDir;
     this.configFilePath = path.join(configDir, 'extension-enablement.json');
+    this.enabledExtensionNamesOverride =
+      enabledExtensionNames?.map((name) => name.toLowerCase()) ?? [];
   }
 
+  validateExtensionOverrides(extensions: Extension[]) {
+    for (const name of this.enabledExtensionNamesOverride) {
+      if (
+        !extensions.some(
+          (ext) => ext.config.name.toLowerCase() === name.toLowerCase(),
+        )
+      ) {
+        console.error(`Extension not found: ${name}`);
+      }
+    }
+  }
+
+  /**
+   * Determines if an extension is enabled based on its name and the current
+   * path. The last matching rule in the overrides list wins.
+   *
+   * @param extensionName The name of the extension.
+   * @param currentPath The absolute path of the current working directory.
+   * @returns True if the extension is enabled, false otherwise.
+   */
   isEnabled(extensionName: string, currentPath: string): boolean {
+    // If we have a single override called 'none', this disables all extensions.
+    // Typically, this comes from the user passing `-e none`.
+    if (
+      this.enabledExtensionNamesOverride.length === 1 &&
+      this.enabledExtensionNamesOverride[0] === 'none'
+    ) {
+      return false;
+    }
+
+    // If we have explicit overrides, only enable those extensions.
+    if (this.enabledExtensionNamesOverride.length > 0) {
+      return this.enabledExtensionNamesOverride.includes(extensionName);
+    }
+
+    // Otherwise, we use the configuration settings
     const config = this.readConfig();
     const extensionConfig = config[extensionName];
     // Extensions are enabled by default.

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

@@ -10,6 +10,7 @@ import * as os from 'node:os';
 import * as path from 'node:path';
 import {
   EXTENSIONS_CONFIG_FILENAME,
+  ExtensionStorage,
   INSTALL_METADATA_FILENAME,
   annotateActiveExtensions,
   loadExtension,
@@ -19,6 +20,7 @@ import { GEMINI_DIR } from '@google/gemini-cli-core';
 import { isWorkspaceTrusted } from '../trustedFolders.js';
 import { ExtensionUpdateState } from '../../ui/state/extensions.js';
 import { createExtension } from '../../test-utils/createExtension.js';
+import { ExtensionEnablementManager } from './extensionEnablement.js';
 
 const mockGit = {
   clone: vi.fn(),
@@ -134,8 +136,8 @@ describe('update tests', () => {
             workspaceDir: tempWorkspaceDir,
           })!,
         ],
-        [],
         process.cwd(),
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
       )[0];
       const updateInfo = await updateExtension(
         extension,
@@ -192,8 +194,8 @@ describe('update tests', () => {
             workspaceDir: tempWorkspaceDir,
           })!,
         ],
-        [],
         process.cwd(),
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
       )[0];
       await updateExtension(
         extension,
@@ -234,8 +236,8 @@ describe('update tests', () => {
             workspaceDir: tempWorkspaceDir,
           })!,
         ],
-        [],
         process.cwd(),
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
       )[0];
       await expect(
         updateExtension(
@@ -274,8 +276,8 @@ describe('update tests', () => {
             workspaceDir: tempWorkspaceDir,
           })!,
         ],
-        [],
         process.cwd(),
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
       )[0];
 
       mockGit.getRemotes.mockResolvedValue([
@@ -317,8 +319,8 @@ describe('update tests', () => {
             workspaceDir: tempWorkspaceDir,
           })!,
         ],
-        [],
         process.cwd(),
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
       )[0];
 
       mockGit.getRemotes.mockResolvedValue([
@@ -364,8 +366,8 @@ describe('update tests', () => {
             workspaceDir: tempWorkspaceDir,
           })!,
         ],
-        [],
         process.cwd(),
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
       )[0];
       let extensionState = new Map();
       const results = await checkForAllExtensionUpdates(
@@ -405,8 +407,8 @@ describe('update tests', () => {
             workspaceDir: tempWorkspaceDir,
           })!,
         ],
-        [],
         process.cwd(),
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
       )[0];
       let extensionState = new Map();
       const results = await checkForAllExtensionUpdates(
@@ -442,8 +444,8 @@ describe('update tests', () => {
             workspaceDir: tempWorkspaceDir,
           })!,
         ],
-        [],
         process.cwd(),
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
       )[0];
 
       mockGit.getRemotes.mockRejectedValue(new Error('Git error'));

packages/cli/src/gemini.tsx

@@ -26,7 +26,7 @@ import { getStartupWarnings } from './utils/startupWarnings.js';
 import { getUserStartupWarnings } from './utils/userStartupWarnings.js';
 import { ConsolePatcher } from './ui/utils/ConsolePatcher.js';
 import { runNonInteractive } from './nonInteractiveCli.js';
-import { loadExtensions } from './config/extension.js';
+import { ExtensionStorage, loadExtensions } from './config/extension.js';
 import {
   cleanupCheckpoints,
   registerCleanup,
@@ -113,6 +113,7 @@ function getNodeMemoryArgs(isDebugMode: boolean): string[] {
 
 import { runZedIntegration } from './zed-integration/zedIntegration.js';
 import { loadSandboxConfig } from './config/sandboxConfig.js';
+import { ExtensionEnablementManager } from './config/extensions/extensionEnablement.js';
 
 export function setupUnhandledRejectionHandler() {
   let unhandledRejectionOccurred = false;
@@ -266,6 +267,7 @@ export async function main() {
       const partialConfig = await loadCliConfig(
         settings.merged,
         [],
+        new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
         sessionId,
         argv,
       );
@@ -336,10 +338,15 @@ export async function main() {
   // to run Gemini CLI. It is now safe to perform expensive initialization that
   // may have side effects.
   {
-    const extensions = loadExtensions();
+    const extensionEnablementManager = new ExtensionEnablementManager(
+      ExtensionStorage.getUserExtensionsDir(),
+      argv.extensions,
+    );
+    const extensions = loadExtensions(extensionEnablementManager);
     const config = await loadCliConfig(
       settings.merged,
       extensions,
+      extensionEnablementManager,
       sessionId,
       argv,
     );

packages/cli/src/ui/hooks/useExtensionUpdates.test.ts

@@ -10,6 +10,7 @@ import * as os from 'node:os';
 import * as path from 'node:path';
 import {
   EXTENSIONS_CONFIG_FILENAME,
+  ExtensionStorage,
   annotateActiveExtensions,
   loadExtension,
 } from '../../config/extension.js';
@@ -19,6 +20,7 @@ import { GEMINI_DIR, type GeminiCLIExtension } from '@google/gemini-cli-core';
 import { isWorkspaceTrusted } from '../../config/trustedFolders.js';
 import { renderHook, waitFor } from '@testing-library/react';
 import { MessageType } from '../types.js';
+import { ExtensionEnablementManager } from '../../config/extensions/extensionEnablement.js';
 
 const mockGit = {
   clone: vi.fn(),
@@ -163,8 +165,8 @@ describe('useExtensionUpdates', () => {
     });
     const extension = annotateActiveExtensions(
       [loadExtension({ extensionDir, workspaceDir: tempHomeDir })!],
-      [],
       tempHomeDir,
+      new ExtensionEnablementManager(ExtensionStorage.getUserExtensionsDir()),
     )[0];
 
     const addItem = vi.fn();

packages/cli/src/zed-integration/zedIntegration.ts

@@ -40,9 +40,10 @@ import * as path from 'node:path';
 import { z } from 'zod';
 
 import { randomUUID } from 'node:crypto';
-import type { Extension } from '../config/extension.js';
+import { ExtensionStorage, type Extension } from '../config/extension.js';
 import type { CliArgs } from '../config/config.js';
 import { loadCliConfig } from '../config/config.js';
+import { ExtensionEnablementManager } from '../config/extensions/extensionEnablement.js';
 
 /**
  * Resolves the model to use based on the current configuration.
@@ -204,6 +205,10 @@ class GeminiAgent {
     const config = await loadCliConfig(
       settings,
       this.extensions,
+      new ExtensionEnablementManager(
+        ExtensionStorage.getUserExtensionsDir(),
+        this.argv.extensions,
+      ),
       sessionId,
       this.argv,
       cwd,