Update extension enablement logic (#8544)

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

@@ -14,7 +14,7 @@ interface DisableArgs {
   scope: SettingScope;
 }
 
-export async function handleDisable(args: DisableArgs) {
+export function handleDisable(args: DisableArgs) {
   try {
     disableExtension(args.name, args.scope);
     console.log(
@@ -42,8 +42,8 @@ export const disableCommand: CommandModule = {
         choices: [SettingScope.User, SettingScope.Workspace],
       })
       .check((_argv) => true),
-  handler: async (argv) => {
-    await handleDisable({
+  handler: (argv) => {
+    handleDisable({
       name: argv['name'] as string,
       scope: argv['scope'] as SettingScope,
     });

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

@@ -14,12 +14,10 @@ interface EnableArgs {
   scope?: SettingScope;
 }
 
-export async function handleEnable(args: EnableArgs) {
+export function handleEnable(args: EnableArgs) {
   try {
-    const scopes = args.scope
-      ? [args.scope]
-      : [SettingScope.User, SettingScope.Workspace];
-    enableExtension(args.name, scopes);
+    const scope = args.scope ? args.scope : SettingScope.User;
+    enableExtension(args.name, scope);
     if (args.scope) {
       console.log(
         `Extension "${args.name}" successfully enabled for scope "${args.scope}".`,
@@ -50,8 +48,8 @@ export const enableCommand: CommandModule = {
         choices: [SettingScope.User, SettingScope.Workspace],
       })
       .check((_argv) => true),
-  handler: async (argv) => {
-    await handleEnable({
+  handler: (argv) => {
+    handleEnable({
       name: argv['name'] as string,
       scope: argv['scope'] as SettingScope,
     });

packages/cli/src/config/extension.ts

@@ -27,6 +27,7 @@ import { isWorkspaceTrusted } from './trustedFolders.js';
 import { resolveEnvVarsInObject } from '../utils/envVarResolver.js';
 import { randomUUID } from 'node:crypto';
 import { ExtensionUpdateState } from '../ui/state/extensions.js';
+import { ExtensionEnablementManager } from './extensions/extensionEnablement.js';
 
 export const EXTENSIONS_DIRECTORY_NAME = path.join(GEMINI_DIR, 'extensions');
 
@@ -140,7 +141,6 @@ export function loadExtensions(
   workspaceDir: string = process.cwd(),
 ): Extension[] {
   const settings = loadSettings(workspaceDir).merged;
-  const disabledExtensions = settings.extensions?.disabled ?? [];
   const allExtensions = [...loadUserExtensions()];
 
   if (
@@ -152,10 +152,14 @@ 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) &&
-      !disabledExtensions.includes(extension.config.name)
+      manager.isEnabled(extension.config.name, workspaceDir)
     ) {
       uniqueExtensions.set(extension.config.name, extension);
     }
@@ -198,9 +202,6 @@ export function loadExtensionsFromDir(dir: string): Extension[] {
 
 export function loadExtension(extensionDir: string): Extension | null {
   if (!fs.statSync(extensionDir).isDirectory()) {
-    console.error(
-      `Warning: unexpected file ${extensionDir} in extensions directory.`,
-    );
     return null;
   }
 
@@ -284,7 +285,7 @@ function getContextFileNames(config: ExtensionConfig): string[] {
 
 /**
  * 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 in list of disabled extensions in settings.
+ * 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.
@@ -294,16 +295,16 @@ export function annotateActiveExtensions(
   enabledExtensionNames: string[],
   workspaceDir: string,
 ): GeminiCLIExtension[] {
-  const settings = loadSettings(workspaceDir).merged;
-  const disabledExtensions = settings.extensions?.disabled ?? [];
+  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: !disabledExtensions.includes(extension.config.name),
+      isActive: manager.isEnabled(extension.config.name, workspaceDir),
       path: extension.path,
       source: extension.installMetadata?.source,
       type: extension.installMetadata?.type,
@@ -526,6 +527,7 @@ export async function installExtension(
       ),
     );
 
+    enableExtension(newExtensionConfig!.name, SettingScope.User);
     return newExtensionConfig!.name;
   } catch (error) {
     // Attempt to load config from the source path even if installation fails
@@ -581,11 +583,10 @@ export async function uninstallExtension(
   ) {
     throw new Error(`Extension "${extensionName}" not found.`);
   }
-  removeFromDisabledExtensions(
-    extensionName,
-    [SettingScope.User, SettingScope.Workspace],
-    cwd,
+  const manager = new ExtensionEnablementManager(
+    ExtensionStorage.getUserExtensionsDir(),
   );
+  manager.remove(extensionName);
   const storage = new ExtensionStorage(extensionName);
 
   await fs.promises.rm(storage.getExtensionDir(), {
@@ -710,45 +711,27 @@ export function disableExtension(
   if (scope === SettingScope.System || scope === SettingScope.SystemDefaults) {
     throw new Error('System and SystemDefaults scopes are not supported.');
   }
-  const settings = loadSettings(cwd);
-  const settingsFile = settings.forScope(scope);
-  const extensionSettings = settingsFile.settings.extensions || {
-    disabled: [],
-  };
-  const disabledExtensions = extensionSettings.disabled || [];
-  if (!disabledExtensions.includes(name)) {
-    disabledExtensions.push(name);
-    extensionSettings.disabled = disabledExtensions;
-    settings.setValue(scope, 'extensions', extensionSettings);
-  }
+
+  const manager = new ExtensionEnablementManager(
+    ExtensionStorage.getUserExtensionsDir(),
+  );
+  const scopePath = scope === SettingScope.Workspace ? cwd : os.homedir();
+  manager.disable(name, true, scopePath);
 }
 
-export function enableExtension(name: string, scopes: SettingScope[]) {
-  removeFromDisabledExtensions(name, scopes);
-}
-
-/**
- * Removes an extension from the list of disabled extensions.
- * @param name The name of the extension to remove.
- * @param scope The scopes to remove the name from.
- */
-function removeFromDisabledExtensions(
+export function enableExtension(
   name: string,
-  scopes: SettingScope[],
+  scope: SettingScope,
   cwd: string = process.cwd(),
 ) {
-  const settings = loadSettings(cwd);
-  for (const scope of scopes) {
-    const settingsFile = settings.forScope(scope);
-    const extensionSettings = settingsFile.settings.extensions || {
-      disabled: [],
-    };
-    const disabledExtensions = extensionSettings.disabled || [];
-    extensionSettings.disabled = disabledExtensions.filter(
-      (extension) => extension !== name,
-    );
-    settings.setValue(scope, 'extensions', extensionSettings);
+  if (scope === SettingScope.System || scope === SettingScope.SystemDefaults) {
+    throw new Error('System and SystemDefaults scopes are not supported.');
   }
+  const manager = new ExtensionEnablementManager(
+    ExtensionStorage.getUserExtensionsDir(),
+  );
+  const scopePath = scope === SettingScope.Workspace ? cwd : os.homedir();
+  manager.enable(name, true, scopePath);
 }
 
 export async function updateAllUpdatableExtensions(

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

@@ -0,0 +1,142 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import fs from 'node:fs';
+import os from 'node:os';
+import path from 'node:path';
+import { afterEach, beforeEach, describe, expect, it } from 'vitest';
+import { ExtensionEnablementManager } from './extensionEnablement.js';
+
+// Helper to create a temporary directory for testing
+function createTestDir() {
+  const dirPath = fs.mkdtempSync(path.join(os.tmpdir(), 'gemini-test-'));
+  return {
+    path: dirPath,
+    cleanup: () => fs.rmSync(dirPath, { recursive: true, force: true }),
+  };
+}
+
+let testDir: { path: string; cleanup: () => void };
+let configDir: string;
+let manager: ExtensionEnablementManager;
+
+describe('ExtensionEnablementManager', () => {
+  beforeEach(() => {
+    testDir = createTestDir();
+    configDir = path.join(testDir.path, '.gemini');
+    manager = new ExtensionEnablementManager(configDir);
+  });
+
+  afterEach(() => {
+    testDir.cleanup();
+    // Reset the singleton instance for test isolation
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    (ExtensionEnablementManager as any).instance = undefined;
+  });
+
+  describe('isEnabled', () => {
+    it('should return true if extension is not configured', () => {
+      expect(manager.isEnabled('ext-test', '/any/path')).toBe(true);
+    });
+
+    it('should return true if no overrides match', () => {
+      manager.disable('ext-test', false, '/another/path');
+      expect(manager.isEnabled('ext-test', '/any/path')).toBe(true);
+    });
+
+    it('should enable a path based on an override rule', () => {
+      manager.disable('ext-test', true, '*'); // Disable globally
+      manager.enable('ext-test', true, '/home/user/projects/');
+      expect(manager.isEnabled('ext-test', '/home/user/projects/my-app')).toBe(
+        true,
+      );
+    });
+
+    it('should disable a path based on a disable override rule', () => {
+      manager.enable('ext-test', true, '*'); // Enable globally
+      manager.disable('ext-test', true, '/home/user/projects/');
+      expect(manager.isEnabled('ext-test', '/home/user/projects/my-app')).toBe(
+        false,
+      );
+    });
+
+    it('should respect the last matching rule (enable wins)', () => {
+      manager.disable('ext-test', true, '/home/user/projects/');
+      manager.enable('ext-test', false, '/home/user/projects/my-app');
+      expect(manager.isEnabled('ext-test', '/home/user/projects/my-app')).toBe(
+        true,
+      );
+    });
+
+    it('should respect the last matching rule (disable wins)', () => {
+      manager.enable('ext-test', true, '/home/user/projects/');
+      manager.disable('ext-test', false, '/home/user/projects/my-app');
+      expect(manager.isEnabled('ext-test', '/home/user/projects/my-app')).toBe(
+        false,
+      );
+    });
+  });
+
+  describe('includeSubdirs', () => {
+    it('should add a glob when enabling with includeSubdirs', () => {
+      manager.enable('ext-test', true, '/path/to/dir');
+      const config = manager.readConfig();
+      expect(config['ext-test'].overrides).toContain('/path/to/dir*');
+    });
+
+    it('should not add a glob when enabling without includeSubdirs', () => {
+      manager.enable('ext-test', false, '/path/to/dir');
+      const config = manager.readConfig();
+      expect(config['ext-test'].overrides).toContain('/path/to/dir');
+      expect(config['ext-test'].overrides).not.toContain('/path/to/dir*');
+    });
+
+    it('should add a glob when disabling with includeSubdirs', () => {
+      manager.disable('ext-test', true, '/path/to/dir');
+      const config = manager.readConfig();
+      expect(config['ext-test'].overrides).toContain('!/path/to/dir*');
+    });
+
+    it('should remove conflicting glob rule when enabling without subdirs', () => {
+      manager.enable('ext-test', true, '/path/to/dir'); // Adds /path/to/dir*
+      manager.enable('ext-test', false, '/path/to/dir'); // Should remove the glob
+      const config = manager.readConfig();
+      expect(config['ext-test'].overrides).toContain('/path/to/dir');
+      expect(config['ext-test'].overrides).not.toContain('/path/to/dir*');
+    });
+
+    it('should remove conflicting non-glob rule when enabling with subdirs', () => {
+      manager.enable('ext-test', false, '/path/to/dir'); // Adds /path/to/dir
+      manager.enable('ext-test', true, '/path/to/dir'); // Should remove the non-glob
+      const config = manager.readConfig();
+      expect(config['ext-test'].overrides).toContain('/path/to/dir*');
+      expect(config['ext-test'].overrides).not.toContain('/path/to/dir');
+    });
+
+    it('should remove conflicting rules when disabling', () => {
+      manager.enable('ext-test', true, '/path/to/dir'); // enabled with glob
+      manager.disable('ext-test', false, '/path/to/dir'); // disabled without
+      const config = manager.readConfig();
+      expect(config['ext-test'].overrides).toContain('!/path/to/dir');
+      expect(config['ext-test'].overrides).not.toContain('/path/to/dir*');
+    });
+
+    it('should correctly evaluate isEnabled with subdirs', () => {
+      manager.disable('ext-test', true, '*');
+      manager.enable('ext-test', true, '/path/to/dir');
+      expect(manager.isEnabled('ext-test', '/path/to/dir')).toBe(true);
+      expect(manager.isEnabled('ext-test', '/path/to/dir/sub')).toBe(true);
+      expect(manager.isEnabled('ext-test', '/path/to/another')).toBe(false);
+    });
+
+    it('should correctly evaluate isEnabled without subdirs', () => {
+      manager.disable('ext-test', true, '*');
+      manager.enable('ext-test', false, '/path/to/dir');
+      expect(manager.isEnabled('ext-test', '/path/to/dir')).toBe(true);
+      expect(manager.isEnabled('ext-test', '/path/to/dir/sub')).toBe(false);
+    });
+  });
+});

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

@@ -0,0 +1,158 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import fs from 'node:fs';
+import path from 'node:path';
+
+export interface ExtensionEnablementConfig {
+  overrides: string[];
+}
+
+export interface AllExtensionsEnablementConfig {
+  [extensionName: string]: ExtensionEnablementConfig;
+}
+
+/**
+ * Converts a glob pattern to a RegExp object.
+ * This is a simplified implementation that supports `*`.
+ *
+ * @param glob The glob pattern to convert.
+ * @returns A RegExp object.
+ */
+function globToRegex(glob: string): RegExp {
+  const regexString = glob
+    .replace(/[.+?^${}()|[\]\\]/g, '\\$&') // Escape special regex characters
+    .replace(/\*/g, '.*'); // Convert * to .*
+
+  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;
+
+  constructor(configDir: string) {
+    this.configDir = configDir;
+    this.configFilePath = path.join(configDir, 'extension-enablement.json');
+  }
+
+  isEnabled(extensionName: string, currentPath: string): boolean {
+    const config = this.readConfig();
+    const extensionConfig = config[extensionName];
+    // Extensions are enabled by default.
+    let enabled = true;
+
+    for (const rule of extensionConfig?.overrides ?? []) {
+      const isDisableRule = rule.startsWith('!');
+      const globPattern = isDisableRule ? rule.substring(1) : rule;
+      const regex = globToRegex(globPattern);
+      if (regex.test(currentPath)) {
+        enabled = !isDisableRule;
+      }
+    }
+
+    return enabled;
+  }
+
+  readConfig(): AllExtensionsEnablementConfig {
+    try {
+      const content = fs.readFileSync(this.configFilePath, 'utf-8');
+      return JSON.parse(content);
+    } catch (error) {
+      if (
+        error instanceof Error &&
+        'code' in error &&
+        error.code === 'ENOENT'
+      ) {
+        return {};
+      }
+      console.error('Error reading extension enablement config:', error);
+      return {};
+    }
+  }
+
+  writeConfig(config: AllExtensionsEnablementConfig): void {
+    fs.mkdirSync(this.configDir, { recursive: true });
+    fs.writeFileSync(this.configFilePath, JSON.stringify(config, null, 2));
+  }
+
+  enable(
+    extensionName: string,
+    includeSubdirs: boolean,
+    scopePath: string,
+  ): void {
+    const config = this.readConfig();
+    if (!config[extensionName]) {
+      config[extensionName] = { overrides: [] };
+    }
+
+    const pathWithGlob = `${scopePath}*`;
+    const pathWithoutGlob = scopePath;
+
+    const newPath = includeSubdirs ? pathWithGlob : pathWithoutGlob;
+    const conflictingPath = includeSubdirs ? pathWithoutGlob : pathWithGlob;
+
+    config[extensionName].overrides = config[extensionName].overrides.filter(
+      (rule) =>
+        rule !== conflictingPath &&
+        rule !== `!${conflictingPath}` &&
+        rule !== `!${newPath}`,
+    );
+
+    if (!config[extensionName].overrides.includes(newPath)) {
+      config[extensionName].overrides.push(newPath);
+    }
+
+    this.writeConfig(config);
+  }
+
+  disable(
+    extensionName: string,
+    includeSubdirs: boolean,
+    scopePath: string,
+  ): void {
+    const config = this.readConfig();
+    if (!config[extensionName]) {
+      config[extensionName] = { overrides: [] };
+    }
+
+    const pathWithGlob = `${scopePath}*`;
+    const pathWithoutGlob = scopePath;
+
+    const targetPath = includeSubdirs ? pathWithGlob : pathWithoutGlob;
+    const newRule = `!${targetPath}`;
+    const conflictingPath = includeSubdirs ? pathWithoutGlob : pathWithGlob;
+
+    config[extensionName].overrides = config[extensionName].overrides.filter(
+      (rule) =>
+        rule !== conflictingPath &&
+        rule !== `!${conflictingPath}` &&
+        rule !== targetPath,
+    );
+
+    if (!config[extensionName].overrides.includes(newRule)) {
+      config[extensionName].overrides.push(newRule);
+    }
+
+    this.writeConfig(config);
+  }
+
+  remove(extensionName: string): void {
+    const config = this.readConfig();
+    if (config[extensionName]) {
+      delete config[extensionName];
+      this.writeConfig(config);
+    }
+  }
+}

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

@@ -49,6 +49,7 @@ 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';
 
 // These imports will get the versions from the vi.mock('./settings.js', ...) factory.
 import {
@@ -61,6 +62,8 @@ import {
   needsMigration,
   type Settings,
   loadEnvironment,
+  migrateDeprecatedSettings,
+  SettingScope,
 } from './settings.js';
 import { FatalConfigError, GEMINI_DIR } from '@google/gemini-cli-core';
 
@@ -90,6 +93,10 @@ vi.mock('fs', async (importOriginal) => {
   };
 });
 
+vi.mock('./extension.js', () => ({
+  disableExtension: vi.fn(),
+}));
+
 vi.mock('strip-json-comments', () => ({
   default: vi.fn((content) => content),
 }));
@@ -2311,4 +2318,122 @@ describe('Settings Loading and Merging', () => {
       expect(needsMigration(settings)).toBe(false);
     });
   });
+
+  describe('migrateDeprecatedSettings', () => {
+    let mockFsExistsSync: Mocked<typeof fs.existsSync>;
+    let mockFsReadFileSync: Mocked<typeof fs.readFileSync>;
+    let mockDisableExtension: Mocked<typeof disableExtension>;
+
+    beforeEach(() => {
+      vi.resetAllMocks();
+
+      mockFsExistsSync = vi.mocked(fs.existsSync);
+      mockFsReadFileSync = vi.mocked(fs.readFileSync);
+      mockDisableExtension = vi.mocked(disableExtension);
+
+      (mockFsExistsSync as Mock).mockReturnValue(true);
+      vi.mocked(isWorkspaceTrusted).mockReturnValue(true);
+    });
+
+    afterEach(() => {
+      vi.restoreAllMocks();
+    });
+
+    it('should migrate disabled extensions from user and workspace settings', () => {
+      const userSettingsContent = {
+        extensions: {
+          disabled: ['user-ext-1', 'shared-ext'],
+        },
+      };
+      const workspaceSettingsContent = {
+        extensions: {
+          disabled: ['workspace-ext-1', 'shared-ext'],
+        },
+      };
+
+      (mockFsReadFileSync as Mock).mockImplementation(
+        (p: fs.PathOrFileDescriptor) => {
+          if (p === USER_SETTINGS_PATH)
+            return JSON.stringify(userSettingsContent);
+          if (p === MOCK_WORKSPACE_SETTINGS_PATH)
+            return JSON.stringify(workspaceSettingsContent);
+          return '{}';
+        },
+      );
+
+      const loadedSettings = loadSettings(MOCK_WORKSPACE_DIR);
+      const setValueSpy = vi.spyOn(loadedSettings, 'setValue');
+
+      migrateDeprecatedSettings(loadedSettings, MOCK_WORKSPACE_DIR);
+
+      // Check user settings migration
+      expect(mockDisableExtension).toHaveBeenCalledWith(
+        'user-ext-1',
+        SettingScope.User,
+        MOCK_WORKSPACE_DIR,
+      );
+      expect(mockDisableExtension).toHaveBeenCalledWith(
+        'shared-ext',
+        SettingScope.User,
+        MOCK_WORKSPACE_DIR,
+      );
+
+      // Check workspace settings migration
+      expect(mockDisableExtension).toHaveBeenCalledWith(
+        'workspace-ext-1',
+        SettingScope.Workspace,
+        MOCK_WORKSPACE_DIR,
+      );
+      expect(mockDisableExtension).toHaveBeenCalledWith(
+        'shared-ext',
+        SettingScope.Workspace,
+        MOCK_WORKSPACE_DIR,
+      );
+
+      // Check that setValue was called to remove the deprecated setting
+      expect(setValueSpy).toHaveBeenCalledWith(
+        SettingScope.User,
+        'extensions',
+        {
+          disabled: undefined,
+        },
+      );
+      expect(setValueSpy).toHaveBeenCalledWith(
+        SettingScope.Workspace,
+        'extensions',
+        {
+          disabled: undefined,
+        },
+      );
+    });
+
+    it('should not do anything if there are no deprecated settings', () => {
+      const userSettingsContent = {
+        extensions: {
+          enabled: ['user-ext-1'],
+        },
+      };
+      const workspaceSettingsContent = {
+        someOtherSetting: 'value',
+      };
+
+      (mockFsReadFileSync as Mock).mockImplementation(
+        (p: fs.PathOrFileDescriptor) => {
+          if (p === USER_SETTINGS_PATH)
+            return JSON.stringify(userSettingsContent);
+          if (p === MOCK_WORKSPACE_SETTINGS_PATH)
+            return JSON.stringify(workspaceSettingsContent);
+          return '{}';
+        },
+      );
+
+      const loadedSettings = loadSettings(MOCK_WORKSPACE_DIR);
+      const setValueSpy = vi.spyOn(loadedSettings, 'setValue');
+
+      migrateDeprecatedSettings(loadedSettings, MOCK_WORKSPACE_DIR);
+
+      expect(mockDisableExtension).not.toHaveBeenCalled();
+      expect(setValueSpy).not.toHaveBeenCalled();
+    });
+  });
 });

packages/cli/src/config/settings.ts

@@ -30,6 +30,7 @@ import {
 import { resolveEnvVarsInObject } from '../utils/envVarResolver.js';
 import { customDeepMerge } from '../utils/deepMerge.js';
 import { updateSettingsFilePreservingFormat } from '../utils/commentJson.js';
+import { disableExtension } from './extension.js';
 
 function getMergeStrategyForPath(path: string[]): MergeStrategy | undefined {
   let current: SettingDefinition | undefined = undefined;
@@ -707,6 +708,31 @@ export function loadSettings(
   );
 }
 
+export function migrateDeprecatedSettings(
+  loadedSettings: LoadedSettings,
+  workspaceDir: string = process.cwd(),
+): void {
+  const processScope = (scope: SettingScope) => {
+    const settings = loadedSettings.forScope(scope).settings;
+    if (settings.extensions?.disabled) {
+      console.log(
+        `Migrating deprecated extensions.disabled settings from ${scope} settings...`,
+      );
+      for (const extension of settings.extensions.disabled ?? []) {
+        disableExtension(extension, scope, workspaceDir);
+      }
+
+      const newExtensionsValue = { ...settings.extensions };
+      newExtensionsValue.disabled = undefined;
+
+      loadedSettings.setValue(scope, 'extensions', newExtensionsValue);
+    }
+  };
+
+  processScope(SettingScope.User);
+  processScope(SettingScope.Workspace);
+}
+
 export function saveSettings(settingsFile: SettingsFile): void {
   try {
     // Ensure the directory exists

packages/cli/src/gemini.test.tsx

@@ -214,6 +214,7 @@ describe('gemini.tsx main function kitty protocol', () => {
         ui: {},
       },
       setValue: vi.fn(),
+      forScope: () => ({ settings: {}, originalSettings: {}, path: '' }),
     } as never);
     vi.mocked(parseArguments).mockResolvedValue({
       model: undefined,

packages/cli/src/gemini.tsx

@@ -15,7 +15,11 @@ import dns from 'node:dns';
 import { spawn } from 'node:child_process';
 import { start_sandbox } from './utils/sandbox.js';
 import type { DnsResolutionOrder, LoadedSettings } from './config/settings.js';
-import { loadSettings, SettingScope } from './config/settings.js';
+import {
+  loadSettings,
+  migrateDeprecatedSettings,
+  SettingScope,
+} from './config/settings.js';
 import { themeManager } from './ui/themes/theme-manager.js';
 import { getStartupWarnings } from './utils/startupWarnings.js';
 import { getUserStartupWarnings } from './utils/userStartupWarnings.js';
@@ -196,7 +200,7 @@ export async function startInteractiveUI(
 export async function main() {
   setupUnhandledRejectionHandler();
   const settings = loadSettings();
-
+  migrateDeprecatedSettings(settings);
   await cleanupCheckpoints();
 
   const argv = await parseArguments(settings.merged);