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(