Merge tag 'v0.3.0' into chore/sync-gemini-cli-v0.3.0

packages/cli/src/commands/extensions.tsx

@@ -0,0 +1,32 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import type { CommandModule } from 'yargs';
+import { installCommand } from './extensions/install.js';
+import { uninstallCommand } from './extensions/uninstall.js';
+import { listCommand } from './extensions/list.js';
+import { updateCommand } from './extensions/update.js';
+import { disableCommand } from './extensions/disable.js';
+import { enableCommand } from './extensions/enable.js';
+
+export const extensionsCommand: CommandModule = {
+  command: 'extensions <command>',
+  describe: 'Manage Gemini CLI extensions.',
+  builder: (yargs) =>
+    yargs
+      .command(installCommand)
+      .command(uninstallCommand)
+      .command(listCommand)
+      .command(updateCommand)
+      .command(disableCommand)
+      .command(enableCommand)
+      .demandCommand(1, 'You need at least one command before continuing.')
+      .version(false),
+  handler: () => {
+    // This handler is not called when a subcommand is provided.
+    // Yargs will show the help menu.
+  },
+};

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

@@ -0,0 +1,51 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { type CommandModule } from 'yargs';
+import { disableExtension } from '../../config/extension.js';
+import { SettingScope } from '../../config/settings.js';
+import { getErrorMessage } from '../../utils/errors.js';
+
+interface DisableArgs {
+  name: string;
+  scope: SettingScope;
+}
+
+export async function handleDisable(args: DisableArgs) {
+  try {
+    disableExtension(args.name, args.scope);
+    console.log(
+      `Extension "${args.name}" successfully disabled for scope "${args.scope}".`,
+    );
+  } catch (error) {
+    console.error(getErrorMessage(error));
+    process.exit(1);
+  }
+}
+
+export const disableCommand: CommandModule = {
+  command: 'disable [--scope] <name>',
+  describe: 'Disables an extension.',
+  builder: (yargs) =>
+    yargs
+      .positional('name', {
+        describe: 'The name of the extension to disable.',
+        type: 'string',
+      })
+      .option('scope', {
+        describe: 'The scope to disable the extenison in.',
+        type: 'string',
+        default: SettingScope.User,
+        choices: [SettingScope.User, SettingScope.Workspace],
+      })
+      .check((_argv) => true),
+  handler: async (argv) => {
+    await handleDisable({
+      name: argv['name'] as string,
+      scope: argv['scope'] as SettingScope,
+    });
+  },
+};

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

@@ -0,0 +1,59 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { type CommandModule } from 'yargs';
+import { FatalConfigError, getErrorMessage } from '@qwen-code/qwen-code-core';
+import { enableExtension } from '../../config/extension.js';
+import { SettingScope } from '../../config/settings.js';
+
+interface EnableArgs {
+  name: string;
+  scope?: SettingScope;
+}
+
+export async function handleEnable(args: EnableArgs) {
+  try {
+    const scopes = args.scope
+      ? [args.scope]
+      : [SettingScope.User, SettingScope.Workspace];
+    enableExtension(args.name, scopes);
+    if (args.scope) {
+      console.log(
+        `Extension "${args.name}" successfully enabled for scope "${args.scope}".`,
+      );
+    } else {
+      console.log(
+        `Extension "${args.name}" successfully enabled in all scopes.`,
+      );
+    }
+  } catch (error) {
+    throw new FatalConfigError(getErrorMessage(error));
+  }
+}
+
+export const enableCommand: CommandModule = {
+  command: 'disable [--scope] <name>',
+  describe: 'Enables an extension.',
+  builder: (yargs) =>
+    yargs
+      .positional('name', {
+        describe: 'The name of the extension to enable.',
+        type: 'string',
+      })
+      .option('scope', {
+        describe:
+          'The scope to enable the extenison in. If not set, will be enabled in all scopes.',
+        type: 'string',
+        choices: [SettingScope.User, SettingScope.Workspace],
+      })
+      .check((_argv) => true),
+  handler: async (argv) => {
+    await handleEnable({
+      name: argv['name'] as string,
+      scope: argv['scope'] as SettingScope,
+    });
+  },
+};

packages/cli/src/commands/extensions/install.test.ts

@@ -0,0 +1,31 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect } from 'vitest';
+import { installCommand } from './install.js';
+import yargs from 'yargs';
+
+describe('extensions install command', () => {
+  it('should fail if no source is provided', () => {
+    const validationParser = yargs([])
+      .locale('en')
+      .command(installCommand)
+      .fail(false);
+    expect(() => validationParser.parse('install')).toThrow(
+      'Either a git URL --source or a --path must be provided.',
+    );
+  });
+
+  it('should fail if both git source and local path are provided', () => {
+    const validationParser = yargs([])
+      .locale('en')
+      .command(installCommand)
+      .fail(false);
+    expect(() =>
+      validationParser.parse('install --source some-url --path /some/path'),
+    ).toThrow('Arguments source and path are mutually exclusive');
+  });
+});

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

@@ -0,0 +1,64 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import type { CommandModule } from 'yargs';
+import {
+  installExtension,
+  type ExtensionInstallMetadata,
+} from '../../config/extension.js';
+
+import { getErrorMessage } from '../../utils/errors.js';
+
+interface InstallArgs {
+  source?: string;
+  path?: string;
+}
+
+export async function handleInstall(args: InstallArgs) {
+  try {
+    const installMetadata: ExtensionInstallMetadata = {
+      source: (args.source || args.path) as string,
+      type: args.source ? 'git' : 'local',
+    };
+    const extensionName = await installExtension(installMetadata);
+    console.log(
+      `Extension "${extensionName}" installed successfully and enabled.`,
+    );
+  } catch (error) {
+    console.error(getErrorMessage(error));
+    process.exit(1);
+  }
+}
+
+export const installCommand: CommandModule = {
+  command: 'install [--source | --path ]',
+  describe: 'Installs an extension from a git repository or a local path.',
+  builder: (yargs) =>
+    yargs
+      .option('source', {
+        describe: 'The git URL of the extension to install.',
+        type: 'string',
+      })
+      .option('path', {
+        describe: 'Path to a local extension directory.',
+        type: 'string',
+      })
+      .conflicts('source', 'path')
+      .check((argv) => {
+        if (!argv.source && !argv.path) {
+          throw new Error(
+            'Either a git URL --source or a --path must be provided.',
+          );
+        }
+        return true;
+      }),
+  handler: async (argv) => {
+    await handleInstall({
+      source: argv['source'] as string | undefined,
+      path: argv['path'] as string | undefined,
+    });
+  },
+};

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

@@ -0,0 +1,36 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import type { CommandModule } from 'yargs';
+import { loadUserExtensions, toOutputString } from '../../config/extension.js';
+import { getErrorMessage } from '../../utils/errors.js';
+
+export async function handleList() {
+  try {
+    const extensions = loadUserExtensions();
+    if (extensions.length === 0) {
+      console.log('No extensions installed.');
+      return;
+    }
+    console.log(
+      extensions
+        .map((extension, _): string => toOutputString(extension))
+        .join('\n\n'),
+    );
+  } catch (error) {
+    console.error(getErrorMessage(error));
+    process.exit(1);
+  }
+}
+
+export const listCommand: CommandModule = {
+  command: 'list',
+  describe: 'Lists installed extensions.',
+  builder: (yargs) => yargs,
+  handler: async () => {
+    await handleList();
+  },
+};

packages/cli/src/commands/extensions/uninstall.test.ts

@@ -0,0 +1,21 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect } from 'vitest';
+import { uninstallCommand } from './uninstall.js';
+import yargs from 'yargs';
+
+describe('extensions uninstall command', () => {
+  it('should fail if no source is provided', () => {
+    const validationParser = yargs([])
+      .locale('en')
+      .command(uninstallCommand)
+      .fail(false);
+    expect(() => validationParser.parse('uninstall')).toThrow(
+      'Not enough non-option arguments: got 0, need at least 1',
+    );
+  });
+});

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

@@ -0,0 +1,47 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import type { CommandModule } from 'yargs';
+import { uninstallExtension } from '../../config/extension.js';
+import { getErrorMessage } from '../../utils/errors.js';
+
+interface UninstallArgs {
+  name: string;
+}
+
+export async function handleUninstall(args: UninstallArgs) {
+  try {
+    await uninstallExtension(args.name);
+    console.log(`Extension "${args.name}" successfully uninstalled.`);
+  } catch (error) {
+    console.error(getErrorMessage(error));
+    process.exit(1);
+  }
+}
+
+export const uninstallCommand: CommandModule = {
+  command: 'uninstall <name>',
+  describe: 'Uninstalls an extension.',
+  builder: (yargs) =>
+    yargs
+      .positional('name', {
+        describe: 'The name of the extension to uninstall.',
+        type: 'string',
+      })
+      .check((argv) => {
+        if (!argv.name) {
+          throw new Error(
+            'Please include the name of the extension to uninstall as a positional argument.',
+          );
+        }
+        return true;
+      }),
+  handler: async (argv) => {
+    await handleUninstall({
+      name: argv['name'] as string,
+    });
+  },
+};

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

@@ -0,0 +1,47 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import type { CommandModule } from 'yargs';
+import { updateExtension } from '../../config/extension.js';
+import { getErrorMessage } from '../../utils/errors.js';
+
+interface UpdateArgs {
+  name: string;
+}
+
+export async function handleUpdate(args: UpdateArgs) {
+  try {
+    // TODO(chrstnb): we should list extensions if the requested extension is not installed.
+    const updatedExtensionInfo = await updateExtension(args.name);
+    if (!updatedExtensionInfo) {
+      console.log(`Extension "${args.name}" failed to update.`);
+      return;
+    }
+    console.log(
+      `Extension "${args.name}" successfully updated: ${updatedExtensionInfo.originalVersion} → ${updatedExtensionInfo.updatedVersion}.`,
+    );
+  } catch (error) {
+    console.error(getErrorMessage(error));
+    process.exit(1);
+  }
+}
+
+export const updateCommand: CommandModule = {
+  command: 'update <name>',
+  describe: 'Updates an extension.',
+  builder: (yargs) =>
+    yargs
+      .positional('name', {
+        describe: 'The name of the extension to update.',
+        type: 'string',
+      })
+      .check((_argv) => true),
+  handler: async (argv) => {
+    await handleUpdate({
+      name: argv['name'] as string,
+    });
+  },
+};

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

@@ -7,7 +7,7 @@
 // File for 'gemini mcp add' command
 import type { CommandModule } from 'yargs';
 import { loadSettings, SettingScope } from '../../config/settings.js';
-import { MCPServerConfig } from '@qwen-code/qwen-code-core';
+import type { MCPServerConfig } from '@qwen-code/qwen-code-core';
 
 async function addMcpServer(
   name: string,

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

@@ -11,9 +11,27 @@ import { loadExtensions } from '../../config/extension.js';
 import { createTransport } from '@qwen-code/qwen-code-core';
 import { Client } from '@modelcontextprotocol/sdk/client/index.js';
 
-vi.mock('../../config/settings.js');
-vi.mock('../../config/extension.js');
-vi.mock('@qwen-code/qwen-code-core');
+vi.mock('../../config/settings.js', () => ({
+  loadSettings: vi.fn(),
+}));
+vi.mock('../../config/extension.js', () => ({
+  loadExtensions: vi.fn(),
+}));
+vi.mock('@qwen-code/qwen-code-core', () => ({
+  createTransport: vi.fn(),
+  MCPServerStatus: {
+    CONNECTED: 'CONNECTED',
+    CONNECTING: 'CONNECTING',
+    DISCONNECTED: 'DISCONNECTED',
+  },
+  Storage: vi.fn().mockImplementation((_cwd: string) => ({
+    getGlobalSettingsPath: () => '/tmp/qwen/settings.json',
+    getWorkspaceSettingsPath: () => '/tmp/qwen/workspace-settings.json',
+    getProjectTempDir: () => '/test/home/.qwen/tmp/mocked_hash',
+  })),
+  GEMINI_CONFIG_DIR: '.qwen',
+  getErrorMessage: (e: unknown) => (e instanceof Error ? e.message : String(e)),
+}));
 vi.mock('@modelcontextprotocol/sdk/client/index.js');
 
 const mockedLoadSettings = loadSettings as vi.Mock;

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

@@ -7,11 +7,8 @@
 // File for 'gemini mcp list' command
 import type { CommandModule } from 'yargs';
 import { loadSettings } from '../../config/settings.js';
-import {
-  MCPServerConfig,
-  MCPServerStatus,
-  createTransport,
-} from '@qwen-code/qwen-code-core';
+import type { MCPServerConfig } from '@qwen-code/qwen-code-core';
+import { MCPServerStatus, createTransport } from '@qwen-code/qwen-code-core';
 import { Client } from '@modelcontextprotocol/sdk/client/index.js';
 import { loadExtensions } from '../../config/extension.js';
 

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

@@ -5,14 +5,14 @@
  */
 
 import { describe, it, expect, beforeEach, vi, afterEach } from 'vitest';
-import * as fs from 'fs';
-import * as path from 'path';
-import { tmpdir } from 'os';
-import {
-  Config,
+import * as fs from 'node:fs';
+import * as path from 'node:path';
+import { tmpdir } from 'node:os';
+import type {
   ConfigParameters,
   ContentGeneratorConfig,
 } from '@qwen-code/qwen-code-core';
+import { Config } from '@qwen-code/qwen-code-core';
 import { http, HttpResponse } from 'msw';
 import { setupServer } from 'msw/node';
 
@@ -282,7 +282,7 @@ describe('Configuration Integration Tests', () => {
           'test',
         ];
 
-        const argv = await parseArguments();
+        const argv = await parseArguments({} as Settings);
 
         // Verify that the argument was parsed correctly
         expect(argv.approvalMode).toBe('auto_edit');
@@ -306,7 +306,7 @@ describe('Configuration Integration Tests', () => {
           'test',
         ];
 
-        const argv = await parseArguments();
+        const argv = await parseArguments({} as Settings);
 
         expect(argv.approvalMode).toBe('yolo');
         expect(argv.prompt).toBe('test');
@@ -329,7 +329,7 @@ describe('Configuration Integration Tests', () => {
           'test',
         ];
 
-        const argv = await parseArguments();
+        const argv = await parseArguments({} as Settings);
 
         expect(argv.approvalMode).toBe('default');
         expect(argv.prompt).toBe('test');
@@ -345,7 +345,7 @@ describe('Configuration Integration Tests', () => {
       try {
         process.argv = ['node', 'script.js', '--yolo', '-p', 'test'];
 
-        const argv = await parseArguments();
+        const argv = await parseArguments({} as Settings);
 
         expect(argv.yolo).toBe(true);
         expect(argv.approvalMode).toBeUndefined(); // Should NOT be set when using --yolo
@@ -362,7 +362,7 @@ describe('Configuration Integration Tests', () => {
         process.argv = ['node', 'script.js', '--approval-mode', 'invalid_mode'];
 
         // Should throw during argument parsing due to yargs validation
-        await expect(parseArguments()).rejects.toThrow();
+        await expect(parseArguments({} as Settings)).rejects.toThrow();
       } finally {
         process.argv = originalArgv;
       }
@@ -381,7 +381,7 @@ describe('Configuration Integration Tests', () => {
         ];
 
         // Should throw during argument parsing due to conflict validation
-        await expect(parseArguments()).rejects.toThrow();
+        await expect(parseArguments({} as Settings)).rejects.toThrow();
       } finally {
         process.argv = originalArgv;
       }
@@ -394,7 +394,7 @@ describe('Configuration Integration Tests', () => {
         // Test that no approval mode arguments defaults to no flags set
         process.argv = ['node', 'script.js', '-p', 'test'];
 
-        const argv = await parseArguments();
+        const argv = await parseArguments({} as Settings);
 
         expect(argv.approvalMode).toBeUndefined();
         expect(argv.yolo).toBe(false);

packages/cli/src/config/config.ts

@@ -4,37 +4,41 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import * as fs from 'fs';
-import * as path from 'path';
-import { homedir } from 'node:os';
-import yargs from 'yargs/yargs';
-import { hideBin } from 'yargs/helpers';
-import process from 'node:process';
-import { mcpCommand } from '../commands/mcp.js';
+import type {
+  ConfigParameters,
+  FileFilteringOptions,
+  MCPServerConfig,
+  TelemetryTarget,
+} from '@qwen-code/qwen-code-core';
 import {
+  ApprovalMode,
   Config,
+  DEFAULT_GEMINI_EMBEDDING_MODEL,
+  DEFAULT_GEMINI_MODEL,
+  DEFAULT_MEMORY_FILE_FILTERING_OPTIONS,
+  EditTool,
+  FileDiscoveryService,
+  getCurrentGeminiMdFilename,
   loadServerHierarchicalMemory,
   setGeminiMdFilename as setServerGeminiMdFilename,
-  getCurrentGeminiMdFilename,
-  ApprovalMode,
-  DEFAULT_GEMINI_MODEL,
-  DEFAULT_GEMINI_EMBEDDING_MODEL,
-  DEFAULT_MEMORY_FILE_FILTERING_OPTIONS,
-  FileDiscoveryService,
-  TelemetryTarget,
-  FileFilteringOptions,
   ShellTool,
-  EditTool,
   WriteFileTool,
-  MCPServerConfig,
-  ConfigParameters,
 } from '@qwen-code/qwen-code-core';
-import { Settings } from './settings.js';
+import * as fs from 'node:fs';
+import { homedir } from 'node:os';
+import * as path from 'node:path';
+import process from 'node:process';
+import { hideBin } from 'yargs/helpers';
+import yargs from 'yargs/yargs';
+import { extensionsCommand } from '../commands/extensions.js';
+import { mcpCommand } from '../commands/mcp.js';
+import type { Settings } from './settings.js';
 
-import { Extension, annotateActiveExtensions } from './extension.js';
-import { getCliVersion } from '../utils/version.js';
-import { loadSandboxConfig } from './sandboxConfig.js';
 import { resolvePath } from '../utils/resolvePath.js';
+import { getCliVersion } from '../utils/version.js';
+import type { Extension } from './extension.js';
+import { annotateActiveExtensions } from './extension.js';
+import { loadSandboxConfig } from './sandboxConfig.js';
 
 import { isWorkspaceTrusted } from './trustedFolders.js';
 
@@ -56,9 +60,7 @@ export interface CliArgs {
   prompt: string | undefined;
   promptInteractive: string | undefined;
   allFiles: boolean | undefined;
-  all_files: boolean | undefined;
   showMemoryUsage: boolean | undefined;
-  show_memory_usage: boolean | undefined;
   yolo: boolean | undefined;
   approvalMode: string | undefined;
   telemetry: boolean | undefined;
@@ -69,6 +71,7 @@ export interface CliArgs {
   telemetryLogPrompts: boolean | undefined;
   telemetryOutfile: string | undefined;
   allowedMcpServerNames: string[] | undefined;
+  allowedTools: string[] | undefined;
   experimentalAcp: boolean | undefined;
   extensions: string[] | undefined;
   listExtensions: boolean | undefined;
@@ -78,9 +81,10 @@ export interface CliArgs {
   proxy: string | undefined;
   includeDirectories: string[] | undefined;
   tavilyApiKey: string | undefined;
+  screenReader: boolean | undefined;
 }
 
-export async function parseArguments(): Promise<CliArgs> {
+export async function parseArguments(settings: Settings): Promise<CliArgs> {
   const yargsInstance = yargs(hideBin(process.argv))
     // Set locale to English for consistent output, especially in tests
     .locale('en')
@@ -128,29 +132,11 @@ export async function parseArguments(): Promise<CliArgs> {
           description: 'Include ALL files in context?',
           default: false,
         })
-        .option('all_files', {
-          type: 'boolean',
-          description: 'Include ALL files in context?',
-          default: false,
-        })
-        .deprecateOption(
-          'all_files',
-          'Use --all-files instead. We will be removing --all_files in the coming weeks.',
-        )
         .option('show-memory-usage', {
           type: 'boolean',
           description: 'Show memory usage in status bar',
           default: false,
         })
-        .option('show_memory_usage', {
-          type: 'boolean',
-          description: 'Show memory usage in status bar',
-          default: false,
-        })
-        .deprecateOption(
-          'show_memory_usage',
-          'Use --show-memory-usage instead. We will be removing --show_memory_usage in the coming weeks.',
-        )
         .option('yolo', {
           alias: 'y',
           type: 'boolean',
@@ -210,6 +196,11 @@ export async function parseArguments(): Promise<CliArgs> {
           string: true,
           description: 'Allowed MCP server names',
         })
+        .option('allowed-tools', {
+          type: 'array',
+          string: true,
+          description: 'Tools that are allowed to run without confirmation',
+        })
         .option('extensions', {
           alias: 'e',
           type: 'array',
@@ -253,7 +244,11 @@ export async function parseArguments(): Promise<CliArgs> {
           type: 'string',
           description: 'Tavily API key for web search functionality',
         })
-
+        .option('screen-reader', {
+          type: 'boolean',
+          description: 'Enable screen reader mode for accessibility.',
+          default: false,
+        })
         .check((argv) => {
           if (argv.prompt && argv['promptInteractive']) {
             throw new Error(
@@ -269,7 +264,13 @@ export async function parseArguments(): Promise<CliArgs> {
         }),
     )
     // Register MCP subcommands
-    .command(mcpCommand)
+    .command(mcpCommand);
+
+  if (settings?.experimental?.extensionManagement ?? false) {
+    yargsInstance.command(extensionsCommand);
+  }
+
+  yargsInstance
     .version(await getCliVersion()) // This will enable the --version flag based on package.json
     .alias('v', 'version')
     .help()
@@ -282,7 +283,10 @@ export async function parseArguments(): Promise<CliArgs> {
 
   // Handle case where MCP subcommands are executed - they should exit the process
   // and not return to main CLI logic
-  if (result._.length > 0 && result._[0] === 'mcp') {
+  if (
+    result._.length > 0 &&
+    (result._[0] === 'mcp' || result._[0] === 'extensions')
+  ) {
     // MCP commands handle their own execution and process exit
     process.exit(0);
   }
@@ -329,7 +333,7 @@ export async function loadHierarchicalGeminiMemory(
     extensionContextFilePaths,
     memoryImportFormat,
     fileFilteringOptions,
-    settings.memoryDiscoveryMaxDirs,
+    settings.context?.discoveryMaxDirs,
   );
 }
 
@@ -346,18 +350,20 @@ export async function loadCliConfig(
       (v) => v === 'true' || v === '1',
     ) ||
     false;
-  const memoryImportFormat = settings.memoryImportFormat || 'tree';
+  const memoryImportFormat = settings.context?.importFormat || 'tree';
 
-  const ideMode = settings.ideMode ?? false;
+  const ideMode = settings.ide?.enabled ?? false;
 
-  const folderTrustFeature = settings.folderTrustFeature ?? false;
-  const folderTrustSetting = settings.folderTrust ?? true;
+  const folderTrustFeature =
+    settings.security?.folderTrust?.featureEnabled ?? false;
+  const folderTrustSetting = settings.security?.folderTrust?.enabled ?? true;
   const folderTrust = folderTrustFeature && folderTrustSetting;
   const trustedFolder = isWorkspaceTrusted(settings);
 
   const allExtensions = annotateActiveExtensions(
     extensions,
     argv.extensions || [],
+    cwd,
   );
 
   const activeExtensions = extensions.filter(
@@ -382,8 +388,8 @@ export async function loadCliConfig(
   // 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.
   // However, loadHierarchicalGeminiMemory is called *before* createServerConfig.
-  if (settings.contextFileName) {
-    setServerGeminiMdFilename(settings.contextFileName);
+  if (settings.context?.fileName) {
+    setServerGeminiMdFilename(settings.context.fileName);
   } else {
     // Reset to default if not provided in settings.
     setServerGeminiMdFilename(getCurrentGeminiMdFilename());
@@ -397,17 +403,19 @@ export async function loadCliConfig(
 
   const fileFiltering = {
     ...DEFAULT_MEMORY_FILE_FILTERING_OPTIONS,
-    ...settings.fileFiltering,
+    ...settings.context?.fileFiltering,
   };
 
-  const includeDirectories = (settings.includeDirectories || [])
+  const includeDirectories = (settings.context?.includeDirectories || [])
     .map(resolvePath)
     .concat((argv.includeDirectories || []).map(resolvePath));
 
   // Call the (now wrapper) loadHierarchicalGeminiMemory which calls the server's version
   const { memoryContent, fileCount } = await loadHierarchicalGeminiMemory(
     cwd,
-    settings.loadMemoryFromIncludeDirectories ? includeDirectories : [],
+    settings.context?.loadMemoryFromIncludeDirectories
+      ? includeDirectories
+      : [],
     debugMode,
     fileService,
     settings,
@@ -444,6 +452,14 @@ export async function loadCliConfig(
       argv.yolo || false ? ApprovalMode.YOLO : ApprovalMode.DEFAULT;
   }
 
+  // Force approval mode to default if the folder is not trusted.
+  if (!trustedFolder && approvalMode !== ApprovalMode.DEFAULT) {
+    logger.warn(
+      `Approval mode overridden to "default" because the current folder is not trusted.`,
+    );
+    approvalMode = ApprovalMode.DEFAULT;
+  }
+
   const interactive =
     !!argv.promptInteractive || (process.stdin.isTTY && question.length === 0);
   // In non-interactive mode, exclude tools that require a prompt.
@@ -475,16 +491,16 @@ export async function loadCliConfig(
   const blockedMcpServers: Array<{ name: string; extensionName: string }> = [];
 
   if (!argv.allowedMcpServerNames) {
-    if (settings.allowMCPServers) {
+    if (settings.mcp?.allowed) {
       mcpServers = allowedMcpServers(
         mcpServers,
-        settings.allowMCPServers,
+        settings.mcp.allowed,
         blockedMcpServers,
       );
     }
 
-    if (settings.excludeMCPServers) {
-      const excludedNames = new Set(settings.excludeMCPServers.filter(Boolean));
+    if (settings.mcp?.excluded) {
+      const excludedNames = new Set(settings.mcp.excluded.filter(Boolean));
       if (excludedNames.size > 0) {
         mcpServers = Object.fromEntries(
           Object.entries(mcpServers).filter(([key]) => !excludedNames.has(key)),
@@ -504,6 +520,10 @@ export async function loadCliConfig(
   const sandboxConfig = await loadSandboxConfig(settings, argv);
   const cliVersion = await getCliVersion();
 
+  const screenReader =
+    argv.screenReader !== undefined
+      ? argv.screenReader
+      : (settings.ui?.accessibility?.screenReader ?? false);
   return new Config({
     sessionId,
     embeddingModel: DEFAULT_GEMINI_EMBEDDING_MODEL,
@@ -511,25 +531,26 @@ export async function loadCliConfig(
     targetDir: cwd,
     includeDirectories,
     loadMemoryFromIncludeDirectories:
-      settings.loadMemoryFromIncludeDirectories || false,
+      settings.context?.loadMemoryFromIncludeDirectories || false,
     debugMode,
     question,
-    fullContext: argv.allFiles || argv.all_files || false,
-    coreTools: settings.coreTools || undefined,
+    fullContext: argv.allFiles || false,
+    coreTools: settings.tools?.core || undefined,
+    allowedTools: argv.allowedTools || settings.tools?.allowed || undefined,
     excludeTools,
-    toolDiscoveryCommand: settings.toolDiscoveryCommand,
-    toolCallCommand: settings.toolCallCommand,
-    mcpServerCommand: settings.mcpServerCommand,
+    toolDiscoveryCommand: settings.tools?.discoveryCommand,
+    toolCallCommand: settings.tools?.callCommand,
+    mcpServerCommand: settings.mcp?.serverCommand,
     mcpServers,
     userMemory: memoryContent,
     geminiMdFileCount: fileCount,
     approvalMode,
     showMemoryUsage:
-      argv.showMemoryUsage ||
-      argv.show_memory_usage ||
-      settings.showMemoryUsage ||
-      false,
-    accessibility: settings.accessibility,
+      argv.showMemoryUsage || settings.ui?.showMemoryUsage || false,
+    accessibility: {
+      ...settings.ui?.accessibility,
+      screenReader,
+    },
     telemetry: {
       enabled: argv.telemetry ?? settings.telemetry?.enabled,
       target: (argv.telemetryTarget ??
@@ -546,15 +567,17 @@ export async function loadCliConfig(
       logPrompts: argv.telemetryLogPrompts ?? settings.telemetry?.logPrompts,
       outfile: argv.telemetryOutfile ?? settings.telemetry?.outfile,
     },
-    usageStatisticsEnabled: settings.usageStatisticsEnabled ?? true,
+    usageStatisticsEnabled: settings.privacy?.usageStatisticsEnabled ?? true,
     // Git-aware file filtering settings
     fileFiltering: {
-      respectGitIgnore: settings.fileFiltering?.respectGitIgnore,
-      respectGeminiIgnore: settings.fileFiltering?.respectGeminiIgnore,
+      respectGitIgnore: settings.context?.fileFiltering?.respectGitIgnore,
+      respectGeminiIgnore: settings.context?.fileFiltering?.respectGeminiIgnore,
       enableRecursiveFileSearch:
-        settings.fileFiltering?.enableRecursiveFileSearch,
+        settings.context?.fileFiltering?.enableRecursiveFileSearch,
+      disableFuzzySearch: settings.context?.fileFiltering?.disableFuzzySearch,
     },
-    checkpointing: argv.checkpointing || settings.checkpointing?.enabled,
+    checkpointing:
+      argv.checkpointing || settings.general?.checkpointing?.enabled,
     proxy:
       argv.proxy ||
       process.env['HTTPS_PROXY'] ||
@@ -563,18 +586,16 @@ export async function loadCliConfig(
       process.env['http_proxy'],
     cwd,
     fileDiscoveryService: fileService,
-    bugCommand: settings.bugCommand,
-    model: argv.model || settings.model || DEFAULT_GEMINI_MODEL,
+    bugCommand: settings.advanced?.bugCommand,
+    model: argv.model || settings.model?.name || DEFAULT_GEMINI_MODEL,
     extensionContextFilePaths,
-    maxSessionTurns: settings.maxSessionTurns ?? -1,
     sessionTokenLimit: settings.sessionTokenLimit ?? -1,
+    maxSessionTurns: settings.model?.maxSessionTurns ?? -1,
     experimentalZedIntegration: argv.experimentalAcp || false,
     listExtensions: argv.listExtensions || false,
     extensions: allExtensions,
     blockedMcpServers,
     noBrowser: !!process.env['NO_BROWSER'],
-    summarizeToolOutput: settings.summarizeToolOutput,
-    ideMode,
     enableOpenAILogging:
       (typeof argv.openaiLogging === 'undefined'
         ? settings.enableOpenAILogging
@@ -590,20 +611,24 @@ export async function loadCliConfig(
           'SYSTEM_TEMPLATE:{"name":"qwen3_coder","params":{"is_git_repository":{RUNTIME_VARS_IS_GIT_REPO},"sandbox":"{RUNTIME_VARS_SANDBOX}"}}',
       },
     ]) as ConfigParameters['systemPromptMappings'],
-    authType: settings.selectedAuthType,
+    authType: settings.security?.auth?.selectedType,
     contentGenerator: settings.contentGenerator,
     cliVersion,
     tavilyApiKey:
       argv.tavilyApiKey ||
       settings.tavilyApiKey ||
       process.env['TAVILY_API_KEY'],
-    chatCompression: settings.chatCompression,
+    summarizeToolOutput: settings.model?.summarizeToolOutput,
+    ideMode,
+    chatCompression: settings.model?.chatCompression,
     folderTrustFeature,
     folderTrust,
     interactive,
     trustedFolder,
-    shouldUseNodePtyShell: settings.shouldUseNodePtyShell,
-    skipNextSpeakerCheck: settings.skipNextSpeakerCheck,
+    useRipgrep: settings.tools?.useRipgrep,
+    shouldUseNodePtyShell: settings.tools?.usePty,
+    skipNextSpeakerCheck: settings.model?.skipNextSpeakerCheck,
+    enablePromptCompletion: settings.general?.enablePromptCompletion ?? false,
   });
 }
 
@@ -665,7 +690,7 @@ function mergeExcludeTools(
   extraExcludes?: string[] | undefined,
 ): string[] {
   const allExcludeTools = new Set([
-    ...(settings.excludeTools || []),
+    ...(settings.tools?.exclude || []),
     ...(extraExcludes || []),
   ]);
   for (const extension of extensions) {

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

@@ -5,24 +5,52 @@
  */
 
 import { vi } from 'vitest';
-import * as fs from 'fs';
-import * as os from 'os';
-import * as path from 'path';
+import * as fs from 'node:fs';
+import * as os from 'node:os';
+import * as path from 'node:path';
 import {
   EXTENSIONS_CONFIG_FILENAME,
-  EXTENSIONS_DIRECTORY_NAME,
+  INSTALL_METADATA_FILENAME,
   annotateActiveExtensions,
+  disableExtension,
+  enableExtension,
+  installExtension,
+  loadExtension,
   loadExtensions,
+  performWorkspaceExtensionMigration,
+  uninstallExtension,
+  updateExtension,
 } from './extension.js';
+import {
+  type GeminiCLIExtension,
+  type MCPServerConfig,
+} from '@qwen-code/qwen-code-core';
+import { execSync } from 'node:child_process';
+import { SettingScope, loadSettings } from './settings.js';
+import { type SimpleGit, simpleGit } from 'simple-git';
+
+vi.mock('simple-git', () => ({
+  simpleGit: vi.fn(),
+}));
 
 vi.mock('os', async (importOriginal) => {
-  const os = await importOriginal<typeof import('os')>();
+  const os = await importOriginal<typeof os>();
   return {
     ...os,
     homedir: vi.fn(),
   };
 });
 
+vi.mock('child_process', async (importOriginal) => {
+  const actual = await importOriginal<typeof import('child_process')>();
+  return {
+    ...actual,
+    execSync: vi.fn(),
+  };
+});
+
+const EXTENSIONS_DIRECTORY_NAME = path.join('.qwen', 'extensions');
+
 describe('loadExtensions', () => {
   let tempWorkspaceDir: string;
   let tempHomeDir: string;
@@ -40,56 +68,7 @@ describe('loadExtensions', () => {
   afterEach(() => {
     fs.rmSync(tempWorkspaceDir, { recursive: true, force: true });
     fs.rmSync(tempHomeDir, { recursive: true, force: true });
-  });
-
-  it('should include extension path in loaded extension', () => {
-    const workspaceExtensionsDir = path.join(
-      tempWorkspaceDir,
-      EXTENSIONS_DIRECTORY_NAME,
-    );
-    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
-
-    const extensionDir = path.join(workspaceExtensionsDir, 'test-extension');
-    fs.mkdirSync(extensionDir, { recursive: true });
-
-    const config = {
-      name: 'test-extension',
-      version: '1.0.0',
-    };
-    fs.writeFileSync(
-      path.join(extensionDir, EXTENSIONS_CONFIG_FILENAME),
-      JSON.stringify(config),
-    );
-
-    const extensions = loadExtensions(tempWorkspaceDir);
-    expect(extensions).toHaveLength(1);
-    expect(extensions[0].path).toBe(extensionDir);
-    expect(extensions[0].config.name).toBe('test-extension');
-  });
-
-  it('should include extension path in loaded extension', () => {
-    const workspaceExtensionsDir = path.join(
-      tempWorkspaceDir,
-      EXTENSIONS_DIRECTORY_NAME,
-    );
-    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
-
-    const extensionDir = path.join(workspaceExtensionsDir, 'test-extension');
-    fs.mkdirSync(extensionDir, { recursive: true });
-
-    const config = {
-      name: 'test-extension',
-      version: '1.0.0',
-    };
-    fs.writeFileSync(
-      path.join(extensionDir, EXTENSIONS_CONFIG_FILENAME),
-      JSON.stringify(config),
-    );
-
-    const extensions = loadExtensions(tempWorkspaceDir);
-    expect(extensions).toHaveLength(1);
-    expect(extensions[0].path).toBe(extensionDir);
-    expect(extensions[0].config.name).toBe('test-extension');
+    vi.restoreAllMocks();
   });
 
   it('should include extension path in loaded extension', () => {
@@ -159,26 +138,101 @@ describe('loadExtensions', () => {
       path.join(workspaceExtensionsDir, 'ext1', 'my-context-file.md'),
     ]);
   });
+
+  it('should filter out disabled extensions', () => {
+    const workspaceExtensionsDir = path.join(
+      tempWorkspaceDir,
+      EXTENSIONS_DIRECTORY_NAME,
+    );
+    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
+
+    createExtension(workspaceExtensionsDir, 'ext1', '1.0.0');
+    createExtension(workspaceExtensionsDir, 'ext2', '2.0.0');
+
+    const settingsDir = path.join(tempWorkspaceDir, '.qwen');
+    fs.mkdirSync(settingsDir, { recursive: true });
+    fs.writeFileSync(
+      path.join(settingsDir, 'settings.json'),
+      JSON.stringify({ extensions: { disabled: ['ext1'] } }),
+    );
+
+    const extensions = loadExtensions(tempWorkspaceDir);
+    const activeExtensions = annotateActiveExtensions(
+      extensions,
+      [],
+      tempWorkspaceDir,
+    ).filter((e) => e.isActive);
+    expect(activeExtensions).toHaveLength(1);
+    expect(activeExtensions[0].name).toBe('ext2');
+  });
+
+  it('should hydrate variables', () => {
+    const workspaceExtensionsDir = path.join(
+      tempWorkspaceDir,
+      EXTENSIONS_DIRECTORY_NAME,
+    );
+    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
+
+    createExtension(
+      workspaceExtensionsDir,
+      'test-extension',
+      '1.0.0',
+      false,
+      undefined,
+      {
+        'test-server': {
+          cwd: '${extensionPath}${/}server',
+        },
+      },
+    );
+
+    const extensions = loadExtensions(tempWorkspaceDir);
+    expect(extensions).toHaveLength(1);
+    const loadedConfig = extensions[0].config;
+    const expectedCwd = path.join(
+      workspaceExtensionsDir,
+      'test-extension',
+      'server',
+    );
+    expect(loadedConfig.mcpServers?.['test-server'].cwd).toBe(expectedCwd);
+  });
 });
 
 describe('annotateActiveExtensions', () => {
   const extensions = [
-    { config: { name: 'ext1', version: '1.0.0' }, contextFiles: [] },
-    { config: { name: 'ext2', version: '1.0.0' }, contextFiles: [] },
-    { config: { name: 'ext3', version: '1.0.0' }, contextFiles: [] },
+    {
+      path: '/path/to/ext1',
+      config: { name: 'ext1', version: '1.0.0' },
+      contextFiles: [],
+    },
+    {
+      path: '/path/to/ext2',
+      config: { name: 'ext2', version: '1.0.0' },
+      contextFiles: [],
+    },
+    {
+      path: '/path/to/ext3',
+      config: { name: 'ext3', version: '1.0.0' },
+      contextFiles: [],
+    },
   ];
 
   it('should mark all extensions as active if no enabled extensions are provided', () => {
-    const activeExtensions = annotateActiveExtensions(extensions, []);
+    const activeExtensions = annotateActiveExtensions(
+      extensions,
+      [],
+      '/path/to/workspace',
+    );
     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, [
-      'ext1',
-      'ext3',
-    ]);
+    const activeExtensions = annotateActiveExtensions(
+      extensions,
+      ['ext1', 'ext3'],
+      '/path/to/workspace',
+    );
     expect(activeExtensions).toHaveLength(3);
     expect(activeExtensions.find((e) => e.name === 'ext1')?.isActive).toBe(
       true,
@@ -192,13 +246,21 @@ describe('annotateActiveExtensions', () => {
   });
 
   it('should mark all extensions as inactive when "none" is provided', () => {
-    const activeExtensions = annotateActiveExtensions(extensions, ['none']);
+    const activeExtensions = annotateActiveExtensions(
+      extensions,
+      ['none'],
+      '/path/to/workspace',
+    );
     expect(activeExtensions).toHaveLength(3);
     expect(activeExtensions.every((e) => !e.isActive)).toBe(true);
   });
 
   it('should handle case-insensitivity', () => {
-    const activeExtensions = annotateActiveExtensions(extensions, ['EXT1']);
+    const activeExtensions = annotateActiveExtensions(
+      extensions,
+      ['EXT1'],
+      '/path/to/workspace',
+    );
     expect(activeExtensions.find((e) => e.name === 'ext1')?.isActive).toBe(
       true,
     );
@@ -206,24 +268,258 @@ describe('annotateActiveExtensions', () => {
 
   it('should log an error for unknown extensions', () => {
     const consoleSpy = vi.spyOn(console, 'error').mockImplementation(() => {});
-    annotateActiveExtensions(extensions, ['ext4']);
+    annotateActiveExtensions(extensions, ['ext4'], '/path/to/workspace');
     expect(consoleSpy).toHaveBeenCalledWith('Extension not found: ext4');
     consoleSpy.mockRestore();
   });
 });
 
+describe('installExtension', () => {
+  let tempHomeDir: string;
+  let userExtensionsDir: string;
+
+  beforeEach(() => {
+    tempHomeDir = fs.mkdtempSync(
+      path.join(os.tmpdir(), 'qwen-code-test-home-'),
+    );
+    vi.mocked(os.homedir).mockReturnValue(tempHomeDir);
+    userExtensionsDir = path.join(tempHomeDir, '.qwen', 'extensions');
+    // Clean up before each test
+    fs.rmSync(userExtensionsDir, { recursive: true, force: true });
+    fs.mkdirSync(userExtensionsDir, { recursive: true });
+
+    vi.mocked(execSync).mockClear();
+  });
+
+  afterEach(() => {
+    fs.rmSync(tempHomeDir, { recursive: true, force: true });
+  });
+
+  it('should install an extension from a local path', async () => {
+    const sourceExtDir = createExtension(
+      tempHomeDir,
+      'my-local-extension',
+      '1.0.0',
+    );
+    const targetExtDir = path.join(userExtensionsDir, 'my-local-extension');
+    const metadataPath = path.join(targetExtDir, INSTALL_METADATA_FILENAME);
+
+    await installExtension({ source: sourceExtDir, type: 'local' });
+
+    expect(fs.existsSync(targetExtDir)).toBe(true);
+    expect(fs.existsSync(metadataPath)).toBe(true);
+    const metadata = JSON.parse(fs.readFileSync(metadataPath, 'utf-8'));
+    expect(metadata).toEqual({
+      source: sourceExtDir,
+      type: 'local',
+    });
+    fs.rmSync(targetExtDir, { recursive: true, force: true });
+  });
+
+  it('should throw an error if the extension already exists', async () => {
+    const sourceExtDir = createExtension(
+      tempHomeDir,
+      'my-local-extension',
+      '1.0.0',
+    );
+    await installExtension({ source: sourceExtDir, type: 'local' });
+    await expect(
+      installExtension({ source: sourceExtDir, type: 'local' }),
+    ).rejects.toThrow(
+      'Extension "my-local-extension" is already installed. Please uninstall it first.',
+    );
+  });
+
+  it('should throw an error and cleanup if gemini-extension.json is missing', async () => {
+    const sourceExtDir = path.join(tempHomeDir, 'bad-extension');
+    fs.mkdirSync(sourceExtDir, { recursive: true });
+
+    await expect(
+      installExtension({ source: sourceExtDir, type: 'local' }),
+    ).rejects.toThrow(
+      `Invalid extension at ${sourceExtDir}. Please make sure it has a valid gemini-extension.json file.`,
+    );
+
+    const targetExtDir = path.join(userExtensionsDir, 'bad-extension');
+    expect(fs.existsSync(targetExtDir)).toBe(false);
+  });
+
+  it('should install an extension from a git URL', async () => {
+    const gitUrl = 'https://github.com/google/gemini-extensions.git';
+    const extensionName = 'gemini-extensions';
+    const targetExtDir = path.join(userExtensionsDir, extensionName);
+    const metadataPath = path.join(targetExtDir, INSTALL_METADATA_FILENAME);
+
+    const clone = vi.fn().mockImplementation(async (_, destination) => {
+      fs.mkdirSync(destination, { recursive: true });
+      fs.writeFileSync(
+        path.join(destination, EXTENSIONS_CONFIG_FILENAME),
+        JSON.stringify({ name: extensionName, version: '1.0.0' }),
+      );
+    });
+
+    const mockedSimpleGit = simpleGit as vi.MockedFunction<typeof simpleGit>;
+    mockedSimpleGit.mockReturnValue({ clone } as unknown as SimpleGit);
+
+    await installExtension({ source: gitUrl, type: 'git' });
+
+    expect(fs.existsSync(targetExtDir)).toBe(true);
+    expect(fs.existsSync(metadataPath)).toBe(true);
+    const metadata = JSON.parse(fs.readFileSync(metadataPath, 'utf-8'));
+    expect(metadata).toEqual({
+      source: gitUrl,
+      type: 'git',
+    });
+    fs.rmSync(targetExtDir, { recursive: true, force: true });
+  });
+});
+
+describe('uninstallExtension', () => {
+  let tempHomeDir: string;
+  let userExtensionsDir: string;
+
+  beforeEach(() => {
+    tempHomeDir = fs.mkdtempSync(
+      path.join(os.tmpdir(), 'qwen-code-test-home-'),
+    );
+    vi.mocked(os.homedir).mockReturnValue(tempHomeDir);
+    userExtensionsDir = path.join(tempHomeDir, '.qwen', 'extensions');
+    // Clean up before each test
+    fs.rmSync(userExtensionsDir, { recursive: true, force: true });
+    fs.mkdirSync(userExtensionsDir, { recursive: true });
+
+    vi.mocked(execSync).mockClear();
+  });
+
+  afterEach(() => {
+    fs.rmSync(tempHomeDir, { recursive: true, force: true });
+  });
+
+  it('should uninstall an extension by name', async () => {
+    const sourceExtDir = createExtension(
+      userExtensionsDir,
+      'my-local-extension',
+      '1.0.0',
+    );
+
+    await uninstallExtension('my-local-extension');
+
+    expect(fs.existsSync(sourceExtDir)).toBe(false);
+  });
+
+  it('should uninstall an extension by name and retain existing extensions', async () => {
+    const sourceExtDir = createExtension(
+      userExtensionsDir,
+      'my-local-extension',
+      '1.0.0',
+    );
+    const otherExtDir = createExtension(
+      userExtensionsDir,
+      'other-extension',
+      '1.0.0',
+    );
+
+    await uninstallExtension('my-local-extension');
+
+    expect(fs.existsSync(sourceExtDir)).toBe(false);
+    expect(loadExtensions(tempHomeDir)).toHaveLength(1);
+    expect(fs.existsSync(otherExtDir)).toBe(true);
+  });
+
+  it('should throw an error if the extension does not exist', async () => {
+    await expect(uninstallExtension('nonexistent-extension')).rejects.toThrow(
+      'Extension "nonexistent-extension" not found.',
+    );
+  });
+});
+
+describe('performWorkspaceExtensionMigration', () => {
+  let tempWorkspaceDir: string;
+  let tempHomeDir: string;
+
+  beforeEach(() => {
+    tempWorkspaceDir = fs.mkdtempSync(
+      path.join(os.tmpdir(), 'qwen-code-test-workspace-'),
+    );
+    tempHomeDir = fs.mkdtempSync(
+      path.join(os.tmpdir(), 'qwen-code-test-home-'),
+    );
+    vi.mocked(os.homedir).mockReturnValue(tempHomeDir);
+  });
+
+  afterEach(() => {
+    fs.rmSync(tempWorkspaceDir, { recursive: true, force: true });
+    fs.rmSync(tempHomeDir, { recursive: true, force: true });
+    vi.restoreAllMocks();
+  });
+
+  it('should install the extensions in the user directory', async () => {
+    const workspaceExtensionsDir = path.join(
+      tempWorkspaceDir,
+      EXTENSIONS_DIRECTORY_NAME,
+    );
+    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
+    const ext1Path = createExtension(workspaceExtensionsDir, 'ext1', '1.0.0');
+    const ext2Path = createExtension(workspaceExtensionsDir, 'ext2', '1.0.0');
+    const extensionsToMigrate = [
+      loadExtension(ext1Path)!,
+      loadExtension(ext2Path)!,
+    ];
+    const failed =
+      await performWorkspaceExtensionMigration(extensionsToMigrate);
+
+    expect(failed).toEqual([]);
+
+    const userExtensionsDir = path.join(tempHomeDir, '.qwen', 'extensions');
+    const userExt1Path = path.join(userExtensionsDir, 'ext1');
+    const extensions = loadExtensions(tempWorkspaceDir);
+
+    expect(extensions).toHaveLength(2);
+    const metadataPath = path.join(userExt1Path, INSTALL_METADATA_FILENAME);
+    expect(fs.existsSync(metadataPath)).toBe(true);
+    const metadata = JSON.parse(fs.readFileSync(metadataPath, 'utf-8'));
+    expect(metadata).toEqual({
+      source: ext1Path,
+      type: 'local',
+    });
+  });
+
+  it('should return the names of failed installations', async () => {
+    const workspaceExtensionsDir = path.join(
+      tempWorkspaceDir,
+      EXTENSIONS_DIRECTORY_NAME,
+    );
+    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
+
+    const ext1Path = createExtension(workspaceExtensionsDir, 'ext1', '1.0.0');
+
+    const extensions = [
+      loadExtension(ext1Path)!,
+      {
+        path: '/ext/path/1',
+        config: { name: 'ext2', version: '1.0.0' },
+        contextFiles: [],
+      },
+    ];
+
+    const failed = await performWorkspaceExtensionMigration(extensions);
+    expect(failed).toEqual(['ext2']);
+  });
+});
+
 function createExtension(
   extensionsDir: string,
   name: string,
   version: string,
   addContextFile = false,
   contextFileName?: string,
-): void {
+  mcpServers?: Record<string, MCPServerConfig>,
+): string {
   const extDir = path.join(extensionsDir, name);
-  fs.mkdirSync(extDir);
+  fs.mkdirSync(extDir, { recursive: true });
   fs.writeFileSync(
     path.join(extDir, EXTENSIONS_CONFIG_FILENAME),
-    JSON.stringify({ name, version, contextFileName }),
+    JSON.stringify({ name, version, contextFileName, mcpServers }),
   );
 
   if (addContextFile) {
@@ -233,4 +529,193 @@ function createExtension(
   if (contextFileName) {
     fs.writeFileSync(path.join(extDir, contextFileName), 'context');
   }
+  return extDir;
 }
+
+describe('updateExtension', () => {
+  let tempHomeDir: string;
+  let userExtensionsDir: string;
+
+  beforeEach(() => {
+    tempHomeDir = fs.mkdtempSync(
+      path.join(os.tmpdir(), 'qwen-code-test-home-'),
+    );
+    vi.mocked(os.homedir).mockReturnValue(tempHomeDir);
+    userExtensionsDir = path.join(tempHomeDir, '.qwen', 'extensions');
+    // Clean up before each test
+    fs.rmSync(userExtensionsDir, { recursive: true, force: true });
+    fs.mkdirSync(userExtensionsDir, { recursive: true });
+
+    vi.mocked(execSync).mockClear();
+  });
+
+  afterEach(() => {
+    fs.rmSync(tempHomeDir, { recursive: true, force: true });
+  });
+
+  it('should update a git-installed extension', async () => {
+    // 1. "Install" an extension
+    const gitUrl = 'https://github.com/google/gemini-extensions.git';
+    const extensionName = 'gemini-extensions';
+    const targetExtDir = path.join(userExtensionsDir, extensionName);
+    const metadataPath = path.join(targetExtDir, INSTALL_METADATA_FILENAME);
+
+    // Create the "installed" extension directory and files
+    fs.mkdirSync(targetExtDir, { recursive: true });
+    fs.writeFileSync(
+      path.join(targetExtDir, EXTENSIONS_CONFIG_FILENAME),
+      JSON.stringify({ name: extensionName, version: '1.0.0' }),
+    );
+    fs.writeFileSync(
+      metadataPath,
+      JSON.stringify({ source: gitUrl, type: 'git' }),
+    );
+
+    // 2. Mock the git clone for the update
+    const clone = vi.fn().mockImplementation(async (_, destination) => {
+      fs.mkdirSync(destination, { recursive: true });
+      // This is the "updated" version
+      fs.writeFileSync(
+        path.join(destination, EXTENSIONS_CONFIG_FILENAME),
+        JSON.stringify({ name: extensionName, version: '1.1.0' }),
+      );
+    });
+
+    const mockedSimpleGit = simpleGit as vi.MockedFunction<typeof simpleGit>;
+    mockedSimpleGit.mockReturnValue({
+      clone,
+    } as unknown as SimpleGit);
+
+    // 3. Call updateExtension
+    const updateInfo = await updateExtension(extensionName);
+
+    // 4. Assertions
+    expect(updateInfo).toEqual({
+      originalVersion: '1.0.0',
+      updatedVersion: '1.1.0',
+    });
+
+    // Check that the config file reflects the new version
+    const updatedConfig = JSON.parse(
+      fs.readFileSync(
+        path.join(targetExtDir, EXTENSIONS_CONFIG_FILENAME),
+        'utf-8',
+      ),
+    );
+    expect(updatedConfig.version).toBe('1.1.0');
+  });
+});
+
+describe('disableExtension', () => {
+  let tempWorkspaceDir: string;
+  let tempHomeDir: string;
+
+  beforeEach(() => {
+    tempWorkspaceDir = fs.mkdtempSync(
+      path.join(os.tmpdir(), 'qwen-code-test-workspace-'),
+    );
+    tempHomeDir = fs.mkdtempSync(
+      path.join(os.tmpdir(), 'qwen-code-test-home-'),
+    );
+    vi.mocked(os.homedir).mockReturnValue(tempHomeDir);
+    vi.spyOn(process, 'cwd').mockReturnValue(tempWorkspaceDir);
+  });
+
+  afterEach(() => {
+    fs.rmSync(tempWorkspaceDir, { recursive: true, force: true });
+    fs.rmSync(tempHomeDir, { recursive: true, force: true });
+  });
+
+  it('should disable an extension at the user scope', () => {
+    disableExtension('my-extension', SettingScope.User);
+    const settings = loadSettings(tempWorkspaceDir);
+    expect(
+      settings.forScope(SettingScope.User).settings.extensions?.disabled,
+    ).toEqual(['my-extension']);
+  });
+
+  it('should disable an extension at the workspace scope', () => {
+    disableExtension('my-extension', SettingScope.Workspace);
+    const settings = loadSettings(tempWorkspaceDir);
+    expect(
+      settings.forScope(SettingScope.Workspace).settings.extensions?.disabled,
+    ).toEqual(['my-extension']);
+  });
+
+  it('should handle disabling the same extension twice', () => {
+    disableExtension('my-extension', SettingScope.User);
+    disableExtension('my-extension', SettingScope.User);
+    const settings = loadSettings(tempWorkspaceDir);
+    expect(
+      settings.forScope(SettingScope.User).settings.extensions?.disabled,
+    ).toEqual(['my-extension']);
+  });
+
+  it('should throw an error if you request system scope', () => {
+    expect(() => disableExtension('my-extension', SettingScope.System)).toThrow(
+      'System and SystemDefaults scopes are not supported.',
+    );
+  });
+});
+
+describe('enableExtension', () => {
+  let tempWorkspaceDir: string;
+  let tempHomeDir: string;
+  let userExtensionsDir: string;
+
+  beforeEach(() => {
+    tempWorkspaceDir = fs.mkdtempSync(
+      path.join(os.tmpdir(), 'qwen-code-test-workspace-'),
+    );
+    tempHomeDir = fs.mkdtempSync(
+      path.join(os.tmpdir(), 'qwen-code-test-home-'),
+    );
+    userExtensionsDir = path.join(tempHomeDir, '.qwen', 'extensions');
+    vi.mocked(os.homedir).mockReturnValue(tempHomeDir);
+    vi.spyOn(process, 'cwd').mockReturnValue(tempWorkspaceDir);
+  });
+
+  afterEach(() => {
+    fs.rmSync(tempWorkspaceDir, { recursive: true, force: true });
+    fs.rmSync(tempHomeDir, { recursive: true, force: true });
+    fs.rmSync(userExtensionsDir, { recursive: true, force: true });
+  });
+
+  afterAll(() => {
+    vi.restoreAllMocks();
+  });
+
+  const getActiveExtensions = (): GeminiCLIExtension[] => {
+    const extensions = loadExtensions(tempWorkspaceDir);
+    const activeExtensions = annotateActiveExtensions(
+      extensions,
+      [],
+      tempWorkspaceDir,
+    );
+    return activeExtensions.filter((e) => e.isActive);
+  };
+
+  it('should enable an extension at the user scope', () => {
+    createExtension(userExtensionsDir, 'ext1', '1.0.0');
+    disableExtension('ext1', SettingScope.User);
+    let activeExtensions = getActiveExtensions();
+    expect(activeExtensions).toHaveLength(0);
+
+    enableExtension('ext1', [SettingScope.User]);
+    activeExtensions = getActiveExtensions();
+    expect(activeExtensions).toHaveLength(1);
+    expect(activeExtensions[0].name).toBe('ext1');
+  });
+
+  it('should enable an extension at the workspace scope', () => {
+    createExtension(userExtensionsDir, 'ext1', '1.0.0');
+    disableExtension('ext1', SettingScope.Workspace);
+    let activeExtensions = getActiveExtensions();
+    expect(activeExtensions).toHaveLength(0);
+
+    enableExtension('ext1', [SettingScope.Workspace]);
+    activeExtensions = getActiveExtensions();
+    expect(activeExtensions).toHaveLength(1);
+    expect(activeExtensions[0].name).toBe('ext1');
+  });
+});

packages/cli/src/config/extension.ts

@@ -4,19 +4,29 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { MCPServerConfig, GeminiCLIExtension } from '@qwen-code/qwen-code-core';
-import * as fs from 'fs';
-import * as path from 'path';
-import * as os from 'os';
+import type {
+  MCPServerConfig,
+  GeminiCLIExtension,
+} from '@qwen-code/qwen-code-core';
+import { Storage } from '@qwen-code/qwen-code-core';
+import * as fs from 'node:fs';
+import * as path from 'node:path';
+import * as os from 'node:os';
+import { simpleGit } from 'simple-git';
+import { SettingScope, loadSettings } from '../config/settings.js';
+import { getErrorMessage } from '../utils/errors.js';
+import { recursivelyHydrateStrings } from './extensions/variables.js';
 
 export const EXTENSIONS_DIRECTORY_NAME = path.join('.qwen', 'extensions');
 export const EXTENSIONS_CONFIG_FILENAME = 'qwen-extension.json';
 export const EXTENSIONS_CONFIG_FILENAME_OLD = 'gemini-extension.json';
+export const INSTALL_METADATA_FILENAME = '.qwen-extension-install.json';
 
 export interface Extension {
   path: string;
   config: ExtensionConfig;
   contextFiles: string[];
+  installMetadata?: ExtensionInstallMetadata | undefined;
 }
 
 export interface ExtensionConfig {
@@ -27,14 +37,103 @@ export interface ExtensionConfig {
   excludeTools?: string[];
 }
 
+export interface ExtensionInstallMetadata {
+  source: string;
+  type: 'git' | 'local';
+}
+
+export interface ExtensionUpdateInfo {
+  originalVersion: string;
+  updatedVersion: string;
+}
+
+export class ExtensionStorage {
+  private readonly extensionName: string;
+
+  constructor(extensionName: string) {
+    this.extensionName = extensionName;
+  }
+
+  getExtensionDir(): string {
+    return path.join(
+      ExtensionStorage.getUserExtensionsDir(),
+      this.extensionName,
+    );
+  }
+
+  getConfigPath(): string {
+    return path.join(this.getExtensionDir(), EXTENSIONS_CONFIG_FILENAME);
+  }
+
+  static getUserExtensionsDir(): string {
+    const storage = new Storage(os.homedir());
+    return storage.getExtensionsDir();
+  }
+
+  static async createTmpDir(): Promise<string> {
+    return await fs.promises.mkdtemp(
+      path.join(os.tmpdir(), 'gemini-extension'),
+    );
+  }
+}
+
+export function getWorkspaceExtensions(workspaceDir: string): Extension[] {
+  return loadExtensionsFromDir(workspaceDir);
+}
+
+async function copyExtension(
+  source: string,
+  destination: string,
+): Promise<void> {
+  await fs.promises.cp(source, destination, { recursive: true });
+}
+
+export async function performWorkspaceExtensionMigration(
+  extensions: Extension[],
+): Promise<string[]> {
+  const failedInstallNames: string[] = [];
+
+  for (const extension of extensions) {
+    try {
+      const installMetadata: ExtensionInstallMetadata = {
+        source: extension.path,
+        type: 'local',
+      };
+      await installExtension(installMetadata);
+    } catch (_) {
+      failedInstallNames.push(extension.config.name);
+    }
+  }
+  return failedInstallNames;
+}
+
 export function loadExtensions(workspaceDir: string): Extension[] {
-  const allExtensions = [
-    ...loadExtensionsFromDir(workspaceDir),
-    ...loadExtensionsFromDir(os.homedir()),
-  ];
+  const settings = loadSettings(workspaceDir).merged;
+  const disabledExtensions = settings.extensions?.disabled ?? [];
+  const allExtensions = [...loadUserExtensions()];
+
+  if (!settings.experimental?.extensionManagement) {
+    allExtensions.push(...getWorkspaceExtensions(workspaceDir));
+  }
 
   const uniqueExtensions = new Map<string, Extension>();
   for (const extension of allExtensions) {
+    if (
+      !uniqueExtensions.has(extension.config.name) &&
+      !disabledExtensions.includes(extension.config.name)
+    ) {
+      uniqueExtensions.set(extension.config.name, extension);
+    }
+  }
+
+  return Array.from(uniqueExtensions.values());
+}
+
+export function loadUserExtensions(): Extension[] {
+  const userExtensions = loadExtensionsFromDir(os.homedir());
+
+  const uniqueExtensions = new Map<string, Extension>();
+  for (const extension of userExtensions) {
     if (!uniqueExtensions.has(extension.config.name)) {
       uniqueExtensions.set(extension.config.name, extension);
     }
@@ -43,8 +142,9 @@ export function loadExtensions(workspaceDir: string): Extension[] {
   return Array.from(uniqueExtensions.values());
 }
 
-function loadExtensionsFromDir(dir: string): Extension[] {
-  const extensionsDir = path.join(dir, EXTENSIONS_DIRECTORY_NAME);
+export function loadExtensionsFromDir(dir: string): Extension[] {
+  const storage = new Storage(dir);
+  const extensionsDir = storage.getExtensionsDir();
   if (!fs.existsSync(extensionsDir)) {
     return [];
   }
@@ -61,7 +161,7 @@ function loadExtensionsFromDir(dir: string): Extension[] {
   return extensions;
 }
 
-function loadExtension(extensionDir: string): Extension | null {
+export function loadExtension(extensionDir: string): Extension | null {
   if (!fs.statSync(extensionDir).isDirectory()) {
     console.error(
       `Warning: unexpected file ${extensionDir} in extensions directory.`,
@@ -86,7 +186,11 @@ function loadExtension(extensionDir: string): Extension | null {
 
   try {
     const configContent = fs.readFileSync(configFilePath, 'utf-8');
-    const config = JSON.parse(configContent) as ExtensionConfig;
+    const config = recursivelyHydrateStrings(JSON.parse(configContent), {
+      extensionPath: extensionDir,
+      '/': path.sep,
+      pathSeparator: path.sep,
+    }) as unknown as ExtensionConfig;
     if (!config.name || !config.version) {
       console.error(
         `Invalid extension config in ${configFilePath}: missing name or version.`,
@@ -102,15 +206,31 @@ function loadExtension(extensionDir: string): Extension | null {
       path: extensionDir,
       config,
       contextFiles,
+      installMetadata: loadInstallMetadata(extensionDir),
     };
   } catch (e) {
     console.error(
-      `Warning: error parsing extension config in ${configFilePath}: ${e}`,
+      `Warning: error parsing extension config in ${configFilePath}: ${getErrorMessage(
+        e,
+      )}`,
     );
     return null;
   }
 }
 
+function loadInstallMetadata(
+  extensionDir: string,
+): ExtensionInstallMetadata | undefined {
+  const metadataFilePath = path.join(extensionDir, INSTALL_METADATA_FILENAME);
+  try {
+    const configContent = fs.readFileSync(metadataFilePath, 'utf-8');
+    const metadata = JSON.parse(configContent) as ExtensionInstallMetadata;
+    return metadata;
+  } catch (_e) {
+    return undefined;
+  }
+}
+
 function getContextFileNames(config: ExtensionConfig): string[] {
   if (!config.contextFileName) {
     return ['QWEN.md'];
@@ -120,17 +240,28 @@ 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 in list of disabled extensions in settings.
+ * @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: Extension[],
   enabledExtensionNames: string[],
+  workspaceDir: string,
 ): GeminiCLIExtension[] {
+  const settings = loadSettings(workspaceDir).merged;
+  const disabledExtensions = settings.extensions?.disabled ?? [];
+
   const annotatedExtensions: GeminiCLIExtension[] = [];
 
   if (enabledExtensionNames.length === 0) {
     return extensions.map((extension) => ({
       name: extension.config.name,
       version: extension.config.version,
-      isActive: true,
+      isActive: !disabledExtensions.includes(extension.config.name),
       path: extension.path,
     }));
   }
@@ -175,3 +306,230 @@ export function annotateActiveExtensions(
 
   return annotatedExtensions;
 }
+
+/**
+ * Clones a Git repository to a specified local path.
+ * @param gitUrl The Git URL to clone.
+ * @param destination The destination path to clone the repository to.
+ */
+async function cloneFromGit(
+  gitUrl: string,
+  destination: string,
+): Promise<void> {
+  try {
+    // TODO(chrstnb): Download the archive instead to avoid unnecessary .git info.
+    await simpleGit().clone(gitUrl, destination, ['--depth', '1']);
+  } catch (error) {
+    throw new Error(`Failed to clone Git repository from ${gitUrl}`, {
+      cause: error,
+    });
+  }
+}
+
+export async function installExtension(
+  installMetadata: ExtensionInstallMetadata,
+  cwd: string = process.cwd(),
+): Promise<string> {
+  const extensionsDir = ExtensionStorage.getUserExtensionsDir();
+  await fs.promises.mkdir(extensionsDir, { recursive: true });
+
+  // Convert relative paths to absolute paths for the metadata file.
+  if (
+    installMetadata.type === 'local' &&
+    !path.isAbsolute(installMetadata.source)
+  ) {
+    installMetadata.source = path.resolve(cwd, installMetadata.source);
+  }
+
+  let localSourcePath: string;
+  let tempDir: string | undefined;
+  if (installMetadata.type === 'git') {
+    tempDir = await ExtensionStorage.createTmpDir();
+    await cloneFromGit(installMetadata.source, tempDir);
+    localSourcePath = tempDir;
+  } else {
+    localSourcePath = installMetadata.source;
+  }
+  let newExtensionName: string | undefined;
+  try {
+    const newExtension = loadExtension(localSourcePath);
+    if (!newExtension) {
+      throw new Error(
+        `Invalid extension at ${installMetadata.source}. Please make sure it has a valid gemini-extension.json file.`,
+      );
+    }
+
+    // ~/.gemini/extensions/{ExtensionConfig.name}.
+    newExtensionName = newExtension.config.name;
+    const extensionStorage = new ExtensionStorage(newExtensionName);
+    const destinationPath = extensionStorage.getExtensionDir();
+
+    const installedExtensions = loadUserExtensions();
+    if (
+      installedExtensions.some(
+        (installed) => installed.config.name === newExtensionName,
+      )
+    ) {
+      throw new Error(
+        `Extension "${newExtensionName}" is already installed. Please uninstall it first.`,
+      );
+    }
+
+    await copyExtension(localSourcePath, destinationPath);
+
+    const metadataString = JSON.stringify(installMetadata, null, 2);
+    const metadataPath = path.join(destinationPath, INSTALL_METADATA_FILENAME);
+    await fs.promises.writeFile(metadataPath, metadataString);
+  } finally {
+    if (tempDir) {
+      await fs.promises.rm(tempDir, { recursive: true, force: true });
+    }
+  }
+
+  return newExtensionName;
+}
+
+export async function uninstallExtension(
+  extensionName: string,
+  cwd: string = process.cwd(),
+): Promise<void> {
+  const installedExtensions = loadUserExtensions();
+  if (
+    !installedExtensions.some(
+      (installed) => installed.config.name === extensionName,
+    )
+  ) {
+    throw new Error(`Extension "${extensionName}" not found.`);
+  }
+  removeFromDisabledExtensions(
+    extensionName,
+    [SettingScope.User, SettingScope.Workspace],
+    cwd,
+  );
+  const storage = new ExtensionStorage(extensionName);
+  return await fs.promises.rm(storage.getExtensionDir(), {
+    recursive: true,
+    force: true,
+  });
+}
+
+export function toOutputString(extension: Extension): string {
+  let output = `${extension.config.name} (${extension.config.version})`;
+  output += `\n Path: ${extension.path}`;
+  if (extension.installMetadata) {
+    output += `\n Source: ${extension.installMetadata.source}`;
+  }
+  if (extension.contextFiles.length > 0) {
+    output += `\n Context files:`;
+    extension.contextFiles.forEach((contextFile) => {
+      output += `\n  ${contextFile}`;
+    });
+  }
+  if (extension.config.mcpServers) {
+    output += `\n MCP servers:`;
+    Object.keys(extension.config.mcpServers).forEach((key) => {
+      output += `\n  ${key}`;
+    });
+  }
+  if (extension.config.excludeTools) {
+    output += `\n Excluded tools:`;
+    extension.config.excludeTools.forEach((tool) => {
+      output += `\n  ${tool}`;
+    });
+  }
+  return output;
+}
+
+export async function updateExtension(
+  extensionName: string,
+  cwd: string = process.cwd(),
+): Promise<ExtensionUpdateInfo | undefined> {
+  const installedExtensions = loadUserExtensions();
+  const extension = installedExtensions.find(
+    (installed) => installed.config.name === extensionName,
+  );
+  if (!extension) {
+    throw new Error(
+      `Extension "${extensionName}" not found. Run gemini extensions list to see available extensions.`,
+    );
+  }
+  if (!extension.installMetadata) {
+    throw new Error(
+      `Extension cannot be updated because it is missing the .gemini-extension.install.json file. To update manually, uninstall and then reinstall the updated version.`,
+    );
+  }
+  const originalVersion = extension.config.version;
+  const tempDir = await ExtensionStorage.createTmpDir();
+  try {
+    await copyExtension(extension.path, tempDir);
+    await uninstallExtension(extensionName, cwd);
+    await installExtension(extension.installMetadata, cwd);
+
+    const updatedExtension = loadExtension(extension.path);
+    if (!updatedExtension) {
+      throw new Error('Updated extension not found after installation.');
+    }
+    const updatedVersion = updatedExtension.config.version;
+    return {
+      originalVersion,
+      updatedVersion,
+    };
+  } catch (e) {
+    console.error(
+      `Error updating extension, rolling back. ${getErrorMessage(e)}`,
+    );
+    await copyExtension(tempDir, extension.path);
+    throw e;
+  } finally {
+    await fs.promises.rm(tempDir, { recursive: true, force: true });
+  }
+}
+
+export function disableExtension(
+  name: string,
+  scope: SettingScope,
+  cwd: string = process.cwd(),
+) {
+  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);
+  }
+}
+
+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(
+  name: string,
+  scopes: 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);
+  }
+}

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

@@ -0,0 +1,30 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+export interface VariableDefinition {
+  type: 'string';
+  description: string;
+  default?: string;
+  required?: boolean;
+}
+
+export interface VariableSchema {
+  [key: string]: VariableDefinition;
+}
+
+const PATH_SEPARATOR_DEFINITION = {
+  type: 'string',
+  description: 'The path separator.',
+} as const;
+
+export const VARIABLE_SCHEMA = {
+  extensionPath: {
+    type: 'string',
+    description: 'The path of the extension in the filesystem.',
+  },
+  '/': PATH_SEPARATOR_DEFINITION,
+  pathSeparator: PATH_SEPARATOR_DEFINITION,
+} as const;

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

@@ -0,0 +1,18 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { expect, describe, it } from 'vitest';
+import { hydrateString } from './variables.js';
+
+describe('hydrateString', () => {
+  it('should replace a single variable', () => {
+    const context = {
+      extensionPath: 'path/my-extension',
+    };
+    const result = hydrateString('Hello, ${extensionPath}!', context);
+    expect(result).toBe('Hello, path/my-extension!');
+  });
+});

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

@@ -0,0 +1,65 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { type VariableSchema, VARIABLE_SCHEMA } from './variableSchema.js';
+
+export type JsonObject = { [key: string]: JsonValue };
+export type JsonArray = JsonValue[];
+export type JsonValue =
+  | string
+  | number
+  | boolean
+  | null
+  | JsonObject
+  | JsonArray;
+
+export type VariableContext = {
+  [key in keyof typeof VARIABLE_SCHEMA]?: string;
+};
+
+export function validateVariables(
+  variables: VariableContext,
+  schema: VariableSchema,
+) {
+  for (const key in schema) {
+    const definition = schema[key];
+    if (definition.required && !variables[key as keyof VariableContext]) {
+      throw new Error(`Missing required variable: ${key}`);
+    }
+  }
+}
+
+export function hydrateString(str: string, context: VariableContext): string {
+  validateVariables(context, VARIABLE_SCHEMA);
+  const regex = /\${(.*?)}/g;
+  return str.replace(regex, (match, key) =>
+    context[key as keyof VariableContext] == null
+      ? match
+      : (context[key as keyof VariableContext] as string),
+  );
+}
+
+export function recursivelyHydrateStrings(
+  obj: JsonValue,
+  values: VariableContext,
+): JsonValue {
+  if (typeof obj === 'string') {
+    return hydrateString(obj, values);
+  }
+  if (Array.isArray(obj)) {
+    return obj.map((item) => recursivelyHydrateStrings(item, values));
+  }
+  if (typeof obj === 'object' && obj !== null) {
+    const newObj: JsonObject = {};
+    for (const key in obj) {
+      if (Object.prototype.hasOwnProperty.call(obj, key)) {
+        newObj[key] = recursivelyHydrateStrings(obj[key], values);
+      }
+    }
+    return newObj;
+  }
+  return obj;
+}

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

@@ -5,11 +5,8 @@
  */
 
 import { describe, it, expect } from 'vitest';
-import {
-  Command,
-  KeyBindingConfig,
-  defaultKeyBindings,
-} from './keyBindings.js';
+import type { KeyBindingConfig } from './keyBindings.js';
+import { Command, defaultKeyBindings } from './keyBindings.js';
 
 describe('keyBindings config', () => {
   describe('defaultKeyBindings', () => {

packages/cli/src/config/sandboxConfig.ts

@@ -4,11 +4,12 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { SandboxConfig } from '@qwen-code/qwen-code-core';
+import type { SandboxConfig } from '@qwen-code/qwen-code-core';
+import { FatalSandboxError } from '@qwen-code/qwen-code-core';
 import commandExists from 'command-exists';
 import * as os from 'node:os';
 import { getPackageJson } from '../utils/package.js';
-import { Settings } from './settings.js';
+import type { Settings } from './settings.js';
 
 // This is a stripped-down version of the CliArgs interface from config.ts
 // to avoid circular dependencies.
@@ -51,21 +52,19 @@ function getSandboxCommand(
 
   if (typeof sandbox === 'string' && sandbox) {
     if (!isSandboxCommand(sandbox)) {
-      console.error(
-        `ERROR: invalid sandbox command '${sandbox}'. Must be one of ${VALID_SANDBOX_COMMANDS.join(
+      throw new FatalSandboxError(
+        `Invalid sandbox command '${sandbox}'. Must be one of ${VALID_SANDBOX_COMMANDS.join(
           ', ',
         )}`,
       );
-      process.exit(1);
     }
     // confirm that specified command exists
     if (commandExists.sync(sandbox)) {
       return sandbox;
     }
-    console.error(
-      `ERROR: missing sandbox command '${sandbox}' (from GEMINI_SANDBOX)`,
+    throw new FatalSandboxError(
+      `Missing sandbox command '${sandbox}' (from GEMINI_SANDBOX)`,
     );
-    process.exit(1);
   }
 
   // look for seatbelt, docker, or podman, in that order
@@ -80,11 +79,10 @@ function getSandboxCommand(
 
   // throw an error if user requested sandbox but no command was found
   if (sandbox === true) {
-    console.error(
-      'ERROR: GEMINI_SANDBOX is true but failed to determine command for sandbox; ' +
+    throw new FatalSandboxError(
+      'GEMINI_SANDBOX is true but failed to determine command for sandbox; ' +
         'install docker or podman or specify command in GEMINI_SANDBOX',
     );
-    process.exit(1);
   }
 
   return '';
@@ -94,7 +92,7 @@ export async function loadSandboxConfig(
   settings: Settings,
   argv: SandboxCliArgs,
 ): Promise<SandboxConfig | undefined> {
-  const sandboxOption = argv.sandbox ?? settings.sandbox;
+  const sandboxOption = argv.sandbox ?? settings.tools?.sandbox;
   const command = getSandboxCommand(sandboxOption);
 
   const packageJson = await getPackageJson();

packages/cli/src/config/settings.ts

@@ -4,29 +4,84 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import * as fs from 'fs';
-import * as path from 'path';
-import { homedir, platform } from 'os';
+import * as fs from 'node:fs';
+import * as path from 'node:path';
+import { homedir, platform } from 'node:os';
 import * as dotenv from 'dotenv';
 import {
   GEMINI_CONFIG_DIR as GEMINI_DIR,
   getErrorMessage,
+  Storage,
 } from '@qwen-code/qwen-code-core';
 import stripJsonComments from 'strip-json-comments';
 import { DefaultLight } from '../ui/themes/default-light.js';
 import { DefaultDark } from '../ui/themes/default.js';
-import { Settings, MemoryImportFormat } from './settingsSchema.js';
+import { isWorkspaceTrusted } from './trustedFolders.js';
+import type { Settings, MemoryImportFormat } from './settingsSchema.js';
+import { mergeWith } from 'lodash-es';
 
 export type { Settings, MemoryImportFormat };
 
 export const SETTINGS_DIRECTORY_NAME = '.qwen';
-export const USER_SETTINGS_DIR = path.join(homedir(), SETTINGS_DIRECTORY_NAME);
-export const USER_SETTINGS_PATH = path.join(USER_SETTINGS_DIR, 'settings.json');
+export const USER_SETTINGS_PATH = Storage.getGlobalSettingsPath();
+export const USER_SETTINGS_DIR = path.dirname(USER_SETTINGS_PATH);
 export const DEFAULT_EXCLUDED_ENV_VARS = ['DEBUG', 'DEBUG_MODE'];
 
+const MIGRATE_V2_OVERWRITE = false;
+
+const MIGRATION_MAP: Record<string, string> = {
+  preferredEditor: 'general.preferredEditor',
+  vimMode: 'general.vimMode',
+  disableAutoUpdate: 'general.disableAutoUpdate',
+  disableUpdateNag: 'general.disableUpdateNag',
+  checkpointing: 'general.checkpointing',
+  theme: 'ui.theme',
+  customThemes: 'ui.customThemes',
+  hideWindowTitle: 'ui.hideWindowTitle',
+  hideTips: 'ui.hideTips',
+  hideBanner: 'ui.hideBanner',
+  hideFooter: 'ui.hideFooter',
+  showMemoryUsage: 'ui.showMemoryUsage',
+  showLineNumbers: 'ui.showLineNumbers',
+  accessibility: 'ui.accessibility',
+  ideMode: 'ide.enabled',
+  hasSeenIdeIntegrationNudge: 'ide.hasSeenNudge',
+  usageStatisticsEnabled: 'privacy.usageStatisticsEnabled',
+  telemetry: 'telemetry',
+  model: 'model.name',
+  maxSessionTurns: 'model.maxSessionTurns',
+  summarizeToolOutput: 'model.summarizeToolOutput',
+  chatCompression: 'model.chatCompression',
+  skipNextSpeakerCheck: 'model.skipNextSpeakerCheck',
+  contextFileName: 'context.fileName',
+  memoryImportFormat: 'context.importFormat',
+  memoryDiscoveryMaxDirs: 'context.discoveryMaxDirs',
+  includeDirectories: 'context.includeDirectories',
+  loadMemoryFromIncludeDirectories: 'context.loadFromIncludeDirectories',
+  fileFiltering: 'context.fileFiltering',
+  sandbox: 'tools.sandbox',
+  shouldUseNodePtyShell: 'tools.usePty',
+  allowedTools: 'tools.allowed',
+  coreTools: 'tools.core',
+  excludeTools: 'tools.exclude',
+  toolDiscoveryCommand: 'tools.discoveryCommand',
+  toolCallCommand: 'tools.callCommand',
+  mcpServerCommand: 'mcp.serverCommand',
+  allowMCPServers: 'mcp.allowed',
+  excludeMCPServers: 'mcp.excluded',
+  folderTrustFeature: 'security.folderTrust.featureEnabled',
+  folderTrust: 'security.folderTrust.enabled',
+  selectedAuthType: 'security.auth.selectedType',
+  useExternalAuth: 'security.auth.useExternal',
+  autoConfigureMaxOldSpaceSize: 'advanced.autoConfigureMemory',
+  dnsResolutionOrder: 'advanced.dnsResolutionOrder',
+  excludedProjectEnvVars: 'advanced.excludedEnvVars',
+  bugCommand: 'advanced.bugCommand',
+};
+
 export function getSystemSettingsPath(): string {
-  if (process.env['GEMINI_CLI_SYSTEM_SETTINGS_PATH']) {
-    return process.env['GEMINI_CLI_SYSTEM_SETTINGS_PATH'];
+  if (process.env['QWEN_CODE_SYSTEM_SETTINGS_PATH']) {
+    return process.env['QWEN_CODE_SYSTEM_SETTINGS_PATH'];
   }
   if (platform() === 'darwin') {
     return '/Library/Application Support/QwenCode/settings.json';
@@ -37,8 +92,14 @@ export function getSystemSettingsPath(): string {
   }
 }
 
-export function getWorkspaceSettingsPath(workspaceDir: string): string {
-  return path.join(workspaceDir, SETTINGS_DIRECTORY_NAME, 'settings.json');
+export function getSystemDefaultsPath(): string {
+  if (process.env['QWEN_CODE_SYSTEM_DEFAULTS_PATH']) {
+    return process.env['QWEN_CODE_SYSTEM_DEFAULTS_PATH'];
+  }
+  return path.join(
+    path.dirname(getSystemSettingsPath()),
+    'system-defaults.json',
+  );
 }
 
 export type { DnsResolutionOrder } from './settingsSchema.js';
@@ -47,6 +108,7 @@ export enum SettingScope {
   User = 'User',
   Workspace = 'Workspace',
   System = 'System',
+  SystemDefaults = 'SystemDefaults',
 }
 
 export interface CheckpointingSettings {
@@ -59,6 +121,7 @@ export interface SummarizeToolOutputSettings {
 
 export interface AccessibilitySettings {
   disableLoadingPhrases?: boolean;
+  screenReader?: boolean;
 }
 
 export interface SettingsError {
@@ -71,38 +134,290 @@ export interface SettingsFile {
   path: string;
 }
 
+function setNestedProperty(
+  obj: Record<string, unknown>,
+  path: string,
+  value: unknown,
+) {
+  const keys = path.split('.');
+  const lastKey = keys.pop();
+  if (!lastKey) return;
+
+  let current: Record<string, unknown> = obj;
+  for (const key of keys) {
+    if (current[key] === undefined) {
+      current[key] = {};
+    }
+    const next = current[key];
+    if (typeof next === 'object' && next !== null) {
+      current = next as Record<string, unknown>;
+    } else {
+      // This path is invalid, so we stop.
+      return;
+    }
+  }
+  current[lastKey] = value;
+}
+
+function needsMigration(settings: Record<string, unknown>): boolean {
+  return !('general' in settings);
+}
+
+function migrateSettingsToV2(
+  flatSettings: Record<string, unknown>,
+): Record<string, unknown> | null {
+  if (!needsMigration(flatSettings)) {
+    return null;
+  }
+
+  const v2Settings: Record<string, unknown> = {};
+  const flatKeys = new Set(Object.keys(flatSettings));
+
+  for (const [oldKey, newPath] of Object.entries(MIGRATION_MAP)) {
+    if (flatKeys.has(oldKey)) {
+      setNestedProperty(v2Settings, newPath, flatSettings[oldKey]);
+      flatKeys.delete(oldKey);
+    }
+  }
+
+  // Preserve mcpServers at the top level
+  if (flatSettings['mcpServers']) {
+    v2Settings['mcpServers'] = flatSettings['mcpServers'];
+    flatKeys.delete('mcpServers');
+  }
+
+  // Carry over any unrecognized keys
+  for (const remainingKey of flatKeys) {
+    v2Settings[remainingKey] = flatSettings[remainingKey];
+  }
+
+  return v2Settings;
+}
+
+function getNestedProperty(
+  obj: Record<string, unknown>,
+  path: string,
+): unknown {
+  const keys = path.split('.');
+  let current: unknown = obj;
+  for (const key of keys) {
+    if (typeof current !== 'object' || current === null || !(key in current)) {
+      return undefined;
+    }
+    current = (current as Record<string, unknown>)[key];
+  }
+  return current;
+}
+
+const REVERSE_MIGRATION_MAP: Record<string, string> = Object.fromEntries(
+  Object.entries(MIGRATION_MAP).map(([key, value]) => [value, key]),
+);
+
+// Dynamically determine the top-level keys from the V2 settings structure.
+const KNOWN_V2_CONTAINERS = new Set(
+  Object.values(MIGRATION_MAP).map((path) => path.split('.')[0]),
+);
+
+export function migrateSettingsToV1(
+  v2Settings: Record<string, unknown>,
+): Record<string, unknown> {
+  const v1Settings: Record<string, unknown> = {};
+  const v2Keys = new Set(Object.keys(v2Settings));
+
+  for (const [newPath, oldKey] of Object.entries(REVERSE_MIGRATION_MAP)) {
+    const value = getNestedProperty(v2Settings, newPath);
+    if (value !== undefined) {
+      v1Settings[oldKey] = value;
+      v2Keys.delete(newPath.split('.')[0]);
+    }
+  }
+
+  // Preserve mcpServers at the top level
+  if (v2Settings['mcpServers']) {
+    v1Settings['mcpServers'] = v2Settings['mcpServers'];
+    v2Keys.delete('mcpServers');
+  }
+
+  // Carry over any unrecognized keys
+  for (const remainingKey of v2Keys) {
+    const value = v2Settings[remainingKey];
+    if (value === undefined) {
+      continue;
+    }
+
+    // Don't carry over empty objects that were just containers for migrated settings.
+    if (
+      KNOWN_V2_CONTAINERS.has(remainingKey) &&
+      typeof value === 'object' &&
+      value !== null &&
+      !Array.isArray(value) &&
+      Object.keys(value).length === 0
+    ) {
+      continue;
+    }
+
+    v1Settings[remainingKey] = value;
+  }
+
+  return v1Settings;
+}
+
 function mergeSettings(
   system: Settings,
+  systemDefaults: Settings,
   user: Settings,
   workspace: Settings,
+  isTrusted: boolean,
 ): Settings {
-  // folderTrust is not supported at workspace level.
-  // eslint-disable-next-line @typescript-eslint/no-unused-vars
-  const { folderTrust, ...workspaceWithoutFolderTrust } = workspace;
+  const safeWorkspace = isTrusted ? workspace : ({} as Settings);
 
+  // folderTrust is not supported at workspace level.
+  const { security, ...restOfWorkspace } = safeWorkspace;
+  const safeWorkspaceWithoutFolderTrust = security
+    ? {
+        ...restOfWorkspace,
+        // eslint-disable-next-line @typescript-eslint/no-unused-vars
+        security: (({ folderTrust, ...rest }) => rest)(security),
+      }
+    : {
+        ...restOfWorkspace,
+        security: {},
+      };
+
+  // Settings are merged with the following precedence (last one wins for
+  // single values):
+  // 1. System Defaults
+  // 2. User Settings
+  // 3. Workspace Settings
+  // 4. System Settings (as overrides)
+  //
+  // For properties that are arrays (e.g., includeDirectories), the arrays
+  // are concatenated. For objects (e.g., customThemes), they are merged.
   return {
+    ...systemDefaults,
     ...user,
-    ...workspaceWithoutFolderTrust,
+    ...safeWorkspaceWithoutFolderTrust,
     ...system,
-    customThemes: {
-      ...(user.customThemes || {}),
-      ...(workspace.customThemes || {}),
-      ...(system.customThemes || {}),
+    general: {
+      ...(systemDefaults.general || {}),
+      ...(user.general || {}),
+      ...(safeWorkspaceWithoutFolderTrust.general || {}),
+      ...(system.general || {}),
+    },
+    ui: {
+      ...(systemDefaults.ui || {}),
+      ...(user.ui || {}),
+      ...(safeWorkspaceWithoutFolderTrust.ui || {}),
+      ...(system.ui || {}),
+      customThemes: {
+        ...(systemDefaults.ui?.customThemes || {}),
+        ...(user.ui?.customThemes || {}),
+        ...(safeWorkspaceWithoutFolderTrust.ui?.customThemes || {}),
+        ...(system.ui?.customThemes || {}),
+      },
+    },
+    ide: {
+      ...(systemDefaults.ide || {}),
+      ...(user.ide || {}),
+      ...(safeWorkspaceWithoutFolderTrust.ide || {}),
+      ...(system.ide || {}),
+    },
+    privacy: {
+      ...(systemDefaults.privacy || {}),
+      ...(user.privacy || {}),
+      ...(safeWorkspaceWithoutFolderTrust.privacy || {}),
+      ...(system.privacy || {}),
+    },
+    telemetry: {
+      ...(systemDefaults.telemetry || {}),
+      ...(user.telemetry || {}),
+      ...(safeWorkspaceWithoutFolderTrust.telemetry || {}),
+      ...(system.telemetry || {}),
+    },
+    security: {
+      ...(systemDefaults.security || {}),
+      ...(user.security || {}),
+      ...(safeWorkspaceWithoutFolderTrust.security || {}),
+      ...(system.security || {}),
+    },
+    mcp: {
+      ...(systemDefaults.mcp || {}),
+      ...(user.mcp || {}),
+      ...(safeWorkspaceWithoutFolderTrust.mcp || {}),
+      ...(system.mcp || {}),
     },
     mcpServers: {
+      ...(systemDefaults.mcpServers || {}),
       ...(user.mcpServers || {}),
-      ...(workspace.mcpServers || {}),
+      ...(safeWorkspaceWithoutFolderTrust.mcpServers || {}),
       ...(system.mcpServers || {}),
     },
-    includeDirectories: [
-      ...(system.includeDirectories || []),
-      ...(user.includeDirectories || []),
-      ...(workspace.includeDirectories || []),
-    ],
-    chatCompression: {
-      ...(system.chatCompression || {}),
-      ...(user.chatCompression || {}),
-      ...(workspace.chatCompression || {}),
+    tools: {
+      ...(systemDefaults.tools || {}),
+      ...(user.tools || {}),
+      ...(safeWorkspaceWithoutFolderTrust.tools || {}),
+      ...(system.tools || {}),
+    },
+    context: {
+      ...(systemDefaults.context || {}),
+      ...(user.context || {}),
+      ...(safeWorkspaceWithoutFolderTrust.context || {}),
+      ...(system.context || {}),
+      includeDirectories: [
+        ...(systemDefaults.context?.includeDirectories || []),
+        ...(user.context?.includeDirectories || []),
+        ...(safeWorkspaceWithoutFolderTrust.context?.includeDirectories || []),
+        ...(system.context?.includeDirectories || []),
+      ],
+    },
+    model: {
+      ...(systemDefaults.model || {}),
+      ...(user.model || {}),
+      ...(safeWorkspaceWithoutFolderTrust.model || {}),
+      ...(system.model || {}),
+      chatCompression: {
+        ...(systemDefaults.model?.chatCompression || {}),
+        ...(user.model?.chatCompression || {}),
+        ...(safeWorkspaceWithoutFolderTrust.model?.chatCompression || {}),
+        ...(system.model?.chatCompression || {}),
+      },
+    },
+    advanced: {
+      ...(systemDefaults.advanced || {}),
+      ...(user.advanced || {}),
+      ...(safeWorkspaceWithoutFolderTrust.advanced || {}),
+      ...(system.advanced || {}),
+      excludedEnvVars: [
+        ...new Set([
+          ...(systemDefaults.advanced?.excludedEnvVars || []),
+          ...(user.advanced?.excludedEnvVars || []),
+          ...(safeWorkspaceWithoutFolderTrust.advanced?.excludedEnvVars || []),
+          ...(system.advanced?.excludedEnvVars || []),
+        ]),
+      ],
+    },
+    extensions: {
+      ...(systemDefaults.extensions || {}),
+      ...(user.extensions || {}),
+      ...(safeWorkspaceWithoutFolderTrust.extensions || {}),
+      ...(system.extensions || {}),
+      disabled: [
+        ...new Set([
+          ...(systemDefaults.extensions?.disabled || []),
+          ...(user.extensions?.disabled || []),
+          ...(safeWorkspaceWithoutFolderTrust.extensions?.disabled || []),
+          ...(system.extensions?.disabled || []),
+        ]),
+      ],
+      workspacesWithMigrationNudge: [
+        ...new Set([
+          ...(systemDefaults.extensions?.workspacesWithMigrationNudge || []),
+          ...(user.extensions?.workspacesWithMigrationNudge || []),
+          ...(safeWorkspaceWithoutFolderTrust.extensions
+            ?.workspacesWithMigrationNudge || []),
+          ...(system.extensions?.workspacesWithMigrationNudge || []),
+        ]),
+      ],
     },
   };
 }
@@ -110,21 +425,30 @@ function mergeSettings(
 export class LoadedSettings {
   constructor(
     system: SettingsFile,
+    systemDefaults: SettingsFile,
     user: SettingsFile,
     workspace: SettingsFile,
     errors: SettingsError[],
+    isTrusted: boolean,
+    migratedInMemorScopes: Set<SettingScope>,
   ) {
     this.system = system;
+    this.systemDefaults = systemDefaults;
     this.user = user;
     this.workspace = workspace;
     this.errors = errors;
+    this.isTrusted = isTrusted;
+    this.migratedInMemorScopes = migratedInMemorScopes;
     this._merged = this.computeMergedSettings();
   }
 
   readonly system: SettingsFile;
+  readonly systemDefaults: SettingsFile;
   readonly user: SettingsFile;
   readonly workspace: SettingsFile;
   readonly errors: SettingsError[];
+  readonly isTrusted: boolean;
+  readonly migratedInMemorScopes: Set<SettingScope>;
 
   private _merged: Settings;
 
@@ -135,8 +459,10 @@ export class LoadedSettings {
   private computeMergedSettings(): Settings {
     return mergeSettings(
       this.system.settings,
+      this.systemDefaults.settings,
       this.user.settings,
       this.workspace.settings,
+      this.isTrusted,
     );
   }
 
@@ -148,18 +474,16 @@ export class LoadedSettings {
         return this.workspace;
       case SettingScope.System:
         return this.system;
+      case SettingScope.SystemDefaults:
+        return this.systemDefaults;
       default:
         throw new Error(`Invalid scope: ${scope}`);
     }
   }
 
-  setValue<K extends keyof Settings>(
-    scope: SettingScope,
-    key: K,
-    value: Settings[K],
-  ): void {
+  setValue(scope: SettingScope, key: string, value: unknown): void {
     const settingsFile = this.forScope(scope);
-    settingsFile.settings[key] = value;
+    setNestedProperty(settingsFile.settings, key, value);
     this._merged = this.computeMergedSettings();
     saveSettings(settingsFile);
   }
@@ -269,7 +593,9 @@ export function loadEnvironment(settings?: Settings): void {
   // If no settings provided, try to load workspace settings for exclusions
   let resolvedSettings = settings;
   if (!resolvedSettings) {
-    const workspaceSettingsPath = getWorkspaceSettingsPath(process.cwd());
+    const workspaceSettingsPath = new Storage(
+      process.cwd(),
+    ).getWorkspaceSettingsPath();
     try {
       if (fs.existsSync(workspaceSettingsPath)) {
         const workspaceContent = fs.readFileSync(
@@ -294,7 +620,8 @@ export function loadEnvironment(settings?: Settings): void {
       const parsedEnv = dotenv.parse(envFileContent);
 
       const excludedVars =
-        resolvedSettings?.excludedProjectEnvVars || DEFAULT_EXCLUDED_ENV_VARS;
+        resolvedSettings?.advanced?.excludedEnvVars ||
+        DEFAULT_EXCLUDED_ENV_VARS;
       const isProjectEnvFile = !envFilePath.includes(GEMINI_DIR);
 
       for (const key in parsedEnv) {
@@ -322,10 +649,13 @@ export function loadEnvironment(settings?: Settings): void {
  */
 export function loadSettings(workspaceDir: string): LoadedSettings {
   let systemSettings: Settings = {};
+  let systemDefaultSettings: Settings = {};
   let userSettings: Settings = {};
   let workspaceSettings: Settings = {};
   const settingsErrors: SettingsError[] = [];
   const systemSettingsPath = getSystemSettingsPath();
+  const systemDefaultsPath = getSystemDefaultsPath();
+  const migratedInMemorScopes = new Set<SettingScope>();
 
   // Resolve paths to their canonical representation to handle symlinks
   const resolvedWorkspaceDir = path.resolve(workspaceDir);
@@ -342,70 +672,102 @@ export function loadSettings(workspaceDir: string): LoadedSettings {
   // We expect homedir to always exist and be resolvable.
   const realHomeDir = fs.realpathSync(resolvedHomeDir);
 
-  const workspaceSettingsPath = getWorkspaceSettingsPath(workspaceDir);
+  const workspaceSettingsPath = new Storage(
+    workspaceDir,
+  ).getWorkspaceSettingsPath();
 
-  // Load system settings
-  try {
-    if (fs.existsSync(systemSettingsPath)) {
-      const systemContent = fs.readFileSync(systemSettingsPath, 'utf-8');
-      systemSettings = JSON.parse(stripJsonComments(systemContent)) as Settings;
-    }
-  } catch (error: unknown) {
-    settingsErrors.push({
-      message: getErrorMessage(error),
-      path: systemSettingsPath,
-    });
-  }
-
-  // Load user settings
-  try {
-    if (fs.existsSync(USER_SETTINGS_PATH)) {
-      const userContent = fs.readFileSync(USER_SETTINGS_PATH, 'utf-8');
-      userSettings = JSON.parse(stripJsonComments(userContent)) as Settings;
-      // Support legacy theme names
-      if (userSettings.theme && userSettings.theme === 'VS') {
-        userSettings.theme = DefaultLight.name;
-      } else if (userSettings.theme && userSettings.theme === 'VS2015') {
-        userSettings.theme = DefaultDark.name;
-      }
-    }
-  } catch (error: unknown) {
-    settingsErrors.push({
-      message: getErrorMessage(error),
-      path: USER_SETTINGS_PATH,
-    });
-  }
-
-  if (realWorkspaceDir !== realHomeDir) {
-    // Load workspace settings
+  const loadAndMigrate = (filePath: string, scope: SettingScope): Settings => {
     try {
-      if (fs.existsSync(workspaceSettingsPath)) {
-        const projectContent = fs.readFileSync(workspaceSettingsPath, 'utf-8');
-        workspaceSettings = JSON.parse(
-          stripJsonComments(projectContent),
-        ) as Settings;
-        if (workspaceSettings.theme && workspaceSettings.theme === 'VS') {
-          workspaceSettings.theme = DefaultLight.name;
-        } else if (
-          workspaceSettings.theme &&
-          workspaceSettings.theme === 'VS2015'
+      if (fs.existsSync(filePath)) {
+        const content = fs.readFileSync(filePath, 'utf-8');
+        const rawSettings: unknown = JSON.parse(stripJsonComments(content));
+
+        if (
+          typeof rawSettings !== 'object' ||
+          rawSettings === null ||
+          Array.isArray(rawSettings)
         ) {
-          workspaceSettings.theme = DefaultDark.name;
+          settingsErrors.push({
+            message: 'Settings file is not a valid JSON object.',
+            path: filePath,
+          });
+          return {};
         }
+
+        let settingsObject = rawSettings as Record<string, unknown>;
+        if (needsMigration(settingsObject)) {
+          const migratedSettings = migrateSettingsToV2(settingsObject);
+          if (migratedSettings) {
+            if (MIGRATE_V2_OVERWRITE) {
+              try {
+                fs.renameSync(filePath, `${filePath}.orig`);
+                fs.writeFileSync(
+                  filePath,
+                  JSON.stringify(migratedSettings, null, 2),
+                  'utf-8',
+                );
+              } catch (e) {
+                console.error(
+                  `Error migrating settings file on disk: ${getErrorMessage(
+                    e,
+                  )}`,
+                );
+              }
+            } else {
+              migratedInMemorScopes.add(scope);
+            }
+            settingsObject = migratedSettings;
+          }
+        }
+        return settingsObject as Settings;
       }
     } catch (error: unknown) {
       settingsErrors.push({
         message: getErrorMessage(error),
-        path: workspaceSettingsPath,
+        path: filePath,
       });
     }
+    return {};
+  };
+
+  systemSettings = loadAndMigrate(systemSettingsPath, SettingScope.System);
+  systemDefaultSettings = loadAndMigrate(
+    systemDefaultsPath,
+    SettingScope.SystemDefaults,
+  );
+  userSettings = loadAndMigrate(USER_SETTINGS_PATH, SettingScope.User);
+
+  if (realWorkspaceDir !== realHomeDir) {
+    workspaceSettings = loadAndMigrate(
+      workspaceSettingsPath,
+      SettingScope.Workspace,
+    );
   }
 
+  // Support legacy theme names
+  if (userSettings.ui?.theme === 'VS') {
+    userSettings.ui.theme = DefaultLight.name;
+  } else if (userSettings.ui?.theme === 'VS2015') {
+    userSettings.ui.theme = DefaultDark.name;
+  }
+  if (workspaceSettings.ui?.theme === 'VS') {
+    workspaceSettings.ui.theme = DefaultLight.name;
+  } else if (workspaceSettings.ui?.theme === 'VS2015') {
+    workspaceSettings.ui.theme = DefaultDark.name;
+  }
+
+  // For the initial trust check, we can only use user and system settings.
+  const initialTrustCheckSettings = mergeWith({}, systemSettings, userSettings);
+  const isTrusted =
+    isWorkspaceTrusted(initialTrustCheckSettings as Settings) ?? true;
+
   // Create a temporary merged settings object to pass to loadEnvironment.
   const tempMergedSettings = mergeSettings(
     systemSettings,
+    systemDefaultSettings,
     userSettings,
     workspaceSettings,
+    isTrusted,
   );
 
   // loadEnviroment depends on settings so we have to create a temp version of
@@ -423,6 +785,10 @@ export function loadSettings(workspaceDir: string): LoadedSettings {
       path: systemSettingsPath,
       settings: systemSettings,
     },
+    {
+      path: systemDefaultsPath,
+      settings: systemDefaultSettings,
+    },
     {
       path: USER_SETTINGS_PATH,
       settings: userSettings,
@@ -432,21 +798,10 @@ export function loadSettings(workspaceDir: string): LoadedSettings {
       settings: workspaceSettings,
     },
     settingsErrors,
+    isTrusted,
+    migratedInMemorScopes,
   );
 
-  // Validate chatCompression settings
-  const chatCompression = loadedSettings.merged.chatCompression;
-  const threshold = chatCompression?.contextPercentageThreshold;
-  if (
-    threshold != null &&
-    (typeof threshold !== 'number' || threshold < 0 || threshold > 1)
-  ) {
-    console.warn(
-      `Invalid value for chatCompression.contextPercentageThreshold: "${threshold}". Please use a value between 0 and 1. Using default compression settings.`,
-    );
-    delete loadedSettings.merged.chatCompression;
-  }
-
   return loadedSettings;
 }
 
@@ -458,9 +813,16 @@ export function saveSettings(settingsFile: SettingsFile): void {
       fs.mkdirSync(dirPath, { recursive: true });
     }
 
+    let settingsToSave = settingsFile.settings;
+    if (!MIGRATE_V2_OVERWRITE) {
+      settingsToSave = migrateSettingsToV1(
+        settingsToSave as Record<string, unknown>,
+      ) as Settings;
+    }
+
     fs.writeFileSync(
       settingsFile.path,
-      JSON.stringify(settingsFile.settings, null, 2),
+      JSON.stringify(settingsToSave, null, 2),
       'utf-8',
     );
   } catch (error) {

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

@@ -5,53 +5,25 @@
  */
 
 import { describe, it, expect } from 'vitest';
-import { SETTINGS_SCHEMA, Settings } from './settingsSchema.js';
+import type { Settings } from './settingsSchema.js';
+import { SETTINGS_SCHEMA } from './settingsSchema.js';
 
 describe('SettingsSchema', () => {
   describe('SETTINGS_SCHEMA', () => {
     it('should contain all expected top-level settings', () => {
       const expectedSettings = [
-        'theme',
-        'customThemes',
-        'showMemoryUsage',
-        'usageStatisticsEnabled',
-        'autoConfigureMaxOldSpaceSize',
-        'preferredEditor',
-        'maxSessionTurns',
-        'memoryImportFormat',
-        'memoryDiscoveryMaxDirs',
-        'contextFileName',
-        'vimMode',
-        'ideMode',
-        'accessibility',
-        'checkpointing',
-        'fileFiltering',
-        'disableAutoUpdate',
-        'hideWindowTitle',
-        'hideTips',
-        'hideBanner',
-        'selectedAuthType',
-        'useExternalAuth',
-        'sandbox',
-        'coreTools',
-        'excludeTools',
-        'toolDiscoveryCommand',
-        'toolCallCommand',
-        'mcpServerCommand',
         'mcpServers',
-        'allowMCPServers',
-        'excludeMCPServers',
+        'general',
+        'ui',
+        'ide',
+        'privacy',
         'telemetry',
-        'bugCommand',
-        'summarizeToolOutput',
-        'dnsResolutionOrder',
-        'excludedProjectEnvVars',
-        'disableUpdateNag',
-        'includeDirectories',
-        'loadMemoryFromIncludeDirectories',
         'model',
-        'hasSeenIdeIntegrationNudge',
-        'folderTrustFeature',
+        'context',
+        'tools',
+        'mcp',
+        'security',
+        'advanced',
       ];
 
       expectedSettings.forEach((setting) => {
@@ -77,9 +49,16 @@ describe('SettingsSchema', () => {
 
     it('should have correct nested setting structure', () => {
       const nestedSettings = [
-        'accessibility',
-        'checkpointing',
-        'fileFiltering',
+        'general',
+        'ui',
+        'ide',
+        'privacy',
+        'model',
+        'context',
+        'tools',
+        'mcp',
+        'security',
+        'advanced',
       ];
 
       nestedSettings.forEach((setting) => {
@@ -96,29 +75,36 @@ describe('SettingsSchema', () => {
 
     it('should have accessibility nested properties', () => {
       expect(
-        SETTINGS_SCHEMA.accessibility.properties?.disableLoadingPhrases,
+        SETTINGS_SCHEMA.ui?.properties?.accessibility?.properties,
       ).toBeDefined();
       expect(
-        SETTINGS_SCHEMA.accessibility.properties?.disableLoadingPhrases.type,
+        SETTINGS_SCHEMA.ui?.properties?.accessibility.properties
+          ?.disableLoadingPhrases.type,
       ).toBe('boolean');
     });
 
     it('should have checkpointing nested properties', () => {
-      expect(SETTINGS_SCHEMA.checkpointing.properties?.enabled).toBeDefined();
-      expect(SETTINGS_SCHEMA.checkpointing.properties?.enabled.type).toBe(
-        'boolean',
-      );
+      expect(
+        SETTINGS_SCHEMA.general?.properties?.checkpointing.properties?.enabled,
+      ).toBeDefined();
+      expect(
+        SETTINGS_SCHEMA.general?.properties?.checkpointing.properties?.enabled
+          .type,
+      ).toBe('boolean');
     });
 
     it('should have fileFiltering nested properties', () => {
       expect(
-        SETTINGS_SCHEMA.fileFiltering.properties?.respectGitIgnore,
+        SETTINGS_SCHEMA.context.properties.fileFiltering.properties
+          ?.respectGitIgnore,
       ).toBeDefined();
       expect(
-        SETTINGS_SCHEMA.fileFiltering.properties?.respectGeminiIgnore,
+        SETTINGS_SCHEMA.context.properties.fileFiltering.properties
+          ?.respectGeminiIgnore,
       ).toBeDefined();
       expect(
-        SETTINGS_SCHEMA.fileFiltering.properties?.enableRecursiveFileSearch,
+        SETTINGS_SCHEMA.context.properties.fileFiltering.properties
+          ?.enableRecursiveFileSearch,
       ).toBeDefined();
     });
 
@@ -147,11 +133,6 @@ describe('SettingsSchema', () => {
       expect(categories.size).toBeGreaterThan(0);
       expect(categories).toContain('General');
       expect(categories).toContain('UI');
-      expect(categories).toContain('Mode');
-      expect(categories).toContain('Updates');
-      expect(categories).toContain('Accessibility');
-      expect(categories).toContain('Checkpointing');
-      expect(categories).toContain('File Filtering');
       expect(categories).toContain('Advanced');
     });
 
@@ -180,73 +161,148 @@ describe('SettingsSchema', () => {
 
     it('should have showInDialog property configured', () => {
       // Check that user-facing settings are marked for dialog display
-      expect(SETTINGS_SCHEMA.showMemoryUsage.showInDialog).toBe(true);
-      expect(SETTINGS_SCHEMA.vimMode.showInDialog).toBe(true);
-      expect(SETTINGS_SCHEMA.ideMode.showInDialog).toBe(true);
-      expect(SETTINGS_SCHEMA.disableAutoUpdate.showInDialog).toBe(true);
-      expect(SETTINGS_SCHEMA.hideWindowTitle.showInDialog).toBe(true);
-      expect(SETTINGS_SCHEMA.hideTips.showInDialog).toBe(true);
-      expect(SETTINGS_SCHEMA.hideBanner.showInDialog).toBe(true);
-      expect(SETTINGS_SCHEMA.usageStatisticsEnabled.showInDialog).toBe(false);
+      expect(SETTINGS_SCHEMA.ui.properties.showMemoryUsage.showInDialog).toBe(
+        true,
+      );
+      expect(SETTINGS_SCHEMA.general.properties.vimMode.showInDialog).toBe(
+        true,
+      );
+      expect(SETTINGS_SCHEMA.ide.properties.enabled.showInDialog).toBe(true);
+      expect(
+        SETTINGS_SCHEMA.general.properties.disableAutoUpdate.showInDialog,
+      ).toBe(true);
+      expect(SETTINGS_SCHEMA.ui.properties.hideWindowTitle.showInDialog).toBe(
+        true,
+      );
+      expect(SETTINGS_SCHEMA.ui.properties.hideTips.showInDialog).toBe(true);
+      expect(SETTINGS_SCHEMA.ui.properties.hideBanner.showInDialog).toBe(true);
+      expect(
+        SETTINGS_SCHEMA.privacy.properties.usageStatisticsEnabled.showInDialog,
+      ).toBe(false);
 
       // Check that advanced settings are hidden from dialog
-      expect(SETTINGS_SCHEMA.selectedAuthType.showInDialog).toBe(false);
-      expect(SETTINGS_SCHEMA.coreTools.showInDialog).toBe(false);
+      expect(SETTINGS_SCHEMA.security.properties.auth.showInDialog).toBe(false);
+      expect(SETTINGS_SCHEMA.tools.properties.core.showInDialog).toBe(false);
       expect(SETTINGS_SCHEMA.mcpServers.showInDialog).toBe(false);
       expect(SETTINGS_SCHEMA.telemetry.showInDialog).toBe(false);
 
       // Check that some settings are appropriately hidden
-      expect(SETTINGS_SCHEMA.theme.showInDialog).toBe(false); // Changed to false
-      expect(SETTINGS_SCHEMA.customThemes.showInDialog).toBe(false); // Managed via theme editor
-      expect(SETTINGS_SCHEMA.checkpointing.showInDialog).toBe(false); // Experimental feature
-      expect(SETTINGS_SCHEMA.accessibility.showInDialog).toBe(false); // Changed to false
-      expect(SETTINGS_SCHEMA.fileFiltering.showInDialog).toBe(false); // Changed to false
-      expect(SETTINGS_SCHEMA.preferredEditor.showInDialog).toBe(false); // Changed to false
-      expect(SETTINGS_SCHEMA.autoConfigureMaxOldSpaceSize.showInDialog).toBe(
-        true,
-      );
+      expect(SETTINGS_SCHEMA.ui.properties.theme.showInDialog).toBe(false); // Changed to false
+      expect(SETTINGS_SCHEMA.ui.properties.customThemes.showInDialog).toBe(
+        false,
+      ); // Managed via theme editor
+      expect(
+        SETTINGS_SCHEMA.general.properties.checkpointing.showInDialog,
+      ).toBe(false); // Experimental feature
+      expect(SETTINGS_SCHEMA.ui.properties.accessibility.showInDialog).toBe(
+        false,
+      ); // Changed to false
+      expect(
+        SETTINGS_SCHEMA.context.properties.fileFiltering.showInDialog,
+      ).toBe(false); // Changed to false
+      expect(
+        SETTINGS_SCHEMA.general.properties.preferredEditor.showInDialog,
+      ).toBe(false); // Changed to false
+      expect(
+        SETTINGS_SCHEMA.advanced.properties.autoConfigureMemory.showInDialog,
+      ).toBe(false);
     });
 
     it('should infer Settings type correctly', () => {
       // This test ensures that the Settings type is properly inferred from the schema
       const settings: Settings = {
-        theme: 'dark',
-        includeDirectories: ['/path/to/dir'],
-        loadMemoryFromIncludeDirectories: true,
+        ui: {
+          theme: 'dark',
+        },
+        context: {
+          includeDirectories: ['/path/to/dir'],
+          loadMemoryFromIncludeDirectories: true,
+        },
       };
 
       // TypeScript should not complain about these properties
-      expect(settings.theme).toBe('dark');
-      expect(settings.includeDirectories).toEqual(['/path/to/dir']);
-      expect(settings.loadMemoryFromIncludeDirectories).toBe(true);
+      expect(settings.ui?.theme).toBe('dark');
+      expect(settings.context?.includeDirectories).toEqual(['/path/to/dir']);
+      expect(settings.context?.loadMemoryFromIncludeDirectories).toBe(true);
     });
 
     it('should have includeDirectories setting in schema', () => {
-      expect(SETTINGS_SCHEMA.includeDirectories).toBeDefined();
-      expect(SETTINGS_SCHEMA.includeDirectories.type).toBe('array');
-      expect(SETTINGS_SCHEMA.includeDirectories.category).toBe('General');
-      expect(SETTINGS_SCHEMA.includeDirectories.default).toEqual([]);
+      expect(
+        SETTINGS_SCHEMA.context?.properties.includeDirectories,
+      ).toBeDefined();
+      expect(SETTINGS_SCHEMA.context?.properties.includeDirectories.type).toBe(
+        'array',
+      );
+      expect(
+        SETTINGS_SCHEMA.context?.properties.includeDirectories.category,
+      ).toBe('Context');
+      expect(
+        SETTINGS_SCHEMA.context?.properties.includeDirectories.default,
+      ).toEqual([]);
     });
 
     it('should have loadMemoryFromIncludeDirectories setting in schema', () => {
-      expect(SETTINGS_SCHEMA.loadMemoryFromIncludeDirectories).toBeDefined();
-      expect(SETTINGS_SCHEMA.loadMemoryFromIncludeDirectories.type).toBe(
-        'boolean',
-      );
-      expect(SETTINGS_SCHEMA.loadMemoryFromIncludeDirectories.category).toBe(
-        'General',
-      );
-      expect(SETTINGS_SCHEMA.loadMemoryFromIncludeDirectories.default).toBe(
-        false,
-      );
+      expect(
+        SETTINGS_SCHEMA.context?.properties.loadMemoryFromIncludeDirectories,
+      ).toBeDefined();
+      expect(
+        SETTINGS_SCHEMA.context?.properties.loadMemoryFromIncludeDirectories
+          .type,
+      ).toBe('boolean');
+      expect(
+        SETTINGS_SCHEMA.context?.properties.loadMemoryFromIncludeDirectories
+          .category,
+      ).toBe('Context');
+      expect(
+        SETTINGS_SCHEMA.context?.properties.loadMemoryFromIncludeDirectories
+          .default,
+      ).toBe(false);
     });
 
     it('should have folderTrustFeature setting in schema', () => {
-      expect(SETTINGS_SCHEMA.folderTrustFeature).toBeDefined();
-      expect(SETTINGS_SCHEMA.folderTrustFeature.type).toBe('boolean');
-      expect(SETTINGS_SCHEMA.folderTrustFeature.category).toBe('General');
-      expect(SETTINGS_SCHEMA.folderTrustFeature.default).toBe(false);
-      expect(SETTINGS_SCHEMA.folderTrustFeature.showInDialog).toBe(true);
+      expect(
+        SETTINGS_SCHEMA.security.properties.folderTrust.properties.enabled,
+      ).toBeDefined();
+      expect(
+        SETTINGS_SCHEMA.security.properties.folderTrust.properties.enabled.type,
+      ).toBe('boolean');
+      expect(
+        SETTINGS_SCHEMA.security.properties.folderTrust.properties.enabled
+          .category,
+      ).toBe('Security');
+      expect(
+        SETTINGS_SCHEMA.security.properties.folderTrust.properties.enabled
+          .default,
+      ).toBe(false);
+      expect(
+        SETTINGS_SCHEMA.security.properties.folderTrust.properties.enabled
+          .showInDialog,
+      ).toBe(true);
+    });
+
+    it('should have debugKeystrokeLogging setting in schema', () => {
+      expect(
+        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging,
+      ).toBeDefined();
+      expect(
+        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging.type,
+      ).toBe('boolean');
+      expect(
+        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging.category,
+      ).toBe('General');
+      expect(
+        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging.default,
+      ).toBe(false);
+      expect(
+        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging
+          .requiresRestart,
+      ).toBe(false);
+      expect(
+        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging.showInDialog,
+      ).toBe(true);
+      expect(
+        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging.description,
+      ).toBe('Enable debug logging of keystrokes to the console.');
     });
   });
 });

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

@@ -5,7 +5,7 @@
  */
 
 // Mock 'os' first.
-import * as osActual from 'os';
+import * as osActual from 'node:os';
 vi.mock('os', async (importOriginal) => {
   const actualOs = await importOriginal<typeof osActual>();
   return {
@@ -25,9 +25,9 @@ import {
   type Mocked,
   type Mock,
 } from 'vitest';
-import * as fs from 'fs';
+import * as fs from 'node:fs';
 import stripJsonComments from 'strip-json-comments';
-import * as path from 'path';
+import * as path from 'node:path';
 
 import {
   loadTrustedFolders,
@@ -35,7 +35,7 @@ import {
   TrustLevel,
   isWorkspaceTrusted,
 } from './trustedFolders.js';
-import { Settings } from './settings.js';
+import type { Settings } from './settings.js';
 
 vi.mock('fs', async (importOriginal) => {
   const actualFs = await importOriginal<typeof fs>();
@@ -132,8 +132,12 @@ describe('isWorkspaceTrusted', () => {
   let mockCwd: string;
   const mockRules: Record<string, TrustLevel> = {};
   const mockSettings: Settings = {
-    folderTrustFeature: true,
-    folderTrust: true,
+    security: {
+      folderTrust: {
+        featureEnabled: true,
+        enabled: true,
+      },
+    },
   };
 
   beforeEach(() => {

packages/cli/src/config/trustedFolders.ts

@@ -4,11 +4,11 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import * as fs from 'fs';
-import * as path from 'path';
-import { homedir } from 'os';
+import * as fs from 'node:fs';
+import * as path from 'node:path';
+import { homedir } from 'node:os';
 import { getErrorMessage, isWithinRoot } from '@qwen-code/qwen-code-core';
-import { Settings } from './settings.js';
+import type { Settings } from './settings.js';
 import stripJsonComments from 'strip-json-comments';
 
 export const TRUSTED_FOLDERS_FILENAME = 'trustedFolders.json';
@@ -111,8 +111,9 @@ export function saveTrustedFolders(
 }
 
 export function isWorkspaceTrusted(settings: Settings): boolean | undefined {
-  const folderTrustFeature = settings.folderTrustFeature ?? false;
-  const folderTrustSetting = settings.folderTrust ?? true;
+  const folderTrustFeature =
+    settings.security?.folderTrust?.featureEnabled ?? false;
+  const folderTrustSetting = settings.security?.folderTrust?.enabled ?? true;
   const folderTrustEnabled = folderTrustFeature && folderTrustSetting;
 
   if (!folderTrustEnabled) {

packages/cli/src/gemini.test.tsx

@@ -4,19 +4,18 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import stripAnsi from 'strip-ansi';
 import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
 import {
   main,
   setupUnhandledRejectionHandler,
   validateDnsResolutionOrder,
+  startInteractiveUI,
 } from './gemini.js';
-import {
-  LoadedSettings,
-  SettingsFile,
-  loadSettings,
-} from './config/settings.js';
+import type { SettingsFile } from './config/settings.js';
+import { LoadedSettings, loadSettings } from './config/settings.js';
 import { appEvents, AppEvent } from './utils/events.js';
+import type { Config } from '@qwen-code/qwen-code-core';
+import { FatalConfigError } from '@qwen-code/qwen-code-core';
 
 // Custom error to identify mock process.exit calls
 class MockProcessExitError extends Error {
@@ -76,7 +75,6 @@ vi.mock('./utils/sandbox.js', () => ({
 }));
 
 describe('gemini.tsx main function', () => {
-  let consoleErrorSpy: ReturnType<typeof vi.spyOn>;
   let loadSettingsMock: ReturnType<typeof vi.mocked<typeof loadSettings>>;
   let originalEnvGeminiSandbox: string | undefined;
   let originalEnvSandbox: string | undefined;
@@ -98,7 +96,6 @@ describe('gemini.tsx main function', () => {
     delete process.env['GEMINI_SANDBOX'];
     delete process.env['SANDBOX'];
 
-    consoleErrorSpy = vi.spyOn(console, 'error').mockImplementation(() => {});
     initialUnhandledRejectionListeners =
       process.listeners('unhandledRejection');
   });
@@ -127,7 +124,7 @@ describe('gemini.tsx main function', () => {
     vi.restoreAllMocks();
   });
 
-  it('should call process.exit(1) if settings have errors', async () => {
+  it('should throw InvalidConfigurationError if settings have errors', async () => {
     const settingsError = {
       message: 'Test settings error',
       path: '/test/settings.json',
@@ -144,37 +141,23 @@ describe('gemini.tsx main function', () => {
       path: '/system/settings.json',
       settings: {},
     };
+    const systemDefaultsFile: SettingsFile = {
+      path: '/system/system-defaults.json',
+      settings: {},
+    };
     const mockLoadedSettings = new LoadedSettings(
       systemSettingsFile,
+      systemDefaultsFile,
       userSettingsFile,
       workspaceSettingsFile,
       [settingsError],
+      true,
+      new Set(),
     );
 
     loadSettingsMock.mockReturnValue(mockLoadedSettings);
 
-    try {
-      await main();
-      // If main completes without throwing, the test should fail because process.exit was expected
-      expect.fail('main function did not exit as expected');
-    } catch (error) {
-      expect(error).toBeInstanceOf(MockProcessExitError);
-      if (error instanceof MockProcessExitError) {
-        expect(error.code).toBe(1);
-      }
-    }
-
-    // Verify console.error was called with the error message
-    expect(consoleErrorSpy).toHaveBeenCalledTimes(2);
-    expect(stripAnsi(String(consoleErrorSpy.mock.calls[0][0]))).toBe(
-      'Error in /test/settings.json: Test settings error',
-    );
-    expect(stripAnsi(String(consoleErrorSpy.mock.calls[1][0]))).toBe(
-      'Please fix /test/settings.json and try again.',
-    );
-
-    // Verify process.exit was called.
-    expect(processExitSpy).toHaveBeenCalledWith(1);
+    await expect(main()).rejects.toThrow(FatalConfigError);
   });
 
   it('should log unhandled promise rejections and open debug console on first error', async () => {
@@ -250,3 +233,100 @@ describe('validateDnsResolutionOrder', () => {
     );
   });
 });
+
+describe('startInteractiveUI', () => {
+  // Mock dependencies
+  const mockConfig = {
+    getProjectRoot: () => '/root',
+    getScreenReader: () => false,
+  } as Config;
+  const mockSettings = {
+    merged: {
+      ui: {
+        hideWindowTitle: false,
+      },
+    },
+  } as LoadedSettings;
+  const mockStartupWarnings = ['warning1'];
+  const mockWorkspaceRoot = '/root';
+
+  vi.mock('./utils/version.js', () => ({
+    getCliVersion: vi.fn(() => Promise.resolve('1.0.0')),
+  }));
+
+  vi.mock('./ui/utils/kittyProtocolDetector.js', () => ({
+    detectAndEnableKittyProtocol: vi.fn(() => Promise.resolve()),
+  }));
+
+  vi.mock('./ui/utils/updateCheck.js', () => ({
+    checkForUpdates: vi.fn(() => Promise.resolve(null)),
+  }));
+
+  vi.mock('./utils/cleanup.js', () => ({
+    cleanupCheckpoints: vi.fn(() => Promise.resolve()),
+    registerCleanup: vi.fn(),
+  }));
+
+  vi.mock('ink', () => ({
+    render: vi.fn().mockReturnValue({ unmount: vi.fn() }),
+  }));
+
+  beforeEach(() => {
+    vi.clearAllMocks();
+  });
+
+  it('should render the UI with proper React context and exitOnCtrlC disabled', async () => {
+    const { render } = await import('ink');
+    const renderSpy = vi.mocked(render);
+
+    await startInteractiveUI(
+      mockConfig,
+      mockSettings,
+      mockStartupWarnings,
+      mockWorkspaceRoot,
+    );
+
+    // Verify render was called with correct options
+    expect(renderSpy).toHaveBeenCalledTimes(1);
+    const [reactElement, options] = renderSpy.mock.calls[0];
+
+    // Verify render options
+    expect(options).toEqual({
+      exitOnCtrlC: false,
+      isScreenReaderEnabled: false,
+    });
+
+    // Verify React element structure is valid (but don't deep dive into JSX internals)
+    expect(reactElement).toBeDefined();
+  });
+
+  it('should perform all startup tasks in correct order', async () => {
+    const { getCliVersion } = await import('./utils/version.js');
+    const { detectAndEnableKittyProtocol } = await import(
+      './ui/utils/kittyProtocolDetector.js'
+    );
+    const { checkForUpdates } = await import('./ui/utils/updateCheck.js');
+    const { registerCleanup } = await import('./utils/cleanup.js');
+
+    await startInteractiveUI(
+      mockConfig,
+      mockSettings,
+      mockStartupWarnings,
+      mockWorkspaceRoot,
+    );
+
+    // Verify all startup tasks were called
+    expect(getCliVersion).toHaveBeenCalledTimes(1);
+    expect(detectAndEnableKittyProtocol).toHaveBeenCalledTimes(1);
+    expect(registerCleanup).toHaveBeenCalledTimes(1);
+
+    // Verify cleanup handler is registered with unmount function
+    const cleanupFn = vi.mocked(registerCleanup).mock.calls[0][0];
+    expect(typeof cleanupFn).toBe('function');
+
+    // checkForUpdates should be called asynchronously (not waited for)
+    // We need a small delay to let it execute
+    await new Promise((resolve) => setTimeout(resolve, 0));
+    expect(checkForUpdates).toHaveBeenCalledTimes(1);
+  });
+});

packages/cli/src/gemini.tsx

@@ -4,49 +4,47 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import React from 'react';
-import { render } from 'ink';
-import { AppWrapper } from './ui/App.js';
-import { loadCliConfig, parseArguments } from './config/config.js';
-import { readStdin } from './utils/readStdin.js';
-import { basename } from 'node:path';
-import v8 from 'node:v8';
-import os from 'node:os';
-import dns from 'node:dns';
-import { spawn } from 'node:child_process';
-import { start_sandbox } from './utils/sandbox.js';
+import type { Config } from '@qwen-code/qwen-code-core';
 import {
-  DnsResolutionOrder,
-  LoadedSettings,
-  loadSettings,
-  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';
-import { ConsolePatcher } from './ui/utils/ConsolePatcher.js';
-import { runNonInteractive } from './nonInteractiveCli.js';
-import { loadExtensions } from './config/extension.js';
-import { cleanupCheckpoints, registerCleanup } from './utils/cleanup.js';
-import { getCliVersion } from './utils/version.js';
-import {
-  Config,
-  sessionId,
-  logUserPrompt,
   AuthType,
+  FatalConfigError,
   getOauthClient,
-  logIdeConnection,
   IdeConnectionEvent,
   IdeConnectionType,
+  logIdeConnection,
+  logUserPrompt,
+  sessionId,
 } from '@qwen-code/qwen-code-core';
+import { render } from 'ink';
+import { spawn } from 'node:child_process';
+import dns from 'node:dns';
+import os from 'node:os';
+import { basename } from 'node:path';
+import v8 from 'node:v8';
+import React from 'react';
 import { validateAuthMethod } from './config/auth.js';
+import { loadCliConfig, parseArguments } from './config/config.js';
+import { loadExtensions } from './config/extension.js';
+import type { DnsResolutionOrder, LoadedSettings } from './config/settings.js';
+import { loadSettings, SettingScope } from './config/settings.js';
+import { runNonInteractive } from './nonInteractiveCli.js';
+import { AppWrapper } from './ui/App.js';
 import { setMaxSizedBoxDebugging } from './ui/components/shared/MaxSizedBox.js';
-import { validateNonInteractiveAuth } from './validateNonInterActiveAuth.js';
+import { SettingsContext } from './ui/contexts/SettingsContext.js';
+import { themeManager } from './ui/themes/theme-manager.js';
+import { ConsolePatcher } from './ui/utils/ConsolePatcher.js';
 import { detectAndEnableKittyProtocol } from './ui/utils/kittyProtocolDetector.js';
 import { checkForUpdates } from './ui/utils/updateCheck.js';
+import { cleanupCheckpoints, registerCleanup } from './utils/cleanup.js';
+import { AppEvent, appEvents } from './utils/events.js';
 import { handleAutoUpdate } from './utils/handleAutoUpdate.js';
-import { appEvents, AppEvent } from './utils/events.js';
-import { SettingsContext } from './ui/contexts/SettingsContext.js';
+import { readStdin } from './utils/readStdin.js';
+import { start_sandbox } from './utils/sandbox.js';
+import { getStartupWarnings } from './utils/startupWarnings.js';
+import { getUserStartupWarnings } from './utils/userStartupWarnings.js';
+import { getCliVersion } from './utils/version.js';
+import { validateNonInteractiveAuth } from './validateNonInterActiveAuth.js';
+import { runZedIntegration } from './zed-integration/zedIntegration.js';
 
 export function validateDnsResolutionOrder(
   order: string | undefined,
@@ -108,7 +106,6 @@ async function relaunchWithAdditionalArgs(additionalArgs: string[]) {
   await new Promise((resolve) => child.on('close', resolve));
   process.exit(0);
 }
-import { runZedIntegration } from './zed-integration/zedIntegration.js';
 
 export function setupUnhandledRejectionHandler() {
   let unhandledRejectionOccurred = false;
@@ -132,6 +129,44 @@ ${reason.stack}`
   });
 }
 
+export async function startInteractiveUI(
+  config: Config,
+  settings: LoadedSettings,
+  startupWarnings: string[],
+  workspaceRoot: string,
+) {
+  const version = await getCliVersion();
+  // Detect and enable Kitty keyboard protocol once at startup
+  await detectAndEnableKittyProtocol();
+  setWindowTitle(basename(workspaceRoot), settings);
+  const instance = render(
+    <React.StrictMode>
+      <SettingsContext.Provider value={settings}>
+        <AppWrapper
+          config={config}
+          settings={settings}
+          startupWarnings={startupWarnings}
+          version={version}
+        />
+      </SettingsContext.Provider>
+    </React.StrictMode>,
+    { exitOnCtrlC: false, isScreenReaderEnabled: config.getScreenReader() },
+  );
+
+  checkForUpdates()
+    .then((info) => {
+      handleAutoUpdate(info, settings, config.getProjectRoot());
+    })
+    .catch((err) => {
+      // Silently ignore update check errors.
+      if (config.getDebugMode()) {
+        console.error('Update check failed:', err);
+      }
+    });
+
+  registerCleanup(() => instance.unmount());
+}
+
 export async function main() {
   setupUnhandledRejectionHandler();
   const workspaceRoot = process.cwd();
@@ -139,18 +174,15 @@ export async function main() {
 
   await cleanupCheckpoints();
   if (settings.errors.length > 0) {
-    for (const error of settings.errors) {
-      let errorMessage = `Error in ${error.path}: ${error.message}`;
-      if (!process.env['NO_COLOR']) {
-        errorMessage = `\x1b[31m${errorMessage}\x1b[0m`;
-      }
-      console.error(errorMessage);
-      console.error(`Please fix ${error.path} and try again.`);
-    }
-    process.exit(1);
+    const errorMessages = settings.errors.map(
+      (error) => `Error in ${error.path}: ${error.message}`,
+    );
+    throw new FatalConfigError(
+      `${errorMessages.join('\n')}\nPlease fix the configuration file(s) and try again.`,
+    );
   }
 
-  const argv = await parseArguments();
+  const argv = await parseArguments(settings.merged);
   const extensions = loadExtensions(workspaceRoot);
   const config = await loadCliConfig(
     settings.merged,
@@ -167,7 +199,7 @@ export async function main() {
   registerCleanup(consolePatcher.cleanup);
 
   dns.setDefaultResultOrder(
-    validateDnsResolutionOrder(settings.merged.dnsResolutionOrder),
+    validateDnsResolutionOrder(settings.merged.advanced?.dnsResolutionOrder),
   );
 
   if (argv.promptInteractive && !process.stdin.isTTY) {
@@ -186,7 +218,7 @@ export async function main() {
   }
 
   // Set a default auth type if one isn't set.
-  if (!settings.merged.selectedAuthType) {
+  if (!settings.merged.security?.auth?.selectedType) {
     if (process.env['CLOUD_SHELL'] === 'true') {
       settings.setValue(
         SettingScope.User,
@@ -195,6 +227,14 @@ export async function main() {
       );
     }
   }
+  // Empty key causes issues with the GoogleGenAI package.
+  if (process.env['GEMINI_API_KEY']?.trim() === '') {
+    delete process.env['GEMINI_API_KEY'];
+  }
+
+  if (process.env['GOOGLE_API_KEY']?.trim() === '') {
+    delete process.env['GOOGLE_API_KEY'];
+  }
 
   setMaxSizedBoxDebugging(config.getDebugMode());
 
@@ -206,40 +246,72 @@ export async function main() {
   }
 
   // Load custom themes from settings
-  themeManager.loadCustomThemes(settings.merged.customThemes);
+  themeManager.loadCustomThemes(settings.merged.ui?.customThemes);
 
-  if (settings.merged.theme) {
-    if (!themeManager.setActiveTheme(settings.merged.theme)) {
+  if (settings.merged.ui?.theme) {
+    if (!themeManager.setActiveTheme(settings.merged.ui?.theme)) {
       // If the theme is not found during initial load, log a warning and continue.
       // The useThemeCommand hook in App.tsx will handle opening the dialog.
-      console.warn(`Warning: Theme "${settings.merged.theme}" not found.`);
+      console.warn(`Warning: Theme "${settings.merged.ui?.theme}" not found.`);
     }
   }
 
   // hop into sandbox if we are outside and sandboxing is enabled
   if (!process.env['SANDBOX']) {
-    const memoryArgs = settings.merged.autoConfigureMaxOldSpaceSize
+    const memoryArgs = settings.merged.advanced?.autoConfigureMemory
       ? getNodeMemoryArgs(config)
       : [];
     const sandboxConfig = config.getSandbox();
     if (sandboxConfig) {
       if (
-        settings.merged.selectedAuthType &&
-        !settings.merged.useExternalAuth
+        settings.merged.security?.auth?.selectedType &&
+        !settings.merged.security?.auth?.useExternal
       ) {
         // Validate authentication here because the sandbox will interfere with the Oauth2 web redirect.
         try {
-          const err = validateAuthMethod(settings.merged.selectedAuthType);
+          const err = validateAuthMethod(
+            settings.merged.security.auth.selectedType,
+          );
           if (err) {
             throw new Error(err);
           }
-          await config.refreshAuth(settings.merged.selectedAuthType);
+          await config.refreshAuth(settings.merged.security.auth.selectedType);
         } catch (err) {
           console.error('Error authenticating:', err);
           process.exit(1);
         }
       }
-      await start_sandbox(sandboxConfig, memoryArgs, config);
+      let stdinData = '';
+      if (!process.stdin.isTTY) {
+        stdinData = await readStdin();
+      }
+
+      // This function is a copy of the one from sandbox.ts
+      // It is moved here to decouple sandbox.ts from the CLI's argument structure.
+      const injectStdinIntoArgs = (
+        args: string[],
+        stdinData?: string,
+      ): string[] => {
+        const finalArgs = [...args];
+        if (stdinData) {
+          const promptIndex = finalArgs.findIndex(
+            (arg) => arg === '--prompt' || arg === '-p',
+          );
+          if (promptIndex > -1 && finalArgs.length > promptIndex + 1) {
+            // If there's a prompt argument, prepend stdin to it
+            finalArgs[promptIndex + 1] =
+              `${stdinData}\n\n${finalArgs[promptIndex + 1]}`;
+          } else {
+            // If there's no prompt argument, add stdin as the prompt
+            finalArgs.push('--prompt', stdinData);
+          }
+        }
+        return finalArgs;
+      };
+
+      const sandboxArgs = injectStdinIntoArgs(process.argv, stdinData);
+
+      await start_sandbox(sandboxConfig, memoryArgs, config, sandboxArgs);
       process.exit(0);
     } else {
       // Not in a sandbox and not entering one, so relaunch with additional
@@ -252,11 +324,12 @@ export async function main() {
   }
 
   if (
-    settings.merged.selectedAuthType === AuthType.LOGIN_WITH_GOOGLE &&
+    settings.merged.security?.auth?.selectedType ===
+      AuthType.LOGIN_WITH_GOOGLE &&
     config.isBrowserLaunchSuppressed()
   ) {
     // Do oauth before app renders to make copying the link possible.
-    await getOauthClient(settings.merged.selectedAuthType, config);
+    await getOauthClient(settings.merged.security.auth.selectedType, config);
   }
 
   if (config.getExperimentalZedIntegration()) {
@@ -271,36 +344,7 @@ export async function main() {
 
   // Render UI, passing necessary config values. Check that there is no command line question.
   if (config.isInteractive()) {
-    const version = await getCliVersion();
-    // Detect and enable Kitty keyboard protocol once at startup
-    await detectAndEnableKittyProtocol();
-    setWindowTitle(basename(workspaceRoot), settings);
-    const instance = render(
-      <React.StrictMode>
-        <SettingsContext.Provider value={settings}>
-          <AppWrapper
-            config={config}
-            settings={settings}
-            startupWarnings={startupWarnings}
-            version={version}
-          />
-        </SettingsContext.Provider>
-      </React.StrictMode>,
-      { exitOnCtrlC: false },
-    );
-
-    checkForUpdates()
-      .then((info) => {
-        handleAutoUpdate(info, settings, config.getProjectRoot());
-      })
-      .catch((err) => {
-        // Silently ignore update check errors.
-        if (config.getDebugMode()) {
-          console.error('Update check failed:', err);
-        }
-      });
-
-    registerCleanup(() => instance.unmount());
+    await startInteractiveUI(config, settings, startupWarnings, workspaceRoot);
     return;
   }
   // If not a TTY, read from stdin
@@ -312,7 +356,9 @@ export async function main() {
     }
   }
   if (!input) {
-    console.error('No input provided via stdin.');
+    console.error(
+      `No input provided via stdin. Input can be provided by piping data into gemini or using the --prompt option.`,
+    );
     process.exit(1);
   }
 
@@ -327,17 +373,21 @@ export async function main() {
   });
 
   const nonInteractiveConfig = await validateNonInteractiveAuth(
-    settings.merged.selectedAuthType,
-    settings.merged.useExternalAuth,
+    settings.merged.security?.auth?.selectedType,
+    settings.merged.security?.auth?.useExternal,
     config,
   );
 
+  if (config.getDebugMode()) {
+    console.log('Session ID: %s', sessionId);
+  }
+
   await runNonInteractive(nonInteractiveConfig, input, prompt_id);
   process.exit(0);
 }
 
 function setWindowTitle(title: string, settings: LoadedSettings) {
-  if (!settings.merged.hideWindowTitle) {
+  if (!settings.merged.ui?.hideWindowTitle) {
     const windowTitle = (process.env['CLI_TITLE'] || `Qwen - ${title}`).replace(
       // eslint-disable-next-line no-control-regex
       /[\x00-\x1F\x7F]/g,

packages/cli/src/nonInteractiveCli.test.ts

@@ -5,19 +5,20 @@
  */
 
 import {
-  Config,
+  type Config,
+  type ToolRegistry,
   executeToolCall,
-  ToolRegistry,
   ToolErrorType,
   shutdownTelemetry,
   GeminiEventType,
-  ServerGeminiStreamEvent,
+  type ServerGeminiStreamEvent,
 } from '@qwen-code/qwen-code-core';
-import { Part } from '@google/genai';
+import { type Part } from '@google/genai';
 import { runNonInteractive } from './nonInteractiveCli.js';
 import { vi } from 'vitest';
 
 // Mock core modules
+vi.mock('./ui/hooks/atCommandProcessor.js');
 vi.mock('@qwen-code/qwen-code-core', async (importOriginal) => {
   const original =
     await importOriginal<typeof import('@qwen-code/qwen-code-core')>();
@@ -35,20 +36,16 @@ describe('runNonInteractive', () => {
   let mockCoreExecuteToolCall: vi.Mock;
   let mockShutdownTelemetry: vi.Mock;
   let consoleErrorSpy: vi.SpyInstance;
-  let processExitSpy: vi.SpyInstance;
   let processStdoutSpy: vi.SpyInstance;
   let mockGeminiClient: {
     sendMessageStream: vi.Mock;
   };
 
-  beforeEach(() => {
+  beforeEach(async () => {
     mockCoreExecuteToolCall = vi.mocked(executeToolCall);
     mockShutdownTelemetry = vi.mocked(shutdownTelemetry);
 
     consoleErrorSpy = vi.spyOn(console, 'error').mockImplementation(() => {});
-    processExitSpy = vi
-      .spyOn(process, 'exit')
-      .mockImplementation((() => {}) as (code?: number) => never);
     processStdoutSpy = vi
       .spyOn(process.stdout, 'write')
       .mockImplementation(() => true);
@@ -72,6 +69,14 @@ describe('runNonInteractive', () => {
       getContentGeneratorConfig: vi.fn().mockReturnValue({}),
       getDebugMode: vi.fn().mockReturnValue(false),
     } as unknown as Config;
+
+    const { handleAtCommand } = await import(
+      './ui/hooks/atCommandProcessor.js'
+    );
+    vi.mocked(handleAtCommand).mockImplementation(async ({ query }) => ({
+      processedQuery: [{ text: query }],
+      shouldProceed: true,
+    }));
   });
 
   afterEach(() => {
@@ -163,14 +168,16 @@ describe('runNonInteractive', () => {
     mockCoreExecuteToolCall.mockResolvedValue({
       error: new Error('Execution failed'),
       errorType: ToolErrorType.EXECUTION_FAILED,
-      responseParts: {
-        functionResponse: {
-          name: 'errorTool',
-          response: {
-            output: 'Error: Execution failed',
+      responseParts: [
+        {
+          functionResponse: {
+            name: 'errorTool',
+            response: {
+              output: 'Error: Execution failed',
+            },
           },
         },
-      },
+      ],
       resultDisplay: 'Execution failed',
     });
     const finalResponse: ServerGeminiStreamEvent[] = [
@@ -189,7 +196,6 @@ describe('runNonInteractive', () => {
     expect(consoleErrorSpy).toHaveBeenCalledWith(
       'Error executing tool errorTool: Execution failed',
     );
-    expect(processExitSpy).not.toHaveBeenCalled();
     expect(mockGeminiClient.sendMessageStream).toHaveBeenCalledTimes(2);
     expect(mockGeminiClient.sendMessageStream).toHaveBeenNthCalledWith(
       2,
@@ -215,12 +221,9 @@ describe('runNonInteractive', () => {
       throw apiError;
     });
 
-    await runNonInteractive(mockConfig, 'Initial fail', 'prompt-id-4');
-
-    expect(consoleErrorSpy).toHaveBeenCalledWith(
-      '[API Error: API connection failed]',
-    );
-    expect(processExitSpy).toHaveBeenCalledWith(1);
+    await expect(
+      runNonInteractive(mockConfig, 'Initial fail', 'prompt-id-4'),
+    ).rejects.toThrow(apiError);
   });
 
   it('should not exit if a tool is not found, and should send error back to model', async () => {
@@ -259,7 +262,6 @@ describe('runNonInteractive', () => {
     expect(consoleErrorSpy).toHaveBeenCalledWith(
       'Error executing tool nonexistentTool: Tool "nonexistentTool" not found in registry.',
     );
-    expect(processExitSpy).not.toHaveBeenCalled();
     expect(mockGeminiClient.sendMessageStream).toHaveBeenCalledTimes(2);
     expect(processStdoutSpy).toHaveBeenCalledWith(
       "Sorry, I can't find that tool.",
@@ -268,9 +270,54 @@ describe('runNonInteractive', () => {
 
   it('should exit when max session turns are exceeded', async () => {
     vi.mocked(mockConfig.getMaxSessionTurns).mockReturnValue(0);
-    await runNonInteractive(mockConfig, 'Trigger loop', 'prompt-id-6');
-    expect(consoleErrorSpy).toHaveBeenCalledWith(
-      '\n Reached max session turns for this session. Increase the number of turns by specifying maxSessionTurns in settings.json.',
+    await expect(
+      runNonInteractive(mockConfig, 'Trigger loop', 'prompt-id-6'),
+    ).rejects.toThrow(
+      'Reached max session turns for this session. Increase the number of turns by specifying maxSessionTurns in settings.json.',
     );
   });
+
+  it('should preprocess @include commands before sending to the model', async () => {
+    // 1. Mock the imported atCommandProcessor
+    const { handleAtCommand } = await import(
+      './ui/hooks/atCommandProcessor.js'
+    );
+    const mockHandleAtCommand = vi.mocked(handleAtCommand);
+
+    // 2. Define the raw input and the expected processed output
+    const rawInput = 'Summarize @file.txt';
+    const processedParts: Part[] = [
+      { text: 'Summarize @file.txt' },
+      { text: '\n--- Content from referenced files ---\n' },
+      { text: 'This is the content of the file.' },
+      { text: '\n--- End of content ---' },
+    ];
+
+    // 3. Setup the mock to return the processed parts
+    mockHandleAtCommand.mockResolvedValue({
+      processedQuery: processedParts,
+      shouldProceed: true,
+    });
+
+    // Mock a simple stream response from the Gemini client
+    const events: ServerGeminiStreamEvent[] = [
+      { type: GeminiEventType.Content, value: 'Summary complete.' },
+    ];
+    mockGeminiClient.sendMessageStream.mockReturnValue(
+      createStreamFromEvents(events),
+    );
+
+    // 4. Run the non-interactive mode with the raw input
+    await runNonInteractive(mockConfig, rawInput, 'prompt-id-7');
+
+    // 5. Assert that sendMessageStream was called with the PROCESSED parts, not the raw input
+    expect(mockGeminiClient.sendMessageStream).toHaveBeenCalledWith(
+      processedParts,
+      expect.any(AbortSignal),
+      'prompt-id-7',
+    );
+
+    // 6. Assert the final output is correct
+    expect(processStdoutSpy).toHaveBeenCalledWith('Summary complete.');
+  });
 });

packages/cli/src/nonInteractiveCli.ts

@@ -4,18 +4,20 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
+import type { Config, ToolCallRequestInfo } from '@qwen-code/qwen-code-core';
 import {
-  Config,
-  ToolCallRequestInfo,
   executeToolCall,
   shutdownTelemetry,
   isTelemetrySdkInitialized,
   GeminiEventType,
   parseAndFormatApiError,
+  FatalInputError,
+  FatalTurnLimitedError,
 } from '@qwen-code/qwen-code-core';
-import { Content, Part, FunctionCall } from '@google/genai';
+import type { Content, Part } from '@google/genai';
 
 import { ConsolePatcher } from './ui/utils/ConsolePatcher.js';
+import { handleAtCommand } from './ui/hooks/atCommandProcessor.js';
 
 export async function runNonInteractive(
   config: Config,
@@ -40,9 +42,28 @@ export async function runNonInteractive(
     const geminiClient = config.getGeminiClient();
 
     const abortController = new AbortController();
+
+    const { processedQuery, shouldProceed } = await handleAtCommand({
+      query: input,
+      config,
+      addItem: (_item, _timestamp) => 0,
+      onDebugMessage: () => {},
+      messageId: Date.now(),
+      signal: abortController.signal,
+    });
+
+    if (!shouldProceed || !processedQuery) {
+      // An error occurred during @include processing (e.g., file not found).
+      // The error message is already logged by handleAtCommand.
+      throw new FatalInputError(
+        'Exiting due to an error processing the @ command.',
+      );
+    }
+
     let currentMessages: Content[] = [
-      { role: 'user', parts: [{ text: input }] },
+      { role: 'user', parts: processedQuery as Part[] },
     ];
+
     let turnCount = 0;
     while (true) {
       turnCount++;
@@ -50,12 +71,11 @@ export async function runNonInteractive(
         config.getMaxSessionTurns() >= 0 &&
         turnCount > config.getMaxSessionTurns()
       ) {
-        console.error(
-          '\n Reached max session turns for this session. Increase the number of turns by specifying maxSessionTurns in settings.json.',
+        throw new FatalTurnLimitedError(
+          'Reached max session turns for this session. Increase the number of turns by specifying maxSessionTurns in settings.json.',
         );
-        return;
       }
-      const functionCalls: FunctionCall[] = [];
+      const toolCallRequests: ToolCallRequestInfo[] = [];
 
       const responseStream = geminiClient.sendMessageStream(
         currentMessages[0]?.parts || [],
@@ -72,29 +92,13 @@ export async function runNonInteractive(
         if (event.type === GeminiEventType.Content) {
           process.stdout.write(event.value);
         } else if (event.type === GeminiEventType.ToolCallRequest) {
-          const toolCallRequest = event.value;
-          const fc: FunctionCall = {
-            name: toolCallRequest.name,
-            args: toolCallRequest.args,
-            id: toolCallRequest.callId,
-          };
-          functionCalls.push(fc);
+          toolCallRequests.push(event.value);
         }
       }
 
-      if (functionCalls.length > 0) {
+      if (toolCallRequests.length > 0) {
         const toolResponseParts: Part[] = [];
-
-        for (const fc of functionCalls) {
-          const callId = fc.id ?? `${fc.name}-${Date.now()}`;
-          const requestInfo: ToolCallRequestInfo = {
-            callId,
-            name: fc.name as string,
-            args: (fc.args ?? {}) as Record<string, unknown>,
-            isClientInitiated: false,
-            prompt_id,
-          };
-
+        for (const requestInfo of toolCallRequests) {
           const toolResponse = await executeToolCall(
             config,
             requestInfo,
@@ -103,21 +107,12 @@ export async function runNonInteractive(
 
           if (toolResponse.error) {
             console.error(
-              `Error executing tool ${fc.name}: ${toolResponse.resultDisplay || toolResponse.error.message}`,
+              `Error executing tool ${requestInfo.name}: ${toolResponse.resultDisplay || toolResponse.error.message}`,
             );
           }
 
           if (toolResponse.responseParts) {
-            const parts = Array.isArray(toolResponse.responseParts)
-              ? toolResponse.responseParts
-              : [toolResponse.responseParts];
-            for (const part of parts) {
-              if (typeof part === 'string') {
-                toolResponseParts.push({ text: part });
-              } else if (part) {
-                toolResponseParts.push(part);
-              }
-            }
+            toolResponseParts.push(...toolResponse.responseParts);
           }
         }
         currentMessages = [{ role: 'user', parts: toolResponseParts }];
@@ -133,7 +128,7 @@ export async function runNonInteractive(
         config.getContentGeneratorConfig()?.authType,
       ),
     );
-    process.exit(1);
+    throw error;
   } finally {
     consolePatcher.cleanup();
     if (isTelemetrySdkInitialized()) {

packages/cli/src/services/BuiltinCommandLoader.test.ts

@@ -22,7 +22,7 @@ vi.mock('../ui/commands/restoreCommand.js', () => ({
 
 import { describe, it, expect, vi, beforeEach, type Mock } from 'vitest';
 import { BuiltinCommandLoader } from './BuiltinCommandLoader.js';
-import { Config } from '@qwen-code/qwen-code-core';
+import type { Config } from '@qwen-code/qwen-code-core';
 import { CommandKind } from '../ui/commands/types.js';
 
 import { ideCommand } from '../ui/commands/ideCommand.js';

packages/cli/src/services/BuiltinCommandLoader.ts

@@ -4,9 +4,9 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { ICommandLoader } from './types.js';
-import { SlashCommand } from '../ui/commands/types.js';
-import { Config } from '@qwen-code/qwen-code-core';
+import type { ICommandLoader } from './types.js';
+import type { SlashCommand } from '../ui/commands/types.js';
+import type { Config } from '@qwen-code/qwen-code-core';
 import { aboutCommand } from '../ui/commands/aboutCommand.js';
 import { authCommand } from '../ui/commands/authCommand.js';
 import { bugCommand } from '../ui/commands/bugCommand.js';

packages/cli/src/services/CommandService.ts

@@ -4,8 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { SlashCommand } from '../ui/commands/types.js';
-import { ICommandLoader } from './types.js';
+import type { SlashCommand } from '../ui/commands/types.js';
+import type { ICommandLoader } from './types.js';
 
 /**
  * Orchestrates the discovery and loading of all slash commands for the CLI.

packages/cli/src/services/FileCommandLoader.test.ts

@@ -5,11 +5,8 @@
  */
 
 import * as path from 'node:path';
-import {
-  Config,
-  getProjectCommandsDir,
-  getUserCommandsDir,
-} from '@qwen-code/qwen-code-core';
+import type { Config } from '@qwen-code/qwen-code-core';
+import { Storage } from '@qwen-code/qwen-code-core';
 import mock from 'mock-fs';
 import { FileCommandLoader } from './FileCommandLoader.js';
 import { assert, vi } from 'vitest';
@@ -17,15 +14,23 @@ import { createMockCommandContext } from '../test-utils/mockCommandContext.js';
 import {
   SHELL_INJECTION_TRIGGER,
   SHORTHAND_ARGS_PLACEHOLDER,
+  type PromptPipelineContent,
 } from './prompt-processors/types.js';
 import {
   ConfirmationRequiredError,
   ShellProcessor,
 } from './prompt-processors/shellProcessor.js';
 import { DefaultArgumentProcessor } from './prompt-processors/argumentProcessor.js';
-import { CommandContext } from '../ui/commands/types.js';
+import type { CommandContext } from '../ui/commands/types.js';
+import { AtFileProcessor } from './prompt-processors/atFileProcessor.js';
 
 const mockShellProcess = vi.hoisted(() => vi.fn());
+const mockAtFileProcess = vi.hoisted(() => vi.fn());
+vi.mock('./prompt-processors/atFileProcessor.js', () => ({
+  AtFileProcessor: vi.fn().mockImplementation(() => ({
+    process: mockAtFileProcess,
+  })),
+}));
 vi.mock('./prompt-processors/shellProcessor.js', () => ({
   ShellProcessor: vi.fn().mockImplementation(() => ({
     process: mockShellProcess,
@@ -57,6 +62,7 @@ vi.mock('@qwen-code/qwen-code-core', async (importOriginal) => {
     await importOriginal<typeof import('@qwen-code/qwen-code-core')>();
   return {
     ...original,
+    Storage: original.Storage,
     isCommandAllowed: vi.fn(),
     ShellExecutionService: {
       execute: vi.fn(),
@@ -70,15 +76,28 @@ describe('FileCommandLoader', () => {
   beforeEach(() => {
     vi.clearAllMocks();
     mockShellProcess.mockImplementation(
-      (prompt: string, context: CommandContext) => {
+      (prompt: PromptPipelineContent, context: CommandContext) => {
         const userArgsRaw = context?.invocation?.args || '';
-        const processedPrompt = prompt.replaceAll(
+        // This is a simplified mock. A real implementation would need to iterate
+        // through all parts and process only the text parts.
+        const firstTextPart = prompt.find(
+          (p) => typeof p === 'string' || 'text' in p,
+        );
+        let textContent = '';
+        if (typeof firstTextPart === 'string') {
+          textContent = firstTextPart;
+        } else if (firstTextPart && 'text' in firstTextPart) {
+          textContent = firstTextPart.text ?? '';
+        }
+
+        const processedText = textContent.replaceAll(
           SHORTHAND_ARGS_PLACEHOLDER,
           userArgsRaw,
         );
-        return Promise.resolve(processedPrompt);
+        return Promise.resolve([{ text: processedText }]);
       },
     );
+    mockAtFileProcess.mockImplementation(async (prompt: string) => prompt);
   });
 
   afterEach(() => {
@@ -86,7 +105,7 @@ describe('FileCommandLoader', () => {
   });
 
   it('loads a single command from a file', async () => {
-    const userCommandsDir = getUserCommandsDir();
+    const userCommandsDir = Storage.getUserCommandsDir();
     mock({
       [userCommandsDir]: {
         'test.toml': 'prompt = "This is a test prompt"',
@@ -112,7 +131,7 @@ describe('FileCommandLoader', () => {
       '',
     );
     if (result?.type === 'submit_prompt') {
-      expect(result.content).toBe('This is a test prompt');
+      expect(result.content).toEqual([{ text: 'This is a test prompt' }]);
     } else {
       assert.fail('Incorrect action type');
     }
@@ -127,7 +146,7 @@ describe('FileCommandLoader', () => {
   itif(process.platform !== 'win32')(
     'loads commands from a symlinked directory',
     async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       const realCommandsDir = '/real/commands';
       mock({
         [realCommandsDir]: {
@@ -152,7 +171,7 @@ describe('FileCommandLoader', () => {
   itif(process.platform !== 'win32')(
     'loads commands from a symlinked subdirectory',
     async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       const realNamespacedDir = '/real/namespaced-commands';
       mock({
         [userCommandsDir]: {
@@ -176,7 +195,7 @@ describe('FileCommandLoader', () => {
   );
 
   it('loads multiple commands', async () => {
-    const userCommandsDir = getUserCommandsDir();
+    const userCommandsDir = Storage.getUserCommandsDir();
     mock({
       [userCommandsDir]: {
         'test1.toml': 'prompt = "Prompt 1"',
@@ -191,7 +210,7 @@ describe('FileCommandLoader', () => {
   });
 
   it('creates deeply nested namespaces correctly', async () => {
-    const userCommandsDir = getUserCommandsDir();
+    const userCommandsDir = Storage.getUserCommandsDir();
 
     mock({
       [userCommandsDir]: {
@@ -213,7 +232,7 @@ describe('FileCommandLoader', () => {
   });
 
   it('creates namespaces from nested directories', async () => {
-    const userCommandsDir = getUserCommandsDir();
+    const userCommandsDir = Storage.getUserCommandsDir();
     mock({
       [userCommandsDir]: {
         git: {
@@ -232,8 +251,10 @@ describe('FileCommandLoader', () => {
   });
 
   it('returns both user and project commands in order', async () => {
-    const userCommandsDir = getUserCommandsDir();
-    const projectCommandsDir = getProjectCommandsDir(process.cwd());
+    const userCommandsDir = Storage.getUserCommandsDir();
+    const projectCommandsDir = new Storage(
+      process.cwd(),
+    ).getProjectCommandsDir();
     mock({
       [userCommandsDir]: {
         'test.toml': 'prompt = "User prompt"',
@@ -262,7 +283,7 @@ describe('FileCommandLoader', () => {
       '',
     );
     if (userResult?.type === 'submit_prompt') {
-      expect(userResult.content).toBe('User prompt');
+      expect(userResult.content).toEqual([{ text: 'User prompt' }]);
     } else {
       assert.fail('Incorrect action type for user command');
     }
@@ -277,14 +298,14 @@ describe('FileCommandLoader', () => {
       '',
     );
     if (projectResult?.type === 'submit_prompt') {
-      expect(projectResult.content).toBe('Project prompt');
+      expect(projectResult.content).toEqual([{ text: 'Project prompt' }]);
     } else {
       assert.fail('Incorrect action type for project command');
     }
   });
 
   it('ignores files with TOML syntax errors', async () => {
-    const userCommandsDir = getUserCommandsDir();
+    const userCommandsDir = Storage.getUserCommandsDir();
     mock({
       [userCommandsDir]: {
         'invalid.toml': 'this is not valid toml',
@@ -300,7 +321,7 @@ describe('FileCommandLoader', () => {
   });
 
   it('ignores files that are semantically invalid (missing prompt)', async () => {
-    const userCommandsDir = getUserCommandsDir();
+    const userCommandsDir = Storage.getUserCommandsDir();
     mock({
       [userCommandsDir]: {
         'no_prompt.toml': 'description = "This file is missing a prompt"',
@@ -316,7 +337,7 @@ describe('FileCommandLoader', () => {
   });
 
   it('handles filename edge cases correctly', async () => {
-    const userCommandsDir = getUserCommandsDir();
+    const userCommandsDir = Storage.getUserCommandsDir();
     mock({
       [userCommandsDir]: {
         'test.v1.toml': 'prompt = "Test prompt"',
@@ -338,7 +359,7 @@ describe('FileCommandLoader', () => {
   });
 
   it('uses a default description if not provided', async () => {
-    const userCommandsDir = getUserCommandsDir();
+    const userCommandsDir = Storage.getUserCommandsDir();
     mock({
       [userCommandsDir]: {
         'test.toml': 'prompt = "Test prompt"',
@@ -353,7 +374,7 @@ describe('FileCommandLoader', () => {
   });
 
   it('uses the provided description', async () => {
-    const userCommandsDir = getUserCommandsDir();
+    const userCommandsDir = Storage.getUserCommandsDir();
     mock({
       [userCommandsDir]: {
         'test.toml': 'prompt = "Test prompt"\ndescription = "My test command"',
@@ -368,7 +389,7 @@ describe('FileCommandLoader', () => {
   });
 
   it('should sanitize colons in filenames to prevent namespace conflicts', async () => {
-    const userCommandsDir = getUserCommandsDir();
+    const userCommandsDir = Storage.getUserCommandsDir();
     mock({
       [userCommandsDir]: {
         'legacy:command.toml': 'prompt = "This is a legacy command"',
@@ -388,7 +409,7 @@ describe('FileCommandLoader', () => {
 
   describe('Processor Instantiation Logic', () => {
     it('instantiates only DefaultArgumentProcessor if no {{args}} or !{} are present', async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       mock({
         [userCommandsDir]: {
           'simple.toml': `prompt = "Just a regular prompt"`,
@@ -403,7 +424,7 @@ describe('FileCommandLoader', () => {
     });
 
     it('instantiates only ShellProcessor if {{args}} is present (but not !{})', async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       mock({
         [userCommandsDir]: {
           'args.toml': `prompt = "Prompt with {{args}}"`,
@@ -418,7 +439,7 @@ describe('FileCommandLoader', () => {
     });
 
     it('instantiates ShellProcessor and DefaultArgumentProcessor if !{} is present (but not {{args}})', async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       mock({
         [userCommandsDir]: {
           'shell.toml': `prompt = "Prompt with !{cmd}"`,
@@ -433,7 +454,7 @@ describe('FileCommandLoader', () => {
     });
 
     it('instantiates only ShellProcessor if both {{args}} and !{} are present', async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       mock({
         [userCommandsDir]: {
           'both.toml': `prompt = "Prompt with {{args}} and !{cmd}"`,
@@ -446,12 +467,62 @@ describe('FileCommandLoader', () => {
       expect(ShellProcessor).toHaveBeenCalledTimes(1);
       expect(DefaultArgumentProcessor).not.toHaveBeenCalled();
     });
+
+    it('instantiates AtFileProcessor and DefaultArgumentProcessor if @{} is present', async () => {
+      const userCommandsDir = Storage.getUserCommandsDir();
+      mock({
+        [userCommandsDir]: {
+          'at-file.toml': `prompt = "Context: @{./my-file.txt}"`,
+        },
+      });
+
+      const loader = new FileCommandLoader(null as unknown as Config);
+      await loader.loadCommands(signal);
+
+      expect(AtFileProcessor).toHaveBeenCalledTimes(1);
+      expect(ShellProcessor).not.toHaveBeenCalled();
+      expect(DefaultArgumentProcessor).toHaveBeenCalledTimes(1);
+    });
+
+    it('instantiates ShellProcessor and AtFileProcessor if !{} and @{} are present', async () => {
+      const userCommandsDir = Storage.getUserCommandsDir();
+      mock({
+        [userCommandsDir]: {
+          'shell-and-at.toml': `prompt = "Run !{cmd} with @{file.txt}"`,
+        },
+      });
+
+      const loader = new FileCommandLoader(null as unknown as Config);
+      await loader.loadCommands(signal);
+
+      expect(ShellProcessor).toHaveBeenCalledTimes(1);
+      expect(AtFileProcessor).toHaveBeenCalledTimes(1);
+      expect(DefaultArgumentProcessor).toHaveBeenCalledTimes(1); // because no {{args}}
+    });
+
+    it('instantiates only ShellProcessor and AtFileProcessor if {{args}} and @{} are present', async () => {
+      const userCommandsDir = Storage.getUserCommandsDir();
+      mock({
+        [userCommandsDir]: {
+          'args-and-at.toml': `prompt = "Run {{args}} with @{file.txt}"`,
+        },
+      });
+
+      const loader = new FileCommandLoader(null as unknown as Config);
+      await loader.loadCommands(signal);
+
+      expect(ShellProcessor).toHaveBeenCalledTimes(1);
+      expect(AtFileProcessor).toHaveBeenCalledTimes(1);
+      expect(DefaultArgumentProcessor).not.toHaveBeenCalled();
+    });
   });
 
   describe('Extension Command Loading', () => {
     it('loads commands from active extensions', async () => {
-      const userCommandsDir = getUserCommandsDir();
-      const projectCommandsDir = getProjectCommandsDir(process.cwd());
+      const userCommandsDir = Storage.getUserCommandsDir();
+      const projectCommandsDir = new Storage(
+        process.cwd(),
+      ).getProjectCommandsDir();
       const extensionDir = path.join(
         process.cwd(),
         '.gemini/extensions/test-ext',
@@ -499,8 +570,10 @@ describe('FileCommandLoader', () => {
     });
 
     it('extension commands have extensionName metadata for conflict resolution', async () => {
-      const userCommandsDir = getUserCommandsDir();
-      const projectCommandsDir = getProjectCommandsDir(process.cwd());
+      const userCommandsDir = Storage.getUserCommandsDir();
+      const projectCommandsDir = new Storage(
+        process.cwd(),
+      ).getProjectCommandsDir();
       const extensionDir = path.join(
         process.cwd(),
         '.gemini/extensions/test-ext',
@@ -555,7 +628,7 @@ describe('FileCommandLoader', () => {
       );
       expect(result0?.type).toBe('submit_prompt');
       if (result0?.type === 'submit_prompt') {
-        expect(result0.content).toBe('User deploy command');
+        expect(result0.content).toEqual([{ text: 'User deploy command' }]);
       }
 
       expect(commands[1].name).toBe('deploy');
@@ -572,7 +645,7 @@ describe('FileCommandLoader', () => {
       );
       expect(result1?.type).toBe('submit_prompt');
       if (result1?.type === 'submit_prompt') {
-        expect(result1.content).toBe('Project deploy command');
+        expect(result1.content).toEqual([{ text: 'Project deploy command' }]);
       }
 
       expect(commands[2].name).toBe('deploy');
@@ -590,7 +663,7 @@ describe('FileCommandLoader', () => {
       );
       expect(result2?.type).toBe('submit_prompt');
       if (result2?.type === 'submit_prompt') {
-        expect(result2.content).toBe('Extension deploy command');
+        expect(result2.content).toEqual([{ text: 'Extension deploy command' }]);
       }
     });
 
@@ -733,7 +806,9 @@ describe('FileCommandLoader', () => {
         '',
       );
       if (result?.type === 'submit_prompt') {
-        expect(result.content).toBe('Nested command from extension a');
+        expect(result.content).toEqual([
+          { text: 'Nested command from extension a' },
+        ]);
       } else {
         assert.fail('Incorrect action type');
       }
@@ -742,7 +817,7 @@ describe('FileCommandLoader', () => {
 
   describe('Argument Handling Integration (via ShellProcessor)', () => {
     it('correctly processes a command with {{args}}', async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       mock({
         [userCommandsDir]: {
           'shorthand.toml':
@@ -767,14 +842,16 @@ describe('FileCommandLoader', () => {
       );
       expect(result?.type).toBe('submit_prompt');
       if (result?.type === 'submit_prompt') {
-        expect(result.content).toBe('The user wants to: do something cool');
+        expect(result.content).toEqual([
+          { text: 'The user wants to: do something cool' },
+        ]);
       }
     });
   });
 
   describe('Default Argument Processor Integration', () => {
     it('correctly processes a command without {{args}}', async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       mock({
         [userCommandsDir]: {
           'model_led.toml':
@@ -801,14 +878,14 @@ describe('FileCommandLoader', () => {
       if (result?.type === 'submit_prompt') {
         const expectedContent =
           'This is the instruction.\n\n/model_led 1.2.0 added "a feature"';
-        expect(result.content).toBe(expectedContent);
+        expect(result.content).toEqual([{ text: expectedContent }]);
       }
     });
   });
 
   describe('Shell Processor Integration', () => {
     it('instantiates ShellProcessor if {{args}} is present (even without shell trigger)', async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       mock({
         [userCommandsDir]: {
           'args_only.toml': `prompt = "Hello {{args}}"`,
@@ -821,7 +898,7 @@ describe('FileCommandLoader', () => {
       expect(ShellProcessor).toHaveBeenCalledWith('args_only');
     });
     it('instantiates ShellProcessor if the trigger is present', async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       mock({
         [userCommandsDir]: {
           'shell.toml': `prompt = "Run this: ${SHELL_INJECTION_TRIGGER}echo hello}"`,
@@ -835,7 +912,7 @@ describe('FileCommandLoader', () => {
     });
 
     it('does not instantiate ShellProcessor if no triggers ({{args}} or !{}) are present', async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       mock({
         [userCommandsDir]: {
           'regular.toml': `prompt = "Just a regular prompt"`,
@@ -849,13 +926,13 @@ describe('FileCommandLoader', () => {
     });
 
     it('returns a "submit_prompt" action if shell processing succeeds', async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       mock({
         [userCommandsDir]: {
           'shell.toml': `prompt = "Run !{echo 'hello'}"`,
         },
       });
-      mockShellProcess.mockResolvedValue('Run hello');
+      mockShellProcess.mockResolvedValue([{ text: 'Run hello' }]);
 
       const loader = new FileCommandLoader(null as unknown as Config);
       const commands = await loader.loadCommands(signal);
@@ -871,12 +948,12 @@ describe('FileCommandLoader', () => {
 
       expect(result?.type).toBe('submit_prompt');
       if (result?.type === 'submit_prompt') {
-        expect(result.content).toBe('Run hello');
+        expect(result.content).toEqual([{ text: 'Run hello' }]);
       }
     });
 
     it('returns a "confirm_shell_commands" action if shell processing requires it', async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       const rawInvocation = '/shell rm -rf /';
       mock({
         [userCommandsDir]: {
@@ -910,7 +987,7 @@ describe('FileCommandLoader', () => {
     });
 
     it('re-throws other errors from the processor', async () => {
-      const userCommandsDir = getUserCommandsDir();
+      const userCommandsDir = Storage.getUserCommandsDir();
       mock({
         [userCommandsDir]: {
           'shell.toml': `prompt = "Run !{something}"`,
@@ -934,23 +1011,36 @@ describe('FileCommandLoader', () => {
         ),
       ).rejects.toThrow('Something else went wrong');
     });
-    it('assembles the processor pipeline in the correct order (Shell -> Default)', async () => {
-      const userCommandsDir = getUserCommandsDir();
+    it('assembles the processor pipeline in the correct order (AtFile -> Shell -> Default)', async () => {
+      const userCommandsDir = Storage.getUserCommandsDir();
       mock({
         [userCommandsDir]: {
-          // This prompt uses !{} but NOT {{args}}, so both processors should be active.
+          // This prompt uses !{}, @{}, but NOT {{args}}, so all processors should be active.
           'pipeline.toml': `
-              prompt = "Shell says: ${SHELL_INJECTION_TRIGGER}echo foo}."
+              prompt = "Shell says: !{echo foo}. File says: @{./bar.txt}"
             `,
         },
+        './bar.txt': 'bar content',
       });
 
       const defaultProcessMock = vi
         .fn()
-        .mockImplementation((p) => Promise.resolve(`${p}-default-processed`));
+        .mockImplementation((p: PromptPipelineContent) =>
+          Promise.resolve([
+            { text: `${(p[0] as { text: string }).text}-default-processed` },
+          ]),
+        );
 
-      mockShellProcess.mockImplementation((p) =>
-        Promise.resolve(`${p}-shell-processed`),
+      mockShellProcess.mockImplementation((p: PromptPipelineContent) =>
+        Promise.resolve([
+          { text: `${(p[0] as { text: string }).text}-shell-processed` },
+        ]),
+      );
+
+      mockAtFileProcess.mockImplementation((p: PromptPipelineContent) =>
+        Promise.resolve([
+          { text: `${(p[0] as { text: string }).text}-at-file-processed` },
+        ]),
       );
 
       vi.mocked(DefaultArgumentProcessor).mockImplementation(
@@ -968,35 +1058,115 @@ describe('FileCommandLoader', () => {
       const result = await command!.action!(
         createMockCommandContext({
           invocation: {
-            raw: '/pipeline bar',
+            raw: '/pipeline baz',
             name: 'pipeline',
-            args: 'bar',
+            args: 'baz',
           },
         }),
-        'bar',
+        'baz',
       );
 
+      expect(mockAtFileProcess.mock.invocationCallOrder[0]).toBeLessThan(
+        mockShellProcess.mock.invocationCallOrder[0],
+      );
       expect(mockShellProcess.mock.invocationCallOrder[0]).toBeLessThan(
         defaultProcessMock.mock.invocationCallOrder[0],
       );
 
       // Verify the flow of the prompt through the processors
-      // 1. Shell processor runs first
-      expect(mockShellProcess).toHaveBeenCalledWith(
-        expect.stringContaining(SHELL_INJECTION_TRIGGER),
+      // 1. AtFile processor runs first
+      expect(mockAtFileProcess).toHaveBeenCalledWith(
+        [{ text: expect.stringContaining('@{./bar.txt}') }],
         expect.any(Object),
       );
-      // 2. Default processor runs second
+      // 2. Shell processor runs second
+      expect(mockShellProcess).toHaveBeenCalledWith(
+        [{ text: expect.stringContaining('-at-file-processed') }],
+        expect.any(Object),
+      );
+      // 3. Default processor runs third
       expect(defaultProcessMock).toHaveBeenCalledWith(
-        expect.stringContaining('-shell-processed'),
+        [{ text: expect.stringContaining('-shell-processed') }],
         expect.any(Object),
       );
 
       if (result?.type === 'submit_prompt') {
-        expect(result.content).toContain('-shell-processed-default-processed');
+        const contentAsArray = Array.isArray(result.content)
+          ? result.content
+          : [result.content];
+        expect(contentAsArray.length).toBeGreaterThan(0);
+        const firstPart = contentAsArray[0];
+
+        if (typeof firstPart === 'object' && firstPart && 'text' in firstPart) {
+          expect(firstPart.text).toContain(
+            '-at-file-processed-shell-processed-default-processed',
+          );
+        } else {
+          assert.fail(
+            'First part of content is not a text part or is a string',
+          );
+        }
       } else {
         assert.fail('Incorrect action type');
       }
     });
   });
+
+  describe('@-file Processor Integration', () => {
+    it('correctly processes a command with @{file}', async () => {
+      const userCommandsDir = Storage.getUserCommandsDir();
+      mock({
+        [userCommandsDir]: {
+          'at-file.toml':
+            'prompt = "Context from file: @{./test.txt}"\ndescription = "@-file test"',
+        },
+        './test.txt': 'file content',
+      });
+
+      mockAtFileProcess.mockImplementation(
+        async (prompt: PromptPipelineContent) => {
+          // A simplified mock of AtFileProcessor's behavior
+          const textContent = (prompt[0] as { text: string }).text;
+          if (textContent.includes('@{./test.txt}')) {
+            return [
+              {
+                text: textContent.replace('@{./test.txt}', 'file content'),
+              },
+            ];
+          }
+          return prompt;
+        },
+      );
+
+      // Prevent default processor from interfering
+      vi.mocked(DefaultArgumentProcessor).mockImplementation(
+        () =>
+          ({
+            process: (p: PromptPipelineContent) => Promise.resolve(p),
+          }) as unknown as DefaultArgumentProcessor,
+      );
+
+      const loader = new FileCommandLoader(null as unknown as Config);
+      const commands = await loader.loadCommands(signal);
+      const command = commands.find((c) => c.name === 'at-file');
+      expect(command).toBeDefined();
+
+      const result = await command!.action?.(
+        createMockCommandContext({
+          invocation: {
+            raw: '/at-file',
+            name: 'at-file',
+            args: '',
+          },
+        }),
+        '',
+      );
+      expect(result?.type).toBe('submit_prompt');
+      if (result?.type === 'submit_prompt') {
+        expect(result.content).toEqual([
+          { text: 'Context from file: file content' },
+        ]);
+      }
+    });
+  });
 });

packages/cli/src/services/FileCommandLoader.ts

@@ -4,33 +4,35 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { promises as fs } from 'fs';
-import path from 'path';
+import { promises as fs } from 'node:fs';
+import path from 'node:path';
 import toml from '@iarna/toml';
 import { glob } from 'glob';
 import { z } from 'zod';
-import {
-  Config,
-  getProjectCommandsDir,
-  getUserCommandsDir,
-} from '@qwen-code/qwen-code-core';
-import { ICommandLoader } from './types.js';
-import {
+import type { Config } from '@qwen-code/qwen-code-core';
+import { Storage } from '@qwen-code/qwen-code-core';
+import type { ICommandLoader } from './types.js';
+import type {
   CommandContext,
-  CommandKind,
   SlashCommand,
   SlashCommandActionReturn,
 } from '../ui/commands/types.js';
+import { CommandKind } from '../ui/commands/types.js';
 import { DefaultArgumentProcessor } from './prompt-processors/argumentProcessor.js';
-import {
+import type {
   IPromptProcessor,
+  PromptPipelineContent,
+} from './prompt-processors/types.js';
+import {
   SHORTHAND_ARGS_PLACEHOLDER,
   SHELL_INJECTION_TRIGGER,
+  AT_FILE_INJECTION_TRIGGER,
 } from './prompt-processors/types.js';
 import {
   ConfirmationRequiredError,
   ShellProcessor,
 } from './prompt-processors/shellProcessor.js';
+import { AtFileProcessor } from './prompt-processors/atFileProcessor.js';
 
 interface CommandDirectory {
   path: string;
@@ -130,11 +132,13 @@ export class FileCommandLoader implements ICommandLoader {
   private getCommandDirectories(): CommandDirectory[] {
     const dirs: CommandDirectory[] = [];
 
+    const storage = this.config?.storage ?? new Storage(this.projectRoot);
+
     // 1. User commands
-    dirs.push({ path: getUserCommandsDir() });
+    dirs.push({ path: Storage.getUserCommandsDir() });
 
     // 2. Project commands (override user commands)
-    dirs.push({ path: getProjectCommandsDir(this.projectRoot) });
+    dirs.push({ path: storage.getProjectCommandsDir() });
 
     // 3. Extension commands (processed last to detect all conflicts)
     if (this.config) {
@@ -225,16 +229,25 @@ export class FileCommandLoader implements ICommandLoader {
     const usesShellInjection = validDef.prompt.includes(
       SHELL_INJECTION_TRIGGER,
     );
+    const usesAtFileInjection = validDef.prompt.includes(
+      AT_FILE_INJECTION_TRIGGER,
+    );
 
-    // Interpolation (Shell Execution and Argument Injection)
-    // If the prompt uses either shell injection OR argument placeholders,
-    // we must use the ShellProcessor.
+    // 1. @-File Injection (Security First).
+    // This runs first to ensure we're not executing shell commands that
+    // could dynamically generate malicious @-paths.
+    if (usesAtFileInjection) {
+      processors.push(new AtFileProcessor(baseCommandName));
+    }
+
+    // 2. Argument and Shell Injection.
+    // This runs after file content has been safely injected.
     if (usesShellInjection || usesArgs) {
       processors.push(new ShellProcessor(baseCommandName));
     }
 
-    // Default Argument Handling
-    // If NO explicit argument injection ({{args}}) was used, we append the raw invocation.
+    // 3. Default Argument Handling.
+    // Appends the raw invocation if no explicit {{args}} are used.
     if (!usesArgs) {
       processors.push(new DefaultArgumentProcessor());
     }
@@ -254,19 +267,24 @@ export class FileCommandLoader implements ICommandLoader {
           );
           return {
             type: 'submit_prompt',
-            content: validDef.prompt, // Fallback to unprocessed prompt
+            content: [{ text: validDef.prompt }], // Fallback to unprocessed prompt
           };
         }
 
         try {
-          let processedPrompt = validDef.prompt;
+          let processedContent: PromptPipelineContent = [
+            { text: validDef.prompt },
+          ];
           for (const processor of processors) {
-            processedPrompt = await processor.process(processedPrompt, context);
+            processedContent = await processor.process(
+              processedContent,
+              context,
+            );
           }
 
           return {
             type: 'submit_prompt',
-            content: processedPrompt,
+            content: processedContent,
           };
         } catch (e) {
           // Check if it's our specific error type

packages/cli/src/services/McpPromptLoader.test.ts

@@ -0,0 +1,128 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { McpPromptLoader } from './McpPromptLoader.js';
+import type { Config } from '@qwen-code/qwen-code-core';
+import type { PromptArgument } from '@modelcontextprotocol/sdk/types.js';
+import { describe, it, expect } from 'vitest';
+
+describe('McpPromptLoader', () => {
+  const mockConfig = {} as Config;
+
+  describe('parseArgs', () => {
+    it('should handle multi-word positional arguments', () => {
+      const loader = new McpPromptLoader(mockConfig);
+      const promptArgs: PromptArgument[] = [
+        { name: 'arg1', required: true },
+        { name: 'arg2', required: true },
+      ];
+      const userArgs = 'hello world';
+      const result = loader.parseArgs(userArgs, promptArgs);
+      expect(result).toEqual({ arg1: 'hello', arg2: 'world' });
+    });
+
+    it('should handle quoted multi-word positional arguments', () => {
+      const loader = new McpPromptLoader(mockConfig);
+      const promptArgs: PromptArgument[] = [
+        { name: 'arg1', required: true },
+        { name: 'arg2', required: true },
+      ];
+      const userArgs = '"hello world" foo';
+      const result = loader.parseArgs(userArgs, promptArgs);
+      expect(result).toEqual({ arg1: 'hello world', arg2: 'foo' });
+    });
+
+    it('should handle a single positional argument with multiple words', () => {
+      const loader = new McpPromptLoader(mockConfig);
+      const promptArgs: PromptArgument[] = [{ name: 'arg1', required: true }];
+      const userArgs = 'hello world';
+      const result = loader.parseArgs(userArgs, promptArgs);
+      expect(result).toEqual({ arg1: 'hello world' });
+    });
+
+    it('should handle escaped quotes in positional arguments', () => {
+      const loader = new McpPromptLoader(mockConfig);
+      const promptArgs: PromptArgument[] = [{ name: 'arg1', required: true }];
+      const userArgs = '"hello \\"world\\""';
+      const result = loader.parseArgs(userArgs, promptArgs);
+      expect(result).toEqual({ arg1: 'hello "world"' });
+    });
+
+    it('should handle escaped backslashes in positional arguments', () => {
+      const loader = new McpPromptLoader(mockConfig);
+      const promptArgs: PromptArgument[] = [{ name: 'arg1', required: true }];
+      const userArgs = '"hello\\\\world"';
+      const result = loader.parseArgs(userArgs, promptArgs);
+      expect(result).toEqual({ arg1: 'hello\\world' });
+    });
+
+    it('should handle named args followed by positional args', () => {
+      const loader = new McpPromptLoader(mockConfig);
+      const promptArgs: PromptArgument[] = [
+        { name: 'named', required: true },
+        { name: 'pos', required: true },
+      ];
+      const userArgs = '--named="value" positional';
+      const result = loader.parseArgs(userArgs, promptArgs);
+      expect(result).toEqual({ named: 'value', pos: 'positional' });
+    });
+
+    it('should handle positional args followed by named args', () => {
+      const loader = new McpPromptLoader(mockConfig);
+      const promptArgs: PromptArgument[] = [
+        { name: 'pos', required: true },
+        { name: 'named', required: true },
+      ];
+      const userArgs = 'positional --named="value"';
+      const result = loader.parseArgs(userArgs, promptArgs);
+      expect(result).toEqual({ pos: 'positional', named: 'value' });
+    });
+
+    it('should handle positional args interspersed with named args', () => {
+      const loader = new McpPromptLoader(mockConfig);
+      const promptArgs: PromptArgument[] = [
+        { name: 'pos1', required: true },
+        { name: 'named', required: true },
+        { name: 'pos2', required: true },
+      ];
+      const userArgs = 'p1 --named="value" p2';
+      const result = loader.parseArgs(userArgs, promptArgs);
+      expect(result).toEqual({ pos1: 'p1', named: 'value', pos2: 'p2' });
+    });
+
+    it('should treat an escaped quote at the start as a literal', () => {
+      const loader = new McpPromptLoader(mockConfig);
+      const promptArgs: PromptArgument[] = [
+        { name: 'arg1', required: true },
+        { name: 'arg2', required: true },
+      ];
+      const userArgs = '\\"hello world';
+      const result = loader.parseArgs(userArgs, promptArgs);
+      expect(result).toEqual({ arg1: '"hello', arg2: 'world' });
+    });
+
+    it('should handle a complex mix of args', () => {
+      const loader = new McpPromptLoader(mockConfig);
+      const promptArgs: PromptArgument[] = [
+        { name: 'pos1', required: true },
+        { name: 'named1', required: true },
+        { name: 'pos2', required: true },
+        { name: 'named2', required: true },
+        { name: 'pos3', required: true },
+      ];
+      const userArgs =
+        'p1 --named1="value 1" "p2 has spaces" --named2=value2 "p3 \\"with quotes\\""';
+      const result = loader.parseArgs(userArgs, promptArgs);
+      expect(result).toEqual({
+        pos1: 'p1',
+        named1: 'value 1',
+        pos2: 'p2 has spaces',
+        named2: 'value2',
+        pos3: 'p3 "with quotes"',
+      });
+    });
+  });
+});

packages/cli/src/services/McpPromptLoader.ts

@@ -4,19 +4,19 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
+import type { Config } from '@qwen-code/qwen-code-core';
 import {
-  Config,
   getErrorMessage,
   getMCPServerPrompts,
 } from '@qwen-code/qwen-code-core';
-import {
+import type {
   CommandContext,
-  CommandKind,
   SlashCommand,
   SlashCommandActionReturn,
 } from '../ui/commands/types.js';
-import { ICommandLoader } from './types.js';
-import { PromptArgument } from '@modelcontextprotocol/sdk/types.js';
+import { CommandKind } from '../ui/commands/types.js';
+import type { ICommandLoader } from './types.js';
+import type { PromptArgument } from '@modelcontextprotocol/sdk/types.js';
 
 /**
  * Discovers and loads executable slash commands from prompts exposed by
@@ -169,7 +169,16 @@ export class McpPromptLoader implements ICommandLoader {
     return Promise.resolve(promptCommands);
   }
 
-  private parseArgs(
+  /**
+   * Parses the `userArgs` string representing the prompt arguments (all the text
+   * after the command) into a record matching the shape of the `promptArgs`.
+   *
+   * @param userArgs
+   * @param promptArgs
+   * @returns A record of the parsed arguments
+   * @visibleForTesting
+   */
+  parseArgs(
     userArgs: string,
     promptArgs: PromptArgument[] | undefined,
   ): Record<string, unknown> | Error {
@@ -177,28 +186,36 @@ export class McpPromptLoader implements ICommandLoader {
     const promptInputs: Record<string, unknown> = {};
 
     // arg parsing: --key="value" or --key=value
-    const namedArgRegex = /--([^=]+)=(?:"((?:\\.|[^"\\])*)"|([^ ]*))/g;
+    const namedArgRegex = /--([^=]+)=(?:"((?:\\.|[^"\\])*)"|([^ ]+))/g;
     let match;
-    const remainingArgs: string[] = [];
     let lastIndex = 0;
+    const positionalParts: string[] = [];
 
     while ((match = namedArgRegex.exec(userArgs)) !== null) {
       const key = match[1];
-      const value = match[2] ?? match[3]; // Quoted or unquoted value
+      // Extract the quoted or unquoted argument and remove escape chars.
+      const value = (match[2] ?? match[3]).replace(/\\(.)/g, '$1');
       argValues[key] = value;
       // Capture text between matches as potential positional args
       if (match.index > lastIndex) {
-        remainingArgs.push(userArgs.substring(lastIndex, match.index).trim());
+        positionalParts.push(userArgs.substring(lastIndex, match.index));
       }
       lastIndex = namedArgRegex.lastIndex;
     }
 
     // Capture any remaining text after the last named arg
     if (lastIndex < userArgs.length) {
-      remainingArgs.push(userArgs.substring(lastIndex).trim());
+      positionalParts.push(userArgs.substring(lastIndex));
     }
 
-    const positionalArgs = remainingArgs.join(' ').split(/ +/);
+    const positionalArgsString = positionalParts.join('').trim();
+    // extracts either quoted strings or non-quoted sequences of non-space characters.
+    const positionalArgRegex = /(?:"((?:\\.|[^"\\])*)"|([^ ]+))/g;
+    const positionalArgs: string[] = [];
+    while ((match = positionalArgRegex.exec(positionalArgsString)) !== null) {
+      // Extract the quoted or unquoted argument and remove escape chars.
+      positionalArgs.push((match[1] ?? match[2]).replace(/\\(.)/g, '$1'));
+    }
 
     if (!promptArgs) {
       return promptInputs;
@@ -213,19 +230,27 @@ export class McpPromptLoader implements ICommandLoader {
       (arg) => arg.required && !promptInputs[arg.name],
     );
 
-    const missingArgs: string[] = [];
-    for (let i = 0; i < unfilledArgs.length; i++) {
-      if (positionalArgs.length > i && positionalArgs[i]) {
-        promptInputs[unfilledArgs[i].name] = positionalArgs[i];
-      } else {
-        missingArgs.push(unfilledArgs[i].name);
+    if (unfilledArgs.length === 1) {
+      // If we have only one unfilled arg, we don't require quotes we just
+      // join all the given arguments together as if they were quoted.
+      promptInputs[unfilledArgs[0].name] = positionalArgs.join(' ');
+    } else {
+      const missingArgs: string[] = [];
+      for (let i = 0; i < unfilledArgs.length; i++) {
+        if (positionalArgs.length > i) {
+          promptInputs[unfilledArgs[i].name] = positionalArgs[i];
+        } else {
+          missingArgs.push(unfilledArgs[i].name);
+        }
+      }
+      if (missingArgs.length > 0) {
+        const missingArgNames = missingArgs
+          .map((name) => `--${name}`)
+          .join(', ');
+        return new Error(`Missing required argument(s): ${missingArgNames}`);
       }
     }
 
-    if (missingArgs.length > 0) {
-      const missingArgNames = missingArgs.map((name) => `--${name}`).join(', ');
-      return new Error(`Missing required argument(s): ${missingArgNames}`);
-    }
     return promptInputs;
   }
 }

packages/cli/src/services/prompt-processors/argumentProcessor.test.ts

@@ -13,7 +13,7 @@ describe('Argument Processors', () => {
     const processor = new DefaultArgumentProcessor();
 
     it('should append the full command if args are provided', async () => {
-      const prompt = 'Parse the command.';
+      const prompt = [{ text: 'Parse the command.' }];
       const context = createMockCommandContext({
         invocation: {
           raw: '/mycommand arg1 "arg two"',
@@ -22,11 +22,13 @@ describe('Argument Processors', () => {
         },
       });
       const result = await processor.process(prompt, context);
-      expect(result).toBe('Parse the command.\n\n/mycommand arg1 "arg two"');
+      expect(result).toEqual([
+        { text: 'Parse the command.\n\n/mycommand arg1 "arg two"' },
+      ]);
     });
 
     it('should NOT append the full command if no args are provided', async () => {
-      const prompt = 'Parse the command.';
+      const prompt = [{ text: 'Parse the command.' }];
       const context = createMockCommandContext({
         invocation: {
           raw: '/mycommand',
@@ -35,7 +37,7 @@ describe('Argument Processors', () => {
         },
       });
       const result = await processor.process(prompt, context);
-      expect(result).toBe('Parse the command.');
+      expect(result).toEqual([{ text: 'Parse the command.' }]);
     });
   });
 });

packages/cli/src/services/prompt-processors/argumentProcessor.ts

@@ -4,8 +4,9 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { IPromptProcessor } from './types.js';
-import { CommandContext } from '../../ui/commands/types.js';
+import { appendToLastTextPart } from '@qwen-code/qwen-code-core';
+import type { IPromptProcessor, PromptPipelineContent } from './types.js';
+import type { CommandContext } from '../../ui/commands/types.js';
 
 /**
  * Appends the user's full command invocation to the prompt if arguments are
@@ -14,9 +15,12 @@ import { CommandContext } from '../../ui/commands/types.js';
  * This processor is only used if the prompt does NOT contain {{args}}.
  */
 export class DefaultArgumentProcessor implements IPromptProcessor {
-  async process(prompt: string, context: CommandContext): Promise<string> {
-    if (context.invocation!.args) {
-      return `${prompt}\n\n${context.invocation!.raw}`;
+  async process(
+    prompt: PromptPipelineContent,
+    context: CommandContext,
+  ): Promise<PromptPipelineContent> {
+    if (context.invocation?.args) {
+      return appendToLastTextPart(prompt, context.invocation.raw);
     }
     return prompt;
   }

packages/cli/src/services/prompt-processors/atFileProcessor.test.ts

@@ -0,0 +1,221 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect, beforeEach, vi } from 'vitest';
+import { createMockCommandContext } from '../../test-utils/mockCommandContext.js';
+import { type CommandContext } from '../../ui/commands/types.js';
+import { AtFileProcessor } from './atFileProcessor.js';
+import { MessageType } from '../../ui/types.js';
+import type { Config } from '@qwen-code/qwen-code-core';
+import type { PartUnion } from '@google/genai';
+
+// Mock the core dependency
+const mockReadPathFromWorkspace = vi.hoisted(() => vi.fn());
+vi.mock('@qwen-code/qwen-code-core', async (importOriginal) => {
+  const original = await importOriginal<object>();
+  return {
+    ...original,
+    readPathFromWorkspace: mockReadPathFromWorkspace,
+  };
+});
+
+describe('AtFileProcessor', () => {
+  let context: CommandContext;
+  let mockConfig: Config;
+
+  beforeEach(() => {
+    vi.clearAllMocks();
+
+    mockConfig = {
+      // The processor only passes the config through, so we don't need a full mock.
+    } as unknown as Config;
+
+    context = createMockCommandContext({
+      services: {
+        config: mockConfig,
+      },
+    });
+
+    // Default mock success behavior: return content wrapped in a text part.
+    mockReadPathFromWorkspace.mockImplementation(
+      async (path: string): Promise<PartUnion[]> => [
+        { text: `content of ${path}` },
+      ],
+    );
+  });
+
+  it('should not change the prompt if no @{ trigger is present', async () => {
+    const processor = new AtFileProcessor();
+    const prompt: PartUnion[] = [{ text: 'This is a simple prompt.' }];
+    const result = await processor.process(prompt, context);
+    expect(result).toEqual(prompt);
+    expect(mockReadPathFromWorkspace).not.toHaveBeenCalled();
+  });
+
+  it('should not change the prompt if config service is missing', async () => {
+    const processor = new AtFileProcessor();
+    const prompt: PartUnion[] = [{ text: 'Analyze @{file.txt}' }];
+    const contextWithoutConfig = createMockCommandContext({
+      services: {
+        config: null,
+      },
+    });
+    const result = await processor.process(prompt, contextWithoutConfig);
+    expect(result).toEqual(prompt);
+    expect(mockReadPathFromWorkspace).not.toHaveBeenCalled();
+  });
+
+  describe('Parsing Logic', () => {
+    it('should replace a single valid @{path/to/file.txt} placeholder', async () => {
+      const processor = new AtFileProcessor();
+      const prompt: PartUnion[] = [
+        { text: 'Analyze this file: @{path/to/file.txt}' },
+      ];
+      const result = await processor.process(prompt, context);
+      expect(mockReadPathFromWorkspace).toHaveBeenCalledWith(
+        'path/to/file.txt',
+        mockConfig,
+      );
+      expect(result).toEqual([
+        { text: 'Analyze this file: ' },
+        { text: 'content of path/to/file.txt' },
+      ]);
+    });
+
+    it('should replace multiple different @{...} placeholders', async () => {
+      const processor = new AtFileProcessor();
+      const prompt: PartUnion[] = [
+        { text: 'Compare @{file1.js} with @{file2.js}' },
+      ];
+      const result = await processor.process(prompt, context);
+      expect(mockReadPathFromWorkspace).toHaveBeenCalledTimes(2);
+      expect(mockReadPathFromWorkspace).toHaveBeenCalledWith(
+        'file1.js',
+        mockConfig,
+      );
+      expect(mockReadPathFromWorkspace).toHaveBeenCalledWith(
+        'file2.js',
+        mockConfig,
+      );
+      expect(result).toEqual([
+        { text: 'Compare ' },
+        { text: 'content of file1.js' },
+        { text: ' with ' },
+        { text: 'content of file2.js' },
+      ]);
+    });
+
+    it('should handle placeholders at the beginning, middle, and end', async () => {
+      const processor = new AtFileProcessor();
+      const prompt: PartUnion[] = [
+        { text: '@{start.txt} in the @{middle.txt} and @{end.txt}' },
+      ];
+      const result = await processor.process(prompt, context);
+      expect(result).toEqual([
+        { text: 'content of start.txt' },
+        { text: ' in the ' },
+        { text: 'content of middle.txt' },
+        { text: ' and ' },
+        { text: 'content of end.txt' },
+      ]);
+    });
+
+    it('should correctly parse paths that contain balanced braces', async () => {
+      const processor = new AtFileProcessor();
+      const prompt: PartUnion[] = [
+        { text: 'Analyze @{path/with/{braces}/file.txt}' },
+      ];
+      const result = await processor.process(prompt, context);
+      expect(mockReadPathFromWorkspace).toHaveBeenCalledWith(
+        'path/with/{braces}/file.txt',
+        mockConfig,
+      );
+      expect(result).toEqual([
+        { text: 'Analyze ' },
+        { text: 'content of path/with/{braces}/file.txt' },
+      ]);
+    });
+
+    it('should throw an error if the prompt contains an unclosed trigger', async () => {
+      const processor = new AtFileProcessor();
+      const prompt: PartUnion[] = [{ text: 'Hello @{world' }];
+      // The new parser throws an error for unclosed injections.
+      await expect(processor.process(prompt, context)).rejects.toThrow(
+        /Unclosed injection/,
+      );
+    });
+  });
+
+  describe('Integration and Error Handling', () => {
+    it('should leave the placeholder unmodified if readPathFromWorkspace throws', async () => {
+      const processor = new AtFileProcessor();
+      const prompt: PartUnion[] = [
+        { text: 'Analyze @{not-found.txt} and @{good-file.txt}' },
+      ];
+      mockReadPathFromWorkspace.mockImplementation(async (path: string) => {
+        if (path === 'not-found.txt') {
+          throw new Error('File not found');
+        }
+        return [{ text: `content of ${path}` }];
+      });
+
+      const result = await processor.process(prompt, context);
+      expect(result).toEqual([
+        { text: 'Analyze ' },
+        { text: '@{not-found.txt}' }, // Placeholder is preserved as a text part
+        { text: ' and ' },
+        { text: 'content of good-file.txt' },
+      ]);
+    });
+  });
+
+  describe('UI Feedback', () => {
+    it('should call ui.addItem with an ERROR on failure', async () => {
+      const processor = new AtFileProcessor();
+      const prompt: PartUnion[] = [{ text: 'Analyze @{bad-file.txt}' }];
+      mockReadPathFromWorkspace.mockRejectedValue(new Error('Access denied'));
+
+      await processor.process(prompt, context);
+
+      expect(context.ui.addItem).toHaveBeenCalledTimes(1);
+      expect(context.ui.addItem).toHaveBeenCalledWith(
+        {
+          type: MessageType.ERROR,
+          text: "Failed to inject content for '@{bad-file.txt}': Access denied",
+        },
+        expect.any(Number),
+      );
+    });
+
+    it('should call ui.addItem with a WARNING if the file was ignored', async () => {
+      const processor = new AtFileProcessor();
+      const prompt: PartUnion[] = [{ text: 'Analyze @{ignored.txt}' }];
+      // Simulate an ignored file by returning an empty array.
+      mockReadPathFromWorkspace.mockResolvedValue([]);
+
+      const result = await processor.process(prompt, context);
+
+      // The placeholder should be removed, resulting in only the prefix.
+      expect(result).toEqual([{ text: 'Analyze ' }]);
+
+      expect(context.ui.addItem).toHaveBeenCalledTimes(1);
+      expect(context.ui.addItem).toHaveBeenCalledWith(
+        {
+          type: MessageType.INFO,
+          text: "File '@{ignored.txt}' was ignored by .gitignore or .geminiignore and was not included in the prompt.",
+        },
+        expect.any(Number),
+      );
+    });
+
+    it('should NOT call ui.addItem on success', async () => {
+      const processor = new AtFileProcessor();
+      const prompt: PartUnion[] = [{ text: 'Analyze @{good-file.txt}' }];
+      await processor.process(prompt, context);
+      expect(context.ui.addItem).not.toHaveBeenCalled();
+    });
+  });
+});

packages/cli/src/services/prompt-processors/atFileProcessor.ts

@@ -0,0 +1,96 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import {
+  flatMapTextParts,
+  readPathFromWorkspace,
+} from '@qwen-code/qwen-code-core';
+import type { CommandContext } from '../../ui/commands/types.js';
+import { MessageType } from '../../ui/types.js';
+import {
+  AT_FILE_INJECTION_TRIGGER,
+  type IPromptProcessor,
+  type PromptPipelineContent,
+} from './types.js';
+import { extractInjections } from './injectionParser.js';
+
+export class AtFileProcessor implements IPromptProcessor {
+  constructor(private readonly commandName?: string) {}
+
+  async process(
+    input: PromptPipelineContent,
+    context: CommandContext,
+  ): Promise<PromptPipelineContent> {
+    const config = context.services.config;
+    if (!config) {
+      return input;
+    }
+
+    return flatMapTextParts(input, async (text) => {
+      if (!text.includes(AT_FILE_INJECTION_TRIGGER)) {
+        return [{ text }];
+      }
+
+      const injections = extractInjections(
+        text,
+        AT_FILE_INJECTION_TRIGGER,
+        this.commandName,
+      );
+      if (injections.length === 0) {
+        return [{ text }];
+      }
+
+      const output: PromptPipelineContent = [];
+      let lastIndex = 0;
+
+      for (const injection of injections) {
+        const prefix = text.substring(lastIndex, injection.startIndex);
+        if (prefix) {
+          output.push({ text: prefix });
+        }
+
+        const pathStr = injection.content;
+        try {
+          const fileContentParts = await readPathFromWorkspace(pathStr, config);
+          if (fileContentParts.length === 0) {
+            const uiMessage = `File '@{${pathStr}}' was ignored by .gitignore or .geminiignore and was not included in the prompt.`;
+            context.ui.addItem(
+              { type: MessageType.INFO, text: uiMessage },
+              Date.now(),
+            );
+          }
+          output.push(...fileContentParts);
+        } catch (error) {
+          const message =
+            error instanceof Error ? error.message : String(error);
+          const uiMessage = `Failed to inject content for '@{${pathStr}}': ${message}`;
+
+          console.error(
+            `[AtFileProcessor] ${uiMessage}. Leaving placeholder in prompt.`,
+          );
+          context.ui.addItem(
+            { type: MessageType.ERROR, text: uiMessage },
+            Date.now(),
+          );
+
+          const placeholder = text.substring(
+            injection.startIndex,
+            injection.endIndex,
+          );
+          output.push({ text: placeholder });
+        }
+        lastIndex = injection.endIndex;
+      }
+
+      const suffix = text.substring(lastIndex);
+      if (suffix) {
+        output.push({ text: suffix });
+      }
+
+      return output;
+    });
+  }
+}

packages/cli/src/services/prompt-processors/injectionParser.test.ts

@@ -0,0 +1,223 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect } from 'vitest';
+import { extractInjections } from './injectionParser.js';
+
+describe('extractInjections', () => {
+  const SHELL_TRIGGER = '!{';
+  const AT_FILE_TRIGGER = '@{';
+
+  describe('Basic Functionality', () => {
+    it('should return an empty array if no trigger is present', () => {
+      const prompt = 'This is a simple prompt without injections.';
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toEqual([]);
+    });
+
+    it('should extract a single, simple injection', () => {
+      const prompt = 'Run this command: !{ls -la}';
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toEqual([
+        {
+          content: 'ls -la',
+          startIndex: 18,
+          endIndex: 27,
+        },
+      ]);
+    });
+
+    it('should extract multiple injections', () => {
+      const prompt = 'First: !{cmd1}, Second: !{cmd2}';
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toHaveLength(2);
+      expect(result[0]).toEqual({
+        content: 'cmd1',
+        startIndex: 7,
+        endIndex: 14,
+      });
+      expect(result[1]).toEqual({
+        content: 'cmd2',
+        startIndex: 24,
+        endIndex: 31,
+      });
+    });
+
+    it('should handle different triggers (e.g., @{)', () => {
+      const prompt = 'Read this file: @{path/to/file.txt}';
+      const result = extractInjections(prompt, AT_FILE_TRIGGER);
+      expect(result).toEqual([
+        {
+          content: 'path/to/file.txt',
+          startIndex: 16,
+          endIndex: 35,
+        },
+      ]);
+    });
+  });
+
+  describe('Positioning and Edge Cases', () => {
+    it('should handle injections at the start and end of the prompt', () => {
+      const prompt = '!{start} middle text !{end}';
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toHaveLength(2);
+      expect(result[0]).toEqual({
+        content: 'start',
+        startIndex: 0,
+        endIndex: 8,
+      });
+      expect(result[1]).toEqual({
+        content: 'end',
+        startIndex: 21,
+        endIndex: 27,
+      });
+    });
+
+    it('should handle adjacent injections', () => {
+      const prompt = '!{A}!{B}';
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toHaveLength(2);
+      expect(result[0]).toEqual({ content: 'A', startIndex: 0, endIndex: 4 });
+      expect(result[1]).toEqual({ content: 'B', startIndex: 4, endIndex: 8 });
+    });
+
+    it('should handle empty injections', () => {
+      const prompt = 'Empty: !{}';
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toEqual([
+        {
+          content: '',
+          startIndex: 7,
+          endIndex: 10,
+        },
+      ]);
+    });
+
+    it('should trim whitespace within the content', () => {
+      const prompt = '!{  \n command with space  \t }';
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toEqual([
+        {
+          content: 'command with space',
+          startIndex: 0,
+          endIndex: 29,
+        },
+      ]);
+    });
+
+    it('should ignore similar patterns that are not the exact trigger', () => {
+      const prompt = 'Not a trigger: !(cmd) or {cmd} or ! {cmd}';
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toEqual([]);
+    });
+
+    it('should ignore extra closing braces before the trigger', () => {
+      const prompt = 'Ignore this } then !{run}';
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toEqual([
+        {
+          content: 'run',
+          startIndex: 19,
+          endIndex: 25,
+        },
+      ]);
+    });
+
+    it('should stop parsing at the first balanced closing brace (non-greedy)', () => {
+      // This tests that the parser doesn't greedily consume extra closing braces
+      const prompt = 'Run !{ls -l}} extra braces';
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toEqual([
+        {
+          content: 'ls -l',
+          startIndex: 4,
+          endIndex: 12,
+        },
+      ]);
+    });
+  });
+
+  describe('Nested Braces (Balanced)', () => {
+    it('should correctly parse content with simple nested braces (e.g., JSON)', () => {
+      const prompt = `Send JSON: !{curl -d '{"key": "value"}'}`;
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toHaveLength(1);
+      expect(result[0].content).toBe(`curl -d '{"key": "value"}'`);
+    });
+
+    it('should correctly parse content with shell constructs (e.g., awk)', () => {
+      const prompt = `Process text: !{awk '{print $1}' file.txt}`;
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toHaveLength(1);
+      expect(result[0].content).toBe(`awk '{print $1}' file.txt`);
+    });
+
+    it('should correctly parse multiple levels of nesting', () => {
+      const prompt = `!{level1 {level2 {level3}} suffix}`;
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toHaveLength(1);
+      expect(result[0].content).toBe(`level1 {level2 {level3}} suffix`);
+      expect(result[0].endIndex).toBe(prompt.length);
+    });
+
+    it('should correctly parse paths containing balanced braces', () => {
+      const prompt = 'Analyze @{path/with/{braces}/file.txt}';
+      const result = extractInjections(prompt, AT_FILE_TRIGGER);
+      expect(result).toHaveLength(1);
+      expect(result[0].content).toBe('path/with/{braces}/file.txt');
+    });
+
+    it('should correctly handle an injection containing the trigger itself', () => {
+      // This works because the parser counts braces, it doesn't look for the trigger again until the current one is closed.
+      const prompt = '!{echo "The trigger is !{ confusing }"}';
+      const expectedContent = 'echo "The trigger is !{ confusing }"';
+      const result = extractInjections(prompt, SHELL_TRIGGER);
+      expect(result).toHaveLength(1);
+      expect(result[0].content).toBe(expectedContent);
+    });
+  });
+
+  describe('Error Handling (Unbalanced/Unclosed)', () => {
+    it('should throw an error for a simple unclosed injection', () => {
+      const prompt = 'This prompt has !{an unclosed trigger';
+      expect(() => extractInjections(prompt, SHELL_TRIGGER)).toThrow(
+        /Invalid syntax: Unclosed injection starting at index 16 \('!{'\)/,
+      );
+    });
+
+    it('should throw an error if the prompt ends inside a nested block', () => {
+      const prompt = 'This fails: !{outer {inner';
+      expect(() => extractInjections(prompt, SHELL_TRIGGER)).toThrow(
+        /Invalid syntax: Unclosed injection starting at index 12 \('!{'\)/,
+      );
+    });
+
+    it('should include the context name in the error message if provided', () => {
+      const prompt = 'Failing !{command';
+      const contextName = 'test-command';
+      expect(() =>
+        extractInjections(prompt, SHELL_TRIGGER, contextName),
+      ).toThrow(
+        /Invalid syntax in command 'test-command': Unclosed injection starting at index 8/,
+      );
+    });
+
+    it('should throw if content contains unbalanced braces (e.g., missing closing)', () => {
+      // This is functionally the same as an unclosed injection from the parser's perspective.
+      const prompt = 'Analyze @{path/with/braces{example.txt}';
+      expect(() => extractInjections(prompt, AT_FILE_TRIGGER)).toThrow(
+        /Invalid syntax: Unclosed injection starting at index 8 \('@{'\)/,
+      );
+    });
+
+    it('should clearly state that unbalanced braces in content are not supported in the error', () => {
+      const prompt = 'Analyze @{path/with/braces{example.txt}';
+      expect(() => extractInjections(prompt, AT_FILE_TRIGGER)).toThrow(
+        /Paths or commands with unbalanced braces are not supported directly/,
+      );
+    });
+  });
+});

packages/cli/src/services/prompt-processors/injectionParser.ts

@@ -0,0 +1,89 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+/**
+ * Represents a single detected injection site in a prompt string.
+ */
+export interface Injection {
+  /** The content extracted from within the braces (e.g., the command or path), trimmed. */
+  content: string;
+  /** The starting index of the injection (inclusive, points to the start of the trigger). */
+  startIndex: number;
+  /** The ending index of the injection (exclusive, points after the closing '}'). */
+  endIndex: number;
+}
+
+/**
+ * Iteratively parses a prompt string to extract injections (e.g., !{...} or @{...}),
+ * correctly handling nested braces within the content.
+ *
+ * This parser relies on simple brace counting and does not support escaping.
+ *
+ * @param prompt The prompt string to parse.
+ * @param trigger The opening trigger sequence (e.g., '!{', '@{').
+ * @param contextName Optional context name (e.g., command name) for error messages.
+ * @returns An array of extracted Injection objects.
+ * @throws Error if an unclosed injection is found.
+ */
+export function extractInjections(
+  prompt: string,
+  trigger: string,
+  contextName?: string,
+): Injection[] {
+  const injections: Injection[] = [];
+  let index = 0;
+
+  while (index < prompt.length) {
+    const startIndex = prompt.indexOf(trigger, index);
+
+    if (startIndex === -1) {
+      break;
+    }
+
+    let currentIndex = startIndex + trigger.length;
+    let braceCount = 1;
+    let foundEnd = false;
+
+    while (currentIndex < prompt.length) {
+      const char = prompt[currentIndex];
+
+      if (char === '{') {
+        braceCount++;
+      } else if (char === '}') {
+        braceCount--;
+        if (braceCount === 0) {
+          const injectionContent = prompt.substring(
+            startIndex + trigger.length,
+            currentIndex,
+          );
+          const endIndex = currentIndex + 1;
+
+          injections.push({
+            content: injectionContent.trim(),
+            startIndex,
+            endIndex,
+          });
+
+          index = endIndex;
+          foundEnd = true;
+          break;
+        }
+      }
+      currentIndex++;
+    }
+
+    // Check if the inner loop finished without finding the closing brace.
+    if (!foundEnd) {
+      const contextInfo = contextName ? ` in command '${contextName}'` : '';
+      // Enforce strict parsing (Comment 1) and clarify limitations (Comment 2).
+      throw new Error(
+        `Invalid syntax${contextInfo}: Unclosed injection starting at index ${startIndex} ('${trigger}'). Ensure braces are balanced. Paths or commands with unbalanced braces are not supported directly.`,
+      );
+    }
+  }
+
+  return injections;
+}

packages/cli/src/services/prompt-processors/shellProcessor.test.ts

@@ -7,14 +7,16 @@
 import { describe, it, expect, beforeEach, vi, type Mock } from 'vitest';
 import { ConfirmationRequiredError, ShellProcessor } from './shellProcessor.js';
 import { createMockCommandContext } from '../../test-utils/mockCommandContext.js';
-import { CommandContext } from '../../ui/commands/types.js';
-import { ApprovalMode, Config } from '@qwen-code/qwen-code-core';
-import os from 'os';
+import type { CommandContext } from '../../ui/commands/types.js';
+import type { Config } from '@qwen-code/qwen-code-core';
+import { ApprovalMode } from '@qwen-code/qwen-code-core';
+import os from 'node:os';
 import { quote } from 'shell-quote';
+import { createPartFromText } from '@google/genai';
+import type { PromptPipelineContent } from './types.js';
 
 // Helper function to determine the expected escaped string based on the current OS,
-// mirroring the logic in the actual `escapeShellArg` implementation. This makes
-// our tests robust and platform-agnostic.
+// mirroring the logic in the actual `escapeShellArg` implementation.
 function getExpectedEscapedArgForPlatform(arg: string): string {
   if (os.platform() === 'win32') {
     const comSpec = (process.env['ComSpec'] || 'cmd.exe').toLowerCase();
@@ -31,6 +33,11 @@ function getExpectedEscapedArgForPlatform(arg: string): string {
   }
 }
 
+// Helper to create PromptPipelineContent
+function createPromptPipelineContent(text: string): PromptPipelineContent {
+  return [createPartFromText(text)];
+}
+
 const mockCheckCommandPermissions = vi.hoisted(() => vi.fn());
 const mockShellExecute = vi.hoisted(() => vi.fn());
 
@@ -92,7 +99,7 @@ describe('ShellProcessor', () => {
 
   it('should throw an error if config is missing', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = '!{ls}';
+    const prompt: PromptPipelineContent = createPromptPipelineContent('!{ls}');
     const contextWithoutConfig = createMockCommandContext({
       services: {
         config: null,
@@ -106,15 +113,19 @@ describe('ShellProcessor', () => {
 
   it('should not change the prompt if no shell injections are present', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = 'This is a simple prompt with no injections.';
+    const prompt: PromptPipelineContent = createPromptPipelineContent(
+      'This is a simple prompt with no injections.',
+    );
     const result = await processor.process(prompt, context);
-    expect(result).toBe(prompt);
+    expect(result).toEqual(prompt);
     expect(mockShellExecute).not.toHaveBeenCalled();
   });
 
   it('should process a single valid shell injection if allowed', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = 'The current status is: !{git status}';
+    const prompt: PromptPipelineContent = createPromptPipelineContent(
+      'The current status is: !{git status}',
+    );
     mockCheckCommandPermissions.mockReturnValue({
       allAllowed: true,
       disallowedCommands: [],
@@ -137,12 +148,14 @@ describe('ShellProcessor', () => {
       expect.any(Object),
       false,
     );
-    expect(result).toBe('The current status is: On branch main');
+    expect(result).toEqual([{ text: 'The current status is: On branch main' }]);
   });
 
   it('should process multiple valid shell injections if all are allowed', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = '!{git status} in !{pwd}';
+    const prompt: PromptPipelineContent = createPromptPipelineContent(
+      '!{git status} in !{pwd}',
+    );
     mockCheckCommandPermissions.mockReturnValue({
       allAllowed: true,
       disallowedCommands: [],
@@ -163,12 +176,14 @@ describe('ShellProcessor', () => {
 
     expect(mockCheckCommandPermissions).toHaveBeenCalledTimes(2);
     expect(mockShellExecute).toHaveBeenCalledTimes(2);
-    expect(result).toBe('On branch main in /usr/home');
+    expect(result).toEqual([{ text: 'On branch main in /usr/home' }]);
   });
 
   it('should throw ConfirmationRequiredError if a command is not allowed in default mode', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = 'Do something dangerous: !{rm -rf /}';
+    const prompt: PromptPipelineContent = createPromptPipelineContent(
+      'Do something dangerous: !{rm -rf /}',
+    );
     mockCheckCommandPermissions.mockReturnValue({
       allAllowed: false,
       disallowedCommands: ['rm -rf /'],
@@ -181,7 +196,9 @@ describe('ShellProcessor', () => {
 
   it('should NOT throw ConfirmationRequiredError if a command is not allowed but approval mode is YOLO', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = 'Do something dangerous: !{rm -rf /}';
+    const prompt: PromptPipelineContent = createPromptPipelineContent(
+      'Do something dangerous: !{rm -rf /}',
+    );
     mockCheckCommandPermissions.mockReturnValue({
       allAllowed: false,
       disallowedCommands: ['rm -rf /'],
@@ -202,12 +219,14 @@ describe('ShellProcessor', () => {
       expect.any(Object),
       false,
     );
-    expect(result).toBe('Do something dangerous: deleted');
+    expect(result).toEqual([{ text: 'Do something dangerous: deleted' }]);
   });
 
   it('should still throw an error for a hard-denied command even in YOLO mode', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = 'Do something forbidden: !{reboot}';
+    const prompt: PromptPipelineContent = createPromptPipelineContent(
+      'Do something forbidden: !{reboot}',
+    );
     mockCheckCommandPermissions.mockReturnValue({
       allAllowed: false,
       disallowedCommands: ['reboot'],
@@ -227,7 +246,9 @@ describe('ShellProcessor', () => {
 
   it('should throw ConfirmationRequiredError with the correct command', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = 'Do something dangerous: !{rm -rf /}';
+    const prompt: PromptPipelineContent = createPromptPipelineContent(
+      'Do something dangerous: !{rm -rf /}',
+    );
     mockCheckCommandPermissions.mockReturnValue({
       allAllowed: false,
       disallowedCommands: ['rm -rf /'],
@@ -249,7 +270,9 @@ describe('ShellProcessor', () => {
 
   it('should throw ConfirmationRequiredError with multiple commands if multiple are disallowed', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = '!{cmd1} and !{cmd2}';
+    const prompt: PromptPipelineContent = createPromptPipelineContent(
+      '!{cmd1} and !{cmd2}',
+    );
     mockCheckCommandPermissions.mockImplementation((cmd) => {
       if (cmd === 'cmd1') {
         return { allAllowed: false, disallowedCommands: ['cmd1'] };
@@ -274,7 +297,9 @@ describe('ShellProcessor', () => {
 
   it('should not execute any commands if at least one requires confirmation', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = 'First: !{echo "hello"}, Second: !{rm -rf /}';
+    const prompt: PromptPipelineContent = createPromptPipelineContent(
+      'First: !{echo "hello"}, Second: !{rm -rf /}',
+    );
 
     mockCheckCommandPermissions.mockImplementation((cmd) => {
       if (cmd.includes('rm')) {
@@ -293,7 +318,9 @@ describe('ShellProcessor', () => {
 
   it('should only request confirmation for disallowed commands in a mixed prompt', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = 'Allowed: !{ls -l}, Disallowed: !{rm -rf /}';
+    const prompt: PromptPipelineContent = createPromptPipelineContent(
+      'Allowed: !{ls -l}, Disallowed: !{rm -rf /}',
+    );
 
     mockCheckCommandPermissions.mockImplementation((cmd) => ({
       allAllowed: !cmd.includes('rm'),
@@ -313,7 +340,9 @@ describe('ShellProcessor', () => {
 
   it('should execute all commands if they are on the session allowlist', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = 'Run !{cmd1} and !{cmd2}';
+    const prompt: PromptPipelineContent = createPromptPipelineContent(
+      'Run !{cmd1} and !{cmd2}',
+    );
 
     // Add commands to the session allowlist
     context.session.sessionShellAllowlist = new Set(['cmd1', 'cmd2']);
@@ -345,12 +374,14 @@ describe('ShellProcessor', () => {
       context.session.sessionShellAllowlist,
     );
     expect(mockShellExecute).toHaveBeenCalledTimes(2);
-    expect(result).toBe('Run output1 and output2');
+    expect(result).toEqual([{ text: 'Run output1 and output2' }]);
   });
 
   it('should trim whitespace from the command inside the injection before interpolation', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = 'Files: !{  ls {{args}} -l  }';
+    const prompt: PromptPipelineContent = createPromptPipelineContent(
+      'Files: !{  ls {{args}} -l  }',
+    );
 
     const rawArgs = context.invocation!.args;
 
@@ -384,7 +415,8 @@ describe('ShellProcessor', () => {
 
   it('should handle an empty command inside the injection gracefully (skips execution)', async () => {
     const processor = new ShellProcessor('test-command');
-    const prompt = 'This is weird: !{}';
+    const prompt: PromptPipelineContent =
+      createPromptPipelineContent('This is weird: !{}');
 
     const result = await processor.process(prompt, context);
 
@@ -392,77 +424,14 @@ describe('ShellProcessor', () => {
     expect(mockShellExecute).not.toHaveBeenCalled();
 
     // It replaces !{} with an empty string.
-    expect(result).toBe('This is weird: ');
-  });
-
-  describe('Robust Parsing (Balanced Braces)', () => {
-    it('should correctly parse commands containing nested braces (e.g., awk)', async () => {
-      const processor = new ShellProcessor('test-command');
-      const command = "awk '{print $1}' file.txt";
-      const prompt = `Output: !{${command}}`;
-      mockShellExecute.mockReturnValue({
-        result: Promise.resolve({ ...SUCCESS_RESULT, output: 'result' }),
-      });
-
-      const result = await processor.process(prompt, context);
-
-      expect(mockCheckCommandPermissions).toHaveBeenCalledWith(
-        command,
-        expect.any(Object),
-        context.session.sessionShellAllowlist,
-      );
-      expect(mockShellExecute).toHaveBeenCalledWith(
-        command,
-        expect.any(String),
-        expect.any(Function),
-        expect.any(Object),
-        false,
-      );
-      expect(result).toBe('Output: result');
-    });
-
-    it('should handle deeply nested braces correctly', async () => {
-      const processor = new ShellProcessor('test-command');
-      const command = "echo '{{a},{b}}'";
-      const prompt = `!{${command}}`;
-      mockShellExecute.mockReturnValue({
-        result: Promise.resolve({ ...SUCCESS_RESULT, output: '{{a},{b}}' }),
-      });
-
-      const result = await processor.process(prompt, context);
-      expect(mockShellExecute).toHaveBeenCalledWith(
-        command,
-        expect.any(String),
-        expect.any(Function),
-        expect.any(Object),
-        false,
-      );
-      expect(result).toBe('{{a},{b}}');
-    });
-
-    it('should throw an error for unclosed shell injections', async () => {
-      const processor = new ShellProcessor('test-command');
-      const prompt = 'This prompt is broken: !{ls -l';
-
-      await expect(processor.process(prompt, context)).rejects.toThrow(
-        /Unclosed shell injection/,
-      );
-    });
-
-    it('should throw an error for unclosed nested braces', async () => {
-      const processor = new ShellProcessor('test-command');
-      const prompt = 'Broken: !{echo {a}';
-
-      await expect(processor.process(prompt, context)).rejects.toThrow(
-        /Unclosed shell injection/,
-      );
-    });
+    expect(result).toEqual([{ text: 'This is weird: ' }]);
   });
 
   describe('Error Reporting', () => {
     it('should append exit code and command name on failure', async () => {
       const processor = new ShellProcessor('test-command');
-      const prompt = '!{cmd}';
+      const prompt: PromptPipelineContent =
+        createPromptPipelineContent('!{cmd}');
       mockShellExecute.mockReturnValue({
         result: Promise.resolve({
           ...SUCCESS_RESULT,
@@ -474,14 +443,17 @@ describe('ShellProcessor', () => {
 
       const result = await processor.process(prompt, context);
 
-      expect(result).toBe(
-        "some error output\n[Shell command 'cmd' exited with code 1]",
-      );
+      expect(result).toEqual([
+        {
+          text: "some error output\n[Shell command 'cmd' exited with code 1]",
+        },
+      ]);
     });
 
     it('should append signal info and command name if terminated by signal', async () => {
       const processor = new ShellProcessor('test-command');
-      const prompt = '!{cmd}';
+      const prompt: PromptPipelineContent =
+        createPromptPipelineContent('!{cmd}');
       mockShellExecute.mockReturnValue({
         result: Promise.resolve({
           ...SUCCESS_RESULT,
@@ -494,14 +466,17 @@ describe('ShellProcessor', () => {
 
       const result = await processor.process(prompt, context);
 
-      expect(result).toBe(
-        "output\n[Shell command 'cmd' terminated by signal SIGTERM]",
-      );
+      expect(result).toEqual([
+        {
+          text: "output\n[Shell command 'cmd' terminated by signal SIGTERM]",
+        },
+      ]);
     });
 
     it('should throw a detailed error if the shell fails to spawn', async () => {
       const processor = new ShellProcessor('test-command');
-      const prompt = '!{bad-command}';
+      const prompt: PromptPipelineContent =
+        createPromptPipelineContent('!{bad-command}');
       const spawnError = new Error('spawn EACCES');
       mockShellExecute.mockReturnValue({
         result: Promise.resolve({
@@ -521,7 +496,9 @@ describe('ShellProcessor', () => {
 
     it('should report abort status with command name if aborted', async () => {
       const processor = new ShellProcessor('test-command');
-      const prompt = '!{long-running-command}';
+      const prompt: PromptPipelineContent = createPromptPipelineContent(
+        '!{long-running-command}',
+      );
       const spawnError = new Error('Aborted');
       mockShellExecute.mockReturnValue({
         result: Promise.resolve({
@@ -535,9 +512,11 @@ describe('ShellProcessor', () => {
       });
 
       const result = await processor.process(prompt, context);
-      expect(result).toBe(
-        "partial output\n[Shell command 'long-running-command' aborted]",
-      );
+      expect(result).toEqual([
+        {
+          text: "partial output\n[Shell command 'long-running-command' aborted]",
+        },
+      ]);
     });
   });
 
@@ -551,29 +530,35 @@ describe('ShellProcessor', () => {
 
     it('should perform raw replacement if no shell injections are present (optimization path)', async () => {
       const processor = new ShellProcessor('test-command');
-      const prompt = 'The user said: {{args}}';
+      const prompt: PromptPipelineContent = createPromptPipelineContent(
+        'The user said: {{args}}',
+      );
 
       const result = await processor.process(prompt, context);
 
-      expect(result).toBe(`The user said: ${rawArgs}`);
+      expect(result).toEqual([{ text: `The user said: ${rawArgs}` }]);
       expect(mockShellExecute).not.toHaveBeenCalled();
     });
 
     it('should perform raw replacement outside !{} blocks', async () => {
       const processor = new ShellProcessor('test-command');
-      const prompt = 'Outside: {{args}}. Inside: !{echo "hello"}';
+      const prompt: PromptPipelineContent = createPromptPipelineContent(
+        'Outside: {{args}}. Inside: !{echo "hello"}',
+      );
       mockShellExecute.mockReturnValue({
         result: Promise.resolve({ ...SUCCESS_RESULT, output: 'hello' }),
       });
 
       const result = await processor.process(prompt, context);
 
-      expect(result).toBe(`Outside: ${rawArgs}. Inside: hello`);
+      expect(result).toEqual([{ text: `Outside: ${rawArgs}. Inside: hello` }]);
     });
 
     it('should perform escaped replacement inside !{} blocks', async () => {
       const processor = new ShellProcessor('test-command');
-      const prompt = 'Command: !{grep {{args}} file.txt}';
+      const prompt: PromptPipelineContent = createPromptPipelineContent(
+        'Command: !{grep {{args}} file.txt}',
+      );
       mockShellExecute.mockReturnValue({
         result: Promise.resolve({ ...SUCCESS_RESULT, output: 'match found' }),
       });
@@ -591,12 +576,14 @@ describe('ShellProcessor', () => {
         false,
       );
 
-      expect(result).toBe('Command: match found');
+      expect(result).toEqual([{ text: 'Command: match found' }]);
     });
 
     it('should handle both raw (outside) and escaped (inside) injection simultaneously', async () => {
       const processor = new ShellProcessor('test-command');
-      const prompt = 'User "({{args}})" requested search: !{search {{args}}}';
+      const prompt: PromptPipelineContent = createPromptPipelineContent(
+        'User "({{args}})" requested search: !{search {{args}}}',
+      );
       mockShellExecute.mockReturnValue({
         result: Promise.resolve({ ...SUCCESS_RESULT, output: 'results' }),
       });
@@ -613,12 +600,15 @@ describe('ShellProcessor', () => {
         false,
       );
 
-      expect(result).toBe(`User "(${rawArgs})" requested search: results`);
+      expect(result).toEqual([
+        { text: `User "(${rawArgs})" requested search: results` },
+      ]);
     });
 
     it('should perform security checks on the final, resolved (escaped) command', async () => {
       const processor = new ShellProcessor('test-command');
-      const prompt = '!{rm {{args}}}';
+      const prompt: PromptPipelineContent =
+        createPromptPipelineContent('!{rm {{args}}}');
 
       const expectedEscapedArgs = getExpectedEscapedArgForPlatform(rawArgs);
       const expectedResolvedCommand = `rm ${expectedEscapedArgs}`;
@@ -641,7 +631,8 @@ describe('ShellProcessor', () => {
 
     it('should report the resolved command if a hard denial occurs', async () => {
       const processor = new ShellProcessor('test-command');
-      const prompt = '!{rm {{args}}}';
+      const prompt: PromptPipelineContent =
+        createPromptPipelineContent('!{rm {{args}}}');
       const expectedEscapedArgs = getExpectedEscapedArgForPlatform(rawArgs);
       const expectedResolvedCommand = `rm ${expectedEscapedArgs}`;
       mockCheckCommandPermissions.mockReturnValue({
@@ -661,7 +652,9 @@ describe('ShellProcessor', () => {
       const processor = new ShellProcessor('test-command');
       const multilineArgs = 'first line\nsecond line';
       context.invocation!.args = multilineArgs;
-      const prompt = 'Commit message: !{git commit -m {{args}}}';
+      const prompt: PromptPipelineContent = createPromptPipelineContent(
+        'Commit message: !{git commit -m {{args}}}',
+      );
 
       const expectedEscapedArgs =
         getExpectedEscapedArgForPlatform(multilineArgs);
@@ -690,7 +683,8 @@ describe('ShellProcessor', () => {
     ])('should safely escape args containing $name', async ({ input }) => {
       const processor = new ShellProcessor('test-command');
       context.invocation!.args = input;
-      const prompt = '!{echo {{args}}}';
+      const prompt: PromptPipelineContent =
+        createPromptPipelineContent('!{echo {{args}}}');
 
       const expectedEscapedArgs = getExpectedEscapedArgForPlatform(input);
       const expectedCommand = `echo ${expectedEscapedArgs}`;

packages/cli/src/services/prompt-processors/shellProcessor.ts

@@ -10,14 +10,16 @@ import {
   escapeShellArg,
   getShellConfiguration,
   ShellExecutionService,
+  flatMapTextParts,
 } from '@qwen-code/qwen-code-core';
 
-import { CommandContext } from '../../ui/commands/types.js';
+import type { CommandContext } from '../../ui/commands/types.js';
+import type { IPromptProcessor, PromptPipelineContent } from './types.js';
 import {
-  IPromptProcessor,
   SHELL_INJECTION_TRIGGER,
   SHORTHAND_ARGS_PLACEHOLDER,
 } from './types.js';
+import { extractInjections, type Injection } from './injectionParser.js';
 
 export class ConfirmationRequiredError extends Error {
   constructor(
@@ -30,15 +32,10 @@ export class ConfirmationRequiredError extends Error {
 }
 
 /**
- * Represents a single detected shell injection site in the prompt.
+ * Represents a single detected shell injection site in the prompt,
+ * after resolution of arguments. Extends the base Injection interface.
  */
-interface ShellInjection {
-  /** The shell command extracted from within !{...}, trimmed. */
-  command: string;
-  /** The starting index of the injection (inclusive, points to '!'). */
-  startIndex: number;
-  /** The ending index of the injection (exclusive, points after '}'). */
-  endIndex: number;
+interface ResolvedShellInjection extends Injection {
   /** The command after {{args}} has been escaped and substituted. */
   resolvedCommand?: string;
 }
@@ -56,11 +53,25 @@ interface ShellInjection {
 export class ShellProcessor implements IPromptProcessor {
   constructor(private readonly commandName: string) {}
 
-  async process(prompt: string, context: CommandContext): Promise<string> {
+  async process(
+    prompt: PromptPipelineContent,
+    context: CommandContext,
+  ): Promise<PromptPipelineContent> {
+    return flatMapTextParts(prompt, (text) =>
+      this.processString(text, context),
+    );
+  }
+
+  private async processString(
+    prompt: string,
+    context: CommandContext,
+  ): Promise<PromptPipelineContent> {
     const userArgsRaw = context.invocation?.args || '';
 
     if (!prompt.includes(SHELL_INJECTION_TRIGGER)) {
-      return prompt.replaceAll(SHORTHAND_ARGS_PLACEHOLDER, userArgsRaw);
+      return [
+        { text: prompt.replaceAll(SHORTHAND_ARGS_PLACEHOLDER, userArgsRaw) },
+      ];
     }
 
     const config = context.services.config;
@@ -71,26 +82,37 @@ export class ShellProcessor implements IPromptProcessor {
     }
     const { sessionShellAllowlist } = context.session;
 
-    const injections = this.extractInjections(prompt);
+    const injections = extractInjections(
+      prompt,
+      SHELL_INJECTION_TRIGGER,
+      this.commandName,
+    );
+
     // If extractInjections found no closed blocks (and didn't throw), treat as raw.
     if (injections.length === 0) {
-      return prompt.replaceAll(SHORTHAND_ARGS_PLACEHOLDER, userArgsRaw);
+      return [
+        { text: prompt.replaceAll(SHORTHAND_ARGS_PLACEHOLDER, userArgsRaw) },
+      ];
     }
 
     const { shell } = getShellConfiguration();
     const userArgsEscaped = escapeShellArg(userArgsRaw, shell);
 
-    const resolvedInjections = injections.map((injection) => {
-      if (injection.command === '') {
-        return injection;
-      }
-      // Replace {{args}} inside the command string with the escaped version.
-      const resolvedCommand = injection.command.replaceAll(
-        SHORTHAND_ARGS_PLACEHOLDER,
-        userArgsEscaped,
-      );
-      return { ...injection, resolvedCommand };
-    });
+    const resolvedInjections: ResolvedShellInjection[] = injections.map(
+      (injection) => {
+        const command = injection.content;
+
+        if (command === '') {
+          return { ...injection, resolvedCommand: undefined };
+        }
+
+        const resolvedCommand = command.replaceAll(
+          SHORTHAND_ARGS_PLACEHOLDER,
+          userArgsEscaped,
+        );
+        return { ...injection, resolvedCommand };
+      },
+    );
 
     const commandsToConfirm = new Set<string>();
     for (const injection of resolvedInjections) {
@@ -180,69 +202,6 @@ export class ShellProcessor implements IPromptProcessor {
       userArgsRaw,
     );
 
-    return processedPrompt;
-  }
-
-  /**
-   * Iteratively parses the prompt string to extract shell injections (!{...}),
-   * correctly handling nested braces within the command.
-   *
-   * @param prompt The prompt string to parse.
-   * @returns An array of extracted ShellInjection objects.
-   * @throws Error if an unclosed injection (`!{`) is found.
-   */
-  private extractInjections(prompt: string): ShellInjection[] {
-    const injections: ShellInjection[] = [];
-    let index = 0;
-
-    while (index < prompt.length) {
-      const startIndex = prompt.indexOf(SHELL_INJECTION_TRIGGER, index);
-
-      if (startIndex === -1) {
-        break;
-      }
-
-      let currentIndex = startIndex + SHELL_INJECTION_TRIGGER.length;
-      let braceCount = 1;
-      let foundEnd = false;
-
-      while (currentIndex < prompt.length) {
-        const char = prompt[currentIndex];
-
-        // We count literal braces. This parser does not interpret shell quoting/escaping.
-        if (char === '{') {
-          braceCount++;
-        } else if (char === '}') {
-          braceCount--;
-          if (braceCount === 0) {
-            const commandContent = prompt.substring(
-              startIndex + SHELL_INJECTION_TRIGGER.length,
-              currentIndex,
-            );
-            const endIndex = currentIndex + 1;
-
-            injections.push({
-              command: commandContent.trim(),
-              startIndex,
-              endIndex,
-            });
-
-            index = endIndex;
-            foundEnd = true;
-            break;
-          }
-        }
-        currentIndex++;
-      }
-
-      // Check if the inner loop finished without finding the closing brace.
-      if (!foundEnd) {
-        throw new Error(
-          `Invalid syntax in command '${this.commandName}': Unclosed shell injection starting at index ${startIndex} ('!{'). Ensure braces are balanced.`,
-        );
-      }
-    }
-
-    return injections;
+    return [{ text: processedPrompt }];
   }
 }

packages/cli/src/services/prompt-processors/types.ts

@@ -4,7 +4,13 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { CommandContext } from '../../ui/commands/types.js';
+import type { CommandContext } from '../../ui/commands/types.js';
+import type { PartUnion } from '@google/genai';
+
+/**
+ * Defines the input/output type for prompt processors.
+ */
+export type PromptPipelineContent = PartUnion[];
 
 /**
  * Defines the interface for a prompt processor, a module that can transform
@@ -13,12 +19,8 @@ import { CommandContext } from '../../ui/commands/types.js';
  */
 export interface IPromptProcessor {
   /**
-   * Processes a prompt string, applying a specific transformation as part of a pipeline.
-   *
-   * Each processor in a command's pipeline receives the output of the previous
-   * processor. This method provides the full command context, allowing for
-   * complex transformations that may require access to invocation details,
-   * application services, or UI state.
+   * Processes a prompt input (which may contain text and multi-modal parts),
+   * applying a specific transformation as part of a pipeline.
    *
    * @param prompt The current state of the prompt string. This may have been
    *   modified by previous processors in the pipeline.
@@ -28,7 +30,10 @@ export interface IPromptProcessor {
    * @returns A promise that resolves to the transformed prompt string, which
    *   will be passed to the next processor or, if it's the last one, sent to the model.
    */
-  process(prompt: string, context: CommandContext): Promise<string>;
+  process(
+    prompt: PromptPipelineContent,
+    context: CommandContext,
+  ): Promise<PromptPipelineContent>;
 }
 
 /**
@@ -42,3 +47,8 @@ export const SHORTHAND_ARGS_PLACEHOLDER = '{{args}}';
  * The trigger string for shell command injection in custom commands.
  */
 export const SHELL_INJECTION_TRIGGER = '!{';
+
+/**
+ * The trigger string for at file injection in custom commands.
+ */
+export const AT_FILE_INJECTION_TRIGGER = '@{';

packages/cli/src/services/types.ts

@@ -4,7 +4,7 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { SlashCommand } from '../ui/commands/types.js';
+import type { SlashCommand } from '../ui/commands/types.js';
 
 /**
  * Defines the contract for any class that can load and provide slash commands.

packages/cli/src/test-utils/customMatchers.ts

@@ -12,7 +12,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { Assertion, expect } from 'vitest';
+import type { Assertion } from 'vitest';
+import { expect } from 'vitest';
 import type { TextBuffer } from '../ui/components/shared/text-buffer.js';
 
 // RegExp to detect invalid characters: backspace, and ANSI escape codes

packages/cli/src/test-utils/mockCommandContext.ts

@@ -5,10 +5,10 @@
  */
 
 import { vi } from 'vitest';
-import { CommandContext } from '../ui/commands/types.js';
-import { LoadedSettings } from '../config/settings.js';
-import { GitService } from '@qwen-code/qwen-code-core';
-import { SessionStatsState } from '../ui/contexts/SessionContext.js';
+import type { CommandContext } from '../ui/commands/types.js';
+import type { LoadedSettings } from '../config/settings.js';
+import type { GitService } from '@qwen-code/qwen-code-core';
+import type { SessionStatsState } from '../ui/contexts/SessionContext.js';
 
 // A utility type to make all properties of an object, and its nested objects, partial.
 type DeepPartial<T> = T extends object

packages/cli/src/test-utils/render.tsx

@@ -5,7 +5,7 @@
  */
 
 import { render } from 'ink-testing-library';
-import React from 'react';
+import type React from 'react';
 import { KeypressProvider } from '../ui/contexts/KeypressContext.js';
 
 export const renderWithProviders = (

packages/cli/src/ui/App.test.tsx

@@ -4,31 +4,41 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { describe, it, expect, vi, beforeEach, afterEach, Mock } from 'vitest';
-import { renderWithProviders } from '../test-utils/render.js';
-import { AppWrapper as App } from './App.js';
-import {
-  Config as ServerConfig,
-  MCPServerConfig,
-  ApprovalMode,
-  ToolRegistry,
+import type {
   AccessibilitySettings,
-  SandboxConfig,
+  AuthType,
   GeminiClient,
-  ideContext,
-  type AuthType,
+  MCPServerConfig,
+  SandboxConfig,
+  ToolRegistry,
 } from '@qwen-code/qwen-code-core';
-import { LoadedSettings, SettingsFile, Settings } from '../config/settings.js';
+import {
+  ApprovalMode,
+  Config as ServerConfig,
+  ideContext,
+} from '@qwen-code/qwen-code-core';
+import { waitFor } from '@testing-library/react';
+import { EventEmitter } from 'node:events';
 import process from 'node:process';
-import { useGeminiStream } from './hooks/useGeminiStream.js';
-import { useConsoleMessages } from './hooks/useConsoleMessages.js';
-import { StreamingState, ConsoleMessageItem } from './types.js';
-import { Tips } from './components/Tips.js';
-import { checkForUpdates, UpdateObject } from './utils/updateCheck.js';
-import { EventEmitter } from 'events';
-import { updateEventEmitter } from '../utils/updateEventEmitter.js';
+import type { Mock } from 'vitest';
+import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest';
 import * as auth from '../config/auth.js';
+import {
+  LoadedSettings,
+  type Settings,
+  type SettingsFile,
+} from '../config/settings.js';
+import { renderWithProviders } from '../test-utils/render.js';
+import { updateEventEmitter } from '../utils/updateEventEmitter.js';
+import { AppWrapper as App } from './App.js';
+import { Tips } from './components/Tips.js';
+import { useConsoleMessages } from './hooks/useConsoleMessages.js';
+import { useGeminiStream } from './hooks/useGeminiStream.js';
 import * as useTerminalSize from './hooks/useTerminalSize.js';
+import type { ConsoleMessageItem } from './types.js';
+import { StreamingState, ToolCallStatus } from './types.js';
+import type { UpdateObject } from './utils/updateCheck.js';
+import { checkForUpdates } from './utils/updateCheck.js';
 
 // Define a more complete mock server config based on actual Config
 interface MockServerConfig {
@@ -52,6 +62,7 @@ interface MockServerConfig {
   showMemoryUsage?: boolean;
   accessibility?: AccessibilitySettings;
   embeddingModel: string;
+  checkpointing?: boolean;
 
   getApiKey: Mock<() => string>;
   getModel: Mock<() => string>;
@@ -66,6 +77,7 @@ interface MockServerConfig {
   getToolCallCommand: Mock<() => string | undefined>;
   getMcpServerCommand: Mock<() => string | undefined>;
   getMcpServers: Mock<() => Record<string, MCPServerConfig> | undefined>;
+  getPromptRegistry: Mock<() => Record<string, unknown>>;
   getExtensions: Mock<
     () => Array<{ name: string; version: string; isActive: boolean }>
   >;
@@ -83,10 +95,34 @@ interface MockServerConfig {
   getShowMemoryUsage: Mock<() => boolean>;
   getAccessibility: Mock<() => AccessibilitySettings>;
   getProjectRoot: Mock<() => string | undefined>;
-  getAllGeminiMdFilenames: Mock<() => string[]>;
+  getEnablePromptCompletion: Mock<() => boolean>;
   getGeminiClient: Mock<() => GeminiClient | undefined>;
+  getCheckpointingEnabled: Mock<() => boolean>;
+  getAllGeminiMdFilenames: Mock<() => string[]>;
+  setFlashFallbackHandler: Mock<(handler: (fallback: boolean) => void) => void>;
+  getSessionId: Mock<() => string>;
   getUserTier: Mock<() => Promise<string | undefined>>;
-  getIdeClient: Mock<() => { getCurrentIde: Mock<() => string | undefined> }>;
+  getIdeMode: Mock<() => boolean>;
+  getWorkspaceContext: Mock<
+    () => {
+      getDirectories: Mock<() => string[]>;
+    }
+  >;
+  getIdeClient: Mock<
+    () => {
+      getCurrentIde: Mock<() => string | undefined>;
+      getDetectedIdeDisplayName: Mock<() => string>;
+      addStatusChangeListener: Mock<
+        (listener: (status: string) => void) => void
+      >;
+      removeStatusChangeListener: Mock<
+        (listener: (status: string) => void) => void
+      >;
+      getConnectionStatus: Mock<() => string>;
+    }
+  >;
+  isTrustedFolder: Mock<() => boolean>;
+  getScreenReader: Mock<() => boolean>;
 }
 
 // Mock @qwen-code/qwen-code-core and its Config class
@@ -147,6 +183,7 @@ vi.mock('@qwen-code/qwen-code-core', async (importOriginal) => {
         getShowMemoryUsage: vi.fn(() => opts.showMemoryUsage ?? false),
         getAccessibility: vi.fn(() => opts.accessibility ?? {}),
         getProjectRoot: vi.fn(() => opts.targetDir),
+        getEnablePromptCompletion: vi.fn(() => false),
         getGeminiClient: vi.fn(() => ({
           getUserTier: vi.fn(),
         })),
@@ -167,6 +204,7 @@ vi.mock('@qwen-code/qwen-code-core', async (importOriginal) => {
           getConnectionStatus: vi.fn(() => 'connected'),
         })),
         isTrustedFolder: vi.fn(() => true),
+        getScreenReader: vi.fn(() => false),
       };
     });
 
@@ -193,6 +231,7 @@ vi.mock('./hooks/useGeminiStream', () => ({
     initError: null,
     pendingHistoryItems: [],
     thought: null,
+    cancelOngoingRequest: vi.fn(),
   })),
 }));
 
@@ -209,8 +248,10 @@ vi.mock('./hooks/useAuthCommand', () => ({
 
 vi.mock('./hooks/useFolderTrust', () => ({
   useFolderTrust: vi.fn(() => ({
+    isTrusted: undefined,
     isFolderTrustDialogOpen: false,
     handleFolderTrustSelect: vi.fn(),
+    isRestarting: false,
   })),
 }));
 
@@ -283,6 +324,10 @@ describe('App UI', () => {
       path: '/system/settings.json',
       settings: settings.system || {},
     };
+    const systemDefaultsFile: SettingsFile = {
+      path: '/system/system-defaults.json',
+      settings: {},
+    };
     const userSettingsFile: SettingsFile = {
       path: '/user/settings.json',
       settings: settings.user || {},
@@ -293,9 +338,12 @@ describe('App UI', () => {
     };
     return new LoadedSettings(
       systemSettingsFile,
+      systemDefaultsFile,
       userSettingsFile,
       workspaceSettingsFile,
       [],
+      true,
+      new Set(),
     );
   };
 
@@ -327,7 +375,9 @@ describe('App UI', () => {
     mockConfig.getShowMemoryUsage.mockReturnValue(false); // Default for most tests
 
     // Ensure a theme is set so the theme dialog does not appear.
-    mockSettings = createMockSettings({ workspace: { theme: 'Default' } });
+    mockSettings = createMockSettings({
+      workspace: { ui: { theme: 'Default' } },
+    });
 
     // Ensure getWorkspaceContext is available if not added by the constructor
     if (!mockConfig.getWorkspaceContext) {
@@ -352,9 +402,19 @@ describe('App UI', () => {
     beforeEach(async () => {
       const { spawn } = await import('node:child_process');
       spawnEmitter = new EventEmitter();
-      spawnEmitter.stdout = new EventEmitter();
-      spawnEmitter.stderr = new EventEmitter();
-      (spawn as vi.Mock).mockReturnValue(spawnEmitter);
+      (
+        spawnEmitter as EventEmitter & {
+          stdout: EventEmitter;
+          stderr: EventEmitter;
+        }
+      ).stdout = new EventEmitter();
+      (
+        spawnEmitter as EventEmitter & {
+          stdout: EventEmitter;
+          stderr: EventEmitter;
+        }
+      ).stderr = new EventEmitter();
+      (spawn as Mock).mockReturnValue(spawnEmitter);
     });
 
     afterEach(() => {
@@ -368,6 +428,7 @@ describe('App UI', () => {
           name: '@qwen-code/qwen-code',
           latest: '1.1.0',
           current: '1.0.0',
+          type: 'major' as const,
         },
         message: 'Qwen Code update available!',
       };
@@ -383,9 +444,10 @@ describe('App UI', () => {
       );
       currentUnmount = unmount;
 
-      await new Promise((resolve) => setTimeout(resolve, 10));
-
-      expect(spawn).not.toHaveBeenCalled();
+      // Wait for any potential async operations to complete
+      await waitFor(() => {
+        expect(spawn).not.toHaveBeenCalled();
+      });
     });
 
     it('should show a success message when update succeeds', async () => {
@@ -395,6 +457,7 @@ describe('App UI', () => {
           name: '@qwen-code/qwen-code',
           latest: '1.1.0',
           current: '1.0.0',
+          type: 'major' as const,
         },
         message: 'Update available',
       };
@@ -411,11 +474,12 @@ describe('App UI', () => {
 
       updateEventEmitter.emit('update-success', info);
 
-      await new Promise((resolve) => setTimeout(resolve, 10));
-
-      expect(lastFrame()).toContain(
-        'Update successful! The new version will be used on your next run.',
-      );
+      // Wait for the success message to appear
+      await waitFor(() => {
+        expect(lastFrame()).toContain(
+          'Update successful! The new version will be used on your next run.',
+        );
+      });
     });
 
     it('should show an error message when update fails', async () => {
@@ -425,6 +489,7 @@ describe('App UI', () => {
           name: '@qwen-code/qwen-code',
           latest: '1.1.0',
           current: '1.0.0',
+          type: 'major' as const,
         },
         message: 'Update available',
       };
@@ -441,11 +506,12 @@ describe('App UI', () => {
 
       updateEventEmitter.emit('update-failed', info);
 
-      await new Promise((resolve) => setTimeout(resolve, 10));
-
-      expect(lastFrame()).toContain(
-        'Automatic update failed. Please try updating manually',
-      );
+      // Wait for the error message to appear
+      await waitFor(() => {
+        expect(lastFrame()).toContain(
+          'Automatic update failed. Please try updating manually',
+        );
+      });
     });
 
     it('should show an error message when spawn fails', async () => {
@@ -455,6 +521,7 @@ describe('App UI', () => {
           name: '@qwen-code/qwen-code',
           latest: '1.1.0',
           current: '1.0.0',
+          type: 'major' as const,
         },
         message: 'Update available',
       };
@@ -473,11 +540,12 @@ describe('App UI', () => {
       // which is what should be emitted when a spawn error occurs elsewhere.
       updateEventEmitter.emit('update-failed', info);
 
-      await new Promise((resolve) => setTimeout(resolve, 10));
-
-      expect(lastFrame()).toContain(
-        'Automatic update failed. Please try updating manually',
-      );
+      // Wait for the error message to appear
+      await waitFor(() => {
+        expect(lastFrame()).toContain(
+          'Automatic update failed. Please try updating manually',
+        );
+      });
     });
 
     it('should not auto-update if GEMINI_CLI_DISABLE_AUTOUPDATER is true', async () => {
@@ -488,6 +556,7 @@ describe('App UI', () => {
           name: '@qwen-code/qwen-code',
           latest: '1.1.0',
           current: '1.0.0',
+          type: 'major' as const,
         },
         message: 'Update available',
       };
@@ -503,9 +572,10 @@ describe('App UI', () => {
       );
       currentUnmount = unmount;
 
-      await new Promise((resolve) => setTimeout(resolve, 10));
-
-      expect(spawn).not.toHaveBeenCalled();
+      // Wait for any potential async operations to complete
+      await waitFor(() => {
+        expect(spawn).not.toHaveBeenCalled();
+      });
     });
   });
 
@@ -659,7 +729,10 @@ describe('App UI', () => {
 
   it('should display custom contextFileName in footer when set and count is 1', async () => {
     mockSettings = createMockSettings({
-      workspace: { contextFileName: 'AGENTS.md', theme: 'Default' },
+      workspace: {
+        context: { fileName: 'AGENTS.md' },
+        ui: { theme: 'Default' },
+      },
     });
     mockConfig.getGeminiMdFileCount.mockReturnValue(1);
     mockConfig.getAllGeminiMdFilenames.mockReturnValue(['AGENTS.md']);
@@ -681,8 +754,8 @@ describe('App UI', () => {
   it('should display a generic message when multiple context files with different names are provided', async () => {
     mockSettings = createMockSettings({
       workspace: {
-        contextFileName: ['AGENTS.md', 'CONTEXT.md'],
-        theme: 'Default',
+        context: { fileName: ['AGENTS.md', 'CONTEXT.md'] },
+        ui: { theme: 'Default' },
       },
     });
     mockConfig.getGeminiMdFileCount.mockReturnValue(2);
@@ -707,7 +780,10 @@ describe('App UI', () => {
 
   it('should display custom contextFileName with plural when set and count is > 1', async () => {
     mockSettings = createMockSettings({
-      workspace: { contextFileName: 'MY_NOTES.TXT', theme: 'Default' },
+      workspace: {
+        context: { fileName: 'MY_NOTES.TXT' },
+        ui: { theme: 'Default' },
+      },
     });
     mockConfig.getGeminiMdFileCount.mockReturnValue(3);
     mockConfig.getAllGeminiMdFilenames.mockReturnValue([
@@ -732,7 +808,10 @@ describe('App UI', () => {
 
   it('should not display context file message if count is 0, even if contextFileName is set', async () => {
     mockSettings = createMockSettings({
-      workspace: { contextFileName: 'ANY_FILE.MD', theme: 'Default' },
+      workspace: {
+        context: { fileName: 'ANY_FILE.MD' },
+        ui: { theme: 'Default' },
+      },
     });
     mockConfig.getGeminiMdFileCount.mockReturnValue(0);
     mockConfig.getAllGeminiMdFilenames.mockReturnValue([]);
@@ -810,7 +889,7 @@ describe('App UI', () => {
   it('should not display Tips component when hideTips is true', async () => {
     mockSettings = createMockSettings({
       workspace: {
-        hideTips: true,
+        ui: { hideTips: true },
       },
     });
 
@@ -843,7 +922,7 @@ describe('App UI', () => {
   it('should not display Header component when hideBanner is true', async () => {
     const { Header } = await import('./components/Header.js');
     mockSettings = createMockSettings({
-      user: { hideBanner: true },
+      user: { ui: { hideBanner: true } },
     });
 
     const { unmount } = renderWithProviders(
@@ -874,7 +953,7 @@ describe('App UI', () => {
 
   it('should not display Footer component when hideFooter is true', async () => {
     mockSettings = createMockSettings({
-      user: { hideFooter: true },
+      user: { ui: { hideFooter: true } },
     });
 
     const { lastFrame, unmount } = renderWithProviders(
@@ -892,9 +971,9 @@ describe('App UI', () => {
 
   it('should show footer if system says show, but workspace and user settings say hide', async () => {
     mockSettings = createMockSettings({
-      system: { hideFooter: false },
-      user: { hideFooter: true },
-      workspace: { hideFooter: true },
+      system: { ui: { hideFooter: false } },
+      user: { ui: { hideFooter: true } },
+      workspace: { ui: { hideFooter: true } },
     });
 
     const { lastFrame, unmount } = renderWithProviders(
@@ -912,9 +991,9 @@ describe('App UI', () => {
 
   it('should show tips if system says show, but workspace and user settings say hide', async () => {
     mockSettings = createMockSettings({
-      system: { hideTips: false },
-      user: { hideTips: true },
-      workspace: { hideTips: true },
+      system: { ui: { hideTips: false } },
+      user: { ui: { hideTips: true } },
+      workspace: { ui: { hideTips: true } },
     });
 
     const { unmount } = renderWithProviders(
@@ -995,6 +1074,7 @@ describe('App UI', () => {
       initError: null,
       pendingHistoryItems: [],
       thought: null,
+      cancelOngoingRequest: vi.fn(),
     });
 
     const { lastFrame, unmount } = renderWithProviders(
@@ -1020,6 +1100,7 @@ describe('App UI', () => {
         initError: null,
         pendingHistoryItems: [],
         thought: null,
+        cancelOngoingRequest: vi.fn(),
       });
 
       mockConfig.getGeminiClient.mockReturnValue({
@@ -1089,9 +1170,13 @@ describe('App UI', () => {
       const validateAuthMethodSpy = vi.spyOn(auth, 'validateAuthMethod');
       mockSettings = createMockSettings({
         workspace: {
-          selectedAuthType: 'USE_GEMINI' as AuthType,
-          useExternalAuth: false,
-          theme: 'Default',
+          security: {
+            auth: {
+              selectedType: 'USE_GEMINI' as AuthType,
+              useExternal: false,
+            },
+          },
+          ui: { theme: 'Default' },
         },
       });
 
@@ -1111,9 +1196,13 @@ describe('App UI', () => {
       const validateAuthMethodSpy = vi.spyOn(auth, 'validateAuthMethod');
       mockSettings = createMockSettings({
         workspace: {
-          selectedAuthType: 'USE_GEMINI' as AuthType,
-          useExternalAuth: true,
-          theme: 'Default',
+          security: {
+            auth: {
+              selectedType: 'USE_GEMINI' as AuthType,
+              useExternal: true,
+            },
+          },
+          ui: { theme: 'Default' },
         },
       });
 
@@ -1181,8 +1270,10 @@ describe('App UI', () => {
     it('should display the folder trust dialog when isFolderTrustDialogOpen is true', async () => {
       const { useFolderTrust } = await import('./hooks/useFolderTrust.js');
       vi.mocked(useFolderTrust).mockReturnValue({
+        isTrusted: undefined,
         isFolderTrustDialogOpen: true,
         handleFolderTrustSelect: vi.fn(),
+        isRestarting: false,
       });
 
       const { lastFrame, unmount } = renderWithProviders(
@@ -1200,8 +1291,10 @@ describe('App UI', () => {
     it('should display the folder trust dialog when the feature is enabled but the folder is not trusted', async () => {
       const { useFolderTrust } = await import('./hooks/useFolderTrust.js');
       vi.mocked(useFolderTrust).mockReturnValue({
+        isTrusted: false,
         isFolderTrustDialogOpen: true,
         handleFolderTrustSelect: vi.fn(),
+        isRestarting: false,
       });
       mockConfig.isTrustedFolder.mockReturnValue(false);
 
@@ -1220,8 +1313,10 @@ describe('App UI', () => {
     it('should not display the folder trust dialog when the feature is disabled', async () => {
       const { useFolderTrust } = await import('./hooks/useFolderTrust.js');
       vi.mocked(useFolderTrust).mockReturnValue({
+        isTrusted: false,
         isFolderTrustDialogOpen: false,
         handleFolderTrustSelect: vi.fn(),
+        isRestarting: false,
       });
       mockConfig.isTrustedFolder.mockReturnValue(false);
 
@@ -1239,7 +1334,7 @@ describe('App UI', () => {
   });
 
   describe('Message Queuing', () => {
-    let mockSubmitQuery: typeof vi.fn;
+    let mockSubmitQuery: Mock;
 
     beforeEach(() => {
       mockSubmitQuery = vi.fn();
@@ -1257,6 +1352,7 @@ describe('App UI', () => {
         initError: null,
         pendingHistoryItems: [],
         thought: null,
+        cancelOngoingRequest: vi.fn(),
       });
 
       const { unmount } = renderWithProviders(
@@ -1282,6 +1378,7 @@ describe('App UI', () => {
         initError: null,
         pendingHistoryItems: [],
         thought: null,
+        cancelOngoingRequest: vi.fn(),
       });
 
       const { unmount, rerender } = renderWithProviders(
@@ -1300,6 +1397,7 @@ describe('App UI', () => {
         initError: null,
         pendingHistoryItems: [],
         thought: null,
+        cancelOngoingRequest: vi.fn(),
       });
 
       // Rerender to trigger the useEffect with new state
@@ -1328,7 +1426,8 @@ describe('App UI', () => {
         submitQuery: mockSubmitQuery,
         initError: null,
         pendingHistoryItems: [],
-        thought: 'Processing...',
+        thought: { subject: 'Processing', description: 'Processing...' },
+        cancelOngoingRequest: vi.fn(),
       });
 
       const { unmount, lastFrame } = renderWithProviders(
@@ -1356,6 +1455,7 @@ describe('App UI', () => {
         initError: null,
         pendingHistoryItems: [],
         thought: null,
+        cancelOngoingRequest: vi.fn(),
       });
 
       const { unmount, lastFrame } = renderWithProviders(
@@ -1385,6 +1485,7 @@ describe('App UI', () => {
         initError: null,
         pendingHistoryItems: [],
         thought: null,
+        cancelOngoingRequest: vi.fn(),
       });
 
       const { unmount } = renderWithProviders(
@@ -1413,6 +1514,7 @@ describe('App UI', () => {
         initError: null,
         pendingHistoryItems: [],
         thought: null,
+        cancelOngoingRequest: vi.fn(),
       });
 
       const { unmount, lastFrame } = renderWithProviders(
@@ -1440,7 +1542,8 @@ describe('App UI', () => {
         submitQuery: mockSubmitQuery,
         initError: null,
         pendingHistoryItems: [],
-        thought: 'Processing...',
+        thought: { subject: 'Processing', description: 'Processing...' },
+        cancelOngoingRequest: vi.fn(),
       });
 
       const { lastFrame, unmount } = renderWithProviders(
@@ -1471,7 +1574,8 @@ describe('App UI', () => {
         submitQuery: mockSubmitQuery,
         initError: null,
         pendingHistoryItems: [],
-        thought: 'Processing...',
+        thought: { subject: 'Processing', description: 'Processing...' },
+        cancelOngoingRequest: vi.fn(),
       });
 
       const { lastFrame, unmount } = renderWithProviders(
@@ -1493,4 +1597,142 @@ describe('App UI', () => {
       expect(output).toContain('esc to cancel');
     });
   });
+
+  describe('debug keystroke logging', () => {
+    let consoleLogSpy: ReturnType<typeof vi.spyOn>;
+
+    beforeEach(() => {
+      consoleLogSpy = vi.spyOn(console, 'log').mockImplementation(() => {});
+    });
+
+    afterEach(() => {
+      consoleLogSpy.mockRestore();
+    });
+
+    it('should pass debugKeystrokeLogging setting to KeypressProvider', () => {
+      const mockSettingsWithDebug = createMockSettings({
+        workspace: {
+          ui: { theme: 'Default' },
+          general: { debugKeystrokeLogging: true },
+        },
+      });
+
+      const { lastFrame, unmount } = renderWithProviders(
+        <App
+          config={mockConfig as unknown as ServerConfig}
+          settings={mockSettingsWithDebug}
+          version={mockVersion}
+        />,
+      );
+      currentUnmount = unmount;
+
+      const output = lastFrame();
+
+      expect(output).toBeDefined();
+      expect(mockSettingsWithDebug.merged.general?.debugKeystrokeLogging).toBe(
+        true,
+      );
+    });
+
+    it('should use default false value when debugKeystrokeLogging is not set', () => {
+      const { lastFrame, unmount } = renderWithProviders(
+        <App
+          config={mockConfig as unknown as ServerConfig}
+          settings={mockSettings}
+          version={mockVersion}
+        />,
+      );
+      currentUnmount = unmount;
+
+      const output = lastFrame();
+
+      expect(output).toBeDefined();
+      expect(
+        mockSettings.merged.general?.debugKeystrokeLogging,
+      ).toBeUndefined();
+    });
+  });
+
+  describe('Ctrl+C behavior', () => {
+    it('should call cancel but only clear the prompt when a tool is executing', async () => {
+      const mockCancel = vi.fn();
+      let onCancelSubmitCallback = () => {};
+
+      // Simulate a tool in the "Executing" state.
+      vi.mocked(useGeminiStream).mockImplementation(
+        (
+          _client,
+          _history,
+          _addItem,
+          _config,
+          _onDebugMessage,
+          _handleSlashCommand,
+          _shellModeActive,
+          _getPreferredEditor,
+          _onAuthError,
+          _performMemoryRefresh,
+          _modelSwitchedFromQuotaError,
+          _setModelSwitchedFromQuotaError,
+          _onEditorClose,
+          onCancelSubmit, // Capture the cancel callback from App.tsx
+        ) => {
+          onCancelSubmitCallback = onCancelSubmit;
+          return {
+            streamingState: StreamingState.Responding,
+            submitQuery: vi.fn(),
+            initError: null,
+            pendingHistoryItems: [
+              {
+                type: 'tool_group',
+                tools: [
+                  {
+                    name: 'test_tool',
+                    status: ToolCallStatus.Executing,
+                    callId: 'test-call-id',
+                    description: 'Test tool description',
+                    resultDisplay: 'Test result',
+                    confirmationDetails: undefined,
+                  },
+                ],
+              },
+            ],
+            thought: null,
+            cancelOngoingRequest: () => {
+              mockCancel();
+              onCancelSubmitCallback(); // <--- This is the key change
+            },
+          };
+        },
+      );
+
+      const { stdin, lastFrame, unmount } = renderWithProviders(
+        <App
+          config={mockConfig as unknown as ServerConfig}
+          settings={mockSettings}
+          version={mockVersion}
+        />,
+      );
+      currentUnmount = unmount;
+
+      // Simulate user typing something into the prompt while a tool is running.
+      stdin.write('some text');
+      await new Promise((resolve) => setTimeout(resolve, 100));
+
+      // Verify the text is in the prompt.
+      expect(lastFrame()).toContain('some text');
+
+      // Simulate Ctrl+C.
+      stdin.write('\x03');
+      await new Promise((resolve) => setTimeout(resolve, 100));
+
+      // The main cancellation handler SHOULD be called.
+      expect(mockCancel).toHaveBeenCalled();
+
+      // The prompt should now be empty as a result of the cancellation handler's logic.
+      // We can't directly test the buffer's state, but we can see the rendered output.
+      await waitFor(() => {
+        expect(lastFrame()).not.toContain('some text');
+      });
+    });
+  });
 });

packages/cli/src/ui/App.tsx

@@ -7,14 +7,20 @@
 import { useCallback, useEffect, useMemo, useState, useRef } from 'react';
 import {
   Box,
-  DOMElement,
+  type DOMElement,
   measureElement,
   Static,
   Text,
   useStdin,
   useStdout,
 } from 'ink';
-import { StreamingState, type HistoryItem, MessageType } from './types.js';
+import {
+  StreamingState,
+  type HistoryItem,
+  MessageType,
+  ToolCallStatus,
+  type HistoryItemWithoutId,
+} from './types.js';
 import { useTerminalSize } from './hooks/useTerminalSize.js';
 import { useGeminiStream } from './hooks/useGeminiStream.js';
 import { useLoadingIndicator } from './hooks/useLoadingIndicator.js';
@@ -43,7 +49,8 @@ import { ShellConfirmationDialog } from './components/ShellConfirmationDialog.js
 import { RadioButtonSelect } from './components/shared/RadioButtonSelect.js';
 import { Colors } from './colors.js';
 import { loadHierarchicalGeminiMemory } from '../config/config.js';
-import { LoadedSettings, SettingScope } from '../config/settings.js';
+import type { LoadedSettings } from '../config/settings.js';
+import { SettingScope } from '../config/settings.js';
 import { Tips } from './components/Tips.js';
 import { ConsolePatcher } from './utils/ConsolePatcher.js';
 import { registerCleanup } from '../utils/cleanup.js';
@@ -52,23 +59,22 @@ import { HistoryItemDisplay } from './components/HistoryItemDisplay.js';
 import { ContextSummaryDisplay } from './components/ContextSummaryDisplay.js';
 import { useHistory } from './hooks/useHistoryManager.js';
 import process from 'node:process';
+import type { EditorType, Config, IdeContext } from '@qwen-code/qwen-code-core';
 import {
-  getErrorMessage,
-  type Config,
-  getAllGeminiMdFilenames,
   ApprovalMode,
+  getAllGeminiMdFilenames,
   isEditorAvailable,
-  EditorType,
-  FlashFallbackEvent,
-  logFlashFallback,
+  getErrorMessage,
   AuthType,
-  type IdeContext,
+  logFlashFallback,
+  FlashFallbackEvent,
   ideContext,
+  isProQuotaExceededError,
+  isGenericQuotaExceededError,
+  UserTierId,
 } from '@qwen-code/qwen-code-core';
-import {
-  IdeIntegrationNudge,
-  IdeIntegrationNudgeResult,
-} from './IdeIntegrationNudge.js';
+import type { IdeIntegrationNudgeResult } from './IdeIntegrationNudge.js';
+import { IdeIntegrationNudge } from './IdeIntegrationNudge.js';
 import { validateAuthMethod } from '../config/auth.js';
 import { useLogger } from './hooks/useLogger.js';
 import { StreamingContext } from './contexts/StreamingContext.js';
@@ -82,18 +88,14 @@ import { useBracketedPaste } from './hooks/useBracketedPaste.js';
 import { useTextBuffer } from './components/shared/text-buffer.js';
 import { useVimMode, VimModeProvider } from './contexts/VimModeContext.js';
 import { useVim } from './hooks/vim.js';
-import { useKeypress, Key } from './hooks/useKeypress.js';
+import type { Key } from './hooks/useKeypress.js';
+import { useKeypress } from './hooks/useKeypress.js';
 import { KeypressProvider } from './contexts/KeypressContext.js';
 import { useKittyKeyboardProtocol } from './hooks/useKittyKeyboardProtocol.js';
 import { keyMatchers, Command } from './keyMatchers.js';
-import * as fs from 'fs';
+import * as fs from 'node:fs';
 import { UpdateNotification } from './components/UpdateNotification.js';
-import {
-  isProQuotaExceededError,
-  isGenericQuotaExceededError,
-  UserTierId,
-} from '@qwen-code/qwen-code-core';
-import { UpdateObject } from './utils/updateCheck.js';
+import type { UpdateObject } from './utils/updateCheck.js';
 import ansiEscapes from 'ansi-escapes';
 import { OverflowProvider } from './contexts/OverflowContext.js';
 import { ShowMoreLines } from './components/ShowMoreLines.js';
@@ -103,6 +105,8 @@ import { SettingsDialog } from './components/SettingsDialog.js';
 import { setUpdateHandler } from '../utils/handleAutoUpdate.js';
 import { appEvents, AppEvent } from '../utils/events.js';
 import { isNarrowWidth } from './utils/isNarrowWidth.js';
+import { useWorkspaceMigration } from './hooks/useWorkspaceMigration.js';
+import { WorkspaceMigrationDialog } from './components/WorkspaceMigrationDialog.js';
 
 const CTRL_EXIT_PROMPT_DURATION_MS = 1000;
 // Maximum number of queued messages to display in UI to prevent performance issues
@@ -115,12 +119,26 @@ interface AppProps {
   version: string;
 }
 
+function isToolExecuting(pendingHistoryItems: HistoryItemWithoutId[]) {
+  return pendingHistoryItems.some((item) => {
+    if (item && item.type === 'tool_group') {
+      return item.tools.some(
+        (tool) => ToolCallStatus.Executing === tool.status,
+      );
+    }
+    return false;
+  });
+}
+
 export const AppWrapper = (props: AppProps) => {
   const kittyProtocolStatus = useKittyKeyboardProtocol();
   return (
     <KeypressProvider
       kittyProtocolEnabled={kittyProtocolStatus.enabled}
       config={props.config}
+      debugKeystrokeLogging={
+        props.settings.merged.general?.debugKeystrokeLogging
+      }
     >
       <SessionStatsProvider>
         <VimModeProvider settings={props.settings}>
@@ -147,7 +165,7 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
   const shouldShowIdePrompt =
     currentIDE &&
     !config.getIdeMode() &&
-    !settings.merged.hasSeenIdeIntegrationNudge &&
+    !settings.merged.ide?.hasSeenNudge &&
     !idePromptAnswered;
 
   useEffect(() => {
@@ -211,6 +229,12 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
   >();
   const [showEscapePrompt, setShowEscapePrompt] = useState(false);
   const [isProcessing, setIsProcessing] = useState<boolean>(false);
+  const {
+    showWorkspaceMigrationDialog,
+    workspaceExtensions,
+    onWorkspaceMigrationDialogOpen,
+    onWorkspaceMigrationDialogClose,
+  } = useWorkspaceMigration(settings);
 
   useEffect(() => {
     const unsubscribe = ideContext.subscribeToIdeContext(setIdeContextState);
@@ -269,10 +293,8 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
   const { isSettingsDialogOpen, openSettingsDialog, closeSettingsDialog } =
     useSettingsCommand();
 
-  const { isFolderTrustDialogOpen, handleFolderTrustSelect } = useFolderTrust(
-    settings,
-    setIsTrustedFolder,
-  );
+  const { isFolderTrustDialogOpen, handleFolderTrustSelect, isRestarting } =
+    useFolderTrust(settings, setIsTrustedFolder);
 
   const {
     isAuthDialogOpen,
@@ -292,16 +314,21 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
   } = useQwenAuth(settings, isAuthenticating);
 
   useEffect(() => {
-    if (settings.merged.selectedAuthType && !settings.merged.useExternalAuth) {
-      const error = validateAuthMethod(settings.merged.selectedAuthType);
+    if (
+      settings.merged.security?.auth?.selectedType &&
+      !settings.merged.security?.auth?.useExternal
+    ) {
+      const error = validateAuthMethod(
+        settings.merged.security.auth.selectedType,
+      );
       if (error) {
         setAuthError(error);
         openAuthDialog();
       }
     }
   }, [
-    settings.merged.selectedAuthType,
-    settings.merged.useExternalAuth,
+    settings.merged.security?.auth?.selectedType,
+    settings.merged.security?.auth?.useExternal,
     openAuthDialog,
     setAuthError,
   ]);
@@ -357,14 +384,14 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
     try {
       const { memoryContent, fileCount } = await loadHierarchicalGeminiMemory(
         process.cwd(),
-        settings.merged.loadMemoryFromIncludeDirectories
+        settings.merged.context?.loadMemoryFromIncludeDirectories
           ? config.getWorkspaceContext().getDirectories()
           : [],
         config.getDebugMode(),
         config.getFileService(),
         settings.merged,
         config.getExtensionContextFilePaths(),
-        settings.merged.memoryImportFormat || 'tree', // Use setting or default to 'tree'
+        settings.merged.context?.importFormat || 'tree', // Use setting or default to 'tree'
         config.getFileFilteringOptions(),
       );
 
@@ -522,7 +549,7 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
   }, []);
 
   const getPreferredEditor = useCallback(() => {
-    const editorType = settings.merged.preferredEditor;
+    const editorType = settings.merged.general?.preferredEditor;
     const isValidEditor = isEditorAvailable(editorType);
     if (!isValidEditor) {
       openEditorDialog();
@@ -608,6 +635,11 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
     () => cancelHandlerRef.current(),
   );
 
+  const pendingHistoryItems = useMemo(
+    () => [...pendingSlashCommandHistoryItems, ...pendingGeminiHistoryItems],
+    [pendingSlashCommandHistoryItems, pendingGeminiHistoryItems],
+  );
+
   // Message queue for handling input during streaming
   const { messageQueue, addMessage, clearQueue, getQueuedMessagesText } =
     useMessageQueue({
@@ -617,6 +649,11 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
 
   // Update the cancel handler with message queue support
   cancelHandlerRef.current = useCallback(() => {
+    if (isToolExecuting(pendingHistoryItems)) {
+      buffer.setText(''); // Just clear the prompt
+      return;
+    }
+
     const lastUserMessage = userMessages.at(-1);
     let textToSet = lastUserMessage || '';
 
@@ -630,7 +667,13 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
     if (textToSet) {
       buffer.setText(textToSet);
     }
-  }, [buffer, userMessages, getQueuedMessagesText, clearQueue]);
+  }, [
+    buffer,
+    userMessages,
+    getQueuedMessagesText,
+    clearQueue,
+    pendingHistoryItems,
+  ]);
 
   // Input handling - queue messages for processing
   const handleFinalSubmit = useCallback(
@@ -666,12 +709,10 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
   );
 
   const { handleInput: vimHandleInput } = useVim(buffer, handleFinalSubmit);
-  const pendingHistoryItems = [...pendingSlashCommandHistoryItems];
-  pendingHistoryItems.push(...pendingGeminiHistoryItems);
 
   const { elapsedTime, currentLoadingPhrase } =
     useLoadingIndicator(streamingState);
-  const showAutoAcceptIndicator = useAutoAcceptIndicator({ config });
+  const showAutoAcceptIndicator = useAutoAcceptIndicator({ config, addItem });
 
   const handleExit = useCallback(
     (
@@ -698,6 +739,11 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
 
   const handleGlobalKeypress = useCallback(
     (key: Key) => {
+      // Debug log keystrokes if enabled
+      if (settings.merged.general?.debugKeystrokeLogging) {
+        console.log('[DEBUG] Keystroke:', JSON.stringify(key));
+      }
+
       let enteringConstrainHeightMode = false;
       if (!constrainHeight) {
         enteringConstrainHeightMode = true;
@@ -761,6 +807,7 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
       handleSlashCommand,
       isAuthenticating,
       cancelOngoingRequest,
+      settings.merged.general?.debugKeystrokeLogging,
     ],
   );
 
@@ -774,7 +821,7 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
     }
   }, [config, config.getGeminiMdFileCount]);
 
-  const logger = useLogger();
+  const logger = useLogger(config.storage);
 
   useEffect(() => {
     const fetchUserMessages = async () => {
@@ -876,12 +923,12 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
   const branchName = useGitBranchName(config.getTargetDir());
 
   const contextFileNames = useMemo(() => {
-    const fromSettings = settings.merged.contextFileName;
+    const fromSettings = settings.merged.context?.fileName;
     if (fromSettings) {
       return Array.isArray(fromSettings) ? fromSettings : [fromSettings];
     }
     return getAllGeminiMdFilenames();
-  }, [settings.merged.contextFileName]);
+  }, [settings.merged.context?.fileName]);
 
   const initialPrompt = useMemo(() => config.getQuestion(), [config]);
   const geminiClient = config.getGeminiClient();
@@ -957,10 +1004,12 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
           key={staticKey}
           items={[
             <Box flexDirection="column" key="header">
-              {!settings.merged.hideBanner && (
-                <Header version={version} nightly={nightly} />
+              {!(
+                settings.merged.ui?.hideBanner || config.getScreenReader()
+              ) && <Header version={version} nightly={nightly} />}
+              {!(settings.merged.ui?.hideTips || config.getScreenReader()) && (
+                <Tips config={config} />
               )}
-              {!settings.merged.hideTips && <Tips config={config} />}
             </Box>,
             ...history.map((h) => (
               <HistoryItemDisplay
@@ -1016,14 +1065,22 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
               ))}
             </Box>
           )}
-
-          {shouldShowIdePrompt && currentIDE ? (
+          {showWorkspaceMigrationDialog ? (
+            <WorkspaceMigrationDialog
+              workspaceExtensions={workspaceExtensions}
+              onOpen={onWorkspaceMigrationDialogOpen}
+              onClose={onWorkspaceMigrationDialogClose}
+            />
+          ) : shouldShowIdePrompt && currentIDE ? (
             <IdeIntegrationNudge
               ide={currentIDE}
               onComplete={handleIdePromptComplete}
             />
           ) : isFolderTrustDialogOpen ? (
-            <FolderTrustDialog onSelect={handleFolderTrustSelect} />
+            <FolderTrustDialog
+              onSelect={handleFolderTrustSelect}
+              isRestarting={isRestarting}
+            />
           ) : shellConfirmationRequest ? (
             <ShellConfirmationDialog request={shellConfirmationRequest} />
           ) : confirmationRequest ? (
@@ -1146,12 +1203,14 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
               <LoadingIndicator
                 thought={
                   streamingState === StreamingState.WaitingForConfirmation ||
-                  config.getAccessibility()?.disableLoadingPhrases
+                  config.getAccessibility()?.disableLoadingPhrases ||
+                  config.getScreenReader()
                     ? undefined
                     : thought
                 }
                 currentLoadingPhrase={
-                  config.getAccessibility()?.disableLoadingPhrases
+                  config.getAccessibility()?.disableLoadingPhrases ||
+                  config.getScreenReader()
                     ? undefined
                     : currentLoadingPhrase
                 }
@@ -1182,8 +1241,7 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
                     <Box paddingLeft={2}>
                       <Text dimColor>
                         ... (+
-                        {messageQueue.length -
-                          MAX_DISPLAYED_QUEUED_MESSAGES}{' '}
+                        {messageQueue.length - MAX_DISPLAYED_QUEUED_MESSAGES}
                         more)
                       </Text>
                     </Box>
@@ -1303,7 +1361,7 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
               )}
             </Box>
           )}
-          {!settings.merged.hideFooter && (
+          {!settings.merged.ui?.hideFooter && (
             <Footer
               model={currentModel}
               targetDir={config.getTargetDir()}
@@ -1315,7 +1373,7 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
               showErrorDetails={showErrorDetails}
               showMemoryUsage={
                 config.getDebugMode() ||
-                settings.merged.showMemoryUsage ||
+                settings.merged.ui?.showMemoryUsage ||
                 false
               }
               promptTokenCount={sessionStats.lastPromptTokenCount}

packages/cli/src/ui/IdeIntegrationNudge.tsx

@@ -4,12 +4,10 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { DetectedIde, getIdeInfo } from '@qwen-code/qwen-code-core';
+import { type DetectedIde, getIdeInfo } from '@qwen-code/qwen-code-core';
 import { Box, Text } from 'ink';
-import {
-  RadioButtonSelect,
-  RadioSelectItem,
-} from './components/shared/RadioButtonSelect.js';
+import type { RadioSelectItem } from './components/shared/RadioButtonSelect.js';
+import { RadioButtonSelect } from './components/shared/RadioButtonSelect.js';
 import { useKeypress } from './hooks/useKeypress.js';
 
 export type IdeIntegrationNudgeResult = {
@@ -88,7 +86,7 @@ export function IdeIntegrationNudge({
       <Box marginBottom={1} flexDirection="column">
         <Text>
           <Text color="yellow">{'> '}</Text>
-          {`Do you want to connect ${ideName ?? 'your'} editor to Qwen Code?`}
+          {`Do you want to connect ${ideName ?? 'your editor'} to Qwen Code?`}
         </Text>
         <Text dimColor>{installText}</Text>
       </Box>

packages/cli/src/ui/colors.ts

@@ -5,7 +5,7 @@
  */
 
 import { themeManager } from './themes/theme-manager.js';
-import { ColorsTheme } from './themes/theme.js';
+import type { ColorsTheme } from './themes/theme.js';
 
 export const Colors: ColorsTheme = {
   get type() {

packages/cli/src/ui/commands/aboutCommand.test.ts

@@ -11,7 +11,7 @@ import { createMockCommandContext } from '../../test-utils/mockCommandContext.js
 import * as versionUtils from '../../utils/version.js';
 import { MessageType } from '../types.js';
 
-import { IdeClient } from '../../../../core/src/ide/ide-client.js';
+import type { IdeClient } from '../../../../core/src/ide/ide-client.js';
 
 vi.mock('../../utils/version.js', () => ({
   getCliVersion: vi.fn(),
@@ -32,7 +32,11 @@ describe('aboutCommand', () => {
         },
         settings: {
           merged: {
-            selectedAuthType: 'test-auth',
+            security: {
+              auth: {
+                selectedType: 'test-auth',
+              },
+            },
           },
         },
       },

packages/cli/src/ui/commands/aboutCommand.ts

@@ -5,7 +5,8 @@
  */
 
 import { getCliVersion } from '../../utils/version.js';
-import { CommandKind, SlashCommand } from './types.js';
+import type { SlashCommand } from './types.js';
+import { CommandKind } from './types.js';
 import process from 'node:process';
 import { MessageType, type HistoryItemAbout } from '../types.js';
 
@@ -26,7 +27,7 @@ export const aboutCommand: SlashCommand = {
     const modelVersion = context.services.config?.getModel() || 'Unknown';
     const cliVersion = await getCliVersion();
     const selectedAuthType =
-      context.services.settings.merged.selectedAuthType || '';
+      context.services.settings.merged.security?.auth?.selectedType || '';
     const gcpProject = process.env['GOOGLE_CLOUD_PROJECT'] || '';
     const ideClient =
       (context.services.config?.getIdeMode() &&

packages/cli/src/ui/commands/authCommand.ts

@@ -4,7 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { CommandKind, OpenDialogActionReturn, SlashCommand } from './types.js';
+import type { OpenDialogActionReturn, SlashCommand } from './types.js';
+import { CommandKind } from './types.js';
 
 export const authCommand: SlashCommand = {
   name: 'auth',

packages/cli/src/ui/commands/chatCommand.test.ts

@@ -4,29 +4,22 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import {
-  vi,
-  describe,
-  it,
-  expect,
-  beforeEach,
-  afterEach,
-  Mocked,
-} from 'vitest';
+import type { Mocked } from 'vitest';
+import { vi, describe, it, expect, beforeEach, afterEach } from 'vitest';
 
-import {
-  type CommandContext,
+import type {
   MessageActionReturn,
   SlashCommand,
+  CommandContext,
 } from './types.js';
 import { createMockCommandContext } from '../../test-utils/mockCommandContext.js';
-import { Content } from '@google/genai';
-import { GeminiClient } from '@qwen-code/qwen-code-core';
+import type { Content } from '@google/genai';
+import type { GeminiClient } from '@qwen-code/qwen-code-core';
 
-import * as fsPromises from 'fs/promises';
+import * as fsPromises from 'node:fs/promises';
 import { chatCommand } from './chatCommand.js';
-import { Stats } from 'fs';
-import { HistoryItemWithoutId } from '../types.js';
+import type { Stats } from 'node:fs';
+import type { HistoryItemWithoutId } from '../types.js';
 
 vi.mock('fs/promises', () => ({
   stat: vi.fn(),
@@ -67,11 +60,14 @@ describe('chatCommand', () => {
     mockContext = createMockCommandContext({
       services: {
         config: {
-          getProjectTempDir: () => '/tmp/gemini',
+          getProjectRoot: () => '/project/root',
           getGeminiClient: () =>
             ({
               getChat: mockGetChat,
             }) as unknown as GeminiClient,
+          storage: {
+            getProjectTempDir: () => '/project/root/.gemini/tmp/mockhash',
+          },
         },
         logger: {
           saveCheckpoint: mockSaveCheckpoint,

packages/cli/src/ui/commands/chatCommand.ts

@@ -4,20 +4,21 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import * as fsPromises from 'fs/promises';
+import * as fsPromises from 'node:fs/promises';
 import React from 'react';
 import { Text } from 'ink';
 import { Colors } from '../colors.js';
-import {
+import type {
   CommandContext,
   SlashCommand,
   MessageActionReturn,
-  CommandKind,
   SlashCommandActionReturn,
 } from './types.js';
+import { CommandKind } from './types.js';
 import { decodeTagName } from '@qwen-code/qwen-code-core';
-import path from 'path';
-import { HistoryItemWithoutId, MessageType } from '../types.js';
+import path from 'node:path';
+import type { HistoryItemWithoutId } from '../types.js';
+import { MessageType } from '../types.js';
 
 interface ChatDetail {
   name: string;
@@ -28,7 +29,8 @@ const getSavedChatTags = async (
   context: CommandContext,
   mtSortDesc: boolean,
 ): Promise<ChatDetail[]> => {
-  const geminiDir = context.services.config?.getProjectTempDir();
+  const cfg = context.services.config;
+  const geminiDir = cfg?.storage?.getProjectTempDir();
   if (!geminiDir) {
     return [];
   }

packages/cli/src/ui/commands/clearCommand.test.ts

@@ -4,7 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { vi, describe, it, expect, beforeEach, Mock } from 'vitest';
+import type { Mock } from 'vitest';
+import { vi, describe, it, expect, beforeEach } from 'vitest';
 import { clearCommand } from './clearCommand.js';
 import { type CommandContext } from './types.js';
 import { createMockCommandContext } from '../../test-utils/mockCommandContext.js';
@@ -20,7 +21,8 @@ vi.mock('@qwen-code/qwen-code-core', async () => {
   };
 });
 
-import { GeminiClient, uiTelemetryService } from '@qwen-code/qwen-code-core';
+import type { GeminiClient } from '@qwen-code/qwen-code-core';
+import { uiTelemetryService } from '@qwen-code/qwen-code-core';
 
 describe('clearCommand', () => {
   let mockContext: CommandContext;

packages/cli/src/ui/commands/clearCommand.ts

@@ -5,7 +5,8 @@
  */
 
 import { uiTelemetryService } from '@qwen-code/qwen-code-core';
-import { CommandKind, SlashCommand } from './types.js';
+import type { SlashCommand } from './types.js';
+import { CommandKind } from './types.js';
 
 export const clearCommand: SlashCommand = {
   name: 'clear',

packages/cli/src/ui/commands/compressCommand.test.ts

@@ -4,7 +4,11 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { GeminiClient } from '@qwen-code/qwen-code-core';
+import {
+  CompressionStatus,
+  type ChatCompressionInfo,
+  type GeminiClient,
+} from '@qwen-code/qwen-code-core';
 import { vi, describe, it, expect, beforeEach } from 'vitest';
 import { compressCommand } from './compressCommand.js';
 import { createMockCommandContext } from '../../test-utils/mockCommandContext.js';
@@ -35,6 +39,7 @@ describe('compressCommand', () => {
         isPending: true,
         originalTokenCount: null,
         newTokenCount: null,
+        compressionStatus: null,
       },
     };
     await compressCommand.action!(context, '');
@@ -50,25 +55,24 @@ describe('compressCommand', () => {
   });
 
   it('should set pending item, call tryCompressChat, and add result on success', async () => {
-    const compressedResult = {
+    const compressedResult: ChatCompressionInfo = {
       originalTokenCount: 200,
+      compressionStatus: CompressionStatus.COMPRESSED,
       newTokenCount: 100,
     };
     mockTryCompressChat.mockResolvedValue(compressedResult);
 
     await compressCommand.action!(context, '');
 
-    expect(context.ui.setPendingItem).toHaveBeenNthCalledWith(
-      1,
-      expect.objectContaining({
-        type: MessageType.COMPRESSION,
-        compression: {
-          isPending: true,
-          originalTokenCount: null,
-          newTokenCount: null,
-        },
-      }),
-    );
+    expect(context.ui.setPendingItem).toHaveBeenNthCalledWith(1, {
+      type: MessageType.COMPRESSION,
+      compression: {
+        isPending: true,
+        compressionStatus: null,
+        originalTokenCount: null,
+        newTokenCount: null,
+      },
+    });
 
     expect(mockTryCompressChat).toHaveBeenCalledWith(
       expect.stringMatching(/^compress-\d+$/),
@@ -76,14 +80,15 @@ describe('compressCommand', () => {
     );
 
     expect(context.ui.addItem).toHaveBeenCalledWith(
-      expect.objectContaining({
+      {
         type: MessageType.COMPRESSION,
         compression: {
           isPending: false,
+          compressionStatus: CompressionStatus.COMPRESSED,
           originalTokenCount: 200,
           newTokenCount: 100,
         },
-      }),
+      },
       expect.any(Number),
     );
 

packages/cli/src/ui/commands/compressCommand.ts

@@ -4,8 +4,10 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { HistoryItemCompression, MessageType } from '../types.js';
-import { CommandKind, SlashCommand } from './types.js';
+import type { HistoryItemCompression } from '../types.js';
+import { MessageType } from '../types.js';
+import type { SlashCommand } from './types.js';
+import { CommandKind } from './types.js';
 
 export const compressCommand: SlashCommand = {
   name: 'compress',
@@ -31,6 +33,7 @@ export const compressCommand: SlashCommand = {
         isPending: true,
         originalTokenCount: null,
         newTokenCount: null,
+        compressionStatus: null,
       },
     };
 
@@ -48,6 +51,7 @@ export const compressCommand: SlashCommand = {
               isPending: false,
               originalTokenCount: compressed.originalTokenCount,
               newTokenCount: compressed.newTokenCount,
+              compressionStatus: compressed.compressionStatus,
             },
           } as HistoryItemCompression,
           Date.now(),

packages/cli/src/ui/commands/copyCommand.test.ts

@@ -4,7 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { vi, describe, it, expect, beforeEach, Mock } from 'vitest';
+import type { Mock } from 'vitest';
+import { vi, describe, it, expect, beforeEach } from 'vitest';
 import { copyCommand } from './copyCommand.js';
 import { type CommandContext } from './types.js';
 import { createMockCommandContext } from '../../test-utils/mockCommandContext.js';
@@ -227,7 +228,7 @@ describe('copyCommand', () => {
     expect(result).toEqual({
       type: 'message',
       messageType: 'error',
-      content: 'Failed to copy to the clipboard.',
+      content: `Failed to copy to the clipboard. ${clipboardError.message}`,
     });
   });
 
@@ -242,14 +243,15 @@ describe('copyCommand', () => {
     ];
 
     mockGetHistory.mockReturnValue(historyWithAiMessage);
-    mockCopyToClipboard.mockRejectedValue('String error');
+    const rejectedValue = 'String error';
+    mockCopyToClipboard.mockRejectedValue(rejectedValue);
 
     const result = await copyCommand.action(mockContext, '');
 
     expect(result).toEqual({
       type: 'message',
       messageType: 'error',
-      content: 'Failed to copy to the clipboard.',
+      content: `Failed to copy to the clipboard. ${rejectedValue}`,
     });
   });
 

packages/cli/src/ui/commands/copyCommand.ts

@@ -5,11 +5,8 @@
  */
 
 import { copyToClipboard } from '../utils/commandUtils.js';
-import {
-  CommandKind,
-  SlashCommand,
-  SlashCommandActionReturn,
-} from './types.js';
+import type { SlashCommand, SlashCommandActionReturn } from './types.js';
+import { CommandKind } from './types.js';
 
 export const copyCommand: SlashCommand = {
   name: 'copy',
@@ -53,7 +50,7 @@ export const copyCommand: SlashCommand = {
         return {
           type: 'message',
           messageType: 'error',
-          content: 'Failed to copy to the clipboard.',
+          content: `Failed to copy to the clipboard. ${message}`,
         };
       }
     } else {

packages/cli/src/ui/commands/directoryCommand.test.tsx

@@ -6,11 +6,11 @@
 
 import { describe, it, expect, vi, beforeEach } from 'vitest';
 import { directoryCommand, expandHomeDir } from './directoryCommand.js';
-import { Config, WorkspaceContext } from '@qwen-code/qwen-code-core';
-import { CommandContext } from './types.js';
+import type { Config, WorkspaceContext } from '@qwen-code/qwen-code-core';
+import type { CommandContext } from './types.js';
 import { MessageType } from '../types.js';
-import * as os from 'os';
-import * as path from 'path';
+import * as os from 'node:os';
+import * as path from 'node:path';
 
 describe('directoryCommand', () => {
   let mockContext: CommandContext;

packages/cli/src/ui/commands/directoryCommand.tsx

@@ -4,10 +4,11 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { SlashCommand, CommandContext, CommandKind } from './types.js';
+import type { SlashCommand, CommandContext } from './types.js';
+import { CommandKind } from './types.js';
 import { MessageType } from '../types.js';
-import * as os from 'os';
-import * as path from 'path';
+import * as os from 'node:os';
+import * as path from 'node:path';
 import { loadServerHierarchicalMemory } from '@qwen-code/qwen-code-core';
 
 export function expandHomeDir(p: string): string {
@@ -91,34 +92,36 @@ export const directoryCommand: SlashCommand = {
           }
         }
 
-        if (added.length > 0) {
-          try {
-            if (config.shouldLoadMemoryFromIncludeDirectories()) {
-              const { memoryContent, fileCount } =
-                await loadServerHierarchicalMemory(
-                  config.getWorkingDir(),
-                  [...config.getWorkspaceContext().getDirectories()],
-                  config.getDebugMode(),
-                  config.getFileService(),
-                  config.getExtensionContextFilePaths(),
-                  context.services.settings.merged.memoryImportFormat || 'tree', // Use setting or default to 'tree'
-                  config.getFileFilteringOptions(),
-                  context.services.settings.merged.memoryDiscoveryMaxDirs,
-                );
-              config.setUserMemory(memoryContent);
-              config.setGeminiMdFileCount(fileCount);
-              context.ui.setGeminiMdFileCount(fileCount);
-            }
-            addItem(
-              {
-                type: MessageType.INFO,
-                text: `Successfully added memory files from the following directories if there are:\n- ${added.join('\n- ')}`,
-              },
-              Date.now(),
-            );
-          } catch (error) {
-            errors.push(`Error refreshing memory: ${(error as Error).message}`);
+        try {
+          if (config.shouldLoadMemoryFromIncludeDirectories()) {
+            const { memoryContent, fileCount } =
+              await loadServerHierarchicalMemory(
+                config.getWorkingDir(),
+                [
+                  ...config.getWorkspaceContext().getDirectories(),
+                  ...pathsToAdd,
+                ],
+                config.getDebugMode(),
+                config.getFileService(),
+                config.getExtensionContextFilePaths(),
+                context.services.settings.merged.context?.importFormat ||
+                  'tree', // Use setting or default to 'tree'
+                config.getFileFilteringOptions(),
+                context.services.settings.merged.context?.discoveryMaxDirs,
+              );
+            config.setUserMemory(memoryContent);
+            config.setGeminiMdFileCount(fileCount);
+            context.ui.setGeminiMdFileCount(fileCount);
           }
+          addItem(
+            {
+              type: MessageType.INFO,
+              text: `Successfully added GEMINI.md files from the following directories if there are:\n- ${added.join('\n- ')}`,
+            },
+            Date.now(),
+          );
+        } catch (error) {
+          errors.push(`Error refreshing memory: ${(error as Error).message}`);
         }
 
         if (added.length > 0) {

packages/cli/src/ui/commands/helpCommand.ts

@@ -4,7 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { CommandKind, SlashCommand } from './types.js';
+import type { SlashCommand } from './types.js';
+import { CommandKind } from './types.js';
 import { MessageType, type HistoryItemHelp } from '../types.js';
 
 export const helpCommand: SlashCommand = {

packages/cli/src/ui/commands/ideCommand.test.ts

@@ -4,15 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import {
-  MockInstance,
-  vi,
-  describe,
-  it,
-  expect,
-  beforeEach,
-  afterEach,
-} from 'vitest';
+import type { MockInstance } from 'vitest';
+import { vi, describe, it, expect, beforeEach, afterEach } from 'vitest';
 import { ideCommand } from './ideCommand.js';
 import { type CommandContext } from './types.js';
 import { type Config, DetectedIde } from '@qwen-code/qwen-code-core';
@@ -20,7 +13,14 @@ import * as core from '@qwen-code/qwen-code-core';
 
 vi.mock('child_process');
 vi.mock('glob');
-vi.mock('@qwen-code/qwen-code-core');
+vi.mock('@qwen-code/qwen-code-core', async (importOriginal) => {
+  const original = await importOriginal<typeof core>();
+  return {
+    ...original,
+    getOauthClient: vi.fn(original.getOauthClient),
+    getIdeInstaller: vi.fn(original.getIdeInstaller),
+  };
+});
 
 describe('ideCommand', () => {
   let mockContext: CommandContext;

packages/cli/src/ui/commands/ideCommand.ts

@@ -4,24 +4,20 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
+import type { Config, IdeClient, File } from '@qwen-code/qwen-code-core';
 import {
-  Config,
-  DetectedIde,
   QWEN_CODE_COMPANION_EXTENSION_NAME,
-  IDEConnectionStatus,
-  getIdeInfo,
   getIdeInstaller,
-  IdeClient,
-  type File,
+  IDEConnectionStatus,
   ideContext,
 } from '@qwen-code/qwen-code-core';
 import path from 'node:path';
-import {
+import type {
   CommandContext,
   SlashCommand,
   SlashCommandActionReturn,
-  CommandKind,
 } from './types.js';
+import { CommandKind } from './types.js';
 import { SettingScope } from '../../config/settings.js';
 
 function getIdeStatusMessage(ideClient: IdeClient): {
@@ -130,11 +126,7 @@ export const ideCommand = (config: Config | null): SlashCommand | null => {
         ({
           type: 'message',
           messageType: 'error',
-          content: `IDE integration is not supported in your current environment. To use this feature, run Qwen Code in one of these supported IDEs: ${Object.values(
-            DetectedIde,
-          )
-            .map((ide) => getIdeInfo(ide).displayName)
-            .join(', ')}`,
+          content: `IDE integration is not supported in your current environment. To use this feature, run Qwen Code in one of these supported IDEs: VS Code or VS Code forks.`,
         }) as const,
     };
   }
@@ -195,7 +187,11 @@ export const ideCommand = (config: Config | null): SlashCommand | null => {
         Date.now(),
       );
       if (result.success) {
-        context.services.settings.setValue(SettingScope.User, 'ideMode', true);
+        context.services.settings.setValue(
+          SettingScope.User,
+          'ide.enabled',
+          true,
+        );
         // Poll for up to 5 seconds for the extension to activate.
         for (let i = 0; i < 10; i++) {
           await config.setIdeModeAndSyncConnection(true);
@@ -235,7 +231,11 @@ export const ideCommand = (config: Config | null): SlashCommand | null => {
     description: 'enable IDE integration',
     kind: CommandKind.BUILT_IN,
     action: async (context: CommandContext) => {
-      context.services.settings.setValue(SettingScope.User, 'ideMode', true);
+      context.services.settings.setValue(
+        SettingScope.User,
+        'ide.enabled',
+        true,
+      );
       await config.setIdeModeAndSyncConnection(true);
       const { messageType, content } = getIdeStatusMessage(ideClient);
       context.ui.addItem(
@@ -253,7 +253,11 @@ export const ideCommand = (config: Config | null): SlashCommand | null => {
     description: 'disable IDE integration',
     kind: CommandKind.BUILT_IN,
     action: async (context: CommandContext) => {
-      context.services.settings.setValue(SettingScope.User, 'ideMode', false);
+      context.services.settings.setValue(
+        SettingScope.User,
+        'ide.enabled',
+        false,
+      );
       await config.setIdeModeAndSyncConnection(false);
       const { messageType, content } = getIdeStatusMessage(ideClient);
       context.ui.addItem(

packages/cli/src/ui/commands/initCommand.test.ts

@@ -5,8 +5,8 @@
  */
 
 import { vi, describe, it, expect, beforeEach, afterEach } from 'vitest';
-import * as fs from 'fs';
-import * as path from 'path';
+import * as fs from 'node:fs';
+import * as path from 'node:path';
 import { initCommand } from './initCommand.js';
 import { createMockCommandContext } from '../../test-utils/mockCommandContext.js';
 import { type CommandContext } from './types.js';

packages/cli/src/ui/commands/initCommand.ts

@@ -4,15 +4,15 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import * as fs from 'fs';
-import * as path from 'path';
-import {
+import * as fs from 'node:fs';
+import * as path from 'node:path';
+import type {
   CommandContext,
   SlashCommand,
   SlashCommandActionReturn,
-  CommandKind,
 } from './types.js';
 import { getCurrentGeminiMdFilename } from '@qwen-code/qwen-code-core';
+import { CommandKind } from './types.js';
 
 export const initCommand: SlashCommand = {
   name: 'init',

packages/cli/src/ui/commands/mcpCommand.test.ts

@@ -15,8 +15,9 @@ import {
   DiscoveredMCPTool,
 } from '@qwen-code/qwen-code-core';
 
-import { MessageActionReturn } from './types.js';
-import { Type, CallableTool } from '@google/genai';
+import type { MessageActionReturn } from './types.js';
+import type { CallableTool } from '@google/genai';
+import { Type } from '@google/genai';
 
 vi.mock('@qwen-code/qwen-code-core', async (importOriginal) => {
   const actual =

packages/cli/src/ui/commands/mcpCommand.ts

@@ -4,15 +4,15 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import {
+import type {
   SlashCommand,
   SlashCommandActionReturn,
   CommandContext,
-  CommandKind,
   MessageActionReturn,
 } from './types.js';
+import { CommandKind } from './types.js';
+import type { DiscoveredMCPPrompt } from '@qwen-code/qwen-code-core';
 import {
-  DiscoveredMCPPrompt,
   DiscoveredMCPTool,
   getMCPDiscoveryState,
   getMCPServerStatus,

packages/cli/src/ui/commands/memoryCommand.test.ts

@@ -4,12 +4,13 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { vi, describe, it, expect, beforeEach, Mock } from 'vitest';
+import type { Mock } from 'vitest';
+import { vi, describe, it, expect, beforeEach } from 'vitest';
 import { memoryCommand } from './memoryCommand.js';
-import { type CommandContext, SlashCommand } from './types.js';
+import type { SlashCommand, type CommandContext } from './types.js';
 import { createMockCommandContext } from '../../test-utils/mockCommandContext.js';
 import { MessageType } from '../types.js';
-import { LoadedSettings } from '../../config/settings.js';
+import type { LoadedSettings } from '../../config/settings.js';
 import {
   getErrorMessage,
   loadServerHierarchicalMemory,

packages/cli/src/ui/commands/memoryCommand.ts

@@ -13,11 +13,8 @@ import path from 'node:path';
 import os from 'os';
 import fs from 'fs/promises';
 import { MessageType } from '../types.js';
-import {
-  CommandKind,
-  SlashCommand,
-  SlashCommandActionReturn,
-} from './types.js';
+import type { SlashCommand, SlashCommandActionReturn } from './types.js';
+import { CommandKind } from './types.js';
 
 export const memoryCommand: SlashCommand = {
   name: 'memory',
@@ -269,9 +266,10 @@ export const memoryCommand: SlashCommand = {
                 config.getDebugMode(),
                 config.getFileService(),
                 config.getExtensionContextFilePaths(),
-                context.services.settings.merged.memoryImportFormat || 'tree', // Use setting or default to 'tree'
+                context.services.settings.merged.context?.importFormat ||
+                  'tree', // Use setting or default to 'tree'
                 config.getFileFilteringOptions(),
-                context.services.settings.merged.memoryDiscoveryMaxDirs,
+                context.services.settings.merged.context?.discoveryMaxDirs,
               );
             config.setUserMemory(memoryContent);
             config.setGeminiMdFileCount(fileCount);

packages/cli/src/ui/commands/privacyCommand.ts

@@ -4,7 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { CommandKind, OpenDialogActionReturn, SlashCommand } from './types.js';
+import type { OpenDialogActionReturn, SlashCommand } from './types.js';
+import { CommandKind } from './types.js';
 
 export const privacyCommand: SlashCommand = {
   name: 'privacy',

packages/cli/src/ui/commands/restoreCommand.test.ts

@@ -5,13 +5,13 @@
  */
 
 import { vi, describe, it, expect, beforeEach, afterEach } from 'vitest';
-import * as fs from 'fs/promises';
-import * as os from 'os';
-import * as path from 'path';
+import * as fs from 'node:fs/promises';
+import * as os from 'node:os';
+import * as path from 'node:path';
 import { restoreCommand } from './restoreCommand.js';
 import { type CommandContext } from './types.js';
 import { createMockCommandContext } from '../../test-utils/mockCommandContext.js';
-import { Config, GitService } from '@qwen-code/qwen-code-core';
+import type { Config, GitService } from '@qwen-code/qwen-code-core';
 
 describe('restoreCommand', () => {
   let mockContext: CommandContext;
@@ -39,7 +39,10 @@ describe('restoreCommand', () => {
 
     mockConfig = {
       getCheckpointingEnabled: vi.fn().mockReturnValue(true),
-      getProjectTempDir: vi.fn().mockReturnValue(geminiTempDir),
+      storage: {
+        getProjectTempCheckpointsDir: vi.fn().mockReturnValue(checkpointsDir),
+        getProjectTempDir: vi.fn().mockReturnValue(geminiTempDir),
+      },
       getGeminiClient: vi.fn().mockReturnValue({
         setHistory: mockSetHistory,
       }),
@@ -77,7 +80,9 @@ describe('restoreCommand', () => {
 
   describe('action', () => {
     it('should return an error if temp dir is not found', async () => {
-      vi.mocked(mockConfig.getProjectTempDir).mockReturnValue('');
+      vi.mocked(
+        mockConfig.storage.getProjectTempCheckpointsDir,
+      ).mockReturnValue('');
 
       expect(
         await restoreCommand(mockConfig)?.action?.(mockContext, ''),
@@ -219,7 +224,7 @@ describe('restoreCommand', () => {
 
   describe('completion', () => {
     it('should return an empty array if temp dir is not found', async () => {
-      vi.mocked(mockConfig.getProjectTempDir).mockReturnValue('');
+      vi.mocked(mockConfig.storage.getProjectTempDir).mockReturnValue('');
       const command = restoreCommand(mockConfig);
 
       expect(await command?.completion?.(mockContext, '')).toEqual([]);

packages/cli/src/ui/commands/restoreCommand.ts

@@ -4,15 +4,15 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import * as fs from 'fs/promises';
-import path from 'path';
+import * as fs from 'node:fs/promises';
+import path from 'node:path';
 import {
   type CommandContext,
   type SlashCommand,
   type SlashCommandActionReturn,
   CommandKind,
 } from './types.js';
-import { Config } from '@qwen-code/qwen-code-core';
+import type { Config } from '@qwen-code/qwen-code-core';
 
 async function restoreAction(
   context: CommandContext,
@@ -22,9 +22,7 @@ async function restoreAction(
   const { config, git: gitService } = services;
   const { addItem, loadHistory } = ui;
 
-  const checkpointDir = config?.getProjectTempDir()
-    ? path.join(config.getProjectTempDir(), 'checkpoints')
-    : undefined;
+  const checkpointDir = config?.storage.getProjectTempCheckpointsDir();
 
   if (!checkpointDir) {
     return {
@@ -125,9 +123,7 @@ async function completion(
 ): Promise<string[]> {
   const { services } = context;
   const { config } = services;
-  const checkpointDir = config?.getProjectTempDir()
-    ? path.join(config.getProjectTempDir(), 'checkpoints')
-    : undefined;
+  const checkpointDir = config?.storage.getProjectTempCheckpointsDir();
   if (!checkpointDir) {
     return [];
   }

packages/cli/src/ui/commands/settingsCommand.ts

@@ -4,7 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { CommandKind, OpenDialogActionReturn, SlashCommand } from './types.js';
+import type { OpenDialogActionReturn, SlashCommand } from './types.js';
+import { CommandKind } from './types.js';
 
 export const settingsCommand: SlashCommand = {
   name: 'settings',

packages/cli/src/ui/commands/setupGithubCommand.test.ts

@@ -15,7 +15,7 @@ import {
   updateGitignore,
   GITHUB_WORKFLOW_PATHS,
 } from './setupGithubCommand.js';
-import { CommandContext, ToolActionReturn } from './types.js';
+import type { CommandContext, ToolActionReturn } from './types.js';
 import * as commandUtils from '../utils/commandUtils.js';
 
 vi.mock('child_process');

packages/cli/src/ui/commands/setupGithubCommand.ts

@@ -9,7 +9,7 @@ import * as fs from 'node:fs';
 import { Writable } from 'node:stream';
 import { ProxyAgent } from 'undici';
 
-import { CommandContext } from '../../ui/commands/types.js';
+import type { CommandContext } from '../../ui/commands/types.js';
 import {
   getGitRepoRoot,
   getLatestGitHubRelease,
@@ -17,11 +17,8 @@ import {
   getGitHubRepoInfo,
 } from '../../utils/gitUtils.js';
 
-import {
-  CommandKind,
-  SlashCommand,
-  SlashCommandActionReturn,
-} from './types.js';
+import type { SlashCommand, SlashCommandActionReturn } from './types.js';
+import { CommandKind } from './types.js';
 import { getUrlOpenCommand } from '../../ui/utils/commandUtils.js';
 
 export const GITHUB_WORKFLOW_PATHS = [

packages/cli/src/ui/commands/statsCommand.ts

@@ -4,7 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { MessageType, HistoryItemStats } from '../types.js';
+import type { HistoryItemStats } from '../types.js';
+import { MessageType } from '../types.js';
 import { formatDuration } from '../utils/formatters.js';
 import {
   type CommandContext,

packages/cli/src/ui/commands/terminalSetupCommand.test.ts

@@ -7,7 +7,7 @@
 import { describe, it, expect, vi, beforeEach } from 'vitest';
 import { terminalSetupCommand } from './terminalSetupCommand.js';
 import * as terminalSetupModule from '../utils/terminalSetup.js';
-import { CommandContext } from './types.js';
+import type { CommandContext } from './types.js';
 
 vi.mock('../utils/terminalSetup.js');
 

packages/cli/src/ui/commands/terminalSetupCommand.ts

@@ -4,7 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { MessageActionReturn, SlashCommand, CommandKind } from './types.js';
+import type { MessageActionReturn, SlashCommand } from './types.js';
+import { CommandKind } from './types.js';
 import { terminalSetup } from '../utils/terminalSetup.js';
 
 /**

packages/cli/src/ui/commands/themeCommand.ts

@@ -4,7 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { CommandKind, OpenDialogActionReturn, SlashCommand } from './types.js';
+import type { OpenDialogActionReturn, SlashCommand } from './types.js';
+import { CommandKind } from './types.js';
 
 export const themeCommand: SlashCommand = {
   name: 'theme',

packages/cli/src/ui/commands/toolsCommand.test.ts

@@ -4,11 +4,11 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { describe, it, expect, vi } from 'vitest';
+import { describe, it, expect } from 'vitest';
 import { toolsCommand } from './toolsCommand.js';
 import { createMockCommandContext } from '../../test-utils/mockCommandContext.js';
 import { MessageType } from '../types.js';
-import { Tool } from '@qwen-code/qwen-code-core';
+import type { Tool } from '@qwen-code/qwen-code-core';
 
 // Mock tools for testing
 const mockTools = [

packages/cli/src/ui/commands/toolsCommand.ts

@@ -13,7 +13,7 @@ import { MessageType } from '../types.js';
 
 export const toolsCommand: SlashCommand = {
   name: 'tools',
-  description: 'list available Qwen Codetools',
+  description: 'list available Qwen Code tools. Usage: /tools [desc]',
   kind: CommandKind.BUILT_IN,
   action: async (context: CommandContext, args?: string): Promise<void> => {
     const subCommand = args?.trim();

packages/cli/src/ui/commands/types.ts

@@ -5,13 +5,12 @@
  */
 
 import { type ReactNode } from 'react';
-import { Content } from '@google/genai';
-import { HistoryItemWithoutId } from '../types.js';
-import { Config, GitService, Logger } from '@qwen-code/qwen-code-core';
-import { LoadedSettings } from '../../config/settings.js';
-import { UseHistoryManagerReturn } from '../hooks/useHistoryManager.js';
-import type { HistoryItem } from '../types.js';
-import { SessionStatsState } from '../contexts/SessionContext.js';
+import type { Content, PartListUnion } from '@google/genai';
+import type { HistoryItemWithoutId, HistoryItem } from '../types.js';
+import type { Config, GitService, Logger } from '@qwen-code/qwen-code-core';
+import type { LoadedSettings } from '../../config/settings.js';
+import type { UseHistoryManagerReturn } from '../hooks/useHistoryManager.js';
+import type { SessionStatsState } from '../contexts/SessionContext.js';
 
 // Grouped dependencies for clarity and easier mocking
 export interface CommandContext {
@@ -123,7 +122,7 @@ export interface LoadHistoryActionReturn {
  */
 export interface SubmitPromptActionReturn {
   type: 'submit_prompt';
-  content: string;
+  content: PartListUnion;
 }
 
 /**

packages/cli/src/ui/commands/vimCommand.ts

@@ -4,7 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { CommandKind, SlashCommand } from './types.js';
+import type { SlashCommand } from './types.js';
+import { CommandKind } from './types.js';
 
 export const vimCommand: SlashCommand = {
   name: 'vim',

packages/cli/src/ui/components/AboutBox.tsx

@@ -4,7 +4,7 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import React from 'react';
+import type React from 'react';
 import { Box, Text } from 'ink';
 import { Colors } from '../colors.js';
 import { GIT_COMMIT_INFO } from '../../generated/git-commit.js';

packages/cli/src/ui/components/AuthDialog.test.tsx

@@ -18,7 +18,7 @@ describe('AuthDialog', () => {
   beforeEach(() => {
     originalEnv = { ...process.env };
     process.env['GEMINI_API_KEY'] = '';
-    process.env['GEMINI_DEFAULT_AUTH_TYPE'] = '';
+    process.env['QWEN_DEFAULT_AUTH_TYPE'] = '';
     vi.clearAllMocks();
   });
 
@@ -31,20 +31,30 @@ describe('AuthDialog', () => {
 
     const settings: LoadedSettings = new LoadedSettings(
       {
-        settings: { customThemes: {}, mcpServers: {} },
+        settings: { ui: { customThemes: {} }, mcpServers: {} },
+        path: '',
+      },
+      {
+        settings: {},
         path: '',
       },
       {
         settings: {
-          selectedAuthType: AuthType.USE_GEMINI,
+          security: {
+            auth: {
+              selectedType: AuthType.USE_GEMINI,
+            },
+          },
         },
         path: '',
       },
       {
-        settings: { customThemes: {}, mcpServers: {} },
+        settings: { ui: { customThemes: {} }, mcpServers: {} },
         path: '',
       },
       [],
+      true,
+      new Set(),
     );
 
     const { lastFrame } = renderWithProviders(
@@ -67,21 +77,27 @@ describe('AuthDialog', () => {
       const settings: LoadedSettings = new LoadedSettings(
         {
           settings: {
-            selectedAuthType: undefined,
-            customThemes: {},
+            security: { auth: { selectedType: undefined } },
+            ui: { customThemes: {} },
             mcpServers: {},
           },
           path: '',
         },
         {
-          settings: { customThemes: {}, mcpServers: {} },
+          settings: {},
           path: '',
         },
         {
-          settings: { customThemes: {}, mcpServers: {} },
+          settings: { ui: { customThemes: {} }, mcpServers: {} },
+          path: '',
+        },
+        {
+          settings: { ui: { customThemes: {} }, mcpServers: {} },
           path: '',
         },
         [],
+        true,
+        new Set(),
       );
 
       const { lastFrame } = renderWithProviders(
@@ -93,28 +109,34 @@ describe('AuthDialog', () => {
       expect(lastFrame()).toContain('OpenAI');
     });
 
-    it('should not show the GEMINI_API_KEY message if GEMINI_DEFAULT_AUTH_TYPE is set to something else', () => {
+    it('should not show the GEMINI_API_KEY message if QWEN_DEFAULT_AUTH_TYPE is set to something else', () => {
       process.env['GEMINI_API_KEY'] = 'foobar';
-      process.env['GEMINI_DEFAULT_AUTH_TYPE'] = AuthType.LOGIN_WITH_GOOGLE;
+      process.env['QWEN_DEFAULT_AUTH_TYPE'] = AuthType.LOGIN_WITH_GOOGLE;
 
       const settings: LoadedSettings = new LoadedSettings(
         {
           settings: {
-            selectedAuthType: undefined,
-            customThemes: {},
+            security: { auth: { selectedType: undefined } },
+            ui: { customThemes: {} },
             mcpServers: {},
           },
           path: '',
         },
         {
-          settings: { customThemes: {}, mcpServers: {} },
+          settings: {},
           path: '',
         },
         {
-          settings: { customThemes: {}, mcpServers: {} },
+          settings: { ui: { customThemes: {} }, mcpServers: {} },
+          path: '',
+        },
+        {
+          settings: { ui: { customThemes: {} }, mcpServers: {} },
           path: '',
         },
         [],
+        true,
+        new Set(),
       );
 
       const { lastFrame } = renderWithProviders(
@@ -126,28 +148,34 @@ describe('AuthDialog', () => {
       );
     });
 
-    it('should show the GEMINI_API_KEY message if GEMINI_DEFAULT_AUTH_TYPE is set to use api key', () => {
+    it('should show the GEMINI_API_KEY message if QWEN_DEFAULT_AUTH_TYPE is set to use api key', () => {
       process.env['GEMINI_API_KEY'] = 'foobar';
-      process.env['GEMINI_DEFAULT_AUTH_TYPE'] = AuthType.USE_GEMINI;
+      process.env['QWEN_DEFAULT_AUTH_TYPE'] = AuthType.USE_GEMINI;
 
       const settings: LoadedSettings = new LoadedSettings(
         {
           settings: {
-            selectedAuthType: undefined,
-            customThemes: {},
+            security: { auth: { selectedType: undefined } },
+            ui: { customThemes: {} },
             mcpServers: {},
           },
           path: '',
         },
         {
-          settings: { customThemes: {}, mcpServers: {} },
+          settings: {},
           path: '',
         },
         {
-          settings: { customThemes: {}, mcpServers: {} },
+          settings: { ui: { customThemes: {} }, mcpServers: {} },
+          path: '',
+        },
+        {
+          settings: { ui: { customThemes: {} }, mcpServers: {} },
           path: '',
         },
         [],
+        true,
+        new Set(),
       );
 
       const { lastFrame } = renderWithProviders(
@@ -160,28 +188,34 @@ describe('AuthDialog', () => {
     });
   });
 
-  describe('GEMINI_DEFAULT_AUTH_TYPE environment variable', () => {
-    it('should select the auth type specified by GEMINI_DEFAULT_AUTH_TYPE', () => {
-      process.env['GEMINI_DEFAULT_AUTH_TYPE'] = AuthType.USE_OPENAI;
+  describe('QWEN_DEFAULT_AUTH_TYPE environment variable', () => {
+    it('should select the auth type specified by QWEN_DEFAULT_AUTH_TYPE', () => {
+      process.env['QWEN_DEFAULT_AUTH_TYPE'] = AuthType.USE_OPENAI;
 
       const settings: LoadedSettings = new LoadedSettings(
         {
           settings: {
-            selectedAuthType: undefined,
-            customThemes: {},
+            security: { auth: { selectedType: undefined } },
+            ui: { customThemes: {} },
             mcpServers: {},
           },
           path: '',
         },
         {
-          settings: { customThemes: {}, mcpServers: {} },
+          settings: {},
           path: '',
         },
         {
-          settings: { customThemes: {}, mcpServers: {} },
+          settings: { ui: { customThemes: {} }, mcpServers: {} },
+          path: '',
+        },
+        {
+          settings: { ui: { customThemes: {} }, mcpServers: {} },
           path: '',
         },
         [],
+        true,
+        new Set(),
       );
 
       const { lastFrame } = renderWithProviders(
@@ -192,25 +226,31 @@ describe('AuthDialog', () => {
       expect(lastFrame()).toContain('● 2. OpenAI');
     });
 
-    it('should fall back to default if GEMINI_DEFAULT_AUTH_TYPE is not set', () => {
+    it('should fall back to default if QWEN_DEFAULT_AUTH_TYPE is not set', () => {
       const settings: LoadedSettings = new LoadedSettings(
         {
           settings: {
-            selectedAuthType: undefined,
-            customThemes: {},
+            security: { auth: { selectedType: undefined } },
+            ui: { customThemes: {} },
             mcpServers: {},
           },
           path: '',
         },
         {
-          settings: { customThemes: {}, mcpServers: {} },
+          settings: {},
           path: '',
         },
         {
-          settings: { customThemes: {}, mcpServers: {} },
+          settings: { ui: { customThemes: {} }, mcpServers: {} },
+          path: '',
+        },
+        {
+          settings: { ui: { customThemes: {} }, mcpServers: {} },
           path: '',
         },
         [],
+        true,
+        new Set(),
       );
 
       const { lastFrame } = renderWithProviders(
@@ -221,59 +261,116 @@ describe('AuthDialog', () => {
       expect(lastFrame()).toContain('● 1. Qwen OAuth');
     });
 
-    it('should show an error and fall back to default if GEMINI_DEFAULT_AUTH_TYPE is invalid', () => {
-      process.env['GEMINI_DEFAULT_AUTH_TYPE'] = 'invalid-auth-type';
+    it('should show an error and fall back to default if QWEN_DEFAULT_AUTH_TYPE is invalid', () => {
+      process.env['QWEN_DEFAULT_AUTH_TYPE'] = 'invalid-auth-type';
 
       const settings: LoadedSettings = new LoadedSettings(
         {
           settings: {
-            selectedAuthType: undefined,
-            customThemes: {},
+            security: { auth: { selectedType: undefined } },
+            ui: { customThemes: {} },
             mcpServers: {},
           },
           path: '',
         },
         {
-          settings: { customThemes: {}, mcpServers: {} },
+          settings: {},
           path: '',
         },
         {
-          settings: { customThemes: {}, mcpServers: {} },
+          settings: { ui: { customThemes: {} }, mcpServers: {} },
+          path: '',
+        },
+        {
+          settings: { ui: { customThemes: {} }, mcpServers: {} },
           path: '',
         },
         [],
+        true,
+        new Set(),
       );
 
       const { lastFrame } = renderWithProviders(
         <AuthDialog onSelect={() => {}} settings={settings} />,
       );
 
-      // Since the auth dialog doesn't show GEMINI_DEFAULT_AUTH_TYPE errors anymore,
+      // Since the auth dialog doesn't show QWEN_DEFAULT_AUTH_TYPE errors anymore,
       // it will just show the default Qwen OAuth option
       expect(lastFrame()).toContain('● 1. Qwen OAuth');
     });
   });
 
+  it('should prevent exiting when no auth method is selected and show error message', async () => {
+    const onSelect = vi.fn();
+    const settings: LoadedSettings = new LoadedSettings(
+      {
+        settings: { ui: { customThemes: {} }, mcpServers: {} },
+        path: '',
+      },
+      {
+        settings: {},
+        path: '',
+      },
+      {
+        settings: {
+          security: { auth: { selectedType: undefined } },
+          ui: { customThemes: {} },
+          mcpServers: {},
+        },
+        path: '',
+      },
+      {
+        settings: { ui: { customThemes: {} }, mcpServers: {} },
+        path: '',
+      },
+      [],
+      true,
+      new Set(),
+    );
+
+    const { lastFrame, stdin, unmount } = renderWithProviders(
+      <AuthDialog onSelect={onSelect} settings={settings} />,
+    );
+    await wait();
+
+    // Simulate pressing escape key
+    stdin.write('\u001b'); // ESC key
+    await wait();
+
+    // Should show error message instead of calling onSelect
+    expect(lastFrame()).toContain(
+      'You must select an auth method to proceed. Press Ctrl+C twice to exit.',
+    );
+    expect(onSelect).not.toHaveBeenCalled();
+    unmount();
+  });
+
   it('should not exit if there is already an error message', async () => {
     const onSelect = vi.fn();
     const settings: LoadedSettings = new LoadedSettings(
       {
-        settings: { customThemes: {}, mcpServers: {} },
+        settings: { ui: { customThemes: {} }, mcpServers: {} },
+        path: '',
+      },
+      {
+        settings: {},
         path: '',
       },
       {
         settings: {
-          selectedAuthType: undefined,
-          customThemes: {},
+          security: { auth: { selectedType: undefined } },
+          ui: { customThemes: {} },
           mcpServers: {},
         },
         path: '',
       },
       {
-        settings: { customThemes: {}, mcpServers: {} },
+        settings: { ui: { customThemes: {} }, mcpServers: {} },
         path: '',
       },
       [],
+      true,
+      new Set(),
     );
 
     const { lastFrame, stdin, unmount } = renderWithProviders(
@@ -300,22 +397,28 @@ describe('AuthDialog', () => {
     const onSelect = vi.fn();
     const settings: LoadedSettings = new LoadedSettings(
       {
-        settings: { customThemes: {}, mcpServers: {} },
+        settings: { ui: { customThemes: {} }, mcpServers: {} },
+        path: '',
+      },
+      {
+        settings: {},
         path: '',
       },
       {
         settings: {
-          selectedAuthType: AuthType.USE_GEMINI,
-          customThemes: {},
+          security: { auth: { selectedType: AuthType.LOGIN_WITH_GOOGLE } },
+          ui: { customThemes: {} },
           mcpServers: {},
         },
         path: '',
       },
       {
-        settings: { customThemes: {}, mcpServers: {} },
+        settings: { ui: { customThemes: {} }, mcpServers: {} },
         path: '',
       },
       [],
+      true,
+      new Set(),
     );
 
     const { stdin, unmount } = renderWithProviders(

packages/cli/src/ui/components/AuthDialog.tsx

@@ -4,16 +4,17 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
+import type React from 'react';
+import { useState } from 'react';
 import { AuthType } from '@qwen-code/qwen-code-core';
 import { Box, Text } from 'ink';
-import React, { useState } from 'react';
 import {
   setOpenAIApiKey,
   setOpenAIBaseUrl,
   setOpenAIModel,
   validateAuthMethod,
 } from '../../config/auth.js';
-import { LoadedSettings, SettingScope } from '../../config/settings.js';
+import { type LoadedSettings, SettingScope } from '../../config/settings.js';
 import { Colors } from '../colors.js';
 import { useKeypress } from '../hooks/useKeypress.js';
 import { OpenAIKeyPrompt } from './OpenAIKeyPrompt.js';
@@ -54,12 +55,12 @@ export function AuthDialog({
   const initialAuthIndex = Math.max(
     0,
     items.findIndex((item) => {
-      if (settings.merged.selectedAuthType) {
-        return item.value === settings.merged.selectedAuthType;
+      if (settings.merged.security?.auth?.selectedType) {
+        return item.value === settings.merged.security?.auth?.selectedType;
       }
 
       const defaultAuthType = parseDefaultAuthType(
-        process.env['GEMINI_DEFAULT_AUTH_TYPE'],
+        process.env['QWEN_DEFAULT_AUTH_TYPE'],
       );
       if (defaultAuthType) {
         return item.value === defaultAuthType;
@@ -120,7 +121,7 @@ export function AuthDialog({
         if (errorMessage) {
           return;
         }
-        if (settings.merged.selectedAuthType === undefined) {
+        if (settings.merged.security?.auth?.selectedType === undefined) {
           // Prevent exiting if no auth method is set
           setErrorMessage(
             'You must select an auth method to proceed. Press Ctrl+C twice to exit.',

packages/cli/src/ui/components/AuthInProgress.tsx

@@ -4,7 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import React, { useState, useEffect } from 'react';
+import type React from 'react';
+import { useState, useEffect } from 'react';
 import { Box, Text } from 'ink';
 import Spinner from 'ink-spinner';
 import { Colors } from '../colors.js';

packages/cli/src/ui/components/AutoAcceptIndicator.tsx

@@ -4,7 +4,7 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import React from 'react';
+import type React from 'react';
 import { Box, Text } from 'ink';
 import { Colors } from '../colors.js';
 import { ApprovalMode } from '@qwen-code/qwen-code-core';

packages/cli/src/ui/components/ConsoleSummaryDisplay.tsx

@@ -4,7 +4,7 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import React from 'react';
+import type React from 'react';
 import { Box, Text } from 'ink';
 import { Colors } from '../colors.js';
 

packages/cli/src/ui/components/ContextSummaryDisplay.test.tsx

@@ -4,7 +4,7 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import React from 'react';
+import type React from 'react';
 import { render } from 'ink-testing-library';
 import { describe, it, expect, vi } from 'vitest';
 import { ContextSummaryDisplay } from './ContextSummaryDisplay.js';

packages/cli/src/ui/components/ContextSummaryDisplay.tsx

@@ -4,7 +4,7 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import React from 'react';
+import type React from 'react';
 import { Box, Text } from 'ink';
 import { Colors } from '../colors.js';
 import {