feat(mcp): project .mcp.json + workspace approval gating with aligned scope precedence (#4615)

packages/cli/src/acp-integration/acpAgent.ts

@@ -6683,7 +6683,12 @@ class QwenAgent implements Agent {
     resume?: boolean,
   ): Promise<Config> {
     this.settings = loadSettings(cwd);
-    const mergedMcpServers = { ...this.settings.merged.mcpServers };
+    // ACP/IDE-injected servers are session-level: they must outrank a project
+    // `.mcp.json` and stay un-gated. Collect them separately and pass them as
+    // `sessionMcpServers` (top precedence tier) rather than merging into
+    // `settings.mcpServers`, where `assembleMcpServers` would demote them below
+    // `.mcp.json` (#4615).
+    const sessionMcpServers: Record<string, MCPServerConfig> = {};
 
     for (const server of mcpServers) {
       const stdioServer = toStdioServer(server);
@@ -6692,7 +6697,7 @@ class QwenAgent implements Agent {
         for (const { name: envName, value } of stdioServer.env) {
           env[envName] = value;
         }
-        mergedMcpServers[stdioServer.name] = new MCPServerConfig(
+        sessionMcpServers[stdioServer.name] = new MCPServerConfig(
           stdioServer.command,
           stdioServer.args,
           env,
@@ -6707,7 +6712,7 @@ class QwenAgent implements Agent {
         for (const { name: headerName, value } of sseServer.headers) {
           headers[headerName] = value;
         }
-        mergedMcpServers[sseServer.name] = new MCPServerConfig(
+        sessionMcpServers[sseServer.name] = new MCPServerConfig(
           undefined,
           undefined,
           undefined,
@@ -6725,7 +6730,7 @@ class QwenAgent implements Agent {
         for (const { name: headerName, value } of httpServer.headers) {
           headers[headerName] = value;
         }
-        mergedMcpServers[httpServer.name] = new MCPServerConfig(
+        sessionMcpServers[httpServer.name] = new MCPServerConfig(
           undefined,
           undefined,
           undefined,
@@ -6738,7 +6743,7 @@ class QwenAgent implements Agent {
       }
     }
 
-    const settings = { ...this.settings.merged, mcpServers: mergedMcpServers };
+    const settings = this.settings.merged;
     const argvForSession = {
       ...this.argv,
       ...(resume ? { resume: sessionId } : { sessionId }),
@@ -6762,6 +6767,7 @@ class QwenAgent implements Agent {
       // sessions otherwise leak persisted disabled skills into the first
       // <available_skills> at cold start.
       buildDisabledSkillNamesProvider(this.settings),
+      sessionMcpServers,
     );
     // Inject the workspace-shared MCP transport pool BEFORE
     // `config.initialize()` so the ToolRegistry picks it up.

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

@@ -17,10 +17,14 @@ describe('mcp command', () => {
     expect(typeof mcpCommand.handler).toBe('function');
   });
 
-  it('should have exactly one option (help flag)', () => {
+  it('should have exactly one option (help flag)', async () => {
     // Test to ensure that the global 'gemini' flags are not added to the mcp command
     const yargsInstance = yargs();
-    const builtYargs = mcpCommand.builder(yargsInstance);
+    const builder = mcpCommand.builder;
+    if (typeof builder !== 'function') {
+      throw new Error('mcp command builder must be a function');
+    }
+    const builtYargs = await builder(yargsInstance);
     const options = builtYargs.getOptions();
 
     // Should have exactly 1 option (help flag)
@@ -35,9 +39,13 @@ describe('mcp command', () => {
       version: vi.fn().mockReturnThis(),
     };
 
-    mcpCommand.builder(mockYargs as unknown as Argv);
+    const builder = mcpCommand.builder;
+    if (typeof builder !== 'function') {
+      throw new Error('mcp command builder must be a function');
+    }
+    builder(mockYargs as unknown as Argv);
 
-    expect(mockYargs.command).toHaveBeenCalledTimes(4);
+    expect(mockYargs.command).toHaveBeenCalledTimes(6);
 
     // Verify that the specific subcommands are registered
     const commandCalls = mockYargs.command.mock.calls;
@@ -47,6 +55,8 @@ describe('mcp command', () => {
     expect(commandNames).toContain('remove <name>');
     expect(commandNames).toContain('list');
     expect(commandNames).toContain('reconnect [server-name]');
+    expect(commandNames).toContain('approve [name]');
+    expect(commandNames).toContain('reject [name]');
 
     expect(mockYargs.demandCommand).toHaveBeenCalledWith(
       1,

packages/cli/src/commands/mcp.ts

@@ -10,6 +10,7 @@ import { addCommand } from './mcp/add.js';
 import { removeCommand } from './mcp/remove.js';
 import { listCommand } from './mcp/list.js';
 import { reconnectCommand } from './mcp/reconnect.js';
+import { approveCommand, rejectCommand } from './mcp/approve.js';
 
 export const mcpCommand: CommandModule = {
   command: 'mcp',
@@ -20,6 +21,8 @@ export const mcpCommand: CommandModule = {
       .command(removeCommand)
       .command(listCommand)
       .command(reconnectCommand)
+      .command(approveCommand)
+      .command(rejectCommand)
       .demandCommand(1, 'You need at least one command before continuing.')
       .version(false),
   handler: () => {

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

@@ -0,0 +1,146 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect, beforeEach, afterEach, vi } from 'vitest';
+import * as fs from 'node:fs';
+import * as os from 'node:os';
+import * as path from 'node:path';
+
+const mockWriteStdoutLine = vi.hoisted(() => vi.fn());
+vi.mock('../../utils/stdioHelpers.js', () => ({
+  writeStdoutLine: mockWriteStdoutLine,
+  writeStderrLine: vi.fn(),
+  clearScreen: vi.fn(),
+}));
+
+import { approveCommand, rejectCommand } from './approve.js';
+import {
+  loadMcpApprovals,
+  resetMcpApprovalsForTesting,
+  MCP_APPROVALS_FILENAME,
+} from '../../config/mcpApprovals.js';
+import { loadProjectMcpServers } from '../../config/mcpJson.js';
+
+describe('qwen mcp approve / reject', () => {
+  let dir: string;
+  let cwdSpy: ReturnType<typeof vi.spyOn>;
+
+  const output = () =>
+    mockWriteStdoutLine.mock.calls.map((c) => c[0]).join('\n');
+
+  const run = async (
+    cmd: typeof approveCommand,
+    argv: Record<string, unknown>,
+  ) => {
+    await (cmd.handler as (a: Record<string, unknown>) => Promise<void>)({
+      _: [],
+      $0: 'qwen',
+      ...argv,
+    });
+  };
+
+  beforeEach(() => {
+    dir = fs.mkdtempSync(path.join(os.tmpdir(), 'mcp-approve-'));
+    process.env['QWEN_CODE_MCP_APPROVALS_PATH'] = path.join(
+      dir,
+      MCP_APPROVALS_FILENAME,
+    );
+    resetMcpApprovalsForTesting();
+    cwdSpy = vi.spyOn(process, 'cwd').mockReturnValue(dir);
+    mockWriteStdoutLine.mockClear();
+  });
+
+  afterEach(() => {
+    delete process.env['QWEN_CODE_MCP_APPROVALS_PATH'];
+    resetMcpApprovalsForTesting();
+    cwdSpy.mockRestore();
+    fs.rmSync(dir, { recursive: true, force: true });
+  });
+
+  const writeMcpJson = (servers: Record<string, unknown>) =>
+    fs.writeFileSync(
+      path.join(dir, '.mcp.json'),
+      JSON.stringify({ mcpServers: servers }),
+    );
+
+  const stateOf = (name: string) => {
+    resetMcpApprovalsForTesting();
+    const { servers } = loadProjectMcpServers(dir);
+    return loadMcpApprovals().getState(dir, name, servers[name]!);
+  };
+
+  const writeWorkspaceSettings = (servers: Record<string, unknown>) => {
+    const qwenDir = path.join(dir, '.qwen');
+    fs.mkdirSync(qwenDir, { recursive: true });
+    fs.writeFileSync(
+      path.join(qwenDir, 'settings.json'),
+      JSON.stringify({ mcpServers: servers }),
+    );
+  };
+
+  /** Read the persisted approval status straight off disk (scope-agnostic). */
+  const persistedStatus = (name: string): string | undefined => {
+    const raw = fs.readFileSync(
+      process.env['QWEN_CODE_MCP_APPROVALS_PATH']!,
+      'utf-8',
+    );
+    return JSON.parse(raw)[dir]?.[name]?.status;
+  };
+
+  it('reports when there are no gated servers', async () => {
+    await run(approveCommand, { name: 'slack', all: false });
+    expect(output()).toContain('No approval-requiring MCP servers found');
+  });
+
+  it('approves a named project server (pending -> approved)', async () => {
+    writeMcpJson({ slack: { command: 'node', args: ['slack.js'] } });
+    expect(stateOf('slack')).toBe('pending');
+
+    await run(approveCommand, { name: 'slack', all: false });
+
+    expect(stateOf('slack')).toBe('approved');
+    expect(output()).toContain('Approved MCP server "slack"');
+  });
+
+  it('approves a workspace .qwen/settings.json server', async () => {
+    writeWorkspaceSettings({ ws: { command: 'node', args: ['ws.js'] } });
+
+    await run(approveCommand, { name: 'ws', all: false });
+
+    expect(output()).toContain('Approved MCP server "ws"');
+    expect(persistedStatus('ws')).toBe('approved');
+  });
+
+  it('rejects a named project server', async () => {
+    writeMcpJson({ slack: { command: 'node' } });
+    await run(rejectCommand, { name: 'slack', all: false });
+    expect(stateOf('slack')).toBe('rejected');
+  });
+
+  it('approves all with --all', async () => {
+    writeMcpJson({ a: { command: 'a' }, b: { command: 'b' } });
+    await run(approveCommand, { name: undefined, all: true });
+    expect(stateOf('a')).toBe('approved');
+    expect(stateOf('b')).toBe('approved');
+  });
+
+  it('reports an unknown server name', async () => {
+    writeMcpJson({ slack: { command: 'node' } });
+    await run(approveCommand, { name: 'ghost', all: false });
+    expect(output()).toContain('not found');
+    expect(stateOf('slack')).toBe('pending');
+  });
+
+  it('binds approval to the config hash: editing .mcp.json reverts to pending', async () => {
+    writeMcpJson({ slack: { command: 'node', args: ['slack.js'] } });
+    await run(approveCommand, { name: 'slack', all: false });
+    expect(stateOf('slack')).toBe('approved');
+
+    // Edit the server's command — approval must no longer apply.
+    writeMcpJson({ slack: { command: 'curl', args: ['slack.js'] } });
+    expect(stateOf('slack')).toBe('pending');
+  });
+});

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

@@ -0,0 +1,132 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+// Files for 'qwen mcp approve' / 'qwen mcp reject' commands (issue #4615).
+import type { CommandModule } from 'yargs';
+import type { MCPServerConfig } from '@qwen-code/qwen-code-core';
+import { isGatedMcpScope } from '@qwen-code/qwen-code-core';
+import { writeStdoutLine } from '../../utils/stdioHelpers.js';
+import { loadSettings } from '../../config/settings.js';
+import { assembleMcpServers } from '../../config/mcpServers.js';
+import {
+  loadMcpApprovals,
+  type McpApprovalStatus,
+} from '../../config/mcpApprovals.js';
+
+/**
+ * All gated (approval-requiring) servers visible from `cwd` — project
+ * `.mcp.json` plus workspace `.qwen/settings.json` (#4615). Non-gated sources
+ * (user/system/extension) never need approval and are excluded.
+ */
+function loadGatedServers(cwd: string): Record<string, MCPServerConfig> {
+  const settings = loadSettings(cwd);
+  const all = assembleMcpServers(settings.merged.mcpServers, cwd);
+  const gated: Record<string, MCPServerConfig> = {};
+  for (const [serverName, config] of Object.entries(all)) {
+    if (isGatedMcpScope(config.scope)) {
+      gated[serverName] = config;
+    }
+  }
+  return gated;
+}
+
+async function setProjectServerStatus(
+  name: string | undefined,
+  status: McpApprovalStatus,
+  all: boolean,
+): Promise<void> {
+  const cwd = process.cwd();
+  const servers = loadGatedServers(cwd);
+
+  const names = Object.keys(servers);
+  if (names.length === 0) {
+    writeStdoutLine(
+      'No approval-requiring MCP servers found (looked in .mcp.json and .qwen/settings.json).',
+    );
+    return;
+  }
+
+  const verb = status === 'approved' ? 'Approved' : 'Rejected';
+  const approvals = loadMcpApprovals();
+
+  const targets = all ? names : name ? [name] : [];
+  if (targets.length === 0) {
+    writeStdoutLine('Specify a server name or pass --all.');
+    return;
+  }
+
+  for (const target of targets) {
+    const config = servers[target];
+    if (!config) {
+      writeStdoutLine(
+        `Server "${target}" not found. Available: ${names.join(', ')}`,
+      );
+      continue;
+    }
+    // The decision binds to this exact config's hash: editing the server in
+    // its source file later returns it to pending (issue #4615).
+    await approvals.setState(cwd, target, config, status);
+    writeStdoutLine(
+      `${verb} MCP server "${target}" (bound to its current config).`,
+    );
+  }
+
+  if (status === 'approved') {
+    writeStdoutLine(
+      'Approved servers connect in your next interactive session.',
+    );
+  }
+}
+
+export const approveCommand: CommandModule = {
+  command: 'approve [name]',
+  describe:
+    'Approve a gated MCP server (.mcp.json or workspace .qwen/settings.json)',
+  builder: (yargs) =>
+    yargs
+      .usage('Usage: qwen mcp approve [options] [name]')
+      .positional('name', {
+        describe: 'Name of the gated server to approve',
+        type: 'string',
+      })
+      .option('all', {
+        describe: 'Approve all gated servers in this workspace',
+        type: 'boolean',
+        default: false,
+      }),
+  handler: async (argv) => {
+    await setProjectServerStatus(
+      argv['name'] as string | undefined,
+      'approved',
+      argv['all'] as boolean,
+    );
+  },
+};
+
+export const rejectCommand: CommandModule = {
+  command: 'reject [name]',
+  describe:
+    'Reject a gated MCP server (.mcp.json or workspace .qwen/settings.json)',
+  builder: (yargs) =>
+    yargs
+      .usage('Usage: qwen mcp reject [options] [name]')
+      .positional('name', {
+        describe: 'Name of the gated server to reject',
+        type: 'string',
+      })
+      .option('all', {
+        describe: 'Reject all gated servers in this workspace',
+        type: 'boolean',
+        default: false,
+      }),
+  handler: async (argv) => {
+    await setProjectServerStatus(
+      argv['name'] as string | undefined,
+      'rejected',
+      argv['all'] as boolean,
+    );
+  },
+};