fix(mcp): fix MCP server removal not persisting to settings (#10098)

Co-authored-by: Jacob Richman <jacob314@gmail.com>

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

@@ -4,66 +4,214 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { vi, describe, it, expect, beforeEach } from 'vitest';
+import { vi, describe, it, expect, beforeEach, afterEach } from 'vitest';
 import yargs from 'yargs';
-import { loadSettings, SettingScope } from '../../config/settings.js';
+import { SettingScope, type LoadedSettings } from '../../config/settings.js';
 import { removeCommand } from './remove.js';
+import * as fs from 'node:fs';
+import * as path from 'node:path';
+import * as os from 'node:os';
 
 vi.mock('fs/promises', () => ({
   readFile: vi.fn(),
   writeFile: vi.fn(),
 }));
 
-vi.mock('../../config/settings.js', async () => {
-  const actual = await vi.importActual('../../config/settings.js');
-  return {
-    ...actual,
-    loadSettings: vi.fn(),
-  };
-});
-
-const mockedLoadSettings = loadSettings as vi.Mock;
-
 describe('mcp remove command', () => {
-  let parser: yargs.Argv;
-  let mockSetValue: vi.Mock;
-  let mockSettings: Record<string, unknown>;
+  describe('unit tests with mocks', () => {
+    let parser: yargs.Argv;
+    let mockSetValue: vi.Mock;
+    let mockSettings: Record<string, unknown>;
 
-  beforeEach(() => {
-    vi.resetAllMocks();
-    const yargsInstance = yargs([]).command(removeCommand);
-    parser = yargsInstance;
-    mockSetValue = vi.fn();
-    mockSettings = {
-      mcpServers: {
-        'test-server': {
-          command: 'echo "hello"',
+    beforeEach(async () => {
+      vi.resetAllMocks();
+
+      mockSetValue = vi.fn();
+      mockSettings = {
+        mcpServers: {
+          'test-server': {
+            command: 'echo "hello"',
+          },
         },
-      },
-    };
-    mockedLoadSettings.mockReturnValue({
-      forScope: () => ({ settings: mockSettings }),
-      setValue: mockSetValue,
+      };
+
+      vi.spyOn(
+        await import('../../config/settings.js'),
+        'loadSettings',
+      ).mockReturnValue({
+        forScope: () => ({ settings: mockSettings }),
+        setValue: mockSetValue,
+      } as Partial<LoadedSettings> as LoadedSettings);
+
+      const yargsInstance = yargs([]).command(removeCommand);
+      parser = yargsInstance;
+    });
+
+    it('should remove a server from project settings', async () => {
+      await parser.parseAsync('remove test-server');
+
+      expect(mockSetValue).toHaveBeenCalledWith(
+        SettingScope.Workspace,
+        'mcpServers',
+        {},
+      );
+    });
+
+    it('should show a message if server not found', async () => {
+      const consoleSpy = vi.spyOn(console, 'log').mockImplementation(() => {});
+      await parser.parseAsync('remove non-existent-server');
+
+      expect(mockSetValue).not.toHaveBeenCalled();
+      expect(consoleSpy).toHaveBeenCalledWith(
+        'Server "non-existent-server" not found in project settings.',
+      );
     });
   });
 
-  it('should remove a server from project settings', async () => {
-    await parser.parseAsync('remove test-server');
+  describe('integration tests with real file I/O', () => {
+    let tempDir: string;
+    let settingsDir: string;
+    let settingsPath: string;
+    let parser: yargs.Argv;
+    let cwdSpy: ReturnType<typeof vi.spyOn>;
 
-    expect(mockSetValue).toHaveBeenCalledWith(
-      SettingScope.Workspace,
-      'mcpServers',
-      {},
-    );
-  });
+    beforeEach(() => {
+      vi.resetAllMocks();
+      vi.restoreAllMocks();
 
-  it('should show a message if server not found', async () => {
-    const consoleSpy = vi.spyOn(console, 'log').mockImplementation(() => {});
-    await parser.parseAsync('remove non-existent-server');
+      tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'mcp-remove-test-'));
+      settingsDir = path.join(tempDir, '.gemini');
+      settingsPath = path.join(settingsDir, 'settings.json');
+      fs.mkdirSync(settingsDir, { recursive: true });
 
-    expect(mockSetValue).not.toHaveBeenCalled();
-    expect(consoleSpy).toHaveBeenCalledWith(
-      'Server "non-existent-server" not found in project settings.',
-    );
+      cwdSpy = vi.spyOn(process, 'cwd').mockReturnValue(tempDir);
+
+      parser = yargs([]).command(removeCommand);
+    });
+
+    afterEach(() => {
+      cwdSpy.mockRestore();
+
+      if (fs.existsSync(tempDir)) {
+        fs.rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    it('should actually remove a server from the settings file', async () => {
+      const originalContent = `{
+        "mcpServers": {
+          "server-to-keep": {
+            "command": "node",
+            "args": ["keep.js"]
+          },
+          "server-to-remove": {
+            "command": "node",
+            "args": ["remove.js"]
+          }
+        }
+      }`;
+      fs.writeFileSync(settingsPath, originalContent, 'utf-8');
+
+      const consoleSpy = vi.spyOn(console, 'log').mockImplementation(() => {});
+      await parser.parseAsync('remove server-to-remove');
+
+      const updatedContent = fs.readFileSync(settingsPath, 'utf-8');
+      expect(updatedContent).toContain('"server-to-keep"');
+      expect(updatedContent).not.toContain('"server-to-remove"');
+
+      expect(consoleSpy).toHaveBeenCalledWith(
+        'Server "server-to-remove" removed from project settings.',
+      );
+
+      consoleSpy.mockRestore();
+    });
+
+    it('should preserve comments when removing a server', async () => {
+      const originalContent = `{
+        "mcpServers": {
+          // Server to keep
+          "context7": {
+            "command": "node",
+            "args": ["server.js"]
+          },
+          // Server to remove
+          "oldServer": {
+            "command": "old",
+            "args": ["old.js"]
+          }
+        }
+      }`;
+      fs.writeFileSync(settingsPath, originalContent, 'utf-8');
+
+      const consoleSpy = vi.spyOn(console, 'log').mockImplementation(() => {});
+      await parser.parseAsync('remove oldServer');
+
+      const updatedContent = fs.readFileSync(settingsPath, 'utf-8');
+      expect(updatedContent).toContain('// Server to keep');
+      expect(updatedContent).toContain('"context7"');
+      expect(updatedContent).not.toContain('"oldServer"');
+      expect(updatedContent).toContain('// Server to remove');
+
+      consoleSpy.mockRestore();
+    });
+
+    it('should handle removing the only server', async () => {
+      const originalContent = `{
+        "mcpServers": {
+          "only-server": {
+            "command": "node",
+            "args": ["server.js"]
+          }
+        }
+      }`;
+      fs.writeFileSync(settingsPath, originalContent, 'utf-8');
+
+      const consoleSpy = vi.spyOn(console, 'log').mockImplementation(() => {});
+      await parser.parseAsync('remove only-server');
+
+      const updatedContent = fs.readFileSync(settingsPath, 'utf-8');
+      expect(updatedContent).toContain('"mcpServers"');
+      expect(updatedContent).not.toContain('"only-server"');
+      expect(updatedContent).toMatch(/"mcpServers"\s*:\s*\{\s*\}/);
+
+      consoleSpy.mockRestore();
+    });
+
+    it('should preserve other settings when removing a server', async () => {
+      // Create settings file with other settings
+      // Note: "model" will be migrated to "model": { "name": ... } format
+      const originalContent = `{
+        "model": {
+          "name": "gemini-2.5-pro"
+        },
+        "mcpServers": {
+          "server1": {
+            "command": "node",
+            "args": ["s1.js"]
+          },
+          "server2": {
+            "command": "node",
+            "args": ["s2.js"]
+          }
+        },
+        "ui": {
+          "theme": "dark"
+        }
+      }`;
+      fs.writeFileSync(settingsPath, originalContent, 'utf-8');
+
+      const consoleSpy = vi.spyOn(console, 'log').mockImplementation(() => {});
+      await parser.parseAsync('remove server1');
+
+      const updatedContent = fs.readFileSync(settingsPath, 'utf-8');
+      expect(updatedContent).toContain('"model"');
+      expect(updatedContent).toContain('"gemini-2.5-pro"');
+      expect(updatedContent).toContain('"server2"');
+      expect(updatedContent).toContain('"ui"');
+      expect(updatedContent).toContain('"theme": "dark"');
+      expect(updatedContent).not.toContain('"server1"');
+
+      consoleSpy.mockRestore();
+    });
   });
 });