fix(mcp): Notifications/tools/list_changed support not working (#21050)

Co-authored-by: Bryan Morgan <bryanmorgan@google.com>

packages/core/src/resources/resource-registry.ts

@@ -69,4 +69,17 @@ export class ResourceRegistry {
   clear(): void {
     this.resources.clear();
   }
+
+  /**
+   * Returns an array of resources registered from a specific MCP server.
+   */
+  getResourcesByServer(serverName: string): MCPResource[] {
+    const serverResources: MCPResource[] = [];
+    for (const resource of this.resources.values()) {
+      if (resource.serverName === serverName) {
+        serverResources.push(resource);
+      }
+    }
+    return serverResources.sort((a, b) => a.uri.localeCompare(b.uri));
+  }
 }

packages/core/src/tools/mcp-client-manager.ts

@@ -173,7 +173,7 @@ export class McpClientManager {
         return Promise.resolve();
       }),
     );
-    await this.cliConfig.refreshMcpContext();
+    await this.scheduleMcpContextRefresh();
   }
 
   /**
@@ -193,7 +193,7 @@ export class McpClientManager {
         }),
       ),
     );
-    await this.cliConfig.refreshMcpContext();
+    await this.scheduleMcpContextRefresh();
   }
 
   /**
@@ -251,7 +251,7 @@ export class McpClientManager {
         if (!skipRefresh) {
           // This is required to update the content generator configuration with the
           // new tool configuration and system instructions.
-          await this.cliConfig.refreshMcpContext();
+          await this.scheduleMcpContextRefresh();
         }
       }
     }
@@ -321,7 +321,7 @@ export class McpClientManager {
             this.cliConfig.getDebugMode(),
             this.clientVersion,
             async () => {
-              debugLogger.log('Tools changed, updating Gemini context...');
+              debugLogger.log(`🔔 Refreshing context for server '${name}'...`);
               await this.scheduleMcpContextRefresh();
             },
           );
@@ -431,7 +431,7 @@ export class McpClientManager {
       this.eventEmitter?.emit('mcp-client-update', this.clients);
     }
 
-    await this.cliConfig.refreshMcpContext();
+    await this.scheduleMcpContextRefresh();
   }
 
   /**
@@ -451,7 +451,7 @@ export class McpClientManager {
         },
       ),
     );
-    await this.cliConfig.refreshMcpContext();
+    await this.scheduleMcpContextRefresh();
   }
 
   /**
@@ -463,7 +463,7 @@ export class McpClientManager {
       throw new Error(`No MCP server registered with the name "${name}"`);
     }
     await this.maybeDiscoverMcpServer(name, config);
-    await this.cliConfig.refreshMcpContext();
+    await this.scheduleMcpContextRefresh();
   }
 
   /**
@@ -517,21 +517,51 @@ export class McpClientManager {
     return instructions.join('\n\n');
   }
 
+  private isRefreshingMcpContext: boolean = false;
+  private pendingMcpContextRefresh: boolean = false;
+
   private async scheduleMcpContextRefresh(): Promise<void> {
+    this.pendingMcpContextRefresh = true;
+
+    if (this.isRefreshingMcpContext) {
+      debugLogger.log(
+        'MCP context refresh already in progress, queuing trailing execution.',
+      );
+      return this.pendingRefreshPromise ?? Promise.resolve();
+    }
+
     if (this.pendingRefreshPromise) {
+      debugLogger.log(
+        'MCP context refresh already scheduled, coalescing with existing request.',
+      );
       return this.pendingRefreshPromise;
     }
 
+    debugLogger.log('Scheduling MCP context refresh...');
     this.pendingRefreshPromise = (async () => {
-      // Debounce to coalesce multiple rapid updates
+      this.isRefreshingMcpContext = true;
-      await new Promise((resolve) => setTimeout(resolve, 300));
       try {
-        await this.cliConfig.refreshMcpContext();
+        do {
+          this.pendingMcpContextRefresh = false;
+          debugLogger.log('Executing MCP context refresh...');
+          await this.cliConfig.refreshMcpContext();
+          debugLogger.log('MCP context refresh complete.');
+
+          // If more refresh requests came in during the execution, wait a bit
+          // to coalesce them before the next iteration.
+          if (this.pendingMcpContextRefresh) {
+            debugLogger.log(
+              'Coalescing burst refresh requests (300ms delay)...',
+            );
+            await new Promise((resolve) => setTimeout(resolve, 300));
+          }
+        } while (this.pendingMcpContextRefresh);
       } catch (error) {
         debugLogger.error(
           `Error refreshing MCP context: ${getErrorMessage(error)}`,
         );
       } finally {
+        this.isRefreshingMcpContext = false;
         this.pendingRefreshPromise = null;
       }
     })();

packages/core/src/tools/mcp-client.test.ts

@@ -22,6 +22,7 @@ import {
   PromptListChangedNotificationSchema,
   ResourceListChangedNotificationSchema,
   ToolListChangedNotificationSchema,
+  ProgressNotificationSchema,
 } from '@modelcontextprotocol/sdk/types.js';
 import type { DiscoveredMCPTool } from './mcp-tool.js';
 
@@ -102,6 +103,7 @@ describe('mcp-client', () => {
 
   afterEach(() => {
     vi.restoreAllMocks();
+    vi.useRealTimers();
   });
 
   describe('McpClient', () => {
@@ -140,13 +142,16 @@ describe('mcp-client', () => {
       const mockedToolRegistry = {
         registerTool: vi.fn(),
         sortTools: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
         getMessageBus: vi.fn().mockReturnValue(undefined),
       } as unknown as ToolRegistry;
       const promptRegistry = {
         registerPrompt: vi.fn(),
+        getPromptsByServer: vi.fn().mockReturnValue([]),
         removePromptsByServer: vi.fn(),
       } as unknown as PromptRegistry;
       const resourceRegistry = {
+        getResourcesByServer: vi.fn().mockReturnValue([]),
         setResourcesForServer: vi.fn(),
         removeResourcesByServer: vi.fn(),
       } as unknown as ResourceRegistry;
@@ -221,13 +226,16 @@ describe('mcp-client', () => {
       const mockedToolRegistry = {
         registerTool: vi.fn(),
         sortTools: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
         getMessageBus: vi.fn().mockReturnValue(undefined),
       } as unknown as ToolRegistry;
       const promptRegistry = {
         registerPrompt: vi.fn(),
+        getPromptsByServer: vi.fn().mockReturnValue([]),
         removePromptsByServer: vi.fn(),
       } as unknown as PromptRegistry;
       const resourceRegistry = {
+        getResourcesByServer: vi.fn().mockReturnValue([]),
         setResourcesForServer: vi.fn(),
         removeResourcesByServer: vi.fn(),
       } as unknown as ResourceRegistry;
@@ -328,13 +336,16 @@ describe('mcp-client', () => {
       const mockedToolRegistry = {
         registerTool: vi.fn(),
         sortTools: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
         getMessageBus: vi.fn().mockReturnValue(undefined),
       } as unknown as ToolRegistry;
       const promptRegistry = {
         registerPrompt: vi.fn(),
+        getPromptsByServer: vi.fn().mockReturnValue([]),
         removePromptsByServer: vi.fn(),
       } as unknown as PromptRegistry;
       const resourceRegistry = {
+        getResourcesByServer: vi.fn().mockReturnValue([]),
         setResourcesForServer: vi.fn(),
         removeResourcesByServer: vi.fn(),
       } as unknown as ResourceRegistry;
@@ -388,13 +399,16 @@ describe('mcp-client', () => {
       const mockedToolRegistry = {
         registerTool: vi.fn(),
         sortTools: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
         getMessageBus: vi.fn().mockReturnValue(undefined),
       } as unknown as ToolRegistry;
       const promptRegistry = {
         registerPrompt: vi.fn(),
+        getPromptsByServer: vi.fn().mockReturnValue([]),
         removePromptsByServer: vi.fn(),
       } as unknown as PromptRegistry;
       const resourceRegistry = {
+        getResourcesByServer: vi.fn().mockReturnValue([]),
         setResourcesForServer: vi.fn(),
         removeResourcesByServer: vi.fn(),
       } as unknown as ResourceRegistry;
@@ -701,13 +715,16 @@ describe('mcp-client', () => {
       const mockedToolRegistry = {
         registerTool: vi.fn(),
         sortTools: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
         getMessageBus: vi.fn().mockReturnValue(undefined),
       } as unknown as ToolRegistry;
       const promptRegistry = {
         registerPrompt: vi.fn(),
+        getPromptsByServer: vi.fn().mockReturnValue([]),
         removePromptsByServer: vi.fn(),
       } as unknown as PromptRegistry;
       const resourceRegistry = {
+        getResourcesByServer: vi.fn().mockReturnValue([]),
         setResourcesForServer: vi.fn(),
         removeResourcesByServer: vi.fn(),
       } as unknown as ResourceRegistry;
@@ -778,13 +795,16 @@ describe('mcp-client', () => {
       const mockedToolRegistry = {
         registerTool: vi.fn(),
         sortTools: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
         getMessageBus: vi.fn().mockReturnValue(undefined),
       } as unknown as ToolRegistry;
       const promptRegistry = {
         registerPrompt: vi.fn(),
+        getPromptsByServer: vi.fn().mockReturnValue([]),
         removePromptsByServer: vi.fn(),
       } as unknown as PromptRegistry;
       const resourceRegistry = {
+        getResourcesByServer: vi.fn().mockReturnValue([]),
         setResourcesForServer: vi.fn(),
         removeResourcesByServer: vi.fn(),
       } as unknown as ResourceRegistry;
@@ -864,13 +884,16 @@ describe('mcp-client', () => {
       const mockedToolRegistry = {
         registerTool: vi.fn(),
         sortTools: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
         getMessageBus: vi.fn().mockReturnValue(undefined),
       } as unknown as ToolRegistry;
       const promptRegistry = {
         registerPrompt: vi.fn(),
+        getPromptsByServer: vi.fn().mockReturnValue([]),
         removePromptsByServer: vi.fn(),
       } as unknown as PromptRegistry;
       const resourceRegistry = {
+        getResourcesByServer: vi.fn().mockReturnValue([]),
         setResourcesForServer: vi.fn(),
         removeResourcesByServer: vi.fn(),
       } as unknown as ResourceRegistry;
@@ -950,13 +973,16 @@ describe('mcp-client', () => {
       const mockedToolRegistry = {
         registerTool: vi.fn(),
         sortTools: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
         getMessageBus: vi.fn().mockReturnValue(undefined),
       } as unknown as ToolRegistry;
       const promptRegistry = {
         registerPrompt: vi.fn(),
+        getPromptsByServer: vi.fn().mockReturnValue([]),
         removePromptsByServer: vi.fn(),
       } as unknown as PromptRegistry;
       const resourceRegistry = {
+        getResourcesByServer: vi.fn().mockReturnValue([]),
         setResourcesForServer: vi.fn(),
         removeResourcesByServer: vi.fn(),
       } as unknown as ResourceRegistry;
@@ -1086,6 +1112,7 @@ describe('mcp-client', () => {
         setNotificationHandler: vi.fn(),
         listTools: vi.fn().mockResolvedValue({ tools: [] }),
         listPrompts: vi.fn().mockResolvedValue({ prompts: [] }),
+        listResources: vi.fn().mockResolvedValue({ resources: [] }),
         request: vi.fn().mockResolvedValue({}),
       };
 
@@ -1096,12 +1123,27 @@ describe('mcp-client', () => {
         {} as SdkClientStdioLib.StdioClientTransport,
       );
 
+      const mockedToolRegistry = {
+        registerTool: vi.fn(),
+        sortTools: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
+        getMessageBus: vi.fn().mockReturnValue(undefined),
+      } as unknown as ToolRegistry;
+
       const client = new McpClient(
         'test-server',
         { command: 'test-command' },
-        {} as ToolRegistry,
+        mockedToolRegistry,
-        {} as PromptRegistry,
+        {
-        {} as ResourceRegistry,
+          getPromptsByServer: vi.fn().mockReturnValue([]),
+          registerPrompt: vi.fn(),
+        } as unknown as PromptRegistry,
+        {
+          getResourcesByServer: vi.fn().mockReturnValue([]),
+          registerResource: vi.fn(),
+          removeResourcesByServer: vi.fn(),
+          setResourcesForServer: vi.fn(),
+        } as unknown as ResourceRegistry,
         workspaceContext,
         MOCK_CONTEXT,
         false,
@@ -1136,9 +1178,21 @@ describe('mcp-client', () => {
       const client = new McpClient(
         'test-server',
         { command: 'test-command' },
-        {} as ToolRegistry,
+        {
-        {} as PromptRegistry,
+          getToolsByServer: vi.fn().mockReturnValue([]),
-        {} as ResourceRegistry,
+          registerTool: vi.fn(),
+          sortTools: vi.fn(),
+        } as unknown as ToolRegistry,
+        {
+          getPromptsByServer: vi.fn().mockReturnValue([]),
+          registerPrompt: vi.fn(),
+        } as unknown as PromptRegistry,
+        {
+          getResourcesByServer: vi.fn().mockReturnValue([]),
+          registerResource: vi.fn(),
+          removeResourcesByServer: vi.fn(),
+          setResourcesForServer: vi.fn(),
+        } as unknown as ResourceRegistry,
         workspaceContext,
         MOCK_CONTEXT,
         false,
@@ -1147,7 +1201,62 @@ describe('mcp-client', () => {
 
       await client.connect();
 
-      expect(mockedClient.setNotificationHandler).toHaveBeenCalledOnce();
+      // Should be called for ProgressNotificationSchema, even if no other capabilities
+      expect(mockedClient.setNotificationHandler).toHaveBeenCalled();
+      const progressCall = mockedClient.setNotificationHandler.mock.calls.find(
+        (call) => call[0] === ProgressNotificationSchema,
+      );
+      expect(progressCall).toBeDefined();
+    });
+
+    it('should set up notification handler even if listChanged is false (robustness)', async () => {
+      // Setup mocks
+      const mockedClient = {
+        connect: vi.fn(),
+        getServerCapabilities: vi
+          .fn()
+          .mockReturnValue({ tools: { listChanged: false } }),
+        setNotificationHandler: vi.fn(),
+        request: vi.fn().mockResolvedValue({}),
+        registerCapabilities: vi.fn().mockResolvedValue({}),
+        setRequestHandler: vi.fn().mockResolvedValue({}),
+      };
+
+      vi.mocked(ClientLib.Client).mockReturnValue(
+        mockedClient as unknown as ClientLib.Client,
+      );
+
+      const client = new McpClient(
+        'test-server',
+        { command: 'test-command' },
+        {
+          getToolsByServer: vi.fn().mockReturnValue([]),
+          registerTool: vi.fn(),
+          sortTools: vi.fn(),
+        } as unknown as ToolRegistry,
+        {
+          getPromptsByServer: vi.fn().mockReturnValue([]),
+          registerPrompt: vi.fn(),
+        } as unknown as PromptRegistry,
+        {
+          getResourcesByServer: vi.fn().mockReturnValue([]),
+          registerResource: vi.fn(),
+          removeResourcesByServer: vi.fn(),
+          setResourcesForServer: vi.fn(),
+        } as unknown as ResourceRegistry,
+        workspaceContext,
+        MOCK_CONTEXT,
+        false,
+        '0.0.1',
+      );
+
+      await client.connect();
+
+      const toolUpdateCall =
+        mockedClient.setNotificationHandler.mock.calls.find(
+          (call) => call[0] === ToolListChangedNotificationSchema,
+        );
+      expect(toolUpdateCall).toBeDefined();
     });
 
     it('should refresh tools and notify manager when notification is received', async () => {
@@ -1167,6 +1276,7 @@ describe('mcp-client', () => {
           ],
         }),
         listPrompts: vi.fn().mockResolvedValue({ prompts: [] }),
+        listResources: vi.fn().mockResolvedValue({ resources: [] }),
         request: vi.fn().mockResolvedValue({}),
         registerCapabilities: vi.fn().mockResolvedValue({}),
         setRequestHandler: vi.fn().mockResolvedValue({}),
@@ -1183,31 +1293,38 @@ describe('mcp-client', () => {
         removeMcpToolsByServer: vi.fn(),
         registerTool: vi.fn(),
         sortTools: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
         getMessageBus: vi.fn().mockReturnValue(undefined),
       } as unknown as ToolRegistry;
 
-      const onToolsUpdatedSpy = vi.fn().mockResolvedValue(undefined);
+      const onContextUpdatedSpy = vi.fn().mockResolvedValue(undefined);
 
-      // Initialize client with onToolsUpdated callback
+      // Initialize client with onContextUpdated callback
       const client = new McpClient(
         'test-server',
         { command: 'test-command' },
         mockedToolRegistry,
         {} as PromptRegistry,
-        {} as ResourceRegistry,
+        {
+          removeMcpResourcesByServer: vi.fn(),
+          registerResource: vi.fn(),
+        } as unknown as ResourceRegistry,
         workspaceContext,
         MOCK_CONTEXT,
         false,
         '0.0.1',
-        onToolsUpdatedSpy,
+        onContextUpdatedSpy,
       );
 
       // 1. Connect (sets up listener)
       await client.connect();
 
-      // 2. Extract the callback passed to setNotificationHandler
+      // 2. Extract the callback passed to setNotificationHandler for tools
-      const notificationCallback =
+      const toolUpdateCall =
-        mockedClient.setNotificationHandler.mock.calls[0][1];
+        mockedClient.setNotificationHandler.mock.calls.find(
+          (call) => call[0] === ToolListChangedNotificationSchema,
+        );
+      const notificationCallback = toolUpdateCall![1];
 
       // 3. Trigger the notification manually
       await notificationCallback();
@@ -1225,7 +1342,7 @@ describe('mcp-client', () => {
       expect(mockedToolRegistry.registerTool).toHaveBeenCalled();
 
       // It should notify the manager
-      expect(onToolsUpdatedSpy).toHaveBeenCalled();
+      expect(onContextUpdatedSpy).toHaveBeenCalled();
 
       // It should emit feedback event
       expect(MOCK_CONTEXT.emitMcpDiagnostic).toHaveBeenCalledWith(
@@ -1259,6 +1376,7 @@ describe('mcp-client', () => {
 
       const mockedToolRegistry = {
         removeMcpToolsByServer: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
         getMessageBus: vi.fn().mockReturnValue(undefined),
       } as unknown as ToolRegistry;
 
@@ -1276,8 +1394,11 @@ describe('mcp-client', () => {
 
       await client.connect();
 
-      const notificationCallback =
+      const toolUpdateCall =
-        mockedClient.setNotificationHandler.mock.calls[0][1];
+        mockedClient.setNotificationHandler.mock.calls.find(
+          (call) => call[0] === ToolListChangedNotificationSchema,
+        );
+      const notificationCallback = toolUpdateCall![1];
 
       // Trigger notification - should fail internally but catch the error
       await notificationCallback();
@@ -1328,10 +1449,11 @@ describe('mcp-client', () => {
         removeMcpToolsByServer: vi.fn(),
         registerTool: vi.fn(),
         sortTools: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
         getMessageBus: vi.fn().mockReturnValue(undefined),
       } as unknown as ToolRegistry;
 
-      const onToolsUpdatedSpy = vi.fn().mockResolvedValue(undefined);
+      const onContextUpdatedSpy = vi.fn().mockResolvedValue(undefined);
 
       const clientA = new McpClient(
         'server-A',
@@ -1343,7 +1465,7 @@ describe('mcp-client', () => {
         MOCK_CONTEXT,
         false,
         '0.0.1',
-        onToolsUpdatedSpy,
+        onContextUpdatedSpy,
       );
 
       const clientB = new McpClient(
@@ -1356,14 +1478,23 @@ describe('mcp-client', () => {
         MOCK_CONTEXT,
         false,
         '0.0.1',
-        onToolsUpdatedSpy,
+        onContextUpdatedSpy,
       );
 
       await clientA.connect();
       await clientB.connect();
 
-      const handlerA = mockClientA.setNotificationHandler.mock.calls[0][1];
+      const toolUpdateCallA =
-      const handlerB = mockClientB.setNotificationHandler.mock.calls[0][1];
+        mockClientA.setNotificationHandler.mock.calls.find(
+          (call) => call[0] === ToolListChangedNotificationSchema,
+        );
+      const handlerA = toolUpdateCallA![1];
+
+      const toolUpdateCallB =
+        mockClientB.setNotificationHandler.mock.calls.find(
+          (call) => call[0] === ToolListChangedNotificationSchema,
+        );
+      const handlerB = toolUpdateCallB![1];
 
       // Trigger burst updates simultaneously
       await Promise.all([handlerA(), handlerB()]);
@@ -1383,12 +1514,11 @@ describe('mcp-client', () => {
       expect(mockedToolRegistry.registerTool).toHaveBeenCalledTimes(2);
 
       // Verify the update callback was triggered for both
-      expect(onToolsUpdatedSpy).toHaveBeenCalledTimes(2);
+      expect(onContextUpdatedSpy).toHaveBeenCalledTimes(2);
     });
 
     it('should abort discovery and log error if timeout is exceeded during refresh', async () => {
       vi.useFakeTimers();
-
       const mockedClient = {
         connect: vi.fn(),
         getServerCapabilities: vi
@@ -1412,6 +1542,7 @@ describe('mcp-client', () => {
             }),
         ),
         listPrompts: vi.fn().mockResolvedValue({ prompts: [] }),
+        listResources: vi.fn().mockResolvedValue({ resources: [] }),
         request: vi.fn().mockResolvedValue({}),
         registerCapabilities: vi.fn().mockResolvedValue({}),
         setRequestHandler: vi.fn().mockResolvedValue({}),
@@ -1428,16 +1559,26 @@ describe('mcp-client', () => {
         removeMcpToolsByServer: vi.fn(),
         registerTool: vi.fn(),
         sortTools: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
         getMessageBus: vi.fn().mockReturnValue(undefined),
       } as unknown as ToolRegistry;
 
       const client = new McpClient(
         'test-server',
-        // Set a short timeout
+        // Set a very short timeout
-        { command: 'test-command', timeout: 100 },
+        { command: 'test-command', timeout: 50 },
         mockedToolRegistry,
-        {} as PromptRegistry,
+        {
-        {} as ResourceRegistry,
+          getPromptsByServer: vi.fn().mockReturnValue([]),
+          registerPrompt: vi.fn(),
+          removePromptsByServer: vi.fn(),
+        } as unknown as PromptRegistry,
+        {
+          getResourcesByServer: vi.fn().mockReturnValue([]),
+          registerResource: vi.fn(),
+          removeResourcesByServer: vi.fn(),
+          setResourcesForServer: vi.fn(),
+        } as unknown as ResourceRegistry,
         workspaceContext,
         MOCK_CONTEXT,
         false,
@@ -1446,13 +1587,16 @@ describe('mcp-client', () => {
 
       await client.connect();
 
-      const notificationCallback =
+      const toolUpdateCall =
-        mockedClient.setNotificationHandler.mock.calls[0][1];
+        mockedClient.setNotificationHandler.mock.calls.find(
+          (call) => call[0] === ToolListChangedNotificationSchema,
+        );
+      const notificationCallback = toolUpdateCall![1];
 
       const refreshPromise = notificationCallback();
 
-      vi.advanceTimersByTime(150);
+      // Advance timers to trigger the timeout (11 minutes to cover even the default timeout)
-
+      await vi.advanceTimersByTimeAsync(11 * 60 * 1000);
       await refreshPromise;
 
       expect(mockedClient.listTools).toHaveBeenCalledWith(
@@ -1463,8 +1607,6 @@ describe('mcp-client', () => {
       );
 
       expect(mockedToolRegistry.registerTool).not.toHaveBeenCalled();
-
-      vi.useRealTimers();
     });
 
     it('should pass abort signal to onToolsUpdated callback', async () => {
@@ -1492,35 +1634,51 @@ describe('mcp-client', () => {
         removeMcpToolsByServer: vi.fn(),
         registerTool: vi.fn(),
         sortTools: vi.fn(),
+        getToolsByServer: vi.fn().mockReturnValue([]),
         getMessageBus: vi.fn().mockReturnValue(undefined),
       } as unknown as ToolRegistry;
 
-      const onToolsUpdatedSpy = vi.fn().mockResolvedValue(undefined);
+      const onContextUpdatedSpy = vi.fn().mockResolvedValue(undefined);
 
       const client = new McpClient(
         'test-server',
         { command: 'test-command' },
         mockedToolRegistry,
-        {} as PromptRegistry,
+        {
-        {} as ResourceRegistry,
+          getPromptsByServer: vi.fn().mockReturnValue([]),
+          registerPrompt: vi.fn(),
+          removePromptsByServer: vi.fn(),
+        } as unknown as PromptRegistry,
+        {
+          getResourcesByServer: vi.fn().mockReturnValue([]),
+          registerResource: vi.fn(),
+          removeResourcesByServer: vi.fn(),
+          setResourcesForServer: vi.fn(),
+        } as unknown as ResourceRegistry,
         workspaceContext,
         MOCK_CONTEXT,
         false,
         '0.0.1',
-        onToolsUpdatedSpy,
+        onContextUpdatedSpy,
       );
 
       await client.connect();
 
-      const notificationCallback =
+      const toolUpdateCall =
-        mockedClient.setNotificationHandler.mock.calls[0][1];
+        mockedClient.setNotificationHandler.mock.calls.find(
+          (call) => call[0] === ToolListChangedNotificationSchema,
+        );
+      const notificationCallback = toolUpdateCall![1];
 
-      await notificationCallback();
+      vi.useFakeTimers();
+      const refreshPromise = notificationCallback();
+      await vi.advanceTimersByTimeAsync(500);
+      await refreshPromise;
 
-      expect(onToolsUpdatedSpy).toHaveBeenCalledWith(expect.any(AbortSignal));
+      expect(onContextUpdatedSpy).toHaveBeenCalledWith(expect.any(AbortSignal));
 
       // Verify the signal passed was not aborted (happy path)
-      const signal = onToolsUpdatedSpy.mock.calls[0][0];
+      const signal = onContextUpdatedSpy.mock.calls[0][0];
       expect(signal.aborted).toBe(false);
     });
   });

packages/core/src/tools/mcp-client.ts

@@ -70,7 +70,10 @@ import type { ToolRegistry } from './tool-registry.js';
 import { debugLogger } from '../utils/debugLogger.js';
 import { type MessageBus } from '../confirmation-bus/message-bus.js';
 import { coreEvents } from '../utils/events.js';
-import type { ResourceRegistry } from '../resources/resource-registry.js';
+import {
+  type ResourceRegistry,
+  type MCPResource,
+} from '../resources/resource-registry.js';
 import { validateMcpPolicyToolNames } from '../policy/toml-loader.js';
 import {
   sanitizeEnvironment,
@@ -156,7 +159,7 @@ export class McpClient implements McpProgressReporter {
     private readonly cliConfig: McpContext,
     private readonly debugMode: boolean,
     private readonly clientVersion: string,
-    private readonly onToolsUpdated?: (signal?: AbortSignal) => Promise<void>,
+    private readonly onContextUpdated?: (signal?: AbortSignal) => Promise<void>,
   ) {}
 
   /**
@@ -352,10 +355,21 @@ export class McpClient implements McpProgressReporter {
 
     const capabilities = this.client.getServerCapabilities();
 
-    if (capabilities?.tools?.listChanged) {
+    debugLogger.log(
-      debugLogger.log(
+      `Registering notification handlers for server '${this.serverName}'. Capabilities:`,
-        `Server '${this.serverName}' supports tool updates. Listening for changes...`,
+      capabilities,
-      );
+    );
+
+    if (capabilities?.tools) {
+      if (capabilities.tools.listChanged) {
+        debugLogger.log(
+          `Server '${this.serverName}' supports tool updates. Listening for changes...`,
+        );
+      } else {
+        debugLogger.log(
+          `Server '${this.serverName}' has tools but did not declare 'listChanged' capability. Listening anyway for robustness...`,
+        );
+      }
 
       this.client.setNotificationHandler(
         ToolListChangedNotificationSchema,
@@ -368,10 +382,16 @@ export class McpClient implements McpProgressReporter {
       );
     }
 
-    if (capabilities?.resources?.listChanged) {
+    if (capabilities?.resources) {
-      debugLogger.log(
+      if (capabilities.resources.listChanged) {
-        `Server '${this.serverName}' supports resource updates. Listening for changes...`,
+        debugLogger.log(
-      );
+          `Server '${this.serverName}' supports resource updates. Listening for changes...`,
+        );
+      } else {
+        debugLogger.log(
+          `Server '${this.serverName}' has resources but did not declare 'listChanged' capability. Listening anyway for robustness...`,
+        );
+      }
 
       this.client.setNotificationHandler(
         ResourceListChangedNotificationSchema,
@@ -384,10 +404,16 @@ export class McpClient implements McpProgressReporter {
       );
     }
 
-    if (capabilities?.prompts?.listChanged) {
+    if (capabilities?.prompts) {
-      debugLogger.log(
+      if (capabilities.prompts.listChanged) {
-        `Server '${this.serverName}' supports prompt updates. Listening for changes...`,
+        debugLogger.log(
-      );
+          `Server '${this.serverName}' supports prompt updates. Listening for changes...`,
+        );
+      } else {
+        debugLogger.log(
+          `Server '${this.serverName}' has prompts but did not declare 'listChanged' capability. Listening anyway for robustness...`,
+        );
+      }
 
       this.client.setNotificationHandler(
         PromptListChangedNotificationSchema,
@@ -451,6 +477,25 @@ export class McpClient implements McpProgressReporter {
         let newResources;
         try {
           newResources = await this.discoverResources();
+
+          // Verification Retry: If no resources are found or resources didn't change,
+          // wait briefly and try one more time. Some servers notify before they're fully ready.
+          const currentResources =
+            this.resourceRegistry.getResourcesByServer(this.serverName) || [];
+          const resourceMatch =
+            newResources.length === currentResources.length &&
+            newResources.every((nr: Resource) =>
+              currentResources.some((cr: MCPResource) => cr.uri === nr.uri),
+            );
+
+          if (resourceMatch && !this.pendingResourceRefresh) {
+            debugLogger.log(
+              `No resource changes detected for '${this.serverName}'. Retrying once in 500ms...`,
+            );
+            const retryDelay = 500;
+            await new Promise((resolve) => setTimeout(resolve, retryDelay));
+            newResources = await this.discoverResources();
+          }
         } catch (err) {
           debugLogger.error(
             `Resource discovery failed during refresh: ${getErrorMessage(err)}`,
@@ -461,6 +506,10 @@ export class McpClient implements McpProgressReporter {
 
         this.updateResourceRegistry(newResources);
 
+        if (this.onContextUpdated) {
+          await this.onContextUpdated(abortController.signal);
+        }
+
         clearTimeout(timeoutId);
 
         this.cliConfig.emitMcpDiagnostic(
@@ -476,7 +525,6 @@ export class McpClient implements McpProgressReporter {
       );
     } finally {
       this.isRefreshingResources = false;
-      this.pendingResourceRefresh = false;
     }
   }
 
@@ -519,9 +567,31 @@ export class McpClient implements McpProgressReporter {
         const timeoutId = setTimeout(() => abortController.abort(), timeoutMs);
 
         try {
-          const newPrompts = await this.fetchPrompts({
+          let newPrompts = await this.fetchPrompts({
             signal: abortController.signal,
           });
+
+          // Verification Retry: If no prompts are found or prompts didn't change,
+          // wait briefly and try one more time. Some servers notify before they're fully ready.
+          const currentPrompts =
+            this.promptRegistry.getPromptsByServer(this.serverName) || [];
+          const promptsMatch =
+            newPrompts.length === currentPrompts.length &&
+            newPrompts.every((np) =>
+              currentPrompts.some((cp) => cp.name === np.name),
+            );
+
+          if (promptsMatch && !this.pendingPromptRefresh) {
+            debugLogger.log(
+              `No prompt changes detected for '${this.serverName}'. Retrying once in 500ms...`,
+            );
+            const retryDelay = 500;
+            await new Promise((resolve) => setTimeout(resolve, retryDelay));
+            newPrompts = await this.fetchPrompts({
+              signal: abortController.signal,
+            });
+          }
+
           this.promptRegistry.removePromptsByServer(this.serverName);
           for (const prompt of newPrompts) {
             this.promptRegistry.registerPrompt(prompt);
@@ -534,6 +604,10 @@ export class McpClient implements McpProgressReporter {
           break;
         }
 
+        if (this.onContextUpdated) {
+          await this.onContextUpdated(abortController.signal);
+        }
+
         clearTimeout(timeoutId);
 
         this.cliConfig.emitMcpDiagnostic(
@@ -549,7 +623,6 @@ export class McpClient implements McpProgressReporter {
       );
     } finally {
       this.isRefreshingPrompts = false;
-      this.pendingPromptRefresh = false;
     }
   }
 
@@ -594,6 +667,38 @@ export class McpClient implements McpProgressReporter {
           newTools = await this.discoverTools(this.cliConfig, {
             signal: abortController.signal,
           });
+          debugLogger.log(
+            `Refresh for '${this.serverName}' discovered ${newTools.length} tools.`,
+          );
+
+          // Verification Retry (Option 3): If no tools are found or tools didn't change,
+          // wait briefly and try one more time. Some servers notify before they're fully ready.
+          const currentTools =
+            this.toolRegistry.getToolsByServer(this.serverName) || [];
+          const toolNamesMatch =
+            newTools.length === currentTools.length &&
+            newTools.every((nt) =>
+              currentTools.some(
+                (ct) =>
+                  ct.name === nt.name ||
+                  (ct instanceof DiscoveredMCPTool &&
+                    ct.serverToolName === nt.serverToolName),
+              ),
+            );
+
+          if (toolNamesMatch && !this.pendingToolRefresh) {
+            debugLogger.log(
+              `No tool changes detected for '${this.serverName}'. Retrying once in 500ms...`,
+            );
+            const retryDelay = 500;
+            await new Promise((resolve) => setTimeout(resolve, retryDelay));
+            newTools = await this.discoverTools(this.cliConfig, {
+              signal: abortController.signal,
+            });
+            debugLogger.log(
+              `Retry refresh for '${this.serverName}' discovered ${newTools.length} tools.`,
+            );
+          }
         } catch (err) {
           debugLogger.error(
             `Discovery failed during refresh: ${getErrorMessage(err)}`,
@@ -609,8 +714,8 @@ export class McpClient implements McpProgressReporter {
         }
         this.toolRegistry.sortTools();
 
-        if (this.onToolsUpdated) {
+        if (this.onContextUpdated) {
-          await this.onToolsUpdated(abortController.signal);
+          await this.onContextUpdated(abortController.signal);
         }
 
         clearTimeout(timeoutId);
@@ -628,7 +733,6 @@ export class McpClient implements McpProgressReporter {
       );
     } finally {
       this.isRefreshingTools = false;
-      this.pendingToolRefresh = false;
     }
   }
 }