fix: Prevent duplicate or inactive tools/prompts after server refresh (#5850)

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

@@ -881,9 +881,14 @@ describe('mcpCommand', () => {
             }),
             getToolRegistry: vi.fn().mockResolvedValue(mockToolRegistry),
             getGeminiClient: vi.fn().mockReturnValue(mockGeminiClient),
+            getPromptRegistry: vi.fn().mockResolvedValue({
+              removePromptsByServer: vi.fn(),
+            }),
           },
         },
       });
+      // Mock the reloadCommands function
+      context.ui.reloadCommands = vi.fn();
 
       const { MCPOAuthProvider } = await import('@google/gemini-cli-core');
 
@@ -901,6 +906,7 @@ describe('mcpCommand', () => {
         'test-server',
       );
       expect(mockGeminiClient.setTools).toHaveBeenCalled();
+      expect(context.ui.reloadCommands).toHaveBeenCalledTimes(1);
 
       expect(isMessageAction(result)).toBe(true);
       if (isMessageAction(result)) {
@@ -985,6 +991,8 @@ describe('mcpCommand', () => {
           },
         },
       });
+      // Mock the reloadCommands function, which is new logic.
+      context.ui.reloadCommands = vi.fn();
 
       const refreshCommand = mcpCommand.subCommands?.find(
         (cmd) => cmd.name === 'refresh',
@@ -1002,6 +1010,7 @@ describe('mcpCommand', () => {
       );
       expect(mockToolRegistry.discoverMcpTools).toHaveBeenCalled();
       expect(mockGeminiClient.setTools).toHaveBeenCalled();
+      expect(context.ui.reloadCommands).toHaveBeenCalledTimes(1);
 
       expect(isMessageAction(result)).toBe(true);
       if (isMessageAction(result)) {

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

@@ -417,6 +417,9 @@ const authCommand: SlashCommand = {
         await geminiClient.setTools();
       }
 
+      // Reload the slash commands to reflect the changes.
+      context.ui.reloadCommands();
+
       return {
         type: 'message',
         messageType: 'info',
@@ -507,6 +510,9 @@ const refreshCommand: SlashCommand = {
       await geminiClient.setTools();
     }
 
+    // Reload the slash commands to reflect the changes.
+    context.ui.reloadCommands();
+
     return getMcpStatus(context, false, false, false);
   },
 };

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

@@ -61,6 +61,7 @@ export interface CommandContext {
     toggleCorgiMode: () => void;
     toggleVimEnabled: () => Promise<boolean>;
     setGeminiMdFileCount: (count: number) => void;
+    reloadCommands: () => void;
   };
   // Session-specific data
   session: {

packages/cli/src/ui/hooks/slashCommandProcessor.ts

@@ -57,6 +57,11 @@ export const useSlashCommandProcessor = (
 ) => {
   const session = useSessionStats();
   const [commands, setCommands] = useState<readonly SlashCommand[]>([]);
+  const [reloadTrigger, setReloadTrigger] = useState(0);
+
+  const reloadCommands = useCallback(() => {
+    setReloadTrigger((v) => v + 1);
+  }, []);
   const [shellConfirmationRequest, setShellConfirmationRequest] =
     useState<null | {
       commands: string[];
@@ -172,6 +177,7 @@ export const useSlashCommandProcessor = (
         toggleCorgiMode,
         toggleVimEnabled,
         setGeminiMdFileCount,
+        reloadCommands,
       },
       session: {
         stats: session.stats,
@@ -195,6 +201,7 @@ export const useSlashCommandProcessor = (
       toggleVimEnabled,
       sessionShellAllowlist,
       setGeminiMdFileCount,
+      reloadCommands,
     ],
   );
 
@@ -220,7 +227,7 @@ export const useSlashCommandProcessor = (
     return () => {
       controller.abort();
     };
-  }, [config, ideMode]);
+  }, [config, ideMode, reloadTrigger]);
 
   const handleSlashCommand = useCallback(
     async (

packages/core/src/tools/tool-registry.ts

@@ -158,6 +158,18 @@ export class ToolRegistry {
     }
   }
 
+  /**
+   * Removes all tools from a specific MCP server.
+   * @param serverName The name of the server to remove tools from.
+   */
+  removeMcpToolsByServer(serverName: string): void {
+    for (const [name, tool] of this.tools.entries()) {
+      if (tool instanceof DiscoveredMCPTool && tool.serverName === serverName) {
+        this.tools.delete(name);
+      }
+    }
+  }
+
   /**
    * Discovers tools from project (if available and configured).
    * Can be called multiple times to update discovered tools.