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

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.