Fix mcp instructions (#16439)

packages/core/src/config/config.ts

@@ -1278,6 +1278,24 @@ export class Config {
     return this.userMemory;
   }
 
+  /**
+   * Refreshes the MCP context, including memory, tools, and system instructions.
+   */
+  async refreshMcpContext(): Promise<void> {
+    if (this.experimentalJitContext && this.contextManager) {
+      await this.contextManager.refresh();
+    } else {
+      const { refreshServerHierarchicalMemory } = await import(
+        '../utils/memoryDiscovery.js'
+      );
+      await refreshServerHierarchicalMemory(this);
+    }
+    if (this.geminiClient?.isInitialized()) {
+      await this.geminiClient.setTools();
+      await this.geminiClient.updateSystemInstruction();
+    }
+  }
+
   setUserMemory(newUserMemory: string): void {
     this.userMemory = newUserMemory;
   }