diff --git a/packages/core/src/config/config.ts b/packages/core/src/config/config.ts
index 901eb269d8..e5ee70c040 100644
--- a/packages/core/src/config/config.ts
+++ b/packages/core/src/config/config.ts
@@ -2832,7 +2832,11 @@ export class Config implements McpContext, AgentLoopContext {
   }
 
   async createToolRegistry(): Promise<ToolRegistry> {
-    const registry = new ToolRegistry(this, this.messageBus, true);
+    const registry = new ToolRegistry(
+      this,
+      this.messageBus,
+      /* isMainRegistry= */ true,
+    );
 
     // helper to create & register core tools that are enabled
     const maybeRegister = (
diff --git a/packages/core/src/tools/tools.ts b/packages/core/src/tools/tools.ts
index f00aeb2d33..5add6823b5 100644
--- a/packages/core/src/tools/tools.ts
+++ b/packages/core/src/tools/tools.ts
@@ -381,6 +381,8 @@ export abstract class DeclarativeTool<
   ) {}
 
   clone(messageBus?: MessageBus): this {
+    // Note: we cannot use structuredClone() here because it does not preserve
+    // prototype chains or handle non-serializable properties (like functions).
     // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
     const cloned = Object.assign(
       Object.create(Object.getPrototypeOf(this)),