chore: address PR feedback by adding inline comments

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 = (

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)),