refactor(core): finish test layer node conversion (#34385)

packages/core/test/tool-question.test.ts

@@ -31,9 +31,6 @@ const permission = Layer.succeed(
     list: () => Effect.die("unused"),
   }),
 )
-const registry = AppNodeBuilder.build(LayerNode.group([ToolRegistry.node, ToolRegistry.toolsNode]), [
-  [ToolOutputStore.node, ToolOutputStore.nodeWithoutConfig],
-])
 const question = Layer.succeed(
   QuestionV2.Service,
   QuestionV2.Service.of({
@@ -46,8 +43,13 @@ const question = Layer.succeed(
     list: () => Effect.die("unused"),
   }),
 )
-const tool = QuestionTool.layer.pipe(Layer.provide(registry), Layer.provide(permission), Layer.provide(question))
-const it = testEffect(Layer.mergeAll(permission, registry, question, tool))
+const it = testEffect(
+  AppNodeBuilder.build(LayerNode.group([ToolRegistry.node, ToolRegistry.toolsNode, QuestionTool.node]), [
+    [PermissionV2.node, permission],
+    [QuestionV2.node, question],
+    [ToolOutputStore.node, ToolOutputStore.nodeWithoutConfig],
+  ]),
+)
 
 describe("QuestionTool", () => {
   it.effect("omits a denied built-in question and terminally settles a stale call", () =>