refactor(core): refine layer node replacements (#34377)

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

@@ -2,6 +2,8 @@ import fs from "fs/promises"
 import path from "path"
 import { describe, expect } from "bun:test"
 import { Effect, Layer } from "effect"
+import { AppNodeBuilder } from "@opencode-ai/core/effect/app-node-builder"
+import { LayerNode } from "@opencode-ai/core/effect/layer-node"
 import { FSUtil } from "@opencode-ai/core/fs-util"
 import { PermissionV2 } from "@opencode-ai/core/permission"
 import { AbsolutePath } from "@opencode-ai/core/schema"
@@ -9,6 +11,7 @@ import { SessionV2 } from "@opencode-ai/core/session"
 import { SkillV2 } from "@opencode-ai/core/skill"
 import { SkillTool } from "@opencode-ai/core/tool/skill"
 import { ToolRegistry } from "@opencode-ai/core/tool/registry"
+import { ToolOutputStore } from "@opencode-ai/core/tool-output-store"
 import { tmpdir } from "./fixture/tmpdir"
 import { it } from "./lib/effect"
 import { toolIdentity, executeTool, settleTool, toolDefinitions } from "./lib/tool"
@@ -63,11 +66,14 @@ describe("SkillTool", () => {
               list: () => Effect.succeed(current),
             }),
           )
-          const registry = ToolRegistry.defaultLayer.pipe(Layer.provide(permission))
+          const registry = AppNodeBuilder.build(
+            LayerNode.group([ToolRegistry.node, ToolRegistry.toolsNode]),
+            [[ToolOutputStore.node, ToolOutputStore.nodeWithoutConfig]],
+          )
           const tool = SkillTool.layer.pipe(
             Layer.provide(registry),
             Layer.provide(permission),
-            Layer.provide(FSUtil.defaultLayer),
+            Layer.provide(LayerNode.compile(FSUtil.node)),
             Layer.provide(skills),
           )
           const layer = Layer.mergeAll(permission, skills, registry, tool)