fix(tests): properly stub notifyParentSession and fix timer-based tests

- Add stubNotifyParentSession implementation to stub manager's notifyParentSession method
- Add stubNotifyParentSession calls to checkAndInterruptStaleTasks tests
- Add messages mock to client mocks for completeness
- Fix timer-based tests by using real timers (fakeTimers.restore) with wait()
- Increase timeout for tests that need real time delays

src/hooks/atlas/index.test.ts

@@ -2,7 +2,7 @@ import { describe, expect, test, beforeEach, afterEach, mock } from "bun:test"
 import { existsSync, mkdirSync, rmSync, writeFileSync } from "node:fs"
 import { join } from "node:path"
 import { tmpdir } from "node:os"
-import { createAtlasHook } from "./index"
+import { randomUUID } from "node:crypto"
 import {
   writeBoulderState,
   clearBoulderState,
@@ -10,11 +10,22 @@ import {
 } from "../../features/boulder-state"
 import type { BoulderState } from "../../features/boulder-state"
 
-import { MESSAGE_STORAGE } from "../../features/hook-message-injector"
+const TEST_STORAGE_ROOT = join(tmpdir(), `atlas-message-storage-${randomUUID()}`)
+const TEST_MESSAGE_STORAGE = join(TEST_STORAGE_ROOT, "message")
+const TEST_PART_STORAGE = join(TEST_STORAGE_ROOT, "part")
+
+mock.module("../../features/hook-message-injector/constants", () => ({
+  OPENCODE_STORAGE: TEST_STORAGE_ROOT,
+  MESSAGE_STORAGE: TEST_MESSAGE_STORAGE,
+  PART_STORAGE: TEST_PART_STORAGE,
+}))
+
+const { createAtlasHook } = await import("./index")
+const { MESSAGE_STORAGE } = await import("../../features/hook-message-injector")
 
 describe("atlas hook", () => {
-   const TEST_DIR = join(tmpdir(), "atlas-test-" + Date.now())
-  const SISYPHUS_DIR = join(TEST_DIR, ".sisyphus")
+  let TEST_DIR: string
+  let SISYPHUS_DIR: string
 
   function createMockPluginInput(overrides?: { promptMock?: ReturnType<typeof mock> }) {
     const promptMock = overrides?.promptMock ?? mock(() => Promise.resolve())
@@ -49,6 +60,8 @@ describe("atlas hook", () => {
   }
 
   beforeEach(() => {
+    TEST_DIR = join(tmpdir(), `atlas-test-${randomUUID()}`)
+    SISYPHUS_DIR = join(TEST_DIR, ".sisyphus")
     if (!existsSync(TEST_DIR)) {
       mkdirSync(TEST_DIR, { recursive: true })
     }
@@ -63,6 +76,7 @@ describe("atlas hook", () => {
     if (existsSync(TEST_DIR)) {
       rmSync(TEST_DIR, { recursive: true, force: true })
     }
+    rmSync(TEST_STORAGE_ROOT, { recursive: true, force: true })
   })
 
   describe("tool.execute.after handler", () => {