fix: harden scoped tools and settings persistence

src/main/shutdown.test.ts

@@ -1,5 +1,9 @@
 import { afterEach, describe, expect, it, vi } from 'vitest'
-import { waitForCleanup } from './shutdown'
+import {
+  runCleanupBeforeDeadline,
+  settleCleanupPhases,
+  waitForCleanup
+} from './shutdown'
 
 afterEach(() => {
   vi.useRealTimers()
@@ -23,4 +27,49 @@ describe('waitForCleanup', () => {
 
     await expect(result).resolves.toBe(false)
   })
+
+  it('runs dependent cleanup phases in order despite failures', async () => {
+    const order: string[] = []
+
+    await settleCleanupPhases([
+      [
+        async () => {
+          order.push('ipc')
+          throw new Error('cleanup failed')
+        }
+      ],
+      [
+        async () => {
+          order.push('gateway')
+        }
+      ],
+      [
+        async () => {
+          order.push('knowledge')
+        }
+      ]
+    ])
+
+    expect(order).toEqual(['ipc', 'gateway', 'knowledge'])
+  })
+
+  it('finalizes databases only after cleanup beats the deadline', async () => {
+    const finalize = vi.fn()
+    await expect(
+      runCleanupBeforeDeadline(Promise.resolve(), 100, finalize)
+    ).resolves.toBe(true)
+    expect(finalize).toHaveBeenCalledOnce()
+
+    vi.useFakeTimers()
+    const timedOutFinalize = vi.fn()
+    const result = runCleanupBeforeDeadline(
+      new Promise(() => {}),
+      100,
+      timedOutFinalize
+    )
+    await vi.advanceTimersByTimeAsync(100)
+
+    await expect(result).resolves.toBe(false)
+    expect(timedOutFinalize).not.toHaveBeenCalled()
+  })
 })