feat(storage): move desktop SQLite ownership into a storage utility process

Main no longer opens desktop business SQLite. A single utility-process
storage owner holds the Assistant, Knowledge, attachment, document-result,
remote-binding and native model-ledger databases and runs whole domain
transactions; Main and Runtime callers use explicit async domain operations.

- Remove the Main readWithFallback path and the supervision worker's
  separate business write connection; manifests are scanned read-only and
  committed by the sole writer.
- Remote events are ACKed only after commit; process loss reports
  unconfirmed writes instead of replaying them.
- Use native utilityProcess messaging with one in-flight bound (32) and
  ordered waiting instead of capacity rejection and retries.
- Start the storage process before the window so startup overlaps.
- Keep short tool output in memory and store full output once in owned
  storage; paging, branching, restart and deletion reuse that copy.
- Put required runtime launch files under goodbuddy-prefixed owned temp
  directories and reclaim confirmed stale ones; stop writing duplicate
  parsed.md.
- Add lint guards for SQLite ownership and architecture, concurrency
  acceptance fixtures, and maintenance/architecture documentation.

Validation: typecheck and lint pass. Alternating baseline (edf019aa) vs
candidate runs show no regression on single-session, C01, C02, C04 and a
5-minute C06; Main p99 drops from ~21 ms to ~16.7 ms under concurrency.
Fresh portable copy (1.75M events) upgrade content unchanged; real-model
output paging passes with 4 external requests. Full npm test runs had
1-9 different timing-sensitive failures per run that pass when rerun.
Not covered: C03 review publication, C07 source body, app-level C05.

src/main/magic-notes/magic-note-analyzer.test.ts

@@ -1,4 +1,4 @@
-import { describe, expect, it } from 'vitest'
+import { describe, expect, it, vi } from 'vitest'
 import type { AgentExecutionRequest, AgentRuntime, RuntimeModelUsageEvent } from '../agent/runtime'
 import type {
   MagicNoteEntry,
@@ -23,6 +23,17 @@ const entry: MagicNoteEntry = {
 }
 
 describe('magic note analyzer', () => {
+  it('awaits model usage persistence and rejects analysis if the write fails', async () => {
+    const { runtime } = recordingRuntime()
+    let reject!: (error: Error) => void
+    const persist = vi.fn(() => new Promise<void>((_resolve, fail) => { reject = fail }))
+    const pending = analyzeMagicNoteEntry(runtime, entry, options, undefined, persist)
+    const rejected = expect(pending).rejects.toThrow('Usage write failed')
+    await vi.waitFor(() => expect(persist).toHaveBeenCalledOnce())
+    reject(new Error('Usage write failed'))
+    await rejected
+  })
+
   const png = 'iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAQAAAC1HAwCAAAAC0lEQVR42mP8/x8AAwMCAO+/l9sAAAAASUVORK5CYII='
   const canvasEntry = {
     ...entry,
@@ -127,7 +138,7 @@ describe('magic note analyzer', () => {
     const usage: RuntimeModelUsageEvent[] = []
     const comments = await analyzeMagicNoteEntry(
       runtime, canvasEntry, options, undefined,
-      (event) => usage.push(event), { supportsImageInput: true, canvasPageCount: 2 }
+      (event) => { usage.push(event) }, { supportsImageInput: true, canvasPageCount: 2 }
     )
     expect(requests).toHaveLength(1)
     expect(requests[0]?.images).toEqual([