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/shutdown.test.ts

@@ -18,7 +18,7 @@ describe('waitForCleanup', () => {
       'utf8'
     )
     const cleanup = source.match(
-      /const cleanup = settleCleanupPhases\(\[[\s\S]*?\]\)\s+globalShortcut/u
+      /const cleanup = settleCleanupPhases\(\[[\s\S]*?\s+globalShortcut/u
     )?.[0] ?? ''
 
     expect(cleanup).toContain('runtime?.detachForApplicationExit()')
@@ -28,6 +28,26 @@ describe('waitForCleanup', () => {
     expect(cleanup.indexOf('runtime?.detachForApplicationExit()')).toBeLessThan(
       cleanup.indexOf('runtime?.dispose()')
     )
+    const storageClose = cleanup.indexOf('desktopStorage?.close()')
+    expect(storageClose).toBeGreaterThan(0)
+    for (const drain of [
+      'applicationStartup', 'runtimeTemporaryCleanup', 'removeIpcHandlers?.()',
+      'startupSubagentService?.dispose()', 'imageGenerationService?.dispose()',
+      'nativeClientCoordinator?.dispose()', 'startupContextManager?.dispose()',
+      'runtime?.dispose()', 'selectedRuntimeManager?.dispose()',
+      'terminalSessionManager?.dispose()', 'managedRemoteExecutionServices?.dispose()',
+      'knowledgeGateway?.dispose()', 'knowledgeService?.dispose()',
+      'documentParsingService?.dispose()'
+    ]) {
+      expect(cleanup.indexOf(drain), drain).toBeGreaterThanOrEqual(0)
+      expect(cleanup.indexOf(drain), drain).toBeLessThan(storageClose)
+    }
+    expect(source).not.toContain('assistantDatabase?.close()')
+    const quitting = source.slice(source.indexOf("app.on('before-quit'"))
+    expect(quitting.indexOf('runtimeTemporaryCleanupController.abort()')).toBeLessThan(
+      quitting.indexOf('const cleanup = settleCleanupPhases')
+    )
+    expect(quitting).toContain('clearTimeout(runtimeTemporaryCleanupTimer)')
   })
 
   it('reports completed and failed cleanup as settled', async () => {