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/shared/contracts.ts

@@ -1321,6 +1321,7 @@ export type AgentEvent =
       summary: string
       input?: string
       output?: string
+      outputReferences?: import('./assistant-contracts').ToolOutputReference[]
       error?: string
     }
   | {
@@ -2335,6 +2336,7 @@ export type DesktopApi = {
     cancelParsing: (operationId: string) => Promise<void>
     sendOriginal: (conversationId: string, id: string) => Promise<ContextAttachment[]>
     openOriginal: (id: string) => Promise<void>
+    readOutput: (input: { conversationId: string; handle: string; cursor?: number; limitBytes?: number }) => Promise<import('./conversation-output').ConversationOutputPage>
     addResultImages: (conversationId: string, resultId: string, imageIds: string[]) => Promise<ContextAttachment[]>
     onDraftChanged: (listener: (conversationId: string, attachments: ContextAttachment[]) => void) => () => void
     getDraft: (conversationId: string) => Promise<ContextAttachment[]>
@@ -2434,6 +2436,11 @@ export type DesktopApi = {
       files: File[],
       graphStrategy?: 'rules' | 'model' | 'hybrid'
     ) => Promise<void>
+    importPaths?: (
+      libraryId: string,
+      paths: string[],
+      graphStrategy?: 'rules' | 'model' | 'hybrid'
+    ) => Promise<void>
     importUrl: (
       libraryId: string,
       url: string,