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/assistant-contracts.ts

@@ -344,6 +344,14 @@ export type ConversationQueueItem = z.infer<
   typeof conversationQueueItemSchema
 >
 
+export const toolOutputReferenceSchema = z.object({
+  handle: z.string().min(1),
+  nextCursor: z.number().int().nonnegative(),
+  totalBytes: z.number().int().nonnegative()
+}).strict()
+
+export type ToolOutputReference = z.infer<typeof toolOutputReferenceSchema>
+
 export const conversationToolActivitySchema = z
   .object({
     callId: z.string().optional(),
@@ -360,6 +368,7 @@ export const conversationToolActivitySchema = z
     summary: z.string(),
     input: z.string().optional(),
     output: z.string().optional(),
+    outputReferences: z.array(toolOutputReferenceSchema).optional(),
     error: z.string().optional()
   })
   .strict()
@@ -436,6 +445,7 @@ const conversationSubagentActivityBaseSchema = z.object({
   reason: z.string().trim().min(1).max(240).optional(),
   progress: conversationMessageBlocksSchema.optional(),
   output: z.string().optional(),
+  outputReference: toolOutputReferenceSchema.optional(),
   error: z.string().trim().min(1).max(1_000).optional()
 })