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.

docs/architecture/desktop-storage-knowledge.md

@@ -0,0 +1,66 @@
+# Knowledge Main Storage Migration (S03)
+
+Knowledge Main now receives `KnowledgeServiceOptions.database`, a
+`KnowledgeStoragePort`. Production composition constructs it with
+`createKnowledgeStoragePort(storageClient)` after `storageClient.ready`.
+`KnowledgeService` no longer opens, initializes, closes, or starts readers for
+the business database. The application storage owner retains those duties.
+
+The adapter sends explicit `knowledge` and `external` domain calls. Search
+signals travel as transport options, not serialized arguments. The port's
+`Awaitable` return type permits synchronous owner-local test implementations;
+the production adapter always returns the storage client's promises.
+
+Main awaits source, document, task, graph, embedding and external metadata
+operations. IPC mutations await their writes before returning or refreshing a
+snapshot. Parsing, models, credentials and source watchers remain in their
+existing Main services. Embedding batches retain their existing sizes and
+staging/publication sequence.
+
+Publication passes the extracted graph through foundation
+`publishDocument(..., { graph })`. Graph-only replacement calls
+`replaceDocumentGraph(library, document, result)`. Its implementation in
+`src/main/desktop-storage-knowledge-operations.ts` runs the existing synchronous
+graph algorithm inside `replaceEvidenceForDocument`'s transaction. No callback
+or SQL crosses the storage boundary.
+
+Shutdown aborts producers immediately, drains tracked work and observes the
+task-interruption write and embedding status persistence. The service does not
+close the shared storage client. Embedding allocation returns its replacement
+ID even if cancellation arrives with the reply, allowing cleanup; a committed
+finish is not reported as rolled back. Rebuild admission remains occupied
+until its final status write settles, and status-write failures reach the
+completion barrier.
+
+## Current Production Boundary
+
+The following boundary is implemented in the current production composition:
+
+- `replaceDocumentGraph(library: KnowledgeBase, document: Document,
+  result: GraphExtractionResult): void` to the knowledge domain contract and
+  dispatch it to the exported owner-local operation, passing the owned database
+  as its first argument. It is not part of the concrete database method
+  allowlist because it is a composite owner operation.
+- Foundation publication reuses the exported `storeExtractedGraph` helper.
+- `StorageData` preserves the existing recursive JSON type without rebuilding it
+  in the adapter.
+- Persistent document lookup is resolved by the storage owner through the
+  Knowledge domain; Main does not register a second lookup.
+- Application composition injects the port, awaits asynchronous gateway and
+  tool-provider calls, and closes shared storage after Knowledge disposal.
+
+## Validation
+
+The focused Knowledge service, external service, embedding coordinator and
+embedding repository suites use a Promise-backed adapter over a test-owned
+SQLite connection. Coverage includes publication rollback, embedding batch
+ordering, late cancellation, replacement cleanup, external request cancellation,
+credential persistence and restart. The production gateway now awaits its library
+and search operations. Remaining evidence is limited to the focused suites and
+does not establish full concurrent desktop acceptance.
+
+Owned production files pass ESLint. The current worktree typecheck and focused
+storage validation cover the injected production port and owner dispatch. Global
+architecture acceptance, packaged checks and concurrent performance acceptance
+remain with the parent delivery; these tests do not establish a new performance
+baseline.