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/agent/create-runtime.ts

@@ -46,6 +46,8 @@ import {
 import type { LaunchEnvironmentProvider } from '../local-tool-environment/launch-environment-provider'
 import type { DesktopDiagnosticFailureObserver } from '../desktop-diagnostics'
 export type AgentCapabilityContext = {
+  outputStore?: ModelRuntimeOptions['outputStore']
+  outputAdopt?: ModelRuntimeOptions['outputAdopt']
   observeFailure?: DesktopDiagnosticFailureObserver
   localRuntimeRegistry?: LocalRuntimeRegistry
   skillInstructions?: string
@@ -219,7 +221,11 @@ export function createAgentRuntime(
       createToolProvider: (directory) => new ModelToolProvider(
         new LocalWorkspaceAccess(directory), capabilities.mcpServers, undefined,
         capabilities.knowledgeGateway, capabilities.webSearchEnabled === true,
-        { runtimeTarget: 'deepseek-harness' }, capabilities.launchEnvironmentProvider
+        {
+          runtimeTarget: 'deepseek-harness',
+          outputStore: capabilities.outputStore,
+          outputAdopt: capabilities.outputAdopt
+        }, capabilities.launchEnvironmentProvider
       )
     }
     const create = () => new DeepSeekHarnessRuntime(options)
@@ -353,6 +359,8 @@ export function createAgentRuntime(
       (modelAuthentication === 'none' || modelApiKey))
   ) {
     return new ModelAgentRuntime({
+      outputStore: capabilities.outputStore,
+      outputAdopt: capabilities.outputAdopt,
       apiKey: modelApiKey ?? '',
       baseUrl:
         defaultModelProfile?.baseUrl ||