fix: checkpoint worker before native stop

[wbugitlab1]

Summary

• add worker-owned mem::shutdown-flush plus authenticated POST /agentmemory/shutdown/flush
• flush BM25/vector index state before native stop signals worker or engine processes
• make Windows non-force stop fail closed when persistence cannot be confirmed, while --force warns clearly
• gate shutdown flush until persisted indexes are loaded or a complete rebuild is available

Fixes #338.

Verification

• corepack pnpm run lint
• corepack pnpm exec vitest run test/index-persistence.test.ts test/search.test.ts test/shutdown-flush.test.ts test/api-boundary-coverage.test.ts test/cli-stop-port-detection.test.ts test/reconnect-registration.test.ts test/engine-launch.test.ts test/runtime-config.test.ts test/cli-iii-config.test.ts test/consistency.test.ts
• corepack pnpm run build
• corepack pnpm test
• semgrep scan --config p/default --error --metrics=off .
• gitleaks protect --staged --redact