Use graceful Lima stops for restart and lifecycle cleanup

[jimpudar]

Summary

• Split VM stopping into graceful and forced paths, then route lifecycle stop and agent restart through the graceful path.
• Added a Lima graceful-stop timeout with fallback to --force only when the clean stop does not complete.
• Updated the VM provider contract and added unit coverage for the new stop behavior.

Testing

• npm run typecheck
• npm run lint
• npm run test -- src/rootcell/rootcell.test.ts
• bun run test:integration -- src/rootcell/integration/common/provider-contract.integration.test.ts