Optimize Web CLI run state updates

[Vickykykykykykyky]

Summary

• reuse the bootstrap run list when building thread metadata, avoiding a duplicate checkpoint scan
• return run/thread deltas from run, resume, image, and 3D endpoints and merge them locally instead of refreshing all Web CLI state
• use canonical project/thread indexes for project history and latest-run lookups
• add coverage for single-scan bootstrap behavior and lossless client-side delta merging

Testing

• npm run typecheck
• npx tsx --test test/run-store.test.mts test/run-manager.test.mts test/web-server.test.mts test/web-state.test.mts (52 passed)
• full npm test: 178 tests passed; the local public-release audit test only flagged ignored root artifacts (.DS_Store and orbit-game) that are absent from a clean checkout