fix: make json store writes atomic

[gaoshiweiGit]

Summary

• add a shared writeJsonSafe() helper that writes JSON through a unique temp file and atomic rename
• add a small in-process JSON write queue and use it for registry agent saves
• switch orchestrator JSON stores to the shared atomic writer for initialization and saves
• add regression tests for atomic writes and queued writes

Closes #2

Verification

• npm test
• C:\Program Files\Git\bin\bash.exe scripts/typecheck.sh
• npm run lint (passes with existing warnings only)
• git diff --check