Add run manifest for stage state tracking

[Zefan-Cai]

Summary

This PR isolates TODO 1 from the larger CLI branch: add a machine-readable run_manifest.json as the primary per-run stage status source.

What Changed

• added src/manifest.py
• added run_manifest.json to the run layout via RunPaths
• initialized a run manifest when creating a run
• ensured a run manifest exists when resuming a run
• updated stage status in the manifest during:
  • stage start
  • stage human review
  • stage approval
  • stage failure
  • run completion / cancellation
• added a focused regression test in tests/test_run_manifest.py

Scope

This PR is intentionally limited to TODO 1 only.

Not included here:

• cross-stage rollback and stale invalidation
• operator session recovery hardening
• stage handoff / context compression
• paper/release package generation

Validation

• python -m py_compile main.py src/*.py tests/*.py
• python -m unittest discover -s tests -v

[huangwei0102]

Thanks for the clear PR description and focused scope. LGTM.