Add run manifest for stage state tracking#3

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Zefan-Cai wants to merge 1 commit intomainfrom

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Zefan-Cai commented Mar 31, 2026

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


          Add run manifest for stage state tracking

6a12f92

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