Fix stage finalize output rehydration

[MaxGhenis]

Summary

• rehydrate serialized stage outputs during final artifact-manifest finalization
• allow a previously failed finalize to become complete when required outputs are present on disk
• add a regression covering a failed stage-09 manifest with persisted validation evidence and benchmark summary

Root cause

The H5 and stage-09 outputs were written, but finalize reconstructed typed outputs from the artifact manifest and dropped the serialized benchmark_summary already present in stage_artifacts/manifests/09_validation_benchmarking.json. The stage validator then saw an empty structured output and raised even though the output existed on disk.

Validation

• UV_PROJECT_ENVIRONMENT=.venv313 uv run --python 3.13 --extra dev --extra policyengine python -m ruff check src/microplex_us/pipelines/stage_runtime.py tests/pipelines/test_stage_runtime.py
• UV_PROJECT_ENVIRONMENT=.venv313 uv run --python 3.13 --extra dev --extra policyengine python -m pytest tests/pipelines/test_stage_runtime.py tests/pipelines/test_stage_run.py -q

Artifact recovery

Applied the fix locally to the existing target_source_gaps_a1f19e0 version directory; stage 09 now has complete: true, lifecycleStatus: complete, and no missing required outputs without rerunning the build.