fix(pipeline): preserve screening checkpoints across resume

[spignotti]

Summary

• Preserve screening checkpoint state so resume can skip redundant re-screening after --stop-after-screening.
• Keep run metrics across pause/resume by reusing existing metrics.json on resume and appending stage metrics.
• Improve UX and coverage with clearer paused CLI output and new unit tests for analysis/pipeline/model resume behavior.

Validation

• uv run nox (lint, typecheck, test)
• pytest: 50 passed