[codex] Add in-flight background experiment harvester

[morganmcg1]

Summary

Adds a small harness-level in-flight handoff for backgrounded student runs, so a later session can finish the PR handoff if the launching session dies.

Changes

• add plugins/senpai/scripts/in_flight.py with new-tag, record, harvest, and clear
• run harvest from the student heartbeat before polling for new work
• track continuity with --wandb_tag; keep --wandb_group as optional human-facing grouping only
• keep harvested PR comments metric-agnostic: the harness links runs and marks completion, but does not guess task-specific metrics or configs
• promote reusable helpers into plugins/senpai/scripts/senpai-gh.sh:
  • comment_pr_with_file
  • current_pr_number
  • require_clean_tracked_worktree
  • require_pushed_head
• make mark_ready_for_review tolerate already-ready PRs
• update student/advisor docs and submission flow for the tracked background-run path

Validation

• bash -n plugins/senpai/scripts/senpai-gh.sh
• python3 -m py_compile plugins/senpai/scripts/in_flight.py cfd_tandemfoil/train.py
• bash -lc 'source plugins/senpai/scripts/senpai-gh.sh && current_pr_number'
• python3 plugins/senpai/scripts/in_flight.py new-tag

Notes

Programmatic PR comments and state transitions are explicitly labeled HARNESS: so later model sessions do not mistake them for model-authored work.