Checkpoint

When invoked (or when the user says checkpoint), do this in order.

1) Preflight (must do; show output)

• git status
• git diff --stat

2) Sanity guardrails (must do)

• Never run: git push, git commit --amend, git rebase, git reset --hard, git clean -fdx, or modify git remotes.
• Never stage/commit secrets/credentials: .env*, *.pem, *.key, id_rsa*, id_ed25519*, tokens.
• Never stage/commit bulky artifacts: data/** (except data/README.md), secrets/**, most of runs/** (except runs/**/summary.md and runs/**/report.md), and typical artifact payloads (*.npz, *.parquet, large *.csv).

3) Ensure runs markdown is link-only (must do)

• If any runs/**/summary.md or runs/**/report.md contain embedded images (![](...)), fix before committing:
  • Run: python scripts/sanitize_runs_markdown.py --root runs --write

4) Stage (default: include safe untracked files)

Stage:

• agent_logs/current.md if modified.
• All changed files under: src/, scripts/, configs/, docs/, plus small root-level *.md/*.yml/*.toml.
• runs/**/summary.md and runs/**/report.md (only those).

If there are new/untracked files:

• Include them only if they are clearly source/config/docs (no artifacts) and reasonably small.
• If there are “too many” files to stage (e.g., >50 paths) or anything looks suspicious, stop and ask before staging.

Before committing, show:

• git diff --cached --stat

5) Commit (auto message; no human message required)

• Create a message checkpoint: <short summary> derived from the staged paths (e.g., “checkpoint: add script + tweak plots”).
• If you can’t derive a meaningful summary, use checkpoint: wip.
• Run git commit -m "<message>".

6) Postflight (must do; show output)

• git status
• Report the commit hash.