Commands

Commands

research-diff [--repo PATH] [--config FILE] COMMAND (also resdiff).

• map [--at REF|.] [--out DIR] [--check]: research.json and research.svg of the working tree (default) or a commit.
• diff [--base checkpoint|REF] [--head .|REF] [--out DIR]: what changed, as headline.txt, plan.txt, diff.svg and diff.json. Defaults: from the checkpoint to the working tree.
• checkpoint [--ref REF]: mark the working tree (or REF) as understood. It is kept under refs/research-diff/checkpoint, in your clone only. Before the first checkpoint, the diff starts from HEAD.
• watch [--port 8766]: a live page of the diff since the checkpoint, with Mark as seen.
• sync: copies MLflow (mlruns/) and W&B (wandb/) runs tagged with an experiment id into the tracked research/runs.json, so they are results on the map and in the diff. The hook, the live page and the MCP tools run it themselves.
• suggest [FILE…] [--out PATCH]: your LLM proposes markers for files with none (or the files named), as a patch in .git/research-diff/suggest.patch. Proposals that name an unknown file or line, are not markers, or reuse an id are refused, with the reason. Nothing changes until you git apply it.
• readme [--check]: rewrites the README section between <!-- research-map:begin --> and <!-- research-map:end -->, and its picture.
• setup claude [--scope user|project|local] [--undo], hook, mcp: see With AI coding agents.

The working tree is read as a snapshot: untracked files count, and nothing you use changes (not your index, HEAD or branches).