Auto-Research Repo

Use this skill to work in repositories whose purpose is cumulative research, not one-off answers. Preserve source evidence, compile it into a durable wiki, and publish portable HTML outputs only when their evidence status is clear.

Core Pattern

Follow a one-way pipeline:

ref/ -> docs/wiki/ -> docs/public/

• Keep ref/ as immutable evidence: papers, datasets, scans, archives, source bundles, and provenance records.
• Keep plans/notes/notebook/ as a mutable scratchpad for rough project thoughts, hunches, outlines, dead ends, meeting notes, copied snippets, prompts, and other useful junk that is not yet evidence or synthesis.
• Keep docs/wiki/ as the maintained synthesis layer: concepts, entities, source notes, evidence maps, questions, conjectures, contradictions, and paper seeds.
• Keep docs/public/ as the publication output lane, with docs/public/index.html as the public table of contents.
• Use docs/public/exploratory/ for publishable working reports, labs, evidence browsers, and conjecture pressure tests.
• Use docs/public/treatise/ for mature paper-shaped publications promoted from wiki synthesis, not as the starting point.
• Keep ref/inbox/ as a mutable intake tray for user-provided files; files become immutable after they are identified and moved elsewhere under ref/.
• Keep plans/to-do/sources.md as the source queue for missing, blocked, paywalled, or strategically important sources.