# Research Second Brain Workspace

This is a research second brain. You (Claude Code) build and query the knowledge
graph with `/graphify`, organize files, and draft outputs. The researcher owns
all judgment.

## Folder semantics

- `inbox/` — raw, untouched incoming notes. Never rename, rewrite, or merge files here.
- `sources/` — original evidence files (PDFs, exports). Read-only; never modify.
- `graphify-out/` — generated graph artifacts (`graph.html`, `graph.json`,
  `GRAPH_REPORT.md`, `manifest.json`, `cache/`). Regenerate with `/graphify`;
  never hand-edit.
- `fallback/graphify-out/` — pre-built copy of the graph, shipped with the kit.
  Fallback only: if the researcher's own build fails, copy it to the workspace
  root as `graphify-out/`. Never treat it as corpus input or update it in place.

## Hard rules

1. **Inbox first.** New material lands in `inbox/` untouched. `/graphify` reads
   files in place — never rename, rewrite, or merge inbox files unless the
   researcher explicitly asks for it.
2. **Never guess metadata.** Missing citations, years, venues, or DOIs get
   `TODO-VERIFY` flags, never invented values.
3. **Judgment fields are human.** `Relevance`, researcher comments, and
   interpretation fields belong to the researcher. Draft around them; never
   overwrite or fill them in.
4. **Keep the paper separate from the reader.** What the paper says (claims,
   evidence, stated limitations) stays separate from what the researcher thinks.
5. **Preserve source context.** Original excerpts, links, and the researcher's
   own wording move into the source-context section of any note you craft —
   never deleted.
6. **Show your work.** After any change, list what was created, moved, or edited.
7. **One step at a time.** Make one change, show it, then continue.
   Speed comes from the loop, not from batch trust.

## Workshop tooling

- `.claude/commands/setup-check.md` defines `/setup-check` — the environment check
  run at the start of class. If the researcher asks to "check my setup" or a tool
  seems missing, follow that command's flow.
- `/setup-check` installs the Graphify CLI (pinned to the class-tested version) and
  registers the `/graphify` skill machine-wide via `graphify install --platform claude`,
  so it keeps working in the researcher's other folders after the course. Do not
  upgrade Graphify mid-workshop.
