omcr-setup

# Setup Install-style flow that lays down the **infrastructure** OMCR needs to operate in a project. This is OMCR's analog of OMC's `/omc-setup` — no research-interview questions, no preset selection, no manuscript scaffolding. Just makes the plugin work. After `/omcr-setup` completes, the user should run `/start-research` for interview-style first-project initialization. **When this skill is invoked, immediately execute the workflow below. Do not only restate or summarize these instructions back to the user.** Safe to re-run. Diffs against current state; only adds what is missing. ## What this installs 1. **CLAUDE.md infrastructure** — `## Project context`, `## Research stack`, `## Language preference` blocks with placeholder fields. (Filled in later by `/start-research`.) 2. **Agent memory directories** — `.claude/agent-memory/<agent>/MEMORY.md` for the 6 core agents, seeded from the canonical template. Existing files are never touched. 3. **Bibliography files** — empty `paper/references.bib` (with header comment) and `references.csv` (with header row) at default paths. Existing files are never touched. 4. **Permission allowlist** — curated `.claude/settings.json` so common research-flow tools (read-only git, file search, edits, LaTeX build, citation lookups, figure crop) don't prompt every time. Dangerous operations (git write, file deletion, wildcard bash) are intentionally excluded so they always prompt. ## What this explicitly does NOT do - Ask about your project (working title, hypothesis, target venue, datasets, etc.) - Pick or apply a domain preset (`neuro-fmri`, etc.) - Scaffold the LaTeX manuscript directory - Clone Overleaf or commit anything All of those belong to `/start-research`. ## Phase execution Execute phases sequentially. For each phase, read the linked file and follow its instructions exactly. 1. **Phase 1 — State check.** Read [`phases/01-state-check.md`](phases/01-state-check.md). 2. **Phase 2 — CLAUDE.md scaffold.** Read [`phases/02-claude-md-scaffold.md`](phases/02-claude-md-scaffold.md). 3. **Phase 3 — Agent memory.** Read [`phases/03-agent-memory.md`](phases/03-agent-memory.md). 4. **Phase 4 — Bibliography.** Read [`phases/04-bibliography.md`](phases/04-bibliography.md). 5. **Phase 5 — Permissions.** Read [`phases/05-permissions.md`](phases/05-permissions.md). 6. **Phase 6 — Report.** Read [`phases/06-report.md`](phases/06-report.md). ## Re-running policy - `CLAUDE.md` marker blocks are inserted only if missing. Existing blocks are inspected but not overwritten. - Existing `MEMORY.md` files are never overwritten (phase 3). - Existing `references.bib` / `references.csv` are never overwritten (phase 4). - Permission allowlist (phase 5) prompts the user before replacing or merging. Existing broad wildcards trigger a narrowing offer with backup to `.claude/settings.json.backup.YYYY-MM-DD`. ## Final recommendation After phase 6's report, recommend the user run `/start-research` to fill in their project context and scaffold the manuscript.