--- name: Brain Setup slug: brain-setup category: DevOps description: Brain Setup bootstraps the Open Project Brain Standard into a project by creating BRAIN.md, scaffolding the brain data directory, and wiring CLAUDE.md and AGENTS.md. Use it when initializing a project memory setup or adding optional hooks. github: "https://github.com/mindmuxai/brain.md/tree/main/skills/brain-setup" language: JavaScript stars: 506 forks: 47 install: "npx degit https://github.com/mindmuxai/brain.md/tree/main/skills/brain-setup ~/.claude/skills/brain-setup" installs_to: ~/.claude/skills/brain-setup source_path: skills/brain-setup/SKILL.md collection_size: 4 category_size: 798 collection_url: "https://dirskills.com/collections/mindmuxai/brain.md" added: 2026-08-26T05:12:49.089Z last_synced: 2026-08-26T05:12:49.089Z canonical_url: "https://dirskills.com/skills/brain-setup" --- # Brain Setup Brain Setup bootstraps the Open Project Brain Standard into a project by creating BRAIN.md, scaffolding the brain data directory, and wiring CLAUDE.md and AGENTS.md. Use it when initializing a project memory setup or adding optional hooks. **Install:** ```bash npx degit https://github.com/mindmuxai/brain.md/tree/main/skills/brain-setup ~/.claude/skills/brain-setup ``` ## README # brain-setup This skill bootstraps a project into the **Open Project Brain Standard**: it drops in the protocol entry point and the `brain/` skeleton so the **brain-page** and **brain-ingest** skills (and the `brain` CLI) have something to work with. It is **idempotent** — safe to run again on an already-initialized project. **Preferred one-shot path:** from the project root run: ``` node /bin/brain.mjs init ``` That command ensures `BRAIN.md`, scaffolds empty brain data (brainRoot-aware), and **default-wires** `CLAUDE.md` + `AGENTS.md` (create if missing; if present, only update/append the marked brain block — never whole-file overwrite). Use the steps below when you need the optional pre-commit hook, the optional Claude Code SessionStart hook, or are explaining the flow. > **NEVER hand-edit any file under the brain directory. All reads and writes MUST go through the `brain` CLI. Manual edits are unsupported and illegitimate.** This scaffold creates the brain once; from then on every read and write is a `brain` subcommand. There is no validator and nothing at the file layer can catch a bad manual edit, so a hand edit silently breaks the brain's invariants. Run this from the **target project's root**. The skill bundle ships the templates under `assets/` and the hook under `hooks/`; resolve `` to the directory this `SKILL.md` lives in. > **Core invariant: there is exactly one brain, at the resolved location.** The brain's data directory is **location-independent** — it lives at `./brain` by default, but a MindMux-managed project redirects it via `brainRoot` in `./.mindmux/preferences.json` (often an absolute path to an external sidecar directory). This skill MUST resolve that location before scaffolding, and MUST NOT create a second, local `./brain` when a `brainRoot` is set — doing so produces a **split brain** (an empty local skeleton shadowing the real external brain). The `BRAIN.md` protocol document is separate: it always lives in the project root regardless of where the brain data lives. ## Steps ### 1. Ensure `BRAIN.md` (the protocol document) is in the project root `BRAIN.md` is the read/write contract that the agent reads to learn how to use the brain. It **always** belongs in the **project root**, independent of where the brain *data* lives. - **Present** → leave it untouched (never overwrite project content). - **Absent** → copy `assets/BRAIN.md` → `./BRAIN.md`. Do **not** stop here just because `BRAIN.md` exists — its presence says nothing about whether the brain data is set up. Always continue to step 2 to resolve and check the data location. ### 2. Resolve the brain data location, then scaffold there only if empty First, resolve where the brain data actually lives — never assume `./brain`. Ask the CLI: ``` node /bin/brain.mjs brain-dir ``` (The brain-page skill carries the CLI; in the brain.md source repo it is `skills/brain-page/bin/brain.mjs`, globally it is e.g. `~/.claude/skills/brain-page/bin/brain.mjs`.) `brain brain-dir` reads `brainRoot` from `./.mindmux/preferences.json` when present (otherwise falls back to `./brain`) and prints, on separate lines: the **resolved directory**, a human-readable origin, `source:` (`brainRoot` or `default`), `exists:` (`true`/`false`), and `populated:` (`true`/`false` — whether the location already holds a root page or any page under `pages/`). Read those lines instead of guessing or `stat`-ing by hand. Branch on the resolved state: - **`populated: true` → the brain already exists. Do NOT scaffold.** Tell the user the brain lives at ``. If `source: brainRoot`, make it explicit: *"this project's brain is redirected to an external directory (``) and is managed there — leaving it untouched."* Then continue to step 3 (wire) and the optional hooks (steps 4–5). Never lay down a local `./brain` in this case. - **`populated: false` → scaffold the skeleton into the resolved directory** (the `brainRoot` target when redirected, otherwise `./brain`). Copy `assets/brain/` → `/` — this brings the six root page templates (`background` / `architecture` / `flow` / `mindmap` / `stack` / `roadmap`), a generated `index.md`, and an empty `pages/` directory. Copy each destination file **only if it does not already exist** (never overwrite). **Never create a second local `./brain` when `source: brainRoot`** — always scaffold at the resolved path. After copying, run `reindex` so the index reflects the present pages: ``` node /bin/brain.mjs reindex ``` (`reindex` resolves the same location, so it writes the index in the right place automatically.) No example pages are scaffolded; the page format is documented in `BRAIN.md` and the **brain-page** skill. ### 3. Wire the agent-config files via `brain wire` (default both files) The project's agent-config files must point at `BRAIN.md` so agents pick up the contract. Wiring is **deterministic — done by the CLI, not by hand.** Do not hand-write `@import` lines or template paragraphs. **Do not ask which agents to wire** — default to both config files unless the user explicitly requests a subset. Run (default — no `--agent` required): ``` node /bin/brain.mjs wire ``` Equivalent: `wire --agent all`. Optional subset: `--agent claude-code` or comma-separated list. Supported ids: `claude-code`, `codex`, `opencode`, `cursor`, `pi`, `all`. What the command does (so you can explain it): - Default maps to **both** `./CLAUDE.md` (claude-code block with `@import`) and `./AGENTS.md` (shared block for codex / opencode / cursor / pi). - Writes one **unified, neutral, self-contained brain block** — wrapped in `` … `` — that tells the agent to read `./BRAIN.md`, states the **session-companion** rules (load brain at task start; capture decisions/constraints when they settle during coding; skip pure implementation; reverse/update when overturning; all via the `brain` CLI; never hand-edit), and notes the four brain skills are installed globally. - Both files get the **same** block body; the only difference is that `CLAUDE.md` additionally carries an `@import ./BRAIN.md` line (Claude Code-specific — other agents don't understand `@import`). - **Idempotent** via the markers: absent file → created; existing file without markers → block **appended** (preserve user content); existing marked block → replaced in place (upgrades, never duplicates). Never whole-file overwrite outside the markers. ### 4. Optionally install a pre-commit hook Offer to install the local index + link backstop (no CI required). Only if the project is a git repository (`.git/` exists) and the user agrees: - Copy `hooks/pre-commit` → `.git/hooks/pre-commit` and make it executable (`chmod +x`). - If a `.git/hooks/pre-commit` already exists, do **not** overwrite it — tell the user and show them the hook contents so they can merge it manually. The hook runs `reindex → lint-links` on every commit and folds any index changes back in. (There is deliberately no validator — correctness is guaranteed by the CLI being the only way to write.) ### 5. Optionally install a Claude Code SessionStart hook Offer a project-local SessionStart hook so Claude Code sessions start with a compact `brain list-pages` snapshot. **Never** write `~/.claude/settings.json` — a global hook would fire in projects that have no brain. Do **not** hand-edit `.claude/settings.json` for this; the CLI merge is the installer. Only if the user agrees: ``` node /bin/brain.mjs install-hooks ``` Reverse with `… uninstall-hooks`. Both are **idempotent**: install copies `hooks/session-start` → `.claude/hooks/brain-session-start` and merges a `SessionStart` command into `.claude/settings.json` without clobbering other settings or duplicating the command; uninstall removes only that command and the copied script. The hook itself only shells out to `brain brain-dir` and `brain list-pages`. It no-ops when `populated:` is not `true`, and any failure exits 0 with no output (convenience layer, not a hard dependency). It does not inject page bodies, and it does not install UserPromptSubmit / Stop hooks. ## After setup The scaffold leaves the brain empty — six root page **templates** plus an empty `pages/`. The valuable next step is to **seed it with real project knowledge**, and that is exactly what the **brain-bootstrap** skill does: > **Recommend the user run the brain-bootstrap skill next.** On an existing (brownfield) project it reads the code, docs, and `git log` to draft the six root pages and capture the key historical decisions; on a near-empty (greenfield) project it interviews the user to seed `background` and friends. brain-setup does **not** run it automatically — initialization and knowledge-seeding are separate steps, so the user stays in control of what gets written. Also point them at: read `BRAIN.md`, then use the **brain-page** skill to author or modify pages directly and the **brain-ingest** skill to digest scattered input into the brain. **Every read and write goes through the `brain` CLI — never hand-edit a brain file.**