/brain-setup

name: brain-setup
description: Bootstrap the Open Project Brain Standard into the current project — prefer `brain init` (ensure BRAIN.md, scaffold empty brain brainRoot-aware, default-wire CLAUDE.md + AGENTS.md). Optionally install a pre-commit hook and a Claude Code or Codex SessionStart hook.

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 <brain-page-bundle>/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 or Codex 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 `<this-skill-bundle>` 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 <brain-page-bundle>/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 `<resolved dir>`. If `source: brainRoot`, make it explicit: *"this project's brain is redirected to an external directory (`<resolved dir>`) 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/` → `<resolved dir>/` — 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 <brain-page-bundle>/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 <brain-page-bundle>/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 **