GitHub - mindmuxai/brain.md: A persistent, file-based memory layer for coding agents — give Claude Code, Codex & others a project brain (dur

brain.md

A persistent memory layer for your coding agents.

An open, agent-agnostic standard for capturing a project's durable knowledge as plain Markdown — read and written through one small CLI. It lives in your repo and travels across agents, machines, and models.

Why · Quick start · See it work · CLI · How it works

This repository is the toolkit , not a brain itself. Install it once, then in any project run brain init : it scaffolds a BRAIN.md protocol file, a brain/ directory, and default-wires agent config files into your repo.

From then on, any coding agent — Claude Code, Codex, anything that reads files — learns to use that brain just by reading the project's BRAIN.md . The brain is plain Markdown, lives in the repo, and outlives every session.

Why a brain

A coding agent's knowledge lives nowhere durable. The reasons behind a decision, the constraints you agreed on, the path not taken — they sit in chat logs and in your head, and they vanish the moment the session ends. The next agent starts from zero.

A brain fixes that. It is the project's persistent memory : the durable decisions, requirements, and constraints, written down as plain Markdown next to the code.

• Repo-native — Markdown that lives in your project and travels in git, with or without a runtime on top.

• Agent-agnostic — the contract is a file ( BRAIN.md ). Any agent that can read it can use the brain.

invariants can't be broken by a malformed edit. There is no validator because none is needed.

• Correct by construction — every write goes through the brain CLI, so the brain's

The test for what belongs in it: will this still matter in six months, and is it hard to reconstruct from the code itself? If yes, it goes in the brain. Pure implementation details and anything readable straight from the code and git history stay where they are.

Quick start

1. Install the tools once (global) — no clone required. This puts brain on your PATH and copies skills into every detected agent ( ~/.claude/skills , …):

npm install -g @mindmux/brain-md

brain setup -y

reverse: brain uninstall # never touches any project's brain data

Prefer not to install globally? Use npx for both steps (npx does not leave brain on your PATH ):

npx @mindmux/brain-md setup -y

npx @mindmux/brain-md init # same as step 2 — not bare `brain init`

reverse: npx @mindmux/brain-md uninstall

From a git checkout of this repo you can still run ./setup (same installer; use --symlink while developing the toolkit).

1. Initialize a project (from the project root; requires the global install from step 1, or use npx @mindmux/brain-md init above):

brain init

or, after setup only (no global bin): node ~/.claude/skills/brain-page/bin/brain.mjs init

This ensures BRAIN.md , scaffolds empty brain data (brainRoot-aware), and default-wires CLAUDE.md + AGENTS.md (creates them if missing; if they already exist, only updates the marked brain block — never whole-file overwrite).

Optionally use the brain-setup skill for the same flow plus a pre-commit hook.

the code, docs, and git log to draft the root pages and capture key decisions; on a near-empty one it interviews you. (Init leaves content seeding as a deliberate next step.)

1. Seed real knowledge — run the brain-bootstrap skill. On an existing project it reads

capture decisions/constraints when they settle; skip pure implementation noise; reverse when overturning. All reads/writes go through the brain CLI following BRAIN.md — never hand-edit brain files.

1. Work as usual. Maintain the brain while coding : load relevant pages at task start;

See it work

The point of a brain is what happens across sessions — a decision made today is still there, with its rationale, weeks later:

You Let's store config as Markdown, not SQLite — easier to diff and migrate.

Agent Capturing that as a decision so it outlives this session. $ brain create-page --id config-as-markdown --category decision \ --title "Store config as Markdown, not SQLite" ✓ page created · indexed

— three weeks and a fresh session later —

You Why aren't we using a database for config?

Agent $ brain read-page config-as-markdown We chose Markdown for diff-ability and zero migrations. Here's the original call and the trade-offs we weighed …

The brain CLI

Reading and writing the brain both go through one zero-dependency Node CLI (run with node ):

brain () { node skills/brain-page/bin/brain.mjs " $@ " ; } # or use the global brain bin after npm install -g

brain init # BRAIN.md + skeleton + default wire CLAUDE.md / AGENTS.md brain wire # same default wire (no --agent needed) brain brain-dir # where is the brain?

brain list-pages # list pages brain read-page my-decision # read a page brain create-page --id my-decision --category decision --title " Use X over Y " echo " the new understanding " | brain update-truth --id my-decision --summary " why it changed " brain append-timeline --id my-decision --kind evidence --summary " benchmark confirmed it " echo " ## Overview … " | brain update-root architecture brain reindex && brain lint-links

A page carries a rewritable compiled_truth (the current best understanding) plus an append-only timeline (the chain of evidence). update-truth rewrites the truth and appends its timeline entry in one atomic write — so the understanding can never change without a trace.

How it works

Three design choices keep the brain durable and tamper-evident:

generated, and update-truth rewrites understanding + records why in a single atomic write. The two things a validator used to guard are now structurally impossible.

• Correct by construction, no validator. The CLI is the only writer. Frontmatter is always

redirect it via brainRoot in .mindmux/preferences.json (e.g. an external sidecar). Every command resolves the location itself — tools never create a second, shadow brain.

• Exactly one brain, location-independent. It defaults to ./brain , but a project can

and travels in git, and runtimes (MindMux over MCP, more to come) layer on top of the same files.

• Pure files, portable. The brain is Markdown plus one Node script — it lives in your repo

The skills that drive it all:

skill what it does

brain-setup same scaffold/wire as brain init , plus an optional pre-commit hook — prefer brain init for day-to-day

brain-bootstrap seed the brain from code / docs / git log — or interview you on a greenfield project

brain-page the operating manual for reading and writing pages + root pages (carries the brain CLI)

brain-ingest digest a conversation, document, or research result into the brain

brain.md is led and incubated by MindMux — the standalone open-source landing of MindMux's Brain Spec + coding-agent adapter. The specification layer uses neutral naming so it can be adopted widely; stewardship and maintenance belong to MindMux. Licensed under Apache-2.0.

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