brain

A personal memory engine and MCP server: hybrid RAG (SQLite FTS5 + vector search) over a git-backed markdown store.

Replace OWNER in the CI badge with your GitHub account once you push this to a repo.

Why

An LLM's context is amnesiac: everything it learns about you, your projects, and your decisions evaporates when the session ends. brain fixes that by persisting durable facts as plain markdown in git — the kind of store you can read, edit, grep, and diff by hand — and making it recallable to any MCP client through hybrid search. The markdown is the source of truth; the search index is a rebuildable cache you can delete at any time.

Related MCP server: mem-persistence

Architecture

          SOURCE OF TRUTH (markdown + git)          DERIVED INDEX (rebuildable)
        ┌───────────────────────────────────┐      ┌─────────────────────────┐
        │  memories/     curated facts       │      │  cache/brain.db         │
        │  summaries/    session digests     │─────▶│  ── FTS5 (BM25)         │
        │  ~/.claude/…   ingested transcripts│ ingest  ── sqlite-vec (256-d   │
        │                 (episodes)         │      │     nomic-embed vectors)│
        └───────────────────────────────────┘      └───────────┬─────────────┘
                    ▲                                           │
                    │ writes auto-commit                        │ hybrid recall
                    │ (optional push to a private remote)       ▼
        ┌───────────┴───────────┐                   ┌─────────────────────────┐
        │   remember(fact,type) │◀──── MCP ────────▶│  recall(query,k,scope)  │
        │                       │     (stdio)       │  get_episode(id)        │
        └───────────────────────┘                   └─────────────────────────┘
                                                     any MCP client (Claude Code, …)

• Three kinds of memory. memories/*.md are curated, durable facts (preferences, runbooks, per-project state notes). summaries/YYYY-MM/*.md are per-session digests. Episodes are ingested Claude Code transcripts (read from ~/.claude/projects/**.jsonl). The first two are git-tracked text you own; episodes derive from live transcripts — though on an emitting host, ingest also writes each episode as a git-tracked file under episodes/YYYY/MM/, so a transcript-less machine can index them by git pull alone (see Running across two machines).

• The index is a cache. cache/brain.db holds an FTS5 table and a sqlite-vec table of 256-dimension nomic-embed-text-v1.5 vectors (Matryoshka-truncated from 768). It is always rebuildable and never committed — delete it freely and brain-ingest --full recreates it.

• Hybrid recall. Each query runs both a lexical (FTS5/BM25) and a semantic (vector) leg; the two rankings fuse via reciprocal-rank fusion, then a prior re-weights by kind (a curated memory outranks a raw episode at equal evidence) and recency (exponential decay with a per-kind half-life, floored so age never fully erases relevance). Every hit carries a score in (0, 1]. The whole ranking surface is env-tunable — see Configuration.

• Durability & sync. Memory writes auto-commit, so a fact is safe the moment it is written. Point origin at any private git remote you control and the markdown store syncs across machines; the index never leaves the box. Sync is off unless you configure a remote, and hard-disabled with BRAIN_SYNC=0.

Quickstart

Requires uv and Python 3.12+. This repo ships a tiny synthetic store under examples/ so you can try recall without any data of your own.

uv sync                                              # install deps into .venv

# Build the index over the shipped examples only.
# BRAIN_CLAUDE_PROJECTS points at an empty dir so no real transcripts are read;
# drop it to also ingest your own ~/.claude/projects transcripts.
BRAIN_DIR=$PWD/examples BRAIN_CLAUDE_PROJECTS=$(mktemp -d) \
  uv run brain-ingest --full

# Hybrid recall from the shell.
BRAIN_DIR=$PWD/examples uv run brain-recall "postgres backup"

Expected top hit:

scope=all
mem_…  memory  2026-01-12  …  score=0.67…  How the demo acme-webapp Postgres database is backed up each night. …

Register the MCP server with Claude Code (or any MCP client that speaks stdio):

claude mcp add brain -- uv run --directory "$PWD" brain-server

Need a read-only server — e.g. behind a gate that requires every exposed tool to be auto-allowable? Register brain-server-readonly instead; it exposes only recall + get_episode, dropping the remember write that such a gate would reject.

Write a fact mid-session from the shell (brain-remember reads one JSON object from stdin — only fact is required):

echo '{"fact": "Staging DB resets nightly at 03:00 UTC.", "type": "reference"}' \
  | uv run brain-remember

First run downloads the embedding model (nomic-embed-text-v1.5, a few hundred MB) to $FASTEMBED_CACHE_PATH (default cache/fastembed/, gitignored). Subsequent runs are instant. Everything runs locally — no API key, no external inference calls.

Commands

Every entry point is a console script; run it with uv run <name>.

Memory file format

A memory is YAML frontmatter plus a markdown body (the same shape Claude Code uses for auto-memory), so it stays readable and hand-editable:

---
name: postgres-nightly-backup
description: How the demo acme-webapp Postgres database is backed up each night.
metadata:
  type: reference
date: 2026-01-12
---
The acme-webapp production Postgres runs a nightly logical backup at 02:00 UTC…

• name — kebab-case slug (defaults to the filename).

• description — one line; indexed alongside the body.

• metadata.type — one of user (preferences), feedback, project (per-project living state notes), reference (facts/runbooks).

• date — optional ISO date; drives recency decay.

See examples/memories/ for one of each kind, and examples/summaries/ for the session-digest format.

Configuration

All configuration is environment variables with sensible defaults — see src/brain/config.py for the full surface. Highlights:

Optional integrations (Claude Code)

These are conveniences for a Claude Code workflow and are entirely optional — the core (ingest + recall/remember + MCP server) has no dependency on them.

• Ambient auto-recall — a UserPromptSubmit hook (brain-hook) that runs a fast, read-only FTS pass on every prompt and silently injects the strongest matching memories as context.

• SessionStart injection — brain-session-start injects a project's rolling state note when a session opens, stamped with a freshness banner.

• Skills — skills/reflect (consolidation pass), skills/catchup (deep resume), and skills/handoff.

• Reflect triggering — on a workstation, consolidation is triggered solely by the in-process reflection-debt spawn from the MCP server (no cron or scheduled job); on an always-on box, a systemd timer runs brain-autoreflect --if-debt. See Running across two machines.

Design docs for these live under specs/.

How multi-machine sync works (optional)

The markdown store can sync across machines through any private git remote you control — there is nothing brain-specific about it:

git remote add origin <your-private-repo>   # e.g. git@github.com:you/brain.git
git config user.name  "Your Name"           # any identity you like
git config user.email you@example.com
git push -u origin main

cache/brain.db is rebuildable and never pushed. Sync auto-detects the remote: with no origin, brain behaves exactly as a local-only store, zero config. BRAIN_SYNC=0 disables it entirely regardless of remote. memories/ and proposals/ carry a merge=union attribute so concurrent edits from two machines concatenate losslessly rather than conflict; the next consolidation pass dedups them. See specs/git-sync.md for the full design.

Memory commits record provenance as git trailers (Session, Project, Host) so you can audit which machine and session produced each fact.

Running across two machines (split-host)

The store is built to run split across an emitting workstation and an always-on box (a small VM), both talking to the same markdown store through the private remote from How multi-machine sync works. They divide the labour:

• The workstation emits. It has the live Claude Code transcripts, so its brain-ingest parses them, writes new memories, and — the key part — emits one markdown file per episode under episodes/YYYY/MM/<id>.md. Unlike cache/ (gitignored), episodes/ is git-tracked and committed (as brain-ingest: emit N episodes) and pushed to the remote. The workstation runs its MCP server with BRAIN_NO_AUTOREFLECT=1, so it never spends a reflect itself — it delegates that to the box.

• The always-on box indexes. It has no transcripts of its own, so it git pulls and indexes straight from the committed episode files, then runs the maintenance loops on a timer. It sets BRAIN_INGEST_SOURCE=episodes so ingest reads episodes/**/*.md only and never scans, emits, or commits transcripts — important because the box accrues its own claude -p reflect transcripts that auto would otherwise wrongly index and re-emit.

Episode source selection (BRAIN_INGEST_SOURCE)

A transcript-less box therefore stays current on episodes purely by git pull. See specs/episodes-in-git.md.

reflect triggering

There is no nightly cron or scheduled OS job. reflect is triggered one way per host:

• On the workstation, solely by the in-process reflection-debt spawn from the MCP server: when accrued debt crosses the threshold, the server spawns a headless consolidation pass. BRAIN_NO_AUTOREFLECT=1 disables it (as the split-host workstation does).

• On the always-on box, by a systemd timer running brain-autoreflect --if-debt — a debt-gated reflect that only spends a claude -p /reflect when reflection debt has actually accrued.

systemd timers (deploy/vm/)

The deploy/vm/ dir ships user-level systemd units (plus a README) for the always-on box:

• brain-reflect.timer (hourly, jittered) runs brain-ingest, then brain-autoreflect --if-debt.

• brain-freshness-audit.timer (daily) runs brain-ingest, then brain-freshness-audit: it sweeps the memories/*-state.md project notes, reuses the SessionStart STALE rule (repo drift or enough new episodes since the note was written) to find notes that have fallen behind their project, and dispatches one Opus refresh agent per stale note to rewrite it in-format and auto-land it. Runs are bounded by BRAIN_AUDIT_MAX_REFRESH (default 3) agents; contradictions, archival candidates, and filename mapping-failures are written out as proposals/needs-user-<date>-<note>.md for a human instead.

Scope & honesty

• Single-user personal project. Extracted from a working personal system and published with fresh git history — not a hardened multi-tenant service.

• Developed on macOS. The core is pure Python and portable. The only platform-specific pieces are optional deployment glue: the workstation runs on macOS, and the always-on box uses Linux user-level systemd units (deploy/vm/).

• Local embeddings. Vectors are computed locally via fastembed — no API key and no external inference calls. (CI runs FTS-only, since the model download and native sqlite-vec wheel may be unavailable on the runner; recall degrades gracefully to lexical-only when the vector table is absent.)

• Sync is bring-your-own and off by default. Nothing leaves your machine unless you add a private remote.

License

MIT.