Second Brain Starter Kit

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A starter kit for running Claude Code as a second brain + working assistant, from Palo Alto AI Research Lab. This is the system we run ourselves every day — stripped of personal data and cut down to a portable core: the method, not the data.

Start here — 25 skills worth your first hour

Every one of them ran in production before it was published. One command each.

skill what it gives you in 60 seconds
/secondop a second opinion from a PANEL of external LLMs (Codex + Grok + Gemini) on any plan or diff — a model never reviews itself
/tt the quality gate after every build: run it live, break it on purpose, prove it with a counter — only then say "done"
/retro end-of-session retrospective that routes every durable artifact to its home and hands you a compact handoff
/handoff a self-contained "semicolon" so another session, person or machine continues exactly where you stopped
/skill-gap audits your sessions for repeated manual patterns and tells you which skill to install or build next
/precedent before you decide anything structural: did we already decide it, and did we already reject it?
/declined the registry of rejected ideas, so the agent stops re-pitching what you already said no to
/issue-match measures a target repo's queue before you spend a PR: how many of the last closed PRs were actually merged
/research-swarm turns any hypothesis into an argument map from 5 independent lenses — never a verdict
/last30days deterministic "what changed in the last 30 days on topic X" before a strategic call
/ask semantic search over your curated vault — the smallest relevant slice, not a corpus dump
/search full-text search across every conversation you ever had, locally, 0 tokens
/chat-search find which past Claude Code session discussed a thing — and resume it
/resume-last continue the previous chat after a crash, even on another machine where native resume can't reach
/1 hard-crash recovery: where were we + is everything alive + restore the history, in one command
/arch the deterministic map of everything your system is made of, and what fell off it
/brain one-glance health of a memory/RAG stack so failures stop being silent
/sync-check green/red report on file sync across a machine fleet, including the silent sync-conflict count
/quarantine holds unsigned or unverified incoming deliverables instead of applying them — fail-closed
/obsidian-ingest universal import pipeline: any source becomes well-linked atomic notes with provenance
/defuddle clean web→markdown without ads or nav — 40-60% fewer tokens than a raw fetch
/dedup find and merge near-duplicate notes with a supersede-not-delete policy
/taste-check a content quality gate: is this fit to show, before anyone sees it
/intake one pass routes a new rule into every home it needs, so parallel sessions see it on their own
/mcp health-check your MCP servers and scout new ones before any integration work

Standalone tools (separate repos, same lab):

tool what it does
claude-memory-tidy keeps an agent memory folder clean and deduplicated
sqlite-graph-memory graph memory for agents on plain SQLite — no server, no vector DB
verbatim-citation-gate a deterministic gate that catches invented quotes before they ship
agent-leash an 8-domain leash for delegated agent authority
claude-consensus machines negotiate propose → counter → accept → commit instead of drifting
llm-spend-audit where your LLM subscription budget actually goes
agent-runtime-integrity-bench replay, idempotency and consensus-integrity scenarios from real incidents

Full map of all 101 → skills/INDEX.md

What's inside

Folder / file What it is
SEED.md The opening message for your FIRST Claude Code session — everything starts here
BOOTSTRAP-CLAUDE.md Instructions for Claude itself: how to install and adapt the kit
CLAUDE-EXTERNAL.md Our working principles (assistant behavior) — the base for your own CLAUDE.md
skills/ All 101 skill commands the system runs on every day — map: skills/INDEX.md. Personal data in examples is replaced with fictional stand-ins (how exactly)
templates/ Second-brain note templates (concepts, decisions, weekly/monthly reviews)
crm-template/ CRM: markdown "one card = one file" + an engine with warmth scoring and safe outbound, with demo data
docs/ How to use CLAUDE.md, onboarding, what is shared
HANDOVER.md Already running your own agent fleet? A snapshot of the whole system and a map of our repos — the entry point for you and your model

📖 Repository wiki: what is actually in here · architecture (4 layers) · your first week · adapting it to your machine

One-command install (skills / plugin marketplace)

Don't need the whole kit? Install just the skills, straight into your Claude Code:

/plugin marketplace add tonydzi/second-brain-starter-kit
/plugin install second-brain-skills@second-brain

Or via skills.sh (works for Claude Code, Codex, Cursor, Gemini CLI and any other agent that speaks the Agent Skills format):

npx skills add tonydzi/second-brain-starter-kit

Quick start (10 minutes)

  1. A Claude Pro or Max subscription → install Claude Code: npm install -g @anthropic-ai/claude-code (no npm? Mac: brew install node, Windows: nodejs.org).
  2. Run claude and log in with your subscription.
  3. Install Obsidian — to look at your second brain with your own eyes.
  4. Clone this repository: git clone https://github.com/tonydzi/second-brain-starter-kit.git (or Code → Download ZIP).
  5. Open SEED.md, put your name in, and paste the text as the first message to Claude Code. Claude takes it from there, following BOOTSTRAP-CLAUDE.md.

The principles this stands on

  • A second brain = stop losing what's useful. Every decision, agreement and idea → a note in the vault, linked into the graph.
  • AK-47 rule: the simplest solution the owner can repair themselves.
  • Receipts: the assistant proves it saved something ("recorded X → note Y") instead of saying "understood".
  • A routine repeated twice becomes a skill — a /name command.
  • Privacy: everything lives locally on your machine; money, deletion and anything leaving the house happen only on your explicit OK.

Roadmap

Now — v0.1.0. 101 skills, 246 engines those skills actually call, note templates, a CRM engine with warmth scoring and safe outbound, SEED.md + BOOTSTRAP-CLAUDE.md for the first session, and HANDOVER.md for people who already run their own agent fleet.

Next, in the order we would take it ourselves:

  • Fix the onboarding (#1): ONBOARDING.md walks a newcomer through five folders that do not exist in this repository. It is the first screen a stranger sees, and it lies — top of the queue.
  • A "clone it and it works" check on someone else's machine. Right now the only proof is that we use this ourselves every day. That is usage, not a test: no third-party machine has ever been seen.
  • Localized READMEs for non-English venues (Chinese, Japanese, Korean, Spanish) — the skill bodies stay English, the docs get localized.

Every notable change ships as a release, so the releases feed is an honest record of what is actually in the kit — unlike a commit history.

Which AI worked here

This project is built by a human + AI team, and the commit history shows it: Claude writes most of the code, Codex and Grok review it, Gemini brings research. A model is credited in a commit only if its output actually changed that commit's content — no decorative signatures. Lab-wide rule: AI-CONTRIBUTORS.md.

License and provenance

The method is open — take it, adapt it, share it. There are no secrets and no personal data in the kit (it goes through an automated secret scanner). Questions and ideas → Issues.

Get in touch

Questions, war stories, or you want to run this yourself:

🧩 One piece of a working system

This repository is one piece lifted out of a live operation: one non-technical founder, an AI cofounder, and a fleet of machines that reach consensus with each other and wake the human only for money or the irreversible. It was extracted after it survived production, not written as a demo — and it runs on its own: nothing here phones home to the rest.

See how the whole thing fits together → SYSTEM.md

Its closest neighbours in the memory layer: sqlite-graph-memory · voice2brain

About & contact

Built and battle-tested at Palo Alto AI Research Lab — a fleet of Claude Code machines running 24/7 as a second brain and synthetic cofounder. Every skill here survived real production use before publication.