AI Second Brain

A knowledge base that an AI agent builds and maintains for you, in plain markdown files you own. Everything you read, watch and save gets turned into linked wiki pages, connected to everything already there, and you can ask it questions.

This repo is the full version of the guide: the concepts, the setup, the vault template, the agent skills, the scripts, and the resources. Free, no signup, nothing to install beyond Obsidian and an agent.

Read it on the web: undefined-ui.github.io/second-brain-os — the full guide with search and navigation, plus every vetted link in one filterable page.

Three things live here — pick your entrance:

• The second-brain guide — a path you follow once: build a knowledge base an agent maintains for you. 65 pages, a starter vault, 18 skills.
• The agents course — a path you read in order: seven modules from a single prompt to a production agent, with tools you install in two commands.
• The handbooks — not a path, references: the full menu of techniques, tools and builds for one layer. Open one when that layer starts hurting.

The problem it solves

You save things with the intention of coming back. You never do. Bookmarks, screenshots, read-later queues and half-filled Notion pages accumulate without compounding, because filing and linking them is boring work that humans stop doing after two weeks.

Hand that work to an agent and the system stays alive. That is the whole idea.

Quickstart

One evening. Nine steps, each with a full page behind it.

# copy the starter vault, skills, commands and agents
git clone https://github.com/undefined-ui/second-brain-os.git
cp -r second-brain-os/vault-template ~/brain

mkdir -p ~/brain/.claude
cp -r second-brain-os/skills   ~/brain/.claude/skills
cp -r second-brain-os/commands ~/brain/.claude/commands
cp -r second-brain-os/agents   ~/brain/.claude/agents
cp -r second-brain-os/scripts  ~/brain/scripts

# the folder READMEs are for reading on GitHub, not for the agent
rm ~/brain/.claude/*/README.md ~/brain/scripts/README.md

cd ~/brain && claude

The scripts/ copy is what lets /metrics, /health and /graph-export run scripts/vault_stats.py and friends from inside the vault. On Windows, use python where this guide says python3: the python3 name usually resolves to the Microsoft Store stub and does nothing.

1. Install Obsidian and open the ~/brain folder you just copied with "Open folder as vault"
2. Set up Claude Code, in the terminal or the Code tab of the desktop app
3. Connect over MCP if you want the agent to reach the vault from anywhere. Optional, skip it on day one
4. Get interviewed for your CLAUDE.md instead of writing it by hand
5. Set up the two layers: a wiki for what you know, projects for what you are doing
6. Scope down to one project when you want to ship something
7. Install the Web Clipper, clip an article to raw/, run /ingest
8. Connect live data: calendar, email, chat
9. Put maintenance on a schedule and wake up to a vault that filed itself

Then feed it ten more sources before judging it. The graph is not interesting at five pages and it is hard to look away from at fifty.

Full walkthrough: Setup.

How it works

   you                    raw/                 agent                 wiki/
 ┌───────┐          ┌──────────────┐      ┌────────────┐      ┌──────────────┐
 │ clip  │  ──────> │ articles     │ ───> │  ingest    │ ───> │ sources/     │
 │ save  │          │ transcripts  │      │  extract   │      │ concepts/    │
 │ dump  │          │ pdfs         │      │  link      │      │ entities/    │
 └───────┘          │ chat exports │      │  lint      │      │ synthesis/   │
                    └──────────────┘      └────────────┘      └──────────────┘
                                                │                     │
                                                │   ask anything      │
                                                └─────────────────────┘

Raw material is an archive you never read. The wiki is the artifact, written in plain language, one idea per page, densely linked. New sources update existing pages instead of piling up beside them, which is why the vault gets better as it grows rather than just bigger.

Alongside the wiki sits a project layer: one folder per project, each with its own CLAUDE.md and an Inputs / Process / Outputs / Feedback pipeline. The wiki holds what you know, the projects hold what you are doing, and they feed each other. The two layers covers why keeping them separate matters more than it sounds.

What is in here

The guide

Ten sections, 77 pages, written to be followed rather than skimmed. From the concept through setup, capture, structure, the graph, automation, retrieval, publishing, and what to do when each of them breaks.

The agents course

Seven modules from a single prompt to a production agent, built on Google's agent whitepapers and the five-layer frame: what the agent sees, who decides the next step, who sorts the incoming work, what it can reach, and how you know it works. Theory with sources, a practice page in every module, and a day-one plan at the end.

The course ships its own tools as a Claude Code plugin — a context auditor, a goal-test generator, a gate finder, a harness auditor, an evals bootstrapper and a loop critic, each doing one module's practice page in your repo:

claude plugin marketplace add undefined-ui/second-brain-os
claude plugin install agents-course@second-brain-os

The handbooks

Everything above is the second brain. The handbooks are the wider craft of building with agents — separate subjects, deliberately compact: eight or nine pages each, current as of September 2026, and every one ends in a hands-on build you can finish in an evening.