PlaybookIntermediate12 min read11 June 2026

How to Build a Second Brain

That Actually Gets Smarter Every Day

In short

This is the full build for an AI-maintained second brain using Obsidian and Claude Code. Two tools, free, six steps, plus the schema prompt that turns Claude from a chatbot into a disciplined wiki maintainer. The unlock isn't "AI helps with notes." The unlock is that the AI does all the maintenance (cross-referencing, summarizing, flagging contradictions, updating index pages) that's why every previous knowledge base you've built died. This one doesn't die because the cost of maintenance dropped to zero. Includes four automations that run while you sleep: morning briefing, call transcript processor, weekly synthesis post, and contradiction tracker.

Most entrepreneurs I know have the same problem.

You've read hundreds of books. Listened to thousands of hours of podcasts. Taken notes from a thousand meetings. Had late-night voice memos that felt like breakthroughs. Screenshots of tweets you wanted to remember. Client calls that contained gold.

And where is all of it right now?

Scattered. Dead. Sitting in apps you forgot you subscribed to, in iMessage threads with yourself, in voice memos labeled "New Recording 247." The compounding machine inside your head exists, but the infrastructure around it is held together with duct tape and hope.

At the end of the day, the real asymmetry in business isn't information access. Everyone has the same internet. The asymmetry is whether your knowledge compounds or decays.

Mine used to decay. Now it compounds. I'm going to show you exactly how.

Why Every "AI + Documents" Setup You've Tried Is Broken

Most people's experience with AI and their own knowledge looks like this:

You upload files. The AI retrieves chunks. You ask a question. You get an answer. Move on.

That's how NotebookLM works. That's how ChatGPT file uploads work. That's how pretty much every RAG system out there works. And the fundamental problem with all of them is this: the AI is rediscovering your knowledge from scratch every single time you ask a question.

Nothing accumulates. Nothing compounds. You read 200 articles this year and your AI is no smarter about your world in December than it was in January. You're basically renting intelligence one question at a time.

At the end of the day, that's not a second brain. That's a search engine with a personality.

What I'm going to show you is different. Instead of retrieving from raw documents every time, the AI incrementally builds and maintains a persistent wiki that sits between you and your sources.

It's kind of like the difference between hiring a researcher who starts from zero every morning versus hiring a chief of staff who actually knows your business and gets smarter every week.

When you add a new source:

  • The AI reads it
  • Extracts what matters
  • Updates the existing topic pages
  • Rewrites the summaries
  • Flags where this new information contradicts stuff you already had
  • Strengthens the evolving synthesis

You never write the wiki yourself. The AI writes and maintains all of it. Your job is the sourcing, the exploration, and asking the right questions. The AI handles the summarizing, cross-referencing, filing, and the bookkeeping. Which, let's be honest, is the part nobody ever actually does. That's why most people's "knowledge bases" die within 3 weeks.

This one doesn't die. It compounds.

What You Actually Need (Don't Overthink This)

Two tools. That's it.

Obsidian: download from obsidian.md. It's free. It's a markdown editor with graph views and link navigation. Think of it as the window you look at your wiki through.

Claude Code: download from claude.com/product/claude-code. This is the agent that reads your files, builds the wiki, and maintains the whole thing.

That's the entire stack. Anyone telling you that you need Notion AI + Mem + Reflect + Heptabase + a custom vector database is selling you something. You need two tools and a good schema. Everything else is cope.

Step 1: Create Your Vault

Open Obsidian. Create a new vault. Name it whatever makes sense to you: brain, vault, your name, doesn't matter.

Inside the vault, create exactly these two folders:

raw-sources/ this is your junk drawer. Articles, meeting transcripts, book highlights, podcast notes, screenshots, voice memo transcriptions, client call transcripts, random ideas at 2 AM. Dump everything here. Do NOT organize it. That's not your job.

These files are immutable. The AI reads from them but never edits them. This is your source of truth, the raw signal.

wiki/ this is where the AI writes the organized version. Summaries, concept pages, entity pages, comparisons, overviews, syntheses. The AI owns this folder completely. It creates pages, updates them when new sources arrive, maintains cross-references, keeps everything consistent.

You read it. The AI writes it. You never edit wiki pages by hand. This is the rule that makes the whole system work. The moment you start manually editing wiki pages, you've broken the contract and the AI can't trust its own work anymore.

Inside wiki/ there are two special files the AI maintains:

  • index.md a catalog of every page in the wiki, each with a one-line description, organized by category. The AI updates this on every ingest. When you ask a question, the AI reads the index first to figure out which pages are relevant, then drills in. This is why you don't need embeddings or a vector database. The index IS the retrieval system. And it works surprisingly well even when you hit hundreds of pages.
  • log.md a chronological record of what happened. Every ingest, every query, every health check, appended in order. This is how the AI stays aware of what's been done recently and avoids repeating work.

Step 2: Add the Schema File (this is the most important step)

Create a file in the root of your vault called CLAUDE.md (if you're using Claude Code) or AGENTS.md (if you're using something else).

This is the schema. This is what turns Claude from a generic chatbot into a disciplined wiki maintainer that actually follows your rules.

You and the AI co-evolve this file over time. It starts with Andrej Karpathy's base prompt and over weeks of use, you refine it for your domain, your style, your standards. Think of it as the SOUL.md for your second brain.

Here's the base prompt to paste in. Copy both parts and combine them:

1ST PROMPT

# LLM Wiki

A pattern for building personal knowledge bases using LLMs.

This is an idea file, it is designed to be copy pasted to your own LLM Agent (e.g. OpenAI Codex, Claude Code, OpenCode / Pi, or etc.). Its goal is to communicate the high level idea, but your agent will build out the specifics in collaboration with you.

## The core idea

Most people's experience with LLMs and documents looks like RAG: you upload a collection of files, the LLM retrieves relevant chunks at query time, and generates an answer. This works, but the LLM is rediscovering knowledge from scratch on every question. There's no accumulation. Ask a subtle question that requires synthesizing five documents, and the LLM has to find and piece together the relevant fragments every time. Nothing is built up. NotebookLM, ChatGPT file uploads, and most RAG systems work this way.

The idea here is different. Instead of just retrieving from raw documents at query time, the LLM **incrementally builds and maintains a persistent wiki** — a structured, interlinked collection of markdown files that sits between you and the raw sources. When you add a new source, the LLM doesn't just index it for later retrieval. It reads it, extracts the key information, and integrates it into the existing wiki — updating entity pages, revising topic summaries, noting where new data contradicts old claims, strengthening or challenging the evolving synthesis. The knowledge is compiled once and then *kept current*, not re-derived on every query.

This is the key difference: **the wiki is a persistent, compounding artifact.** The cross-references are already there. The contradictions have already been flagged. The synthesis already reflects everything you've read. The wiki keeps getting richer with every source you add and every question you ask.

You never (or rarely) write the wiki yourself — the LLM writes and maintains all of it. You're in charge of sourcing, exploration, and asking the right questions. The LLM does all the grunt work — the summarizing, cross-referencing, filing, and bookkeeping that makes a knowledge base actually useful over time. In practice, I have the LLM agent open on one side and Obsidian open on the other. The LLM makes edits based on our conversation, and I browse the results in real time — following links, checking the graph view, reading the updated pages. Obsidian is the IDE; the LLM is the programmer; the wiki is the codebase.

This can apply to a lot of different contexts. A few examples:

- **Personal**: tracking your own goals, health, psychology, self-improvement — filing journal entries, articles, podcast notes, and building up a structured picture of yourself over time.
- **Research**: going deep on a topic over weeks or months — reading papers, articles, reports, and incrementally building a comprehensive wiki with an evolving thesis.
- **Reading a book**: filing each chapter as you go, building out pages for characters, themes, plot threads, and how they connect. By the end you have a rich companion wiki. Think of fan wikis like [Tolkien Gateway](<https://tolkiengateway.net/wiki/Main_Page>) — thousands of interlinked pages covering characters, places, events, languages, built by a community of volunteers over years. You could build something like that personally as you read, with the LLM doing all the cross-referencing and maintenance.
- **Business/team**: an internal wiki maintained by LLMs, fed by Slack threads, meeting transcripts, project documents, customer calls. Possibly with humans in the loop reviewing updates. The wiki stays current because the LLM does the maintenance that no one on the team wants to do.
- **Competitive analysis, due diligence, trip planning, course notes, hobby deep-dives** — anything where you're accumulating knowledge over time and want it organized rather than scattered.

## Architecture

There are three layers:

**Raw sources** — your curated collection of source documents. Articles, papers, images, data files. These are immutable — the LLM reads from them but never modifies them. This is your source of truth.

**The wiki** — a directory of LLM-generated markdown files. Summaries, entity pages, concept pages, comparisons, an overview, a synthesis. The LLM owns this layer entirely. It creates pages, updates them when new sources arrive, maintains cross-references, and keeps everything consistent. You read it; the LLM writes it.

**The schema** — a document (e.g. CLAUDE.md for Claude Code or AGENTS.md for Codex) that tells the LLM how the wiki is structured, what the conventions are, and what workflows to follow when ingesting sources, answering questions, or maintaining the wiki. This is the key configuration file — it's what makes the LLM a disciplined wiki maintainer rather than a generic chatbot. You and the LLM co-evolve this over time as you figure out what works for your domain.

## Operations

**Ingest.** You drop a new source into the raw collection and tell the LLM to process it. An example flow: the LLM reads the source, discusses key takeaways with you, writes a summary page in the wiki, updates the index, updates relevant entity and concept pages across the wiki, and appends an entry to the log. A single source might touch 10-15 wiki pages. Personally I prefer to ingest sources one at a time and stay involved — I read the summaries, check the updates, and guide the LLM on what to emphasize. But you could also batch-ingest many sources at once with less supervision. It's up to you to develop the workflow that fits your style and document it in the schema for future sessions.

**Query.** You ask questions against the wiki. The LLM searches for relevant pages, reads them, and synthesizes an answer with citations. Answers can take different forms depending on the question — a markdown page, a comparison table, a slide deck (Marp), a chart (matplotlib), a canvas. The important insight: **good answers can be filed back into the wiki as new pages.** A comparison you asked for, an analysis, a connection you discovered — these are valuable and shouldn't disappear into chat history. This way your explorations compound in the knowledge base just like ingested sources do.

**Lint.** Periodically, ask the LLM to health-check the wiki. Look for: contradictions between pages, stale claims that newer sources have superseded, orphan pages with no inbound links, important concepts mentioned but lacking their own page, missing cross-references, data gaps that could be filled with a web search. The LLM is good at suggesting new questions to investigate and new sources to look for. This keeps the wiki healthy as it grows.

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How to Build a Second Brain · Playbooks · Steve Tan