:classical_building: claude-second-brain

Your notes don't compound. This wiki does.

The fastest way to start your personal knowledge base powered by Obsidian, Claude Code, qmd, and GitHub.

npx claude-second-brain

One command gives you a fully wired knowledge system:

• Claude ingests your sources and maintains a cross-linked wiki
• qmd powers local semantic search
• The scaffolded folder is your Obsidian vault — open it directly in Obsidian, with obsidian-git pre-configured for seamless sync
• GitHub is the source of truth — version history, anywhere access, and a backup you control

You've been reading papers, articles, and books for years. Drop a source in, run /ingest, and Claude reads it — extracts what matters, cross-links it to everything you already know, and files it. Ask a question six months later and get cited answers, not a list of files to re-read.

Inspired by Andrej Karpathy's approach to LLM-powered knowledge management — share an "idea file" with an LLM agent and let it build and maintain your knowledge base.

How this is different

This is not a RAG system. It's not a chatbot over your notes. It's an actively maintained, cross-linked wiki — five structured page types, YAML frontmatter, and a set of Claude Code skills that run the whole thing.

The schema (CLAUDE.md) is that idea file. Claude reads it every session.

The stack

Everything is pre-configured. You bring the sources.

Get started in 3 steps

Step 1 — Scaffold

npx claude-second-brain

Creates your vault (the folder itself is the Obsidian vault), installs mise + bun, and runs git init with an initial commit.

Step 2 — Initialize inside Claude Code

cd my-wiki && claude

Then run:

/setup

Registers the qmd collections and generates local vector embeddings. First run downloads ~2GB of GGUF models — once.

Step 3 — Push to GitHub and open in Obsidian

git remote add origin https://github.com/you/my-wiki.git
git push -u origin main

Open my-wiki/ as a vault in Obsidian — the folder is already a valid Obsidian vault. The Git plugin is pre-configured — enable it and sync is automatic.

Claude Code skills included

The wiki ships with three slash commands that cover the full workflow. No manual prompting, no copy-pasting.

/ingest — Drop a file into sources/articles/, sources/pdfs/, or sources/personal/. Run /ingest. Claude summarizes the source, asks what matters most to you, creates a wiki/sources/ page, updates or creates related topic pages, flags any contradictions with existing knowledge, and logs everything.

/query — Ask anything about what you know. Claude runs hybrid semantic search across the wiki, reads the most relevant pages, and writes an answer with inline [[wiki/page]] citations. If the answer synthesizes multiple pages in a novel way, it offers to file it as a permanent wiki/qa/ entry.

/lint — Health-check the wiki. Surfaces orphan pages, broken links, unresolved contradictions, and data gaps. Reports findings and applies fixes where possible.

Access from anywhere

Edit anywhere — Claude Code on desktop or mobile
Claude Code's GitHub integration lets you open the repo and work from anywhere — ingest a source, run a query, or update a page from your phone.

Read anywhere — Obsidian desktop and mobile
Open the repo as an Obsidian vault. The bundled .obsidian folder pre-configures the obsidian-git community plugin — no setup required, just enable it. Your wiki syncs automatically on every commit. For iOS: put the repo folder inside iCloud Drive — Obsidian Mobile picks it up natively with no extra setup. Graph view, backlinks, offline reading — all working.

Browse anywhere — GitHub
It's a plain GitHub repo. View and edit files directly in the browser at any time.

How it works

┌─────────────────────┐        ┌─────────────────────┐        ┌─────────────────────┐
│   Drop in a source  │        │  /ingest in Claude  │        │     Wiki grows      │
│                     │        │        Code         │        │                     │
│  · article          │──────▶ │                     │──────▶ │  · cross-linked     │
│  · PDF              │        │  reads + extracts   │        │    pages            │
│  · personal note    │        │  key knowledge      │        │  · contradictions   │
│                     │        │                     │        │    flagged          │
└─────────────────────┘        └─────────────────────┘        │  · syntheses        │
                                                              │    written          │
                                                              └─────────────────────┘

Query it anytime with /query. Get answers with inline [[wiki/page]] citations, not a list of files.

Wiki structure

Five page types, all with YAML frontmatter:

All pages cross-link with Obsidian [[wikilinks]]. Contradictions are flagged with [!WARNING] callouts. Full schema in CLAUDE.md.

Directory layout

my-wiki/
├── CLAUDE.md              ← The schema. Claude reads this every session.
├── sources/               ← Your raw inputs. Claude never modifies these.
│   ├── articles/
│   ├── pdfs/
│   └── personal/
├── wiki/                  ← Claude owns this entirely.
│   ├── index.md
│   ├── log.md
│   ├── overview.md
│   ├── sources/
│   └── qa/
└── scripts/qmd/           ← Semantic search setup and re-indexing

Roadmap

• GitHub Actions for scheduled re-indexing
• GitHub agentic workflows — auto-ingest on push, scheduled lint, auto-summary on new sources
• More Claude Code skills (source discovery, topic clustering)

Requirements

• mise — auto-installed by the CLI if missing
• Claude Code — the CLI that runs the wiki
• Obsidian — optional but recommended

License

MIT