~/Documents/Obsidian_Vault/my-brain

built using claude-second-brain

Your notes don't compound. This wiki does.

Drop in a source. Claude reads it, extracts what matters, cross-links it to everything you already know, and files it. Query it 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.

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Quick start

# 1. Install tools (node + pnpm via mise)
mise install

# 2. Install dependencies
pnpm install

# 3. Open Claude Code
claude

Inside Claude Code, run:

/setup

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

Then open this folder in Obsidian. The Git plugin is pre-configured — enable it in Obsidian settings and your wiki syncs automatically.

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Your Claude Code skills

Daily workflow

/brain-ingest — Add a file to raw-sources/articles/, raw-sources/pdfs/, or raw-sources/personal/, then run /brain-ingest. Claude summarizes the source, asks what aspects matter most, updates related wiki pages, flags contradictions, and logs everything.

/brain-search — Ask anything: what do I know about [topic]? Claude searches the wiki semantically and returns a cited answer. If it synthesizes multiple pages in a useful way, it offers to file it as a permanent wiki/qa/ entry.

/lint — Health-check the wiki. Finds orphan pages, broken links, unresolved contradictions, and data gaps. Reports findings and fixes what it can.

Maintenance

/brain-refresh — Re-scan the vault for new or changed files and regenerate vector embeddings. Run after a bulk ingest session or manual edits. Pass force to re-embed every chunk.

/brain-rebuild — Destructive. Redesigns the qmd schema: analyzes the wiki, proposes new collections and contexts, waits for your approval, then patches scripts/qmd/setup.ts, drops the old index, and rebuilds embeddings from scratch.

Setup

/setup — First-time initialization. Registers the qmd collections and generates local vector embeddings. Run once after scaffolding.

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How it works

Sources flow in on the left, Claude synthesizes them into the wiki, qmd indexes every page into a local hybrid search index, and GitHub makes the whole vault editable from Obsidian and Claude Code on any device.

flowchart TB
  subgraph Sources["raw-sources/ — raw, immutable"]
    direction LR
    S1[articles/]
    S2[pdfs/]
    S3[personal/]
  end

  subgraph Skills["Claude Code skills"]
    direction LR
    I["/brain-ingest"]
    Q["/brain-search"]
    R["/brain-refresh"]
  end

  subgraph Wiki["wiki/ — cross-linked synthesis"]
    direction LR
    W1[overview.md]
    W2[topic / entity pages]
    W3[sources/]
    W4[qa/]
  end

  QMD[("qmd.sqlite<br/>vector + BM25<br/>hybrid index")]

  subgraph Remote["GitHub — source of truth"]
    GH[private repo]
  end

  subgraph Read["Read / edit anywhere"]
    direction LR
    OB["Obsidian<br/>graph · backlinks · mobile"]
    CC["Claude Code<br/>desktop + mobile"]
  end

  User((you))

  Sources -->|read| I
  I -->|write pages, cross-link,<br/>flag contradictions| Wiki
  R -.->|chunk + embed<br/>changed files| QMD
  Wiki -.->|indexed by| QMD
  User -->|ask a question| Q
  Q -->|hybrid search| QMD
  QMD -->|top-k pages| Q
  Q -->|cited answer| User
  Wiki <-->|"obsidian-git<br/>auto commit / pull"| GH
  GH --> OB
  GH --> CC

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Obsidian Mobile

If this repo lives inside your iCloud Drive folder, Obsidian Mobile reads it with no extra setup. Graph view, backlinks, offline access — all working. The Git plugin handles sync automatically when you commit and push.

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Wiki structure

Five page types, all with YAML frontmatter:

Type	File	Purpose
overview	wiki/overview.md	Evolving high-level synthesis
topic	wiki/[concept].md	A concept, domain, or idea
entity	wiki/[name].md	A person, tool, company, or project
source-summary	wiki/sources/[slug].md	One page per ingested source
qa	wiki/qa/[slug].md	Filed answers to notable queries

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

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Directory layout

claude-second-brain/
├── CLAUDE.md              ← The schema. Claude reads this every session.
├── raw-sources/           ← Your raw inputs. Claude never modifies these.
│   ├── articles/          ← Web articles saved as markdown
│   ├── pdfs/              ← PDFs or extracted text
│   └── personal/          ← Brain dumps, rough notes
├── wiki/                  ← Claude owns this entirely.
│   ├── index.md           ← Master index
│   ├── log.md             ← Append-only activity log
│   ├── overview.md        ← Evolving synthesis
│   ├── sources/           ← One summary per ingested source
│   └── qa/                ← Filed Q&A answers
└── scripts/qmd/           ← Semantic search setup and re-indexing

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Installing and updating skills

Skills are slash commands Claude Code loads from .claude/skills/[name]/SKILL.md in this vault. The wiki ships with /brain-ingest, /brain-search, /brain-refresh, /brain-rebuild, /lint, /setup, and /qmd-cli pre-installed.

Update built-in wiki skills

Pull the latest skills from the upstream template:

# Install or update all 7 wiki skills
npx skills add https://github.com/jessepinkman9900/claude-second-brain/tree/main/template/.claude/skills -a claude-code -y

# Or update a specific skill
npx skills add https://github.com/jessepinkman9900/claude-second-brain/tree/main/template/.claude/skills --skill brain-ingest -a claude-code -y

Once installed via npx skills, future updates are a single command:

npx skills update -a claude-code

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Re-indexing

After a bulk ingest session, re-index to keep search current:

/brain-refresh

This wraps pnpm qmd:reindex — you can also run that command directly if you're not inside Claude Code. Pass force to /brain-refresh to re-embed every chunk (e.g. after changing the embedding model).

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License

MIT