/second-brain

name: second-brain
description: When you want to capture into, compile, query, lint, or connect your personal Second Brain. Wraps the Karpathy LLM Wiki schema (Obsidian or any markdown vault) — raw/ (unprocessed sources), wiki/ (AI-compiled interlinked topic pages), outputs/ (generated artifacts). Tool-agnostic in design but defaults to a vault at ${SECOND_BRAIN_VAULT:-$HOME/Documents/SecondBrain}/. Six modes — capture (drop something into raw/), compile (process unprocessed raw files into wiki pages, update INDEX.md), query (answer a question from the wiki, save to outputs/), lint (orphans / contradictions / stale / unprocessed raw / topic gaps), connect (suggest new wikilinks between pages), search (quick lookup). Triggers on "/second-brain," "/sb," "capture this," "save this to my brain," "compile the wiki," "process raw notes," "query my wiki," "ask my brain," "lint the wiki," "find connections," "search my notes." Complements deep-research (external corpus) — this is the internal corpus.
metadata:
  version: 0.2.1

/second-brain — Karpathy LLM Wiki workflow

Wraps an existing Second Brain in Obsidian (or any markdown-based vault). The wiki vault's schema doc (`CLAUDE.md` or `AGENTS.md`) is the authoritative schema — the skill orchestrates the operations the user has been doing manually.

Mental model

Three layers, each with a clear role:

raw/      →  wiki/         →  outputs/
sources      compiled         generated
                              artifacts

• **raw/** — unprocessed source material. Articles, highlights, ideas, braindumps, tweets. Type-prefixed (`article-`, `idea-`, `highlights-`, `braindump-`, `note-`, `resource-`, `tweet-`). Never deleted — source of truth.
• **wiki/** — AI-compiled topic pages. One page per concept, not per source. Interlinked via `[[wikilinks]]`. `INDEX.md` at root.
• **outputs/** — generated artifacts from queries: research summaries, analyses, slide decks. Named descriptively.

Folders to leave alone during wiki ops: `Projects/`, `Daily/`, `Templates/`, `Inbox/`, `Notes/`, `Tasks.md`, `Kanban.md`, `Home.md`.

Step 1 — Load vault config + schema

1. Read `references/vault-config.md` for the vault path (default: `${SECOND_BRAIN_VAULT:-$HOME/Documents/SecondBrain}/`) 2. Read the vault's schema doc — `<vault>/CLAUDE.md` or `<vault>/AGENTS.md`, whichever exists (if both, read both) — for the authoritative schema. If present, trust it over `references/schema.md` — the user's vault is the source of truth. 3. If neither exists, fall back to `references/schema.md`.

Step 2 — Parse mode

| Invocation | Mode | |---|---| | `/sb capture` / `/second-brain capture` / "capture this" / "save this to my brain" | **capture** | | `/sb compile` / "compile the wiki" / "process raw notes" | **compile** | | `/sb query <question>` / "ask my brain X" / "what does my brain say about Y" | **query** | | `/sb lint` / "lint the wiki" / "health check my brain" | **lint** | | `/sb connect` / "find connections" / "suggest wikilinks" | **connect** | | `/sb search <term>` / "search my notes for X" | **search** |

Step 3 — Run the mode

capture

Inputs: URL, pasted text, file path, or screenshot.

1. **Detect type** from content:

• URL → `article-`
• Pasted text with quoted highlights → `highlights-`
• User's own thoughts / brainstorm → `braindump-` or `idea-`
• Single tweet / X post → `tweet-`
• PDF, video, podcast → `resource-`
• Quick reference (recipe, command, fact) → `note-`
• If ambiguous, ask.

2. **Generate a descriptive filename**: `<type>-<kebab-case-topic>.md` (e.g., `article-andrew-wilkinson-tiny-manual.md`). Use the source title or topic — not the URL slug. 3. **Add metadata to the top:**

   source: <URL if applicable>
   captured: YYYY-MM-DD

4. **Save to `<vault>/raw/`**. 5. If the source is a URL, fetch the article content (your agent's URL fetch, or agent-browser for auth-walled pages) and save the readable text — not just the URL. 6. **Report** path + a one-line summary of what was saved.

Don't compile into the wiki here — capture is fast intake. Compilation is a separate, deliberate pass.

compile

The expensive but valuable operation. Process unprocessed raw files into wiki pages.

1. **Find unprocessed raw files**: grep `wiki/*.md` for `Sources` sections; the raw files NOT listed are unprocessed. 2. **Read each unprocessed raw file** + the existing `wiki/INDEX.md`. 3. **For each raw file**:

• Extract key concepts, facts, insights
• **Default: merge into an existing wiki page** if the topic overlaps. Only create a new page if the concept doesn't fit anywhere.
• **One page per concept, not per source.**
• Use `[[wikilinks]]` for every related concept
• Add the raw file under the wiki page's `## Sources` section with a one-line note on what was drawn from it

4. **Update `wiki/INDEX.md`**:

• Add new pages under their category (Creative / Health & Longevity / Faith & Personal Growth / Business / Personal Growth / Tech / Hobbies / Sci-Fi / Pets — or new category if needed)
• One line per entry: `- [[Page Name]] — brief description`

5. **Connections section is mandatory** on every wiki page. If a new page has no connections, find one before saving. 6. **Quality > quantity.** If a page would be <100 words, hold the raw file for now and ask the user if it should be merged into an adjacent page.

Output: list of pages created/updated, what merged where, anything held for clarification.

query

Answer a question using ONLY the wiki/raw corpus. Different from `deep-research` (which goes external).

1. **Read `wiki/INDEX.md`** to identify potentially relevant pages 2. **Read those pages** + traverse `[[wikilinks]]` 1–2 hops 3. **Compose the answer**:

• Cite wiki pages by name: *"Per [[Microplastics Detox]]..."*
• If the wiki contradicts itself, surface both sides
• If the wiki doesn't contain the answer, say so and offer to run `/deep-research` to expand

4. **