/second-brain — Karpathy LLM Wiki workflow

Wraps an existing Second Brain in Obsidian (or any markdown-based vault). The wiki vault's CLAUDE.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

Read

references/vault-config.md

for the vault path (default:

${SECOND_BRAIN_VAULT:-$HOME/Documents/SecondBrain}/

)

Read
```
<vault>/CLAUDE.md
```
for the authoritative schema. If present, trust it over
```
references/schema.md
```
— the user's vault is the source of truth.
If no
```
<vault>/CLAUDE.md
```
, 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.

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.
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.

Add metadata to the top:

markdown

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

Save to
<vault>/raw/
.
If the source is a URL, fetch the article content (via WebFetch or agent-browser for auth-walled) and save the readable text — not just the URL.
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.

Find unprocessed raw files: grep
```
wiki/*.md
```
for
```
Sources
```
sections; the raw files NOT listed are unprocessed.
Read each unprocessed raw file + the existing
```
wiki/INDEX.md
```
.
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
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
```
Connections section is mandatory on every wiki page. If a new page has no connections, find one before saving.
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).

Read
wiki/INDEX.md
to identify potentially relevant pages
Read those pages + traverse
```
[[wikilinks]]
```
1–2 hops
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
Save to
outputs/<YYYY-MM-DD>-<question-slug>.md
with:
- The original question
- The answer
- List of wiki pages consulted
Show the answer in chat + path to the saved output
Optional render: if
```
--render pdf
```
or
```
--render html
```
was passed, pipe the output through pandoc using the shared stylesheet. See
```
references/schema.md
```
→ "Publishing alternatives" for the commands.

lint

Health check the wiki.

Check:

Orphan pages — wiki/*.md that aren't in INDEX.md
Connection orphans — pages with no
```
[[wikilinks]]
```
to other pages
Unprocessed raw — raw files not listed under any wiki page's Sources
Stale pages — most recent source >6 months old AND topic is volatile (AI, marketing, finance, health protocols)
Topic gaps — concepts mentioned in 3+ pages without their own dedicated page
Contradictions — wiki pages making opposing claims without flagging it
Missing connections — pages on clearly related topics with no
```
[[wikilink]]
```
between them (suggest
```
/sb connect
```
)

Output: prioritized list. Most important first (broken structure beats stale content).

connect

Find pages that should be linked but aren't.

Build a topic map from INDEX.md + page summaries
For each page, find 2–5 other pages with thematic overlap
Check whether each candidate is already linked
Suggest the missing links — and if the user approves, edit the pages to add them to their
```
## Connections
```
sections

search

Quick grep across

wiki/

raw/

for a term. Return matching files with a 2-line excerpt around the match. Faster than

query

when the user knows what page they're looking for.

Composes with

```
deep-research
```
— when
```
query
```
finds gaps in the wiki, route to deep-research to expand from external sources. Deep-research output can be captured back into
```
raw/
```
for future compilation.
```
paste
```
— capture content cleanly into
```
raw/
```
(especially for terminal/CLI captures).

business-brainstorm

— checks

Portfolio of Businesses

and

Entrepreneurship & Startups

wiki pages for relevant context before brainstorming.

```
decide
```
— pull from
```
Personal Philosophy
```
/
```
Productivity & Systems
```
wiki for principles when scoring Q34 ("what principles are we bending"). New: a
```
Decision Log
```
wiki page accumulates the narrative form of decisions over time (the
```
decide
```
archive is the structured form; the wiki page is the story).
```
jab-hook
```
— a
```
Content Ideas
```
wiki page hoppers hooks, frameworks, and stories.
```
/jab-hook
```
drafts pull candidates from there.
```
slide-deck
```
— content drafted in
```
outputs/
```
becomes deck source; speaker notes can reference relevant wiki pages.
```
pm
```
— Projects/ folder in the vault is off-limits to second-brain; pm owns it. But a
```
Workflow Docs
```
wiki page captures operational patterns that show up across multiple projects.

Sibling implementations (reference)

Two other systems following the same raw → wiki → outputs pattern. Both are worth watching as upgrade paths.

Hermes'
llm-wiki
skill — off-the-shelf implementation of the 3-folder pattern. Pre-built workflows for compile / query / lint. Useful for comparing schema decisions.
Gbrain by Garry Tan — much more sophisticated. Treats the brain as a database (Postgres or PGLite) with synthesis, graph traversal, gap analysis, scheduled cron maintenance, and MCP integration. Powers a 146K-page deployment with 24K people entities. If the user's vault outgrows the markdown-only pattern, Gbrain is the upgrade direction. Borrows worth adopting today even without migrating: people-as-entities (the
```
person-
```
raw type +
```
People
```
wiki page) and scheduled maintenance (wire
```
compile
```
and
```
lint
```
to fire on a recurring schedule via the
```
loop
```
or
```
compound-engineering:schedule
```
skill).

Notes on quality

Quality over quantity. Fewer well-connected wiki pages beat many thin ones. Hold raw files for clarification if compilation would produce a thin page.
Don't flatten nuance. If two raw sources contradict, the wiki page should note the disagreement, not pick a side silently.
Connections section is mandatory — every wiki page must link to at least one other page.
Never delete raw files after compilation. They're the source of truth.
Never modify files in
```
Projects/
```
,
```
Daily/
```
,
```
Templates/
```
,
```
Notes/
```
,
```
Tasks.md
```
,
```
Kanban.md
```
,
```
Home.md
```
, or
```
Inbox/
```
during second-brain operations. Those belong to other workflows.

second-brain

NPX Install

Tags

SKILL.md Content

/second-brain — Karpathy LLM Wiki workflow

Mental model

Step 1 — Load vault config + schema

Step 2 — Parse mode

Step 3 — Run the mode

capture

compile

query

lint

connect

search

Composes with

Sibling implementations (reference)

Notes on quality

Notes on quality