/llm-wiki

name: llm-wiki
description: "Use when building or maintaining an Obsidian second brain that an LLM keeps up to date, or when ingesting a paper, article or book into it. Ingests with ingest_source.py, maintains index and links and checks the vault with lint_wiki.py."
context: fork
license: MIT
metadata:
  version: 2.9.0
  author: claude-code-skills
  tags: [knowledge-management, obsidian, second-brain, pkm, rag-alternative, wiki, karpathy, memex]
  compatible_tools: [claude-code, codex-cli, cursor, antigravity, opencode, gemini-cli]

LLM Wiki — Second Brain for Claude Code + Obsidian

Inspired by Andrej Karpathy's LLM Wiki pattern ([gist](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f)). This skill turns Claude Code (or any agent CLI) into a disciplined wiki maintainer that **incrementally builds and maintains** a persistent, interlinked Obsidian vault as you feed it sources. The knowledge compounds — cross-references, contradictions, and synthesis are already there when you query.

Core principle

Most LLM+docs workflows are **RAG**: retrieve fragments at query time, synthesize from scratch, forget. The wiki is **compounding**: sources are read once, integrated into a persistent markdown knowledge base, and kept current. You curate and ask; the LLM reads, files, cross-references, and maintains.

> Obsidian is the IDE. The LLM is the programmer. The wiki is the codebase.

When to use

• **Personal**: track goals, health, psychology, journaling, self-improvement
• **Research**: deep dives over weeks on a topic — papers, articles, reports, evolving thesis
• **Book companion**: file chapters as you read; build a fan-wiki-style companion for characters, themes, plot threads
• **Business/team**: internal wiki fed by Slack, meeting notes, calls — LLM does maintenance nobody else wants to do
• **Competitive analysis, due diligence, trip planning, course notes, hobby deep-dives**

**Do NOT use when:** you need one-shot Q&A over a fixed document (use RAG), you don't plan to add sources over time, or you don't want Obsidian in the loop.

Architecture (three layers)

vault/
├── raw/                    # Layer 1 — IMMUTABLE source of truth
│   ├── <source files>      # Articles, papers, PDFs, images, data
│   └── assets/             # Downloaded images from clipped articles
├── wiki/                   # Layer 2 — LLM-owned knowledge base
│   ├── index.md            # Content catalog (LLM updates every ingest)
│   ├── log.md              # Append-only timeline (## [YYYY-MM-DD] <op> | <title>)
│   ├── entities/           # Person/Org/Place pages
│   ├── concepts/           # Ideas, theories, frameworks
│   ├── sources/            # One summary page per ingested source
│   ├── comparisons/        # Cross-source analysis pages
│   └── synthesis/          # High-level syntheses, theses, overviews
├── CLAUDE.md               # Schema + conventions (Claude Code)
└── AGENTS.md               # Same content, for Codex/Cursor/Antigravity

• **Layer 1 (raw/)** — you own. LLM only reads; never writes.
• **Layer 2 (wiki/)** — LLM owns. It creates, updates, and cross-references pages. You read it.
• **Layer 3 (CLAUDE.md / AGENTS.md)** — the *schema*. Conventions, workflows, frontmatter rules. Co-evolved by you and the LLM.

Three core operations

1. **Ingest** — LLM reads a source, discusses takeaways with you, writes a source summary, updates 10-15 relevant pages, updates index, appends to log. See `references/ingest-workflow.md`. 2. **Query** — LLM reads `index.md` first, drills into relevant pages, synthesizes with citations. Good answers get **filed back into the wiki** so explorations compound. See `references/query-workflow.md`. 3. **Lint** — Health check: contradictions, stale claims, orphan pages, missing cross-refs, concepts mentioned but lacking their own page, data gaps to fill with web search. See `references/lint-workflow.md`.

Quick start

# 1. Initialize a vault (in Obsidian's vault directory)
python scripts/init_vault.py --path ~/vaults/research --topic "LLM interpretability"

# 2. Drop a source into raw/, then ingest
/wiki-ingest ~/vaults/research/raw/anthropic-monosemanticity.pdf

# 3. Ask questions (answers can be re-filed into the wiki)
/wiki-query "how does monosemanticity compare to mechanistic interpretability?"

# 4. Periodic health check
/wiki-lint

# 5. See the timeline
/wiki-log --last 10

Slash commands (this plugin ships)

| Command | Purpose | |---|---| | `/wiki-init` | Bootstrap a fresh vault with schema files + starter structure | | `/wiki-ingest <path>` | Read a source, discuss, update wiki, log it | | `/wiki-query <question>` | Search wiki, synthesize answer, offer to file back | | `/wiki-lint` | Run health check — contradictions, orphans, stale claims, gaps | | `/wiki-log` | Show recent log entries (uses unix tools on `log.md`) |

Sub-agents (this plugin ships)

| Agent | When dispatched | |---|---| | `wiki-ingestor` | Delegated ingest flow — reads source, proposes updates, applies after your approval | | `wiki-linter` | Runs the health-check workflow independently, reports findings | | `wiki-librarian` | Answers queries using index-first search, synthesizes with citations |

Python tools (`scripts/`)

All tools are **standard library only** (no pip installs). Run with `python scripts/<tool>.py --help`.

| Script | Purpose | |---|---| | `init_vault.py` | Create folder structure + seed CLAUDE.md, AGENTS.md, index.md, log.md | | `ingest_source.py` | Helper: extract text/frontmatter from a source file, ready for LLM review | | `update_index.py` | Regenerate `index.md` from wiki page frontmatter (category, date, source count) | | `append_log.py` | Append a standardized log entry `## [YYYY-MM-DD] <op> \| <title>` | | `wiki_search.py` | BM25 search over wiki pages (standalone fallback when index.md isn't enough) | | `lint_wiki.py` | Find orphans (no inbound links), stale pages, missing cross-refs, broken links | |