) │ ├── 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 ```bash # 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 | | `graph_analyzer.py` | Compute link graph stats — hubs, orphans, clusters, disconnected components | | `export_marp.py` | Render a wiki page (or subtree) to a Marp slide deck | ## Cross-tool compatibility The vault's **schema** lives in CLAUDE.md (Claude Code) or AGENTS.md (Codex/Cursor/Antigravity/OpenCode). The same content works in both. This plugin ships both templates. For per-tool setup instructions see `references/cross-tool-setup.md`. ``` CLAUDE.md → Claude Code AGENTS.md → Codex CLI, Cursor, Antigravity, OpenCode, Gemini CLI .cursorrules → legacy Cursor (pre-AGENTS.md) ``` The scripts are pure Python stdlib → run identically everywhere. Only the loader file changes per tool. ## Obsidian setup (recommended) - **Obsidian Web Clipper** — browser extension; converts web articles to markdown and drops them in `raw/` - **Download images locally** — Settings → Files and links → Attachment folder path = `raw/assets/`. Settings → Hotkeys → bind "Download attachments for current file" to `Ctrl+Shift+D` - **Graph view** — see hubs/orphans; essential for spotting structural problems - **Marp plugin** — Markdown-based slide decks directly from wiki pages - **Dataview plugin** — dynamic tables/lists over page frontmatter (tags, dates, source counts) - **Git** — the vault is a plain markdown repo; version it Full setup walkthrough: `references/obsidian-setup.md` ## Why this works (vs plain RAG) | Plain RAG | LLM Wiki | |---|---| | Rediscover knowledge each query | Knowledge accumulates | | Cross-references re-computed every time | Cross-references pre-written and maintained | | Contradictions surface only if you ask | Contradictions flagged during ingest | | Exploration disappears into chat history | Good answers re-filed as new pages | | Scales by embeddings infrastructure | Scales by markdown + `index.md` + optional local search | At ~100 sources / hundreds of pages, `index.md` + filesystem search is enough. Past that, layer in a local search tool like [qmd](https://github.com/tobi/qmd) or use `scripts/wiki_search.py`. ## Related skills (chains via `context: fork`) This skill is marked `context: fork` so other skills can chain into it: - **`para-memory-files`** — PARA-method memory; complementary as long-term personal memory that feeds sources into the wiki - **`obsidian-vault`** (mattpocock) — lightweight Obsidian note helper; this skill is the maintained-wiki layer on top - **`rag-design`** — when wiki outgrows ~500 pages, use rag-design to bolt on a retrieval layer - **`mcp-design`** — expose the wiki as an MCP tool - **`agent-communication`** — for multi-agent wiki maintenance (ingestor + linter + librarian) ## Reference docs - `references/wiki-schema.md` — full vault layout, page frontmatter, naming conventions - `references/page-formats.md` — entity, concept, source, comparison, synthesis templates - `references/ingest-workflow.md` — the detailed ingest flow the wiki-ingestor agent follows - `references/query-workflow.md` — query patterns, citation format, re-filing answers - `references/lint-workflow.md` — health-check heuristics - `references/obsidian-setup.md` — Obsidian plugins, hotkeys, vault config - `references/cross-tool-setup.md` — per-tool setup (Codex, Cursor, Antigravity, etc.) - `references/memex-principles.md` — Bush's Memex, why the LLM changes the maintenance math ## Templates (`assets/`) - `CLAUDE.md.template`, `AGENTS.md.template`, `.cursorrules.template` — schema loaders per tool - `index.md.template`, `log.md.template` — starter index and log - `page-templates/` — entity, concept, source-summary, comparison, synthesis - `example-vault/` — small worked example you can study or copy ## Iron rule **The LLM never edits files in `raw/`.** Ever. Sources are immutable. All LLM writes go to `wiki/`. If you need to correct a source, do it in `raw/` yourself

--- name: llm-wiki description: Use when building or maintaining a persistent personal knowledge base (second brain) in Obsidian where an LLM incrementally ingests sources, updates entity/concept pages, maintains cross-references, and keeps a synthesis current. Triggers include "second brain", "Obsidian wiki", "personal knowledge management", "ingest this paper/article/book", "build a research wiki", "compound knowledge", "Memex", or whenever the user wants knowledge to accumulate across sessions instead of being re-derived by RAG on every query. context: fork version: 1.0.0 author: claude-code-skills license: MIT 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 │ ├── # 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] | ) │ ├── 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 ```bash # 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 | | `graph_analyzer.py` | Compute link graph stats — hubs, orphans, clusters, disconnected components | | `export_marp.py` | Render a wiki page (or subtree) to a Marp slide deck | ## Cross-tool compatibility The vault's **schema** lives in CLAUDE.md (Claude Code) or AGENTS.md (Codex/Cursor/Antigravity/OpenCode). The same content works in both. This plugin ships both templates. For per-tool setup instructions see `references/cross-tool-setup.md`. ``` CLAUDE.md → Claude Code AGENTS.md → Codex CLI, Cursor, Antigravity, OpenCode, Gemini CLI .cursorrules → legacy Cursor (pre-AGENTS.md) ``` The scripts are pure Python stdlib → run identically everywhere. Only the loader file changes per tool. ## Obsidian setup (recommended) - **Obsidian Web Clipper** — browser extension; converts web articles to markdown and drops them in `raw/` - **Download images locally** — Settings → Files and links → Attachment folder path = `raw/assets/`. Settings → Hotkeys → bind "Download attachments for current file" to `Ctrl+Shift+D` - **Graph view** — see hubs/orphans; essential for spotting structural problems - **Marp plugin** — Markdown-based slide decks directly from wiki pages - **Dataview plugin** — dynamic tables/lists over page frontmatter (tags, dates, source counts) - **Git** — the vault is a plain markdown repo; version it Full setup walkthrough: `references/obsidian-setup.md` ## Why this works (vs plain RAG) | Plain RAG | LLM Wiki | |---|---| | Rediscover knowledge each query | Knowledge accumulates | | Cross-references re-computed every time | Cross-references pre-written and maintained | | Contradictions surface only if you ask | Contradictions flagged during ingest | | Exploration disappears into chat history | Good answers re-filed as new pages | | Scales by embeddings infrastructure | Scales by markdown + `index.md` + optional local search | At ~100 sources / hundreds of pages, `index.md` + filesystem search is enough. Past that, layer in a local search tool like [qmd](https://github.com/tobi/qmd) or use `scripts/wiki_search.py`. ## Related skills (chains via `context: fork`) This skill is marked `context: fork` so other skills can chain into it: - **`para-memory-files`** — PARA-method memory; complementary as long-term personal memory that feeds sources into the wiki - **`obsidian-vault`** (mattpocock) — lightweight Obsidian note helper; this skill is the maintained-wiki layer on top - **`rag-design`** — when wiki outgrows ~500 pages, use rag-design to bolt on a retrieval layer - **`mcp-design`** — expose the wiki as an MCP tool - **`agent-communication`** — for multi-agent wiki maintenance (ingestor + linter + librarian) ## Reference docs - `references/wiki-schema.md` — full vault layout, page frontmatter, naming conventions - `references/page-formats.md` — entity, concept, source, comparison, synthesis templates - `references/ingest-workflow.md` — the detailed ingest flow the wiki-ingestor agent follows - `references/query-workflow.md` — query patterns, citation format, re-filing answers - `references/lint-workflow.md` — health-check heuristics - `references/obsidian-setup.md` — Obsidian plugins, hotkeys, vault config - `references/cross-tool-setup.md` — per-tool setup (Codex, Cursor, Antigravity, etc.) - `references/memex-principles.md` — Bush's Memex, why the LLM changes the maintenance math ## Templates (`assets/`) - `CLAUDE.md.template`, `AGENTS.md.template`, `.cursorrules.template` — schema loaders per tool - `index.md.template`, `log.md.template` — starter index and log - `page-templates/` — entity, concept, source-summary, comparison, synthesis - `example-vault/` — small worked example you can study or copy ## Iron rule **The LLM never edits files in `raw/`.** Ever. Sources are immutable. All LLM writes go to `wiki/`. If you need to correct a source, do it in `raw/` yourself — then re-ingest.