llm-wiki

name llm-wiki description Karpathy's LLM Wiki: build/query interlinked markdown KB. version 2.1.0 author Hermes Agent license MIT platforms ["linux","macos","windows"] metadata {"hermes":{"tags":["wiki","knowledge-base","research","notes","markdown","rag-alternative"],"category":"research","related_skills":["obsidian","arxiv"]}} Karpathy's LLM Wiki Build and maintain a persistent, compounding knowledge base as interlinked markdown files. Based on Andrej Karpathy's LLM Wiki pattern . Unlike traditional RAG (which rediscovers knowledge from scratch per query), the wiki compiles knowledge once and keeps it current. Cross-references are already there. Contradictions have already been flagged. Synthesis reflects everything ingested. Division of labor: The human curates sources and directs analysis. The agent summarizes, cross-references, files, and maintains consistency. When This Skill Activates Use this skill when the user: Asks to create, build, or start a wiki or knowledge base Asks to ingest, add, or process a source into their wiki Asks a question and an existing wiki is present at the configured path Asks to lint, audit, or health-check their wiki References their wiki, knowledge base, or "notes" in a research context Wiki Location Location: Set via WIKI_PATH environment variable (e.g. in ${HERMES_HOME:-~/.hermes}/.env ). If unset, defaults to ~/wiki . WIKI= " ${WIKI_PATH:- $HOME /wiki} " The wiki is just a directory of markdown files — open it in Obsidian, VS Code, or any editor. No database, no special tooling required. Architecture: Three Layers wiki/ ├── SCHEMA.md # Conventions, structure rules, domain config ├── index.md # Sectioned content catalog with one-line summaries ├── log.md # Chronological action log (append-only, rotated yearly) ├── raw/ # Layer 1: Immutable source material │ ├── articles/ # Web articles, clippings │ ├── papers/ # PDFs, arxiv papers │ ├── transcripts/ # Meeting notes, interviews │ └── assets/ # Images, diagrams referenced by sources ├── entities/ # Layer 2: Entity pages (people, orgs, products, models) ├── concepts/ # Layer 2: Concept/topic pages ├── comparisons/ # Layer 2: Side-by-side analyses └── queries/ # Layer 2: Filed query results worth keeping Layer 1 — Raw Sources: Immutable. The agent reads but never modifies these. Layer 2 — The Wiki: Agent-owned markdown files. Created, updated, and cross-referenced by the agent. Layer 3 — The Schema: SCHEMA.md defines structure, conventions, and tag taxonomy. Resuming an Existing Wiki (CRITICAL — do this every session) When the user has an existing wiki, always orient yourself before doing anything : ① Read SCHEMA.md — understand the domain, conventions, and tag taxonomy. ② Read index.md — learn what pages exist and their summaries. ③ Scan recent log.md — read the last 20-30 entries to understand recent activity. WIKI= " ${WIKI_PATH:- $HOME /wiki} " # Orientation reads at session start read_file " $WIKI /SCHEMA.md" read_file " $WIKI /index.md" read_file " $WIKI /log.md" offset=<last 30 lines> Only after orientation should you ingest, query, or lint. This prevents: Creating duplicate pages for entities that already exist Missing cross-references to existing content Contradicting the schema's conventions Repeating work already logged For large wikis (100+ pages), also run a quick search_files for the topic at hand before creating anything new. Initializing a New Wiki When the user asks to create or start a wiki: Determine the wiki path (from $WIKI_PATH env var, or ask the user; default ~/wiki ) Create the directory structure above Ask the user what domain the wiki covers — be specific Write SCHEMA.md customized to the domain (see template below) Write initial index.md with sectioned header Write initial log.md with creation entry Confirm the wiki is ready and suggest first sources to ingest SCHEMA.md Template Adapt to the user's domain. The schema constrains agent behavior and ensures consistency: # Wiki Schema ## Domain [What this wiki covers — e.g., "AI/ML research", "personal health", "startup intelligence"] ## Conventions - File names: lowercase, hyphens, no spaces (e.g., `transformer-architecture.md` ) - Every wiki page starts with YAML frontmatter (see below) - Use `[[wikilinks]]` to link between pages (minimum 2 outbound links per page) - When updating a page, always bump the `updated` date - Every new page must be added to `index.md` under the correct section - Every action must be appended to `log.md` - **Provenance markers:** On pages that synthesize 3+ sources, append `^[raw/articles/source-file.md]` at the end of paragraphs whose claims come from a specific source. This lets a reader trace each claim back without re-reading the whole raw file. Optional on single-source pages where the `sources:` frontmatter is enough. ## Frontmatter ```yaml --- title: Page Title created: YYYY-MM-DD updated: YYYY-MM-DD type: entity | concept | comparison | query | summary tags: [from taxonomy below] sources: [raw/articles/source-name.md] # Optional quality signals: confidence: high | medium | low # how well-supported the claims are contested: true # set when the page has unresolved contradictions contradictions: [other-page-slug] # pages this one conflicts with --- confidence and contested are optional but recommended for opinion-heavy or fast-moving topics. Lint surfaces contested: true and confidence: low pages for review so weak claims don't silently harden into accepted wiki fact. raw/ Frontmatter Raw sources ALSO get a small frontmatter block so re-ingests can detect drift: --- source_url: https://example.com/article # original URL, if applicable ingested: YYYY-MM-DD sha256: <hex digest of the raw content below the frontmatter> --- The sha256: lets a future re-ingest of the same URL skip processing when content is unchanged, and flag drift when it has changed. Compute over the body only (everything after the closing --- ), not the frontmatter itself. Tag Taxonomy [Define 10-20 top-level tags for the domain. Add new tags here BEFORE using them.] Example for AI/ML: Models: model, architecture, benchmark, training People/Orgs: person, company, lab, open-source Techniques: optimization, fine-tuning, inference, alignment, data Meta: comparison, timeline, controversy, prediction Rule: every tag on a page must appear in this taxonomy. If a new tag is needed, add it here first, then use it. This prevents tag sprawl. Page Thresholds Create a page when an entity/concept appears in 2+ sources OR is central to one source Add to existing page when a source mentions something already covered DON'T create a page for passing mentions, minor details, or things outside the domain Split a page when it exceeds ~200 lines — break into sub-topics with cross-links Archive a page when its content is fully superseded — move to _archive/ , remove from index Entity Pages One page per notable entity. Include: Overview / what it is Key facts and dates Relationships to other entities ([[wikilinks]]) Source references Concept Pages One page per concept or topic. Include: Definition / explanation Current state of knowledge Open questions or debates Related concepts ([[wikilinks]]) Comparison Pages Side-by-side analyses. Include: What is being compared and why Dimensions of comparison (table format preferred) Verdict or synthesis Sources Update Policy When new information conflicts with existing content: Check the dates — newer sources generally supersede older ones If genuinely contradictory, note both positions with dates and sources Mark the contradiction in frontmatter: contradictions: [page-name] Flag for user review in the lint report ### index.md Template The index is sectioned by type. Each entry is one line: wikilink + summary. ```markdown # Wiki Index > Content catalog. Every wiki page listed under its type with a one-line summary. > Read this first to find relevant pages for any query. > Last updated: YYYY-MM-DD | Total pages: N ## Entities <!-- Alphabetical within section --> ## Concepts ## Comparisons ## Queries Scaling rule: When any section exceeds 50 entries, split it into sub-sections by first letter or sub-domain. When the index exceeds 200 entries total, create a _meta/topic-map.md that groups pages by theme for faster navigation. log.md Template # Wiki Log > Chronological record of all wiki actions. Append-only. > Format: `## [YYYY-MM-DD] action | subject` > Actions: ingest, update, query, lint, create, archive, delete > When this file exceeds 500 entries, rotate: rename to log-YYYY.md, start fresh. ## [YYYY-MM-DD] create | Wiki initialized - Domain: [domain] - Structure created with SCHEMA.md, index.md, log.md Core Operations 1. Ingest When the user provides a source (URL, file, paste), integrate it into the wiki: ① Capture the raw source: URL → use web_extract to get markdown, save to raw/articles/ PDF → use web_extract (handles PDFs), save to raw/papers/ Pasted text → save to appropriate raw/ subdirectory Name the file descriptively: raw/articles/karpathy-llm-wiki-2026.md Add raw frontmatter ( source_url , ingested , sha256 of the body). On re-ingest of the same URL: recompute the sha256, compare to the stored value — skip if identical, flag drift and update if different. This is cheap enough to do on every re-ingest and catches silent source changes. ② Discuss takeaways with the user — what's interesting, what matters for the domain. (Skip this in automated/cron contexts — proceed directly.) ③ Check what already exists — search index.md and use search_files to find existing pages for mentioned entities/concepts. This is the difference between a growing wiki and a pile of duplicates. ④ Write or update wiki pages: New entities/concepts: Create pages only if they meet the Page Thresholds in SCHEMA.md (2+ source mentions, or central to one source) Existing pages: Add new information, update facts, bump updated date. When new info contradicts existing content, follow the Update Policy. Cross-reference: Every new or updated page must link to at least 2 other pages via [[wikilinks]] . Check that existing pages link back. Tags: Only use tags from the taxonomy in SCHEMA.md Provenance: On pages synthesizing 3+ sources, append ^[raw/articles/source.md] markers to paragraphs whose claims trace to a specific source. Confidence: For opinion-heavy, fast-moving, or single-source claims, set confidence: medium or low in frontmatter. Don't mark high unless the claim is well-supported across multiple sources. ⑤ Update navigation: Add new pages to index.md under the correct section, alphabetically Update the "Total pages" count and "Last updated" date in index header Append to log.md : ## [YYYY-MM-DD] ingest | Source Title List every file created or updated in the log entry ⑥ Report what changed — list every file created or updated to the user. A single source can trigger updates across 5-15 wiki pages. This is normal and desired — it's the compounding effect. 2. Query When the user asks a question about the wiki's domain: ① Read index.md to identify relevant pages. ② For wikis with 100+ pages , also search_files across all .md files for key terms — the index alone may miss relevant content. ③ Read the relevant pages using read_file . ④ Synthesize an answer from the compiled knowledge. Cite the wiki pages you drew from: "Based on [[page-a]] and [[page-b]]..." ⑤ File valuable answers back — if the answer is a substantial comparison, deep dive, or novel synthesis, create a page in queries/ or comparisons/ . Don't file trivial lookups — only answers that would be painful to re-derive. ⑥ Update log.md with the query and whether it was filed. 3. Lint When the user asks to lint, health-check, or audit the wiki: ① Orphan pages: Find pages with no inbound [[wikilinks]] from other pages. # Use execute_code for this — programmatic scan across all wiki pages import os, re from collections import defaultdict wiki = "<WIKI_PATH>" # Scan all .md files in entities/, concepts/, comparisons/, queries/ # Extract all [[wikilinks]] — build inbound link map # Pages with zero inbound links are orphans ② Broken wikilinks: Find [[links]] that point to pages that don't exist. ③ Index completeness: Every wiki page should appear in index.md . Compare the filesystem against index entries. ④ Frontmatter validation: Every wiki page must have all required fields (title, created, updated, type, tags, sources). Tags must be in the taxonomy. ⑤ Stale content: Pages whose updated date is >90 days older than the most recent source that mentions the same entities. ⑥ Contradictions: Pages on the same topic with conflicting claims. Look for pages that share tags/entities but state different facts. Surface all pages with contested: true or contradictions: frontmatter for user review. ⑦ Quality signals: List pages with confidence: low and any page that cites only a single source but has no confidence field set — these are candidates for either finding corroboration or demoting to confidence: medium . ⑧ Source drift: For each file in raw/ with a sha256: frontmatter, recompute the hash and flag mismatches. Mismatches indicate the raw file was edited (shouldn't happen — raw/ is immutable) or ingested from a URL that has since changed. Not a hard error, but worth reporting. ⑨ Page size: Flag pages over 200 lines — candidates for splitting. ⑩ Tag audit: List all tags in use, flag any not in the SCHEMA.md taxonomy. ⑪ Log rotation: If log.md exceeds 500 entries, rotate it. ⑫ Report findings with specific file paths and suggested actions, grouped by severity (broken links > orphans > source drift > contested pages > stale content > style issues). ⑬ Append to log.md: ## [YYYY-MM-DD] lint | N issues found Working with the Wiki Searching # Find pages by content search_files "transformer" path= " $WIKI " file_glob= "*.md" # Find pages by filename search_files "*.md" target= "files" path= " $WIKI " # Find pages by tag search_files "tags:.*alignment" path= " $WIKI " file_glob= "*.md" # Recent activity read_file " $WIKI /log.md" offset=<last 20 lines> Bulk Ingest When ingesting multiple sources at once, batch the updates: Read all sources first Identify all entities and concepts across all sources Check existing pages for all of them (one search pass, not N) Create/update pages in one pass (avoids redundant updates) Update index.md once at the end Write a single log entry covering the batch Archiving When content is fully superseded or the domain scope changes: Create _archive/ directory if it doesn't exist Move the page to _archive/ with its original path (e.g., _archive/entities/old-page.md ) Remove from index.md Update any pages that linked to it — replace wikilink with plain text + "(archived)" Log the archive action Obsidian Integration The wiki directory works as an Obsidian vault out of the box: [[wikilinks]] render as clickable links Graph View visualizes the knowledge network YAML frontmatter powers Dataview queries The raw/assets/ folder holds images referenced via ![[image.png]] For best results: Set Obsidian's attachment folder to raw/assets/ Enable "Wikilinks" in Obsidian settings (usually on by default) Install Dataview plugin for queries like TABLE tags FROM "entities" WHERE contains(tags, "company") If using the Obsidian skill alongside this one, set OBSIDIAN_VAULT_PATH to the same directory as the wiki path. Obsidian Headless (servers and headless machines) On machines without a display, use obsidian-headless instead of the desktop app. It syncs vaults via Obsidian Sync without a GUI — perfect for agents running on servers that write to the wiki while Obsidian desktop reads it on another device. Setup: # Requires Node.js 22+ npm install -g obsidian-headless # Login (requires Obsidian account with Sync subscription) ob login --email <email> --password '<password>' # Create a remote vault for the wiki ob sync-create-remote --name "LLM Wiki" # Connect the wiki directory to the vault cd ~/wiki ob sync-setup --vault "<vault-id>" # Initial sync ob sync # Continuous sync (foreground — use systemd for background) ob sync --continuous Continuous background sync via systemd: # ~/.config/systemd/user/obsidian-wiki-sync.service [Unit] Description =Obsidian LLM Wiki Sync After =network- on line.target Wants =network- on line.target [Service]