llm-wiki

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

~/.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

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

index.md

log.md

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

Initializing a New Wiki

When the user asks to create or start a wiki:

1. Determine the wiki path (from

   $WIKI_PATH

   env var, or ask the user; default

   ~/wiki

   )
2. Create the directory structure above
3. Ask the user what domain the wiki covers — be specific
4. Write

   SCHEMA.md

   customized to the domain (see template below)
5. Write initial

   index.md

   with sectioned header
6. Write initial

   log.md

   with creation entry
7. 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

contested

contested: true

confidence: low

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:

---

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:

1. Check the dates — newer sources generally supersede older ones
2. If genuinely contradictory, note both positions with dates and sources
3. Mark the contradiction in frontmatter:

   contradictions: [page-name]

4. 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

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

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

search_files

.md

read_file

queries/

comparisons/

3. Lint

When the user asks to lint, health-check, or audit the wiki:

① Orphan pages: Find pages with no inbound

[[wikilinks]]

# 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]]

③ Index completeness: Every wiki page should appear in

index.md

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

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

contradictions:

⑦ Quality signals: List pages with

confidence: low

confidence: medium

⑧ Source drift: For each file in

raw/

sha256:

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:

1. Read all sources first
2. Identify all entities and concepts across all sources
3. Check existing pages for all of them (one search pass, not N)
4. Create/update pages in one pass (avoids redundant updates)
5. Update index.md once at the end
6. Write a single log entry covering the batch

Archiving

When content is fully superseded or the domain scope changes:

1. Create

   _archive/

   directory if it doesn't exist
2. Move the page to

   _archive/

   with its original path (e.g.,

   _archive/entities/old-page.md

   )
3. Remove from

   index.md

4. Update any pages that linked to it — replace wikilink with plain text + "(archived)"
5. 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

Obsidian Headless (servers and headless machines)

On machines without a display, use

obsidian-headless

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-online.target
Wants=network-online.target

[Service]
ExecStart=/path/to/ob sync --continuous
WorkingDirectory=/home/user/wiki
Restart=on-failure
RestartSec=10

[Install]
WantedBy=default.target

systemctl --user daemon-reload
systemctl --user enable --now obsidian-wiki-sync
# Enable linger so sync survives logout:
sudo loginctl enable-linger $USER

This lets the agent write to

~/wiki

Pitfalls

• Never modify files in

  raw/

  — sources are immutable. Corrections go in wiki pages.
• Always orient first — read SCHEMA + index + recent log before any operation in a new session. Skipping this causes duplicates and missed cross-references.
• Always update index.md and log.md — skipping this makes the wiki degrade. These are the navigational backbone.
• Don't create pages for passing mentions — follow the Page Thresholds in SCHEMA.md. A name appearing once in a footnote doesn't warrant an entity page.
• Don't create pages without cross-references — isolated pages are invisible. Every page must link to at least 2 other pages.
• Frontmatter is required — it enables search, filtering, and staleness detection.
• Tags must come from the taxonomy — freeform tags decay into noise. Add new tags to SCHEMA.md first, then use them.
• Keep pages scannable — a wiki page should be readable in 30 seconds. Split pages over 200 lines. Move detailed analysis to dedicated deep-dive pages.
• Ask before mass-updating — if an ingest would touch 10+ existing pages, confirm the scope with the user first.
• Rotate the log — when log.md exceeds 500 entries, rename it

  log-YYYY.md

  and start fresh. The agent should check log size during lint.
• Handle contradictions explicitly — don't silently overwrite. Note both claims with dates, mark in frontmatter, flag for user review.

Related Tools

llm-wiki-compiler is a Node.js CLI that compiles sources into a concept wiki with the same Karpathy inspiration. It's Obsidian-compatible, so users who want a scheduled/CLI-driven compile pipeline can point it at the same vault this skill maintains. Trade-offs: it owns page generation (replaces the agent's judgment on page creation) and is tuned for small corpora. Use this skill when you want agent-in-the-loop curation; use llmwiki when you want batch compile of a source directory.