Use when building, querying, or maintaining a Karpathy-style interlinked markdown knowledge base for LLM notes, research synthesis, and lightweight RAG alternatives.
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name
llm-wiki
description
Use when building, querying, or maintaining a Karpathy-style interlinked markdown knowledge base for LLM notes, research synthesis, and lightweight RAG alternatives.
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.
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.
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 applicableingested:YYYY-MM-DDsha256:<hexdigestoftherawcontentbelowthefrontmatter>---
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
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 pagesimport 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 vaultcd ~/wiki
ob sync-setup --vault "<vault-id>"# Initial sync
ob sync# Continuous sync (foreground — use systemd for background)
ob sync --continuous
This lets the agent write to ~/wiki on a server while you browse the same
vault in Obsidian on your laptop/phone — changes appear within seconds.
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.
Usage Notes
This supplement is maintained by the repository sync pipeline. It keeps the
imported upstream skill usable inside this curated collection when the upstream
source is intentionally concise.
Common Patterns
1. Confirm that the user's task matches the skill trigger.
2. Read the relevant project files or user-provided context before acting.
3. Choose the smallest reversible action that advances the task.
4. Run the verification command or manual check that proves the result.
5. Report the outcome, evidence, and any remaining risk.
Boundaries
Prefer the upstream workflow for Llm Wiki; this section only adds local quality
guardrails.
Do not invent project facts when required files, vaults, services, or tools are
unavailable.
Stop and ask for clarification when the next action could overwrite user work,
expose private data, or change production state.
