LLM-Maintained Knowledge Base

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LLM-Maintained Knowledge Base

Complete Setup Guide for Andrej Karpathy's proposed setup

Andrej Karpathy recently proposed LLM Knowledge Bases, a system where an LLM acts as a librarian — ingesting raw sources, compiling a structured wiki, and answering complex queries against it. You rarely edit the wiki directly; the LLM owns it. Here is a quick setup guide to test this setup for yourself.

What we are setting up?

• The core loop is: ingest raw → compile wiki → query & enhance → repeat
• Obsidian is the viewer, the LLM is the writer
• Index files (_master-index.md, per-topic _index.md) replace the need for RAG at small-to-medium scale (~100 articles, ~400K words)
• Every query result can be filed back into the wiki, so exploration compounds over time
• CLAUDE.md is the instruction set that persists the LLM’s behavior across sessions

Architecture Overview

vault/
├── CLAUDE.md              # LLM instructions (the "constitution")
├── raw/                   # Inbox — dump source material here
│   └── _processed/        # Compiled files move here
├── wiki/                  # LLM-maintained knowledge base
│   ├── _master-index.md   # Top-level index of all topics
│   └── <topic>/           # One folder per topic
│       ├── _index.md      # Lists all articles in this topic
│       ├── article.md     # Individual wiki article
│       └── assets/        # Images for this topic
├── output/                # Query results, reports, slides
└── .obsidian/             # Obsidian config and plugins

Step-by-Step Setup

Step 1: Create the Vault Structure

Open a terminal and create the directory skeleton:

mkdir -p vault/{raw/_processed,wiki,output}

Step 2: Initialize Obsidian

• Open Obsidian → “Open folder as vault” → select the vault/ directory
• This creates the .obsidian/ config folder automatically

Step 3: Install Obsidian Plugins

Community plugins (Settings → Community plugins → Browse):

Plugin Purpose Local Images Plus Downloads remote images to local when pasting URLs or clipping articles Marp Slides Renders Marp-format markdown as slide decks Dataview (optional) Query your wiki with SQL-like syntax inside Obsidian

Browser extension:

Extension Purpose Obsidian Web Clipper Clips web articles as .md files directly into raw/

Configure Web Clipper’s default save location to raw/ so clipped content lands in the inbox automatically.

Core plugins to enable (Settings → Core plugins):

• Backlinks
• Outgoing links
• Graph view
• Tags
• Page preview

Step 4: Create the Master Index

Create wiki/_master-index.md:

# Knowledge Base Index

Topics will be listed here as they are created.

This is the entry point the LLM reads first when navigating the wiki.

Step 5: Write CLAUDE.md

Create CLAUDE.md in the vault root. This is the instruction file that tells the LLM how to behave across every session.

Prompt: Core Rules

# Vault - LLM-Maintained Knowledge Base

## Knowledge Base Rules

- This is an LLM-maintained knowledge base. You are the librarian.
- The wiki/ folder is YOUR domain - you write and maintain everything in it.
I rarely edit wiki files directly.
- raw/ is the inbox. When I dump files here, you process them into the wiki
during a "compile" step.
- wiki/_master-index.md is the entry point. It lists every topic folder with
a one-line description. Always keep this up to date.
- Each topic gets its own subfolder in wiki/ (e.g., wiki/ai-agents/) with its
own _index.md that lists all articles in that topic with brief descriptions.
- Always use [[wiki links]] to connect related concepts across topics.

Prompt: Compile Workflow

## Compiling Raw Material

When compiling raw material:
1. Read the raw file
2. Decide which topic it belongs to (or create a new one)
3. Write a wiki article with key takeaways and relevant links
4. Update that topic's _index.md
5. Update wiki/_master-index.md
6. If a raw file spans multiple topics, create articles in both and cross-link
7. Move the compiled file to raw/_processed/

- Keep articles concise - bullet points over paragraphs.
- Include a ## Key Takeaways section in every wiki article.

Prompt: Compiled File Tracking

## Compiled File Tracking

- After compiling a raw file, move it to raw/_processed/.
- This makes it easy to see what's pending (raw/) vs already compiled
(raw/_processed/).
- If a raw file is updated after processing, move it back to raw/ for
recompilation.

Prompt: Image Handling

## Image Handling

- When a raw file or article references images, store them in
wiki/<topic>/assets/.
- Reference images using relative paths: .
- The obsidian-local-images-plus plugin handles pasted images in Obsidian,
but when compiling raw files with images, manually copy them to the
appropriate assets/ folder.

Prompt: Commands

## Commands

- "compile" — Process everything in raw/ that hasn't been compiled yet into
the wiki. Move compiled files to raw/_processed/.
- "audit" or "lint" — Review the wiki for inconsistencies, broken links,
gaps, and suggest improvements.
- "query: [question]" — Research the question across the wiki and write the
answer to output/ as a markdown file.

Prompt: Q&A Workflow

## Q&A Workflow

- When answering questions, read _master-index.md first to navigate, then
drill into the relevant topic _index.md, then read specific articles.
- Write answers to output/ as markdown files so they're viewable in Obsidian.
- For visual outputs, generate the appropriate format:

• Slides — Use Marp-compatible markdown (frontmatter: marp: true)
• Diagrams — Use Mermaid code blocks (rendered natively in Obsidian)
• Charts/images — Generate matplotlib/other scripts and save output PNGs
  to output/

Prompt: Filing Outputs Back

## Filing Outputs Back into Wiki

- When a query result is substantial enough to be a standalone article,
file it into the wiki:

1. Move or adapt the output into the appropriate wiki/<topic>/ folder
2. Update the topic's _index.md
3. Update wiki/_master-index.md
4. Add [[wiki links]] to connect it with existing articles
   - This feedback loop ensures explorations and queries always "add up"
   in the knowledge base.

Step 6: Set Up the Ingest Pipeline

For web articles:

1. Install the Obsidian Web Clipper browser extension
2. Configure it to save clipped articles to raw/
3. Enable “Download images” in the clipper settings or use Local Images Plus to pull them after clipping

For papers/PDFs:

• Save PDFs to raw/ — Claude Code can read PDFs directly during compile

For code repos/datasets:

• Clone or save relevant files to raw/<source-name>/
• The LLM will extract key concepts during compilation

Hotkey tip: Set up a keyboard shortcut to download all images on a page locally, so the LLM can reference them without network access.

Step 7: First Compile

Drop some source material into raw/, then tell the LLM:

compile

It will process each file, create topic folders, write articles, build indexes, and move processed files to raw/_processed/.

Step 8: Query the Wiki

Once you have enough compiled articles, ask questions:

query: What are the main differences between X and Y?
query: Summarize everything we know about Z
query: Generate a slide deck on topic W

Results land in output/ and are viewable in Obsidian.

Step 9: Audit Regularly

Periodically run:

audit

The LLM will:

• Find broken [[wiki links]]
• Spot inconsistent data across articles
• Identify gaps and suggest new articles
• Flag stale content
• Use web search to impute missing data when appropriate

Usage Patterns

The Core Loop

Ingest → Compile → Query → File back → Repeat

1. Ingest: Clip articles, save papers, dump notes into raw/
2. Compile: LLM processes raw into structured wiki articles
3. Query: Ask complex questions, get answers in output/
4. File back: Promote valuable outputs into the wiki
5. Repeat: The knowledge base compounds with every cycle