LLM Wiki Pattern

Build and maintain a persistent, interlinked Obsidian wiki using an LLM. The wiki is a directory of markdown files that the LLM owns — it creates pages, updates them when new sources arrive, maintains cross-references, and keeps everything consistent. You (the human) curate sources, ask questions, and guide the analysis. The LLM does the bookkeeping.

The core idea: Instead of RAG (re-discovering knowledge from raw docs on every query), the LLM incrementally builds a persistent wiki that compounds over time. Cross-references are already there. Contradictions are flagged. The synthesis reflects everything you've read. The wiki gets richer with every source ingested and every question asked.

Think of it like this: Obsidian is the IDE, the LLM is the programmer, the wiki is the codebase.

Three Layers

Raw sources — your curated collection of source documents (articles, papers, notes). Immutable — the LLM reads but never modifies them.
The wiki — a directory of LLM-generated markdown files. The LLM owns this layer entirely.
The schema — conventions for how the wiki is structured (AGENTS.md / CLAUDE.md). Co-evolved with the LLM.

Directory Structure Convention

wiki/
├── raw/                  # Source documents (immutable)
│   ├── articles/
│   ├── papers/
│   └── notes/
├── wiki/                 # The wiki itself
│   ├── index.md          # Content-oriented catalog of all pages
│   ├── log.md            # Chronological, append-only record of operations
│   ├── entities/         # Pages for people, places, organizations
│   ├── concepts/         # Pages for ideas, theories, terms
│   ├── sources/          # Summaries of ingested sources
│   └── synthesis/        # Cross-cutting analyses, comparisons, syntheses
└── assets/               # Images, diagrams, etc.

Operations Workflow

When the user asks you to do something with their wiki, follow the pattern below. Use surgical changes (touch only what must change). Define verifiable success criteria for each operation.

Ingest

When the user provides a new source (article, paper, note, podcast transcript, etc.):

Read the source thoroughly
Discuss key takeaways with the user — ask what to emphasize
Write a summary page in wiki/sources/ with:
- YAML frontmatter (title, date, source type, tags)
- Summary of key points
- Links to relevant entity and concept pages (created or updated as needed)
Update or create entity/concept pages that the source touches
Update wiki/index.md — add the new source and any new pages
Append to wiki/log.md with a consistent date-prefixed entry

Format for log entries:

## [YYYY-MM-DD] ingest | Source Title
- Created/updated: [list of pages touched]

Karpathy guideline: State your plan before starting:

1. Read source → verify: summarized key points with user
2. Create/update wiki pages → verify: index.md updated, log.md appended, cross-references added

Query

When the user asks a question:

Read wiki/index.md to find relevant pages
Drill into specific pages as needed
Synthesize an answer with citations to specific wiki pages
File good answers back into the wiki as new synthesis pages (in wiki/synthesis/)

Good answers don't disappear into chat history — they compound in the knowledge base.

Lint / Health Check

Periodically run a health check:

Contradictions between pages that newer sources superseded
Orphan pages with no inbound links
Missing pages — important concepts mentioned but lacking their own page
Stale claims — assertions contradicted by newer sources
Cross-reference gaps — pages that should link to each other but don't
Data gaps — questions the wiki can't answer that a web search might fill

Create

When starting a new wiki from scratch:

Ask the user: what domain/topic? What's the scope?
Create the directory structure
Create wiki/index.md and wiki/log.md with initial entries
Create initial entity/concept pages based on what the user knows so far
Ask the user for their first sources to ingest

Obsidian Markdown Conventions

Use Obsidian Flavored Markdown for all wiki pages:

Frontmatter (Properties)

---
title: Page Title
date: 2026-04-27
tags:
  - topic
  - status/active
aliases:
  - Alternative Name
sources:
  - "<span class="broken-link" title="Page not found: Source Page">Source Page</span>"
---

Callouts

Use callouts for structure:

> [!note] — General information
> [!warning] — Contradictions or unresolved questions
> [!quote] — Direct quotes from sources
> [!example] — Examples
> [!info] — Additional context
> [!question] — Open questions for future investigation

Embeds

Use !<span class="broken-link" title="Page not found: image.png">image.png</span> for embedded images. Images go in assets/.

Synthesis Pages Format

---
title: Comparison of X and Y
date: 2026-04-27
tags:
  - synthesis
  - topic/comparison
---

# Comparison of X and Y

Key differences between <span class="broken-link" title="Page not found: Entity X">Entity X</span> and <span class="broken-link" title="Page not found: Entity Y">Entity Y</span>.

> [!note]
> This synthesis was generated in response to: [user's question]

llm-wiki