A Knowledge Wiki an Agent Maintains

For a few years this was just notes. Files in Obsidian, written by hand, useful whenever I remembered they existed and inert the rest of the time. In 2026 I rebuilt the whole thing around Andrej Karpathy’s LLM Wiki pattern, and it turned into something that maintains itself.

The vault has two layers. Anything I read goes into raw untouched. The wiki layer holds what came out of it: a note for each source, concept pages for ideas that outlive any single source, analyses, and maps showing how clusters of notes connect.

That is 349 notes at the moment. 127 source notes, 39 concepts, 33 maps, 16 analyses. There are another 127 sitting in a legacy folder, imported from how I used to do this before.

I do not write the wiki layer by hand. I drop a source into raw and an agent ingests it, following rules I wrote in a file called AGENTS.md.

The rules

The pattern gives you the shape: a raw layer and a wiki layer, a schema file the agent reads, and three operations that ingest, query and lint. What goes into that schema is left to you, and that file is the part I actually wrote.

Mine says the system should accumulate. When something new arrives, the instruction is to improve the page that already exists instead of creating a near-duplicate beside it. Links belong inside the sentences where the connection matters, and never in a generic related-notes list at the bottom of a page.

The rule I care about most is that notes have to preserve uncertainty and disagreement rather than flattening them into confident-sounding summaries. That one exists because of what happened with my research paper. A knowledge base that quietly resolves every open question into a clean answer is worse than no knowledge base, because you stop being able to tell which parts you actually know.

There is also a lint pass. It looks for orphan pages that have value but nothing linking to them, duplicate concepts spread across several notes, links that are technically correct but contextually weak, and claims that a better source has since made obsolete.

How I use it

Source goes into raw. The agent ingests it and updates whatever concept, analysis or map pages it touches. When I want an answer I start from the index or the relevant map and read only the pages I need. If the answer turns out to be worth keeping, it goes back in as a durable note instead of being thrown away.

What decayed

wiki/entities is empty.

It was meant to hold pages for people, organisations and specific things. It is written into the rules as one of the four note types. I have never once used it, and it has been sitting there as an empty folder the entire time.

That is the honest state of the structure. Designed in full, used in part.