Clean up, organize, and build a retrieval registry for a markdown knowledge base (Obsidian / PARA second brain) using Karpathy's 3-layer LLM-wiki method: RAW sources, COMPILED wiki, SCHEMA/index. Runs a read-only audit (missing frontmatter, broken or missing [[wikilinks]], orphan pages, missing Related sections, stale files, duplicate names, folders without an INDEX), then fixes them, enforces consistent structure, and generates per-folder + a master INDEX so any file is fast to find. Use when the user says: "clean up my folders / vault", "organize my files", "build an index or registry", "make my notes retrievable", "lint my knowledge base", "tidy my second brain", "standardize frontmatter and wikilinks", or wants a folder reorganized for better recall.
2026-06-19