I organize notes by tags, folders, and links from tree of "map of content" notes. Those documented as rules for AI. All notes came to "Inbox" folder, and from time to time I run special script that checks inbox, formats notes, tags them, and put in the most appropriate place. "git diff" to check results and fix mistakes, reset if it went wrong.
As notes organized by the limited number of well defined rules, they became easy to search and navigate by AI. Claude Code easily finds requested notes, working as advanced search engine, and they became a starting point for "deep research" : find relevant notes, follow links, detect gaps, search internet. Repeat until reach required confidence level.
The most advanced workflow so far is combination of TRIZ (Theory of Inventive Problem Solving) + First Principles Framework. Former generates ideas and hypotheses, later validates them and converge on final answer.