Hierarchies get out of hand quickly too. You will soon find that different people (or the same person at different times) create different hierarchies for the same thing and that the same thing belongs in multiple places.
I have been experimenting with different representations of data in Neo4j, Markdown, and Orgmode. I even tried cludging the polyhierarchies into different file systems using symlinks and tagging,
I'm still researching for better storage techniques.
I want a good mix between hand editing, but robust machine readable formats. Orgmode works pretty good, but it's fairly complicated to parse, and I think it could be improved.
The retrieval and search part could be improved with RAG, but I don't have the hardware or time at the moment to hacking around with the compute intensive AI stuff.