I didn't know this term before, thanks! Are there any examples (e.g., products you like) that demonstrate this One True Way in practice?

Not yet.

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.

Just give me a Neo4j database and Cypher to query it.

That seems like a silly term for a Directed Acyclic Graph