The big central problem here is that non-trivial taxonomies aren't trees but graphs. Trying to get a tree-based filesystem to represent a taxonomy means you're forcing a graph into a tree. Symlinks help because they turn your tree into a graph (albeit one that breaks too easily; I think that could be fixed, though). But in the end, a traditional filesystem is a poor way to represent a taxonomy.
If you really want to organize files basic on semantics you might generate file names based on, say, a SHA-3 hash but keep looking the attributes of the files in a database.
The trouble with that though is that people have different perspectives on documents.
The librarian in me wants to ingest a document and never modify it, such that content addressable storage is what I want. I want to attach metadata in an external database.
There's another culture though where people edit documents, most notable in Adobe's tools which will try to save a JPEG even if all you did was print it! Adobe developed
