The smallest step up from a hierarchical file system is to allow any file to have any number of tags, where each tag is just a simple string (no hidden IDs or anything). I believe most tag proposals implement this concept and not much further. I briefly looked at Tagsistant and numerous software and papers.
I sketched some of my own ideas about identifying immutable files by hash and creating arbitrary tags that reference such files. It turns out that this way of organizing files goes really deep, and I haven't explored all the implications yet. It yields a completely different landscape than the file system that we are used to today - the concepts of path, mutability, attributes, etc. are replaced with different mechanisms.
The article is long, but I would appreciate hearing if the concepts resonate with anybody else: https://www.nayuki.io/page/designing-better-file-organizatio...