> The problem with a fixed / structured filesystem is that it's largely inflexible. The next option would be to have some sort of hybrid -- a persistent data store plus, say, hardlinks or symlinks onto that store based on other elements, could work, but would be somewhat annoying to maintain (though not impossible, and a tools-based approach might well work).

What your are describing here is called a semantic file system, and there are some implementations of this, like for instance https://www.tagsistant.net/