This is one example for why hierarchical directories are bad. They're not all bad, but with all their power and flexibility, they carry some inherent flaws. It's much the same as JSON, which is also versatile and highly useful. However, both of these abstractions tend to lead to the ad-hoc creation of more complexity and more details to remember, while having no clearly delineated way to be self-describing.

(Is JSON an abstraction? Not really, as it's a concrete spec, but its general kind of serialization format is an (incomplete) abstraction.)