Yeah, people keep complaining that apps are hiding the concept of a hierarchical FS from the user, but honestly I can understand why they do it. The hierarchical model just isn't a very good model for almost any nontrivial (i.e. 1-dimensional) logical model of data. For all we rightly complain about how much time is spent reinventing CRUD programs that simply list your files in a relational interface, few people seem to ask why we keep feeling the need to do that

Proper use of file attributes could help a lot, but while almost all modern OSes and FSes support them, AFAIK only MacOS makes much non-system use of them, and they have poor portability across systems. Even copying a file can lose them if the utility is not aware of them