I think the real culprit here are operating systems and file systems, not programmers (of end-user applications). File systems were designed during an era where

I think the real culprit here are operating systems and file systems, not programmers (of end-user applications). File systems were designed during an era where semantic meaning was just not important; all file systems cared about (and still care about) are directories and files. The whole paradigm should've been abandoned long ago for something much cleaner.