Folders/directories are a necessity as long as we continue to distribute collections of files the way we do. I'm not sure what github would look like in a world without directories, nor how file naming would work. Do you have a proposal for the issues that doing away with directories brings up?
Folders are only a human factor necessity. Tags forming a graph of related files are more capable, but harder to manage mentally since they can reach any part of the system and cross boundaries.
