I think the reason why people (I put myself into this camp as well) prefer directories for organization is because there is an entire ecosystem built around them. Backing up, recursive search, exploring via ui, programmable access, programmatic access using language of ones choice are all choices available to the user. Code organization isnt the only place this shows up, organizing music and photos has similar semantics - apps which try to do the organization via higher level metadata rarely put in the engineering effort to come up with robust solutions for all the above use cases I cited abode.