IMO file/folder structure in a project is a geographic mapping exercise. It's not that far off from city planning. I think it's so important to design the structure and naming conventions of a project with the ultimate goal of aesthetically-pleasing, human-understandable spatial organization of digital artifacts. You "go here" to "see that". This "lives here". You travel to the destination of the thing you're looking for, and gain a deeper understanding of how the world is constructed that you are inhabiting.
This is one of my pet peeves with any kind of cloud file storage -- oftentimes they try to reinvent or abstract away the idea of a deeply-nested filesystem tree, and it just feels anti-human to me lol
Edit: I hit submit and then acknowledged I was kind of ranting about something else entirely from the paper itself!