Years ago websites were made of files; now they are made of dependencies.
Perhaps this is the archivist in me, but this process of creating files and flinging them into an unsorted pot and then searching or hoping that the newest one is the one we want gives me the collywobbles. It seems like a rejection of our past work, to just sling all the files into a heap, immediately devaluing them as soon as something newer comes along.
I also prefer files in the filesystem. This goes for photos, notes, journal entries, everything. I treat them with respect and I'm unlikely to screw them up or misplace them. And if I were to screw them up, it would be my own fault and my backups would be right there.