Maybe it's just because I've been using OSX since 10.2 but I've never had any problems keeping files in trees, I have a very nicely pruned set of nested folders

Maybe it's just because I've been using OSX since 10.2 but I've never had any problems keeping files in trees, I have a very nicely pruned set of nested folders that I keep all my work in. If you wanna dump all your shit in ~/Documents then sure you can do it, but it's also super easy to stick folders in the Finder sidebar or the Dock for easy access to your big multifile projects.