One of the things that doesn't leap out at you right away as a new game developer is just how many files start building up, and how important it is to keep them organized. The project I'm working on right now (yeah, the one that's keeping me from Project Jumper. Sorry!) started out in my head as a pretty simple Arkanoid style game. Surely that won't involve too many files, right? I'll just use the standard src/com/developer/name file structure, and that should be fine.
Hah. Maybe I'm just too addicted to making new classes for every little bit of functionality, and maybe I could cram all my graphics into spritesheets, but still, my folders are becoming a cluttered mess. The OCD part of me that makes me rename/reorganize all my music to a very strict scheme is going insane that I haven't sorted my files into categories and subcategories.
Well, while this project is too far along to make a reorganization worthwhile, I think it's actually a good lesson. The aggravation I'm starting to suffer at the end of this small game will teach me to avoid the same aggravation on a larger scale when I start working on more ambitious things. This is just another of those times when mistakes are actually more beneficial than success.