ID:2731806
 
If I separate my files into multiple folders for an easier time finding what I need, do I need to make a copy of the project with the files removed from the folders before I upload?
When you package your project for download it will only include the compiled files, and any extras you specify. If you package the source it will include any files that are used in the compilation (but you have to compile first). You shouldn't have to do anything special.

If you're unsure at any point, create a .zip package and take a look at what's in it.
Thanks for the quick reply.