I'm a little confused and probably confused with how this works in XCode as well.
I have some groups that have two different icons in the project view. One a lighter color folder, the other a darker color folder (With Darcula theme) The lighter color has an underlying folder and I can move files to that group and they'll move on the file system. The darker doesn't and will try to move/create files to the root of the project. Looking at the project.pbxproj file, I see the difference is that one has an element 'Path' and the other has an element 'Name'.
My questions are:
1) How do I change from one to the other? I want to have Paths for everything that makes sense.
2) What did I do wrong in the first place that some of them are set incorrectly?