Is there a way to make xcode use real folder hierarchies in the Project Navigator? I'm finding these pseudo folders somewhat annoying because they do not reflect the project on disk. Or at least have the xcode-made-folders a different color than the real folders?
Thanks.
Not really, although they are colored differently.
You have groups (yellow) -- which can refer to a directory, but does not update automatically to reflect what's on disk. Groups can also represent a group which has no relation to a directory or the structure of its contents.
You also have a reference (blue). This updates automatically, but its contents are not first class project items.
Personally, I just structure projects such that they can be (re)constructed from an on-disk representation easily (e.g. drop the folder), or in another IDE. Quite often, details which could (unnecessarily) be defined in Xcode are moved outside of the xcodeproject. Synchronizing the representation in the Project Navigator is about as easy as drag and drop once you work out how to structure the program/sources/targets.
Edit: I am referring to the Project Navigator. Whether what you refer to as the "project organizer" means the Project Navigator or some part of the Organizer, I am not sure.