This Python script keeps your project.pbxproj file inside of your <ProjectName>.xcodeproj file organized.
Copy pbxproj_organizer.py into your Xcode project's directory so it is a sibling of your .xcodeproj file. Then add the following Run Script to your Build Phases to have Xcode automatically keep your project.pbxproj file organized each time you build your app:
or you can navigate to your project's directory and run it via the Terminal:
$ python pbxproj_organizer.py