I have the following folder structure in xcode for a project.
I recently discovered a Command Line Tool that will do exactly what you need. You can find it here:
https://github.com/venmo/synx
To install the tool, you just need to open the terminal and run the following command (use sudo to run it as a superuser and get permission):
$ sudo gem install synx
Then, just like the instructions on the GitHub webpage above indicate, use the following command to re-organize your folder structure:
$ synx path/to/your/project.xcodeproj
This should do it :).