Preserving Header Directory Structure in Xcode for Static Library
I also needed to preserve the header file directory structure for a C++ library project and I finally managed to do it. It is ridiculously complicated with XCode, compared to the simple nature of the task. The key is to create "folder references" at first, then to copy the header folders in an extra build phase and afterwards to delete .c/.cpp-files from these exported header folders with a script, because XCode will not only copy the .h-files.
I've written a blog post here on how to all achieve that, because it's more tricky in detail. You might also want to check out an example XCode project that I've pot on github.
When you add files to your project, you have to choose next parameter on an additional window "Create folder references for any added folders". And then all your files will have fixed path for your files and will save structure after compilation.