Converting from 2.4.8 to 3.0alpha/open_contrib/includes

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I recently updated from 2.4.8 to 3.0alpha and am having a hard time understanding the how to re-setup the include files. I am running on Win 8.1 64 bit with VS2012 c++/cli and CMake 2.8.11.2 I have CUDA 6.0 and an NVidia card. My code is using SIFT/SURF and Cuda. I re-compiled the code with the OPENCV_EXTRA_MODULES_PATH set and the opencv code builds fine.

Now I have to modify the includes in my own source and that is where I am having a problem. My include section used to work fine and say:

#include <opencv2/opencv.hpp>
#include <opencv2/core/core.hpp>
#include <opencv2/features2d/features2d.hpp>
#include <opencv2/highgui/highgui.hpp>
#include <opencv2/features2d.hpp>
#include <opencv2/stitching.hpp>
#include <opencv2/gpu.hpp>
#include <opencv2/gpumat.hpp>

Now, it cannot find the gpu.hpp or gpumat,hpp files. I tried to follow this question but it is not clear that anything actually happened. Seems like all the header files, etc. need to be coped from various subfolders into a standard include directory.

What is the easiest way to get reset the include files?

Thanks for any help!