Refactored cmake build system to use just one FindCUDA.cmake, under cmake_modules subdirectory,

based on the FindCUDA.cmake that was in the platforms/cuda/cuda-make directory.
Setting of CUDA_NVCC_FLAGS is now in top-level CMakeLists.txt, in case I ever figure out how
to get this working with the cmake 2.8 installed system version of FindCUDA.cmake.
Before this change, there were three separate FindCUDA.cmake areas.  Now there is just one.

plugins/freeEnergy/platforms/cuda/tests/CMakeLists.txt

@@ -2,7 +2,7 @@
 # Testing
 #
 ENABLE_TESTING()
-INCLUDE(${CMAKE_SOURCE_DIR}/platforms/cuda/cuda-cmake/FindCuda.cmake)
+# INCLUDE(${CMAKE_SOURCE_DIR}/platforms/cuda/cuda-cmake/FindCuda.cmake)
 INCLUDE_DIRECTORIES(${CUDA_INCLUDE})
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/include)
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/src)