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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.

Modified Cuda FreeEnergy plugin to use a different windows export macro than main openmm library and cuda library.
Modified CUDA_NVCC_FLAGS to be consistent with Peter's latest version in all three locations they are defined.
Added "-Xcompiler '/MD'" to CUDA_NVCC_FLAGS on Windows to avoid link error in Cuda FreeEnergy plugin.

Incorporate apple-specific OpenCL include directory from the other FindOpenCL.cmake in the platforms/opencl CMakeLists.txt file.
TODO - in future use only one FindOpenCL.cmake file.

Reorganized platform analysis in NML init method.
Failed attempt to get OPENMM_PLUGIN_DIR working for NML test.

Set NVCC_FLAGS to particular value in new cmake_modules/FindCUDA.cmake

Turn on free energy plugin by default.
Better rule for when to default build OpenMM wrappers.
Several tweaks to advanced vs. non-advanced cmake variables.

So nightly builds can build CUDA and API wrappers when prerequisites are present.
While still being gentle on third party cmake builders.
New cmake_modules directory contains FindCUDA.cmake from cmake 2.8.0, and
Find OpenCL.cmake from platforms/OpenCL directory.