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Change Fortran wrapper building script (wrappers/FortranWrapper_Header.xslt) to add line breaks between function and subroutine arguments.  This was needed to keep lines under 132 characters in length

Changed std::fabs to std::abs in AssertionUtilities.h to avoid compile ambiguity error on Windows with TestReferenceCustomHbondForce

Downgraded recent cmake changes to ghastly compliance with cmake 2.4, for the benefit of the simtk dart server.

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.

Export CudaFreeEnergyKernelFactory symbols to avoid link error in test program.

So far tested only on GPU-having windows machine.

Turn default to ON for nightly building Cuda FreeEnergy plugin, since it is desired for pyopenmm release.

Accumulation of Born force was incorrect in USE_OUTPUT_BUFFER_PER_WARP block w/ cell coordinates  x != y

Still doesn't build on windows, but might help with linux (todo next)

Cast exponent in pow() function to RealOpenMM, to avoid overload ambiguity error on Windows when RealOpenMM is defined as double.

Exported some symbols from Cuda plugin, for use by external NML plugin.
  cudaOpenMMInitializeIntegration, gpuSetConstants, CudaPlatform
  (but I couldn't figure out how to export kGenerateRandoms)
Also turned off TestRandomCuda on Windows, since it always fails and makes the dashboard look bad.
Renamed InitializeIntegration method to cudaOpenMMInitializeIntegration, now that symbol is being exported.

Increased the tolerance on two tests that started failing when we switched the reference platform to double precision