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Fixes a hard to catch bug when a boundingBoxSize increases in size in between a timestep, but does not trigger a rebuild of the neighbourlist. Affects the usage of singlePeriodicCopy in nonbonded force.  

Fixes a minor windows compiler invocation issue where C:\Program Files becomes delimited by the space. Also enables debugging libraries to be built in debug mode for WIN32 + Visual Studio. 

When computing kinetic energy, make sure the shifted velocities are perpendicular to the constraints

Reduced memory use for random numbers, eliminated unnecessary calculation when generating random numbers

Fixes nvcc terminals popping up during CUDA JIT compilation due to invoking system("nvcc ..."). Replaced with MSVC's native CreateProcess() function. 

CudaApplyConstraintsKernel::apply() did not set the context as current, leading to errors when using multiple contexts

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Fixes uninitialized bits occurring in the PaddedNumAtoms regions by properly constructing them. This should hopefully get rid of some of the NaN errors we've been seeing.