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NonbondedForce sometimes included energy terms that weren't appropriate to the specified force groups

NonbondedForce sometimes included energy terms that weren't appropriate to the specified force groups

Eliminated having CMake run programs to check for CUDA and OpenCL compatible GPUs.  They mostly just caused problems.

API wrappers are marked as depending on the XSLT files that generate them (Mike Garrahan's patch to bug 1625).

Reimplemented SETTLE velocity constraints with a different algorithm.  The old one produced incorrect results.