sPuReMD: make CoM logic consistent with PuReMD. Other build system updates for debugging and newer versions of MPICH.

PG-PuReMD: fix nvcc build issue where incorrect C++ compiler was utilized. Fix race condition with three body list computation. Remove debug code. Other misc. refactoring.

PG-PuReMD: fix build system linker argument ordering (LDFLAGS -> LDADD). Fix inline functions. Disable optimized CUDA code generation by default (added Makefile flags to enable along with preprocessor defs to enable relevant code paths).

sPuReMD: fix incorrect thread parallelism inside bonded force routines. Update default value of CFLAGS in autotools.