PG-PuReMD: split bond and hbond initialization kernels for future optimizations. Cleanup CUDA code related to far neighbor list being in full format (remove unnecessary conditionals and arithmetic).

PG-PuReMD: merge memory management and step retry logic from MPI+GPU code into MPI-only code. Fix and backport numerous bugs (void pointer arithmetic and dereferences, etc.). Update code to match new data structures. Begin merging changes from OpenMP code (sPuReMD) for preconditioning work.