PG-PuReMD: begin enhancements. Enable sim. step retries. Enable far neighbors list max per atom. Other general code clean-ups.

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).

PG-PuReMD: fix include guards, resolve implicit function declarations, fix inline issues with GCC v5 (C99 std). Other general code clean-up.

PG-PuReMD: fix issue with hydrogen bond cutoff with systems without hydrogen atoms. Remove debugging info for MPI-only version of PG-PuReMD.

PG-PuReMD: include forgotten headers for distribution. Fix CUDA installation check. Additional updates for build system.

sPuReMD: enable debug builds. Fix compilation issues when optimizations disabled (-O0). Fix graph coloring data structure management.

PuReMD-GPU: fix issues with C++ to C calling conventions. Remove function overloading for C compilation.

sPuReMD: complete preconditioner application using level scheduling with permutations based on graph coloring.

sPuReMD: fix Jacobi iteration synchronization issues and change inner SpMV thread scheduling policy to guided for load balancing.

sPuReMD: expand domain-based QEq matrix cut-off and add control file parameter. Update control file.

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