Fix build issue where config.h.in is only generated once (for sPuReMD) => common file across all versions.

Build toos: refactor to remove recurisve Makefiles. Fix issue with OpenMP flags being overridden when user supplied value for CFLAGS variable.

Build systems updates for sPuReMD, PuReMD-GPU, and PG-PuReMD (use safer optimization level defaults).

All: fix issue with pi bonds being incorrectly computed in bond orders. Patch originally submitted to LAMMPS mailing list by Tomas Trnka, SCM (refer to Issue #837 on Github).

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

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