sPuReMD: fix linear solver to work with no preconditioner. Fix issue when precondition recomputation frequency is zero. Other misc. changes.

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.