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.

sPuReMD: refactor tri solve level sched memory management. Change OpenMP thread scheduling policy to static. Modify logging output format.

sPuReMD: fix diagonal preconditioner computation and level scheduling application. Modify preconditioner logic to compute and cache sparsity-based info. Update run script.