sPuReMD: fix issue with incorrect cutoff being applied for periodic neighbors in small simulation boxes (nonb_cut -> vlist_cut). Other clean-up and debug I/O updates.

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

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