PG-PuReMD: fix performance logging code around GPU code. Rearrange header files to allow some preprocessor definitions to be defined via options in configure script. Rework Autoconf and Automake code to allow passing flags directly to nvcc compiler wrapper (for CUDA code). Enable C11 and C++11 standard targets during compilation.

PG-PuReMD: fix issue with some interaction lists not being initialized on first step of simulations from restarted runs. Fix typos in C++ code for utilizing C code (__cplusplus). Clean up C code for utilizing C++ code (unconditional extern's for unmangled member naming). Ensure that CUDA thread and block sizes are correctly set. Tweaks to memory transfers and allocation logic in integration code (GPU). Fix logic error with charge matrix allocation in GPU code. Other code clean-up.

PG-PuReMD: add BiCGStab solver for GPU code. Corrections to CUDA block and thread sizes for some kernels. Fix some variables being used with uninitialized values.

Build: work around Autoconf bug in AC_SEARCH_LIBS preventing both LAPACK and Tensorflow from being used together for sPuReMD.

sPuReMD: fix issue with configure script nuking Tensorflow link variables when LAPACK link variables are set.

sPuReMD: improvements for building in debug mode (add assertion support for run-time checks). Fix issue with Verlet list recomputation logic being incorrect. Fixes to be string comparisons.

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).

PG-PuReMD: fix CUDA compilation error. Revert library building via libtool due to issues with recognizing custom suffix rules for building CUDA source files and revisit at a later date.

Change MPI build target to use newer MPI-only code by default, and add option to build older MPI code (to be removed in the future).

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.

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