PuReMD-old: more clean-up of linear algebra code. Remove or conditionally enable debugging code (DEBUG preprocessor). Fix memory leak in SAI setup. Better memory allocation checks.

PuReMD-old: remove non-source junk files. Clean-up to remove debugging code for neutral territory. Conditionally toggle SpMV implementation (Sparse_MatVec) debugging on if neutral territory is selected.

Merge branch 'full-far-nbrs-list-charge-matrix' into full-far-nbrs-list-charge-matrix-half-full-refactor.

Merge branch 'full-far-nbrs-list-charge-matrix-half-full-refactor' into full-far-nbrs-list-charge-matrix-half-full-refactor2.

Fix issue with bonds list ordering leading to different torsion and conjugation energies due to changing the far neighbors list to a full list.

Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.

PuReMD: refactor to allow selection of far range interaction Verlet list format at runtime (half or full). Similar change for symmetric charge matrix format (half or full). For SAI, toggle between half and full depending on whether it is a refactoring step.

Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.

Tools: fix MPI command. Change control file generation to be in running directory (for temporary directories and files) => necessary for running with MPI (shared filesystem needed across nodes).