sPuReMD: refactor and clean up preconditioner application code (level scheduling, graph coloring, Jacobi iteration). Conditionally change charge matrix for setting up preconditioner for ICHOLT and ILU(T).

sPuReMD: fix issue with graph coloring causing sporadic failures in solver convergence for EE and ACKS2. Conditionally change the charge matrix for ICHOLT and ILU(T) preconditioning. Refactor graph coloring code.

sPuReMD: split into library and driver for, e.g., optimization integration. Fix bug with interaction lists being allocated for hydrogen bonds when no hydorgen atoms present. Fix minimum allocation size of 3-body lists (uncovered with small lithium geometries). Refactor naming of conflicting data structures. Update .gitignore.

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

sPuReMD: enable debug builds. Fix compilation issues when optimizations disabled (-O0). Fix graph coloring data structure management.

sPuReMD: complete preconditioner application using level scheduling with permutations based on graph coloring.

sPuReMD: fix SuperLU build and code. Fix ILU_PAR (compute factors separately). Move diagonal preconditioner computation. Refactor precondition computations. General code clean-up.