Modified saveToDirectory() in UpdateSummariesParallel to add continued directory numbering

saveToDirectory(vector<UpdateSummary> upsumvec ...) has been modified to accept a new boolean argument -> bool stack_updates which allows the user to add to the same master CMA updates directory if multiple optimizations are run for the same dmp. The argument is defaulted to FALSE in UpdateSummariesParallel.hpp. This seemed cleaner than adding a new function, but could pose an issue if the user wanted to overwrite a particular set of optimization runs but use this same continued numbering format. This sort of problem is probably best left to the user because of the particularity of this implementation. Compiles and runs fine.

P.S. I do not know why the .cpp and .hpp files show so many changes but the only changes are lines 96-116 and 157.