Arg parse and make output folder

[drbergman]

Move argument parsing to new class ArgumentParser in modules/PhysiCell_settings.h. This handles the config file as arg away from main.cpp making that file simpler for users. Also, can pass the output folder as an arg (prefixed by a -o flag). Or still set within the config file. Future features are commented (pass in rules, ics, etc as command line args)

This also implements the creating of the output folder if it doesn't exist. This implementation creates the necessary folder structure, i.e. creates all necessary intermediate folders if they don't yet exist.