Removed fortran cpp directory separation, just too many directories to go through

This is so we don't need a pointer to each array held within the actors.

Added command line arguments to output scripts.

Added instructions to resourceUsage script

Scripts for going over data within Summa

Also added file for setting up a read the docs page

Sorted Scripts
Created Configuration Script for Submitting Jobs

Started configuration.py to streamline job submissions

No more booleans are requried to ensure files have been created and HRUs have had their
pamarameters written