Simulation pipeline requires an overarching point of entry #47

Since parts of the sweep had to be split into separate SCons scripts, it has lead to only weak coupling of inter-script dependencies. At present this dependency hierarchy is managed manually -- running each stage in the correct order once the last one finishes. It highlights the need for something.

A overlord script is required, which performs the stages and would naturally take on the "whole simulation" output path and other variables such as seed. This script it itself could use Nestly -- but I would be tentative to do so as the goal isn't Application Inception. :-) Also, it would be a good time to yank out all the bash scripting.