sorting my dir

still sorting
my code

This is now my code & scripts
change dir struct

Just modifying dir structure
JAP code -- lots of updates

Streamlined main.cpp
Updated documentation in README.txt
Small adjustments only

Mostly modified the plotting script
New plotting script: many runs, compare w

plot_compw.sh will plot as many fileIDs as the user gives it.
Useful for comparing e.g., initial conditions
updated read me
Merge pull request #9 from jolyonb/jonathan

Jonathan