initial merge request

I think I had deleted some files in the beginning, so those older versions are missing from mine. The bulk of the changes are in sub_functions.jl. Comments were added to some other files, but any changes I made to Make.jl,  Experiments.jl, or Types.jl were just experimenting on my local machine and shouldn't be replicated. 

script.jl pulls some relevant lines from Make.jl so that at the Julia repl, source codes can be interactively loaded by running include("script.jl"). 

I've installed the "Devectorize" package and added it to the places it works directly for a 10-15% speedup in sim_simple(). 

Thanks,
Angela