integrate VKJ changes
Merge branch 'vkj'

Conflicts:
	main.pdf
Update abstract
Update keywords
MATLAB
cleanup first two P
continue introduction
continue
Finish motivation for now
Add citation for Github
Finish architecture for now

Moved the section on documentation to the using/contributing
section of the introduction.
Rename motivation to introduction section
Finish simulator for now
Knock out MATLAB interface
pack up before sending out
review simulator.tex
review ui.tex

Still needs work...
pdf