added more command line stuff to to-do
added more command line stuff to to-do

stan-dev/math,stan-dev/stan,stan-dev/math,stan-dev/math,stan-dev/math,stan-dev/math,stan-dev/stan,stan-dev/math,stan-dev/math,stan-dev/math,stan-dev/stan,stan-dev/stan,stan-dev/stan,stan-dev/math