added installation dependencies

I noticed I had to install both freetype2 and libpng-dev before
matplotlib could be installed (on a 64 bit machine running linux)
expanded documentation

Added a couple things to output and running sections
added rate rule caveat to documentation

...it might be wise to double check existing rules to ensure there are
not too many instances of this
added molecular constraints to documentation

This regards RMG-Py issue #174. Also made sure
generatedSpeciesConstraints works properly.