Major Description
Right now Fauxton has loads of non-Bootstrap class names and styles for things that Bootstrap has a name for (ex: .button vs. .btn). Often those class names and styles compete and sometimes are even used together causing a pretty tangled mess.
Focusing our use of class names on the Bootstrap defined ones gives new comers to the code documentation on what classes mean what--and we don't even have to maintain it! 
If you know Bootstrap, you should be able to know how to add buttons, etc to Fauxton without getting tripped up by .button .red .outlineGray, etc.