Added a long exposition on how to make decisions about implementation of SIR with the toolkit. Explained what is in a transition, how we choose state. Got rid of BVDV example.
Added more to reference section. Also added references to papers. Moved frogs to the examples section, sadly. Hope to flesh it out and have an intro with frogs.
Small change to language on intro
Added a jenkins image and the list of tests.
Added to the intro.
Added the BVDV model to examples.
Added a figure to the manual.
Added a section on implementation.
Added the files to make Jenkins instance. Added reference to this and how we use github in the FAQ.