Add doxygen to the project so that we can start documenting everything.

[Robert Massaioli]

The part that we should be especially vigilant in documenting is the plugins system. We should make sure that people can write plugins with the full knowledge of what everything does and how to use it.

The sooner we start documenting our interfaces and, in-fact, our entire code-base the better.

[Robert Massaioli]

A Doxygen file has been added to the project.