The source code is divided into several seperate projects, each with its own directory.
dynamo/
This is where all the Event-Driven simulation specific code is and is probably what you are interested in if you're reading this.
magnet/
Magnet is a header-only library, filled with useful and generic C++ functions and classes. DynamO uses the magnet library for stuff like sorting, collision detection, and input/output in XML.
coil/
Coil is a visualization library. It uses OpenCL and OpenGL to perform fast real-time renderings of simulations. In DynamO, the coil library provides the interactive visualiser.