Separate the Dust API from the Kernel. The first contains the communication layer and base classes, essential to communicate between components. The Kernel is the implementation of the API, it contains the main function and the initialization process. Important: it also must contain layers, because there can be various startup environments (for Java: desktop, servlet and GWT client are currently considered).
Start liking GitHub (server and client). Nice "for dummies" environment, perfect for me as I want to waste minimal amount of time on the environment, but make it safe. I use a new repository and also work with the wiki, both are better than enough for me.
On the other hand, it is hard to set up the toolchain. It's great having a mindmap on my tablet, but that is connected to Dropbox, not to GitHub. I type things here that I should add to wiki. In some cases I already feel the limitations of the wiki, I should use UML instead, but where - on the tablet or desktop? Better here because the UML plans should go directly to GitHub...