Detailed documentation is uploaded (i.e. my thesis). It examines the system from the user's perspective, but includes some internal details too. Of course it has some extra chapters here and there to conform to the format of a thesis.
Check it out at the "Files" section (r221). There's also a corresponding src/bin/javadoc bundle there.
The 0.3.1 version introduces buildings, resources (e.g. gold), and the resource overlay.
The 0.2 version contains a map editor and save/load features.
A really huge refactoring happened in the last 2.5 week, I even committed the sin of committing half-done not-running code. (As I'm the sole developer I can use the SVN for backup, but I know it's not good practice.)
Just avoid revision 61.
There's still no networking or genetic algorithm framework.
See Download section.