Documentation is split into four sections - user documentation, API documentation, GM notes and file format.
User documentation describes how to use the software, giving details of the GUI interface. It is best to read this first.
Currently, this just consists of JavaDocs. They are incomplete and variable in their usefulness.
This provides background on the ideas behind map generation, including discussion of the various terrain types and how best to use them.
Map files are stored as XML files which contain binary data for the map itself. This isn't ideal from a readability point of view, but storing each tile in the bitmap has an XML node is very impractical.