We've published the technical documentation to help you to understand the source code of JDEEP. You can find it at https://sourceforge.net/docman/display_doc.php?docid=81381&group_id=208269
If you want to help us to improve our plugin you find a new section "how to contribute" at https://sourceforge.net/docman/display_doc.php?docid=81382&group_id=208269