This refactor implies the following major changes:

delete unused projects ( configuration, general model, gnuprolog) and unused or deprecated classes
incorporate Gradle as build tool
decouple the business logic from the GUI
rename classes and attributes to follow a predefined naming convention
order source file to follow a predefined structure (to get easy of maintenance)
complete documentation for generating javadocs documenation from the main classes
define a coding standard and migrate the source code to respect this standard