For general presentation of the whole, there is a presentation 'slide show' made with LibreOffice (odp format). The presentation can be found from: JavaEERest/doc/presentation.odp
For project specific instructions, see the files in: <project>/doc/
You can also generate the javadocs from the JavaEERest and JPA2 projects. These should provide you the overview of the classes. The javadoc files will be generated in the <project>/doc/ folders. Start by opening the index.html file generated (view in browser).