There are two jar files: runme.jar (contains your class files) and scjda-xxx.jar. The latter contains the former, the database file, your docs, etc.
See the runme.jar as a jar that is used to run your application (
java -jar runme.jar) and the scjda-xxx.jar as a normal zip or lzh file to store all your files together so you can upload everything in one go.
They just decided to use jar instead of zip or lzh for that.