The instruction.html says in the code directory , put the source code and all related part of the project.
What related part it should be?
The code directory should have source code. The unchanged database file should be outside the code directory.
The properties file should be created on the fly on the current working directory and it is not supposed to be submitted.
Related parts could be images for your buttons or for your about dialog. So the code directory will be an exact copy of the src folder of your IDE. I didn't have anything else but java sources, so my code directory in the submission jar contained no related parts.