Hi Lee - I could be completely wrong here, but my understanding of the requirements (at least those for mine) is that first you have to create an executable jar file (called runme.jar in my case). Having done that, you have to package everything up - source code, choices.txt etc AND runme.jar into a second jar file. The assessor then unjars THIS file and is only then able to run the program.
You appear to be trying to run the executable from a jar which contains a Doc directory rather than just your classes...
Yes, there are two JAR files; one inside the other.
Get the executable jar file working first - it will not have the directory prefix '/code/'.
Once you have the executable jar file working, then you can package the executable jar, the doc directory, the source directory, and the additional files into another jar file (which will not be executable).
Make sure you read your instructions carefully to make sure you get packaging perfect. There have been cases of candidates being failed for doing something silly like having source files in a 'source' directory instead of a 'src' directory. You must follow what is written in your instructions to the letter.