I was going through the JNLP file,I found that single jar file is referenced twice in the same JNLP file. Actually ,I am creating a folder structure where I will put jar corresponding to there position in the respective JNLP files in the server. My aim is to create a single executable jar from this folder.
If you want to run the application outside JNLP, you just need to put all the needed jar files onto the classpath. It shouldn't matter that some files were referenced multiple times in the JNLP, though I don't know why should it be so.
Also, you don't need to bundle them together into one jar. As mentioned in the other thread, there are installer that can pack all the necessary files into one installation package.