I found out how to start a java process from an ApplicationMaster. Infact, my problem was based on the command to start the process even if this is the officially documented way provided by the Apache Hadoop project.
What I did no was to specify the packageResource to be a file not an archive:
packageResource.setType(LocalResourceType.FILE);
Now the node manager does not extract the resource but leaves it as file. In my case as JAR. To start the process I call:
java -jar primecalculator.jar
To start a JAR without specifying a main class in command line you have to specify the main class in the MANIFEST file (Manually or let maven do it for you).
To sum it up: I did NOT added the resource as archive but as file and I did not use the -cp command to add the syslink folder that is created by hadoop for the extracted archive folder. I simply startet the JAR via the -jar parameter and that's it.
Hope it helps you guys!