Fix for building standalone jar with included libs and fix for run-mapper.sh

The fix for `run-mapper.sh` skips the use of the -jar argument and gives the main class as an argument instead. When -jar is used -cp is ignored:
http://docs.oracle.com/javase/7/docs/technotes/tools/solaris/java.html#jar
`When you use this option, the JAR file is the source of all user classes, and other user class path settings are ignored.`

The change in `pom.xml` adds a second jar file for the target where all the libraries are included.
This makes the application easier to run without the need of run-mapper.sh`