Remove extra log4j jar file

This removes many of the warnings seen when running applications from
one-jar.

Task #11.
Remove cobertura.classpath from base.classpath

This ensures that we don't find cobertura classes when we build our
one-jar binaries. This removes warnings and reduces the size of the
final jar files.

Fixes #11.
Merge branch 'task_11-classpath-warnings'