Set java lib dir to user directory if ./configur --prefix=... is used

At the current version of the build system, the `--prefix` parameter is ignored for the java target dir configuration: The .jar files are copied into a system directory. With this PR, the .jar files are copied into `$prefix/lib/java`.
The user has to adapt for example the `$CLASSPATH` manually like `$PYTHONPATH` for python.