Problem: can't specify where to send Java and Clojure output

Solution: add -root_path:xxx option, so from src, you can set this
to -root_path:../main.

It's still unclear where the best place is for model files in a
multilanguage project. To be tweaked. For now they're in src.
Merge pull request #136 from hintjens/master

Problem: can't specify where to send Java and Clojure output