Plugin can end up being unresponsive to interruption (build timeout) if a window popups

Unfortunately in some cases, Unity might popup a window even if running in batchmode.

In this case, the process will be hanging, and the output copier will block in the join().

Here are the threaddumps before and after the process was killed manually: https://gist.github.com/1964929

We need to find a proper way to handle this case as I doubt Unity is going to fix their dialog pop-ups anytime soon.