Creates --use-gemfile-git option to use git repos for runtime gems

This patch adds the --use-gemfile-git option which causes the
configure script to use the git repo directories in vendor/cache
directory when copying gems to the runtime/gems directory.

This can be used along with `bundle package --all` to use git
gems specified in the Gemfile instead of downloading the gems
from rubygems.org.

Also adds `make clean` command when building rubinius-melbourne
because copied files for this gem don't always trigger rebuild.