Switch from os.rename to shutil.move to support cross-fs renames when needed.

In each of these cases dst is a file or a new dir.  In these 2 cases the ouput of os.rename and shutil.move are identical (they are only different when dst is an existing dir).

Testing Done:
CI went green here: https://travis-ci.org/pantsbuild/pants/builds/38112860

Bugs closed: 671

Reviewed at https://rbcommons.com/s/twitter/r/1157/