Add a timeout to stop command

It should be able to wait for more than 10 seconds for the master to
tear shut itself down without having to wait for all current builds to
finish. Currently the shutdown wait is kind of all or nothing. This
change should allow for some flexibility.

Also, make waiting true by default in stop.stop, else wait-related
options like --timeout and --clean are never honored.

Conflicts:
	master/buildbot/scripts/runner.py

Change-Id: Ied471ab35ab3880ff222eb5c8a4a50cca07102ac