YML: program.build-instructions.time_limit is effectively ignored during builds

[pdreiter]

Darjeeling generated a patch that did not complete the respective build, hanging the darjeeling tool during candidate patch evaluations.
You can easily duplicate this by adding an additional build command into the YML's program.build-instructions.steps like sleep X, where X>>program.build-instructions.time-limit.

During debug, I found two issues related to this:

1. in BuildInstructions.execute
   time_left = int(max(0, time.duration - self.time_limit))
   which should be:
   time_left = int(max(0, self.time_limit - time.duration ))
   since the StopWatch/timer initial value seems to be 0.0
2. The included DockerBlade module's shell package method check_output (dockerblade/shell.py:242) does not pass time_limit or kill_after values to the called function self.run.