Better suite shutdown behaviour.

Fixes a bug that prevent job kills after issuing a shutdown order.
Fixed a minor bug in stop-after-wallclock-time.
Merge pull request #1117 from hjoliver/shutdown-kill-fix

Shutdown kill fix
Combine job activity logs in a single file

Job submit, poll, kill, event hook standard output and error are now
written to the `job-activity.log` file.

Added a basic test for this change.

Fixed some documentation issues.