Better use of flag to stimulate dependency negotiation.

Incoming messages that change task outputs set a flag to signal that
dependency negotation is required. The flag should only be turned
off again after it has been used, else dependency negotation could be
missed if the flag gets turned on then off in quick succession. This
can result in a stalled suite that requires a "nudge" to get it going.
Turn off unnecessary suite state updates.

Command queue processing was dropping through to a suite state update
even if there were no commands queued.
Merge pull request #281 from hjoliver/matt-test-battery-stuck

Matt test battery stuck
Merge branch 'master' into job-status
job status file: add PID.