Extended use of job log directory.

Captures output from daemon-invoked commands to the job log directory.
Removed vestiges of the old lockserver.
Bug fixes for previous...
Bash bug workaround.
Bug fix previous.
Longer wall_clock_limit.
Test header: graph coords can occasionally be -ve.
Merge pull request #1112 from hjoliver/new-job-log-files

New job log files
Merge branch 'master' into global-cfg

Conflicts:
	lib/cylc/job_submission/job_submit.py