CUG updates post #1056
Update runahead limiting and internal queues documentation.
Removed "Section" from references in the CUG.
Corrected two LaTeX references.
Typo fixed.
Clock-trigger offsets as ISO8601 duration.
Bug fix previous.
Changed clock trigger offset format for the iso test.
Consistent clock-trigger validation errors.
Fixed bug revealed by test battery.
Merge pull request #1059 from hjoliver/1029.clock-trigger-interval

clock trigger offset as duration
cylc.job_submission.job_submit: + pylint score
Merge pull request #1058 from hjoliver/more-cug-updates

Some User Guide Updates
Merge pull request #1062 from matthewrmshin/pylint-job-submit

cylc.job_submission.job_submit: improve pylint score
Squash double spaces in plain graph tests.
Better auto shutdown logic.

Fixes #1054.
Style: removed some superfluous whitespace.
Merge pull request #1063 from hjoliver/fix-new-graph-tests

Squash double spaces in plain graph tests.
Merge pull request #1064 from hjoliver/1054.auto-shutdown

1054. better auto shutdown logic
Restructure suite run time log/job/ and work/

Directory structure now looks like:
* `log/job/CYCLE/TASK/{01,02,...,NN}/{job,job.out,job.err,job.status}`
* `work/CYCLE/TASK/`

which should make it easier to archive the log for the whole cycle or to
housekeep all the work files of a given cycle.

`log/job/CYCLE/TASK/NN` is a symbolic link that points to the job log
directory of the latest submit for `TASK.CYCLE`.