cylc run --warm: decouple start from initial cycle point
alter reference logs
restore cold-start behaviour and fix new warm-start test
update
fix update bugs
unify cylc-run modes, remove raw start
adjust warm-start reference log
Merge pull request #1043 from benfitzpatrick/warm-start.pre-initial

#119: warm start support
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`.