Backport CLI-manager infrastructure from LWR.
I had previously reworked this CLI stuff to work with LWR - this changeset brings those changes back to Galaxy. This version has the advantage of using the job script module - the upshot is that GALAXY_SLOTS, job_conf env directives, and job metrics should all be usable now with the CLI runner. This version also has a local shell variant (to eliminate the use of SSH and run qsub directly on the same machine), a variant of the Torque executor to target slurm's torque compatibility executables (doesn't support -x), and some other small bug fixes.
Merged in jmchilton/galaxy-central-fork-1 (pull request #385)

CLI Job Runner Enhancements