Debug Scan jobrunner (and add a test that proved useful in the process).

Note it turns out to be critical that the same version of Scala build Queue and the plugin.
Add basic Queue script to run GATK pipeline
Add Jobrunner compile script
Take class specs from the commandline, and use the class specs given by jobs
Add support for running with variable number of threads
Permit class specs to include an initial hardware specification, and use that for the GATK pipeline
Fix jobrunner inheritance, and direct output as required by Queue.
Support scatter gather operation