This check-in closes Issue #57.

pipeline executor options now in a single option group, so they are not separately defined in pipeline_executor.py and AbstractApplication.

This will make it easier (and less error-prone!) to add and update options.

Command line options that are unique to AbstractApplication only are also in an option group.
Merge branch 'develop' into pre-1.2-misc-fixes
Updated defaults for executor options:

--num-executors = 0 (Otherwise, due to new launching/killing executor functionality), server would automatically launch an executor even if --num-executors was not specified.
--proc = 1
--mem = 6
--time-to-seppuku=15 minutes
--time-to-accept-jobs=180 minutes (3 hours)

The last two defaults were agreed upon by Matthijs and myself yesterday. They will potentially change as we get more people using this code and we continue to optimize parameters.
Changed default NUC and INORM file names to be shorter.

_nu_corrected --> _nuc

_inormalized --> _inorm
Added a hack (I HATE THIS!) into MBM.py so that prior to NLIN, if the initial target (created via LSQ12) has no mask, the init model mask is associated with this target. This is the default in old MBM.

I did this because otherwise when mincANTS is run, there is no target mask included in the registration. (Similarly for minctracc, but since we have a source mask there, it is less of an issue.)

Creating a github issue for this, so we can write this more seamlessly (e.g. by including it in either the NLIN or LSQ12 modules.)
Updated default number of executors to be -1 per discussion with Jason.

If a user tries to run a pipeline without specifying --num-executors, then it will shutdown with an error message.
Fixed bug I just created with the --num-executors=-1 default.

Now, when the server launches executors, we need to specify --num-executors=1 explicitly.
Merge branch 'pre-1.2-misc-fixes' into develop