ENH: FIXING BUGS IN template use for phase 3.

The process of building the pipeline sould
be contained in one set of files, not distributed
across several files somewhat indeterminantly..

Removed unnecessary code.
Reorganize pipeline to be consistent
Fixed cross sectional bugs in refactoring.
More changes for BAW debugging.
ENH: Added GenerateAverageLmkFile interface.
ENH: Split required and optional items from datagrabber.

Fix data grabbers to grab correct information needed for longitudinal
processing.

Fixed Stage3 BRAINSCut inputs.
BUG: Incorrect syntax for custom pipeline arguments

Must specify the 'overwrite':True option to the dictionary.
ENH: Try to fix Brainstem segmentations.