BUG: Fixed BCD Test failures on Dashboard

All BCD tests are passed successfully on Mac; however, 22 tests were
failed on the Linux system because MSP estimation generates slightly
different results on Mac and Linux. Despite of the difference between
landmark points locations, both results on Linux and Mac are valid.
Therefore, we need to have multiple baselines for the Mac and Linux
systems.
Fortunately, ITKTestDriver supports multiple baselines, and different
baseline names should have following pattern:
baselineFileName.nrrd
baselineFileName.1.nrrd

Also, it seems that the extension of the file name is important! For
example using multiple baselines does NOT work when files are named
as follows!
baselineFileName.nii.gz
baselineFileName.1.nii.gz

Therefore, I changed all the output files extensions to "nrrd" for the
BCD TestSuite.

Furthermore, 6 of the failures were related to the landmark fcsv files
comparison that is run by an internal program named "LandmarksCompare".
This program is modified in a way to support comparing with multiple
baseline files.
BUG: Fix BRAINSFitTest_ROIBSpline test failure
BUG: Replace the baselines of BCD tests based on CDash build
BUG: Fix a bug in BRAINSFit SyN registration
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.