BUG: Partial fix for EMSegment/BRAINSFit integration. See #3561, #2741, #3779

This commit is a follow up of EMSegment commit r23496. It updates BRAINSFit
to integrate the fix done by Kent to specifically address the naming
of .h5 transform files written by BRAINSFit.

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commit e46c99795cedd4c6aeec98e881af9c2b28dc5cf5
Author: Kent Williams <norman-k-williams@uiowa.edu>
Date:   Tue Jul 29 15:24:11 2014 -0500

BUG: don't extend composite transform filenames needlessly.there was some deficient logic that
was changing the filename of composit transforms to force them to hdf5 format, even if the filename
given was already for an HDF5 file.
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git-svn-id: http://svn.slicer.org/Slicer4/trunk@23507 3bd1e089-480b-0410-8dfb-8563597acbee