Removed debugging file output
Fixed image resampling to resample the whole volume

In severly rotated cases, the resampled image was a cropped
version of the original because it did not resample over
the whole axis-aligned bounding box of the rotated image.
This commit fixes that.
Produce all airway pieces in geometry

Before, it just extracted the largest connected component
under the assumption that the airway is a single contiguous
piece. This assusmption isn't always true.
Moved ITK-derived source files to Code directory
Moved unused files to Deprecated directory
Changed file suffixes to match ITK style