Shuffle dependencies around to add modified nak

Well, this is a hack. I built a modified version of nak-1.1.0.jar
to add undo methods to all of the PointTransformer classes, and then I
added the modified nak to the lib directory. Then I also checked in
chalk and all of its dependencies to prevent it from being downloaded
and pulling along the unmodified nak with it.
Print transformed and undone centroids

Previous, the --output-centroids option only printed out the coordinates
of the centroids in the transformed space (i.e. after applying the
z-score transformation or PCA). Now it will also print out the centroids
in the original coordinate system (approximately for PCA).