The not-very-helpful answer is that the old-style bundles do not support source updates.  Also, as you've probably noticed, a lot of documentation is out of date.  What I would suggest is to download one of the newer "plus" bundles here:

These actually include all of the necessary dependencies (which keep changing on short notice, sorry!) and also have a source layout that's more consistent with our development environment.  The current builds incorporate the program you're looking for, but you can also update cctbx in the future by doing this:

cd $CCTBX/modules

rm -rf cctbx_project