Hi Martin,
 
I totally agree - if cherry picking is time consuming then it's not
worth it.  I just wondered if there was a quick way to strip out some
of the top level namespaces completely from the build dependencies.

Yes. The libtbx/configure.py command lists all the top-level names of the modules used. You can simply rm -rf the rest.
 
One other quick question that's quite important to my project: is
there a way to build a debug version cctbx? At the moment I'm having a
lot of problems due to mixing of release/debug CRTs (when I build my
code in debug).

We have libtbx/configure.py --build=debug option. I'm occasionally using this under Linux and Mac OS X. I don't remember if I ever tried this under Windows.

Ralf