Regarding boost, ccp4io_adaptbx, etc: I generally agree with Luc, but
adding subtrees and submodules will make working with the repository
more complex. No idea how it's mapped to svn for those who'd prefer to
keep using svn. It'd be simpler to avoid subtrees and have
ccp4io_adaptbx and other non-external modules in the main cctbx repo
(it should be technically doable during the migration).

You are right: incorporating ccp4io_adaptbx into the cctbx repository is the most sensible option indeed. As for boost, SCons and ccp4io, I guess you propose to just incorporate their whole directory tree in one single commit with a comment like “Upgrade to Boost version xxxx”. That would work too indeed. I would still favour using git submodules for those though.