The present main trunk of maneage has gnuastro and astropy as
targets. While many astronomers working on observational
projects will be happy to have both, many branches of maneage
will most likely be projects with only the minimal additional
packages beyond the basic.mk packages added as targets.
Moreover, many packages will be non-astronomical.

If someone developing a maneage-branched project wishes to update
by merging recent developments from the main maneage trunk to
his/her project, then at the moment, when s/he wishes to do a merge, s/he will have to do a merge of only some of the commits
(git cherry-pick them, for example), carefully avoid merging
the TARGETS.conf file, and also checking various other changes
that might have diverged.

Is it right that the only really annoying divergence that
needs to be checked carefully is TARGETS.conf ?

I'm just thinking aloud here - I haven't tried this yet, but
it would make sense to sooner or later.

Maybe this is already easy - so there may be not much to do
on this task... :)