Currently GARstow just tells packages being installed to stick their
config files in sysconfdir; this works fine for me, but it's not
very convenient when upgrading or downgrading packages that make incompatible
changes to their config file formats.
An alternative would be to make packages install their config files in
packageprefix/etc (while still being compiled with the right
value of sysconfdir), and merge changes at stow time: calculate
a diff between the old provided config files and those currently in
sysconfdir, then try applying it to the new provided config
files, and complain if it fails.
This would require, among other things, knowing what the old installed version
was before stowing.
It might also be nice in the future to enforce that packages should use
sysconfdir/GARNAME.