Andy Piper <andyp(a)parallax.co.uk> writes:
 IMHO "Update Packages" should be on the main package menu
as it is not
 specific to using packages with custom - its just a convenient way of
 getting the latest versions. 
It is supposed to only update the package that were explicitly
selected using custom, see the doc string. However it really doesn't
do that now (to be more precise it just adds all the packages it can
find to the customize variables and then adds only those "selected").
So either
1. what "Update Packages" does now is correct. However then I do not
   see the need to manage a whole set of packages using custom if you
   are never going to use that set. Then using custom is just a bad
   way of getting the menus and the "Manage Packages" menus should
   simply use a menufilter and the "Using Custom" menu should be ditched.
2. The Customize Packages system is really intented to manage an
   orthogonal set of packages and the :initialize functions should be
   ditched.
Jan