RE: always put Customizations in `custom-file', never in `user-init-file'

[Drew Adams]

> Great. And I guess custom-file should be run after .emacs, since that
> makes it possible to chose another custom-file.

No, I think `custom-file' should continue to be loaded only upon explicit
request, never automatically. You should be able to put (load-file
custom-file) wherever you like - the order can sometimes be important.

If an old `user-init-file' already has Customizations, then the explicit
(load-file custom-file) should replace them at the same location.

If it happens (would it?) that an old `user-init-file' has Customizations,
but other code is intermingled with them (e.g. custom-set-variables, then
some other, non-customize stuff, then customize-set-faces), then the user
should be informed and have to decide what to do to remedy the situation.