cli/upgrade: 'doom refresh' after upgrading, before updating
cli/upgrade: 'doom refresh' after upgrading, before updating

Fixes an issue where uninitialized packages aren't installed when 'doom
update' tries to update them.

hlissner/.emacs.d,UndeadKernel/emacs_doom,hlissner/.emacs.d,hlissner/doom-emacs,hlissner/.emacs.d,UndeadKernel/emacs_doom,UndeadKernel/emacs_doom,hlissner/.emacs.d,hlissner/.emacs.d,UndeadKernel/emacs_doom,UndeadKernel/emacs_doom,hlissner/doom-emacs,UndeadKernel/emacs_doom,hlissner/doom-emacs,hlissner/doom-emacs,hlissner/doom-emacs,hlissner/.emacs.d,hlissner/doom-emacs,UndeadKernel/emacs_doom,hlissner/.emacs.d,hlissner/.emacs.d,hlissner/doom-emacs