cli/upgrade: refresh before updating packages
cli/upgrade: refresh before updating packages

So missing packages are installed and orphaned ones are removed (and env
file updated, if necessary).

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