Since version 2.0, multiple distinct actions can be specified in a single invocation of GNU Stow. For example, to update an installation of Emacs from version 21.3 to 21.4a you can now do the following:
stow -D emacs-21.3 -S emacs-21.4a
which will replace emacs-21.3 with emacs-21.4a using a single invocation.
This is much faster and cleaner than performing two separate invocations of stow, because redundant folding/unfolding operations can be factored out. In addition, all the operations are calculated and merged before being executed (see Deferred Operation), so the amount of of time in which GNU Emacs is unavailable is minimised.
You can mix and match any number of actions, for example,
stow -S pkg1 pkg2 -D pkg3 pkg4 -S pkg5 -R pkg6
will unstow pkg3, pkg4 and pkg6, then stow pkg1, pkg2, pkg5 and pkg6.