For instance, on a fresh system ~/.weechat may not exist. If we install weechat with stow then it will create ~/.weechat as a symlink. This will mean that every new file created in ~/.weechat will be added to source control including logs, etc. which we don't want.
The solution to this is to add the --no-folding flag it seems after a little testing. This creates the directory if it doesn't exist. See the man pages for more info. So the command would look like:
stow -S --no-folding *