In yaourt.fish, substitute "complete -c pacman" with "complete -c yaourt"
everywhere, but leave "pacman -Q" and "pacman -Sl" as they are, because
yaourt versions of -Q and -Sl are nice and colorized but not good to be used
for the completion.
This command would do the trick (because without the "g" suffix, sed
substitutes only the first instance for each line):
sed "s/pacman/yaourt/" pacman.fish > yaourt.fish
It works for me.
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