#!/bin/bash
farmerpath=/var/www/dokuwiki-farm
# for each animal reference some of the default configuration files (will be overwritten in the animals)
for animalpath in /var/www/{animal1.example.org,animal2.example.org,example.org/custom/path}; do
ln -sf $farmerpath/conf/{dokuwiki.php,{acl.auth,local,users.auth}.php.dist} $animalpath/conf/.
# invalidate cache
touch $animalpath/conf/local.php
# remove file (not used anymore)
rm $animalpath/conf/msg
done

# alternatively you can find each folder containing a conf/ directory using this:
for animalconf in /var/www/*/conf; do echo $animalconf; done
# if this looks ok (dokuwiki-farm/conf/* cant be overwritten anyway by itself), do
for animalconf in /var/www/*/conf; do
ln -sf $farmerpath/conf/{dokuwiki.php,{acl.auth,local,users.auth}.php.dist} $animalconf/.
# invalidate cache
touch $animalconf/local.php
# remove file (not used anymore)
rm $animalconf/conf/msg
done