That is a bug in the Zuul merger, the reason is it tries to clone operations/software when another repo such as operations/software/conftool has already been created. Since the directory operations/software already exists, git clone bails out.

Fix:

ssh scandium.eqiad.wmnet
sudo -H -u zuul bash -l
cd /srv/ssd/zuul/git/operations/software
git init .
git remote add origin ssh://jenkins-bot@ytterbium.wikimedia.org:29418/operations/software
git remote set-head origin --auto

Did a recheck and zuul merger now manages to merge the patches properly. Thank you for the task filling!