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.
ssh scandium.eqiad.wmnet sudo -H -u zuul bash -l cd /srv/ssd/zuul/git/operations/software git init . git remote add origin ssh://email@example.com: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!