Remove broken repos without certificate and remove code handling that

Historically, repos were added to the DB without much information and could stay in a broken state until manually removed.

If a repo is updating, it should have a cert. So only repos that never did a single index update don't have a cert.

Nowadays, this can not happen anymore as we get the repo and its cert before adding it to the DB. So whenever we update a repo, we know its certificate and fingerprint.

Thus, this MR includes a DB migration removing all broken repos and making the certificate for repos in the DB non-null.