[db] make repo certs non-null and remove repos without cert

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

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