Gracefully handle LetsEncrypt certificate generation failures by throwing warnings instead of failing

When a certificate generation fails, the verify task fails but the task still writes the certificate path to the virtualhost file.

This breaks apache, as the virtualhost config is broken, so apache can't reload or start.

We should:

1. Only throw a warning if certificate generation fails. The site will still work in this situation, so a warning is more appropriate.
2. Don't write the certificate file info to virtualhost configs if there isn't one. See #3020747: Don't add SSL config to configuration files if the crt files aren't there/aren't readable. (especially redirects)