lego already bundles the chain with the certificate,[1] so the current
code, designed for simp_le, was resulting in duplicate certificate
chains, manifesting as "Chain issues: Incorrect order, Extra certs" on
the Qualys SSL Server Test.
cert.pem stays around as a symlink for backwards compatibility.
[1] 5cdc0002e9/acme/api/certificate.go (L40-L44)