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For cert-manager to work you need to have the ingress controller port (or I guess another port) exposed publicly? Or it supports DNS verification? I thought about doing this, but I am essentially having my cluster fully in a private network which I connect with wireguard from outside, but maybe I should reconsider?
I am keen to know a little bit more about your setup
I am using cloudflare DNS, which cert-manager requires an API key to edit the DNS entries. Documentation on this can be found here. It seems to support a number of DNS APIs, you can view those here.