I'm coming into this conversation late, so what I say could be completely irrelevant, but when I recently set up an independent (i.e., not behind httpd) Tomcat server on one of our AWS EC2 instances, and could not get certbot to function at all, to save my life, I ended up using something called "LEGO." It *does* require one to shut the Tomcat server down during the renewal process (because it has to take over the port briefly), but it also *does* play nicely with a Tomcat server that's doing its own SSL.

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James H. H. Lampert

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