This is a primer for installing a Letsencrypt certificate on a Jira server that is running the Jira provided, default Tomcat for serving webpages.
I found lots of information about how to do it using a free-standing Tomcat or nginx, but nothing about this particular combination. I hope it helps you!
Obviously, in all the examples, you need to replace jira.example.com with your own domain! And (duh) you need to use your own password, not 1234
You need to have installed Java (outside the scope of this document). Then in your user's shell RC file and probably root's RC file, add