There's two ways people do this.
The messy and annoying one is to implement SSL in the Tomcat Jira runs on.
The better, easier and more flexible one is to run it behind a proxy that does SSL. The usual one is to use Apache for this, but you can do it with others like Nginx, Lighttpd and so-on. See https://confluence.atlassian.com/kb/securing-your-atlassian-applications-with-apache-using-ssl-838284349.html
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