If you run Jira behind a http proxy, namely https (ssl) then you need to add three options to the server.xml file in /opt/atlassian/jira/conf:

scheme=”https”
proxyName=”sub.domain.tld”
proxyPort=”443″

The only change needed to vanilla Jira.  Then in something like nginx you have the line:

proxy_pass              http://192.168.1.123:8080;

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