I just recently installed Jira and Jira Service Desk on my Ubuntu server. I'm using Apache to create virtual hosts using a proxy and SSL and Jira can be accessed successfully on a computer at jira.domain.com. However, if I try to use the Jira Server app, it tries to login using domain.com. I've tried http://jira.domain.com, https://jira.domain.com, and jira.domain.com.
I was able to get the login page to load by creating a permanent redirect on domain.com's virtual host file to the jira login page, but of course that only allows me to login into the app and not actually use it because it's still trying to use the main domain for every other URL.
Figured this out. Even though I know I set my base URL in jira to jira.domain.com, somehow it got changed to domain.com. Corrected that and the app now works correctly.
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