We have already contacted Atlassian Support due to not being able to get the "Development Panel" working inside Jira when Application Linking to Stash.

They recommended creating the Application Links via HTTP (everything else runs on HTTPS via Apache Proxy)

The issue with this is when clicking something like "Create Branch", it uses the Application URL, not the Display URL which then requires the users to re-authenticate as it is a different domain. I think this will also stop us from using Secure Cookies when we implement Crowd.

Shouldn't the links in Jira through to Stash use Display URL, not Application URL? (... but behind the scenes it uses Application URL to gather that actual data presented in JIRA)