I had JIRA 6.2 with Stash 2.11.x successfully connected using application link. After upgrading to Stash 2.12.3, the JIRA 6.2 Development Tools page shows that the Stash "Create and view pull requests" and "View commits" capabilities are "unsupported", but "Create branches" still works. I have tried removing and adding the application link to no avail.
Are there any errors in the JIRA / Stash logs when you replicate this behaviour?
Have you followed the instructions on the Integrating JIRA with Code Development Tools document and created the AppLink using 2 Legged OAuth authentication?
Are you running these applications behind a reverse proxy or using SSL, and if so, could you please confirm whether the same problem also happens when you remove these variables and connect them directly?
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