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.