I am running Stash 2.8.2 and JIRA 6.1.1.
I have set up application links between the apps, and there are no warnings or errors on the web UI about the links.
I can mention a JIRA issue in a Stash commit and the commit will show up on the Source tab in JIRA. Likewise, the JIRA issue will appear as a link on the Stash Commits tab and I can pop open the issue to view and/or interact with it.
I cannot create a Stash branch from JIRA, no matter what I do. I have deleted and re-created the application links several times, initiating the link from Stash and JIRA without any change in Symptoms.
There is no "development" section on the JIRA issue as described in the JIRA 6.1 documentation. I have checked the permission helper and I have the "View Development Tools" permission for the issue.
On the "Commit" tab of JIRA I just see the 3 ads for BitBucket / Stash / Fisheye. If I click on the "connect" button for Stash, I am taken to the application link page where JIRA shows that I have a good connection to Stash.
If I go to the project admin page in JIRA and choose "Development Tools", the "Connected Developer Tools" says "Create branch from JIRA is unsupported. Upgrade Stash to use this feature". I've tried clicking refresh without change. I am running Stash 2.8.2, so I'm not sure if the version checking isn't working and JIRA thinks that I'm on <= 2.7.x.
There are what appear to be some spurious warnings about i18n in both logs, and about http client thread usage in JIRA.