From: https://answers.atlassian.com/questions/99642/jira-with-stash-browse-source-without-fisheye

I was facing the same problem. I created the trusted link both ways, and committed with Jira Issue Keys in comments but nothing happened. As per the documentation, Stash waits for the first commit with a Jira Issue Key and then indexes the entire repository. However, it did not seem to work for me.

Then I made another commit with issue keys in [], so if a issue key is "IT-567", in comments I put "[IT-567] Making changes to hello" and immediately after doing this, it showed all the commits in JIRA, and from now on, it started showing even the commits without [] in jira keys. So everything works now.

And

well, I had created a new test server, and had created just one project, and one repository in it, and have just added one file so I don't see why it should take time. After app linking, I committed same file three times by making small changes, and it did not work. I waited like 15 minutes, but it did not work. And then later at the day, I used [] in keys and it worked. If it was time, then Atlassian have forgot to put in document to wait for a couple of hours before trying. I am sure the keys entered were correct because I just used the same keys all the time, and after first successful linking, all of them are being shown linked in the repo.

A number of options:

• Indexing is not running / all indexing threads are busy indexing other repositories.
• The UI isn't showing the JIRA keys, even though the application links have been created. In that case the 'Issues' column on the commits list shouldn't be displayed at all. Maybe the conditions that control the visibility of the Issues column use caching?