Whenever I create a new application link from my JIRA instance to another application, such as Confluence, Stash, etc., I'm seeing new items added to the Application Navigator menu in JIRA, having flowed through that application link. This might be ok, except in several cases I already had those links configured in the JIRA instance, and they now show up more than once.

In other words, the automatic adding of Application Navigator menu items is not very intelligent...at the very least, it shouldn't add duplicate entries. Ideally, there would be some way of configuring how the Navigator menu items flow through these links.

I'm sure this problem affects more than just JIRA, but I'm seeing it most often in JIRA. I'm pretty sure it affects Confluence as well. Also, I've listed 6.0.8 as the Affects Version only because that's my current version. Again, I'm sure more versions are actually affected.