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I'm a full administrator so this shouldn't be hidden. I've searched the KB for JIRA 6.4 specific notes but it just says to click Applications from the Cog. I'm trying to set up a trust between Bitbucket Cloud and JIRA so I need to access Application links which I've done before.
Applications only went into that menu in JIRA 7, and it's referring to Core, Service Desk and Software.
For 6.4, hit any of those options you have in the image, and you'll be in the admin interface. Frankly, I have no idea where most things move to in here across all the versions (I started with JIRA 2, things have moved a lot), so I was delighted when Atlassian added the "admin search". Use that, it's at the top of all admin screens, and belt "applications" into there.
That's a fair comment - some docs do it ok (A lot of Atlassian stuff has a version drop-down near the top) but some don't even try to hint at a version. I guess you ran into one of the latter!
I wasn't sure whether you needed applications, as I don't know what doc you'd found, but the search was a start.
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