How to update system plugin in jira

Seems we are hit by this bug:

We are running JIRA version: 6.3.6

How do I udpate the navLinks plugin to 3.3.12?

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Upgrade to 6.3.7 is the official answer, but if you have a look in the comments, you'll see a link to a new .jar you can download.  

Download it, then use the plugin manager to "upload plugin".  I would keep a copy of the .jar from your current installation just in case, but I'm always cautious.

Thank you. I updated the Nav-Links plugin to 3.3.12. It seesm to have solved the problem. However, It now shows up in the user add-ons instead of system add-ons. Should I be worried about this or is it just cosmetic?

No and yes. You do not need to worry about it appearing in the "wrong" list on your current installation. Technically, it is a user-installed plugin because you did it by hand, but the difference between system and user plugins is not much more than "it came in the installation off-the-shelf" However, before you upgrade, you must remember to remove it, or it may interfere with the (fixed) new version in the new installation.

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