How can I select what options appear in the JIRA navigation bar, e.g. Agile, Tempo, Service Desk, etc. As we install more and more plugins I don't see a need to have all of these in the navigation bar especially if they are only being used by a certain user base. I've read articles that describe removing the whole plugin but the point is to keep the plugin, but remove the link in the navigation bar.
It depends on which plugin you want to hide. Some have a module you can disable within them to do this.
I have never used those two so I can't help with them, but I have added their label to this question to help drive the correct traffic here. If you have a staging environment where this can be reproduced, I would look at the plugin's module lists and see if there is an obvious module which can be disabled. If you can't find anything, consider using Javascript in your announcement banner to remove the elements.
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