If we got to brwose->confluence admin and click 'applciation navigator' in the left hand nav, we can see all the links currently established. There is an column for 'restricted to groups' which is editable for each. What we would do is add an entry to each restricting the view to the most basic gorup allowed into Confleunce. By default this is the 'confluence-users' group but could have been changed depending on your user managment setup. Once restrictions are in place for each entry then the application navigator will no longer appear for anonymous users.
P.S the same options will appear in the application navigator screens of Jira.
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