Currently, Teachers can hide Course Navigation links from students to de-clutter, but they cannot remove links for themselves. This means that instructors see all of the tools they are using and all of the tools they aren't using in the navigation.
Instead of links being in a binary state of "Enabled" or "Disabled", add a third state, such as "Disabled for All" that can allow faculty to remove links from the Course Navigation that they have no use for.
