Add-on Addon that controls Navigation Links?

I've tried searching so forgive me if I didn't use the right term but I spent some time trying to find the answer.

I'm using Custom Tabs and it is very useful but I'm wondering if there is any way, outside of making template modifications inside the theme templates, to control the links that appear for Forums, Media, Resources, etc?

I've got way too many links in Forums after I added the CTA Featured Threads addon and I want to be able to control what appears without having to maintain version control of my template modifications across themes.
 
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