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It seems that the "Custom HTML" option in the admin console affects pages and blogs, but not the Application Navigator.
Thanks for any advice,
If you inspect element on any of these links do they have a common css class?
You may be able to use the jQuery in to following KB to filter for those classes instead of ".external-link"
Daniel, thanks for the suggested KB article.
I then inspected the elements and saw that the a href class for all of the Application Navigator links is .aui-dropdown2-radio so I tried this as well, but no luck.
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