|T66321 Personal tools are too crowded (tracking)
|T46448 Consolidate personal portlet links into collapsed control or dropdown (tracking)
|T67467 Courses link is not showing up in the gadgets/extension section of compact personal bar flyout
Jared, I assume the issue is that the Courses link is enabled for a user and shows up normally, but when the Compact Personal Bar version of Personal Tools is used, it doesn't show up.
That link is inserted via a call to the PersonalUrls hook: https://git.wikimedia.org/blob/mediawiki%2Fextensions%2FEducationProgram/254a135c3754fcbfb4ee63f8bc4e1a9888d70e85/EducationProgram.hooks.php#L110
Juliusz et al, if there's another example of using the PersonalUrl hook to insert a link in a way that is compatible with the Compact Personal Bar, I'll try to update this.