Comment 3 for bug 78997

The applications logo icon should still be installed into the system hicolor
theme. From dobey's blog:

"While the application's logo icon for use in the system menus, and the app's about box and window titlebars, should still go into the system hicolor theme, following the guidelines in the Icon Theme and Icon Naming specifications, we can't really do this for other icons."

I agree that it would be easier to fix this with the package rules (this is what I did in Fedora), that running automake on the patched Makefiles.