A *very* preliminary attempt at a "sync" script that works the way I outlined is now in the branch chocolate-update-menus. I've hooked it into postinst and prerm (but the prerm call won't work properly at the very least). I've only implemented Heretic so far whilst testing. Lots of XXX/TODOs, but I hope that this illustrates my idea at the very least. It would need to be hooked into triggers and g-d-p updated to cooperate on a trigger name I think, ideally.
P.S.: I discovered that LXDE's lxpanel is not good at noticing .desktop files being removed (#852316) so if you happen to use LXDE bear that in mind. XFCE at least seems OK.
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