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In all the places where applications are listed, duplicates of some of them may appear. Why? Below are some examples:

ClassicMenu indicator "Open with" menu "Select application" dialogue

Here is an old question of mine that can be considered related. It's about Wine apps only (native Linux apps were not duplicating during those days) and I doubt the reason is the same as Wine is "quite a different opera". I was also not able to find the "Main Menu" app mentioned in the answer there.

Ivan
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Most likely that's because there are multiple .desktop files for those applications in /usr/share/applications/ or $HOME/.local/share/applications/.

To get the "Main Menu" app install the package alacarte.

  • Funny (well, not really) thing, the classic menu indicator (which I assume you are the author of, and that's why I adore you) has gone empty (all the apps disappeared, only Personal, Hardware, System and ClassicMenu Indicator submenus left) as soon as I have visited both directories you have mentioned with an elevated mc (not deleted/changed anything, everything is still there intact) and installed alacarte (not even launched it). Restarting the indicator doesn't help. – Ivan Nov 12 '15 at 22:51
  • Now as I have launched Alacarte all the apps are there (including the duplicates) but not in the ClassicMenu indicator menu. – Ivan Nov 12 '15 at 22:55
  • Everything works just fine as I have restarted the system. Still curious what it was... – Ivan Nov 13 '15 at 02:55
  • Which version of ClassicMenu indicator are you using? – Florian Diesch Nov 13 '15 at 23:40
  • I was using the version included in the standard Ububti 15.10 repositories (as I like its look better - I prefer empty places instead of gears icons where no icon is defined). Now, as I have upgraded thinking it was going to fix the problem, I am using 0.09-1 from the PPA. – Ivan Nov 13 '15 at 23:43
  • Another thing I don't like about the new version is it doesn't show Wine as a separate program group (puts it in "Other" instead) while the older version does. – Ivan Nov 14 '15 at 02:08