Comment 3 for bug 1562409

This problem was there in Ubuntu (GNOME) 16.04, and still remains in 16.10. It seems that the duplicate entries come from multiple .desktop files in /usr/share/applications/. There is also a duplicate entry for Rhythmbox that appears in "Open with..." prompts, etc. (One of the Rhythmbox entries is for selecting an input source, but the name in the .desktop file is the same as the one for the main entry.) All this may be because of providing entries for the Ubuntu Unity desktop.

Deleting or renaming one .desktop file for File Roller does remove the duplicate entry for Archive Manager while having no ill-effects, but deleting or renaming one or other of the .desktop files for Nautilus causes the Files entry to disappear from either the dash or the Applications menu. In any case, an update to any of the applications will put the .desktop file and thus the duplicate entry back again, and it will be a matter of constantly correcting /usr/share/applications/ manually or automatically; a less than desirable workaround. Comparing with another standard GNOME desktop, such as in Fedora Workstation, and investigating possible conflicts with entries meant for the Unity desktop may help. One option may be to tweak the "OnlyShowIn" entries in the .desktop files.