There is an invalid entry left by Atom editor (authors failed to provide an unistaller). Entries are not removable using menulibre - it is not listing them, but ghost entries remain in menus.
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Searching for fitting .desktop files and removing them may help.
In that case removal of /usr/local/share/applications/Atom.desktop fixed problem.
Solution found on http://forum.lxde.org/viewtopic.php?p=48112&sid=51e194b86f5901892036da51a76a55db#p48112
reducing activity
- 1,260