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When I open my menu, it displays two icons for pycharm. Why? Is it an error or did I misunderstand something? Same thing for Skype, it displays two icons.

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Probably you have repeated entries for two different installations or version for those apps.

You can try hitting Right-click on the menu icon and then entering configuration. Take a look at the different folders and you should see the repeated entries.

Although the most system-independent way is to do it manually:

Menu application entries are located in ~/.local/share/applications/ for your personal entries and in /usr/share/applications for default ones.

You should take a look at these dirs so they contain .desktop files for each menu item. It can happen that two different files exist to define the same application.

These are simple text files so you can easily try to create or delete some. Inside this files is specified what categories the belong to (folders in the menu), name, program they really execute, etc.

also if you want to play whith dirs inside the menu the are .directory in /usr/share/desktop-directories for default ones and in ~/.local/share/desktop-directories/ for your personals.

If you chose to make a new folder in the menu, it exists in ~/.local/share/desktop-directories/ as a file with the extension, .directory. If you chose to make a new menu item, it exists in ~/.local/share/applications/ as a file with the extension, .desktop. These were created by alacarte. They are regular text files; and, now that you know their location, you could do this manually, too.

The rest of the files for the menu are located in /usr/share/desktop-directories and /usr/share/applications

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