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Modern desktop environments, such as Gnome and KDE, conveniently offer a nice "workaround" called 'launchers'. Those are small files that describe how something should be started. Just a few lines that specify the name, the icon that should be displayed and the actual command to execute. Conveniently, the syntax of those launcher files is the same for Gnome and KDE. And those launchers don't have to have any execute permissions set on them! Desktop environments treat those files as a special case, so when you click on them Gnome or KDE will happily execute the command that was specified within the launcher description and without the need for the execute bit to be set on the launcher itself.

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our malware needs the ability to install a launcher for itself so that it is started whenever the user logs in. As mentioned, for Gnome that means creating a launcher description in the ~/.config/autostart folder.

http://www.geekzone.co.nz/foobar/6229

How can I fully disable the .desktop file function under GNOME?

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What you're asking for isn't possible. .desktop files are baked into GNOME.

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