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  • org.gnome.Nautilus.desktop

    OK, so if you open up that file (presumably in /usr/share/applications), there should be lines like

    Exec=nautilus --new-window %U
    ... and/or ...
    Exec=nautilus --new-window
    

    So try running nautilus --new-window from the terminal. Does it work?
    If it does, try running nautilus --new-window FOLDER (replace FOLDER by one of the paths you wanted to open from the dock). Does that work?

    Now you should know whether you have a problem with all of nautilus, or whether nautilus just doesn't like one of your folders. Then you need to either figure out how to fix nautilus, or try caja instead (or find some other file manager, or ...).

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