One suggestion, as I just could have used it
Could you add an option (either to menu or by commandline) to restore system menu and have catorise re-aarange it again, i.e. to begin from scratch, just as it was newly installed? Would make it easier to restore some functional menu as well as to restore from some not-so-clever customizing. A backup of customized menu could be done and maybe an option to restore that one again.

Now I'm just finished restoring the menu by completely uninstalling catoriseplus, removing folder /opt/catorise and installing catoriseplus again. Before installing it, all icons were uncategorized. Is that correct? I thought, in case of uninstallation the system menu should get activated again.