Using xfce4 as window manager.

Then using xfce4-menueditor to reorganise and add to the desktop menus.

The changes are saved to ~/.config/xfce4/desktop/menu.xml, and all is fine.

Then I run update-menus and this modified menu.xml file is overwritten by a new one generated by update-menus.

Why is update-menus so rude as to over-write my personal menu settings, and how can I stop it from doing so?

Why are you running 'update-menus' if you are already making the desired changes yourself? You could always rename the xml file before and then after the command to retain your settings.

Agreed, but since update-menus seems to run automatically after new apps with menu entries are installed, that would mean remembering to move or backup the menu.xml file every time a new app is installed.

Painful, and certain to end in tears sooner or later.

You said, "Then I run update-menus...". It was not made plain in your initial post that this was an auto-config problem. Please be more specific in the future.

If you have the menu-xdg package installed, remove it.

By default, xfce4 looks in /usr/share/applications/ to generate it's 'system' menu. This folder is part of the freedesktop.org standard. Gnome and KDE also follow this standard now. The problem is that not all applications are packaged to create a file in this directory. The best way around this is to create files for the apps that don't show up in your menu. The format isn't difficult to understand and by now there's probably even an app out there that will do this for you.

update-menus aims to solve this but it does seem to overwrite the xfce menus.. have a look at the man page for update-menus. In the configuration section it mentions /etc/menu-methods which contains files dealing with each different window manager. It also says users can create their own methods for how a update-menus deals with certain window managers in ~/.menu-methods