After doing a lot of trial and error have come up with a solution. First you'll need some way of starting xterm. Fortunately, even though my applications were gone, I could still run a command through the statusbar-app, which allowed me to run xterm (osso-xterm). After that, I did the following:

1. sudo gainroot (if you do not have becomeroot installed, you may not be able to do this, but I am not sure if it absolutely necessary).

2. run this command: update-desktop-database /usr/share/applications/hildon/

3. then run: cp /etc/xdg/menus/applications.menu /home/user/.osso/menus/applications.menu

This seemed to work for me, so I hope it is of some help!