My /home/user/.osso/menus/applications.menu is empty, but the former file has the default entries as you listed and the directory still has all my .desktop files for all my installed applications.

I guess there is no way to automagically have it regenerate my applications.menu given the .desktop files?

Edit: I just copied the default applications.menu file to the one located within my home folder, and now the defaults show up.... but argh! Wouldn't there be some sort of error when I install applications and it's not able to write an applications menu entry for one reason or another? I guess I'll have to sit down some day and manually recreate all my menus and their entries.

Edit 2: I tried the suggestion from this post but it didn't even seem to do anything. The /etc/xdg/menus/applications.menu was still the default after executing the command in that post. I even tried renaming both the /etc/xdg/menus/applications.menu and the blank one under my home folder to other names and running the command with no success, no files were created. If it makes any difference, I'm running from mmc.

Edit 3: Ok, silly me for not fully checking. Just when I gave up, I started tapping through the default menus and found out all the previous apps were now moved to Extras in one giant list. So now I just have to recreate my custom menu structure and reorganize my application menu items. I'm guessing they were all dumped into Extras because the .desktop files don't have specific menu categories listed in them.