Menudrake keeps files in each user directory under ~/.menu/

One of those files is named 'adding_by_menudrake'.  This is where your edits 
go unless they are deletions in which case they go under their own name and 
show as "available applications" the next time you run menudrake.

Your menu is built from /etc/menu/menu and other files in that directory.  
Menudrake is _supposed_ to be able to place a file in that directory, but it 
appears that it can happen only once.  That file is merged with 
/etc/menu/menu for putposes of updating menus.

If you merge by hand the data stored in your ~/.menu/adding_by_menudrake with 
the file referring to menudrake in your /etc directory, it will become 
available for all users immediately after the next run of update-menus.  It 
will, that is, if you don't make a mistake in the editing.  Otherwise, expect 
to be using a console to delete the merged file and rename the backups to 
their originals.

I do NOT recommend anyone try to open /etc/menu/menu (or any other file in 
/etc/menu) with a text editor of less ability than jed or emacs, and 
specifically suggest you leave it alone with kedit, because text wrapping 
done by some editors causes a disaster.  Anyway, that's how to update menus 
for now.  

For those of you with four copies of every menu item, look at /etc/menu/menu 
and look at other files there as well--those files are merged in making the 
menu--so your problem might lie there.  Detecting and removing duplicates 
should be reasonably easy with a powerful editor.

Civileme

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