The desktop file will not contain empty lines
If empty lines are en ountered, the GNOME skip it
 and does not put into menu entry.
If some installed GUI based apps does not
appear on the menu entry, will be this kind of problem.
Check on 
/usr/share/applications
If corresponding .desktop file exists, edit it using text editor
 and delete empty lines to correct it.

Perphaps, will use "tee" from command line. Need check for their sintax.

Note that the nautilus does not display file name for
.desktop. Thus, need to use ls on command line to
identify.
