I can find this all over the web as far as people installing programs, using which ever method they desire, and having some of them not show up in the menu. An example in my instance is the program "Scribus". If I go to the part of the menu where you can type the name of the application, It finds it. Then I go to the menuedit from the terminal to see where the heck it is in the menu. It seems that it is in the graphics part of the menu, head over there and it is not there. This is just one example, I have more.
It seems that people need to set certain files to executable to make this work? Can anyone let me know how they got through this? Eventually I would like to add menu items (menuedit for instance), but I am not even going there until I see how to make this work.