I think that the first time you download and run an application, Haiku should automatically add it to boot/be/Applications folder so that it automatically shows up in your Leaf Menu/Applications folder so that you can access it more easily.
No, even better. Make it an option on right-click: “Link to Applications Menu” or such like. Then you can get a dialogue to ask if you are sure, just in case you click it accidentally.
I’m sure Tracker could read if that file was an executable, and then only show that option on executable files that don’t have links in the Be menu. Win-win situation i believe.
EDIT: typo city, and clarification
No thanks, I organize my deskbar menu the way I like. I like to categorize my software, and some progtrams do not deserve a menu shortcut. I place a shortcut to /boot/apps in /boot/home/config/be/Applications for all the programs that do not get their own link.
Haiku could just ask if you want to install a shortcut or not.