How to Manage the Main Menu Icons on Gnome
No matter what desktop environment you choose to work with, or if you prefer playful docks to classic menus, your system's main repository of applications will always lie on your main menu, found on a corner of your screen or on the center of it in the case that you are using GNOME Shell. Installing software from here and there may quickly lead to an over-bloated main menu where users cannot easily find what they are looking for, while new users are confused as to how they can add a compiled binary file on their menu. It is imperative that the Main Menu is managed and customized effectively in order to serve its user in the most ergonomic way possible.
The Alacarte way
One easy way to modify your main menu entries is to use the Alacarte menu editor. This simple to use utility allows you to enable/disable entries, add or remove items from the menu and fiddle with the application categories and subcategories.
Using the buttons on the right, you can add new entries and link them with a binary file located in your hard disk. Let's do a step by step example. Suppose that I want to add an entry of the Rigs of Rods simulator in my main menu. First I'll have to locate the binary file which is the “RoR” executable in /home/rigs-of-rods/bin folder.
Now I can go to Alacarte, choose the “Games” category on the left and then press the “New Item” button on the right. The name can be set to anything I want but the command should be the “RoR” binary. Pressing “browse” allows me to locate the file on the file manager, so the new entry can be added by pressing the “Ok” button. Optionally, you may also choose an icon for your new entry by pressing the box on the left and browsing again for the .png or .jpeg file.
After restarting the session (press Alt+F2 and then “r” and enter if you're in GNOME Shell), the new icon should be accessible via your Main Menu.
The File Manager way
As Linux distributions differentiate significantly in some sectors nowadays, it is often the case that Alacarte won't work as intended. This is when you'll have to use your File Manager to access your main menu icons and make the proper changes to them (add/delete/remove/change).
You will find the main menu entries under /home/.local/share/applications. Note that the “.local” folder is hidden so you have to enable the “show hidden files” option in your File Manager to see it. This folder contains the .desktop files that you installed as a user. For the software that was installed by the administrator, the corresponding .desktop files are found in /usr/share/applications. To make changes on this location you will need to open your file manager as the root user. To do this, open a terminal and type: “sudo nautilus” and hit enter (replace “nautilus” with the name of your file manager if you're using something else).