- Launch the application
- Fire up a terminal and run `xprop WM_CLASS`. Click the application window.
- You'll get some output like `WM_CLASS(STRING) = "Navigator", "Firefox"`. Choose one of the classes, eg Firefox in this example
- Add the class as the value of `StartupWMClass` in the .desktop file. For example, `StartupWMClass=Firefox`
- Save the .desktop file, close the application and re-open it. There should now only be 1 icon in the launcher