The patch file in this repo is built against the source code for wpa_supplicant version 2.6.
It changes the default option for wpa_gui to start in the system tray, instead of in the main window. I find that to be a more sensible default since in most cases the device will connect to a saved network, and the window pop-up is just downright annoying.
The patch can be applied to the source code through the following commands:
tar -xf wpa_supplicant-2.6.tar.gz
cd wpa_supplicant-2.6/
patch -Np1 -i ../wpa_gui-default-to-tray.patch
The patch also replaces the startup option -t with -w, which will start the main window. The desktop file and the man page are also edited accordingly.