Download the rusEFI bundle for your hardware.
Launch rusEFI Console. You can find it in the bundle you downloaded, in the "console" folder.
Click the "Update Firmware" button.
The canonical way to update the firmware on Linux is with DFU.
You will need dfu-util:
# Debian/Ubuntu sudo apt install dfu-util # Arch/Manjaro sudo pacman -Syu dfu-util
Once you have dfu-util, you can run this from the extracted bundle directory:
java -jar console/rusefi_console.jar reboot_dfu dfu-util -a 0 -D rusefi.dfu
For more about DFU see HOWTO-DFU
ST-LINK is an advanced mode of firmware update which requires ST-LINK device, either external, or built-in like on Discovery/Nucleo board.
Update TunerStudio Definition
Once you have updated your firmware, you also need to update your TunerStudio definition so it is able to communicate properly.
You can find the .ini file in the USB storage device that rusEFI board presents to your computer, or in the rusEFI bundle. The former is preferable, as it ensures that you have the correct version for the firmware that is installed on your board.