The "Gertboard" requires several link wires to be connected between Pi GPIO inputs and outputs before different python or 'c' programs are run on the Pi.
What "Arduino" code could you suggest I might use on the "Gertboard ATMega" to configure these connections by inputting a sequence of two pin references for any given Pi program. e.g. From the "Gertboard" Manual Page 17 Fig. 13: The wiring diagram necessary to run the "Gertboard" LED test program, leds (12 Pi GPIO connected pins used in this example - too many for ATMega pins?).
This, in an attempt to avoid the requirement to physically wire the pins manually for any given pi or 'c' program.