Add warning about setting up pins in custom firmware

Author: WillB97

programming/sr/ruggeduinos/custom_firmware.md

@@ -25,6 +25,11 @@ If you're using completely custom firmware, you'll need to tell the kit to ignor
 [Extension of the SR firmware](#extension) {#extension}
 ------------------------------
 
+<div class="warning">
+Because the API sets all pins to inputs when the robot is initialised, you cannot set pin modes in the setup function as these will be overridden.
+In order to setup pins you can either create a function on the ruggeduino that you call after your robot is initialised or use the [python functions](/docs/programming/sr/ruggeduinos/) to setup the pins. 
+</div>
+
 You may wish to extend the SR firmware with additional functionality.
 This will allow you to continue using the commands already provided by the SR firmware (e.g. `digital_read()`),
  which means any existing robot code you have won't need modifying very much.