Looks like the SAMA5D2x PIO controller differs from the SAMA5D3x and D4x PIO controllers. So the PIO/ISR configuration probably needs to be updated. I'm giving this a shot, but not sure how best to tackle this. Should I look at the Linux4SAM code? Or is reading the datasheet the best way to go? Deciphering that is pretty slow going.
I would not recommend looking at Linux code at all. First, Linux is to complex to follow the logic and second, it is GPL so you are permitted to leverage anything from there due to the license: I would look at the IRQ number and the RX pin configuation.
