linux: dts: Remove FPGA GPIOs from dts.

Remove GPIOs controlled from FPGA logic. The content of the FPGA is likely to change a lot between gateware options. It would be cleaner to keep the FPGA content inside the overlays associated with the gateware build option/source RTL. The vast majority of these GPIOs do not follow the Beagleboard naming convention and need to be modified anyway.