If the FPGA contains a hard PCIe IP that can act as a host and the proper transceivers and the CPU implemented all of the necessary things to interface with it, it'd be about as difficult as writing a driver for any other machine. Actually building a board for the FPGA with all of the required power supplies, peripherals, and a PCIe host is not a trivial undertaking however, and an FPGA with a hard PCIe controller generally isn't cheap!
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