I've got a working Mega16 design. The system also contains a Xilinx FPGA with a Xilinx system PROM. Today the MCU and FPGA only talk over SPI. They are programmed separately, 6-pin ISP (.hex) for the MCU, Xilinx JTAG dongle for the FPGA (.mcs).
For the future I'd like to upgrade the system with a bootloader for the MCU and for the MCU to program the Xilinx PROM. I'll probably use RS232 or UART over USB for this.
I'd appreciate any comments on the feasibility of this. I'd like to be able to program the FPGA with full verification and a following read-protect-enable.