Собственно всё написано в readme:
How to compile firmware:
All you need is WinAVR. Just type "make hex" in command line to compile firmware or bootloader.
How to build it:
You need to flash ATMEGA64 microcontroll using any AVR programmer. It's recommended to program bootloader first, so you can flash/update firmware via USB. I'm using bootloader by Martin Thomas, you can use already configured one in bootloader folder. There are fuses for it:
LFUSE = E4
HFUSE = DC
EFUSE = FF
You can program it using command like "make program PROGRAMMER_TYPE=avrisp2 PROGRAMMER_PORT=usb" from bootloader folder. Don't forget to replace avrisp2 and usb with you programmer type and port.
Connect device to USB and PC will detect it as virtual serial port. First 8 seconds after power up bootloader is active (all leds are on), so you can program main firmware.
You can use command "make program PROGRAMMER_PORT=COM10" to program main firmware. Replace COM10 with port assigned to your dumper (you can use Windows device manager to see it).
Also it's recommended to reprogram FT232 chip using FT_PROG util to change device name to "Famicom Dumper/Programmer", so it can be detected automatically by software.
That's all! You can use it now.