Here's the hex file I've been using as bootloader,
the pins_arduino.h variant,
and the boards.txt entry:
##############################################################
bobuino.name=Bobuino
bobuino.upload.protocol=arduino
bobuino.upload.maximum_size=130048
bobuino.upload.speed=115200
bobuino.bootloader.low_fuses=0xff
bobuino.bootloader.high_fuses=0xde
bobuino.bootloader.extended_fuses=0xfd
bobuino.bootloader.path=optiboot
bobuino.bootloader.file=optiboot_atmega1284p.hex
bobuino.bootloader.unlock_bits=0x3F
bobuino.bootloader.lock_bits=0x0F
bobuino.build.mcu=atmega1284p
bobuino.build.f_cpu=16000000L
#bobuino.build.core=arduino:arduino
bobuino.build.core=standard
bobuino.build.variant=bobuino
##############################################################
optiboot_atmega1284p.hex (1.47 KB)
pins_arduino.h (6.08 KB)