Elijahg:
There's a small problem with uploading too, for some reason the port for AVRdude to use gets lost somewhere. Changing AVRDUDE_PORT in Avrdude.mk to $(BOARD_PORT) fixes that.
That's strange, AVRDUDE_PORT is defined in Avrdude.mk by:
AVRDUDE_PORT = $(firstword $(wildcard $(BOARD_PORT)))
with BOARD_PORT defined in Arduino UNO.xconfig by
BOARD_PORT = /dev/tty.usbmodem*
or in Step1.mk otherwise by
ifndef BOARD_PORT
BOARD_PORT = /dev/tty.usb*
endif
Arduino UNO.xconfig has priority over Step1.mk.