There's a number of reason why you'd want to program your Arduino device as a regular AVR MCU. For me it was having to do some tests I'd later have to run on a normal AVR board and only having an Arduino board available. Turns out the built-in STK500 ISP on the Mega 2560 is supported by avrdude.
The whole compiling/flashing shebang can be done with the following Makefile (slightly modified from the one found here).
You'll probably have to modify the DEVICE variable if you're using something
other than OSX and the SOURCES one if you're using C++ instead of C.
NAME := main HEX := $(NAME).hex OUT := $(NAME).out MAP := $(NAME).map SOURCES := $(wildcard *.c) HEADERS := $(wildcard *.h) OBJECTS := $(patsubst %.c,%.o,$(SOURCES)) MCU := atmega2560 MCU_AVRDUDE := m2560 PARTNO := stk500v2 DEVICE := /dev/tty.usbmodem* BAUDRATE := 115200 AVRDUDE_FLAGS := -F -V -D -v CC := avr-gcc OBJCOPY := avr-objcopy SIZE := avr-size -A CFLAGS := -Wall -pedantic -mmcu=$(MCU) -std=c99 -g -Os -DF_CPU=16000000UL all: $(HEX) clean: rm -f $(HEX) $(OUT) $(MAP) $(OBJECTS) flash: $(HEX) avrdude $(AVRDUDE_FLAGS) -c $(PARTNO) -p $(MCU_AVRDUDE) -P $(DEVICE) -b $(BAUDRATE) -U flash:w:$(HEX) $(HEX): $(OUT) $(OBJCOPY) -R .eeprom -O ihex $< $@ $(OUT): $(OBJECTS) $(CC) $(CFLAGS) -o $@ -Wl,-Map,$(MAP) $^ @echo @$(SIZE) $@ @echo %.o: %.c $(HEADERS) $(CC) $(CFLAGS) -c -o $@ $< %.pp: %.c $(CC) $(CFLAGS) -E -o $@ $< %.ppo: %.c $(CC) $(CFLAGS) -E $<
With the Makefile in the same folder as your main.c just run:
make make flash
And you should have you program running in the Arduino.
To know the pin mappings from the board to the actual ATMega2560 pins, you can check this useful resource.