What I have is just bare ATMega328 (note the lack of "p"), which I am going to program (using avrispmkii directly). As I already have the MCU assembled, I do not want to change to, say, Arduino Uno to be able to use the library. Most likely, I will "play" with the Bluefruit on Arduino first to get the feel of it, but the code needs to be run on the "bare" ATMega328. The other part of the program (which prepare data to be sent from atmega) is trivial, so I will have no problem to rewrite it from C to Arduino. Porting Adafruit library from C++ to C is probably much more difficult.
Thus, one of the possible approaches is to compile the my code + Bluefruit LE code for Arduino, but upload to the ATMega328.
And this is where I need help:
How to make Arduino (command line tool is ok) to compile to the MCU I have? I guess, the result should be some kind of hex-file for flash (and eeprom?).
And, may be useful, which flags to use with avrdude, if there is anything specific for the Arduino-generated code. (I do not need any bootloaders on the chip, just the program, and I do not have UART-USB connected to atmega).
Of course, please, mention if there are better ways I overlooked, like some Arduino-compatible gcc toolchain to compile C++/C mix into avr code (avr-g++?). Or maybe there is some C-library for the component atmega needs to talk to.
UPDATE: Similar question: http://www.avrfreaks.net/forum/using-arduino-ide-general-atmel-microcontroller-no-bootloader-no-cristal