How is AVR Assembly in Eclipse or at Linux command line done? I'm trying to learn AVR development in C and Assembly for the Arduino Uno (Atmel 328p microprocessor) in Linux. 

I've found many good guides on how to install and setup the AVR plugin for Eclipse, and I've no problem building and uploading C code. 
However there doesn't seem to be any menu options for creating an assembler project, nor can I seem to find the correct syntax for using the cli avr-as for assembling my programs into a .hex file.
If you don't mind using make, I'd recommend copying the Makefiles from ChibiOS. For me it works quite well and it's much more aligned to my daily experience with Linux.