How do I transition from using the Arduino IDE to plain avrdude/make?
The tool I would use in this case is Cduino. Cduino is a tool designed to give greater control over the actions of the ATmega and doesn't require a bootloader. 


  The cduino project tries to make it simpler to migrate from the arduino to simpler hardware setups, in particular those that lack a USB serial interface and bootloader. This may be interesting to users for whom cost definitely is a factor.


You will need a USB programming cable, and a Duemilanove or an Uno as it uses the Mega328p chip. Of course, Uno's and Duemilanove's seem to be the most common, so this shouldn't be an issue. You will also want an ISP (examples given in the first part of the question) for in-system programming (i.e. to avoid the bootloader).


  It's a lots like the excellent arduino project and uses the same open hardware, but avoids the new wiring language, the C++ intermediate layer, and the Java-based IDE.


Cduino itself is a command line tool which allows you to write directly to the Arduino. You will need a few packages installed, including make, avrdude and screen. To make it run without the bootloader, connect the Arduino as I explained in the previous question, and in the generic.mk file change UPLOAD_METHOD from arduino_bl to AVRISPmkII.

Uploading the file itself is a simple command line sequence:

make -R -C &lt;program_name&gt; writeflash


Then, to communicate with the board serially, use:

make -R -C term_io writeflash 
make -R -C term_io run_screen


There is a series of 'lessons' to write code for Cduino here. It is basically C, but with a few library functions specific to the ATMega328p chip - note that it is C, NOT C++.