The new code is in SVN. Basically, you set the upload.using preference in the Arduino preferences file to be the key of the one of the programmers defined in programmers.txt. The upload will then use that programmer. You can add programmers to that file as well, AVRISP, AVRISP mkII, stk500, etc. should work (anything that's serial, parallel, or USB, I think). I didn't know about the avrdude.rc providing default options - I'll look into that. Maybe I'll add the option to set upload.using to "avrdude" or to have it use that.
For the moment, I'm planning to leave this option out of the IDE, because I don't want to confuse people that don't know what a programmer is (and don't need to), which I think is a large portion of our user base.