The first thing I did was get rid of the IDE completely and just replace it with a Makefile, so I can use the emacs compile command to build. You can find the Makefile I use in the "microcode" subdirectory of the source tarball for my project:
http://home.comcast.net/~tomhorsley/hardware/arduino/software.html
It is obviously highly specific to the install directories I have and the hardware I'm using, but it works for me and does get the annoying IDE out of my way.