Makefiles are definitely a useful alternative to the IDE. We used to include one with the distribution, but no one maintained it and I didn't really have the resources to do it myself. There are now a few different Makefiles out there, e.g.:
http://bleaklow.com/2010/06/04/a_makefile_for_arduino_sketches.html
http://mjo.tc/atelier/2009/02/arduino-cli.html
If people standardize on one and keep it maintained, then I can include it in the distribution again.