Here's my current plan for reorganizing the code. Header files are left out of the list, usually in same spot as C file.

octal/
	commands.c
	machine.c
	core.c
	output.c
	package.c   (was util)
	pattern/
		pattern.c
		pattern_model.c
	engine/
		engine.c
		engine_model.c
		mixer.c
	user/
		user.c   (was main)
		engine_view.c
		pattern_trackerview.c
		pattern_pianoview.c
		wavetable_view.c
	machines/
		squaregen.c
		delay.c
	wavetable/
		wavetable.c
		wavetable_model.c

 		

Note the model and view bits, alluding to the MVC-inspired architecture.