Last week I took the whole "standard" Makefile apart (which is used by "everybody" but is really far too complex for simple projects) and made a simple one from scratch that just the job and does it well. The standard makefile isn't good at detecting changes in source files, really the reason why'd want to use a makefile in the first place, otherwise you'd could just use a script as well. It also gets rid of the ridiculous subdirectories, submakefiles, etc.
What I really need now is proper documentation of the hardware, on "datasheet"-level.