Short answer: build it from configure.ac. Useful answer: You'll need to use autoreconf (which is part of the autoconf package) to create the configure script. The autoreconf tool will also run all the other 'auto' tools like automake, aclocal, et c., and do so in the correct order. So the more useful answer boils down to, 'run autoreconf.' I find the '--verbose' and '--force' options are often useful. Once you've run autoreconf, you should have a configure script and Makefile.in files. Each project that uses autoconf has one configure/.ac script in the top directory. There will be one Makefile/.am/.in set for each directory. Once you've run autoreconf and configure once, the Makefiles that are created know how to run the auto tools when various things like a Makefile.am changes. Resit the temptation to check generated files into svn.