Automake takes as input the file Makefile.am and produces Makefile.in.
The "autoconf" program takes as input the file configure.in (or in Autoconf 2.5 the file configure.ac) and generates the ./configure script out of it.
Autoheader takes as input the files acconfig.h and generates the config.h.in template by parsing configure.in.
./configure, when ran by the user generates the normal Makefile out of Makefile.in and optionally processes other files (such as config.h.in -> config.h, an optional RPM Spec, Makefiles in other directories, etc.
