What is Autoconf? What does it have to do with GNOME?

Autoconf is a tool for producing shell scripts that automatically configure source code to adapt to the system you are using. Autoconf is invaluable, since it makes the development of such configure scripts drastically easier. GNOME uses it alongside the related tool, Automake, which allows Autoconf to produce custom Makefiles for your system. Autoconf uses m4 to operate. M4 is a powerful (but arcane) macro language used by many GNU utilities. Most of the macros used to generate these files are found in either /usr/share/aclocal or the macros subdirectory of the source tree.

If you are using the tarballs, Autoconf and Automake have already been run for you, so you don't need them on your system. If you use CVS, you won't get very far without having recent versions of these tools. You can find more information about Autoconf at http://gnu.org/software/autoconf/autoconf.html, and Automake at http://gnu.org/software/automake/automake.html.

Keep in mind, that configure, config.h, Makefile, and even Makefile.in are all constructed files. If you need to change them, you shouldn't patch them directly, but rather modify the files used to create them: configure.in, config.h.in, and Makefile.am.