Good autotools tutorial
Mark Kim as a nice beginners overview of Autotools. Worth the time to read it, if this is something that you're interested in!
To summarize (overly simplistic view!)
autoscan --> creates initial configure.in (called configure.scan to avoid overwriting your pre-existing configure.in)
Note: you will have to edit at least AC_INIT and AC_OUTPUT in the configure.scan template that autoscan produces.
autoconf uses configure.ac to create configure
configure.ac -> autoconf -> configure
|---> ./configure (uses configure.ac and Makefile.in to generate Makefile
You can use automake to generate a Makefile:
Makefile.am is the input to automake
Makefile.am --> automake ---> Makefile.in
autoreconf can be used to regenerate all the derived files when changes are made to input files. autoreconf will run all of the necessary tools in the correct order.