- Makefile.am (the .am stands for automake) is a programmer-defined file and is used by automake to generate the Makefile.in file.
- The configure script itself is generated from a programmer-defined file named either configure.ac (autoconf) or configure.in (deprecated).
- The configure script will use the Makefile.in to generate a Makefile.
Makefile.am --(automake)--> Makefile.in | configure.ac --(autoconf)--> (configure) | Makefile <---+
autoreconf --installgenerates several template files which should be tracked by Git, including Makefile.in. It only needs to be run the first time.