Makefile.am -- a user input file to automake
configure.in -- a user input file to autoconf
autoconf generates configure from configure.in
automake gererates Makefile.in from Makefile.am
configure generates Makefile from Makefile.in
For ex:
$]
configure.in Makefile.in
$] sudo autoconf
configure configure.in Makefile.in ...
$] sudo ./configure
Makefile Makefile.in