build: Add warnings for autogen.sh. Fix AC_CONFIG_SRCDIR.

Added warnings and verbosity for autoreconf, should be useful for debugging.
AC_CONFIG_SRCDIR argument should actually be a unique file in the src dir, not the dir itself.
(http://www.gnu.org/savannah-checkouts/gnu/autoconf/manual/autoconf-2.69/html_node/Input.html)
Also moved two AC_CONFIG calls to a more readable (usual) location.