rename configure.in -> configure.ac

Silences warning on newer autoconf:

aclocal: warning: autoconf input should be named 'configure.ac', not
'configure.in'
add AC_CONFIG_MACRO_DIR([m4]), move *.m4 files to m4/

Silences notice on newer autoconf:

libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.ac and
libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree.

This helps keep the top-level build directory clean, too
s/INCLUDES/AM_CPPFLAGS/g

Silences warnings on recent automake such as:

src/core/Makefile.am:3: warning: 'INCLUDES' is the old name for
'AM_CPPFLAGS' (or '*_CPPFLAGS')
Merge pull request #68 from falconindy/master

Autotools cleanup