autogen.sh: replace custom bootstrap mechanism

autogen.sh is a widespread convention for autotools setup.
configure.ac modernization

- AM_CONFIG_HEADER->AC_CONFIG_HEADERS
  removed from automake 1.13
- AC_PROG_INTLTOOL->IT_PROG_INTLTOOL
  removed from automake 1.13
- AM_PROG_MKDIR_P->AC_PROG_MKDIR_P
  deprecated
- introduce AC_CONFIG_MACRO_DIR
  ensure correct local m4 macros
Makefile.am: INCLUDES->AM_CPPFLAGS

INCLUDES was deprecated.