Autoupdate on configure.ac.  Also remove some really old, commented-out junk and write-only variables.
Update acx_pthread.m4 (now ax_pthread.m4) from the autoconf macro archive.
Squelch unused and definitely unnecessary autoconf checks:

* HAVE_GETHOSTBYNAME_R is redundant to HAVE_GETHOSTBYNAME_R_[653]_ARG
* HAVE_PTHREADS is redundant to HAVE_PTHREAD
  (renamed the PTHREADS automake conditional to PTHREAD for consistency)
* <stdarg.h>, <stddef.h>, and <stdlib.h> are C89, no need to check for them
* fcntl.h, fcntl(), and signal() are used unconditionally
* poll.h and port.h are used under checks which imply their existence
* inet_aton(), splice(), struct in6_addr.s6_addr32 and .s6_addr16,
  and struct so_linger are not used at all
m4/ directory tidying:

Rename ac_backport_259_ssizet.m4 to backports.m4 (since it will
now contain more stuff).
Replace AC_USE_SYSTEM_EXTENSIONS conditional use in configure.ac
with an additional backport (of the autoconf 2.69 version).
Remove ntp_pkg_config.m4; use PKG_PROG_PKG_CONFIG instead.
Monkey-patch AC_INCLUDES_DEFAULT not to do pointless checks. Make sure AC_CHECK_HEADERS is always used in the mode where it doesn't check for everything two different ways.