configure: fix issues that 'autoupdate' detected

- AC_HELP_STRING is an obsolete macro and has been replaced with
  AS_HELP_STRING, so use it instead.

- AC_OUTPUT accepts arguments, but this use is deprecated. Instead, use
  AC_CONFIG_FILES and run AC_OUTPUT with no args.
autogen: enable all warnings for autoreconf

An extra option is needed for autoreconf to make autoconf warnings
visible, helping to detect issues like those fixed in the previous
commit.