I got a copy of preprocessed sources from bryan d. o'connor.
Here's what seems to be the problem:

* <config.h> has "#define __GETOPT_PREFIX rpl_" as expected.

* unexmacosx.c includes the Gnulib <unistd.h>.

* The Gnulib <unistd.h> includes the system unistd.h, which declares
  the getopt-related names itself (without including anything) and then 
finishes.

* The Gnulib <unistd.h> then includes the Gnulib <getopt.h>.

* The Gnulib <getopt.h> includes the system getopt.h.

* The system getopt.h includes the Gnulib <unistd.h>.

* This inner Gnulib <unistd.h> does nothing, and finishes.

* The system getopt.h declares 'struct option' and other stuff, and finishes.

* The Gnulib <getopt.h> then does this:

     #if defined __GETOPT_PREFIX && !defined __need_getopt
     # if !@HAVE_GETOPT_H@
     #  include <stdlib.h>
     #  include <stdio.h>
     #  include <unistd.h>
     # endif
     # undef __need_getopt
     ...
     # undef option
     # define __GETOPT_CONCAT(x, y) x ## y
     # define __GETOPT_XCONCAT(x, y) __GETOPT_CONCAT (x, y)
     # define __GETOPT_ID(y) __GETOPT_XCONCAT (__GETOPT_PREFIX, y)
     ...
     # define option __GETOPT_ID (option)
     ...
     #endif

* This should "#define option rpl_option", but apparently it doesn't.

* Presumably __GETOPT_PREFIX is defined, but __need_getopt is also defined,
  so the entire #if is skipped.

* And when Gnulib <getopt.h> declares a 'struct option', this clashes
  with the 'struct option' declared in the system getopt.h.
       
If my analysis is right, we need to figure out why __need_getopt is
defined.  Can you send the output of the following?

cd emacs
grep -r __need_getopt . /usr/include


PS.  This all seems to be a case where we should be using Gnulib's
identifier replacement mechanism, but I don't understand it that
well and if memory serves it doesn't work with struct tags anyway.

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