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This patch attempts to do what Tim suggested in the python-dev thread about getopt()'s prototype and the difficulties of it. the 'getopt' implementation as provided in Python/getopt.c is renamed to Py_GetOpt(), the exported variables 'opterr', 'optind' and 'optarg' are prefixed with Py_, and all use in the Python sourcetree is adjusted.
The patch is missing the 'pygetopt.h' include file, though :P I'll resubmit a proper patch later. 
There are a couple of issues still open: the name of the getopt.c file, its use of 'fprintf(stderr, ... )', its license, documentation (which this patch lacks) and whether this Py_GetOpt should be an officially exported API at all.