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If this configuration needs an operator decision, I think
this decision is best made in Modules/Setup.local. Anybody
who wants to use the local libffi installation can do so, by
writing a Setup.local that lists the source files, and gives
-lffi as a library option. Setup.dist could provide a
commented version of such a configuration.

setup.py *should* then skip over building _ctypes, as it
should find out that _ctypes was already built through Makefile.