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Patch at http://codereview.appspot.com/1749042.
The idea here is to let the user set CFLAGS on either configure or make (or both), and have later settings appear later in the $CC command line. I left OPT, BASECFLAGS, and EXTRA_CFLAGS around in case people have written scripts using them, but I think they're superfluous as user-visible knobs after this patch.
I prevented AC_PROG_CC from setting a default $CFLAGS value because the values it would set are already put into $BASECFLAGS when appropriate, and @CFLAGS@ needs to appear after @BASECFLAGS@ to allow the user to override Python's defaults at configure time. We could also accomplish this by removing BASECFLAGS and OPT entirely and instead prepending their contents to $CFLAGS in configure. That's a bigger patch, but if any of you feel strongly about it I can do that instead.
I made the same changes for CPPFLAGS and LDFLAGS but no other user-settable variables. I don't have strong opinions about the exact set we support this for, as long as it includes CFLAGS, but these three seemed like a sensible set.