Follow-up Comment #1, bug #18170 (project freeciv):

MD5 in Freeciv is used for user authentication in the server (not an area
into which I've ventured before, as it involves faffing with databases). 

Our MD5 implementation appears to have been pinched from glibc in around 2005
(r10768 <http://svn.gna.org/viewcvs/freeciv?view=rev&revision=10768>). I can't
find a ticket for its addition to Freeciv, so I don't know more about its
exact provenance (a "Mike Kaufman" was involved). Still, if as I suspect it's
a 64-bit cleanliness issue in the code, it might be possible to find the same
bug in glibc's development history and possibly lift a newer version from
glibc.

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