Yes, I think that would work.
A workaround might be quite easy though.
Produce 2 md5s. One from the whole file and another from the file minus 1 byte (first, last or middle). Or make the second md5 just the first half of the file; or from just the 10th, 20th, 30th etc. bytes (or whichever bytes the attack modifies to compromise the md5).
Now the attackers not only have the task of finding a duplicate file with the same md5, they have to produce one that matches two md5s.
Again, my math lets me down, but doesn't that make their job much, *much* harder?
Examine what is said, not who speaks.
"Efficiency is intelligent laziness." -David Dunham
"Think for yourself!" - Abigail
"Memory, processor, disk in that order on the hardware side. Algorithm, algorithm, algorithm on the code side." - tachyon
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