There is no reason to slurp the whole file into memory just to calculate an MD5. See Digest::MD5 for the correct way to do it; efficiently.
It's quite common for a disk file to be larger than the available RAM on a machine, so that's just about the worst algorithm error you could get in there (on an algorithm that works at all).
Though the usefullness of an MD5 here is somewhat suspect in the first place; expensive, and gains nothing over the sollution it would replace.
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