This is a post to record difference methods on linux or wherever for large numbers of files (3m to 4m)
https://stackoverflow.com/questions/4997693/given-two-directory-trees-how-can-i-find-out-which-files-differ
A utility that is useful for such compares is xargs. A tutorial is below
http://www.linuxplanet.com/linuxplanet/tutorials/6522/1
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