If I understand your process correctly, wouldn't there be at least the slightest little worry that two different (original) file names would generate the same MD5 hash?
I suppose that if you just make a list of the file names and their md5 sigs first, you could spot collisions before actually moving stuff into the new directory structure. But if you have to add files to the structure over time, you need to check for the existence of a given md5 "path/name" before storing a new file there (and then figure out a proper way to avoid collisions while maintaining correct mappings between original and hashed names).
