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We quite clearly mention, in the white paper, that we "roughly defragment your system files". We make no claim of directory structure defragmentation, and also suggest people buy iDefrag if fragmentation is a serious issue.
We do nothing weird when we copy files, walking them in "natural folder order" as returned from fts, so I don't see how you'd get different results with other tools... the files are copied sequentially, in order....
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--Dave Nanian
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