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We tried to be clear in the WGTH? section, but basically we don't copy those things that are automatically recreated on the other system when you boot. These include Unix temporary files and virtual memory swap files, plus a few special files that -- again -- are part of the OS and shouldn't be copied.
Note, though, that there are some programs (the latest version of Quark is a good example) that "lock" themselves to the drive that you're physically on. Copying Quark -- even if you copy every file, and we do -- doesn't mean it'll still be activated on the other drive. They're working hard to make sure that isn't the case. So, you'd have to re-activate it, and any other program that tries to do nasty things like that. Otherwise, though, you *are* making an "effective" exact clone. (It's usually best, in this kind of case, to name the backup the same as the original volume, too.) Hope that helps.
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