Setup Manager is a tool you can use to create answer files, such as Sysprep.inf. If you're like most professionals, you'll create your own answer files manually, without the aid of Setup Manager. Setup Manager doesn't factor in to any other part of the disk-cloning process. Create the Sysprep folder, which includes Sysprep.exe, Setupcl.exe and Sysprep.inf, and then run Sysprep.exe to prepare the disk for cloning.
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