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Is there a way to script a snapshot for the purposes of application installation and package creation?

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http://serverfault.com – I know there are solutions that do this in the wild (and some are free) that perform difference based app packaging, but for some reason when I use them for those tough packages (silent install fails when following vendor's instructions, vendor doesn't support silent installs, take your pick) some of those also fail. Also, they miss certain things. If it's pretty easy to script this, I'll take a crack at it, I know that they typically grab File System Changes Registry changes and they don't grab File Permission Changes Driver installs And package them into an msi. I also know a true (HowTos)