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I would like to build an MSI file for Active Directory deployment. Instead of taking a pre install snapshot, installing the application, taking a post install snapshot and packaging the differences in an MSI file. I would like to put a setup.exe file inside a MSI file and run it with the /silent switch.

Is there any free or cheap programs that could do this?

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The Windows Installer Wrapper Wizard will do what you want. It's scant on documentation and you should test the heck out of anything you make with it.

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