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How can I run a program after the Windows Installer? I know how to mount and commit .wim files.

This must be done using the Windows Automated Installation Kit.

Is there a default registry hive where I can create a entry under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run? where do I find the hive on the installation media?

I don't need to automate the install process, except to run a program after the installer finishes.

Update: I just found out about the file %WINDIR%\Setup\Scripts\SetupComplete.cmd is this the proper way? Which .wim file is this in?

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If possible I would highly suggest the use of the MDT2010 package as WAIK has been superseded.

Just because scripted installs and automation are possible with MDT doesn't mean you have to use them - for a long time I simply had a basic OS install with no automation and a couple executables in the post install section.

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