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answers:

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What is the difference between using an MST combined with an MSI, and running the MSI and passing the modified properties through the command line (MSIEXEC)

+1  A: 

An MST can contain all kinds of changes to the MSI--including new or different files, Registry entries, custom actions... and modified properties, as you mention.

On the MSI command line, the only thing you can do differently is change properties...

ewall
A: 

When deploying a package via Active Directory, you can't specify command line properties... so you'll need to use an MST.

Additionally if you want to add/change new files (either uncompressed, or in a CAB) then you'll also need an MST.

sascha

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