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From this article I see I can use msbuild to apply configuration transformations but is there another way using either a command line program or.Net API?
http://msdn.microsoft.com/en-us/gg454290
Update:
I found an answer:
I found an answer on this and provided a quick writeup on it:
http://mbonig.wordpress.com/2012/01/11/using-the-vs2010-publishing-configuration-transformations-outside-of-vs2010/