I have a website project and would like to setup different web.config transformation files for it, but the option doesn't exist when I right-click on the web.config file. Is this option limited to web applications?
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You can use a Web Deployment Project.
For the VS 2010 version, see:

RickNZ
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1Looks like this might be [supported](http://stackoverflow.com/a/10356428/612265) now. – Evan Haas Dec 02 '13 at 17:37