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How can I deploy a new web application to a subdirectory of an IIS site and not have to click “Convert To Application”?

I'm trying to write an automated deployment application that runs on one box but deploys to a remote QA server. Basically each time a branch is created in source control my automated deployment tool will deploy the application. Right now the code all deploys but IIS doesn't like the nested web.config files unless I use the "Convert to Application" function.

Notice in the below screenshot that for the Test-Site which was just created for the new "Test-Site" branch that the folders "Analyze", "Investigate", "Measure" and "Score" aren't applications like the RevECurrent and RevENew have above for those folders. Without actually clicking "Convert To Application" for each folder how do I make the web.config files not generate errors whenever I deploy a new subdirectory like "Test-Site"?

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Check the System.Web.Administration namespace , it will allow you to interact with IIS. I have used it to add/remove bindings, add sites, etc... I would assume it would let you create application folders under a Web Site as well.

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