I am facing the issue how to deploy 2 separate ASP.NET solutions in one IIS website. This is how I plan to deploy. In the root website folder, I put one solution's published files. Then, I create another folder in that root folder and put another solution's published files.
When I run from IIS, only the contents from root folder works but those inside a folder doesn't work.
You can use sub folders (add virtual folder) in IIS.
Remember to set the folders "Convert to Web Application" so it works with dependent configuration context.
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