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Using two values for 'Virtual Directory' in web.config

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I am using two URLs (say url/internal, url/vendor) for my application which has different authentication (one has AD authentication & the other has application login).

I have created two application under the default website in IIS - each of which is mapped to same root folder.

The issue i'm facing is when i login with url/vendor (which is using application login) and navigate to other pages from home page, the URL gets updated to url/internal and it subsequently asks for AD authentication.

Since the Virtual Directory in web.config is "internal" if i create different root folder for url/vendor and Virtual Directory as "Vendor" this issue is resolved.

But i want to use only one root folder.

Question: how can i achieve two values of VirtualDirectory in same web.config for two sites of application.

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