In SharePoint, a web application is a site in IIS. It is where an administrator defines what the root URL of the site will be, type of authentication that will be used, and other site-wide settings.

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Adding a custom web application to a SharePoint site

Has anyone added a custom web application to a sharepoint site? I thought it would be added as a virtual directory and then you'd specify an unmanaged path but i'm not having much luck.
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How to replicate site collections on the same web application?

I need to create a copy of publishing(Collobaration Portal) site collection on the same web application. I can do this by using backup/restore, but the problem is when we restore the same site ...