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Visual Studio generated an error saying that the file web.config is not found when I deploy solution. After that the folder inetpub\wwwroot\wss\VirtualDirectories\80 was empty at all. Also the site is no longer available through the browser, but is somehow available through a SharePoint Manager. Is anyone familiar with this problem?

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Very odd - do you mean that the site does not show up if accessed in a browser but seems to be valid if you open the site in the designer? Have you tried some other tool (for example, does SharePoint manager detect the web site?)? Central admin still shows the site collection in the site collection list? Are you sure there isn't a managed path involved (or some host file redirection)? Do you browse the site on the same machine that runs the designer? I suggest that you try to add some more info - could help people to see what's wrong here. –  SPArchaeologist Jan 16 '13 at 13:29
    
I would recommend you to use ULS viewer to check for errors while trying to hit website through browser –  Muhammad Raja Jan 16 '13 at 22:20
    
There's no host file redirection. When try to access site using the browser 403 error appears, using SharePoint Designer: "Probably on the web server at xxx SharePoint Foundation service is not installed" error. SharePoint Manager opens the web application and shows all sites structure. –  Dmitry Gorbenko Jan 17 '13 at 8:34
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I came across the fact that Windows SharePoint Services Web Application stucks at "starting" status. After I completed the steps described here the site became available.

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