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<a href="~/">Some link to root of site</a>

public class RootHandler : IHttpHandler
    {
        #region IHttpHandler Members

        public bool IsReusable
        {
            get { return true; }
        }

        public void ProcessRequest(HttpContext context)
        {
            context.Response.Clear();
            string toUrl = context.Request.ApplicationPath;
            context.Response.Redirect(toUrl);
            context.Response.End();
        }

        #endregion
    }

    <handlers>
      <remove name="root"/>
      <add name="root" verb="*" path="~/" type="Namespace.RootHandler, Assembly"/>   
    </handlers>

        public void ProcessRequest(HttpContext context)
        {
            context.Response.Clear();
            
            string toUrl = context.Request.ApplicationPath + "/";
            string url = context.Request.RawUrl;

            int idx = url.LastIndexOf("~/");

            url = url.Substring(idx + 2);
            
            url = VirtualPathUtility.Combine(toUrl, url);

            context.Response.Redirect(url);
            context.Response.End();
        }