Suggestion fix for bug https://bugzilla.xamarin.com/show_bug.cgi?id=6327

Edited makefile for create these directories and copy Microsoft.WebApplication.targets into

mono/xbuild/Microsoft/VisualStudio/v10.0/WebApplications/
mono/xbuild/Microsoft/VisualStudio/v11.0/WebApplications/

Based on https://bugzilla.xamarin.com/show_bug.cgi?id=6327 bug report