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In Xamarin Studio 6.0 when the jQuery NuGet package is removed the Scripts folder is not removed from the Solution window. It is removed in Xamarin Studio 5.10.
I believe this is because in Xamarin Studio 6.0 the NuGet addin no longer refreshes the entire project tree node in the solution window and only refreshes the Packages and References tree node.
This is fixed in the latest Xamarin Studio 6.1 (nuget3 branch).
I am unable to reproduce the problem in Xamarin Studio 6.0.
I have checked this issue with latest master XamarinStudio-126.96.36.19913_96009545fe3e9fb1b66fef1325b37027c0664e24 and observed this issue works fine. On uninstalling the jquery NuGet package, it also removed the Scripts folder from the Solution window as shown in screencast: http://www.screencast.com/t/Be3tU3OOAF
This issue is also working fine on Mac XS.
I shall verify this issue once get the Cycle 8 builds.