There's nothing magic going on. A C# project's settings are located in the .csproj file (other .net languages work similarly). This file is normally editied from within Visual Studio, but it's just xml and can be edited by hand fairly easily.

A project file has references [1], which define the project's external dependences, Removing references is easy. [2][3]

[1] http://msdn.microsoft.com/en-us/library/ez524kew(v=vs.110).a...

[2] http://msdn.microsoft.com/en-us/library/hh708954.aspx

[3] http://msdn.microsoft.com/en-us/library/7314433t(v=vs.90).as...