Tooling Inserts Duplicate ProjectReferences In Some Scenarios

[aolszowka]

Consider the following scenario:

1. Project has an AssemblyReference and a ProjectReference to the same project
2. Tooling is run.

As the tooling is written today this will result in a duplicate ProjectReference entry. MSBuild proper and Visual Studio do not seem to care; but when running Roslyn-Based Tooling (such as StyleCop's Stand Alone Fixer) this will throw an exception due to the duplicates. See dotnet/roslyn#31390

This tooling should be a "good neighbor" and not insert this duplicate.