Fix duplicate dependency issue (#2597)

* Fix duplicate dependency issue
If a package has the same name as a framework assembly in the dependency
graph, we usually replace it with the framework assembly if the package
provides no assets. If the framework assembly wasn't resolved, it would
skip this logic and end up adding dupes to the list, which blows up later on.
This is a tactical fix to solve the issue, we need to do some more thinking
to determine how we want to resolve conflicts between framework assemblies,
packages and dlls with the same name.

TestAssets/TestProjects/TestMicrosoftCSharpReferenceMissingFramework/Program.cs

@@ -0,0 +1,10 @@
+namespace TestMicrosoftCSharpReference
+{
+    public class Program
+    {
+        public static int Main(string[] args)
+        {
+            return 0;
+        }
+    }
+}