Fixed two bugs.

src/Generator/Generators/CSharp/CSharpTextTemplate.cs

@@ -133,7 +133,7 @@ namespace CppSharp.Generators.CSharp
             if (reference.GenerationKind == GenerationKind.Generate && Options.GenerateLibraryNamespace)
                 refNames.Push(Options.OutputNamespace);
 
-            while (refNames.Count > 0 && ctxNames.Count > 0 &&refNames.Peek() == ctxNames.Peek())
+            while (refNames.Count > 1 && ctxNames.Count > 1 &&refNames.Peek() == ctxNames.Peek())
             {
                 refNames.Pop();
                 ctxNames.Pop();

src/Generator/Passes/RenameRootNamespaces.cs

@@ -20,7 +20,9 @@ namespace CppSharp.Passes
             var fileName = unit.TranslationUnit.FileName;
             if (Driver.RootNamespaceRenames.ContainsKey(fileName))
             {
-                unit.Name = Driver.RootNamespaceRenames[fileName].rootNamespaceName;
+                var rootNamespace = Driver.RootNamespaceRenames[fileName].rootNamespaceName;
+                if (this.Driver.Options.OutputNamespace != rootNamespace)
+                    unit.Name = rootNamespace;
             }
             else if (unit.GenerationKind == GenerationKind.Generate)
             {