diff --git a/src/Generator.Tests/GeneratorTest.cs b/src/Generator.Tests/GeneratorTest.cs
index a400bc9739..d2f7e75919 100644
--- a/src/Generator.Tests/GeneratorTest.cs
+++ b/src/Generator.Tests/GeneratorTest.cs
@@ -42,9 +42,16 @@ public virtual void Setup(Driver driver)
             testModule.IncludeDirs.Add(path);
 
             Diagnostics.Message("Looking for tests in: {0}", path);
-            var files = Directory.EnumerateFiles(path, "*.h");
+            var files = Directory.EnumerateFiles(path, "*.h", SearchOption.AllDirectories);
             foreach (var file in files)
+            {
+                string includeDir = Path.GetDirectoryName(file);
+                if (!testModule.IncludeDirs.Contains(includeDir))
+                {
+                    testModule.IncludeDirs.Add(includeDir);
+                }
                 testModule.Headers.Add(Path.GetFileName(file));
+            }
         }
 
         public virtual void Preprocess(Driver driver, ASTContext ctx)
diff --git a/src/Generator/Passes/CleanUnitPass.cs b/src/Generator/Passes/CleanUnitPass.cs
index c9978f92fb..0bc9c04782 100644
--- a/src/Generator/Passes/CleanUnitPass.cs
+++ b/src/Generator/Passes/CleanUnitPass.cs
@@ -31,9 +31,14 @@ private Module GetModule(TranslationUnit unit)
                 includeDir = ".";
             includeDir = Path.GetFullPath(includeDir);
 
-            return Options.Modules.FirstOrDefault(
-                m => m.IncludeDirs.Any(i => Path.GetFullPath(i) == includeDir)) ??
-                    Options.Modules[1];
+            Module module = Options.Modules.Find(
+                m => m.IncludeDirs.Any(i => Path.GetFullPath(i) == includeDir));
+            if (module == null)
+            {
+                unit.ExplicitlyIgnore();
+                module = Options.Modules[1];
+            }
+            return module;
         }
 
         public override bool VisitDeclarationContext(DeclarationContext context)
diff --git a/src/Generator/Passes/DelegatesPass.cs b/src/Generator/Passes/DelegatesPass.cs
index 1f427a47ff..68d205faae 100644
--- a/src/Generator/Passes/DelegatesPass.cs
+++ b/src/Generator/Passes/DelegatesPass.cs
@@ -215,7 +215,8 @@ private DeclarationContext GetDeclContextForDelegates(DeclarationContext @namesp
             Namespace parent = null;
             if (string.IsNullOrEmpty(module.OutputNamespace))
             {
-                var groups = module.Units.SelectMany(u => u.Declarations).OfType<Namespace>(
+                var groups = module.Units.Where(u => u.IsGenerated).SelectMany(
+                    u => u.Declarations).OfType<Namespace>(
                     ).GroupBy(d => d.Name).Where(g => g.Any(d => d.HasDeclarations)).ToList();
                 if (groups.Count == 1)
                     parent = groups.Last().Last();
@@ -231,7 +232,7 @@ private DeclarationContext GetDeclContextForDelegates(DeclarationContext @namesp
             }
 
             if (parent == null)
-                parent = module.Units.Last();
+                parent = module.Units.Last(u => u.IsGenerated);
 
             var namespaceDelegates = new Namespace
                 {