diff --git a/src/CLI/Generator.cs b/src/CLI/Generator.cs
index ed215001d..58db9ac72 100644
--- a/src/CLI/Generator.cs
+++ b/src/CLI/Generator.cs
@@ -108,6 +108,9 @@ public bool ValidateOptions(List<string> messages)
             if (string.IsNullOrEmpty(options.OutputNamespace))
                 options.OutputNamespace = moduleName;
 
+            if (options.IncludeDirs.Count == 0)
+                options.IncludeDirs.Add(Path.GetDirectoryName(options.HeaderFiles.First()));
+
             SetupTargetTriple();
 
             return true;
diff --git a/src/Generator/Driver.cs b/src/Generator/Driver.cs
index 29e36d968..82780bfa2 100644
--- a/src/Generator/Driver.cs
+++ b/src/Generator/Driver.cs
@@ -439,7 +439,12 @@ public static void Run(ILibrary library)
             }
 
             new CleanUnitPass { Context = driver.Context }.VisitASTContext(driver.Context.ASTContext);
-            options.Modules.RemoveAll(m => m != options.SystemModule && !m.Units.GetGenerated().Any());
+            foreach (var module in options.Modules.Where(
+                         m => m != options.SystemModule && !m.Units.GetGenerated().Any()))
+            {
+                Diagnostics.Message($"Removing module {module} because no translation units are generated...");
+                options.Modules.Remove(module);
+            }
 
             if (!options.Quiet)
                 Diagnostics.Message("Processing code...");
diff --git a/src/Generator/Passes/CleanUnitPass.cs b/src/Generator/Passes/CleanUnitPass.cs
index 4d1b3750d..3afaa028f 100644
--- a/src/Generator/Passes/CleanUnitPass.cs
+++ b/src/Generator/Passes/CleanUnitPass.cs
@@ -31,6 +31,11 @@ private Module GetModule(TranslationUnit unit)
                 includeDir = ".";
             includeDir = Path.GetFullPath(includeDir);
 
+            // Added in https://github.com/mono/CppSharp/pull/1736, but causes us issues.
+            // 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)