Setup include dirs on the module instead of parser options in the CLI.

src/CLI/Generator.cs

@@ -123,6 +123,7 @@ namespace CppSharp
 
             module.Headers.AddRange(options.HeaderFiles);
             module.Libraries.AddRange(options.Libraries);
+            module.IncludeDirs.AddRange(options.IncludeDirs);
             module.OutputNamespace = options.OutputNamespace;
 
             if (abi == CppAbi.Microsoft)
@@ -139,9 +140,6 @@ namespace CppSharp
             foreach (string s in options.Arguments)
                 parserOptions.AddArguments(s);
 
-            foreach (string s in options.IncludeDirs)
-                parserOptions.AddIncludeDirs(s);
-
             foreach (KeyValuePair<string, string> d in options.Defines)
             {
                 if(string.IsNullOrEmpty(d.Value))