UseHeaderDirectories when true generated files will be outputted to original relative paths, and include will use relative path between headers. When NoGenIncludePrefix is set a string is prepended to the include files that are not generated.

src/Generator/Driver.cs

@@ -320,7 +320,7 @@ namespace CppSharp
 
         public void WriteCode(List<GeneratorOutput> outputs)
         {
-            var outputPath = Options.OutputDir;
+            var outputPath = Path.GetFullPath(Options.OutputDir);
 
             if (!Directory.Exists(outputPath))
                 Directory.CreateDirectory(outputPath);
@@ -329,16 +329,22 @@ namespace CppSharp
             {
                 var fileBase = output.TranslationUnit.FileNameWithoutExtension;
 
+                if (Options.UseHeaderDirectories)
+                {
+                    var dir = Path.Combine(outputPath, output.TranslationUnit.FileRelativeDirectory);
+                    Directory.CreateDirectory(dir);
+                    fileBase = Path.Combine(output.TranslationUnit.FileRelativeDirectory, fileBase);
+                }
+
                 if (Options.GenerateName != null)
                     fileBase = Options.GenerateName(output.TranslationUnit);
 
                 foreach (var template in output.Templates)
                 {
-                    var fileName = string.Format("{0}.{1}", fileBase, template.FileExtension);
+                    var fileRelativePath = string.Format("{0}.{1}", fileBase, template.FileExtension);
-                    Diagnostics.EmitMessage("Generated '{0}'", fileName);
+                    Diagnostics.EmitMessage("Generated '{0}'", fileRelativePath);
 
-                    var filePath = Path.Combine(outputPath, fileName);
+                    var file = Path.Combine(outputPath, fileRelativePath);
-                    string file = Path.GetFullPath(filePath);
                     File.WriteAllText(file, template.Generate());
                     Options.CodeFiles.Add(file);
                 }

src/Generator/Generators/CLI/CLITypeReferences.cs

@@ -1,5 +1,6 @@
 using System;
 using System.Collections.Generic;
+using System.IO;
 using CppSharp.AST;
 using CppSharp.AST.Extensions;
 using CppSharp.Generators.AST;
@@ -109,9 +110,9 @@ namespace CppSharp.Generators.CLI
                 return;
             }
 
-            var declFile = decl.Namespace.TranslationUnit.FileName;
+            var translationUnit = decl.Namespace.TranslationUnit;
 
-            if(decl.Namespace.TranslationUnit.IsSystemHeader)
+            if (translationUnit.IsSystemHeader)
                 return;
 
             if(decl.ExplicityIgnored)
@@ -125,15 +126,35 @@ namespace CppSharp.Generators.CLI
             {
                 typeRef.Include = new Include
                     {
-                        File = declFile,
+                        File = GetIncludePath(translationUnit),
-                        TranslationUnit = decl.Namespace.TranslationUnit,
+                        TranslationUnit = translationUnit,
-                        Kind = Include.IncludeKind.Quoted,
+                        Kind = translationUnit.IsGenerated
+                            ? Include.IncludeKind.Quoted
+                            : Include.IncludeKind.Angled,
                     };
             }
 
             typeRef.Include.InHeader |= IsIncludeInHeader(record);
         }
 
+        private string GetIncludePath(TranslationUnit translationUnit)
+        {
+            if (!translationUnit.IsGenerated)
+                return DriverOptions.NoGenIncludePrefix + translationUnit.FileRelativePath;
+
+            if (!DriverOptions.UseHeaderDirectories)
+                return translationUnit.FileName;
+
+            var rel = PathHelpers.GetRelativePath(
+                TranslationUnit.FileRelativeDirectory,
+                translationUnit.FileRelativeDirectory);
+
+            if (string.IsNullOrEmpty(rel))
+                return translationUnit.FileName;
+
+            return Path.Combine(rel, translationUnit.FileName);
+        }
+
         private bool IsBuiltinTypedef(Declaration decl)
         {
             var typedefDecl = decl as TypedefDecl;

src/Generator/Options.cs

@@ -95,9 +95,11 @@ namespace CppSharp
         public bool GenerateProperties;
         public bool GenerateInternalImports;
         public bool GenerateClassMarshals;
+        public bool UseHeaderDirectories;
 
         //List of include directories that are used but not generated
         public List<string> NoGenIncludeDirs;
+        public string NoGenIncludePrefix = "";
 
         /// <summary>
         /// Enable this option to enable generation of finalizers.

src/Generator/Utils/Utils.cs

@@ -235,4 +235,19 @@ namespace CppSharp
             return assembly.GetTypes().Where(baseType.IsAssignableFrom);
         }
     }
+
+    public static class PathHelpers
+    {
+        public static string GetRelativePath(string fromPath, string toPath)
+        {
+            var path1 = fromPath.Trim('\\', '/');
+            var path2 = toPath.Trim('\\', '/');
+
+            var uri1 = new System.Uri("c:\\" + path1 + "\\");
+            var uri2 = new System.Uri("c:\\" + path2 + "\\");
+
+            return uri1.MakeRelativeUri(uri2).ToString();
+        }
+        
+    }
 }