Don't flatten build directories

Make a really good guess

tools/resources/__init__.py

@@ -482,10 +482,15 @@ class Resources(object):
         self.add_toolchain_labels(toolchain)
         for path in src_paths:
             if exists(path):
+                into_path = relpath(path).strip(".\\/")
                 if exclude:
-                    self.add_directory(path, into_path="", exclude_paths=[toolchain.build_dir])
+                    self.add_directory(
+                        path,
+                        into_path=into_path,
+                        exclude_paths=[toolchain.build_dir]
+                    )
                 else:
-                    self.add_directory(path, into_path="")
+                    self.add_directory(path, into_path=into_path)
 
         # Scan dependency paths for include dirs
         if dependencies_paths is not None: