Make core/ includes absolute, remove subfolders from include path

This allows more consistency in the manner we include core headers,
where previously there would be a mix of absolute, relative and
include path-dependent includes.

modules/mono/mono_gc_handle.h

@@ -33,7 +33,7 @@
 
 #include <mono/jit/jit.h>
 
-#include "reference.h"
+#include "core/reference.h"
 
 class MonoGCHandle : public Reference {