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.

core/ref_ptr.cpp

@@ -30,8 +30,8 @@
 
 #include "ref_ptr.h"
 
-#include "reference.h"
-#include "resource.h"
+#include "core/reference.h"
+#include "core/resource.h"
 
 void RefPtr::operator=(const RefPtr &p_other) {