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.

scene/main/timer.cpp

@@ -30,7 +30,7 @@
 
 #include "timer.h"
 
-#include "engine.h"
+#include "core/engine.h"
 
 void Timer::_notification(int p_what) {