Style: Cleanups, added headers, renamed files

Made sure files in core/ and tools/ have a proper Godot license header
when written by us. Also renamed aabb.{cpp,h} and object_type_db.{cpp,h}
to rect3.{cpp,h} and class_db.{cpp,h} respectively.

Also added a proper header to core/io/base64.{c,h} after clarifying
the licensing with the original author (public domain).

core/reference.h

@@ -32,7 +32,7 @@
 #include "object.h"
 #include "safe_refcount.h"
 #include "ref_ptr.h"
-#include "object_type_db.h"
+#include "class_db.h"
 
 /**
 	@author Juan Linietsky <reduzio@gmail.com>