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).

modules/visual_script/visual_script_builtin_funcs.cpp

@@ -1,6 +1,6 @@
 #include "visual_script_builtin_funcs.h"
 #include "math_funcs.h"
-#include "object_type_db.h"
+#include "class_db.h"
 #include "reference.h"
 #include "func_ref.h"
 #include "os/os.h"