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).