On gcc, our -Werror option during compile causes compilation to fail if you use any deprecated methods.  Reading the header files with the offending APIs gives no hint about how to change your model/script, while inspecting the code of the deprecated methods gives you the clue you need.  These need to be documented as deprecated, along with the part that should also be in CHANGES.html that tells you how to fix your code to use the new API.

List of the deprecated methods in src/ of ns-3-dev as of today:

simulator/simulator.h:
  static void EnableLogTo(char const *)
helper/point-to-point-helper.h: 
  void SetDeviceParameter(std::string,const AttributeValue &)
  void SetChannelParameter(std::string,const AttributeValue &)
helper/csma-helper.h:
  void SetDeviceParameter(std::string,const AttributeValue &)
  void SetChannelParameter(std::string,const AttributeValue &)
common/packet.h:
  static void EnableMetadata (void)