The MooTools 1.3 Upgrade Helper is an uncompressed copy of MooTools 1.3 Core with the Compatibility layer. When accessing 1.2 methods that have been changed for 1.3, it will log to a console like Web Inspector or Firebug, so you can find and replace the deprecated methods.
Simply include the file on your page instead of the existing MooTools 1.3 + Compat file. Open up Firebug or Web Inspector and away you go!
For a list of methods that have changed in 1.3, please see our http://github.com/mootools/mootools-core/wiki/Upgrade-from-1.2-to-1.3