Beyond compare is a great tool, but it has to be used with caution. It will show you the differences between files and folders and there are a couple ways to apply these changes.
I compare the original files from the previous version with the original files from the new version and apply those differences to my existing code. Sometimes this requires creativity to get around the hacks that are already installed but this is not a huge step so it should be pretty smooth.
If there is a better way to use it I'm open to suggestions.
