I use phpstorm to compare.
Compare your current site with a fresh copy of the same PHP-fusion version. Then you know exactly what you have modded.
Now compare the modded files in the fresh copy version, with the same files in the new PHP-fusion version. If the files are the same, you can easy put your modded version back.(most updates only a few files are changed, but they always let you update the whole site, I still don't know why). For the other files you need to make the same mod in the new version.
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