There's dozens of tools that can tell you what has changed. Beyond Compare is one of those.
Select two directories, and it will show u all different files (files added, removed, or content changed). Files you didn't touch to config, you can simply overwrite with the newer version. Files you changed, you'll have to use the built-in file merger to merge the new file into your existing file (or the otherway around, if there's more new content than old content...)
Very easy to use, and there's a trial version.
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