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That’s a science of itself. There’re merging solutions in project managing software like subversion or git, but I’ve never trusted them and they can’t really work if the same lines were changed in both sources. Further I’ve seen how they can’t relate it anymore if there are to many changes. When I’m in such a situation I’m always using programs like WinMerge to see the differences and merge them manually. That’s even easier if you know what files were changed.
Regards