We(small group) have a SocialEngine based project and we made lots and lots of changes in 4.6.0 version including core modules, now we struggle to update to 4.8.0 which is a pain in the ass so question: Which logic to implement in new version of social engine where will be stored our modified code that will help for future update?
We are trying using Decorator Pattern, creating another folder(modules2) for example there creating clones of modules and using only modified files(which is currently unsuccessfully).
You can to compare your files with the latest upgrade package files with Softwares like WinMerge and copy new changes in SocialEngine core to your modified files. Don't forget the database queries in application/MODULE_NAME/settings/my-upgrade sql file of each module. It's gonna take time but I don't think there's any easier solutions.
See, thats where git or subversion comes handy , you exactly know where the code is changed .