@: I use a program called Rsync and there is a Linux and Windows library (haven’t check for Mac yet).
Windows Library: https://github.com/librsync/librsync
On Linux it is a built in command but that would depend on how you decide to implement it I guess.
I normally do a basic checksum on all new files and have that available for the updater … this allows the updater to check for any manually modified files that may have been modified by the user … but once again this depends on your setup.