rsync
rsync -avz --delete "/home/user/A" "/home/user/B"
Explanation by SonicARG
-a Do the sync preserving all filesystem attributes
-v run verbosely
-z compress the data during the sync (transport the data in compressed mode)
--delete delete the files in target folder that do not exist in the source, /home/user/A: source folder, /home/user/B: target folder
exclude .git
--exclude='.git/'
How to use rsync to backup a directory without git subdirectory