rsync is pretty much the default program to synchronize files between directories. Try a command along the lines of:
rsync -r --update --progress --dry-run That will tell you what would be copied and what wouldn't. The --update command only copies files when the source is newer than the destination. If it looks correct, then take off the --dry-run option. If it's not right, check the man page for rsync to see what I did wrong.