That is the problem - it is not just files and folders. You need to copy across any plugins you have installed or you can just reinstall them from the web installer within Moodle. Then you need to set up any settings again on the live site because these settings are stored in the database and and files are buried somewhere deep in the moodledata folder. Because both the moodledata folder and the database are updated continually by the live site there is no way to sync these two items.
Backup and restore
Deploying database changes: dev --> test --> prod
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