I would make a copy of the application-code and the database as it is running right now. Take the site offline and setup one of your latest backups. Then make a diff on the version you deployed (in case you do not have that consider using a VCS next time) and the code you just saved from your webserver, so you can see what has been modified and analyze the consequences.
Besides that I would suggest that you inform your hoster about the possible attack and ask them to investigate it or, in case you are running non-hosted, patch your production system.
regards,
Jens
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