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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