Getting hacked is one of the worst experiences one can go through as a webmaster. Unfortunately, no matter how careful you are, there is always a chance that a smart hacker might get around your defenses. That does not mean you should just give up and do not do your best to protect your website against future hack attacks. Fixing a hacked website is not always difficult. In fact, it can be a very time consuming process.
In order to fix your website and get it back to its original condition, you first have to analyze what has happened. Sometimes all hackers do is deface sites and manipulate their .htaccess files. Those are not that hard to fix. Database and server hacks are a bit more consuming to get a handle on though.
Fixing your website is important. But you also need to understand how you were hacked so you can avoid having to deal with the same issue in the future. There are commandsyou can run on your server to figure out how it was accessed and by whom.
If you are with a decent web host, chances are its team has a guide on how to deal with hacked sites. You do want to pay attention to the date the files on your sites were changed. That helps you identify which files you need to take care of first (I would delete everything though). If your database has been altered, you are better off using a clean backupto save yourself some time in the process. Of course, you can always go through your database and use commands such as thisto find malicious content in it:
This is the first thing I would do after bringing all my sites down. The reason is quite simple. You do not want your website to be visited and flagged as having malware while you are in the process of fixing it. I always put my site in maintenance mode and go to work to fix some of the issues with it. You can use SSH to find the files that have been modified recently. But that is not always perfect and can be very time-consuming if you have multiple sites. I prefer downloading all the files from my server to my local machine and use a software such as BitDefenderto look for viruses and other malicious codes.

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