If you’ve been unfortunate enough to be targetted by hackers who have added malware to your web server, here are a few Linux CLI tools you can use to troubleshoot.
The first is maldet which can be paired with Clam Antivirus to scan for malware. Here’s a good guide on how to do that.
Note you can install maldet via tools like yum or apt usually too. The key is to make sure it is running together with ClamAV which you should keep up to date. You can also get it to alert you and automatically quarantine suspicious files.
Another tool, which is much better at finding hacked PHP code (which is usually encoded) is PHP malware finder. You’ll notice that hacked PHP files aren’t plain PHP code, but have instead be encoded (e.g. base64) to make them unreadable without decoding.
This can be cloned to the server and run from the CLI with PHP. Just a note it will pick up a lot of positives depending on your app (e.g. WordPress) and you’ll need to work through these yourself.
Don’t forget to also have something like [All in One WP Security and Firewall] (https://wordpress.org/plugins/all-in-one-wp-security-and-firewall/) installed to lock down your WordPress site and also to scan for and alert you of any changes.
As a final measure, it helps if your application code is kept under version control on the server using a tool like git. This helps to see any untracked or modified files which you can then investigate and quarantine.