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You essentially need to delete all your files (except /wp-content/uploads and your DB) and install everything fresh from the source e.g. download wordpress from wordpress.org, and download your theme and plugins from their sources. Do not use backups or nulled software.
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Unfortunately yes. On the plus side, this will help ensure they can't get in again. One more thing to add that list... You can use maldet to check for malware/compromised files. It's not the best malware scanner, but it's free and can help find malware in other hidden folders/files: https://www.rfxn.com/projects/linux-malware-detect/
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SonarQube
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