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    Do you have your website in subversion (or similar)? An hourly svn status cron job can alert you very quickly to any changes and a manual svn revert can remove all the changes. Commented Jun 22, 2012 at 9:17
  • I think this answer might apply to your situation. security.stackexchange.com/questions/16305/… Commented Jun 24, 2012 at 13:22
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    "malware injection" is just a symptom of insecure code. An attacker needs a vulnerability such as SQL Injection or a Local File Include vulnerability in order to make this happen. Commented Jul 10, 2013 at 16:36