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I run suphp so the uid of scripts is for the user not the webserver. My log files are also in /home/$user/logs/error.log

CSF only monitors /var/log/apache2/error.log

However because of my setup i dont think the logs go here so how do I add my user's log files to be monitored by CSF firewall.

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CSF not only monitor /var/log/apache2/error.log, it monitor many other service's log like maillog, syslog. You can add your log file, open csf conf as below:

vim /etc/csf/csf.conf

find below file entries and add your one below it.

Log files

HTACCESS_LOG = "/usr/local/apache/logs/error_log"

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