Install it - it's proven excellent for us and stopped many an attempted intrusion. It also gives a heads-up for someone looking for holes in scripts.
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I have near to 50 Perl and PHP scripts running in my website. Will these scripts be affected? Do I need to recode the scripts?
Most likely not. The best thing is to install it with a wide range of filters and gradually change them to suit your environment. All the output from mod_security is stored in a log file which you define on installation (which is extremely easy, btw).
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Will it affect other things?
Other than scripts? Not usually, though it can sometimes affect JavaScript.
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It will protect the server quietly in the background like APF
Yes. it basically scans all HTTP requests that come in and any that match the filters that you define will receive back an error which you can define. So instead of getting a 200 OK, they'll get a 500 or whatever you specify.
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It will email me a warning when there is an intrusion.
It will email me a report like chkrootkit.
No. It does put a single line log into your Apache error_log file which you can look out for if you use logcheck (which I run hourly) and then check the mod_securty specific log for details about the filter hit.
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After a reboot, how do I know if mod_security is working?
It installs as an Apache module, so rebooting has no effect, Apache loads it up on startup together with all its other modules. You can easily test it by putting in a URL like:
http://www.mydomain.com/index.html?bug=/etc/passwd
Which should generate the error that you choose, usually 500 Server Error.