Using NinjaScanner (with NinjaFirewall) is an absolute pleasure. It finds all suspect files (changed/modified/non-standard) in the WordPress installation, even files that I forgot that I had modified!
It leans heavily on the side of security, and will show all suspects including modified files, so you want to add some exclusions here – like cache, etc. – to avoid false positives.
This is a great security tool to add to any WordPress powered site. The guys at NinTechNet really know their stuff, and apply that knowledge well. Their other plugin NinjaFirewall is amazing, and coupled with NinjaScanner, give a really solid security base for WordPress.
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