repair hacked wordpress site will tell you that there's no htaccess from the directory. You may put a.htaccess file within this directory if you desire, and you can use it to control access to the directory or address range. Details of how to do that are readily available on the net.
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Harness Scanner goes seeking anything suspicious through the files on your website comment database and place tables. You are also notified by it for plugin names that are unusual. It doesn't remove anything, it simply warns you for possible threats.
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Do your homework and some searching, but if you are pressed for time and want to get this done once and for all, try out the WordPress safety plugin that I use. It's a relief to know that my site (and business!) are secure.