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phpGraphy is composed of several directories, some of them must NOT being accessible from the evil Internet by browsing your website. There's actually four sensitives directories :
logs/ and if using Flat File database
To check that there aren't accessible, you just need to use your web browser and add the directory name after the normal URL used to access phpGraphy, for example, if the URL to access your phpGraphy installation is http://myprovider.com/phpgraphy/, then just check the following urls :
You must either have a "404 Not Found" (this will be the case if you've moved your directories) or "Not allowed"
If your site seem to or simply isn't secure, then please read the next section Protecting sensitives directories.