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I'm guessing that you're using Plesk, in which case I wouldn't recommend doing it the way you describe. You have two possible alternatives instead:
1) Create a vhost.conf to move your DocumentRoot to a subdirectory of httpdocs (that way you can place your include files in httpdocs and your actual website in the subdirectory)
2) Just have your includes directory in httpdocs as normal, but put a .htaccess into the includes directory to 'deny from all' so that it's not web accessible. This way it will only be accessed by scripts on the filesystem.
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