PHP can access any file on the server's file-system, granted that it has the proper permission.
You can use absolute paths with most of PHP's file functions, such as include and readfile.
Like, say, if you had a DB connection script stored in "/var/www/include", you could simply do:
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include("/var/www/include/dbConnect.php");
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If your web-root is located at "/var/www/html", and the current script is at the web-root, you could also use a relative path, like:
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include("../include/dbConnect.php");
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On Windows, using a path like "C:\\SomeDir\myfile.php" should also be perfectly valid.