You can set the full path linking to your root folder, to make your rule directory-recursive. You can see the path on your cPanel, or using php function getcwd()
in run_me_first.php
.
In my case the path would be like this:
php_value auto_append_file "/home/userID/public_html/run_me_first.php"
Note: If you want to prepend file(in this case your appending the file to the end of every file), use auto_prepend_file
instead.