Hi Andrew,
You could enter the path to the directory, and then add the list of other entities in that directory as things to exclude from the backup. i.e. back up /nfs/c04/h06/mnt/123456/domains/domainname.com/wp-config.php and type in "html" in the list of things to exclude.
Note, though, that unless your wp-config.php contains something more than just your MySQL configuration, then you may not need to back it up.
David
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