You need to set LIMIT_TO_DIRECTORY back to true and then enter links in the textbox like so:
Code:
http://www.domain.com/dir1/
http://www.domain.com/dir1/sub1/
http://www.domain.com/dir1/sub2/
With LIMIT_TO_DIRECTORY set to true, PhpDig indexes that (sub)directory only; no (sub)directories of (sub)directories are indexed.