Assuming you are using PhpDig v.1.8.7, apply the code change in
this post, set LIMIT_TO_DIRECTORY to true and set PHPDIG_IN_DOMAIN to false, both in the config file, and then index http://www.domain.com/subdir/ (with ending slash) from the PhpDig admin panel textbox using whatever "Search depth" and "Links per" you prefer. Note that values present in "Update sites" are used by default, so just choose "no" or edit "Update sites" if you wish to reset the values.