A little more info: I was able to fix the code to generate the correct URL with the com_joomdoc reference by editing line 15. However, the com_linkdoc/views/process/tmpl/default.php refers to the old docman_2 schema. I fixed it by replacing the "#__docman_2" token on line 36 with "#__joomdoc". While I get now the full set of current documents, unfortunately they all appear under the last category. Will take a little more debugging to get them to 1) list the full category hierarchy, and 2) list the documents under their assigned category.