The manual is hopefully self-contained, and it has links to the two papers.
For the DJ-only sample, I forget exactly how I got the “intronic” V genes, but it was something obvious/simple like sort/uniq’ing through whatever occurred to the left of each D gene. The end result was this germline set directory, where a V gene with a name like IGHVxDx1-101 is, as you’d imagine, the intronic sequence that occurred to the 5’ side of IGHD1-101. These are, uh, presumably universal for humans? Others are probably better qualified than I to comment on that. Use the --initial-germline-dir argument (see --help for details) to use this directory instead of the default.