Sorry for not being clear.  Command-line options are overwritten by these conf files and in fact, multiple conf files are overwritten as well, preferring the last-seen values instead of anything else.  So I'm just pointing out that your command-line options to the driver to generate stuff are ignored if the JobGenerator script creates .xml files with anything in them (e.g., JobGenerator sets the `kmerLength`, so `kmerLength` as used on the command line does nothing.