It is the --configfile option. I will check in new versions of irptransmogrifier.bat and irptransmogrifier.sh, hope that is OK.Is there a way that the command line can also be made to use this file?
In the longer time span I plan to merge you changes. In the short time span, using separate versions is likely better. I would suggest that you update the version "number" of if (it is the version attribute of the top level element) to anything unique, for example with a suffix -rm or such. That version number is (at least presently) only used by humans.