'Without having a tool programmatic way to change the SWA in files I may need to look at batch process for creating new files and models from a valid seed and coping elements and application data (extractions tables etc) into the fresh files. '
I've done similar with existing projects Stirling, but what I've done is reference in files using co-world and then merged them. This also gets all files in the same seed format which isn't a bad idea any way.
