DragonDreams Developer Forum

That's really not nice. It's a security feature to avoid file corruption and tampering. But you could disable the checks in if nothing helps:
- https://github.com/LordOfDragons/dragen ... e.cpp#L548
- https://github.com/LordOfDragons/dragen ... n.cpp#L390
You would need to disable the entire if-blocks there to avoid the file based exception.

Is there a way I could generate the manifest files separate from the main build step after the modules have been patched?

The manifest files are XML files. You can use an XML library to load, edit and save them. Most probably simpler would be using an XSLT processor to alter a specific tag content. "xsltproc" is the usual command line tool to do this.