quoted

Please can someone help nudge me in the right direction?

I wonder whether setting up a clean/smudge filter might help. You might want to look into a clean filter that runs your code generator.

Thanks. I'm not clear that this will help, because the main problem is
that the rebase stops when trying to apply a later commit. In this
case, the previous commit will be "clean", but the commit the rebase
is trying to apply will conflict and the rebase process will stop

Reading elsewhere, I'm now looking into whether wrapping the default
mergetool will help provide the "hooks" I need.