I read the linked blog, and I'm still not clear on why you need to distinguish the two. At least as a first cut, wouldn't it be adequate to just print out all of the effects of the use/require? As in, symbol table entries, variable assignments, etc.? You can figure out what package a particular subroutine was defined in via B::Deparse's coderef2text, so you can still group things by package and then output an alias statement (sub A::f {...}; *B::g = *A::f;) rather than a redefinition (sub A::F {...}; sub B::g { ... }) or a chained assignment: *A::f = *B::g = sub { ... }.

I have to admit that I haven't thought very hard about it, though.

I guess I can see the value in making the output code look as much as possible like the input code, although for things where this would be useful, I'm not sure if that's relevant. (If you're debugging something that autogenerates classes, then there's really no input that's useful to imitate.)