> re-factoring a big repo of decades old fortran+C cod

Having been in academia in the past and now in software I can say with a lot of certainty that this will take a lot more upfront work than otherwise.

Academic code does not have a lot of structure. And usually lacks a lot in terms of tests. While AI is best when it can mimic patterns as well as there are tests to target.

So you will probably need to budget a few weeks to establish good patters, docs as well as testing patterns before you can seriously make it really do what you want it to do.