My hope is (was?) to show to A&A exactly what is in the content of the article: it comes directly from Gorski et al 1999a/b, it is independent of whatever may or may not be in the code.
Well, I personally *believe* you were ONLY inspired by Gorski et al 1999a/b, and has NOT used their code. However, since you *had HAD* the code before you submitted the paper to A&A, the HEALPix group - as we all know - claim that you were _not_ smart enough to invent the algebra (almost) from scratch but you _were_ smart enough to derive the algebraic equations from the code and so you stole their intellectual property.
Ouch :(. i'd prefer *not* to look at the HEALPix code.
Fine! So now you have to be smart again and show that... it is not possible to derive the algebra - as it stands in your article - from the HEALPix code. Either because the HEALPix code is too obscure or badly documented or your algebra is different or... I don't know.
Anyway, if you want to win this argument you have to show a proof - or better to say - an alibi that their claims (that you have "undone" their code back to the algebra) are void.
It may be hard to find a clever way to show such an alibi but you have no other way, I'm afraid. This is because when someone is accused she/he has committed a plagiarism, this is the alleged plagiarist duty to bring the evidence that no plagiarism took place.
a.