How to communicate with reviewer who has waived his anonymity? (Within the standard review process) I received review comments on a paper, one of the reviewers, say A, waived his anonymity in the review submitted to the journal (I know A personally). Now, A made some suggestions (essentially about some way of using software developed by students of A) which do not work (suggested feature does not exist). Should I


write an email to A directly asking about clarifications on how to use the software as he suggested, at the risk of the handling editor feeling like I went behind his back
write this email, but include the handling editor as CC:, at the risk of A feeling like I would "belittle" him "in front of" the editor, or
mention in the response that the feature was not implemented in the suggested software, citing documentation / error messages
No matter what, I would suggest keeping all formal communications and responses within the journal system, even though the reviewer has waived anonymity.  That way, you keep a clear record both for yourself and the editor but also for the other anonymous reviewers (if the journal shares reviews between reviewers as many do) and for any other journal staff who might later need to audit the interaction.

Now, given that the reviewer has revealed themselves, you may or may not find it appropriate to communicate informally about concerns that you may have.  If the journal has approved the waver of anonymity (e.g., by the identity being revealed in the review that you were sent), then it's definitely OK. If it's come through a side-channel, however, then some might consider it fine (e.g., "anonymity is just to protect reviewers") and some might consider it unethical (e.g., "talking to your friend gives an unfair advantage").