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I recently submitted a manuscript to a journal that focuses on short papers about software packages. One reviewer gave a very detailed (and helpful) critique of my software/paper with one major objection: another package already exists that has similar functionality. S/he mandated that I clarify what my package offers that the other package does not.

Unfortunately, I was not aware of the other software package when I started my project (which I'm pretty embarrassed about). On further inspection, I realize that this other package is far superior to my own in terms of functionality and performance. I've come to the conclusion that my project is not salvageable. This is disappointing but not soul crushing as it was a side project that is only tangential to my dissertation work. Frankly, I don't have time to improve my software to point of being a significant contribution, and I'd only do so for the sake of "getting a publication," which does not seem fruitful. Improvements wouldn't be immediately useful to me. and thus I don't have the motivation to submit a revision.

That said, I'd really like to submit a genuine word of thanks to the anonymous reviewer for their detailed critique of my paper/software. Through their comments and working through a revision I learned a lot (how to use Docker, sharing and recording terminal sessions through asciinema/asciicast, general improvements to my writing, etc.) Do editors allow authors to respond to reviewers even if their manuscript is essentially rejected? It seems as though editors would generally disallow this since authors responding to a rejection may often want to say something nasty. Would it be best to email the editor directly with my request or respond through the submission system?

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The most likely scenario is that the authors can respond to the editor, and the editor will decide (at their discretion) whether or not to pass back the message to the referees.

After all, there are valid reasons to message the referees afterwards (for example if the main argument for rejection is based on a misunderstanding). For a simple thank you, it will depend on the editor's preference, but it definitely doesn't hurt to try.

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It is unlikely that the editor will allow you to contact the referee directly but it would not be inappropriate for you to contact the editor by email, repeating the essence of your post, and asking the editor to transmit these comments to the referee in question.

Even if the editor chooses not to pass your comments along, you will have acknowledged the constructive work of a referee, something that is quite useful for an editor and she or he might very well ask this referee's opinion again.

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    And, shall you cross the same referee again, s(he) will try the best not to reject! – Alchimista Aug 22 '17 at 13:54
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    @Alchimista this might indeed be a unintended consequence of being nice to a referee! :) – user67075 Aug 22 '17 at 13:56
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    "Might very well ask this referee's opinion again" = No good deed goes unpunished. – Andreas Blass Jul 16 '18 at 12:54
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If you were to write to the editor with your words of thanks to the reviewer, I would be surprised if the editor did not pass it on. A message of thanks to a reviewer is a nice thing to receive, especially one with details of the skills you learned from their review. Reviewers work gratis for journals, so a good editor is unlikely to pass up the opportunity to pass on a nice happy message to the reviewer from a satisfied customer.

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If your situation is anything like what I'm familiar with, then this happened:

  1. The reviewer wrote the critical review, and the editor decided on 'revise'.
  2. The revise letter said something similar to "your revision is due in 60 days".
  3. Since your project is not salvageable, you are not intending to revise your paper. Accordingly, you should notify the editor that you are withdrawing your paper. You don't have to, but it's a courtesy, since if you don't you also clog up their editorial management system. You might e.g. trigger automated reminders to the editor/publisher/yourself that your revision is late.

Since you have to write to the editor anyway, that's the time to tell him what you wrote in the question. If you write something positive, the editor is likely to pass it on. Harsh criticisms of the referees - that might get censored by the editor.

As for whether to use normal email or the editorial management system, both will reach the editor but the latter is preferable. Emails sent by the editorial management system will usually include a line with "click on this link to access the submission" and, as you might expect, that is very convenient.

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