Dear Authors,

Thank you for your recent response to your referees and your revised manuscript.

I have now reviewed both and believe that your manuscript is potentially acceptable for publication in Geoscientific Model Development.

I have identified below a handful of remaining referee points where I think either further clarification of your response is required, or where a minor modification to your manuscript may improve it. Please respond to these or address them in the manuscript.

Finally, in reviewing your Code Availability section, I note some remaining issues with it. I have identified these below also. As reproducibility is of prime importance to GMD, please address these as directed.

If you have any questions, please do not hesitate to contact me.

With best regards,

Andrew Yool.

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Referee 1, “2. The authors diagnose the proportion …”

The response here is fine, but I feel that there is a case for mentioning the failure of this test, at least in passing. Sometimes model improvements turn out not to be improvements, and noting this could save other workers wasted effort.

Referee 1, “p. 3, l. 19: To how many vertical levels …”

I would suggest deleting the comma after "upper layers", and switching "depths" -> "depth" (i.e. "... to 22 m at depth, with ...")

Referee 3, “General comment #2 …”

A figure change is mentioned in your response, but the referee mentions aspects that do not appear to be addressed (or are not stated as being addressed). For instance, the SSS bias and early ice retreat. Can you please clarify whether these have been addressed?

Referee 3, “Why ice melts too early is not clearly attributed …”

Again, a figure has been added, but it is unclear what other changes have been included. The latter point about observational estimates could be fashioned into a limitation or caveat of the study and added to the discussion to prompt future work.

Referee 3, “The comparison of snow at two stations …”

Have you remarked on the lack of availability of data in the text on this point? Again, it may be a useful discussion point to drive future work.

Referee 3, “Revise your conclusions once analysis has been sharpened.”

What has been done here? Your response, "Ok", is fairly non-specific. Are you referring to General Comment #1 of this referee?

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Code availability

While your current text notes the availability and revision number of the underlying NEMO code that your work utilises, it does not document the modifications that you have made to perform the work in this manuscript to the same standard. For the latter, it currently reports the following:

“Our Baltic Sea adopted code, input data, analysis scripts and data used to produce the figures in this study can be made available upon request by the corresponding author.”

The nature of the ”adopted code” (“adapted code”?), is unclear here, no reference is made to whether it is under version control, or, if so, which revision is used in the work here. If the adapted code consists of modified versions of existing NEMO routines, perhaps these could be made available as a supplement for this paper. The same would be possible for wholly new code blocks. If it is not possible to make the code (and the parameter sets or other input data) available in this way, it is important to note why this is. For reference, GMD’s guidance on code availability runs as follows:

“All papers must include a section, at the end of the paper, entitled "Code availability". Here, either instructions for obtaining the code, or the reasons why the code is not available should be clearly stated. It is preferred for the code to be uploaded as a supplement or to be made available at a data repository with an associated DOI (digital object identifier) for the exact model version described in the paper. Alternatively, for established models, there may be an existing means of accessing the code through a particular system. In this case, there must exist a means of permanently accessing the precise model version described in the paper. In some cases, authors may prefer to put models on their own website, or to act as a point of contact for obtaining the code. Given the impermanence of websites and email addresses, this is not encouraged, and authors should consider improving the availability with a more permanent arrangement. After the paper is accepted the model archive should be updated to include a link to the GMD paper.”

Please revisit this guidance and adapt your manuscript, and potentially its supplements, appropriately.

Dear authors,

Thank you for getting back to me so quickly.

I think that the only remaining issue is the code availability section. You replied previously with …

“Our code contains just a few really minor changes which are stated in the beginning of the code availability section. We have it under revision control and can provide a revision number. The repository is available online but a user account is required to download the code. If we provide the link to the repository and an email to me or the admin person, it is perhaps not an optimal solution, but more convenient for us, would that work? If not, then we will provide the relevant subroutines or code blocks as supplemental material.”

Firstly, you overlooked my point about “adopted” (i.e. code you’ve taken from elsewhere) vs. “adapted” (i.e. code from here you’ve modified). That ambiguity still remains in the main text. Can you clear it up please?

Regarding your suggestions around the modified code, reporting the repository address, the revision number and supplying a contact point to get an account should be sufficient for this. The latter would probably best be an administrative contact point rather than an individual, just in case the individual moves to a new job, etc. The information around the repository and revision should be intelligible and sufficient for the contact point to work out what’s being requested some time down the line when this paper isn’t fresh in everyone’s minds. Refer back to the guidance I included last time for more pointers.

And, unless it is very difficult, I would be inclined to add the modified code blocks as supplementary material in addition.

Please feel free to get in contact if you have any questions. And apologies for the delay in resolving these issues.

Best regards,

Andrew Yool.