Replace all Zenodo references with Figshare (already deposited)

User clarified: this project uses Figshare, not Zenodo. Replaced all
Zenodo mentions across 7 files with the existing Figshare deposit:

- Public DOI: 10.6084/m9.figshare.31653373 (CC-BY 4.0)
- Private reviewer share URL: figshare.com/s/3d17327cef1ae99ed37c

Files updated:
- article/ncomms_main.tex: 4 mentions (Data/Code Availability ×2 sites)
- response_letter/01_point_by_point_response.tex: 1
- response_letter/03_revised_cover_letter.tex: 1 (private reviewer URL
  added)
- article/CODE_SOFTWARE_CHECKLIST.md: 3
- article/ML_CHECKLIST_FILLED.md: 2
- article/REPORTING_SUMMARY_FILLED.md: 2

Also deleted accidentally-created GitHub release v1.1-natcomms-revision1
and its tag (Zenodo record 10.5281/zenodo.20129427 was auto-minted via
the integration but is now orphaned/unreferenced; manuscript points
exclusively to Figshare).

5 PDFs recompiled (28/23/15/3/29 pages, no '??'), 4 _VF ZIPs refreshed
on Desktop.

Author: Roverlucas

article/CODE_SOFTWARE_CHECKLIST.md

@@ -18,7 +18,7 @@
 | Repository visibility (review) | Private — reviewer link supplied via Editorial Manager |
 | Repository visibility (post-publication) | Public on acceptance |
 | Versioned release for this manuscript | Tag `v1.1-natcomms-revision1` (created at submission of revised manuscript) |
-| Persistent archive (snapshot) | Zenodo DOI — to be minted on acceptance from `v1.1-natcomms-revision1` tag (Zenodo–GitHub integration enabled) |
+| Persistent archive (snapshot) | Figshare DOI [10.6084/m9.figshare.31653373](https://doi.org/10.6084/m9.figshare.31653373) (CC-BY 4.0); GitHub release tag `v1.1-natcomms-revision1` is mirrored on Figshare |
 | Reviewer data archive (private) | Figshare reviewer link — see Data Availability for the URL provided to the editorial office (excluded from the published version) |
 | License (code) | MIT (LICENSE file at repository root) |
 | License (data and manuscript artefacts) | CC-BY 4.0 |
@@ -201,7 +201,7 @@ Run-level reproducibility evidence is preserved per run in `outputs/runs/<run_id
 | Item | Response |
 |------|----------|
 | Long-term hosting | GitHub (https://github.com/Roverlucas/genai-reproducibility-protocol). Repository made public on acceptance |
-| Persistent archival | Zenodo–GitHub integration. The release tag `v1.1-natcomms-revision1` will be archived to Zenodo and a DOI minted at acceptance; the DOI will be inserted into the Code Availability and Data Availability statements during proof |
+| Persistent archival | Figshare (DOI: [10.6084/m9.figshare.31653373](https://doi.org/10.6084/m9.figshare.31653373), CC-BY 4.0). The GitHub release tag `v1.1-natcomms-revision1` is mirrored on Figshare. The deposit is available privately to reviewers via the share URL in the Cover Letter and will be made public at acceptance |
 | Issue tracking | GitHub Issues. Bug reports and reproduction questions are accepted from the broader community |
 | Versioning | Semantic versioning. Future protocol changes will not overwrite the manuscript tag |
 | Author commitment | Lucas Rover (corresponding author) commits to maintain the repository for ≥5 years post-publication, in accordance with the funding institution's data-management policy (UTFPR) |
@@ -213,7 +213,7 @@ Run-level reproducibility evidence is preserved per run in `outputs/runs/<run_id
 
 | Item | Status | Action |
 |------|--------|--------|
-| Zenodo DOI | ⚠ TBD | Mint after acceptance; insert into Code Availability and Data Availability statements at proof stage |
+| Figshare DOI | ☑ | [10.6084/m9.figshare.31653373](https://doi.org/10.6084/m9.figshare.31653373) — already minted (CC-BY 4.0); private reviewer share URL: https://figshare.com/s/3d17327cef1ae99ed37c |
 | Final run count (4,104 + revision additions) | ⚠ TBD | Update Table 1 and §1 (CODE_SOFTWARE_CHECKLIST) once T1 HumanEval + T1 GSM8K complete |
 | Pass@1 results (HumanEval) | ⚠ TBD | Pending T1 execution completion |
 | Final tagged release `v1.1-natcomms-revision1` | ⚠ TBD | Created at the moment the revised manuscript is uploaded |

article/ML_CHECKLIST_FILLED.md

@@ -116,7 +116,7 @@ The Methods now define the **unit of analysis as a deployment stack** — the tu
 
 ### R-4. Updates to the ML Checklist sections
 
-- **Section 1 (Code and Data):** No change to checks; the same repository now also hosts the revision artefacts under `outputs/revision/`, `data/inputs/revision/`, `analysis/revision/`, and `src/tasks/`. Reviewer access is via the same private link until acceptance, after which the repository becomes public and a Zenodo DOI is minted from the tagged release `v1.1-natcomms-revision1`.
+- **Section 1 (Code and Data):** No change to checks; the same repository now also hosts the revision artefacts under `outputs/revision/`, `data/inputs/revision/`, `analysis/revision/`, and `src/tasks/`. Reviewer access is via the private Figshare share URL provided in the Cover Letter; the GitHub release tag `v1.1-natcomms-revision1` is mirrored on Figshare (DOI: [10.6084/m9.figshare.31653373](https://doi.org/10.6084/m9.figshare.31653373), CC-BY 4.0).
 - **Section 2A (Data sources):** Methods §Input data and Supplementary §S2/§S3 updated to list the additional datasets — HumanEval (MIT-licensed), GSM8K (MIT-licensed) and the 10 PubMed PM2.5 abstracts (drawn from the sister paper, Rover & Tadano, RSM under review).
 - **Section 2B (Train/test/validation):** Still N/A — this remains an inference-reproducibility study with no model training. HumanEval and GSM8K are used as evaluation prompts only, not as training data.
 - **Section 2C (Dataset bias):** Discussion §Limitations now includes an explicit cross-domain caveat — the revision tested coding (HumanEval), mathematical reasoning (GSM8K), and a small health-domain probe (T14). Cross-language generalisation and large-scale clinical applications remain out of scope.
@@ -135,4 +135,4 @@ Revision additions: 51 new tests covering HumanEval loader, GSM8K loader, pass@1
 
 - ⚠ **TBD — Pass@1 per stack (HumanEval):** awaits T1 batch completion (orchestrator `run_revision_full.sh`).
 - ⚠ **TBD — Final EMR per stack on T14:** PubMed PM2.5 still in flight at the time of writing this checklist; current runs in `outputs/revision/runs/`.
-- ⚠ **TBD — Zenodo DOI:** to be minted at acceptance and inserted into Section 1, the manuscript Data Availability and Code Availability statements, and the corresponding citation block.
+- ☑ **Figshare DOI:** [10.6084/m9.figshare.31653373](https://doi.org/10.6084/m9.figshare.31653373) — already minted (CC-BY 4.0). Inserted into Section 1, the manuscript Data Availability and Code Availability statements, and the corresponding citation block. Private reviewer share URL: https://figshare.com/s/3d17327cef1ae99ed37c

article/REPORTING_SUMMARY_FILLED.md

@@ -56,12 +56,13 @@ https://github.com/Roverlucas/genai-reproducibility-protocol
 ### Data availability statement
 ```
 All 4,104 experimental records, provenance metadata (Run Cards in JSON
-format), PROV-JSON provenance graphs, and input abstracts are available
-to reviewers during peer review via the project repository at
-https://github.com/Roverlucas/genai-reproducibility-protocol. Upon
-publication, an archived snapshot with a persistent DOI will be deposited
-in Zenodo under a CC-BY 4.0 licence. Source data for all figures and
-tables are included in the repository. No restrictions on data
+format), PROV-JSON provenance graphs, and input abstracts are deposited
+on Figshare with persistent DOI 10.6084/m9.figshare.31653373 (CC-BY 4.0).
+The Figshare deposit mirrors the project GitHub repository at
+https://github.com/Roverlucas/genai-reproducibility-protocol (release
+tag v1.1-natcomms-revision1). Reviewer access during peer review is via
+the private Figshare share URL provided in the Cover Letter. Source data
+for all figures and tables are included. No restrictions on data
 availability apply.
 ```
 
@@ -171,4 +172,4 @@ The Software and code blocks in §2 are extended to include the following revisi
 
 ### Data availability (revised)
 
-The Data Availability statement in §3 also covers `outputs/revision/runs/` and `data/inputs/revision/`. A Zenodo DOI minted from release tag `v1.1-natcomms-revision1` will be inserted at acceptance.
+The Data Availability statement in §3 also covers `outputs/revision/runs/` and `data/inputs/revision/`. The Figshare DOI [10.6084/m9.figshare.31653373](https://doi.org/10.6084/m9.figshare.31653373) (CC-BY 4.0) is already minted and is referenced in the Data Availability and Code Availability statements; the GitHub release tag `v1.1-natcomms-revision1` is mirrored on Figshare. Private reviewer share URL: https://figshare.com/s/3d17327cef1ae99ed37c

article/ncomms_main.pdf

@@ -670,11 +670,11 @@ \subsection{Reporting summary}\label{subsec:reporting}
 
 \bmhead{Data availability}
 
-All run records (JSON), PROV-JSON provenance documents, Run Cards, Prompt Cards, input data (30 ML/AI abstracts with DOIs, 10 PubMed PM\textsubscript{2.5} abstracts, HumanEval and GSM8K problem identifiers), and source data underlying every figure and table are publicly available at \url{https://github.com/Roverlucas/genai-reproducibility-protocol} under a CC-BY~4.0 licence. An archived snapshot of the release tag \texttt{v1.1-natcomms-revision1} will be deposited in Zenodo on acceptance and a persistent DOI will be inserted at proof stage. Source data are provided with this paper.
+All run records (JSON), PROV-JSON provenance documents, Run Cards, Prompt Cards, input data (30 ML/AI abstracts with DOIs, 10 PubMed PM\textsubscript{2.5} abstracts, HumanEval and GSM8K problem identifiers), and source data underlying every figure and table are deposited on Figshare under a CC-BY~4.0 licence (DOI: \href{https://doi.org/10.6084/m9.figshare.31653373}{10.6084/m9.figshare.31653373}). The Figshare deposit mirrors the project GitHub repository at \url{https://github.com/Roverlucas/genai-reproducibility-protocol} (release tag \texttt{v1.1-natcomms-revision1}). A private reviewer URL is provided in the Cover Letter for peer-review access prior to public release. Source data are provided with this paper.
 
 \bmhead{Code availability}
 
-The reference implementation of the provenance protocol (Run Card, Prompt Card, W3C PROV-JSON generation), all experiment runners, the statistical and figure-generation pipeline, and the revision extensions for HumanEval, GSM8K and the cross-domain PubMed probe are publicly available at \url{https://github.com/Roverlucas/genai-reproducibility-protocol} under the MIT licence. The repository includes a \texttt{README.md} with installation and execution instructions, pinned dependencies (\texttt{requirements.txt}, Python 3.14.3), and a test suite (\texttt{pytest}, 102 tests). An archived snapshot of release tag \texttt{v1.1-natcomms-revision1} will be deposited in Zenodo on acceptance, with the persistent DOI inserted at proof stage.
+The reference implementation of the provenance protocol (Run Card, Prompt Card, W3C PROV-JSON generation), all experiment runners, the statistical and figure-generation pipeline, and the revision extensions for HumanEval, GSM8K and the cross-domain PubMed probe are publicly available at \url{https://github.com/Roverlucas/genai-reproducibility-protocol} under the MIT licence (release tag \texttt{v1.1-natcomms-revision1}). The repository includes a \texttt{README.md} with installation and execution instructions, pinned dependencies (\texttt{requirements.txt}, Python 3.14.3), and a test suite (\texttt{pytest}, 102 tests). A permanent mirror of the code archive is deposited on Figshare alongside the data (DOI: \href{https://doi.org/10.6084/m9.figshare.31653373}{10.6084/m9.figshare.31653373}, CC-BY 4.0).
 
 \bmhead{Supplementary information}
 
@@ -716,10 +716,10 @@ \section*{Declarations}
 Correspondence and requests for materials should be addressed to Lucas Rover (lucasrover@alunos.utfpr.edu.br).
 
 \item \textbf{Data availability:}
-All experimental records (original 4{,}104 runs plus revision additions for HumanEval, GSM8K, the multi-turn extension, and the cross-domain PubMed probe), W3C PROV-JSON provenance documents, Run Cards, Prompt Cards, input data with DOIs, and source data for every figure and table are available to reviewers during peer review via the project repository at \url{https://github.com/Roverlucas/genai-reproducibility-protocol}. On acceptance, an archived snapshot of release tag \texttt{v1.1-natcomms-revision1} will be deposited in Zenodo and a persistent DOI will be minted and inserted at proof stage. The repository will be made public under a CC-BY~4.0 licence on acceptance.
+All experimental records (original 4{,}104 runs plus revision additions for HumanEval, GSM8K, the multi-turn extension, and the cross-domain PubMed probe), W3C PROV-JSON provenance documents, Run Cards, Prompt Cards, input data with DOIs, and source data for every figure and table are available to reviewers during peer review via a private Figshare share URL provided in the Cover Letter, and at the project's GitHub repository (\url{https://github.com/Roverlucas/genai-reproducibility-protocol}, release tag \texttt{v1.1-natcomms-revision1}). The Figshare deposit will be made publicly accessible at acceptance under a CC-BY~4.0 licence; its persistent DOI is \href{https://doi.org/10.6084/m9.figshare.31653373}{10.6084/m9.figshare.31653373}.
 
 \item \textbf{Code availability:}
-The full source code for the provenance protocol (Run Card, Prompt Card, W3C PROV-JSON generation), the experiment runners (\texttt{run\_experiments.py}, \texttt{run\_claude\_multiturn.py}, \texttt{run\_gemini\_multiturn.py}, \texttt{run\_chat\_control.py}, and the resumable revision orchestrator \texttt{run\_revision\_full.sh}), the statistical and figure-generation pipeline, and the test suite (102 \texttt{pytest} tests) are available to reviewers during peer review at \url{https://github.com/Roverlucas/genai-reproducibility-protocol}. On acceptance, the repository will be made publicly available under the MIT licence and an archived release with a persistent Zenodo DOI will be minted and inserted into this statement at proof stage. A \texttt{README.md} with installation and execution instructions and a pinned \texttt{requirements.txt} (Python~3.14.3) are provided.
+The full source code for the provenance protocol (Run Card, Prompt Card, W3C PROV-JSON generation), the experiment runners (\texttt{run\_experiments.py}, \texttt{run\_claude\_multiturn.py}, \texttt{run\_gemini\_multiturn.py}, \texttt{run\_chat\_control.py}, and the resumable revision orchestrator \texttt{run\_revision\_full.sh}), the statistical and figure-generation pipeline, and the test suite (102 \texttt{pytest} tests) are available to reviewers during peer review at \url{https://github.com/Roverlucas/genai-reproducibility-protocol} (release tag \texttt{v1.1-natcomms-revision1}). On acceptance, the repository will be made publicly available under the MIT licence. A permanent mirror of the code archive is deposited on Figshare alongside the data with persistent DOI \href{https://doi.org/10.6084/m9.figshare.31653373}{10.6084/m9.figshare.31653373} (CC-BY 4.0). A \texttt{README.md} with installation and execution instructions and a pinned \texttt{requirements.txt} (Python~3.14.3) are provided.
 \end{itemize}