Software paper for the v3 substrate; README demotes the v1 technical note

README.md

@@ -395,10 +395,16 @@ the GitHub URL).
 | Code | [github.com/lukefwalton/answer-engine](https://github.com/lukefwalton/answer-engine) |
 | About | [lukefwalton.com/ask/about/](https://lukefwalton.com/ask/about/) |
 
-**Artifact note:** cite [10.5281/zenodo.20710897](https://doi.org/10.5281/zenodo.20710897)
-for v1.2 of the formal write-up ([`docs/ARTIFACT-NOTE-v1.2.md`](./docs/ARTIFACT-NOTE-v1.2.md)).
-Its concept DOI, [10.5281/zenodo.20686053](https://doi.org/10.5281/zenodo.20686053),
-is separate from the software archive above and resolves to the latest version.
+**Software paper:** [`paper.md`](./paper.md) (references in [`paper.bib`](./paper.bib))
+describes the v3 substrate: the disclosure-typed contract, its design, and its
+evaluation. It is written in the Journal of Open Source Software form and is not yet
+submitted; until it has a venue, cite the software DOI above.
+
+**Technical note:** cite [10.5281/zenodo.20710897](https://doi.org/10.5281/zenodo.20710897)
+for v1.2 of the earlier technical note on the v1 engine
+([`docs/ARTIFACT-NOTE-v1.2.md`](./docs/ARTIFACT-NOTE-v1.2.md)). Its concept DOI,
+[10.5281/zenodo.20686053](https://doi.org/10.5281/zenodo.20686053), is separate from
+the software archive above and resolves to the latest version.
 
 To pin a specific archived snapshot, pick that release's version DOI on the
 [Zenodo versions page](https://zenodo.org/records/20676773) — no README update
@@ -442,7 +448,8 @@ the latest tag already advanced.
 
 ## Related writing
 
-Formal description of this implementation:
+The software paper for the v3 substrate: [`paper.md`](./paper.md). The earlier
+technical note on the v1 engine:
 [`docs/ARTIFACT-NOTE-v1.2.md`](./docs/ARTIFACT-NOTE-v1.2.md) —
 [DOI](https://doi.org/10.5281/zenodo.20710897) (CC BY-NC-ND 4.0).
 

paper.bib

@@ -0,0 +1,186 @@
+@inproceedings{lewis2020,
+  author    = {Lewis, Patrick and Perez, Ethan and Piktus, Aleksandra and Petroni, Fabio and Karpukhin, Vladimir and Goyal, Naman and K{\"u}ttler, Heinrich and Lewis, Mike and Yih, Wen-tau and Rockt{\"a}schel, Tim and Riedel, Sebastian and Kiela, Douwe},
+  title     = {Retrieval-Augmented Generation for Knowledge-Intensive {NLP} Tasks},
+  booktitle = {Advances in Neural Information Processing Systems 33 (NeurIPS 2020)},
+  year      = {2020},
+  doi       = {10.48550/arXiv.2005.11401}
+}
+
+@article{gao2023,
+  author  = {Gao, Yunfan and Xiong, Yun and Gao, Xinyu and Jia, Kangxiang and Pan, Jinliu and Bi, Yuxi and Dai, Yi and Sun, Jiawei and Wang, Meng and Wang, Haofen},
+  title   = {Retrieval-Augmented Generation for Large Language Models: A Survey},
+  journal = {arXiv preprint},
+  year    = {2023},
+  doi     = {10.48550/arXiv.2312.10997}
+}
+
+@article{rashkin2023,
+  author  = {Rashkin, Hannah and Nikolaev, Vitaly and Lamm, Matthew and Aroyo, Lora and Collins, Michael and Das, Dipanjan and Petrov, Slav and Tomar, Gaurav Singh and Turc, Iulia and Reitter, David},
+  title   = {Measuring Attribution in Natural Language Generation Models},
+  journal = {Computational Linguistics},
+  volume  = {49},
+  number  = {4},
+  pages   = {777--840},
+  year    = {2023},
+  doi     = {10.1162/coli_a_00486}
+}
+
+@inproceedings{liu2023,
+  author    = {Liu, Nelson F. and Zhang, Tianyi and Liang, Percy},
+  title     = {Evaluating Verifiability in Generative Search Engines},
+  booktitle = {Findings of the Association for Computational Linguistics: EMNLP 2023},
+  year      = {2023},
+  pages     = {7001--7025},
+  doi       = {10.18653/v1/2023.findings-emnlp.467}
+}
+
+@article{bohnet2022,
+  author  = {Bohnet, Bernd and Tran, Vinh Q. and Verga, Pat and Aharoni, Roee and Andor, Daniel and Soares, Livio Baldini and Ciaramita, Massimiliano and Eisenstein, Jacob and Ganchev, Kuzman and Herzig, Jonathan and Hui, Kai and Kwiatkowski, Tom and Ma, Ji and Ni, Jianmo and Saralegui, Lierni Sestorain and Schuster, Tal and Cohen, William W. and Collins, Michael and Das, Dipanjan and Metzler, Donald and Petrov, Slav and Webster, Kellie},
+  title   = {Attributed Question Answering: Evaluation and Modeling for Attributed Large Language Models},
+  journal = {arXiv preprint},
+  year    = {2022},
+  doi     = {10.48550/arXiv.2212.08037}
+}
+
+@inproceedings{rebedea2023,
+  author    = {Rebedea, Traian and Dinu, Razvan and Sreedhar, Makesh and Parisien, Christopher and Cohen, Jonathan},
+  title     = {{NeMo} Guardrails: A Toolkit for Controllable and Safe {LLM} Applications with Programmable Rails},
+  booktitle = {Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing: System Demonstrations},
+  year      = {2023},
+  pages     = {431--445},
+  doi       = {10.18653/v1/2023.emnlp-demo.40}
+}
+
+@article{shoemaker2011,
+  author  = {Shoemaker, David},
+  title   = {Attributability, Answerability, and Accountability: Toward a Wider Theory of Moral Responsibility},
+  journal = {Ethics},
+  volume  = {121},
+  number  = {3},
+  pages   = {602--632},
+  year    = {2011},
+  doi     = {10.1086/659003}
+}
+
+@article{sabelfeld2003,
+  author  = {Sabelfeld, Andrei and Myers, Andrew C.},
+  title   = {Language-Based Information-Flow Security},
+  journal = {IEEE Journal on Selected Areas in Communications},
+  volume  = {21},
+  number  = {1},
+  pages   = {5--19},
+  year    = {2003},
+  doi     = {10.1109/JSAC.2002.806121}
+}
+
+@inproceedings{goguen1982,
+  author    = {Goguen, Joseph A. and Meseguer, Jos{\'e}},
+  title     = {Security Policies and Security Models},
+  booktitle = {Proceedings of the 1982 IEEE Symposium on Security and Privacy},
+  year      = {1982},
+  pages     = {11--20},
+  doi       = {10.1109/SP.1982.10014}
+}
+
+@misc{mcp2026,
+  author = {{Model Context Protocol project}},
+  title  = {Model Context Protocol specification, revision 2026-07-28},
+  year   = {2026},
+  url    = {https://modelcontextprotocol.io/specification/2026-07-28}
+}
+
+@misc{langchain,
+  author = {Chase, Harrison},
+  title  = {{LangChain}},
+  year   = {2022},
+  url    = {https://github.com/langchain-ai/langchain}
+}
+
+@misc{llamaindex,
+  author = {Liu, Jerry},
+  title  = {{LlamaIndex}},
+  year   = {2022},
+  url    = {https://github.com/run-llama/llama_index}
+}
+
+@misc{walton2026a,
+  author    = {Walton, Luke F.},
+  title     = {The Decision No One Authored: The Answerability Gap in Generative {AI}},
+  year      = {2026},
+  publisher = {Zenodo},
+  doi       = {10.5281/zenodo.20614374}
+}
+
+@misc{walton2026b,
+  author    = {Walton, Luke F.},
+  title     = {The Captured Oracle: Authorship and Agency in the Ethics of Answer-Engine Optimization},
+  year      = {2026},
+  publisher = {Zenodo},
+  doi       = {10.5281/zenodo.20676327}
+}
+
+@misc{walton2026c,
+  author    = {Walton, Luke F.},
+  title     = {The Invariant of Answerability},
+  year      = {2026},
+  publisher = {Zenodo},
+  doi       = {10.5281/zenodo.20606492}
+}
+
+@misc{walton2026d,
+  author    = {Walton, Luke F.},
+  title     = {Building Answerable {AI}: Why Automation Needs Owned Error},
+  year      = {2026},
+  publisher = {Zenodo},
+  doi       = {10.5281/zenodo.20682306}
+}
+
+@misc{walton2026note,
+  author    = {Walton, Luke F.},
+  title     = {Answer Engine: A Small Reference Implementation for Citation-Grounded Answerability},
+  year      = {2026},
+  publisher = {Zenodo},
+  doi       = {10.5281/zenodo.20686053}
+}
+
+@software{walton2026software,
+  author    = {Walton, Luke F.},
+  title     = {Answer Engine},
+  year      = {2026},
+  publisher = {Zenodo},
+  doi       = {10.5281/zenodo.20676773},
+  url       = {https://github.com/lukefwalton/answer-engine}
+}
+
+@article{almasoud2026,
+  author  = {Al Masoud, Aiman and Arazzi, Marco and Nocera, Antonino},
+  title   = {{SD-RAG}: A Prompt-Injection-Resilient Framework for Selective Disclosure in Retrieval-Augmented Generation},
+  journal = {arXiv preprint},
+  year    = {2026},
+  doi     = {10.48550/arXiv.2601.11199}
+}
+
+@inproceedings{rasul2026,
+  author    = {Rasul, Md Fazle and Aghayarzadeh, Hamed and Ray, Indrakshi},
+  title     = {Information Flow Control for Retrieval-Augmented {LLM} Chatbots},
+  booktitle = {Data and Applications Security and Privacy XL: 40th IFIP WG 11.3 Annual Conference, DBSec 2026},
+  publisher = {Springer},
+  year      = {2026},
+  doi       = {10.1007/978-3-032-33260-8_17}
+}
+
+@article{siddiqui2025,
+  author  = {Siddiqui, Shoaib Ahmed and Gaonkar, Radhika and K{\"o}pf, Boris and Krueger, David and Paverd, Andrew and Salem, Ahmed and Tople, Shruti and Wutschitz, Lukas and Xia, Menglin and Zanella-B{\'e}guelin, Santiago},
+  title   = {Permissive Information-Flow Analysis for Large Language Models},
+  journal = {Transactions on Machine Learning Research},
+  year    = {2025},
+  url     = {https://arxiv.org/abs/2410.03055}
+}
+
+@article{xu2026,
+  author  = {Xu, Jinghan and Fan, Longze and Wang, Zeyuan and Li, Xinjin and Liu, Hankai},
+  title   = {{MNC}: Scope-Bound Semantic Declassification for Private {LLM}-Agent Communication},
+  journal = {arXiv preprint},
+  year    = {2026},
+  doi     = {10.48550/arXiv.2608.01719}
+}