Merge manuscript cleanup and bibliography fixes from main into joss

paper/paper.bib

@@ -3,51 +3,47 @@
 
 ## `paper.bib`
 
-```bibtex
 @misc{anthropic2024mcp,
   title = {Introducing the Model Context Protocol},
-  author = {Anthropic},
+  author = {{Anthropic}},
   year = {2024},
   month = {November},
   url = {https://www.anthropic.com/news/model-context-protocol},
-  howpublished = {\url{https://www.anthropic.com/news/model-context-protocol}},
-  note = {Accessed: August 22, 2025}
+  note = {Accessed: 2025-08-22}
 }
 
 @misc{mcp2024github,
   title = {Model Context Protocol: A protocol for seamless integration between LLM applications and external data sources},
   author = {{Model Context Protocol Contributors}},
   year = {2024},
   url = {https://github.com/modelcontextprotocol},
-  howpublished = {\url{https://github.com/modelcontextprotocol}},
-  note = {Accessed: August 22, 2025}
+  note = {Accessed: 2025-08-22}
 }
 
 @misc{semanticscholar2024api,
   title = {Semantic Scholar Academic Graph API},
   author = {{Semantic Scholar}},
   year = {2024},
   url = {https://www.semanticscholar.org/product/api},
-  howpublished = {\url{https://www.semanticscholar.org/product/api}},
-  note = {Accessed: August 22, 2025}
+  note = {Accessed: 2025-08-22}
 }
 
 @article{Kinney2023TheSS,
-  title={The Semantic Scholar Open Data Platform},
-  author={Rodney Michael Kinney and Chloe Anastasiades and Russell Authur and Iz Beltagy and Jonathan Bragg and Alexandra Buraczynski and Isabel Cachola and Stefan Candra and Yoganand Chandrasekhar and Arman Cohan and Miles Crawford and Doug Downey and Jason Dunkelberger and Oren Etzioni and Rob Evans and Sergey Feldman and Joseph Gorney and David W. Graham and F.Q. Hu and Regan Huff and Daniel King and Sebastian Kohlmeier and Bailey Kuehl and Michael Langan and Daniel Lin and Haokun Liu and Kyle Lo and Jaron Lochner and Kelsey MacMillan and Tyler C. Murray and Christopher Newell and Smita R Rao and Shaurya Rohatgi and Paul Sayre and Zejiang Shen and Amanpreet Singh and Luca Soldaini and Shivashankar Subramanian and A. Tanaka and Alex D Wade and Linda M. Wagner and Lucy Lu Wang and Christopher Wilhelm and Caroline Wu and Jiangjiang Yang and Angele Zamarron and Madeleine van Zuylen and Daniel S. Weld},
-  journal={ArXiv},
-  year={2023},
-  volume={abs/2301.10140},
-  url={https://api.semanticscholar.org/CorpusID:256194545}
+  title = {The Semantic Scholar Open Data Platform},
+  author = {Kinney, Rodney Michael and Anastasiades, Chloe and Authur, Russell and Beltagy, Iz and Bragg, Jonathan and Buraczynski, Alexandra and Cachola, Isabel and Candra, Stefan and Chandrasekhar, Yoganand and Cohan, Arman and Crawford, Miles and Downey, Doug and Dunkelberger, Jason and Etzioni, Oren and Evans, Rob and Feldman, Sergey and Gorney, Joseph and Graham, David W. and Hu, F. Q. and Huff, Regan and King, Daniel and Kohlmeier, Sebastian and Kuehl, Bailey and Langan, Michael and Lin, Daniel and Liu, Haokun and Lo, Kyle and Lochner, Jaron and MacMillan, Kelsey and Murray, Tyler C. and Newell, Christopher and Rao, Smita R. and Rohatgi, Shaurya and Sayre, Paul and Shen, Zejiang and Singh, Amanpreet and Soldaini, Luca and Subramanian, Shivashankar and Tanaka, A. and Wade, Alex D. and Wagner, Linda M. and Wang, Lucy Lu and Wilhelm, Christopher and Wu, Caroline and Yang, Jiangjiang and Zamarron, Angele and van Zuylen, Madeleine and Weld, Daniel S.},
+  journal = {arXiv},
+  year = {2023},
+  volume = {2301.10140},
+  doi = {10.48550/arXiv.2301.10140},
+  url = {https://arxiv.org/abs/2301.10140}
 }
 
 @misc{neo4j2024database,
   title = {Neo4j Graph Database Platform},
   author = {{Neo4j Inc.}},
   year = {2024},
   url = {https://neo4j.com/product/neo4j-graph-database/},
-  howpublished = {\url{https://neo4j.com/product/neo4j-graph-database/}},
-  note = {Accessed: August 22, 2025}
+  note = {Accessed: 2025-08-22}
 }
 
 @article{franz2023cytoscape,
@@ -147,23 +143,23 @@ @inproceedings{wang-etal-2024-leave
 }
 
 @article{gao2023retrieval,
-  title={Retrieval-augmented generation for large language models: A survey},
-  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, Haofen and Wang, Haofen},
-  journal={arXiv preprint arXiv:2312.10997},
-  volume={2},
-  year={2023}
+  title = {Retrieval-augmented generation for large language models: A survey},
+  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, Haofen and Wang, Haofen},
+  journal = {arXiv preprint arXiv:2312.10997},
+  volume = {2},
+  year = {2023}
 }
 
 @inproceedings{reimers-2019-sentence-bert,
-  title     = {Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks},
-  author    = {Reimers, Nils and Gurevych, Iryna},
+  title = {Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks},
+  author = {Reimers, Nils and Gurevych, Iryna},
   booktitle = {Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing},
-  pages     = {3973--3983},
-  month     = {November},
-  year      = {2019},
+  pages = {3973--3983},
+  month = {November},
+  year = {2019},
   publisher = {Association for Computational Linguistics},
-  url       = {http://arxiv.org/abs/1908.10084},
-  doi       = {10.18653/v1/d19-1410}
+  url = {http://arxiv.org/abs/1908.10084},
+  doi = {10.18653/v1/D19-1410}
 }
 
 @article{reinanda2020knowledge,
@@ -230,52 +226,49 @@ @misc{docker2024
   author = {{Docker, Inc.}},
   year = {2024},
   url = {https://www.docker.com/},
-  howpublished = {\url{https://www.docker.com/}},
-  note = {Accessed: August 22, 2025}
+  note = {Accessed: 2025-08-22}
 }
 
 @misc{fastapi2024,
   title = {FastAPI: Modern, fast (high-performance), web framework for building APIs with Python 3.6+ based on standard Python type hints},
   author = {{FastAPI Contributors}},
   year = {2024},
   url = {https://fastapi.tiangolo.com/},
-  howpublished = {\url{https://fastapi.tiangolo.com/}},
-  note = {Accessed: August 22, 2025}
+  note = {Accessed: 2025-08-22}
 }
 
 @misc{rabbitmq2024,
   title = {RabbitMQ: The most widely deployed open source message broker},
   author = {{VMware, Inc.}},
   year = {2024},
   url = {https://www.rabbitmq.com/},
-  howpublished = {\url{https://www.rabbitmq.com/}},
-  note = {Accessed: August 22, 2025}
+  note = {Accessed: 2025-08-22}
 }
 
 @misc{ollama2024,
   title = {Ollama: Get up and running with Llama 3.2, Mistral, Gemma 2, and other large language models},
   author = {{Ollama Team}},
   year = {2024},
   url = {https://ollama.com/},
-  howpublished = {\url{https://ollama.com/}},
-  note = {Accessed: August 22, 2025}
+  note = {Accessed: 2025-08-22}
 }
 
 @misc{openai2023api,
-  title={OpenAI API},
-  author={OpenAI},
-  note={\url{https://platform.openai.com/}},
-  year={2023}
+  title = {OpenAI API Documentation},
+  author = {{OpenAI}},
+  year = {2026},
+  url = {https://developers.openai.com/api/docs},
+  note = {Accessed: 2026-04-01}
 }
 
 @article{nussbaum2025nomic,
-  title={Nomic Embed: Training a Reproducible Long Context Text Embedder},
-  author={Nussbaum, Zach and Morris, John Xavier and Mulyar, Andriy and Duderstadt, Brandon},
-  journal={Transactions on Machine Learning Research},
-  issn={2835-8856},
-  year={2025},
-  url={https://openreview.net/forum?id=IPmzyQSiQE},
-  note={Reproducibility Certification}
+  title = {Nomic Embed: Training a Reproducible Long Context Text Embedder},
+  author = {Nussbaum, Zach and Morris, John Xavier and Mulyar, Andriy and Duderstadt, Brandon},
+  journal = {Transactions on Machine Learning Research},
+  issn = {2835-8856},
+  year = {2025},
+  url = {https://openreview.net/forum?id=IPmzyQSiQE},
+  note = {Reproducibility Certification}
 }
 
 @article{rothacher2023eleven,
@@ -291,81 +284,91 @@ @article{rothacher2023eleven
 }
 
 @article{merkel2014docker,
-  title={Docker: lightweight linux containers for consistent development and deployment},
-  author={Merkel, Dirk},
-  journal={Linux journal},
-  volume={2014},
-  number={239},
-  pages={2},
-  year={2014}
+  title = {Docker: lightweight linux containers for consistent development and deployment},
+  author = {Merkel, Dirk},
+  journal = {Linux Journal},
+  volume = {2014},
+  number = {239},
+  pages = {2},
+  year = {2014}
 }
 
 @misc{langchain2026rag,
-  title        = {Build a RAG agent with LangChain},
-  author       = {{LangChain}},
-  howpublished = {\url{https://docs.langchain.com/oss/python/langchain/rag}},
-  note         = {Accessed: 2026-01-23}
+  title = {Build a RAG agent with LangChain},
+  author = {{LangChain}},
+  year = {2026},
+  url = {https://docs.langchain.com/oss/python/langchain/rag},
+  note = {Accessed: 2026-01-23}
 }
 
 @misc{llamaindex2026rag,
-  title        = {Introduction to RAG (Retrieval-Augmented Generation)},
-  author       = {{LlamaIndex}},
-  howpublished = {\url{https://developers.llamaindex.ai/python/framework/understanding/rag/}},
-  note         = {Accessed: 2026-01-23}
+  title = {Introduction to RAG (Retrieval-Augmented Generation)},
+  author = {{LlamaIndex}},
+  year = {2026},
+  url = {https://developers.llamaindex.ai/python/framework/understanding/rag/},
+  note = {Accessed: 2026-01-23}
 }
 
 @misc{haystack2026,
-  title        = {Get Started (Haystack Documentation)},
-  author       = {{deepset Haystack}},
-  howpublished = {\url{https://docs.haystack.deepset.ai/docs/get-started}},
-  note         = {Accessed: 2026-01-23}
+  title = {Get Started (Haystack Documentation)},
+  author = {{deepset Haystack}},
+  year = {2026},
+  url = {https://docs.haystack.deepset.ai/docs/get-started},
+  note = {Accessed: 2026-01-23}
 }
 
 @misc{llamaindex2026kg,
-  title        = {Knowledge Graph Index (LlamaIndex Python Documentation)},
-  author       = {{LlamaIndex}},
-  howpublished = {\url{https://developers.llamaindex.ai/python/examples/index_structs/knowledge_graph/knowledgegraphdemo/}},
-  note         = {Accessed: 2026-01-23}
+  title = {Knowledge Graph Index (LlamaIndex Python Documentation)},
+  author = {{LlamaIndex}},
+  year = {2026},
+  url = {https://developers.llamaindex.ai/python/examples/index_structs/knowledge_graph/knowledgegraphdemo/},
+  note = {Accessed: 2026-01-23}
 }
 
 @misc{langchain2026neo4j,
-  title        = {Neo4j (LangChain Integration Documentation)},
-  author       = {{LangChain}},
-  howpublished = {\url{https://docs.langchain.com/oss/python/integrations/providers/neo4j}},
-  note         = {Accessed: 2026-01-23}
+  title = {Neo4j (LangChain Integration Documentation)},
+  author = {{LangChain}},
+  year = {2026},
+  url = {https://docs.langchain.com/oss/python/integrations/providers/neo4j},
+  note = {Accessed: 2026-01-23}
 }
 
 @misc{microsoft2026graphrag,
-  title        = {microsoft/graphrag: A modular graph-based Retrieval-Augmented Generation (RAG) system},
-  author       = {{Microsoft}},
-  howpublished = {\url{https://github.com/microsoft/graphrag}},
-  note         = {Accessed: 2026-01-23}
+  title = {microsoft/graphrag: A modular graph-based Retrieval-Augmented Generation (RAG) system},
+  author = {{Microsoft}},
+  year = {2026},
+  url = {https://github.com/microsoft/graphrag},
+  note = {Accessed: 2026-01-23}
 }
 
 @misc{neo4j2026graphrag,
-  title        = {neo4j/neo4j-graphrag-python: Neo4j GraphRAG Package for Python},
-  author       = {{Neo4j}},
-  howpublished = {\url{https://github.com/neo4j/neo4j-graphrag-python}},
-  note         = {Accessed: 2026-01-23}
+  title = {neo4j/neo4j-graphrag-python: Neo4j GraphRAG Package for Python},
+  author = {{Neo4j}},
+  year = {2026},
+  url = {https://github.com/neo4j/neo4j-graphrag-python},
+  note = {Accessed: 2026-01-23}
 }
 
 @misc{connectedpapers2026,
-  title        = {Connected Papers},
-  author       = {{Connected Papers}},
-  howpublished = {\url{https://www.connectedpapers.com/}},
-  note         = {Accessed: 2026-01-23}
+  title = {Connected Papers},
+  author = {{Connected Papers}},
+  year = {2026},
+  url = {https://www.connectedpapers.com/},
+  note = {Accessed: 2026-01-23}
 }
 
 @misc{researchrabbit2026,
-  title        = {ResearchRabbit},
-  author       = {{ResearchRabbit}},
-  howpublished = {\url{https://www.researchrabbit.ai/}},
-  note         = {Accessed: 2026-01-23}
+  title = {ResearchRabbit},
+  author = {{ResearchRabbit}},
+  year = {2026},
+  url = {https://www.researchrabbit.ai/},
+  note = {Accessed: 2026-01-23}
 }
 
 @misc{litmaps2026,
-  title        = {Litmaps},
-  author       = {{Litmaps}},
-  howpublished = {\url{https://www.litmaps.com/}},
-  note         = {Accessed: 2026-01-23}
+  title = {Litmaps},
+  author = {{Litmaps}},
+  year = {2026},
+  url = {https://www.litmaps.com/},
+  note = {Accessed: 2026-01-23}
 }