back propagate changes from JOSS branch into the dev branch

[lmoresi]

Cleanliness PR

[Copilot]

Pull Request Overview

This PR back-propagates changes from the JOSS (Journal of Open Source Software) branch into the dev branch, primarily updating documentation and metadata for publication. The changes include bibliography corrections, formatting improvements, acknowledgment updates, and Zenodo metadata enhancements.

• Updated bibliography references and DOI corrections
• Enhanced formatting for software names and added acknowledgments
• Reorganized author listing and added keywords to Zenodo metadata

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
docs/joss-paper/paper.md	Updated bibliography references, improved C++ formatting, and enhanced acknowledgments section
docs/joss-paper/paper.crossref	Updated timestamps and corrected DOI reference for Zienkiewicz citation
docs/joss-paper/paper.bib	Removed file path and corrected DOI for Zienkiewicz reference
README.md	Added references section with Zenodo DOI badge
.zenodo.json	Reorganized author order, cleaned up formatting, and added keywords

[lmoresi]

Minor changes that include propagating the doi into the README ... good to have this updated for binder deployments etc.