Merge manuscript cleanup and bibliography fixes from main into joss

[tjkerby]

This PR brings the latest JOSS manuscript revisions from main into the joss branch in response to editor feedback.

Why this should be merged

The changes in this PR improve the paper’s correctness, readability, and fit with JOSS expectations without changing the underlying contribution of the software. In particular, they:

• correct front matter metadata so author affiliations map cleanly to the author list
• simplify the manuscript structure to better match the expected JOSS paper format
• remove material that belongs more naturally in repository documentation than in the paper itself
• reduce duplication and awkward phrasing
• clean up bibliography issues identified during review

Overall, this makes the joss branch a cleaner and more accurate version of the manuscript for continued review.

Summary of changes

• Reordered affiliations in the YAML metadata so they match the author order correctly.
• Removed extra subsection headings and the separate Software overview section to better align with the standard JOSS paper structure.
• Standardized heading capitalization and presentation for consistency.
• Consolidated overlapping software-description material into a single Software design section.
• Simplified the design-tradeoffs table for readability.
• Reworked the software capabilities into a more concise presentation.
• Removed installation and runtime command examples from the paper body.
• Removed standalone repository and license boilerplate from the manuscript text.
• Removed the separate Use cases section.
• Removed the separate Quality control section, since testing and operational details are better documented in the repository.
• Condensed the Research impact statement by removing a paragraph that read more like reviewer-facing commentary than manuscript content.
• Removed duplicated content and cleaned up formatting in the AI usage disclosure.
• Smoothed phrasing throughout the manuscript.
• Fixed bibliography issues, including duplicate URLs, the OpenAI reference, and the Kinney et al. (2023) DOI/reference formatting.

Notes

This PR is manuscript-focused. It does not change the software itself. Its purpose is to keep the joss branch aligned with the improved manuscript and reference cleanup already completed on main.