Move book build workflow to uv

[jdebacker]

Summary

This PR moves the book build workflow from the legacy environment.yml / requirements.txt setup to uv, while keeping the project dependency set intentionally small and focused on building and deploying the book.

What changed

• added a root pyproject.toml with a minimal dependency set centered on jupyter-book>=2.0.0,<3
• generated and committed uv.lock for reproducible dependency resolution
• removed environment.yml and requirements.txt
• added a root Makefile with a book target that performs a clean rebuild via make book
• updated the GitHub Actions workflows to use uv instead of Conda and to run make book
• updated the deploy workflow to publish book/_build/site
• updated the README to document the new uv workflow

Build verification

• ran uv lock successfully
• ran make book successfully

Additional compatibility fixes included here

Because the new uv workflow is wired into CI, this PR also includes the minimum Jupyter Book 2 / MyST compatibility fixes needed for the build to pass under the new toolchain:

• converted the glossary page to MyST glossary syntax
• updated the bibliography page and book/myst.yml bibliography configuration
• made the clean step non-interactive for CI with jupyter book clean --all --yes
• ignored the root _build/ directory in .gitignore

Notes

• This branch is stacked on top of codex/low-priority-tutorial-pass.
• The build still emits non-fatal warnings about legacy scale options in some figure directives, but the site now builds successfully end to end with the new uv workflow.