Migrate course site pipeline to Jupyter Book 2 with MyST config

[Copilot]

This updates the course site from Jupyter Book 1.x to 2.x and aligns the repository with the MyST-driven configuration model. It also keeps the Columbia/NYU school rendering flow compatible with the new build path.

• Jupyter Book 2 dependency + CLI migration

  • Bumped jupyter-book to 2.* in requirements.txt.
  • Replaced legacy JB1 build flags in Makefile with JB2-compatible invocation.

• MyST-native project/site configuration

  • Added myst.yml as the authoritative JB2 config.
  • Migrated course metadata and full book navigation into project.toc.
  • Preserved school-specific Jinja conditionals inside TOC entries (Columbia/NYU branches of content).

• Read the Docs pipeline alignment

  • Switched .readthedocs.yaml from Sphinx-prebuild flow to direct JB2/MyST HTML build commands.
  • Added explicit Node runtime and _build/html artifact copy compatible with JB2 output.

• Docs update for maintainers

  • Updated meta/instructor_guide.md to reference myst.yml in site configuration ownership.

site:
	jupyter-book build --html --all --ci

[afeld]

@copilot Rebase and squash on main then fix the build. Keep going until it passes.

[Copilot]

@copilot Rebase and squash on main then fix the build. Keep going until it passes.

Updated in 5e53235 (plus prior 0a84ed1). I merged main instead of rebasing/squashing because this environment cannot safely publish rewritten history (no force-push path). I fixed the failing build path by normalizing .html internal links to JB2 folder-style routes in extras/scripts/broken_links.rb, and the earlier test dependency failure was fixed by adding markdown-it-py.

[afeld]

@copilot There are still merge conflicts.

[Copilot]

@copilot There are still merge conflicts.

Resolved in c7591b6 (merge of latest main) and 060f010 (lockfile update after dependency conflict resolution). The branch now includes current main and the merge conflict on dependency files has been resolved.