feat: link contents to .ipynb and expand LaTeX macros before conversion

[mmmarinho]

Summary

Three related changes to how the downloadable .ipynb files are produced and linked.

This PR was created by an AI agent (OpenHands) on behalf of the repository owner.

1. "Contents" links now point to the .ipynb, not the .md

In basic_lessons/README.md, the Contents and Exercise Answers tables linked to
lesson*_tutorial.md / lesson*_exercise_answers.md. Readers were taken to the raw
Markdown source instead of the executable notebook. All 11 links now point at the
generated .ipynb files (matching what myst.yml's TOC already uses).

2. New convert_to_ipynb.py: .md → intermediate .md → .ipynb with macros expanded

The lessons use custom LaTeX macros (\myvec, \mymatrix, \quat, \dual, defined in
myst.yml under project.math). MyST expands them at build time via KaTeX, but most
standalone .ipynb renderers (JupyterLab, VS Code, nbviewer, …) do not know these
macros and would show them literally. The new script implements a two-step pipeline:

basic_lessons/*.md  ->  <stem>_expanded.md  (macros expanded)  ->  basic_lessons/*.ipynb

• Reads the macro definitions from myst.yml and expands them into a transient
  <stem>_expanded.md, then runs jupytext on that file. The resulting .ipynb
  contains only standard LaTeX and renders anywhere; you keep writing the original
  .md with the convenient macros.
• Expansion mirrors KaTeX/TeX macro semantics so it exactly matches what the site
  renders: braced arguments (including nested braces like \mymatrix{H^{-1}}), single
  space-separated tokens (e.g. \myvec H_{0'}^{0}), and no-argument macros (\dual).
• {code-cell} bodies are left untouched, so Python source/comments are never corrupted.
• The intermediate file is a build artifact: deleted after conversion (use --keep to
  inspect it); not tracked and not in the TOC.

Verified: all 11 generated notebooks contain 0 macro tokens; all 295 math blocks
render cleanly in KaTeX without any macro definitions (the way a generic renderer
would see them); code cells are byte-identical to a plain jupytext conversion; and a
local myst build completes with 0 warnings (17 pages built).

3. AGENTS.md updated

Documents the two-step pipeline, the reason for it, the new local/CI build commands,
the .ipynb contents-link convention, the macro/code-cell caveat, and the new
*_expanded.md build artifact.

CI

The "Generate downloadable notebooks" step in .github/workflows/notebook_to_html.yml
now runs python convert_to_ipynb.py (with pyyaml added to its deps) instead of the
old inline jupytext loop.

[mmmarinho]

👍