feat: change markdown standard to GFM

[tachyonicClock]

Change markdown standard to Github Flavored Markdown (GFM) replacing Pandoc's default markdown. This is consistent with the Jupyter Notebook markdown cells and should improve compatibility (https://nbformat.readthedocs.io/en/latest/format_description.html#markdown-cells).

[pep8speaks]

Hello @tachyonicClock! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file src/nbsphinx/__init__.py:

Line 1044:80: E501 line too long (104 > 79 characters)

Comment last updated at 2024-09-04 22:52:54 UTC

[mgeier]

Thanks for this PR!

I wasn't aware that Jupyter uses GFM. First I thought this was changed recently, but apparently this has been supported for a long time!

So I'm all for also using it in nbsphinx, but this PR seems to break a few things:

• LaTeX environments and macros like \ref{}
• HTML elements
• "warning" box within "note" box

This might not be a full list, for now I only looked at markdown-cells.ipynb.

[douglas-raillard-arm]

Drive-by comment: have you considered also making a similar PR in jupyter nbconvert ? Both projects unfortunately do not share the pandoc invocation, but I think most users would expect them to behave the same way (at least I did).