Fix API documentation generation

[melissawm]

Description

This PR fixes the RTD documentation generation and deployment by eliminating many formatting issues, some importing errors and warnings resulting from the docstring generation via apidoc.

The main issue I fixed was to remove many of the docs dependencies, since they can be mocked in the conf.py file and that makes the docs generation process faster and lighter. I also fixed a couple of typos, and reviewed the installation instructions which looked to me to be outdated (please confirm).

This is a big PR since it involves many files, but changes are all in docstrings, so should not have any effect on actual code. In addition to fixing warnings, I also went ahead and reviewed as many docstrings as I could to fix formatting, make them consistent and better looking for the generated documentation website. Docstrings are written in rst format, and some of them were written in a markdown flavor - this is something to be aware of in the future (see https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html)

Tests

Documentation builds correctly (and quickly) locally.

Checklist

Before submitting this PR, please make sure (put X in square brackets):

• I have performed a self-review of my code. For an optional AI review, add the gemini-review label.
• I have necessary comments in my code, particularly in hard-to-understand areas.
• I have run end-to-end tests tests and provided workload links above if applicable.
• I have made or will make corresponding changes to the doc if needed, including adding new documentation pages to the relevant Table of Contents (toctree directive) as explained in our documentation.

[codecov]

Codecov Report

❌ Patch coverage is 0% with 18 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/MaxText/kernels/jax_flash_attention.py	0.00%	17 Missing ⚠️
src/MaxText/utils/ckpt_conversion/to_maxtext.py	0.00%	1 Missing ⚠️

📢 Thoughts on this report? Let us know!

[melissawm]

mdformat should not be running on all files here, as far as I understand. I'll investigate and solve the remaining CI checks.