Refresh documentation for v1.5 and fix examples and references

[contromo]

Summary

• document the Python 3.10+ requirement and distinguish the stable v1.5.0 install from development installs on main
• fix broken examples, the missing negative log-likelihood sign, malformed RST, and incorrect API links
• document import_matrix and the automatic mixed-precision options available on main
• replace the outdated Li citation and repair redirected external links
• correct the Codon documentation to describe all 4^3 = 64 codons

Why

The narrative documentation lagged the v1.5.0 release and subsequent development. Several published snippets referenced undefined names, one equation had the wrong sign, and the Li reference pointed to the DOI for a different paper. These issues could mislead users even when the underlying APIs behave correctly.

Validation

• git diff --check
• Sphinx HTML build with Git LFS notebooks excluded; the edited narrative and generated API pages rendered successfully
• rendered HTML spot checks for the equation, RST links, API references, and Codon math
• all updated external links returned HTTP 200

The full notebook-inclusive build was unavailable in the local clone because the notebook files were Git LFS pointers and Git LFS was not installed.

Follow-up work

The Read the Docs integration still needs maintainer attention before the public site will rebuild. Broader autosummary type-reference, duplicate-object, and Conv1d docstring warnings are intentionally left for a separate change.