Refactor: 3.1 phase of RESTRUCTURE.md, focussing on setup.sh and related Python dependency & Dockerfile files

[SamuelMarks]

Description

Refactor: 3.1 phase of RESTRUCTURE.md, focussing on setup.sh and related Python dependency & Dockerfile files

Note: merge this before #2361; after which that PR is roughly halved.

Tests

CI and manual

bash ./dependencies/scripts/docker_build_dependency_image.sh DEVICE=tpu MODE=nightly

bash ./dependencies/scripts/docker_build_dependency_image.sh DEVICE=tpu MODE=stable

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.