Multiple small issues of new flow

[daquinteroflex]

• sync to read the docs on the release is happening on the main branch, not the latest branch
• Improve the way the latest branch and develop branch get updated so they don't get too far apart
• Have more clarity on the actual tidy3d-notebooks deployment, review Shaungs documentation
• Improve inherited methods display on documentation
• Pytest options for core, notebooks, etc
• Big ruff update on the repository
• Fix the notebooks testing script
• Notebooks visualisation docstings
• Improve explanations on the new developer flow per Alec feedback
• Finish polishing off the poetry run test <multiple_options>

Pending from docs restructure:

• Add link to colab notebook with the minimal example and API key loaded as environment variable.
• Cooler intro page and pictures
• The user can find more context when reading though the class definitions
• Including equations when needed
• Schematics to show geometric parameters
• An example on how to use that object in a simulation.
• Link to examples and tutorials
• Cleaner API viewer
• Make nice illustration of medium property types, ie anisotropic isotropic for the uninitated
• Make nice illustrations of all the sources and geometrically how they are represented
• Standalone examples for most common class methods etc.
• Update README.md for notebooks
• Upgrade the jax requirements to caret and test across all platforms
• Documentation pdf building #1604
• CLI test single notebook via arguments
• Update the development docs to the latest flow.
• [ ]See if we can remove the extra API classes nder the table
• Include the relevant markdown files inot their corresponding API sections.
• https://github.com/orgs/flexcompute/projects/2/views/1?pane=issue&itemId=49735837
• Sort out the old 404s from old links