Improve documentation

[jank324]

Description

Cleanup the structure of and extend the documentation to make getting started with Cheetah and discovering all of the things it can do easier.

Motivation and Context

• I have raised an issue to propose this change (required for new features and bug fixes)

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation (update in the documentation)

Checklist

• I have updated the changelog accordingly (required).
• My change requires a change to the documentation.
• I have updated the tests accordingly (required for a bug fix or a new feature).
• I have updated the documentation accordingly.
• I have reformatted the code and checked that formatting passes (required).
• I have have fixed all issues found by flake8 (required).
• I have ensured that all pytest tests pass (required).
• I have run pytest on a machine with a CUDA GPU and made sure all tests pass (required).
• I have checked that the documentation builds (required).

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[cr-xu]

Looks good to me in general.

Some minor comments:

• The flat-layout now in the left navigation panel will be overcrowded eventually. Shall we think of smaller subsections dividing by topics? (Getting Started / Physics / Optimizing Simulaiton / Auxiliary) The "API Reference" definitely makes more sense than before.
• Also now the ordering is a bit arbitrary, is it supposed to be sequentially from intro -> deep, it's pretty vague.

If we decide to keep the flat layout, I suggest adding some tags to the page so that later it becomes more findable?