docs: Add a reference for the CLI

[ruben-arts]

Adding a reference to the documentation for the cli.

This PR adds:

• Documentation improvements of the tutorials
• Auto generation of the cli reference with clap-markdown
• A CI stage to test the generated docs, We don't do it on mkdocs hook as the build might be slow and that would be annoying.
• Some misc docs improvements.

This PR doesn't add:

• A fully reviewed and improved documentation, lets do it in steps.