docs: remove CLI internals from generated API docs and add proper CLI reference

[planetf1]

Problem

The cli/ package is included in the generated API reference docs alongside the mellea library API. This is wrong — the CLI is a user-facing tool, not a public Python library. Documenting its internal classes and methods as an API reference exposes implementation details that are not a public contract and adds noise for users looking for the library API.

At the same time, there is no unified CLI reference. Coverage is scattered across a few how-to and guide pages but there is no single place documenting all m subcommands, their flags, and usage.

What needs to happen

1. Remove cli/ from the generated API docs — it should not appear under the API Reference section.

2. Add a proper CLI reference — a user-facing page documenting all m subcommands (alora, decompose, eval, serve), covering invocation, flags, and typical usage.