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

[planetf1]

Problem

The cli/ package is currently included in the generated API reference docs (docs/docs/api/cli/). This is wrong — the CLI is a user-facing tool, not a public Python API. Documenting its internal classes and methods as an API reference is misleading and adds noise to the API docs.

At the same time, there is no unified CLI reference for users. Coverage is scattered across a few how-to and guide pages (m-decompose.md, m-serve.md, refactor-prompts-with-cli.md, lora-and-alora-adapters.md) but no single place that documents all commands, their flags, and usage.

What needs to happen

1. Remove cli/ from generated API docs — exclude cli from the PACKAGES list in generate-ast.py and clean up the corresponding nav entries and coverage scope in audit_coverage.py.

2. Add a proper CLI reference — a user-facing page (or section) documenting all m subcommands: alora, decompose, eval, serve. Should cover invocation, flags, and typical usage. Could be generated from --help output or written as a static guide.

Why

• CLI internals are not a stable public contract; exposing them as API docs sets wrong expectations
• Users currently have no single reference for CLI commands