docs: consolidate CLI docs into command reference

[tobiasraabe]

Summary

• generate a single CLI command reference from the Click command tree
• move that page under Reference Guides as Commands
• remove the old per-command CLI docs and retarget internal links to the new anchors

Validation

• uv run python scripts/generate_cli_reference.py --check
• uv run --group test pytest tests/test_cli.py tests/test_click.py
• just docs