Add docs/cli.md CLI usage guide

[cursor]

Summary

Document the nested CLI in docs/cli.md before the next PyPI release.

Goals

• Describe top-level groups: repo, dependabot, environment
• Document each subcommand with flags, defaults, and examples
• Cover output formats (table / json) and delete confirmation (--yes)
• Cover create visibility flags: --public / --private / --internal (default public)
• Link from README (keep README as install/auth/quick start; point Commands to the guide)

Related

• Nested CLI landed in Refactor CLI to nested command groups #90
• Config already documented in docs/configuration.md
• Blocked for release docs polish; release tracked separately