Fix clean check workflow

[A-Tarski]

What changed

• run the ty pre-commit hook with the cli extra so typer and rich are available in a fresh environment
• format the README tables according to the configured dprint Markdown formatter
• make the documented one-time lint retry actually run after auto-fixing hooks modify files

Why

On a clean checkout, just check created the default development environment without the optional CLI dependencies. As a result, ty reported unresolved imports for typer and rich. The same first run also reformatted README.md and failed, while the justfile comment promised an automatic verification retry that was not implemented.

Impact

just check is now self-contained on a clean checkout and no longer requires a manual uv sync --extra cli or a second manual run after dprint fixes Markdown.

Validation

• just check
• just check in a separate fresh clone with no pre-existing .venv
• 135 tests passed in both runs