bug: dev dependencies (click, PyYAML) not declared in any manifest

**Severity**: LOW
**Files**: pyproject.toml, scripts/cli_documentation/*.py
**Found by**: code-atlas bug hunt

click and PyYAML are used in dev scripts but not declared anywhere. Developers get ImportError on fresh clone.

Fix: Add [project.optional-dependencies] dev = ['click', 'pyyaml']