Refactor article-cli lifecycle commands and add robust setup/doctor workflows

[prudhomm]

Improve article-cli robustness and usability across the paper lifecycle: initialize, setup, diagnose, compile, update bibliography, version, and release.

This includes

• adopting uv consistently,
• making setup idempotent and worktree-safe,
• preserving existing hooks,
• fixing config precedence,
• splitting CLI commands into maintainable modules,
• adding a read-only doctor command with JSON output, and
• preparing the architecture for safer version/release workflows.