Add cross-referencing to all rticles

I think that it could be easier to use cross-referencing in rticles. References to tables, figures and equations are ubiquitous to scientific papers. bookdown provides a generic solution that, I think, is more likely to bring users to success from the start.

\begin{equation}
(\#eq:eq)
c = a \cdot b
\end{equation}
  
see \@ref(eq:eq)

Gives

@cderv suggested that maybe we could provide two possible default outputs in the skeletons. Something like:

output:
  rmarkdown::pdf_document:
    base_format: rticles::mdpi_article
  bookdown::pdf_book: 
    base_format: rticles::mdpi_article

It has the benefit that the default output does not require bookdown, and it shows that other outputs are possible. While cross-referencing would not work from the start, enabling it would be a matter of picking the next output in the list. If using bookdown as the default output is excluded, then I think this solution is pretty good.

Following #327, I believe that the solution might need to be applied to all skeletons.

Start with the output YAML and the repository's article skeletons referenced in the issue, then compare how each skeleton defines its default output. Check the proposed alternative output behavior and determine whether cross-references work consistently across all skeletons. Done means every skeleton has a documented, usable path to cross-referencing without making bookdown mandatory by default.