No links to main body in the appendices in --supplement mode

Until now, in the appendices we were simply using '\ref' to refer to
different parts of the published paper. However, when built in
'--supplement' mode, the main body of the paper is a separate PDF and
having links to a separate PDF is not impossible, but far too complicated.
However, having the links adds to the richness of the text and helps point
readers to specific parts of the paper.

With this commit, there is a LaTeX conditional anywhere in the appendices
that we want to refer the reader to sections/figures in the main body. When
building a separate PDF, the resepective section/figure is cited in a
descriptive mode (like "Seciton discussing longevity of tools"). However,
when the appendices go into the same PDF as the main body, the '\ref's
remain.

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