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Org mode contains a LaTeX exporter written by Bastien Guerry. With
further processing1, this backend is also used to
produce PDF output. Since the LaTeX output uses hyperref to
implement links and cross references, the PDF output file will be fully
linked. Beware of the fact that your org file has to be properly
structured in order to be correctly exported: respect the hierarchy of
sections.
[1] The default LaTeX output is designed for
processing with pdftex or LaTeX. It includes packages that are not
compatible with xetex and possibly luatex. See the variables
org-export-latex-default-packages-alist and
org-export-latex-packages-alist.