Duplicate TOC entries

[Emil Tywoniak <emil.tywoniak-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>]

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Hello everybody,
I'm building a pdf with a latex template, and every single entry in the TOC 
as well as the .toc file is duplicated likle this:

\contentsline {section}{Verification}{11}{section*.20}%
\contentsline {section}{Verification}{11}{section*.20}%

I'm absolutely stumped, I would like to untangle pandoc's and latexmk's 
invocations to at least know what source code to read but I can't figure 
that out. The repository is at 
https://gitlab.com/tywonemi-school-stuff/titania/doc and you need latexmk, 
inkscape, and this latex template/cls <https://github.com/tohecz/ctuthesis> 
to build it. If it helps, here's what the Makefile runs:

pandoc analysis.md \
-s \
--filter pandoc-minted/pandoc-minted.py \
--filter pandoc-svg/pandoc-svg.py \
--data-dir=. \
--template=ctuthesis.tex \
--bibliography bibliography.bib \
--pdf-engine=latexmk \
--pdf-engine-opt=-outdir=temp \
--pdf-engine-opt=-shell-escape \
--pdf-engine-opt=-bibtex \
-o doc.pdf

If I let it generate .tex, it has sections looking as expected:

\hypertarget{verification}{%
\section{Verification}\label{verification}}

Any suggestions where to look would be much appreciated. I found zero cases 
of somebody's .toc items being duplicated and zero information on how the 
.toc is even generated.

Thanks,
Emil J

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