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You are always welcome to improve to make other's life easier! Below are few issues for the amazing developers;
Auto equation enumeration works, but there is a problem with hyperlinks. They should appear like [(1)] in the text when they are referenced, however, they appear with the label names (e.g., eq:fourier) with broken links.
The newer versions of Pandoc can deal with converting native markdowns into various formats. At least for this version of the template repository, we used a BioMed-central based latex template modified for BrainHack 2015 by Cameron Craddock. If you have a Docker container that can convert a native markdown container to a PDF by retaining the LaTeX template, please let us know. I think getting rid of LaTeX components would make this tool more user friendly.