A repeated task I run into when I start working on a new paper is the laying out the initial structure of the repository to store the paper text. I recently pushed a simple skeleton that I use a starting point to GitHub. There’s nothing really fancy here, but it’s a good starting point. I use latexmk to build all my documents since it takes care of running BibTeX among other things. One of the nice other things is that it will automatically try to use make to build any missing files. The repository basically consists of a Makefile that generates the paper along with a simple LaTeX skeleton and an empty BibTeX file. Hope it might be helpful to someone else!
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