This a template I use to bootstrap my papers.
A few features/assumptions/caveats about this template
* GNU make is used to build the paper
* latexmk is used for the preview mode and to call bibtex
* I'm using IEEETran, but you can use another style
* I'm using biblatex with the bibtex backend
* I use pdfLatex
* All Markdown (*.md) files will be converted to auto/*.tex check
* You need pandoc to convert markdown to LateX
* All seqdiag images in imgs/*.seq will be converted to PDF files
You can check the example/ folder for some tips on how to use it.