For code samples I prefer to have them in separate files and include them so it's just one command that imports them and formats them. I wrote both my Master's

For code samples I prefer to have them in separate files and include them so it's just one command that imports them and formats them. I wrote both my Master's and Ph.D. theses in LaTeX and found it much better than the alternatives. With Markdown I'd be resorting to falling back on LaTeX anyway and many of the additional Markdown features weren't available when I wrote them. I had a predefined document class for my Master's but the university changed the guidelines by the time of my Ph.D. so I used the Memoir document class and that had a lot of flexibility and I didn't have to include many other packages to format things. I basically set up the format once at the beginning, checked against the guidelines once at the end and that was it.