Funny. I started my “serious” effort to write in LaTeX (compile to PDF/epub), then over to Scrivener, then back to LaTeX (using my “Bookmaker” gem), then briefly back to Scrivener then to Markdown (compiles to LaTeX/PDF and HTML/epub/mobi) via my “Verku” gem. All the files are in a private github repository, so I can have the novel metadata as README.md, etc. If I could figure out how to compile the PDF/epub/mobi via a post-commit hook without TravisCI (costs to use with ), then I’d just let Git do it.
As I self-publish, I put together a web form on my site (GH hosted) that routes via a Heroku-hosted Sinatra app to create an issue on the private repo. Then beta (or other) readers are able to report problems (if they want).