My initial reaction was: why Markdown? That's (despite its name) a markup language, not some sort of data/configuration format. But then I saw that it allows you to consolidate the documentation and the tasks into a single place, and now I think this is a great idea!

Other comments have pointed it out, but the only issue I see is that shell commands aren't trivially usable on e.g. Windows. I'm sure there are good solutions out there for this, but I haven't found them yet...