Your life in plain .md files.

Why not just, you know, actual plain .md files and your directory navigator and text editor of choice (often the ones that that already come with your Linux distro)? Or code editor if you want them together? Don't forget the terminal if you want to go even simpler. Always worked for me, I don't even use the formatted view half the time because *this* already conveys the same information as this in my mind. Hell throw a git repo in there and you have better version control than full office suites.

I honestly think the fancy wrappers around Markdown files defeat the elegant minimalism of using Markdown in the first place. I've always found my favourite "feature" of Markdown is that you don't need to install anything.