I'd have a couple of repositories of notes on bitbucket, where they're just collections of markdown files. It'd be a lot more convenient to be able to add files as needed within the site, as opposed to needing to clone the repo before creating a new file.
For anyone watching this issue, I created a new ticket, 12095, to specify creating a new file in an empty repo. Since this ticket is marked as resolved, I thought it might be a good idea. Toss your vote on 12095 if you think it's a good idea.