A useful add-on for Atom is md-writer. In particular, it allows me to make internal links to other notes in my notebook by highlighting a term, then hitting command+shift+k. (This brings up a menu to allow me to select the relevant note. Say I wanted to cross-link to the code I used to sonify the topic model of John Adams’ diaries, I’d highlight the term, hit the keystrokes, and there we go. Seems a little thing, but it’s very important for turning this whole thing into a wiki-style notebook.

Once you’ve installed the package, you need to set up a .cson file for markdown that tells it where to find the posts. For reference sake, it should look something like this. The important bits there are these:

siteUrl: "http://smgrojects.github.io/"
# URLs to tags/posts/categories JSON file
urlForTags: "http://smgrojects.github.io/tags.json"
urlForPosts: "http://smgrojects.github.io/posts.json"
urlForCategories: "http://smgrojects.github.io/categories.json"

Those .json files are generated from this code; they live inside my source folder and are generated when I jekyll build. Make sure also, if it still doesn’t seem to work, that the URLs for those json files are entered on the mdwriter configuration page within atom.