Your comments

@Cory I use Cmd+Tab (Mac) or Alt+Tab (Win & Lin) to flip between my MD editor and my desktop file windows. I like that because HarooPad can be fullscreen/distraction free, and then I can quickly flip back and forth between the file tree and my writing with a keystroke -- no mousing necessary. I'm not trying to dissuade anyone from having the file tree in a sidebar, but I find it less than useful in my apps that have it like Evernote and Coda 2.

However, I do want to echo the love for a tabbed interface -- that's one thing I really like about LightPaper markdown editor for Mac, as it helps me keep track of the files I have open. It's great for more complex projects where you need to have a number of files open at a time.
Maybe this document would help? It appears to be the Apple developer guide for integrating Services.
Just for some perspective here -- what's wrong with your desktop file tree? I have been finding since I write in Markdown that I'm actually using my OSX Finder windows more, doing the kinds of file management tasks I used to do in Evernote or Google Drive. Organizing my MD files into folders and tags on the desktop is fast, and I've even been using to speed up those tasks considerably. Maybe I'm missing something, but it seems silly to reproduce this functionality inside of the app if it already exists on the desktop?