Expandable File Tree for obsessive note keepers

If I may add wishes to this suggestion, could you go one step further and make it possible to link to files?
For example like this: 

[see here](path/to/note.md) 
Fix the ninja [bug](ninja.md) 

This syntax probably won't do because you need to figure out whether it's a web or file system link, but just as a rough idea.

Likewise, perhaps instead of or in addition to creating a specialized UI for the directory tree view, you could create a command similar to [TOC] that creates like a table of contents for files in the current or a specified folder?
Users just have to create a "contents" file with the [TOC] statement in it and have their tree view. This gives users the freedom to create multiple such "views" for various folders and the ability to link between them. 

A little background / use case: I currently use Evernote as a personal wiki and have a huge archive of notes with lots of cross links for my various projects and tasks. I want to get away from it and haroopad looks awesome – with some basic file linking / listing it could be used as a personal wiki I believe.

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 AlfredApp.com 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?

@Ted, it may be okay to do so on a Mac but not all OS's are equal, though dir trees can be. That said not all work flows are equal either.

If a tree view was a hotkey away the use of a mouse diminishes. Couple this with the possibility of tabs and we open up a world of ease.

also even with use on a Mac, and correct me if I'm wrong because I'm not a Mac user, having a collapsible file tree with a hot key to open it saves a lot of time and space on the screen and especially helps when trying to use the application in any kind of distraction free mode type sense. Also Haroopad has a pretty slick interface and it would look pretty nice to have a sliding out panel area with the tree view. maybe with a slightly later background color but a flat design and when collapsed is invisible as it would reach the edge of the window.

by the way Glen tabs is a great idea in combination with this tie that in with in a feature to automatically export to HTML and you could use it to manage a flat file website very easily, or alternatively an option to automatically save PDF versions for documentation reasons. I guess that stuff would need to be a new ticket though on userecho.

@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.