Your comments

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.