Generating documentation to match folder structures.

[ghost]

Is it possible where the user can select to output the generated documentation in the same folder structure the project is in?

Currently
For example, if we have a folder structure that is as such:
Project
|______FolderOne
|         |_______FileOne.cs
|                  |_______FileTwo.cs
|______FolderTwo
|         |_______FileThree.cs

The output markdowns will be:
Project
|_____index.md
|_____FolderOne.md
|_____FileOne.md
|_____FileTwo.md
|_____FolderTwo.md
|_____FileThree.md

Desired
It would be much more convenient for large projects if the documentation could be:
Project
|_____FolderOne
|         |_____FileOne.md
|         |_____FileTwo.md
|_____FolderTwo
|         |_____FileThree.md
|______FolderOne.md
|______FolderTwo.md
|
Project.md