The default directory where RSpec Documentation will look for your Markdown files is rspec-documentation/pages.
Add as many files as you like and use you like into the root directory or subdirectories to generate the documentation tree.
rspec-documentation/
└── pages/
├── Introduction.md
├── File System/
│ └── Ordering.md
└── File System.md
Creating a subdirectory inside rspec-documentation/pages adds a new node to the index tree. Add files or more subdirectories to build the tree.
The file you are reading now is located in rspec-documentation/pages/File System.md.
There is also a directory named rspec-documentation/pages/File System which contains a file named Ordering.md.
Take a look at the source to see how it works.