Updating files to move  into root directory

After discussion, getting rid of the `pages/` directory and putting everything in the root so that file paths to `fig/`, `data/`, etc. will be the same in source and generated pages.  This doesn't matter much for simple Markdown, but is important for R Markdown, IPython Notebooks, and other "live" pages.
Just modifed the wording in LAYOUT.md and DESIGN.md to make this clearer.