Extension of the theme doesn't work when defining the content in another directory

[btzo]

I figured out that when you don't put the files in the root of the folder, the theme change doesn't take effect.

For reference, inside my book main folder I created an example folder, put all my markdown files there and set "root" : "./example_folder" in the books.json file. When I did this, all the modifications inside _layouts/website/page.html was ignored.