Generate nested folders in _site and have them reflected in URL?

[jonsnou]

Hi, I have my mds in subfolders within _pages. Currently, in _site, all md are generated as htmls in a flat hierarchy. I want to achieve two things:
a) the _pages folder should be mirrored to _site, i.e. the subfolders should be also reflected in _site as they are in _pages
b) the final URL should show the subfolder + the htmls (not a permalink), i.e. page.com/folder1/folder2/index.html
How can I achieve that?
What do I need to change in these files:

• _config.yml
• front matter
• sidebar.yml
  Hope you can give a tip. Thanks!

Plus: How to solve it that the references (css/scripts) are correctly injected so that the paths work (from _includes/head.html).

[gbv34]

I know this question dates back from a long time, but I am in the same situation.
I have a _site folder with all my HTML pages in a flat hierarchy.
I would like to organize and keep the whole files organized as subfolders. It is possible to change the permalink, but the CSS doesn't apply anymore...
Any help on this, please?