You must be running the recent Jekyll version 3.2, which introduces Gem based themes (from https://jekyllrb.com/docs/themes/):
Jekyll themes package layouts, includes, and stylesheets in a way that can be overridden by your site’s content.
The theme is set in _config.yml:
theme: minima
Initial files that were previously in _layouts, _includes, and _sass are now packaged with the theme.