Ok, here is the thing. By default, doing what you did should work. I can confirm it works because I just tried it (see long block of text at the end of mail).
However, it does look like you edited your FILES setting. The default is
That means "take the content of the files folder and copy it to the output". Seems you have changed it to
That means "take the content of the files folder and copy it to the output in the files subfolder"
So, put it back as it was and all good.
nikola ~/P/nikola master ± nikola init -q foo2
[2018-03-20T15:14:15Z] INFO: init: Created empty site at foo2.
nikola ~/P/nikola master ± cd foo2
nikola ~/P/n/foo2 master ± touch files/CNAME
nikola ~/P/n/foo2 master ± nikola build
Scanning posts........done!
. copy_files:output/CNAME
. copy_assets:output/assets/css/bootstrap.min.css.map
. copy_assets:output/assets/css/docs.css
. copy_assets:output/assets/css/bootstrap-theme.min.css.map
. copy_assets:output/assets/css/bootstrap-theme.min.css
. copy_assets:output/assets/css/bootstrap.min.css
. copy_assets:output/assets/css/theme.css
. copy_assets:output/assets/css/images/ie6/borderTopLeft.png
. copy_assets:output/assets/css/images/ie6/borderTopCenter.png
. copy_assets:output/assets/css/images/ie6/borderMiddleRight.png
. copy_assets:output/assets/css/images/ie6/borderBottomRight.png
. copy_assets:output/assets/css/images/ie6/borderBottomLeft.png
. copy_assets:output/assets/css/images/ie6/borderBottomCenter.png
. copy_assets:output/assets/css/images/ie6/borderTopRight.png
. copy_assets:output/assets/css/images/ie6/borderMiddleLeft.png
. copy_assets:output/assets/js/jquery.min.map
. copy_assets:output/assets/js/jquery.min.js
. copy_assets:output/assets/js/flowr.plugin.js
. copy_assets:output/assets/js/bootstrap.min.js
. copy_assets:output/assets/fonts/glyphicons-halflings-regular.woff
. copy_assets:output/assets/fonts/glyphicons-halflings-regular.woff2
. copy_assets:output/assets/fonts/glyphicons-halflings-regular.svg
. copy_assets:output/assets/fonts/glyphicons-halflings-regular.ttf
. copy_assets:output/assets/fonts/glyphicons-halflings-regular.eot
. copy_assets:output/assets/css/rst_base.css
. copy_assets:output/assets/css/baguetteBox.min.css
. copy_assets:output/assets/css/ipython.min.css
. copy_assets:output/assets/css/nikola_ipython.css
. copy_assets:output/assets/css/nikola_rst.css
. copy_assets:output/assets/css/rst.css
. copy_assets:output/assets/css/html4css1.css
. copy_assets:output/assets/xml/atom.xsl
. copy_assets:output/assets/xml/rss.xsl
. copy_assets:output/assets/js/flowr.js
. copy_assets:output/assets/js/baguetteBox.min.js
. copy_assets:output/assets/js/fancydates.js
. copy_assets:output/assets/js/html5.js
. copy_assets:output/assets/js/moment-with-locales.min.js
. copy_assets:output/assets/js/html5shiv-printshiv.min.js
. copy_assets:output/assets/css/code.css
. render_posts:timeline_changes
. render_galleries:output/galleries
. render_galleries:output/galleries/index.html
. render_galleries:output/galleries/rss.xml
. render_listings:output/listings/index.html
. render_taxonomies:output/archive.html
. render_taxonomies:output/index.html
. render_taxonomies:output/categories/index.html
. render_taxonomies:output/rss.xml
. create_bundles:output/assets/css/all-nocdn.css
. create_bundles:output/assets/js/all.js
. create_bundles:output/assets/css/all.css
. create_bundles:output/assets/js/all-nocdn.js
. sitemap:output/sitemap.xml
. sitemap:output/sitemapindex.xml
. robots_file:output/robots.txt
nikola ~/P/n/foo2 master ± ls -l output/
total 40
-rw-r--r-- 1 ralsina domain^users 3085 mar 20 12:14 archive.html
drwxr-xr-x 6 ralsina domain^users 4096 mar 20 12:14 assets/
drwxr-xr-x 2 ralsina domain^users 4096 mar 20 12:14 categories/
-rw-r--r-- 1 ralsina domain^users 0 mar 20 12:14 CNAME
drwxr-xr-x 2 ralsina domain^users 4096 mar 20 12:14 galleries/
-rw-r--r-- 1 ralsina domain^users 3263 mar 20 12:14 index.html
drwxr-xr-x 2 ralsina domain^users 4096 mar 20 12:14 listings/
-rw-r--r-- 1 ralsina domain^users 79 mar 20 12:14 robots.txt
-rw-r--r-- 1 ralsina domain^users 726 mar 20 12:14 rss.xml
-rw-r--r-- 1 ralsina domain^users 711 mar 20 12:14 sitemapindex.xml
-rw-r--r-- 1 ralsina domain^users 864 mar 20 12:14 sitemap.xml