Howto fix source files (i.e. *.md) being copied over to _site?

In the project i’m currently building i created a folder named /pages to better organize the many pages i’m going to create:


After building with jekyll, the resulting structure in _site is:


This does not happen for *.md files stored in root or _posts directory. Also, when i define a permalink to another directory via front matter, it will only create the final .html.

So how do i stop it from copying over unprocessed source files?

Using jekyll 3.8.5 - any help much appreciated!

This is, indeed, totally unexpected. Just for the heck of it, I just tried your pages> arrangement, and in my case only pages>swfl.html is produced. I’m using Jekyll 4.0, but that can’t be it. Mysterious to me.
Does jekyll doctor produce anything helpful? Or the --verbose option with build?