I wish to organize the my themes directory a little more.
Is it possible to move header.php and footer.php to a sub directory?
I guess it's done by hooking on to some action, but is it possible with just a config setting?
It is not possible to override header/footer via hooks in respective get_header()/get_header() functions.
However it is often overlooked that these function allow input and loading different headers.
For example get_header( 'nested/header' ); will look for header-nested/header.php in theme's folder. It's kind of a hack in regards to subdirectory use, but it works. :)
nested-header directory and a nested-footer directory. I guess I'll just leave the at the root then. A way to do it might be write a function of my own, that loads the files, and triggers the correct actions, but then I would need to maintain it manually for every update. Thanks for the answer! :)