Change directory where get_header(), get_footer() and get_sidebar() look for templates

Simple solution, use get_template_part().

For example:

get_template_part( 'partials/footer' ); 

Which would get the footer.php inside the partials/ directory.

Another example:

get_template_part( 'partials/footer', 'home' ); 

Which would get the footer-home.php inside the partials/ directory.

One more example:

get_template_part( 'partials/footer/blog' ); 

Which would get the blog.php inside the partials/footer/ directory.