As the subject states, I wish to rename these directories. Specifically, I want to nest them under a directory _content. The motivation for this change is that I wish to have a separate Git repo for just the content of the site, which is easy to achieve with a submodule. However, without symlinks, I don’t see how I can get Git to recognize these nested folders.
You probably want to look into jekyll themes, this would allow you to split the content from the site design and code without renaming and moving folders https://jekyllrb.com/docs/themes/