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.
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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/