If you want links like [manual](https://leanpub.com/manual) in the body text to be automatically turned into footnotes spelling out the URL, that works with the correct Theme setting.
However, if you put a link like this [manual](https://leanpub.com/manual) in a footnote, you see the word "manual" formatted as a link, but that link has no footnote spelling out the URL https://leanpub.com/manual, even though you set the theme to have links spelled out in their own footnote.
In this case, you should do the link in the footnote like this:
<https://leanpub.com/manual>
That way, it will be link, and it will be displayed in the footnote as https://leanpub.com/manual.