I’m doing some self-educating on MMD -> LaTeX by using the Scapple manual, and I notice one rather cool feature that I don’t quite understand how Ioa (or Fletcher?) did.
So when there is a bit of MMD text like this:
The generated LaTeX is:
In other words, the LaTeX doesn’t just have the embedded hyperlink, there is also a footnote created with the text of the hyperlink (as well as embedded link). Is this happening via Preset Replacements? Or is this a wonderful trick that I have somehow missed?
You should be getting that behaviour out of the box with MMD->LaTeX (so yes, Fletcher). Here is what I get when I use MMD on the command-line, which is as about as pure an experience as you can get:
$ mmd2tex
Test [links](http://www.literatureandlatte.com/)
<^D>
Output:
Test \href{http://www.literatureandlatte.com/}{links}\footnote{\href{http://www.literatureandlatte.com/}{http:/\slash www.literatureandlatte.com\slash }}
Mind, I’m still using MMD 5.4.0, I’ve not upgraded to 6.0 yet as I ran into issues with some of my XSLT workflow and didn’t have time to sort it out yet.
Huh. Most of my URLs (of late, at least) have been in the footnotes [^Lorem] syntax, and I haven’t observed this behavior.
Is there perhaps some Scrivener option that I’ve enabled that would shut this behavior off? Failing that, I suppose I am just unobservant. 
Okay, it might not do that when using a hyperlink inside of a footnote, if that is what you mean, since that would entail making a footnote of a footnote.
As I say though, the above example was done purely on the shell with the MMD command-line interface. I didn’t use Scrivener for the test and it doesn’t generally mess with MMD syntax at all as a rule of thumb, save for the few things it generates from its own internal features like embedded images and its own footnotes.