I’ve looked around but can’t see this mentioned anywhere: it would be pretty useful for those that write in markdown if the italics, bold, underline shortcuts could be used to create italics bold underline instead of italics bold underline. This has been implemented in other open source projects, and so you ought to be able to pinch the code from somewhere as long as it had the appropriate license. It could be an option in the preferences, and would save the step of making sure you haven’t accidentally got non-markdown formatting kicking about in your long, long document!
Bump.
You know about Format > Covert > Bold and Italics to MMD Syntax? This would ensure you don’t have rogue bold/italics at least…
I know our benign overlord KB has said many times Scrivener is a rich text editor which supports compile time MMD (which is does superlatively), but I suppose having a limited ⌘c ⌘v ⌘u toggle wouldn’t be capitulating too far from the RTF domain?
Scrivener is a rich text application (as nontroppo said I would say…), so this isn’t really practical - and it’s definitely out of scope, I’m afraid. Scrivener is not a Markdown editor. It can export to MultiMarkdown for those that use it, but it’s not a Markdown editor.
nontroppo - that Convert > Bold and Italics to MMD Syntax will be gone in a future update… with a much more powerful rich text -> MMD conversion engine replacing it in Compile. 
Oh, let us beta test for you sooner than soon. 
oooooh, great news, that sounds uttterly lickable; you will find me waiting patiently in the beta testing line, hoping saliva won’t do too much damage to all that shiny…
How do you get underline to be underline in MD/MMD?
I get underline as underline.
I’m pretty pleased with how it’s turned out (although it requires a lot more testing). I’m currently in the final stages of implementing ePub3 support, which is the last part of the major Compile overhaul I’ve been implementing. ePub3 requires HTML5, but Apple’s text system can only export to HTML4. So our ePub3 support pipes everything through MMD to create the HTML5 documents, converting rich text to MMD (with a lot of extra HTML injected too) and making heavy use of the new styles system in the process. But even for regular MMD/LaTex/HTML export, it will be possible to take advantage of that engine, converting bold, italics, block quotes, code, captions, tables and lists from rich text to MMD. Not a small undertaking. 
KB: ePub 3, styles system, MMD conversion – will the shiny ever end??? great to hear you are dogfooding your MMD conversion code, and I at least love your little developer stories.
Briar: I think underline is considered not “semantic” markup so never got embodied in markdown (it also makes something look like a link for HTML). Anyway with KB’s fancy schmancy converter I suspect it may be possible to custom map text here into using html tags…
rdale: perhaps instead of the mythical babel fish, we should all carry a pug around and get them to convert our expressions into a universal pugulese, a universal language for us all…
Yes, not semantic is the reason. The asterisks (or underscore alternates) aren’t mapped to italic and bold, they mapped to emphasis and strong emphasis, or and . Most browsers and converters display the former as italics and the latter as bold, but all of that can be easily changed with a stylesheet. Underlining is… just that. It’s a text adornment and nothing more. Having syntax for that would go against the principles of Markdown, like having syntax for adjusting the font size would. That’s the background anyway.
Since this conversation is involving MMD usage, you can already do that with Replacements:
Replace: __$@__
With: <u>$@</u>
But yes, styles will be even cooler.
That’s fair enough I suppose, I’ve come to realise that I would probably be better off using a slightly different programme, but I’m well invested in scrivener now and I can just about bend it to my workflow. I’ll just have to make sure I don’t miss any markup!
@KB If you’re going to be piping things through an external programme to do your compiling, you should really check out http://pandoc.org which is a much more capable engine for converting between markdown and xyz. If you don’t want to use Pandoc’s markdown syntax (which is largely the same anyway with a few additions) then you can even specify markdown_mmd as an input/output format…
The only problem I could see is that it’s not the fastest when compiling with lots of options and a bibliography etc, but I should think that a straightforward mmd -> html5 would be speedy enough:
Benchmark time for a 45000 word markdown file to html: 1.03 seconds
Support for Pandoc to .docx, DocBook and ePub has already been added for the next major update.
Definitely would be 
if that were bi-directional with for example ePUB to Scrivener on File > Import.
Am using scrivener to create epub and would like to use pandoc to make sure my epub is more consistent.
Any idea when this update is due?
We don’t have any news yet on that release, but to be clear that will be a matter of automation of what already exists (as you probably are aware). With Scrivener right now you can use the MultiMarkdown compile option (just plain to text) and then process that text file with Pandoc to produce your ePub file.
There are further techniques you can use right now to automate the process further. You’ll find details on how to set that up in this forum thread. Do note these techniques require the direct-sale version if you’re using Mac OSX 10.11.2 or greater.
Is there any update on the status of this feature?
The technical answer is when it’s ready, but it does seem to be close.
BUT perhaps you can do what you may need today, in that you can use MMD -> Pandoc and replacements etc. already?