I understand that the Markdown spec allows you to use the actual markup as a backup:
For any markup that is not covered by Markdown Syntax, you simply use the HTML itself. There is no need for a preface to it or to delimit it, indicating that you are switching from Markdown to HTML; you just use tags.
The only limitations are HTML block elements - for example, <div>, <table>, <pre>, <p>, etc. - must be separated from the surrounding empty lines and the beginning and end labels of the block must not be indented with tabs or spaces.
So, if you have a syntax shortcut, you really like that it is not detected automatically, you can just drop the <code> literal block with the corresponding attribute in your Markdown. I don’t think this is particularly against Markdown’s goals, either ... it's a pretty simple indicator.
It may also be not so difficult to collapse your own script, which is executed first after the DOM is ready, finds blocks of code and inserts the appropriate attributes for the selected syntax marker of your choice, depending on several heuristics that you think up for their contents, but if there is a library that is already doing this, obviously that has some advantages. :)
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