Assume we have defined an abbreviation
*[YAFR]: Yet Another Feature Request
Then the following markdown
Our function $f_\text{YAFR}$ does some things
will be expanded to (something like):
Our function $f_\text{<abbr title="Yet Another Feature Request">YAFR</abbr>}$ does some things
This will cause a maths renderer like mathjax to fail. It is actually rather common to add subindices to notation in maths that refer to abbreviations defined in the text, so I think it would be nice to have the extension not try to expand the text.
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