This is a new feature suggestion based on problem solving that turned out to be a conflict between the Moodle glossary and MathJax.
It would be useful to blacklist an expression in the glossary, so that it will not be replaced in an extended expression. For example, “angle” is a valid glossary term, but “\angle” should not be autolinked. Alternately, could ranges of text between arbitrary delimiters be globally nolink’d, such as anything $$between double-dollar signs like this$$.
1. add a glossary to a course and add the term angle to be autolinked throughout the course.
2. add MathJax to the server to render out equations.
3. insert an equation using the \angle TeX command, such as $$ In triangle ABC, \angle a and \angle c are complimentary$$.
We found that since the autolinking of the term angle added the html code within the equation to get the term to link to the glossary as expected. What was unforeseen was that the addition of this code seems to prevent MathJax from being able to display the equation. The solution is to disable linking of that equation using the nolink code which while effective, is very cumbersome in a large course that uses MathJax equations including angles on nearly every page.
Moodle's glossary allows for adding keywords to terms that then also get autolinked, thereby allowing multiple versions of the same word or other words altogether to be linked. Selecting the "Match whole words only" helps to eliminate excessive linking when the term is part of a larger word. Adding a blacklist field of terms to NOT link may help in the prevention of issues as described above.
In the above scenario, the thinking is that adding "\angle" to a blacklist of "angle" in the glossary would prohibit Moodle from trying to autolink a term that appears in the equation code.