Here are a few things I found by simply running git grep -i jax:
There are, however, some traces of MathJax left in the Math extension's code:
- Translatable messages: mw_math_latexml_jax and mw_math_mathjax. They should be simply deleted from en.json,and qqq.json, and the other languages will be auto-updated. (patch)
- README mentions MathJax configuration.
- A reference image for Special:MathStatus. Actually opening that page in the English Wikipedia says "Test Comparing the generated SVG with the reference failed."
- Remove $wgUseMathJax = true; from WMF's CommonSettings.php. (patch)
If MathJax is completely irrelevant for the Math extension, then I guess that the only results for git grep -i jax should be in the HISTORY file.