Update to new jmol patch for `SAGE_ROOT`

.

Also, after applying the changes from #11874, #11503 and this ticket, the doctest of `devel/sagenb-main/sagenb`

passes.

After these changes however, there is a problem with typesetting maths and I get this notice on evaluation of **every** cell, whether it is plot or maths.

`Error typesetting mathematics.`

And sure enough, something as simple as `view(2+2)`

shows the latex code instead of the maths. jsmath is loaded and the button is present on the right hand corner.

UPDATE: I have same problem with sagenb from github with mathjax instead of jsmath. Seems like something is broken in sage and not sagenb.