Thanks. By the time I left that last message I'd already used cp-a, which seems to work at this point (from what I could tell, they do the same thing. I think -a keeps time stamps identical (doubt that's important in my case), and does something in relation to copying hard link references or some such, also prob not relevant, but couldn't be sure.) The directory I was copying had some subdirs, and all that was copied.
Thank you for the phpman app. I grab that now.
So in the end I've got MathJax working via remote server (CDN), as well as locally, and also installed the XyJax commutative diagram package into the HDA's Mediawiki, which will be helpful and which is very cool (
https://www.google.com/#q=xyjax and
http://sonoisa.github.io/xyjax/xyjax.html).
That closes what I was trying to do. Case closed.
Many thanks again.