Don't link to rna.bgsu.edu

WebFR3D shouldn't link directly to rna.bgsu.edu for results. It's cleaner for
testing things if we are self contained despite whatever host we are running on.
Use the Jmol that is part of this repo

Don't use the global Jmol, instead we use the one that is part of this project
to make things more self contained.
Correct link to not hard code rna.bgsu
Ignore .agignore
Remove more links to rna.bgsu

This should make for a more isolated testing environment. We do not want to
always link to rna.bgsu when we are on the test site.