Clean Up The lingering hard coded javascript in jinja2 template land

[iamh2o]

The UI skin is ok. The mechanism to switch skins is there, but confounded by the small # of harcoded css still in the templates. Take a pass to tidy this, and while at it, also tweak it so variables are being used in their expected environments. Unclear how to tacke: cytoscape is it's whole other ting... that might just stay as is.