Improves highlighting of menu buttons
Smoother transitions for the menus
Basic interactivity between different views is now implemented.

The menus have been adjusted to just show things that are relevant in
the context they are used.  The updates now update everything.  All
items in the views are ordered by their relevance score.  Items in the
to-read and core lists are just displayed vertically.
Fixed file permissions
Merge branch 'master' into tooltip-menu

Conflicts:
	d3/update.js
	d3/visParameters.js
	js/papers.js