Replace bad practice of using custom `pure-` classname

This removes the use the `pure-` classname prefix for custom classnames.
Remove commented out CSS
Organize `pure-` classnames to come after custom classnames in layouts
Change menu items in Side Menu example to not be the Pure site's
Fix misspelling in side menu example layout
Merge pull request #189 from ericf/non-pure-core-classes

Replace bad practice of using custom `pure-` classnames