Doc update to please Doxygen

Doxygen doesn't like when a =head2 section is not linked to a method.
We had to move the comments to #-prefixed lines.
Include the CSS for the eHive HTML doc

The CSS file is a copy from 00_general.css (in ensembl-webcode).
Variables have been replaced, and a few tweaks have been made:
 - global padding on <body>
 - font-size in the th/td elements
typo
Added scripts documentation
Added the Doxygen documentation
added docs/index.html