Code style improvements

Major code style improvements, including the following:
- consistent spaces instead of tabs
- removes ?> from EOF
- generally subscribes to PEAR coding styles
- puts documentation into a consistent format
- adds documentation to all Copernicus-original files
- removes some dead code
- consolidates all non-colour styles into one file

In addition, removes the embedded Civil Footnotes plugin and switches footnote style support to WP Markdown on Save Improved as suggested in #37.