Take Rouge class from pre rather than code

Rouge’s HTML formatter was changed so that the class appears on the
`pre` element rather than the `code` element.

See also jneen/rouge#191.
Merge pull request #502 from nanoc/fix-rouge-class

Take Rouge class from pre rather than code
add support for :extra_files config whitelist for extra files, update #492
Test support for dotfiles in data-sources

    .htaccess and .htpasswd were not handled by any data-source
fix code and tests
improved documentation and errors for all_files_and_dirs_in
add more tests for all_files_in
remove the default ht files list
fix (local) tests for rubocop and removed defaults
use concat instead of +=