Remove Bio::KEGG::API and its sample code and documentation files.

 * Remove Bio::KEGG::API and its sample code and documentation files.
   * deleted: lib/bio/io/keggapi.rb
   * deleted: doc/KEGG_API.rd
   * deleted: doc/KEGG_API.rd.ja
   * deleted: sample/demo_keggapi.rb
Delete autoload lines for removed Bio::KEGG::API
Remove KEGG API plugin of BioRuby Shell, due to the removal of Bio::KEGG::API.
Remove description about KEGG API and Bio::KEGG::API.
Remove descriptions about KEGG API and Bio::KEGG::API.
Remove sample/psortplot_html.rb which depend on Bio::KEGG::API.

 * Remove sample/psortplot_html.rb because it strongly depend on
   removed Bio::KEGG::API and discontinued SOAP-based KEGG API.
   It is hard to re-write by using new REST-based KEGG API because
   the new API seems to lack color_pathway_by_objects that returns
   image URL. Moreover, there is no one-by-one API migration guide.
regenerate bioruby.gemspec with rake regemspec
Set html title when generating tutorial html
updated doc/Tutorial.rd.html and doc/Tutorial.rd.ja.html
Convert encoding of the Japanese tutorial files to UTF-8