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
Ruby 2.0 support: Set script encoding to US-ASCII for gff.rb.
Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
Rewrite to use TogoWS REST API instead of SOAP-based KEGG API.

 * Rewrite to use TogoWS REST API instead of deprecated SOAP-based
   KEGG API.
 * Examples are changed to fit with current TogoWS.
 * Now, the script does not depend on any non-standard libraries
   including BioRuby. This means that one can put this script on
   a server without installing BioRuby.
 * New constans SCRIPT_NAME and BASE_URL for easy customizing.
 * Many changes. See "git diff" for details.
add magic comment: coding utf-8
remove excess double quotations in html part
Add metadata cache

 * Add metadata cache. It caches the list of databases and a list of
   available formats for each database. Database entries are not cached.
 * charset=utf-8 in CGI header.
Improvement of parameter checks and error output

 * Improvement of parameter checks
 * To avoid potential XSS in old MSIE which ignores content-type,
   always do CGI.escapeHTML for parameters in error messages