Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files

 * Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files.
   Because ChangeLog is not rdoc format, rdoc bundled with Ruby 2.0
   raises error during parsing.
Update files and directories used to create package without git
regenerate bioruby.gemspec with rake regemspec