fix documentation reflecting recent changes of Bio::Fetch
Change default server to EBI Dbfetch server; remove BioRuby BioFetch server

 * Change default server to EBI Dbfetch server.
 * The BioRuby BioFetch server is removed. When "-r" option (force to use
   BioRuby server) is specified, warning message is shown, and the program
   exits with code 1 (abnormal exit).
 * Usage message is also changed.
remove unused $Id:$ line
Bug fix: use NCBI E-Utilities instead of old deprecated API

 * Bio::PubMed#search, query, pmfetch: remove old code using deprecated
   and/or unofficial web API, and change use esearch or efetch methods
   which use NCBI E-utilities. These methods will be deprecated in the
   future. To indicate this, show warning message if $VERBOSE is true.
 * Update RDoc documentation
Change default tool and email values

 * Default "tool" and "email" values are changed to "bioruby" and
   "staff@bioruby.org" respectively. Now, the author of a script
   do not need to set his/her email address unless the script makes
   excess traffic to NCBI.
 * Update RDoc documentation