Update URIs

 * Update URIs.
 * Remove links to RubyForge and RAA which have already been closed.
 * Add some words for Ruby 1.9 or later.
regenerate bioruby.gemspec with rake regemspec
Documentation bug fix: Return value is Rational or Float.

 * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Return value
   is Rational or Float in recent versions of Ruby. Documentation added for
   the treatment of "u" and to return 0.0 if there are no bases.
   Reported by ctSkennerton (https://github.com/bioruby/bioruby/issues/73 ).
Prevent to repeat calculations of total bases

 * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Prevent to
   repeat calculations of total bases.
Doc bug fix: wrong sample code