Treat values ruby.bin,.. as options

* obsolete ruby.version. use ruby.api_version.
Add note about an obsolete value ruby.version
Remove --bindir option from setup.rb, most of setup.rb does not have this option
Fix wrong value of ruby.version
Add new value ruby.gemdir (from ruby.branch)

${ruby.gemdir} => ${prefix}/lib/ruby/gems/1.8, ${prefix}/lib/ruby1.9/gems/1.9.1