JRubyFXのfxml_rootをjarパッケージング時にも適切に動作する形で設定する ref: http://qiita.com/supermomonga/items/210ab629da519381070b

file0.txt

fxml_root File.dirname(__FILE__)
class KawaiiController
  include JRubyFX::Controller
  fxml "輿水幸子.fxml"
end

file1.txt

def jar_filename
  $LOAD_PATH.map{|it|
    it.split('/')
  }.flatten.uniq.select{|it|
    it.match /^(?!jruby-complete\.jar!)(?!jruby-stdlib-[0-9\.]+\.jar!).+\.jar!$/
  }.first.tap{|it| break it.tr('!','') unless it.nil?}
end
fxml_root File.dirname(__FILE__), jar_filename

file2.txt

if JRubyFX::Application.in_jar?
  fxml_root nil, '乙倉悠貴.jar'
else
  fxml_root File.dirname(__FILE__)
end