[wip] reference/index更新、reference/twig_referenceとreference/configuration/kernel追加

[済]
reference/configuration/mongodb.rst削除
reference/index.rst更新
reference/map.rst.inc更新
reference/mode.rst削除
reference/YAML.rst削除

[作業中]
reference/configuration/kernel.rst追加
reference/twig_reference.rst追加