RuboCop: Split `.rubocop_manual_todo.yml` into `.rubocop_todo/**/*.yml`

This commit moves all RuboCop configuration from the large
`.rubocop_manual_todo.yml` into smaller more focused files within
`.rubocop_todo/**/*.yml`.

This step enables us to split `.rubocop_todo.yml` later which is very
likely needed if we start using `rake rubocop:todo:generate` because it
will produce a huge `.rubocop_todo.yml` (due to much higher "exclude
limit").