All the layout related issues should be fixed. Somehow the actual new layout folders themselves didn't get pushed up to github when Rob committed the changed.
Just FYI, what the new JLayout stuff does is, it moves the HTML markup for the element out of the element's main model PHP, and into a separate layout file, which can be overridden. Layouts are basically little mini templates. So in the same way you can do template overrides in J!, you can do layout overrides. So if you want to change the way an element is rendered, i.e. the actual HTML / DOM structure, you can now do that by overriding an individual element's layout.
So, for example, if you have a J! template which uses Bootstrap v3, and a particular element doesn't render properly because our markup has to assume we are using J!'s standard v2, it would be trivial to override that element's layout, and tweak whatever it is about the markup (usually class names) which is borking up in BS v3.
-- hugh