Window layout and z-ordering isn't preserved in Jalview projects

This probably goes back some time. If a tree, structure view, and alignment window are saved in a project arranged a certain way on the desktop they should not only be loaded back from the project with the same width and height, but also z-order and location should be preserved.

z-ordering is almost certainly due to variation in desktop window ordering behaviour which happened for different Mac implementations over the years. This should be a cross-platform test.