Use 'kill window' to kill a specific window (for example only one specific
popup), use 'kill client' to kill the whole application (or X11 connection to
be specific).
The implementation works like this:
Containers can have a 'sticky-group' attribute. Imagine two different
containers (on two different workspaces) which have the same sticky-group.
Now you open a window in the first container. When you switch to the
other workspace, the window will be re-assigned to the other container.
An obvious problem which is not covered with the code at the moment is
having two containers with the same sticky-group visible at the same time.
