Don't close the popover when the app is showing a modalWindow.
Use windowNumberAtPoint: to determine if clicks actually reach the parentWindow.

This means that if you move a different app window around (that
overlaps the parent window), we won’t accidentally dismiss the popover.
Also use windowNumberAtPoint: to test if we're in the popoverWindow.
Merge pull request #146 from github/dont-dismiss-when-theres-a-modal

Use windowNumberAtPoint: to determine if a mouse event is on a window.