Right now the menus are a little disorganized, especially since the PhenoMap configuration can have 3 windows open at once. The secondary windows should have some of the standard menu items from the main window. Also, it would be nice to use the standard Quit and About menus on Mac OS X. Cut, copy, paste, and undo can be placed within a standard Edit menu.
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This is fixed, primarily due to the new docking framework.