Rectangle Hotkeys

Focus the app, then open the Rectangle menu and select "Ignore app". To un-ignore it, focus the same app again and deselect "Ignore" from the Rectangle menu.

Yes. Use rectangle://execute-action?name=[name]. For example: rectangle://execute-action?name=left-half.

Rectangle stores configuration in NSUserDefaults at ~/Library/Preferences/com.knollsoft.Rectangle.plist. You can also import/export JSON config from the Preferences window.