Ask for close confirmation in beforeunload handler.

src/app/pane-container.coffee

@@ -83,7 +83,9 @@ class PaneContainer extends View
     saved = true
     for pane in @getPanes()
       for item in pane.getItems() when item.isModified?()
-        saved = false if not pane.promptToSaveItem item
+        if not @paneAtIndex(0).promptToSaveItem item
+          saved = false
+          break
     saved
 
   getPanes: ->

src/app/window-event-handler.coffee

@@ -14,13 +14,10 @@ class WindowEventHandler
     @subscribe $(window), 'blur',  -> $("body").addClass('is-blurred')
     @subscribe $(window), 'window:open-path', (event, pathToOpen) ->
       rootView?.open(pathToOpen) unless fsUtils.isDirectorySync(pathToOpen)
+    @subscribe $(window), 'beforeunload', -> rootView?.confirmClose()
 
     @subscribeToCommand $(window), 'window:toggle-full-screen', => atom.toggleFullScreen()
-    @subscribeToCommand $(window), 'window:close', =>
-      if rootView?
-        closeWithoutConfirm() if rootView.confirmClose()
-      else
-        closeWithoutConfirm()
+    @subscribeToCommand $(window), 'window:close', => window.close()
     @subscribeToCommand $(window), 'window:reload', => atom.reload()
 
     @subscribeToCommand $(document), 'core:focus-next', @focusNext

src/app/window.coffee

@@ -210,10 +210,6 @@ window.restoreDimensions = ->
   window.setDimensions(dimensions)
   $(window).on 'unload', -> atom.setWindowState('dimensions', window.getDimensions())
 
-window.closeWithoutConfirm = ->
-  atom.hide()
-  ipc.sendChannel 'close-without-confirm'
-
 window.onerror = ->
   atom.openDevTools()
 

src/atom-application.coffee

@@ -175,11 +175,6 @@ class AtomApplication
       @installUpdate = quitAndUpdate
       @buildApplicationMenu version, quitAndUpdate
 
-    ipc.on 'close-without-confirm', (processId, routingId) ->
-      window = BrowserWindow.fromProcessIdAndRoutingId processId, routingId
-      window.removeAllListeners 'close'
-      window.close()
-
     ipc.on 'open-config', =>
       @openConfig()
 

src/atom-window.coffee

@@ -89,11 +89,6 @@ class AtomWindow
       # Spec window's web view should always have focus
       @browserWindow.on 'blur', =>
         @browserWindow.focusOnWebView()
-    else
-      @browserWindow.on 'close', (event) =>
-        unless @browserWindow.isCrashed()
-          event.preventDefault()
-          @sendCommand 'window:close'
 
   openPath: (pathToOpen) ->
     if @loaded