Include AtomWindow in command options

This ensures that all application commands can use it instead of relying
on the focused window.

src/browser/atom-application.coffee

@@ -140,7 +140,8 @@ class AtomApplication
     @on 'application:open-file', -> @promptForPath(type: 'file')
     @on 'application:open-folder', -> @promptForPath(type: 'folder')
     @on 'application:open-dev', -> @promptForPath(devMode: true)
-    @on 'application:inspect', ({x,y}, atomWindow=@focusedWindow()) ->
+    @on 'application:inspect', ({x,y, atomWindow}) ->
+      atomWindow ?= @focusedWindow()
       atomWindow?.browserWindow?.inspectElement(x, y)
 
     @on 'application:open-documentation', -> shell.openExternal('https://atom.io/docs/latest/?app')
@@ -236,7 +237,7 @@ class AtomApplication
   # atomWindow - The {AtomWindow} to send the command to.
   # args - The optional arguments to pass along.
   sendCommandToWindow: (command, atomWindow, args...) ->
-    unless @emit(command, args..., atomWindow)
+    unless @emit(command, args...)
       if atomWindow?
         atomWindow.sendCommand(command, args...)
       else

src/browser/context-menu.coffee

@@ -13,7 +13,9 @@ class ContextMenu
   createClickHandlers: (template) ->
     for item in template
       if item.command
-        (item.commandOptions ?= {}).contextCommand = true
+        item.commandOptions ?= {}
+        item.commandOptions.contextCommand = true
+        item.commandOptions.atomWindow = @atomWindow
         do (item) =>
           item.click = =>
             global.atomApplication.sendCommandToWindow(item.command, @atomWindow, item.commandOptions)