Reset MenuManager in AtomEnvironment::reset

src/atom-environment.coffee

@@ -245,6 +245,8 @@ class AtomEnvironment extends Model
 
     @styles.restoreSnapshot(@initialStyleElements)
 
+    @menu.clear()
+
   ###
   Section: Event Subscription
   ###

src/menu-manager.coffee

@@ -96,6 +96,10 @@ class MenuManager
     @unmerge(@template, item) for item in items
     @update()
 
+  clear: ->
+    @template = []
+    @update()
+
   # Should the binding for the given selector be included in the menu
   # commands.
   #