Ensure there is clean serialization of RootView state

Everything from RootView to Pane needs to return a serialized clone of
its state, so we don't accidentally further mutate the serialized state
in tests.

src/app/pane-axis.coffee

@@ -15,7 +15,7 @@ class PaneAxis extends View
       @state = args[0]
       @state.get('children').each (child, index) => @addChild(deserialize(child), index, updateState: false)
     else
-      @state = telepath.Document.create(deserializer: @className(), children: [])
+      @state = telepath.create(deserializer: @className(), children: [])
       @addChild(child) for child in args
 
     @state.get('children').on 'changed', ({index, inserted, removed, site}) =>
@@ -27,7 +27,7 @@ class PaneAxis extends View
 
   addChild: (child, index=@children().length, options={}) ->
     @insertAt(index, child)
-    @state.get('children').insert(index, child.serialize()) if options.updateState ? true
+    @state.get('children').insert(index, child.getState()) if options.updateState ? true
     @getContainer()?.adjustPaneDimensions()
 
   removeChild: (child, options={}) ->
@@ -83,8 +83,9 @@ class PaneAxis extends View
     children.insert(childIndex + 1, newChild.getState())
 
   serialize: ->
-    child.serialize() for child in @children().views()
-    @state
+    state = @state.clone()
+    state.set('children', child.serialize() for child in @children().views())
+    state
 
   getState: -> @state
 

src/app/pane-container.coffee

@@ -18,22 +18,24 @@ class PaneContainer extends View
   @content: ->
     @div id: 'panes'
 
-  initialize: (@state) ->
-    if @state?
-      @setRoot(deserialize(@state.get('root')), updateState: false)
+  initialize: (state) ->
+    if state instanceof telepath.Document
+      @state = state
+      @setRoot(deserialize(@state.get('root')))
     else
-      @state = telepath.Document.create(deserializer: 'PaneContainer')
+      @state = telepath.create(deserializer: 'PaneContainer')
 
     @state.on 'changed', ({key, newValue, site}) =>
       return if site is @state.site.id
       if key is 'root'
-        @setRoot(deserialize(newValue), updateState: false)
+        @setRoot(deserialize(newValue))
 
     @destroyedItemStates = []
 
   serialize: ->
-    @getRoot()?.serialize()
-    @state
+    state = @state.clone()
+    state.set('root', @getRoot()?.serialize())
+    state
 
   getState: -> @state
 
@@ -92,7 +94,7 @@ class PaneContainer extends View
   setRoot: (root, options={}) ->
     @empty()
     @append(root) if root?
-    @state.set(root: root?.getState()) if options.updateState ? true
+    @state.set(root: root?.getState())
 
   removeChild: (child) ->
     throw new Error("Removing non-existant child") unless @getRoot() is child

src/app/pane.coffee

@@ -33,7 +33,7 @@ class Pane extends View
       @items = args
       @state = telepath.Document.create
         deserializer: 'Pane'
-        items: @items.map (item) -> item.getState?() ? item.serialize()
+        items: @items.map (item) -> item.getState()
 
     @state.get('items').on 'changed', ({index, removed, inserted, site}) =>
       return if site is @state.site.id
@@ -315,9 +315,10 @@ class Pane extends View
     @viewForItem(@activeItem)
 
   serialize: ->
-    @state.get('items').set(index, item.serialize()) for item, index in @items
-    @state.set focused: @is(':has(:focus)')
-    @state
+    state = @state.clone()
+    state.set('items', item.serialize() for item, index in @items)
+    state.set('focused', @is(':has(:focus)'))
+    state
 
   getState: -> @state
 
@@ -374,7 +375,7 @@ class Pane extends View
     @closest('#panes').view()
 
   copyActiveItem: ->
-    deserialize(@activeItem.serialize())
+    @activeItem.copy?() ? deserialize(@activeItem.serialize())
 
   remove: (selector, keepData) ->
     return super if keepData

src/app/project.coffee

@@ -71,7 +71,11 @@ class Project
       for insertedBuffer, i in inserted
         @addBufferAtIndex(deserialize(insertedBuffer), index + i, updateState: false)
 
-  serialize: -> @state.clone()
+  serialize: ->
+    state = @state.clone()
+    state.set('buffers', buffer.serialize() for buffer in @getBuffers())
+    state
+
   getState: -> @state
 
   # Retrieves the project path.

src/app/root-view.coffee

@@ -32,7 +32,7 @@ class RootView extends View
     @div id: 'root-view', =>
       @div id: 'horizontal', outlet: 'horizontal', =>
         @div id: 'vertical', outlet: 'vertical', =>
-          @subview 'panes', deserialize(state?.get?('panes')) ? new PaneContainer
+          @div outlet: 'panes'
 
   @deserialize: (state) ->
     new RootView(state)
@@ -40,8 +40,16 @@ class RootView extends View
   initialize: (state={}) ->
     if state instanceof telepath.Document
       @state = state
+      panes = deserialize(state.get('panes'))
     else
-      @state = telepath.Document.create(_.extend({version: RootView.version, deserializer: 'RootView', panes: @panes.serialize()}, state))
+      panes = new PaneContainer
+      @state = telepath.create
+        deserializer: @constructor.name
+        version: @constructor.version
+        panes: panes.getState()
+
+    @panes.replaceWith(panes)
+    @panes = panes
 
     @on 'focus', (e) => @handleFocus(e)
     @subscribe $(window), 'focus', (e) =>
@@ -83,9 +91,12 @@ class RootView extends View
     _.nextTick => atom.setFullScreen(@state.get('fullScreen'))
 
   serialize: ->
-    @panes.serialize()
-    @state.set('fullScreen', atom.isFullScreen())
-    @state
+    state = @state.clone()
+    state.set('panes', @panes.serialize())
+    state.set('fullScreen', atom.isFullScreen())
+    state
+
+  getState: -> @state
 
   handleFocus: (e) ->
     if @getActivePane()

src/app/text-buffer.coffee

@@ -90,9 +90,7 @@ class TextBuffer
     this
 
   serialize: ->
-    state = @state.clone()
-    state.remove('text') unless @isModified()
-    state
+    @state.clone()
 
   getState: -> @state