Serialize package states independently of RootView

Previously, package specs needed to deactivate the root view to test
their package serialization. Now, specs can just deactivate and then
reactivate the package, relying on serialization infrastructure that's
independent of the lifecycle of the RootView.

src/app/atom.coffee

@@ -27,11 +27,6 @@ _.extend atom,
   setPackageState: (name, state) ->
     @packageStates[name] = state
 
-  serializeAtomPackages: ->
-    for pack in @getActivePackages()
-      @setPackageState(pack.name, state) if state = pack.serialize?()
-    @packageStates
-
   activatePackages: ->
     @activatePackage(pack.path) for pack in @getLoadedPackages()
 

src/app/root-view.coffee

@@ -29,8 +29,7 @@ class RootView extends View
         @div id: 'vertical', outlet: 'vertical', =>
           @subview 'panes', panes ? new PaneContainer
 
-  @deserialize: ({ panes, packages, projectPath }) ->
-    atom.packageStates = packages ? {}
+  @deserialize: ({ panes }) ->
     panes = deserialize(panes) if panes?.deserializer is 'PaneContainer'
     new RootView({panes})
 
@@ -73,7 +72,6 @@ class RootView extends View
     version: RootView.version
     deserializer: 'RootView'
     panes: @panes.serialize()
-    packages: atom.serializeAtomPackages()
 
   confirmClose: ->
     @panes.confirmClose()
@@ -94,10 +92,6 @@ class RootView extends View
   afterAttach: (onDom) ->
     @focus() if onDom
 
-  deactivate: ->
-    atom.deactivatePackages()
-    @remove()
-
   open: (path, options = {}) ->
     changeFocus = options.changeFocus ? true
     path = project.resolve(path) if path?

src/app/window.coffee

@@ -61,10 +61,12 @@ window.shutdown = ->
   return if not project and not rootView
   atom.setWindowState('pathToOpen', project.getPath())
   atom.setWindowState('project', project.serialize())
-  atom.setWindowState('rootView', rootView.serialize())
   atom.setWindowState('syntax', syntax.serialize())
+  atom.setWindowState('rootView', rootView.serialize())
+  atom.deactivatePackages()
+  atom.setWindowState('packageStates', atom.packageStates)
+  rootView.remove()
   atom.saveWindowState()
-  rootView.deactivate()
   project.destroy()
   git?.destroy()
   $(window).off('focus blur before')
@@ -95,6 +97,7 @@ window.deserializeWindowState = ->
 
   windowState = atom.getWindowState()
 
+  atom.packageStates = windowState.packageStates ? {}
   window.project = deserialize(windowState.project) ? new Project(pathToOpen)
   window.rootView = deserialize(windowState.rootView) ? new RootView