Construct Project during Atom environment construction

Signed-off-by: Max Brunsfeld <maxbrunsfeld@github.com>

src/atom.coffee

@@ -160,6 +160,9 @@ class Atom extends Model
     GrammarRegistry = require './grammar-registry'
     @grammars = new GrammarRegistry({@config})
 
+    Project = require './project'
+    @project = new Project({notificationManager: @notifications, packageManager: @packages, @confirm})
+
   setConfigSchema: ->
     @config.setSchema null, {type: 'object', properties: _.clone(require('./config-schema'))}
 
@@ -651,13 +654,6 @@ class Atom extends Model
 
     false
 
-  deserializeProject: ->
-    Project = require './project'
-    startTime = Date.now()
-    @project = new Project()
-    @project.deserialize(@state.project, @deserializers) if @state.project?
-    @deserializeTimings.project = Date.now() - startTime
-
   deserializeWorkspace: ->
     Workspace = require './workspace'
 
@@ -679,7 +675,6 @@ class Atom extends Model
       @grammars.grammarOverridesByPath = grammarOverridesByPath
 
     @deserializePackageStates()
-    @deserializeProject()
     @deserializeWorkspace()
 
   loadThemes: ->
@@ -741,6 +736,10 @@ class Atom extends Model
 
     @deserializeTimings.atom = Date.now() -  startTime
 
+    startTime = Date.now()
+    @project.deserialize(@state.project, @deserializers) if @state.project?
+    @deserializeTimings.project = Date.now() - startTime
+
   getStateKey: (paths) ->
     if paths?.length > 0
       sha1 = crypto.createHash('sha1').update(paths.slice().sort().join("\n")).digest('hex')

src/project.coffee

@@ -21,7 +21,7 @@ class Project extends Model
   Section: Construction and Destruction
   ###
 
-  constructor: ->
+  constructor: ({@confirm, @notificationManager, packageManager}) ->
     @emitter = new Emitter
     @buffers = []
     @paths = []
@@ -30,7 +30,7 @@ class Project extends Model
 
     @directoryProviders = []
     @defaultDirectoryProvider = new DefaultDirectoryProvider()
-    atom.packages.serviceHub.consume(
+    packageManager.serviceHub.consume(
       'atom.directory-provider',
       '^0.1.0',
       (provider) => @directoryProviders.unshift(provider))
@@ -42,7 +42,7 @@ class Project extends Model
     @repositoryPromisesByPath = new Map()
 
     @repositoryProviders = [new GitRepositoryProvider(this)]
-    atom.packages.serviceHub.consume(
+    packageManager.serviceHub.consume(
       'atom.repository-provider',
       '^0.1.0',
       (provider) =>
@@ -417,9 +417,9 @@ class Project extends Model
 
   subscribeToBuffer: (buffer) ->
     buffer.onDidDestroy => @removeBuffer(buffer)
-    buffer.onWillThrowWatchError ({error, handle}) ->
+    buffer.onWillThrowWatchError ({error, handle}) =>
       handle()
-      atom.notifications.addWarning """
+      @notificationManager.addWarning """
         Unable to read file after file `#{error.eventType}` event.
         Make sure you have permission to access `#{buffer.getPath()}`.
         """,