Fix repository initialization

Author: shana

src/GitHub.Api/Application/ApplicationManagerBase.cs

@@ -104,7 +104,11 @@ public ITask InitializeRepository()
                 }))
                 .Then(GitClient.Add(filesForInitialCommit))
                 .Then(GitClient.Commit("Initial commit", null))
-                .Then(RestartRepository)
+                .Then(_ =>
+                {
+                    Environment.InitializeRepository();
+                    RestartRepository();
+                })
                 .ThenInUI(InitializeUI);
             return task;
         }

src/UnityExtension/Assets/Editor/GitHub.Unity/ApplicationManager.cs

@@ -29,6 +29,7 @@ protected override void SetupMetrics()
         protected override void InitializeUI()
         {
             Logger.Trace("Restarted {0}", Environment.Repository);
+            EnvironmentCache.Instance.Flush();
             ProjectWindowInterface.Initialize(Environment.Repository);
             var window = Window.GetWindow();
             if (window != null)