Hosted apps on OS X now act more like a native app.

chrome/browser/app_controller_mac.mm

Index: chrome/browser/app_controller_mac.mm
diff --git a/chrome/browser/app_controller_mac.mm b/chrome/browser/app_controller_mac.mm
index f234859d815687b6b0dabd654fc198d6c8c3d898..b3711a6cc14f05c2c9fe33898fea5658d7a34390 100644
--- a/chrome/browser/app_controller_mac.mm
+++ b/chrome/browser/app_controller_mac.mm
@@ -74,6 +74,7 @@
 #include "chrome/browser/ui/startup/startup_browser_creator.h"
 #include "chrome/browser/ui/startup/startup_browser_creator_impl.h"
 #include "chrome/browser/ui/user_manager.h"
+#include "chrome/browser/web_applications/web_app_mac.h"
 #include "chrome/common/chrome_paths_internal.h"
 #include "chrome/common/chrome_switches.h"
 #include "chrome/common/cloud_print/cloud_print_class_mac.h"
@@ -93,6 +94,7 @@
 #include "content/public/browser/plugin_service.h"
 #include "content/public/browser/user_metrics.h"
 #include "extensions/browser/extension_system.h"
+#include "extensions/browser/extension_registry.h"
 #include "net/base/filename_util.h"
 #include "ui/base/cocoa/focus_window_set.h"
 #include "ui/base/l10n/l10n_util.h"
@@ -1187,6 +1189,16 @@ class AppControllerProfileObserver : public ProfileInfoCacheObserver {
     std::set<NSWindow*> browserWindows;
     for (chrome::BrowserIterator iter; !iter.done(); iter.Next()) {
       Browser* browser = *iter;
+      if (browser && browser->is_app()) {
+        extensions::ExtensionRegistry* registry =
+            extensions::ExtensionRegistry::Get(browser->profile());
+        const extensions::Extension* extension = registry->GetExtensionById(
+            web_app::GetExtensionIdFromApplicationName(browser->app_name()),
+            extensions::ExtensionRegistry::ENABLED);
+        if (extension->is_hosted_app()) {

[jackhou1, 2014/12/11 02:43:18]

The goal here is to identify windows that are not logically associated with the
Chrome dock icon. I think a better way would be to check
ExtensionAppShimHandler::FindHost. Having a host implies the window has its own
shim and so should not be included here.

[mitchellj, 2014/12/12 00:03:45]

Done.

+          continue;
+        }
+      }
       browserWindows.insert(browser->window()->GetNativeWindow());
     }
     if (!browserWindows.empty()) {