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 2e2dfe57e200c64a0cff295ef819aeefefa3b63b..174b78658808204013d1d1fd6727cccc8dc5091f 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"
@@ -93,11 +94,14 @@
 #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"
 #include "ui/base/l10n/l10n_util_mac.h"
 
+using apps::AppShimHandler;
+using apps::ExtensionAppShimHandler;
 using base::UserMetricsAction;
 using content::BrowserContext;
 using content::BrowserThread;
@@ -1185,8 +1189,22 @@ class AppControllerProfileObserver : public ProfileInfoCacheObserver {
   // notifications so we still need to open a new window.
   if (hasVisibleWindows) {
     std::set<NSWindow*> browserWindows;
+    ExtensionAppShimHandler* appShimHandler =
+        g_browser_process->platform_part()
+            ->app_shim_host_manager()
+            ->extension_app_shim_handler();
     for (chrome::BrowserIterator iter; !iter.done(); iter.Next()) {
       Browser* browser = *iter;
+      // When focusing Chrome, don't focus any browser windows associated with
+      // a currently running app shim, so ignore them.
+      if (browser && browser->is_app()) {
+        AppShimHandler::Host* host = appShimHandler->FindHost(
+            browser->profile(),
+            web_app::GetExtensionIdFromApplicationName(browser->app_name()));
+        if (host) {
+          continue;
+        }
+      }
       browserWindows.insert(browser->window()->GetNativeWindow());
     }
     if (!browserWindows.empty()) {