Instead of marking all default apps as bookmark apps, allow it to be specified per-app.

chrome/browser/extensions/extension_service.cc

 // Copyright (c) 2012 The Chromium Authors. All rights reserved.
 // Use of this source code is governed by a BSD-style license that can be
 // found in the LICENSE file.
 
 #include "chrome/browser/extensions/extension_service.h"
 
 #include <algorithm>
 #include <set>
 
 #include "base/basictypes.h"
@@ skipping 660 matching lines @@
     creation_flags |= Extension::FROM_WEBSTORE;
   }
 
   // Bookmark apps being updated is kind of a contradiction, but that's because
   // we mark the default apps as bookmark apps, and they're hosted in the web
   // store, thus they can get updated. See http://crbug.com/101605 for more
   // details.
   if (extension && extension->from_bookmark())
     creation_flags |= Extension::FROM_BOOKMARK;
 
-  if (extension) {
-    // Additionally, if the extension is an external extension, we preserve the
-    // creation flags (usually from_bookmark), even if the current pref values
-    // don't reflect them. This is to fix http://crbug.com/109791 for users that
-    // had default apps updated and lost the from_bookmark bit.
-    ProviderCollection::const_iterator i;
-    for (i = external_extension_providers_.begin();
-        i != external_extension_providers_.end(); ++i) {
-      ExternalExtensionProviderInterface* provider = i->get();
-      if (provider->HasExtension(extension->id())) {
-        creation_flags |= provider->GetCreationFlags();
-        break;
-      }
-    }
-  }
   installer->set_creation_flags(creation_flags);
 
   installer->set_delete_source(true);
   installer->set_download_url(download_url);
   installer->set_install_cause(extension_misc::INSTALL_CAUSE_UPDATE);
   installer->InstallCrx(extension_path);
 
   if (out_crx_installer)
     *out_crx_installer = installer;
 
@@ skipping 1944 matching lines @@
   // To coexist with certain unit tests that don't have an IO thread message
   // loop available at ExtensionService shutdown, we lazy-initialize this
   // object so that those cases neither create nor destroy an
   // APIResourceController.
   CHECK(BrowserThread::CurrentlyOn(BrowserThread::IO));
   if (!api_resource_controller_) {
     api_resource_controller_ = new extensions::APIResourceController();
   }
   return api_resource_controller_;
 }