Enable permission warnings from ManifestHandlers.

chrome/browser/extensions/active_tab_permission_granter.cc

Index: chrome/browser/extensions/active_tab_permission_granter.cc
diff --git a/chrome/browser/extensions/active_tab_permission_granter.cc b/chrome/browser/extensions/active_tab_permission_granter.cc
index d8c0ce6e64330acaed70dd3bcda2326e00f6e8fe..aebeb39cc8eb208c76eb332d594b4f06b5b9e50b 100644
--- a/chrome/browser/extensions/active_tab_permission_granter.cc
+++ b/chrome/browser/extensions/active_tab_permission_granter.cc
@@ -59,7 +59,8 @@ void ActiveTabPermissionGranter::GrantIfRequested(const Extension* extension) {
   if (!new_apis.empty() || !new_hosts.is_empty()) {
     granted_extensions_.Insert(extension);
     scoped_refptr<const PermissionSet> new_permissions =
-        new PermissionSet(new_apis, new_hosts, URLPatternSet());
+        new PermissionSet(new_apis, ManifestPermissionSet(),
+                          new_hosts, URLPatternSet());
     PermissionsData::UpdateTabSpecificPermissions(extension,
                                                   tab_id_,
                                                   new_permissions);