Some menu items are losing their parent information

@bjalford thanks for submit this.. i think that http://drupal.org/node/1866966 it's very different in that case panelizer is creating a set of permission dynamically for each content type.. and somehow it does not update during the import process. You could be right about that menu missing so menu link can not be pointed, but not sure. Still looking into this.

@bjalford thanks for taking the time of clarifying this.. 1 more question.... This issue apears when you export and import configurations using a tar file? can you confirm that?

@bjalford Another question are you creating the menu entries from Node edit form.. or the menu module UI?

Confirmed this issue only appears when synchronizing, export and import menu and menu-links works correctly.

@bjalford Both processes use basically the same api method ConfigurationManagement::importToActiveStore() the problem as far I see go around dependencies... if you import including dependencies it will work... and fail if you don't include them, the way that method imports dependent components it's kind a different as importing single components 1 by 1. I do not have time to look for this issue right now but let me know if you are working on this and I can assist you, i'm in the IRC.

I'm almost sure this is a consequence of #1908048: Dependency selection doesn't allow multiple modifications.

I cannot replicate this issue using the last development version after the commit mentioned above. Please re-open if you still are having issues.

I'm having the same problem. According to drush I'm using 7.x-2.0-alpha2+10-dev. I'm trying to copy the data store to the active store inside an install profile. The data store includes an exported menu and menu links. I have dependencies set to TRUE, but some of the links fail to appear, and I see notices identical to the one in the summary.

From the install profile:

  $tracking_file = \Drupal\configuration\Config\ConfigurationManagement::readTrackingFile();
  $to_track = array_keys($tracking_file['tracked']);
  \Drupal\configuration\Config\ConfigurationManagement::importToActiveStore($to_track, TRUE, FALSE, TRUE);

I'm still digging, hopefully I'll be able to provide some more information.

@rylowry We were using configuration to manage configuration in a install profile from quite a time using the function configuration_import_directory(). You have a lot of parameters to handling the import check the function definition in configuration.module. This helper function allow you to do a few extra things like enabling modules and other stuff.

This is a callback example that you can use for a profile task, here we keep the files in a configuration folder within the profile:

function my_profile_import_configurations_process() {
  if (module_exists('configuration')) {
    $config_path = drupal_get_path('profile', 'my_profile') . "/configuration/";
    configuration_import_directory($config_path);
    drupal_set_message("Imported configurations");
  }
  else {
    drupal_set_message("Error importing configurations.", 'Error');
  }
}

If it helps with debugging this issue, I'm also seeing similar behaviour but only with menu links that link to views. If I create links manually with the normal Drupal menu UI and the path links to the path of a View, the menu link will not be created when synchronizing. If I create an identical link but using the 'Menu' section on the edit page for the relevant View, the menu link will be created. Both types of links function identically in the 'source' Drupal site, but only the latter type can be imported during synchronization.

update