Site in Subdirs support doesn't work

The culprit seems to be here:

$features = drush_get_option('hosting_features', array());

This array is always empty. That is why this code simply doesn't work as expected:

    if (subdirs_drush_load()) {
      $this->configs['site'][] = 'Provision_Config_Nginx_Subdir';
      $this->configs['site'][] = 'Provision_Config_Nginx_SubdirVhost';
    }

And of course this also shouldn't work for the same reason, I suppose:

    $features = drush_get_option('hosting_features', array());
    if (array_key_exists('subdirs', $features) && $features['subdirs']) {
      $this->configs['site'][] = 'Provision_Config_Apache_Subdir';
      $this->configs['site'][] = 'Provision_Config_Apache_SubdirVhost';
    }

If this code worked before, why it no longer works? No idea :/

OK, it seems that to make it work, in needs ~/.drush/drushrc.php file, but I don't see this file created, for some reason.

====
Issue #2098389: Record enabled Hosting Features in /var/aegir/.drush/drushrc.php.
We want to be able to block unwanted Drush hooks from firing, especially those in
extensions where the front-end module is not enabled. To do so, we need to know
which Hosting Features are enabled very early in the Drush bootstrap process, since
blocking the unwanted hooks from firing is accomplished with hook_drush_load()'s.

Well, I think it is related to our custom Drush hardening we did to improve security. We need to add back this code and restrict it to aegir backend user, I suppose.

+  // Load a drushrc.php file in the ~/.drush directory.
+  drush_load_config('home.drush');

+  // in $HOME/.drush directory
+  $per_user_config_dir = drush_get_context('DRUSH_PER_USER_CONFIGURATION');
+  if (!empty($per_user_config_dir)) {
+    $configs['home.drush'] = $per_user_config_dir . '/' . $config_file;
+  }

Yep, that was it, sorry for the noise. I will submit some fixes we added while debugging this, separately.