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Line 776 of ckeditor.lib.inc
$ckeditor_config_path = $module_drupal_path . "/ckeditor.config.js?" . @filemtime($module_drupal_path . "/ckeditor.config.js");
Should be
$ckeditor_config_path = $module_drupal_path . "/ckeditor.config.js?" . @filemtime($module_drupal_local_path . "/ckeditor.config.js");
or filemtime() fails