Theming custom field directly in custom module folder?
When you define your module's theme info in theme_hook(), you can use drupal_get_path() to find the path to your module, and the path array key in your theme implementation array to point to the directory your tpl is in.

A working example would be:

function field_collection_theme($existing, $type, $theme, $path) {

  $path = drupal_get_path('module', 'field_collection');

  return array(
    'field_collection_op_links' =&gt; array(
      'path' =&gt; $path . '/includes/theme',
      'template' =&gt; 'field-collection-op-links',
      'render element' =&gt; 'op_links',
    ),
  );
}


Where the field_collection_op_links.tpl.php is in field_collection/includes/theme/, no matter where field collection is installed.