How to programmatically clear/refresh module file cache?
Add a MYMODULE.install file to your module. In there implement hook_update_N to flush all caches. When others update your module, and then do database updates, Drupal will pick up this hook and flushes the cache and your new files will be recognized.

/**
 * Pick up new files.
 */
function MYMODULE_update_7100(&amp;$sandbox) {
  drupal_flush_all_caches();
}