Scan directories for files and add them to the Backdrop managed file system

manage_unmanaged_files.php

<?php

// Load file from disk.
echo 'Managing unmanaged files:\n';
// Change the DIRECTORY_NAME below for each directory you'd like to process.
foreach (new DirectoryIterator('DIRECTORY_NAME') as $unmanaged_file) {
  if(($unmanaged_file->isDir()) | ($unmanaged_file->isDot()) | (!$unmanaged_file->valid())) continue;
  $filename = $unmanaged_file->getFilename();
  if($filename == '.htaccess') continue;
  $pathname = $unmanaged_file->getPathname();
  echo $pathname. "\n";
  $contents = file_get_contents($pathname);
  // Make sure to set the "public://" bit below to the full public:// path of the directory you're processing
  $file = file_save_data($contents, 'public://' . $filename , FILE_EXISTS_REPLACE);
  file_usage_add($file, 'user', 'user', '1');
  $count++;
}
print_r('Managed ' . $count . ' files!');

Run this with drush: drush scr --user=1 manage_unmanaged_files.php

Tried this today, nearly three years after writing it, and it totally works! (So long as you are sure to set the public:// bit correctly, tried to quickly note that in the code though I know it's not the clearest.)