Drush command to relocate files into folders based on unchanging file id. http://lechronicles.blogspot.co.uk/2014/03/improve-performance-organize-your-files.html

d7_fid_migration_filepath.drush.inc

<?php
/**
 * Implements of hook_drush_command().
 */
function migration_filepath_drush_command() {
  $items = array();

  $items['migration_filepath'] = array(
    'description' => "Move files to subdirectories",
    'callback' => 'drush_migration_filepath',
    'aliases' => array('mf'),
    // We are using options rather than arguments so the source can be omitted
    // if needed (e.g. files are just directly under sites/default/files).
    'options' => array(
      'source' => array(
        'description' => 'The directory under files where the to be relocated files are.',
        'example_value' => 'field/image',
      ),
      'target' => array(
        'description' => 'The target directory where the files will be moved to and restructured.',
        'example_value' => 'pictures',
      ),
      'limit' => array(
        'description' => 'Use this option to explicitly limit the number of files to move. Do not use this option if you want to move all files.',
        'example_value' => '15',
      ),
      'list-info' => 'Print total number of files remaining to be moved and other helpful info and exit.',
    ),
    'examples' => array(
      'drush migration_filepath' => 'Moves all files located in the public file directory to fid based directory structure.',
   ),
    'bootstrap' => DRUSH_BOOTSTRAP_DRUPAL_FULL
  );

  return $items;
}

/**
 * Command callback to perform the file migration.
 *
 * The two optional options are the source and target directories. By default
 * assumes that these are under the default path, e.g. sites/default/files.
 */
function drush_migration_filepath() {
  // Source directory to be cleaned up. All images in this directory will be relocated.
  $source_directory = rtrim(drush_get_option('source', ''), '/');
  // Directory to place the new structure under. If does not exist will be created.
  $target_directory = rtrim(drush_get_option('target', ''), '/');


  // Regular expression to find files in the source directory.
  // For now assume public files only.
  // public://field/image/imagefield_hENvtS.png
  $extensions = array('jpeg', 'jpg', 'gif', 'png');

  // Construct a expression to find images located in the source directory.
  $file_pattern = "[^\/]*"; // Finds anything that does not contain "/", should be fine.

  // Append the trailing slash for the regular expression.
  // Note, in some instances drupal places under public:/// (three slashes)
  // even when no folder specified. Reason for this is not known yet.
  $source_pattern = $source_directory ? $source_directory . "\/" : '';

  $regex = "^public:\/\/" . $source_pattern . "(" . $file_pattern . ")\.(" . implode($extensions, '|') . ")$";

  // Query the database for files that match this pattern.
  $filetypes = array('image/jpeg', 'image/jpg', 'image/gif', 'image/png');
  $query = db_select('file_managed', 'f')
    ->condition('filemime', $filetypes , 'IN')
    ->condition('uri', $regex, 'REGEXP')
    // Select the files to be moved.
    ->fields('f', array('fid', 'filename', 'uri', 'timestamp'))
    // Start from the oldest so that new additions in between the file move
    // and the site using the new fe_paths path won't be tarnished.
    ->orderBy('timestamp', 'asc');

  // Open a file in the public files/ directory to write redirects into.
  $public_path = variable_get('file_public_path', conf_path() . '/files');
  $redirects_filename = $public_path . "/image-redirects.map";

  // Print helpful information on pending file moves and exit.
  if (drush_get_option('list-info')) {
    print $query;
    print_r($query->arguments());
    // Print total number of files that need moving
    $num_files = $query->countQuery()->execute()->fetchField();
    drush_print(dt('There are ' . $num_files . ' files in total to be moved.'));
    drush_print(dt('The redirects file will be created at: ' . $redirects_filename));
    return TRUE;
  }

  // Limit the number of files.
  if ($limit = drush_get_option('limit')) {
    $files = $query->range(0, $limit)->execute()->fetchAll();
  }
  else {
    $files = $query->execute()->fetchAll();
  }

  $total_files = count($files);
  drush_print(dt($total_files . ' files are set to be moved.'));

  $count = 1;
  // Keep a list of files that have not been moved.
  $files_not_moved = array();

  // Create or open the redirects file for writing.
  $redirects_file = fopen($redirects_filename, 'a') or die("Unable to open redirects file for writing.");

  foreach ($files as $file) {
    preg_match_all("/$regex/i", $file->uri, $matches); // Note, $file->filename can be the SAME for different uri-s!
    $filename = $matches[1][0] . "." . $matches[2][0];

    $old_file_wrapper = file_stream_wrapper_get_instance_by_uri($file->uri);

    // If the file has already been moved, or does not exist in the filesystem, move on.
    if (FALSE === ($status = $old_file_wrapper->url_stat($file->uri, STREAM_URL_STAT_QUIET))) {
      $files_not_moved[] = $file->uri;
      drush_log("File entry in the database does not exist on the filesystem for " . $file->uri, 'notice');
      continue;
    }

    // Each file should go to the directory based on its fid.
    $target_directory_for_file = $target_directory . '/' . generate_directory_name($file);

    // Construct a dummy URI for it so we can use the stream wrappers.
    $new_directory = file_build_uri($target_directory_for_file);
    $wrapper = file_stream_wrapper_get_instance_by_uri($new_directory);
    // Make sure that the new directory exists.
    $wrapper->mkdir($new_directory, 0777, TRUE);

    // Construct the new directory.
    $wrapper = file_stream_wrapper_get_instance_by_uri($file->uri);
    $new_uri = file_build_uri($target_directory_for_file . '/' . $filename);
    if (!$wrapper->rename($file->uri, $new_uri)) {
      $files_not_moved[] = $file->uri;
      drush_log("There was a problem moving " . $file->uri, 'notice');
      continue;
    }

    $progress = round(($count / $total_files) * 100);
    drush_print($progress . '%');
    $query = db_update('file_managed')
      ->fields(array('uri' => $new_uri))
      ->condition('fid', $file->fid)
      ->execute();

    // Append to the image redirects list.
    $rel_old_url = parse_url(file_create_url($file->uri), PHP_URL_PATH);
    $rel_new_url = parse_url(file_create_url($new_uri), PHP_URL_PATH);
    fwrite($redirects_file, '~^' . $rel_old_url . ' ' . $rel_new_url . ';' . PHP_EOL);

    $count++;
  }

  fclose($redirects_file);

  $not_moved = count($files_not_moved) ? count($files_not_moved) : 0;

  drush_print(dt('(' . ($total_files - $not_moved) . '/' . $total_files . ') ' .
                 'files moved.'));

  if ($not_moved) {
    drush_print(dt($not_moved . ' files do not exist in the filesystem.'));
  }
  drush_print(dt('Redirects file: ' . $redirects_filename));
}

/**
 * Generate the new file structure based on the timestamp.
 */
function generate_directory_name($file) {
  $fid = str_pad($file->fid, 10, '0', STR_PAD_LEFT);
  $len = strlen($fid);
  $top_dir = $fid[$len - 3];
  $sub_dir = $fid[$len - 2] . $fid[$len - 1];
  $value = $top_dir . '/' . $sub_dir;
  return $value;
}
?>