' . htmlspecialchars($docblock['source']) . '

, ,  tags.
  // We don't apply any processing to the contents of these tags to avoid messing
  // up code. We look for matched pairs and allow basic nesting. For example:
  // "processed 
 ignored  ignored 
 processed"
  $chunks = preg_split('@(]*>)@i', $text, -1, PREG_SPLIT_DELIM_CAPTURE);
  // Note: PHP ensures the array consists of alternating delimiters and literals
  // and begins and ends with a literal (inserting NULL as required).
  $ignore = FALSE;
  $ignoretag = '';
  $output = '';
  foreach ($chunks as $i => $chunk) {
    if ($i % 2) {
      // Opening or closing tag?
      $open = ($chunk[1] != '/');
      list($tag) = preg_split('/[ >]/', substr($chunk, 2 - $open), 2);
      if (!$ignore) {
        if ($open) {
          $ignore = TRUE;
          $ignoretag = $tag;
        }
      }
      // Only allow a matching tag to close it.
      elseif (!$open && $ignoretag == $tag) {
        $ignore = FALSE;
        $ignoretag = '';
      }
    }
    elseif (!$ignore) {
      $chunk = api_format_documentation_lists($chunk);
      $chunk = preg_replace('|\n*$|', '', $chunk) ."\n\n"; // just to make things a little easier, pad the end
      $chunk = preg_replace('|
\s*
|', "\n\n", $chunk);
      $chunk = preg_replace('!(<'. $block .'[^>]*>)!', "\n$1", $chunk); // Space things out a little
      $chunk = preg_replace('!()!', "$1\n\n", $chunk); // Space things out a little
      $chunk = preg_replace("/\n\n+/", "\n\n", $chunk); // take care of duplicates
      $chunk = preg_replace('/\n?(.+?)(?:\n\s*\n|\z)/s', "
$1
\n", $chunk); // make paragraphs, including one at the end
      $chunk = preg_replace('|
\s*
\n|', '', $chunk); // under certain strange conditions it could create a P of entirely whitespace
      $chunk = preg_replace("|
(|", "$1", $chunk); // problem with nested lists
      $chunk = preg_replace('|
]*)>|i', "
", $chunk);
      $chunk = str_replace('
', '
', $chunk);
      $chunk = preg_replace('!
\s*(]*>)!', "$1", $chunk);
      $chunk = preg_replace('!(]*>)\s*
!', "$1", $chunk);
      $chunk = preg_replace('/&([^#])(?![A-Za-z0-9]{1,8};)/', '&$1', $chunk);
    }
    $output .= $chunk;
  }
  return $output;
}

/**
 * Regular expression callback for @code in api_format_documentation().
 */
function api_format_embedded_php($matches) {
  return "\n\n". api_format_php("") ."\n\n";
}

/**
 * Formats documentation lists as HTML lists.
 *
 * Parses a block of text for lists that uses hyphens or asterisks as bullets,
 * and format the lists as proper HTML lists.
 */
function api_format_documentation_lists($documentation) {
  $lines = explode("\n", $documentation);
  $output = '';
  $bullet_indents = array(-1);

  foreach ($lines as $line) {
    preg_match('!^( *)([*-] )?(.*)$!', $line, $matches);
    $indent = strlen($matches[1]);
    $bullet_exists = $matches[2];

    if ($indent < $bullet_indents[0]) {
      // First close off any lists that have completed.
      while ($indent < $bullet_indents[0]) {
        array_shift($bullet_indents);
        $output .= '';
      }
    }

    if ($indent == $bullet_indents[0]) {
      if ($bullet_exists) {
        // A new bullet at the same indent means a new list item.
        $output .= '
';
      }
      else {
        // If the indent is the same, but there is no bullet, that also
        // signifies the end of the list.
        array_shift($bullet_indents);
        $output .= '
';
      }
    }

    if ($indent > $bullet_indents[0] && $bullet_exists) {
      // A new list at a lower level.
      array_unshift($bullet_indents, $indent);
      $output .= '
';
    }

    $output .= $matches[3] ."\n";
  }

  // Clean up any unclosed lists.
  array_pop($bullet_indents);
  foreach ($bullet_indents as $indent) {
    $output .= '
';
  }

  return $output;
}

/**
 * Retrieves a summary from a documentation block.
 */
function api_documentation_summary($documentation) {
  $pos = strpos($documentation, '
');
  if ($pos !== FALSE) {
    $documentation = substr($documentation, 0, $pos);
  }
  $documentation = trim(strip_tags($documentation));

  if (strlen($documentation) > 255) {
    return substr($documentation, 0, strrpos(substr($documentation, 0, 252), ' ')) . '…';
  }
  else {
    return $documentation;
  }
}

/**
 * Colorizes and formats PHP code.
 *
 * @param $code
 *   PHP code to format.
 *
 * @return
 *   HTML-formatted code, with spans enclosing various PHP elements.
 */
function api_format_php($code) {
  $output = '';

  if (!defined('T_ML_COMMENT')) {
    define('T_ML_COMMENT', T_COMMENT);
  }
  if (!defined('T_DOC_COMMENT')) {
    define('T_DOC_COMMENT', T_COMMENT);
  }

  $tokens = token_get_all($code);

  $in_string = FALSE;

  foreach ($tokens as $token) {
    if ($in_string) {
      if ($token == '"') {
        $output .= '"';
        $in_string = FALSE;
      }
      else {
        $output .= is_array($token) ? htmlspecialchars($token[1]) : htmlspecialchars($token);
      }
      continue;
    }
    elseif ($token == '"') {
      $output .= '"';
      $in_string = TRUE;
      continue;
    }

    if (is_array($token)) {
      $type = $token[0];
      $value = htmlspecialchars($token[1]);

      switch ($type) {
        case T_OPEN_TAG:
        case T_CLOSE_TAG:
          $output .= ''. $value .'';
          break;

        case T_COMMENT:
        case T_ML_COMMENT:
        case T_DOC_COMMENT:
          $output .= ''. $value .'';
          break;

        case T_VARIABLE:
          $output .= ''. $value .'';
          break;

        case T_CONSTANT_ENCAPSED_STRING:
        case T_INLINE_HTML:
          $output .= ''. $value .'';
          break;

        case T_STRING:
          $output .= ''. $value .'';
          break;

        case T_LNUMBER:
        case T_DNUMBER:
          $output .= ''. $value .'';
          break;

        case T_ARRAY_CAST: case T_ARRAY: case T_AS: case T_BOOL_CAST:
        case T_BREAK: case T_CASE: case T_CLASS: case T_CONST:
        case T_CONTINUE: case T_DECLARE: case T_DEFAULT: case T_DO:
        case T_DOUBLE_CAST: case T_ECHO: case T_ELSE: case T_ELSEIF:
        case T_EMPTY: case T_ENDDECLARE: case T_ENDFOR: case T_ENDFOREACH:
        case T_ENDIF: case T_ENDSWITCH: case T_ENDWHILE: case T_EVAL:
        case T_EXIT: case T_EXTENDS: case T_FOR: case T_FOREACH:
        case T_FUNCTION: case T_GLOBAL: case T_IF: case T_INCLUDE_ONCE:
        case T_INCLUDE: case T_INT_CAST: case T_ISSET: case T_LIST:
        case T_NEW: case T_OBJECT_CAST: case T_PRINT:
        case T_REQUIRE_ONCE: case T_REQUIRE: case T_RETURN: case T_STATIC:
        case T_STRING_CAST: case T_SWITCH: case T_UNSET_CAST: case T_UNSET:
        case T_USE: case T_VAR: case T_WHILE:
          $output .= ''. $value .'';
          break;

        default:
          $output .= $value;
      }
    }
    else {
      $output .= $token;
    }
  }

  // Manage whitespace:
  return '
'. trim($output) .'
';
}

/**
 * Keeps track of references while parsing API files.
 *
 * Since we may parse a file containing a reference before we have parsed the
 * file containing the referenced object, we keep track of the references
 * using a scratch table and save the references to the database table after the
 * referenced object has been parsed.
 *
 * @param $branch
 *   Branch the reference is in.
 * @param $to_type
 *   Type of object being referenced.
 * @param $to_name
 *   Name of object being referenced.
 * @param $from_did
 *   Documentation ID of the object that references this object.
 */
function api_reference($branch, $to_type, $to_name, $from_did) {
  static $is_php_function = array();

  if ($to_type == 'function' && !isset($is_php_function[$to_name])) {
    $is_php_function[$to_name] = (db_result(db_query_range("SELECT 1 FROM {api_documentation} d INNER JOIN {api_branch} b ON b.branch_id = d.branch_id AND b.type = 'php' WHERE d.object_name = '%s'", $to_name, 1, 1)));
  }

  if ($to_type != 'function' || !$is_php_function[$to_name]) {
    db_query("INSERT INTO {api_reference_storage} (object_name, branch_id, object_type, from_did) VALUES ('%s', '%s', '%s', %d)", $to_name, $branch->branch_id, $to_type, $from_did);
  }
}

/**
 * Registers a shutdown function for cron, making sure to do it just once.
 *
 * @see api_shutdown()
 */
function api_schedule_shutdown() {
  static $scheduled = FALSE;

  if (!$scheduled) {
    register_shutdown_function('api_shutdown');
    $scheduled = TRUE;
  }
}

/**
 * Cleans up at the end of the cron job.
 *
 * Updates the collected references, updates the JSON object list, and clears
 * the cache.
 */
function api_shutdown() {
  // Figure out all the dids of the object/branch/types.
  db_query('UPDATE {api_reference_storage} r INNER JOIN {api_documentation} d ON r.object_name = d.object_name AND r.branch_id = d.branch_id AND r.object_type = d.object_type SET r.to_did = d.did');

  // Save overrides
  $changed_classes = array();
  $result = db_query("SELECT ad.did, ad.object_type, ad.member_name, ad.class_did, ad.documentation, af.parameters, af.return_value, ad.see, ad.throws, ad.var FROM {api_documentation} ad LEFT JOIN {api_overrides} ao ON ao.did = ad.did LEFT JOIN {api_function} af ON af.did = ad.did WHERE ad.class_did <> 0 AND ao.did IS NULL");
  while ($object = db_fetch_object($result)) {
    $changed_classes[$object->class_did] = TRUE;
    $override = array(
      'did' => $object->did,
      'overrides_did' => 0,
      'documented_did' => api_has_documentation($object) ? $object->did : 0,
      'root_did' => $object->did,
    );
    $overrides_did = 0;
    $parents = array($object->class_did);
    while ($parent = array_shift($parents)) {
      $result_parents = db_query("SELECT ad.did, ars.to_did, ad.summary, ad.documentation, af.parameters, af.return_value, ad.see, ad.throws, ad.var, ad.class_did FROM {api_reference_storage} ars LEFT JOIN {api_documentation} ad ON ad.class_did = ars.to_did AND ad.object_type = '%s' AND ad.member_name = '%s' LEFT JOIN {api_function} af ON af.did = ad.did WHERE ars.from_did = %d AND ars.object_type IN ('class', 'interface')", $object->object_type, $object->member_name, $parent);
      while ($parent_class = db_fetch_object($result_parents)) {
        $parents[] = $parent_class->to_did;
        if (!empty($parent_class->class_did)) {
          $changed_classes[$parent_class->class_did] = TRUE;
        }
        if (!is_null($parent_class->did)) { // If documented
          if ($override['overrides_did'] === 0) {
            $override['overrides_did'] = $parent_class->did;
          }
          if ($override['documented_did'] === 0 && api_has_documentation($parent_class)) {
            $override['documented_did'] = $parent_class->did;
            // Save the inherited summary
            $inherited_summary = array(
              'summary' => $parent_class->summary,
              'did' => $object->did,
            );
            drupal_write_record('api_documentation', $inherited_summary, 'did');
          }
          $override['root_did'] = $parent_class->did;
        }
      }
    }
    drupal_write_record('api_overrides', $override);
  }

  // Save members
  while (list($class_did,) = each($changed_classes)) {
    // Add child classes to $changed_classes
    $result_chidren = db_query("SELECT ars.from_did FROM {api_reference_storage} ars WHERE ars.to_did = %d AND ars.object_type IN ('class', 'interface') AND ars.from_did <> 0", $class_did);
    while ($child = db_fetch_object($result_chidren)) {
      $changed_classes[$child->from_did] = TRUE;
    }
    // Walk up the tree to find members
    $members = array('');
    $parents = array($class_did);
    while ($parent = array_shift($parents)) {
      $result_parents = db_query("SELECT ars.to_did FROM {api_reference_storage} ars WHERE ars.from_did = %d AND ars.object_type IN ('class', 'interface') AND ars.to_did <> 0", $parent);
      while ($object = db_fetch_object($result_parents)) {
        $parents[] = $object->to_did;
      }
      $result_members = db_query("SELECT did, member_name FROM {api_documentation} WHERE class_did = %d AND member_name NOT IN (" . db_placeholders($members, 'text') . ")", array_merge(array($parent), array_keys($members)));
      while ($member = db_fetch_object($result_members)) {
        $members[$member->member_name] = $member->did;
      }
    }
    // Save them
    array_shift($members);
    db_query("DELETE FROM {api_members} WHERE class_did = %d", $class_did);
    foreach ($members as $did) {
      $api_member = array(
        'class_did' => $class_did,
        'did' => $did,
      );
      drupal_write_record('api_members', $api_member);
    }
  }

  // Save JSON autocomplete cache
  $directory = file_directory_path();
  if (is_dir($directory) && is_writable($directory) && (variable_get('file_downloads', FILE_DOWNLOADS_PUBLIC) == FILE_DOWNLOADS_PUBLIC)) {
    $path = file_create_path('api');
    file_check_directory($path, FILE_CREATE_DIRECTORY);
    $date = gmdate('U');
    foreach (api_get_branch_names() as $branch_name) {
      $new_json = api_autocomplete($branch_name, FALSE);

      $old_file_path = variable_get('api_autocomplete_path_' . $branch_name, FALSE);
      if ($old_file_path !== FALSE) {
        if (md5($new_json) === md5(file_get_contents($old_file_path))) {
          continue; // No changes, no file write.
        }
        // Delete in the future, help avoid race conditions.
        job_queue_add('file_delete', t('Remove expired API JSON, %path.'), array('%path' => $old_file_path));
      }

      $file_name = $path . '/api-' . $branch_name . '-' . $date . '.json';
      file_save_data($new_json, $file_name, FILE_EXISTS_REPLACE);
      variable_set('api_autocomplete_path_' . $branch_name, $file_name);
    }
  }

  cache_clear_all();
}

function api_has_documentation($object) {
  foreach (array('documentation', 'parameters', 'return_value', 'see', 'throws', 'var') as $member) {
    if (!empty($object->$member)) {
      return TRUE;
    }
  }
  return FALSE;
}

/**
 * Updates all branches, by calling their update functions.
 *
 * @see api_update_branch_php()
 * @see api_update_branch_files()
 */
function api_update_all_branches() {
  foreach (api_get_branches() as $branch) {
    $function = 'api_update_branch_' . $branch->type;
    $function($branch);
    watchdog('api', 'Updated %project branch %branch_name.', array('%branch_name' => $branch->branch_name, '%project' => $branch->project));
  }
}

/**
 * Updates a PHP branch.
 *
 * Queries the branch URL to get an updated list of functions, and saves each
 * function in the database.
 *
 * @see api_update_all_branches()
 */
function api_update_branch_php($branch) {
  $response = drupal_http_request($branch->summary);
  if ($response->code === '200') {
    $docblocks = array();
    preg_match_all('!^[a-zA-Z0-9_]+ ([a-zA-Z0-9_]+)\(.*\n.*$!m', $response->data, $function_matches, PREG_SET_ORDER);
    foreach ($function_matches as $function_match) {
      $docblocks[] = array(
        'branch' => $branch,
        'file_name' => $branch->summary,
        'object_type' => 'function',
        'object_name' => $function_match[1],
        'title' => $function_match[1],
        'documentation' => $function_match[0],
        'content' => '',
      );
    }
    api_save_documentation($docblocks);
  }
}

/**
 * Updates a files branch.
 *
 * Checks the current directories included in the branch to make an updated
 * list of files. Removes documentation from files that no longer exist, adds
 * documentation from new files, and updates documentation for any files that
 * have changed.
 *
 * @see api_update_all_branches()
 */
function api_update_branch_files($branch) {
  static $parse_functions = array(
    'php' => 'api_parse_php_file',
    'module' => 'api_parse_php_file',
    'inc' => 'api_parse_php_file',
    'install' => 'api_parse_php_file',
    'engine' => 'api_parse_php_file',
    'theme' => 'api_parse_php_file',
    'profile' => 'api_parse_php_file',

    'txt' => 'api_parse_text_file',

    'htm' => 'api_parse_html_file',
    'html' => 'api_parse_html_file',
  );

  // List all documented files for the branch.
  $files = array();
  $result = db_query("SELECT f.did, f.modified, d.object_name FROM {api_documentation} d INNER JOIN {api_file} f ON d.did = f.did WHERE d.branch_id = %d AND d.object_type = 'file'", $branch->branch_id);
  while ($file = db_fetch_object($result)) {
    $files[$file->object_name] = $file;
  }

  foreach (api_scan_directories($branch->directories, $branch->excluded_directories) as $path => $file_name) {
    preg_match('!\.([a-z]*)$!', $file_name, $matches);
    if (isset($matches[1]) && isset($parse_functions[$matches[1]])) {
      if (isset($files[$file_name])) {
        $parse = (filemtime($path) > $files[$file_name]->modified);
        unset($files[$file_name]); // All remaining files will be removed.
      }
      else { // New file.
        $parse = TRUE;
      }
      if ($parse) {
        job_queue_add('api_parse_file', t('API parse %branch %file'), array($parse_functions[$matches[1]], $path, $branch, '%file' => $file_name, '%branch' => $branch->branch_name), drupal_get_path('module', 'api') .'/parser.inc', TRUE);
      }
    }
  }

  // Remove outdated files.
  foreach (array_keys($files) as $file_name) {
    watchdog('api', 'Removing %file.', array('%file' => $file_name));
    $result = db_query("SELECT ad.did FROM {api_documentation} ad WHERE ad.file_name = '%s' AND ad.branch_id = %d", $file_name, $branch->branch_id);
    while ($doc = db_fetch_object($result)) {
      db_query("DELETE FROM {api_documentation} WHERE did = %d", $doc->did);
      db_query("DELETE FROM {api_file} WHERE did = %d", $doc->did);
      db_query("DELETE FROM {api_function} WHERE did = %d", $doc->did);
      db_query("DELETE FROM {api_reference_storage} WHERE from_did = %d OR to_did = %d", $doc->did, $doc->did);
    }
    api_schedule_shutdown();
  }
}

/**
 * Finds all the files in the directories specified for a branch.
 *
 * @param $directories
 *   List of directories to scan, as text (separated by newlines).
 * @param $excluded_directories
 *   List of directories to exclude, as text (separated by newlines).
 *
 * @return
 *   Associative array of files, where the keys are the full paths to the
 *   files and the values are the file names.
 */
function api_scan_directories($directories, $excluded_directories) {
  $directory_array = explode("\n", $directories);
  $excluded_array = explode("\n", $excluded_directories);

  if (count($directory_array) > 1) {
    $directories_components = array();
    foreach ($directory_array as $directory) {
      $directory_components = array();
      $parts = explode(DIRECTORY_SEPARATOR, $directory);
      foreach ($parts as $part) {
        if (strlen($part)) {
          array_unshift($directory_components, reset($directory_components) . DIRECTORY_SEPARATOR . $part);
        }
      }
      $directories_components[] = $directory_components;
    }

    $common_ancestor_components = call_user_func_array('array_intersect', $directories_components);
    $common_ancestor = reset($common_ancestor_components);
  }
  else {
    $common_ancestor = $directories;
  }

  $source_files = array();
  foreach ($directory_array as $directory) {
    $files = file_scan_directory($directory, '.*');
    foreach ($files as $path => $file) {
      if (strpos($path, '/.') !== FALSE) {
        continue;
      }
      $excluded = FALSE;
      // If the file is in an excluded path, ignore it
      foreach ($excluded_array as $excluded_path) {
        if (!empty($excluded_path) && (strpos($path, $excluded_path) === 0)) {
          $excluded = TRUE;
        }
      }
      if (!$excluded) {
        $file_name = substr($path, strlen($common_ancestor) + 1);
        $source_files[$path] = $file_name;
      }
    }
  }
  return $source_files;
}