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To use a custom hook_menu() path on your Drupal site to provide data for an autocomplete, try something like this:

Drupal Module

Place this code into your custom Drupal module:

/**
 * Implements hook_menu().
 */
function my_module_menu() {
 $items['example/autocomplete'] = array(
    'page callback' => '_my_module_autocomplete',
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK
  );
  return $items;
}

Then implement the page callback function in the module:

function _my_module_autocomplete() {
  $title = $_GET['title'];
  $limit = $_GET['limit'] ? $_GET['limit'] : 10;
  $results = db_select('node', 'n')
    ->fields('n', array('nid', 'title'))
    ->condition('title', db_like($title) . '%', 'LIKE')
    ->condition('type', 'article')
    ->range(0, $limit)
    ->execute()
    ->fetchAll();
  drupal_json_output($results);
  drupal_exit();
}

Note, your page callback must return an array of objects, similar to the output provided above, which would look something like this:

[{"nid":"176","title":"Hello World"},{"nid":"207","title":"How to Drupal"}]

App

Place this code into your custom DrupalGap module to create a custom page:

/**
 * Implements hook_menu().
 */
function my_module_menu() {
  var items = {};
  items['my_autocomplete'] = {
    title: 'Autocomplete',
    page_callback: 'my_module_autocomplete_page'
  };
  return items;
}

Then implement the page callback:

/**
 * My autocomplete page callback.
 */
function my_module_autocomplete_page() {
  try {
    var content = {};
    content.my_autocomplete = {
      theme: 'autocomplete',
      remote: true,
      custom: true,
      path: 'example/autocomplete',
      value: 'nid',
      label: 'title',
      filter: 'title',
      params: 'limit=5'
    };
    return content;
  }
  catch (error) { console.log('my_module_autocomplete_page - ' + error); }
}

Notice how we set custom to true, and pass along additional parameters using param.

This code produces an autocomplete that functions identically to the Autocomplete with Remote Views JSON Data example.