Introduce hook_settings() for themes

We're seeing this as well.

I think it's important to resolve this quickly, as people are now beginning to write D7 themes with custom settings, and the resolution might break their code. For example see http://drupal.org/node/177868#comment-4191174

In case it's helpful, here's the exact places the SUBTHEME_form_theme_settings_alter() is being run twice.

First in system.admin.inc:562, in system_theme_settings() :

// Process the theme and all its base themes.
foreach ($theme_keys as $theme) {
  // Include the theme-settings.php file.
  $filename = DRUPAL_ROOT . '/' . str_replace("/$theme.info", '', $themes[$theme]->filename) . '/theme-settings.php';
  if (file_exists($filename)) {
    require_once $filename;
  }

  // Call theme-specific settings.
  $function = $theme . '_form_system_theme_settings_alter';
  if (function_exists($function)) {
    $function($form, $form_state);
  }
}

And again in includes/form.inc:1040, in drupal_prepare_form ():

// Invoke hook_form_alter(), hook_form_BASE_FORM_ID_alter(), and
// hook_form_FORM_ID_alter() implementations.
$hooks = array('form');
if (isset($form_state['build_info']['base_form_id'])) {
  $hooks[] = 'form_' . $form_state['build_info']['base_form_id'];
}
$hooks[] = 'form_' . $form_id;
//$hooks == array('form','form_system_theme_settings');
drupal_alter($hooks, $form, $form_state, $form_id);

And some potentially relevant threads:

http://drupal.org/node/481142#comment-2525928
http://drupal.org/node/563708

Is this the same bug as #943212: hook_form_system_theme_settings_alter() vs. THEME_form_system_theme_settings_alter() name-clash

This is - obviously - a major API change and can only be considered for D8+.