Preserve source code formatting - Geshi

I read a lot about problems where ckeditor removes geshi tags.
The solution to stop that is adding this to the config.js in the root folder of ckeditor

 // do not touch code inside of <foo></foo> and [foo] [/foo]
   config.protectedSource.push( %\[.*\].*\[/.*\]%i );
   config.protectedSource.push( %\<.*\>.*\</.*\>%i );

That works and the correct geshi highlighting is applied.

Somehow there is another problem left. If you switch from source view to normal view. It will kill all formatting of tha code. Example code

/**
 * @file
 * Integrates client-side editors with Drupal.
 */

/**
 * Implements hook_entity_info().
 */
function wysiwyg_entity_info() {
  $types['wysiwyg_profile'] = array(
    'label' => t('Wysiwyg profile'),
    'base table' => 'wysiwyg',
    'controller class' => 'WysiwygProfileController',
    'fieldable' => FALSE,
    // When loading all entities, DrupalDefaultEntityController::load() ignores
    // its static cache. Therefore, wysiwyg_profile_load_all() implements a
    // custom static cache.
    'static cache' => FALSE,
    'entity keys' => array(
      'id' => 'format',
    ),
  );
  return $types;
}

will become:

/** * Implements hook_entity_info(). */ function wysiwyg_entity_info() { $types['wysiwyg_profile'] = array( 'label' => t('Wysiwyg profile'), 'base table' => 'wysiwyg', 'controller class' => 'WysiwygProfileController', 'fieldable' => FALSE, // When loading all entities, DrupalDefaultEntityController::load() ignores // its static cache. Therefore, wysiwyg_profile_load_all() implements a // custom static cache. 'static cache' => FALSE, 'entity keys' => array( 'id' => 'format', ), ); return $types; } 

so it seems the protected source config tag works not for the formatting options so i think it is neccessary to use: http://docs.cksource.com/CKEditor_3.x/Developers_Guide/Output_Formatting

as of another post it seems that the ckeditor-3.0.js needs to be hacked to prevent the reformatting between the geshi tags (only guessing)

opinions? i will post the solution if i find one.