I think I’ve fixed it on my installation, but would be interesting to see if it’s the same for anyone else. Basically I did a clean install on my localhost machine and ran through all the proposed solutions.
Eventually got to replacing the connectors directory as suggested by Bob and clearing the cache which fixed it, so I ran a diff on that directory between the clean install and the upgrade. There were two file differences,
First was connectors/layout/mod.config.js.php
The upgrade version
<?php
define('MODX_REQP',false);
require_once dirname(dirname(__FILE__)).'/index.php';
$_SERVER['HTTP_MODAUTH'] = $modx->site_id;
$modx->request->handleRequest(array('location' => 'system','action' => 'config.js'));
Whereas the clean install file is
<?php
define('MODX_REQP',false);
require_once dirname(dirname(__FILE__)).'/index.php';
$_SERVER['HTTP_MODAUTH'] = $_SESSION["modx.{$modx->context->get('key')}.user.token"];
$modx->request->handleRequest(array('location' => 'system','action' => 'config.js'));
There was a similar difference in connectors/system/phpthump.php
So I changed the two files on my upgrade site
mod.config.js.php
<?php
define('MODX_REQP',false);
require_once dirname(dirname(__FILE__)).'/index.php';
/*$_SERVER['HTTP_MODAUTH'] = $modx->site_id;*/
$_SERVER['HTTP_MODAUTH'] = $_SESSION["modx.{$modx->context->get('key')}.user.token"];
$modx->request->handleRequest(array('location' => 'system','action' => 'config.js'));
and phpthumb.php
<?php
require_once dirname(dirname(__FILE__)).'/index.php';
/*$_SERVER['HTTP_MODAUTH'] = $modx->site_id;*/
$_SERVER['HTTP_MODAUTH'] = $_SESSION["modx.{$modx->context->get('key')}.user.token"];
$modx->request->handleRequest(array('location' => 'system','action' => 'phpthumb'));
I cleared the cache and reloaded the manager and lo and behold the navigation tree appears and works as expected.
So I’d be interested to know if this fixes for the other reported problems.
I don’t really know how the upgrade modifies these files, so I’m not sure whether it’s something wrong with my setup or is it something that needs filing as a bug?
Anyway I hope this helps.
Adrian