If you would like to hide particular documents in the tree, you can do so without assigning them to Resource Groups if you would like to hide them from all users, including the Admin. This will give your MODx manager that fully custom touch.
For instance, say your site has a site wide configuration page, for multiple sites using a template database, and you moved the link to the top menu with a custom title rather than having it in the document tree alongside all your pages. You’d simply add the following line into your "manager>frames>menu.php" under Site Menu after one of the other options (you can specify whether it shows up for admins with proper permissions only or publicly)...
// siteconfig
$sitemenu[] = ’<li><a onclick="this.blur();" href="index.php?a=27&id=1" target="main">Title of Link Goes Here</a></li>’;
The 27 represents the edit resource function and the 1 represents the document ID. Be sure to specify what document you’d like to show up in the menu.
After this, you can remove the page from being seen in the tree by editing the CSS in "manager>media>style>MODXCarbon>style.css" and adding:
#node1 {display:none;} (the 1 is an example of the document ID... in my case is was the first document for the site.)
NOTE: Be sure and keep a backup of both files before editing!
