Integrating menus, taxonomy, sections, roles and permissions

I didn't think of this. This may do the trick. I'll try this out and report back with code

This snippet out put terms and related nodes as nested html lists.
Essentially this lets me create a hierarchy with one master taxonomy vocabulary listing each term and all the nodes in a term sorted by weight. It seems this functionality should be built in but at least Drupal has the flexibility to allow a php hack like this.

<?php
    $vocabulary_id = 4; // vocabulary id for the "master" category 
    $result = db_query("SELECT d.tid, d.name, d.weight  FROM {term_data} d INNER JOIN {term_node} USING (tid) INNER JOIN {node} n USING (nid) WHERE d.vid = $vocabulary_id AND n.status = 1 GROUP BY d.tid, d.name ORDER BY d.weight");
    $items = array();
    $sub_items = array();
    
    while ($category = db_fetch_object($result)) {
        $output .= "<ul>"; // for term list
        $output .= "<li>" . l($category->name, 'taxonomy/term/'. $category->tid) . "</li>";
        $output .= "<ul>"; // for nodes list
        // call function to find all nodes in a term 
        $sub_items = get_nodes_in_term($category->tid);
        // Add nodes to items array
        foreach($sub_items as $val)   {
            $output .= $val;
        }
      $output .= "</ul></li></ul>";   
    }
    print $output;


    function get_nodes_in_term($tid)    {
        $sub_items = array();
        $sql = "SELECT node.title, node.nid FROM node INNER JOIN term_node ON node.nid = term_node.nid WHERE term_node.tid = $tid ";
        $result = db_query($sql);
        while ($anode = db_fetch_object($result)) {
            $sub_items[] = "<li>" . l($anode->title, "node/$anode->nid") . "</li>";
        }
    return $sub_items;
    }
?>