Maybe the update stuff is fixed now.

markdown_sqlite.py

@@ -9,6 +9,7 @@ reflects the current state of the markdown file.
 
 import os
 import sqlite3
+import uuid
 import hashlib
 import argparse
 import logging
@@ -168,6 +169,7 @@ class MarkdownProcessor:
         ''', (document_id,))
         for heading_id, level, title, parent_id, content in self.db_manager.cursor.fetchall():
             structure[heading_id] = {
+                'id': heading_id,  # Add this line to include the id in each node
                 'level': level,
                 'title': title,
                 'parent_id': parent_id,
@@ -175,13 +177,10 @@ class MarkdownProcessor:
                 'children': []
             }
         # Build the tree structure
-        root = {}
         for id, node in structure.items():
             if node['parent_id'] in structure:
                 structure[node['parent_id']]['children'].append(id)
-            else:
-                root[id] = node
-        return root
+        return structure 
 
     def parse_new_structure(self, tokens: List) -> Dict:
         structure = {}