fix(tools): enforce ID uniqueness in TODO store during replace operations

Deduplicate todo items by ID before writing to the store, keeping the
last occurrence. Prevents ghost entries when the model sends duplicate
IDs in a single write() call, which corrupts subsequent merge operations.

Co-authored-by: WAXLYY <WAXLYY@users.noreply.github.com>

tests/tools/test_todo_tool.py

@@ -24,6 +24,18 @@ class TestWriteAndRead:
         items[0]["content"] = "MUTATED"
         assert store.read()[0]["content"] == "Task"
 
+    def test_write_deduplicates_duplicate_ids(self):
+        store = TodoStore()
+        result = store.write([
+            {"id": "1", "content": "First version", "status": "pending"},
+            {"id": "2", "content": "Other task", "status": "pending"},
+            {"id": "1", "content": "Latest version", "status": "in_progress"},
+        ])
+        assert result == [
+            {"id": "2", "content": "Other task", "status": "pending"},
+            {"id": "1", "content": "Latest version", "status": "in_progress"},
+        ]
+
 
 class TestHasItems:
     def test_empty_store(self):

tools/todo_tool.py

@@ -46,11 +46,11 @@ class TodoStore:
         """
         if not merge:
             # Replace mode: new list entirely
-            self._items = [self._validate(t) for t in todos]
+            self._items = [self._validate(t) for t in self._dedupe_by_id(todos)]
         else:
             # Merge mode: update existing items by id, append new ones
             existing = {item["id"]: item for item in self._items}
-            for t in todos:
+            for t in self._dedupe_by_id(todos):
                 item_id = str(t.get("id", "")).strip()
                 if not item_id:
                     continue  # Can't merge without an id
@@ -143,6 +143,15 @@ class TodoStore:
 
         return {"id": item_id, "content": content, "status": status}
 
+    @staticmethod
+    def _dedupe_by_id(todos: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
+        """Collapse duplicate ids, keeping the last occurrence in its position."""
+        last_index: Dict[str, int] = {}
+        for i, item in enumerate(todos):
+            item_id = str(item.get("id", "")).strip() or "?"
+            last_index[item_id] = i
+        return [todos[i] for i in sorted(last_index.values())]
+
 
 def todo_tool(
     todos: Optional[List[Dict[str, Any]]] = None,