feat(api): maintain assistant content parts and file handling in advanced chat (#24663)

Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com>

api/factories/file_factory.py

@@ -41,8 +41,14 @@ def build_from_message_file(
         "url": message_file.url,
         "id": message_file.id,
         "type": message_file.type,
-        "upload_file_id": message_file.upload_file_id,
     }
+
+    # Set the correct ID field based on transfer method
+    if message_file.transfer_method == FileTransferMethod.TOOL_FILE.value:
+        mapping["tool_file_id"] = message_file.upload_file_id
+    else:
+        mapping["upload_file_id"] = message_file.upload_file_id
+
     return build_from_mapping(
         mapping=mapping,
         tenant_id=tenant_id,
@@ -318,6 +324,11 @@ def _is_file_valid_with_config(
     file_transfer_method: FileTransferMethod,
     config: FileUploadConfig,
 ) -> bool:
+    # FIXME(QIN2DIM): Always allow tool files (files generated by the assistant/model)
+    # These are internally generated and should bypass user upload restrictions
+    if file_transfer_method == FileTransferMethod.TOOL_FILE:
+        return True
+
     if (
         config.allowed_file_types
         and input_file_type not in config.allowed_file_types