fix(config): revised config methods

- `write_file` requires an destination file path
- `read_config` -> `merge_from_file`, if no path is provided, reads from `self.init_file_path`
- update app, tests to use new methods
- fix configurator, was overwriting config file data unexpectedly

invokeai/backend/install/invokeai_configure.py

@@ -711,7 +711,8 @@ def run_console_ui(
 ) -> Tuple[Optional[Namespace], Optional[InstallSelections]]:
     first_time = not (config.root_path / "invokeai.yaml").exists()
     invokeai_opts = default_startup_options(initfile) if first_time else config
-    invokeai_opts.set_root(program_opts.root)
+    if program_opts.root:
+        invokeai_opts.set_root(Path(program_opts.root))
 
     if not set_min_terminal_size(MIN_COLS, MIN_LINES):
         raise WindowTooSmallException(
@@ -731,15 +732,13 @@ def write_opts(opts: InvokeAIAppConfig, init_file: Path) -> None:
     """
     Update the invokeai.yaml file with values from current settings.
     """
-    # this will load current settings
     new_config = get_config()
     new_config.set_root(config.root_path)
 
-    for key, value in vars(opts).items():
-        if hasattr(new_config, key):
-            setattr(new_config, key, value)
-
-    new_config.write_file(exclude_defaults=True)
+    # Remove any fields that are not in the model_fields list, like `hf_token`
+    cleaned_opts = {k: v for k, v in vars(opts).items() if k in new_config.model_fields}
+    new_config.update_config(cleaned_opts)
+    new_config.write_file(init_file)
 
     if hasattr(opts, "hf_token") and opts.hf_token:
         HfLogin(opts.hf_token)
@@ -819,12 +818,13 @@ def main() -> None:
         help="path to root of install directory",
     )
     opt = parser.parse_args()
-    invoke_args: dict[str, Any] = {}
+    updates: dict[str, Any] = {}
     if opt.root:
-        invoke_args["root"] = opt.root
+        config.set_root(Path(opt.root))
     if opt.full_precision:
-        invoke_args["precision"] = "float32"
-    config.update_config(invoke_args)
+        updates["precision"] = "float32"
+    config.merge_from_file()
+    config.update_config(updates)
     logger = InvokeAILogger().get_logger(config=config)
 
     errors = set()