fix: preserve config during non-interactive defaults onboarding

Maintainer edit: make explicit --defaults refresh existing configs without prompting when no TTY is available, preserving user values for CI and Docker runs.

docs/cli-reference.md

@@ -8,7 +8,7 @@ Use this page when you know what you want to run and need the command shape. For
 |---|---|---|
 | Check the install | `nanobot --version` | If this fails, try `python -m nanobot --version` |
 | Use guided setup | `nanobot onboard` | Best when you prefer prompts over hand-editing JSON |
-| Create or refresh defaults | `nanobot onboard --defaults` | Creates `~/.nanobot/config.json` and `~/.nanobot/workspace/` without prompts |
+| Create or refresh defaults | `nanobot onboard --defaults` | Creates `~/.nanobot/config.json` and `~/.nanobot/workspace/` without the wizard |
 | Check config without calling a model | `nanobot status` | Reads the default config and summarizes the active model/provider |
 | Send one test message | `nanobot agent -m "Hello!"` | First proof that install, config, provider, model, and workspace all work |
 | Chat in the terminal | `nanobot agent` | Interactive local chat; exit with `exit`, `/exit`, `:q`, or `Ctrl+D` |
@@ -53,11 +53,13 @@ Long-running commands keep working until you stop them. Press `Ctrl+C` in that t
 | Command | Description |
 |---|---|
 | `nanobot onboard` | Use the interactive setup wizard |
-| `nanobot onboard --defaults` | Initialize or refresh the default config and workspace without prompts |
+| `nanobot onboard --defaults` | Initialize or refresh the default config and workspace without the wizard |
-| `nanobot onboard --defaults --config <path> --workspace <path>` | Initialize or refresh a specific instance without prompts |
+| `nanobot onboard --defaults --config <path> --workspace <path>` | Initialize or refresh a specific instance without the wizard |
 
 Without `--defaults`, `nanobot onboard` opens the wizard only when stdin and stdout are attached to a terminal. In scripts, CI, and Docker non-TTY runs, it falls back to the defaults setup.
 
+When `--defaults` refreshes an existing config in scripts, CI, or Docker non-TTY runs, it preserves existing values without prompting. In an interactive terminal, nanobot still asks before replacing an existing config with fresh defaults.
+
 Default paths:
 
 | Path | Default |

nanobot/cli/commands.py

@@ -452,9 +452,11 @@ def onboard(
     from nanobot.config.loader import get_config_path, load_config, save_config, set_config_path
     from nanobot.config.schema import Config
 
+    can_prompt = _onboard_can_prompt()
     wants_wizard = wizard or not defaults
-    use_wizard = wants_wizard and not defaults and _onboard_can_prompt()
+    use_wizard = wants_wizard and not defaults and can_prompt
     default_fallback = wants_wizard and not use_wizard and not defaults
+    default_refresh_without_prompt = defaults and not can_prompt
     if default_fallback:
         console.print(
             "[yellow]No interactive terminal detected; using --defaults setup instead.[/yellow]"
@@ -476,7 +478,7 @@ def onboard(
     if config_path.exists():
         if use_wizard:
             config = _apply_workspace_override(load_config(config_path))
-        elif default_fallback:
+        elif default_fallback or default_refresh_without_prompt:
             config = _apply_workspace_override(load_config(config_path))
             save_config(config, config_path)
             console.print(

tests/cli/test_commands.py

@@ -108,10 +108,11 @@ def test_onboard_fresh_install(mock_paths):
     assert mock_ws.call_args.args == (expected_workspace,)
 
 
-def test_onboard_existing_config_refresh(mock_paths):
+def test_onboard_existing_config_refresh(mock_paths, monkeypatch):
     """Config exists, user declines overwrite — should refresh (load-merge-save)."""
     config_file, workspace_dir, _ = mock_paths
     config_file.write_text('{"existing": true}')
+    monkeypatch.setattr("nanobot.cli.commands._onboard_can_prompt", lambda: True)
 
     result = runner.invoke(app, ["onboard", "--defaults"], input="n\n")
 
@@ -136,10 +137,46 @@ def test_onboard_non_tty_existing_config_refreshes_without_prompt(mock_paths):
     assert workspace_dir.exists()
 
 
-def test_onboard_existing_config_overwrite(mock_paths):
+def test_onboard_defaults_non_tty_existing_config_preserves_values_without_prompt(
+    tmp_path, monkeypatch
+):
+    """Explicit --defaults should refresh existing configs without prompts outside a TTY."""
+    config_path = tmp_path / "config.json"
+    workspace_path = tmp_path / "workspace"
+    config_path.write_text(
+        json.dumps({"agents": {"defaults": {"model": "custom/keep"}}}),
+        encoding="utf-8",
+    )
+
+    monkeypatch.setattr("nanobot.cli.commands._onboard_can_prompt", lambda: False)
+    monkeypatch.setattr("nanobot.channels.registry.discover_all", lambda: {})
+
+    result = runner.invoke(
+        app,
+        [
+            "onboard",
+            "--defaults",
+            "--config",
+            str(config_path),
+            "--workspace",
+            str(workspace_path),
+        ],
+    )
+
+    assert result.exit_code == 0
+    assert "Config already exists" not in result.stdout
+    assert "Overwrite?" not in result.stdout
+    assert "existing values preserved" in result.stdout
+    saved = Config.model_validate(json.loads(config_path.read_text(encoding="utf-8")))
+    assert saved.agents.defaults.model == "custom/keep"
+    assert saved.workspace_path == workspace_path
+
+
+def test_onboard_existing_config_overwrite(mock_paths, monkeypatch):
     """Config exists, user confirms overwrite — should reset to defaults."""
     config_file, workspace_dir, _ = mock_paths
     config_file.write_text('{"existing": true}')
+    monkeypatch.setattr("nanobot.cli.commands._onboard_can_prompt", lambda: True)
 
     result = runner.invoke(app, ["onboard", "--defaults"], input="y\n")
 
@@ -149,11 +186,12 @@ def test_onboard_existing_config_overwrite(mock_paths):
     assert workspace_dir.exists()
 
 
-def test_onboard_existing_workspace_safe_create(mock_paths):
+def test_onboard_existing_workspace_safe_create(mock_paths, monkeypatch):
     """Workspace exists — should not recreate, but still add missing templates."""
     config_file, workspace_dir, _ = mock_paths
     workspace_dir.mkdir(parents=True)
     config_file.write_text("{}")
+    monkeypatch.setattr("nanobot.cli.commands._onboard_can_prompt", lambda: True)
 
     result = runner.invoke(app, ["onboard", "--defaults"], input="n\n")