Fix Config Loading + Base Dirs CLI Flag

cmd/bagel/scan.go

@@ -23,6 +23,7 @@ var (
 	strict       bool
 	noCache      bool
 	noProgress   bool
+	baseDirs     []string
 )
 
 // scanCmd represents the scan command
@@ -42,6 +43,9 @@ func init() {
 	scanCmd.Flags().BoolVar(&strict, "strict", false, "exit with code 2 if any findings are detected")
 	scanCmd.Flags().BoolVar(&noCache, "no-cache", false, "bypass file index cache and force rebuild")
 	scanCmd.Flags().BoolVar(&noProgress, "no-progress", false, "disable progress bars")
+	scanCmd.Flags().StringSliceVar(&baseDirs, "base-dirs", nil,
+		"comma-separated directories to scan; overrides file_index.base_dirs. "+
+			"e.g. --base-dirs /home,/Users,/root")
 }
 
 func runScan(cmd *cobra.Command, args []string) error {
@@ -55,6 +59,12 @@ func runScan(cmd *cobra.Command, args []string) error {
 		return fmt.Errorf("failed to load config: %w", err)
 	}
 
+	// --base-dir takes precedence over config/defaults
+	if len(baseDirs) > 0 {
+		cfg.FileIndex.BaseDirs = baseDirs
+		log.Debug().Strs("base_dirs", baseDirs).Msg("Overriding base dirs from --base-dirs")
+	}
+
 	log.Debug().Msg("Starting scan")
 
 	// Initialize probes

pkg/config/config.go

@@ -37,13 +37,19 @@ func Load(configPath string) (*models.Config, error) {
 	v.SetEnvPrefix("BAGEL")
 	v.AutomaticEnv()
 
-	// Read config file if it exists
+	// Read config file if it exists.
+	// A missing or unreadable config must never block a scan
 	if err := v.ReadInConfig(); err != nil {
 		var configFileNotFoundError viper.ConfigFileNotFoundError
-		if !errors.As(err, &configFileNotFoundError) {
-			return nil, fmt.Errorf("failed to read config file: %w", err)
+		switch {
+		case errors.As(err, &configFileNotFoundError):
+			log.Debug().Msg("config: no config file found; using built-in defaults")
+		case configPath != "":
+			return nil, fmt.Errorf("failed to read config file %q: %w", configPath, err)
+		default:
+			log.Warn().Err(err).Msg(
+				"config: could not read a discovered config file; using built-in defaults")
 		}
-		// Config file not found is OK, we'll use defaults
 	}
 
 	// Unmarshal config

pkg/config/config_test.go

@@ -67,3 +67,44 @@ func TestLoad_DefaultsEnableBothAIProbes(t *testing.T) {
 	assert.True(t, cfg.Probes.AICredentials.Enabled)
 	assert.True(t, cfg.Probes.AIChats.Enabled)
 }
+
+// TestLoad_NoConfigFileUsesDefaults verifies that when auto-discovery finds no
+// config file, Load succeeds with built-in defaults — every probe enabled and
+// the file-index patterns populated.
+func TestLoad_NoConfigFileUsesDefaults(t *testing.T) {
+	t.Setenv("HOME", t.TempDir()) // empty home, no bagel.yaml
+	t.Chdir(t.TempDir())          // empty cwd, no bagel.yaml on "." path
+
+	cfg, err := Load("")
+	require.NoError(t, err)
+	require.NotNil(t, cfg)
+
+	assert.True(t, cfg.Probes.Git.Enabled)
+	assert.True(t, cfg.Probes.Cloud.Enabled)
+	assert.NotEmpty(t, cfg.FileIndex.Patterns)
+}
+
+// TestLoad_DiscoveredConfigUnusableFallsBack verifies that when auto-discovery
+// cannot turn up a usable config file, Load does not abort the scan: it falls
+// back to defaults instead of erroring.
+func TestLoad_DiscoveredConfigUnusableFallsBack(t *testing.T) {
+	dir := t.TempDir()
+	// A directory named bagel.yaml means there's no readable config file to
+	// load, standing in for an absent/inaccessible config under auto-discovery.
+	require.NoError(t, os.Mkdir(filepath.Join(dir, "bagel.yaml"), 0o755))
+	t.Chdir(dir)
+
+	cfg, err := Load("")
+	require.NoError(t, err)
+	require.NotNil(t, cfg)
+	assert.True(t, cfg.Probes.Git.Enabled)
+}
+
+// TestLoad_ExplicitConfigFailsLoudly verifies the opposite contract: when the
+// user explicitly names a --config file that cannot be read, Load returns an
+// error rather than silently using defaults.
+func TestLoad_ExplicitConfigFailsLoudly(t *testing.T) {
+	missing := filepath.Join(t.TempDir(), "does-not-exist.yaml")
+	_, err := Load(missing)
+	require.Error(t, err)
+}