diff --git a/internal/sidekick/internal/config/config.go b/internal/sidekick/internal/config/config.go
index b94363c9a5..bc1acc6089 100644
--- a/internal/sidekick/internal/config/config.go
+++ b/internal/sidekick/internal/config/config.go
@@ -66,10 +66,11 @@ type Config struct {
 // GeneralConfig contains configuration parameters that affect Parsers and Codecs, including the
 // selection of parser and codec.
 type GeneralConfig struct {
-	Language            string `toml:"language,omitempty"`
-	SpecificationFormat string `toml:"specification-format,omitempty"`
-	SpecificationSource string `toml:"specification-source,omitempty"`
-	ServiceConfig       string `toml:"service-config,omitempty"`
+	Language            string   `toml:"language,omitempty"`
+	SpecificationFormat string   `toml:"specification-format,omitempty"`
+	SpecificationSource string   `toml:"specification-source,omitempty"`
+	ServiceConfig       string   `toml:"service-config,omitempty"`
+	IgnoredDirectories  []string `toml:"ignored-directories,omitempty"`
 }
 
 // LoadConfig loads the top-level configuration file and validates its contents.
@@ -130,6 +131,7 @@ func mergeConfigs(rootConfig, local *Config) (*Config, error) {
 		General: GeneralConfig{
 			Language:            rootConfig.General.Language,
 			SpecificationFormat: rootConfig.General.SpecificationFormat,
+			IgnoredDirectories:  rootConfig.General.IgnoredDirectories,
 		},
 		Source:           map[string]string{},
 		Codec:            map[string]string{},
diff --git a/internal/sidekick/internal/config/config_test.go b/internal/sidekick/internal/config/config_test.go
index e9a4db346b..b8e10479ca 100644
--- a/internal/sidekick/internal/config/config_test.go
+++ b/internal/sidekick/internal/config/config_test.go
@@ -69,6 +69,7 @@ func TestLoadRootConfig(t *testing.T) {
 		General: GeneralConfig{
 			Language:            "root-language",
 			SpecificationFormat: "root-specification-format",
+			IgnoredDirectories:  []string{"a", "b"},
 		},
 		Source: map[string]string{
 			"s1": "v1",
@@ -101,6 +102,7 @@ func TestMergeLocalForGeneral(t *testing.T) {
 		General: GeneralConfig{
 			Language:            "root-language",
 			SpecificationFormat: "root-specification-format",
+			IgnoredDirectories:  []string{"a", "b"},
 		},
 	}
 
@@ -123,6 +125,7 @@ func TestMergeLocalForGeneral(t *testing.T) {
 			SpecificationFormat: "local-specification-format",
 			SpecificationSource: "local-specification-source",
 			ServiceConfig:       "local-service-config",
+			IgnoredDirectories:  []string{"a", "b"},
 		},
 		Codec:  map[string]string{},
 		Source: map[string]string{},
diff --git a/internal/sidekick/refreshall.go b/internal/sidekick/refreshall.go
index 1990a46bf1..d6a302ffd8 100644
--- a/internal/sidekick/refreshall.go
+++ b/internal/sidekick/refreshall.go
@@ -22,6 +22,7 @@ import (
 	"os"
 	"path"
 	"path/filepath"
+	"slices"
 	"strings"
 	"sync"
 
@@ -68,7 +69,7 @@ func refreshAll(rootConfig *config.Config, cmdLine *CommandLine) error {
 	if err != nil {
 		return err
 	}
-	directories, err := findAllDirectories()
+	directories, err := findAllDirectories(override)
 	if err != nil {
 		return err
 	}
@@ -104,28 +105,18 @@ func refreshAll(rootConfig *config.Config, cmdLine *CommandLine) error {
 	return errors.Join(failures...)
 }
 
-func findAllDirectories() ([]string, error) {
+func findAllDirectories(config *config.Config) ([]string, error) {
 	var result []string
 	err := fs.WalkDir(os.DirFS("."), ".", func(path string, d fs.DirEntry, _ error) error {
 		if d.IsDir() {
 			return nil
 		}
-		dir := filepath.Dir(path)
-
-		// TODO(https://github.com/googleapis/librarian/issues/1563): do not
-		// harcode
-		if dir == "dart" {
-			return nil
-		}
-		ignored := []string{
-			"dart/",           // Testing
-			"target/package/", // The output from `cargo package`
-		}
-		for _, candidate := range ignored {
-			if strings.Contains(dir, candidate) {
+		for _, ignore := range config.General.IgnoredDirectories {
+			if isInPath(ignore, path) {
 				return nil
 			}
 		}
+		dir := filepath.Dir(path)
 		if d.Name() == ".sidekick.toml" && dir != "." {
 			result = append(result, dir)
 		}
@@ -136,3 +127,8 @@ func findAllDirectories() ([]string, error) {
 	}
 	return result, nil
 }
+
+func isInPath(dir, path string) bool {
+	components := strings.Split(path, string(filepath.Separator))
+	return slices.Contains(components, dir)
+}
diff --git a/internal/sidekick/refreshall_test.go b/internal/sidekick/refreshall_test.go
index 3e25c1153d..9b708e73d6 100644
--- a/internal/sidekick/refreshall_test.go
+++ b/internal/sidekick/refreshall_test.go
@@ -21,3 +21,26 @@ func TestRefreshAll(t *testing.T) {
 		t.Fatal(err)
 	}
 }
+
+func TestIsInPath(t *testing.T) {
+	type TestCase struct {
+		Dir  string
+		Path string
+		Want bool
+	}
+	testCases := []TestCase{
+		{"dart", "dart", true},
+		{"dart", "dartboard", false},
+		{"dart", "dart/v2", true},
+		{"dart", "dart/v2/d2/d4", true},
+		{"dart", "a/b/c/d/dart/v2/d2/d4", true},
+		{"generator", "dart/v2", false},
+		{"generator", "generator/", true},
+	}
+	for _, test := range testCases {
+		got := isInPath(test.Dir, test.Path)
+		if got != test.Want {
+			t.Errorf("got (%v) != want (%v) for %q in %q", got, test.Want, test.Dir, test.Path)
+		}
+	}
+}