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diff --git a/packages/cli/src/utils/settingsUtils.ts b/packages/cli/src/utils/settingsUtils.ts
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+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { Settings, SettingScope, LoadedSettings } from '../config/settings.js';
+import {
+  SETTINGS_SCHEMA,
+  SettingDefinition,
+  SettingsSchema,
+} from '../config/settingsSchema.js';
+
+// The schema is now nested, but many parts of the UI and logic work better
+// with a flattened structure and dot-notation keys. This section flattens the
+// schema into a map for easier lookups.
+
+function flattenSchema(
+  schema: SettingsSchema,
+  prefix = '',
+): Record<string, SettingDefinition & { key: string }> {
+  let result: Record<string, SettingDefinition & { key: string }> = {};
+  for (const key in schema) {
+    const newKey = prefix ? `${prefix}.${key}` : key;
+    const definition = schema[key];
+    result[newKey] = { ...definition, key: newKey };
+    if (definition.properties) {
+      result = { ...result, ...flattenSchema(definition.properties, newKey) };
+    }
+  }
+  return result;
+}
+
+const FLATTENED_SCHEMA = flattenSchema(SETTINGS_SCHEMA);
+
+/**
+ * Get all settings grouped by category
+ */
+export function getSettingsByCategory(): Record<
+  string,
+  Array<SettingDefinition & { key: string }>
+> {
+  const categories: Record<
+    string,
+    Array<SettingDefinition & { key: string }>
+  > = {};
+
+  Object.values(FLATTENED_SCHEMA).forEach((definition) => {
+    const category = definition.category;
+    if (!categories[category]) {
+      categories[category] = [];
+    }
+    categories[category].push(definition);
+  });
+
+  return categories;
+}
+
+/**
+ * Get a setting definition by key
+ */
+export function getSettingDefinition(
+  key: string,
+): (SettingDefinition & { key: string }) | undefined {
+  return FLATTENED_SCHEMA[key];
+}
+
+/**
+ * Check if a setting requires restart
+ */
+export function requiresRestart(key: string): boolean {
+  return FLATTENED_SCHEMA[key]?.requiresRestart ?? false;
+}
+
+/**
+ * Get the default value for a setting
+ */
+export function getDefaultValue(key: string): SettingDefinition['default'] {
+  return FLATTENED_SCHEMA[key]?.default;
+}
+
+/**
+ * Get all setting keys that require restart
+ */
+export function getRestartRequiredSettings(): string[] {
+  return Object.values(FLATTENED_SCHEMA)
+    .filter((definition) => definition.requiresRestart)
+    .map((definition) => definition.key);
+}
+
+/**
+ * Recursively gets a value from a nested object using a key path array.
+ */
+function getNestedValue(obj: Record<string, unknown>, path: string[]): unknown {
+  const [first, ...rest] = path;
+  if (!first || !(first in obj)) {
+    return undefined;
+  }
+  const value = obj[first];
+  if (rest.length === 0) {
+    return value;
+  }
+  if (value && typeof value === 'object' && value !== null) {
+    return getNestedValue(value as Record<string, unknown>, rest);
+  }
+  return undefined;
+}
+
+/**
+ * Get the effective value for a setting, considering inheritance from higher scopes
+ * Always returns a value (never undefined) - falls back to default if not set anywhere
+ */
+export function getEffectiveValue(
+  key: string,
+  settings: Settings,
+  mergedSettings: Settings,
+): SettingDefinition['default'] {
+  const definition = getSettingDefinition(key);
+  if (!definition) {
+    return undefined;
+  }
+
+  const path = key.split('.');
+
+  // Check the current scope's settings first
+  let value = getNestedValue(settings as Record<string, unknown>, path);
+  if (value !== undefined) {
+    return value as SettingDefinition['default'];
+  }
+
+  // Check the merged settings for an inherited value
+  value = getNestedValue(mergedSettings as Record<string, unknown>, path);
+  if (value !== undefined) {
+    return value as SettingDefinition['default'];
+  }
+
+  // Return default value if no value is set anywhere
+  return definition.default;
+}
+
+/**
+ * Get all setting keys from the schema
+ */
+export function getAllSettingKeys(): string[] {
+  return Object.keys(FLATTENED_SCHEMA);
+}
+
+/**
+ * Get settings by type
+ */
+export function getSettingsByType(
+  type: SettingDefinition['type'],
+): Array<SettingDefinition & { key: string }> {
+  return Object.values(FLATTENED_SCHEMA).filter(
+    (definition) => definition.type === type,
+  );
+}
+
+/**
+ * Get settings that require restart
+ */
+export function getSettingsRequiringRestart(): Array<
+  SettingDefinition & {
+    key: string;
+  }
+> {
+  return Object.values(FLATTENED_SCHEMA).filter(
+    (definition) => definition.requiresRestart,
+  );
+}
+
+/**
+ * Validate if a setting key exists in the schema
+ */
+export function isValidSettingKey(key: string): boolean {
+  return key in FLATTENED_SCHEMA;
+}
+
+/**
+ * Get the category for a setting
+ */
+export function getSettingCategory(key: string): string | undefined {
+  return FLATTENED_SCHEMA[key]?.category;
+}
+
+/**
+ * Check if a setting should be shown in the settings dialog
+ */
+export function shouldShowInDialog(key: string): boolean {
+  return FLATTENED_SCHEMA[key]?.showInDialog ?? true; // Default to true for backward compatibility
+}
+
+/**
+ * Get all settings that should be shown in the dialog, grouped by category
+ */
+export function getDialogSettingsByCategory(): Record<
+  string,
+  Array<SettingDefinition & { key: string }>
+> {
+  const categories: Record<
+    string,
+    Array<SettingDefinition & { key: string }>
+  > = {};
+
+  Object.values(FLATTENED_SCHEMA)
+    .filter((definition) => definition.showInDialog !== false)
+    .forEach((definition) => {
+      const category = definition.category;
+      if (!categories[category]) {
+        categories[category] = [];
+      }
+      categories[category].push(definition);
+    });
+
+  return categories;
+}
+
+/**
+ * Get settings by type that should be shown in the dialog
+ */
+export function getDialogSettingsByType(
+  type: SettingDefinition['type'],
+): Array<SettingDefinition & { key: string }> {
+  return Object.values(FLATTENED_SCHEMA).filter(
+    (definition) =>
+      definition.type === type && definition.showInDialog !== false,
+  );
+}
+
+/**
+ * Get all setting keys that should be shown in the dialog
+ */
+export function getDialogSettingKeys(): string[] {
+  return Object.values(FLATTENED_SCHEMA)
+    .filter((definition) => definition.showInDialog !== false)
+    .map((definition) => definition.key);
+}
+
+// ============================================================================
+// BUSINESS LOGIC UTILITIES (Higher-level utilities for setting operations)
+// ============================================================================
+
+/**
+ * Get the current value for a setting in a specific scope
+ * Always returns a value (never undefined) - falls back to default if not set anywhere
+ */
+export function getSettingValue(
+  key: string,
+  settings: Settings,
+  mergedSettings: Settings,
+): boolean {
+  const definition = getSettingDefinition(key);
+  if (!definition) {
+    return false; // Default fallback for invalid settings
+  }
+
+  const value = getEffectiveValue(key, settings, mergedSettings);
+  // Ensure we return a boolean value, converting from the more general type
+  if (typeof value === 'boolean') {
+    return value;
+  }
+  // Fall back to default value, ensuring it's a boolean
+  const defaultValue = definition.default;
+  if (typeof defaultValue === 'boolean') {
+    return defaultValue;
+  }
+  return false; // Final fallback
+}
+
+/**
+ * Check if a setting value is modified from its default
+ */
+export function isSettingModified(key: string, value: boolean): boolean {
+  const defaultValue = getDefaultValue(key);
+  // Handle type comparison properly
+  if (typeof defaultValue === 'boolean') {
+    return value !== defaultValue;
+  }
+  // If default is not a boolean, consider it modified if value is true
+  return value === true;
+}
+
+/**
+ * Check if a setting exists in the original settings file for a scope
+ */
+export function settingExistsInScope(
+  key: string,
+  scopeSettings: Settings,
+): boolean {
+  const path = key.split('.');
+  const value = getNestedValue(scopeSettings as Record<string, unknown>, path);
+  return value !== undefined;
+}
+
+/**
+ * Recursively sets a value in a nested object using a key path array.
+ */
+function setNestedValue(
+  obj: Record<string, unknown>,
+  path: string[],
+  value: unknown,
+): Record<string, unknown> {
+  const [first, ...rest] = path;
+  if (!first) {
+    return obj;
+  }
+
+  if (rest.length === 0) {
+    obj[first] = value;
+    return obj;
+  }
+
+  if (!obj[first] || typeof obj[first] !== 'object') {
+    obj[first] = {};
+  }
+
+  setNestedValue(obj[first] as Record<string, unknown>, rest, value);
+  return obj;
+}
+
+/**
+ * Set a setting value in the pending settings
+ */
+export function setPendingSettingValue(
+  key: string,
+  value: boolean,
+  pendingSettings: Settings,
+): Settings {
+  const path = key.split('.');
+  const newSettings = JSON.parse(JSON.stringify(pendingSettings));
+  setNestedValue(newSettings, path, value);
+  return newSettings;
+}
+
+/**
+ * Check if any modified settings require a restart
+ */
+export function hasRestartRequiredSettings(
+  modifiedSettings: Set<string>,
+): boolean {
+  return Array.from(modifiedSettings).some((key) => requiresRestart(key));
+}
+
+/**
+ * Get the restart required settings from a set of modified settings
+ */
+export function getRestartRequiredFromModified(
+  modifiedSettings: Set<string>,
+): string[] {
+  return Array.from(modifiedSettings).filter((key) => requiresRestart(key));
+}
+
+/**
+ * Save modified settings to the appropriate scope
+ */
+export function saveModifiedSettings(
+  modifiedSettings: Set<string>,
+  pendingSettings: Settings,
+  loadedSettings: LoadedSettings,
+  scope: SettingScope,
+): void {
+  modifiedSettings.forEach((settingKey) => {
+    const path = settingKey.split('.');
+    const value = getNestedValue(
+      pendingSettings as Record<string, unknown>,
+      path,
+    );
+
+    if (value === undefined) {
+      return;
+    }
+
+    const existsInOriginalFile = settingExistsInScope(
+      settingKey,
+      loadedSettings.forScope(scope).settings,
+    );
+
+    const isDefaultValue = value === getDefaultValue(settingKey);
+
+    if (existsInOriginalFile || !isDefaultValue) {
+      // This is tricky because setValue only works on top-level keys.
+      // We need to set the whole parent object.
+      const [parentKey] = path;
+      if (parentKey) {
+        // Ensure value is a boolean for setPendingSettingValue
+        const booleanValue = typeof value === 'boolean' ? value : false;
+        const newParentValue = setPendingSettingValue(
+          settingKey,
+          booleanValue,
+          loadedSettings.forScope(scope).settings,
+        )[parentKey as keyof Settings];
+
+        loadedSettings.setValue(
+          scope,
+          parentKey as keyof Settings,
+          newParentValue,
+        );
+      }
+    }
+  });
+}
+
+/**
+ * Get the display value for a setting, showing current scope value with default change indicator
+ */
+export function getDisplayValue(
+  key: string,
+  settings: Settings,
+  _mergedSettings: Settings,
+  modifiedSettings: Set<string>,
+  pendingSettings?: Settings,
+): string {
+  // Prioritize pending changes if user has modified this setting
+  let value: boolean;
+  if (pendingSettings && settingExistsInScope(key, pendingSettings)) {
+    // Show the value from the pending (unsaved) edits when it exists
+    value = getSettingValue(key, pendingSettings, {});
+  } else if (settingExistsInScope(key, settings)) {
+    // Show the value defined at the current scope if present
+    value = getSettingValue(key, settings, {});
+  } else {
+    // Fall back to the schema default when the key is unset in this scope
+    const defaultValue = getDefaultValue(key);
+    value = typeof defaultValue === 'boolean' ? defaultValue : false;
+  }
+
+  const valueString = String(value);
+
+  // Check if value is different from default OR if it's in modified settings OR if there are pending changes
+  const defaultValue = getDefaultValue(key);
+  const isChangedFromDefault =
+    typeof defaultValue === 'boolean' ? value !== defaultValue : value === true;
+  const isInModifiedSettings = modifiedSettings.has(key);
+  const hasPendingChanges =
+    pendingSettings && settingExistsInScope(key, pendingSettings);
+
+  // Add * indicator when value differs from default, is in modified settings, or has pending changes
+  if (isChangedFromDefault || isInModifiedSettings || hasPendingChanges) {
+    return `${valueString}*`; // * indicates changed from default value
+  }
+
+  return valueString;
+}
+
+/**
+ * Check if a setting doesn't exist in current scope (should be greyed out)
+ */
+export function isDefaultValue(key: string, settings: Settings): boolean {
+  return !settingExistsInScope(key, settings);
+}
+
+/**
+ * Check if a setting value is inherited (not set at current scope)
+ */
+export function isValueInherited(
+  key: string,
+  settings: Settings,
+  _mergedSettings: Settings,
+): boolean {
+  return !settingExistsInScope(key, settings);
+}
+
+/**
+ * Get the effective value for display, considering inheritance
+ * Always returns a boolean value (never undefined)
+ */
+export function getEffectiveDisplayValue(
+  key: string,
+  settings: Settings,
+  mergedSettings: Settings,
+): boolean {
+  return getSettingValue(key, settings, mergedSettings);
+}