gemini-cli/packages/cli/src/config/settings.ts

/**
 * @license
 * Copyright 2025 Google LLC
 * SPDX-License-Identifier: Apache-2.0
 */

import * as fs from 'node:fs';
import * as path from 'node:path';
import { platform } from 'node:os';
import * as dotenv from 'dotenv';
import process from 'node:process';
import {
  CoreEvent,
  FatalConfigError,
  GEMINI_DIR,
  getErrorMessage,
  Storage,
  coreEvents,
  homedir,
  type AdminControlsSettings,
  createCache,
} from '@google/gemini-cli-core';
import stripJsonComments from 'strip-json-comments';
import { DefaultLight } from '../ui/themes/builtin/light/default-light.js';
import { DefaultDark } from '../ui/themes/builtin/dark/default-dark.js';
import { isWorkspaceTrusted } from './trustedFolders.js';
import {
  type Settings,
  type MergedSettings,
  type MemoryImportFormat,
  type MergeStrategy,
  type SettingsSchema,
  type SettingDefinition,
  getSettingsSchema,
} from './settingsSchema.js';

export {
  type Settings,
  type MergedSettings,
  type MemoryImportFormat,
  type MergeStrategy,
  type SettingsSchema,
  type SettingDefinition,
  getSettingsSchema,
};

import { resolveEnvVarsInObject } from '../utils/envVarResolver.js';
import { customDeepMerge } from '../utils/deepMerge.js';
import { updateSettingsFilePreservingFormat } from '../utils/commentJson.js';
import {
  validateSettings,
  formatValidationError,
} from './settings-validation.js';

export function getMergeStrategyForPath(
  path: string[],
): MergeStrategy | undefined {
  let current: SettingDefinition | undefined = undefined;
  let currentSchema: SettingsSchema | undefined = getSettingsSchema();
  let parent: SettingDefinition | undefined = undefined;

  for (const key of path) {
    if (!currentSchema || !currentSchema[key]) {
      // Key not found in schema - check if parent has additionalProperties
      if (parent?.additionalProperties?.mergeStrategy) {
        return parent.additionalProperties.mergeStrategy;
      }
      return undefined;
    }
    parent = current;
    current = currentSchema[key];
    currentSchema = current.properties;
  }

  return current?.mergeStrategy;
}

export const USER_SETTINGS_PATH = Storage.getGlobalSettingsPath();
export const USER_SETTINGS_DIR = path.dirname(USER_SETTINGS_PATH);
export const DEFAULT_EXCLUDED_ENV_VARS = ['DEBUG', 'DEBUG_MODE'];

const AUTH_ENV_VAR_WHITELIST = [
  'GEMINI_API_KEY',
  'GOOGLE_API_KEY',
  'GOOGLE_CLOUD_PROJECT',
  'GOOGLE_CLOUD_LOCATION',
];

/**
 * Sanitizes an environment variable value to prevent shell injection.
 * Restricts values to a safe character set: alphanumeric, -, _, ., /
 */
export function sanitizeEnvVar(value: string): string {
  return value.replace(/[^a-zA-Z0-9\-_./]/g, '');
}

export function getSystemSettingsPath(): string {
  if (process.env['GEMINI_CLI_SYSTEM_SETTINGS_PATH']) {
    return process.env['GEMINI_CLI_SYSTEM_SETTINGS_PATH'];
  }
  if (platform() === 'darwin') {
    return '/Library/Application Support/GeminiCli/settings.json';
  } else if (platform() === 'win32') {
    return 'C:\\ProgramData\\gemini-cli\\settings.json';
  } else {
    return '/etc/gemini-cli/settings.json';
  }
}

export function getSystemDefaultsPath(): string {
  if (process.env['GEMINI_CLI_SYSTEM_DEFAULTS_PATH']) {
    return process.env['GEMINI_CLI_SYSTEM_DEFAULTS_PATH'];
  }
  return path.join(
    path.dirname(getSystemSettingsPath()),
    'system-defaults.json',
  );
}

export type { DnsResolutionOrder } from './settingsSchema.js';

export enum SettingScope {
  User = 'User',
  Workspace = 'Workspace',
  System = 'System',
  SystemDefaults = 'SystemDefaults',
  // Note that this scope is not supported in the settings dialog at this time,
  // it is only supported for extensions.
  Session = 'Session',
}

/**
 * A type representing the settings scopes that are supported for LoadedSettings.
 */
export type LoadableSettingScope =
  | SettingScope.User
  | SettingScope.Workspace
  | SettingScope.System
  | SettingScope.SystemDefaults;

/**
 * The actual values of the loadable settings scopes.
 */
const _loadableSettingScopes = [
  SettingScope.User,
  SettingScope.Workspace,
  SettingScope.System,
  SettingScope.SystemDefaults,
];

/**
 * A type guard function that checks if `scope` is a loadable settings scope,
 * and allows promotion to the `LoadableSettingsScope` type based on the result.
 */
export function isLoadableSettingScope(
  scope: SettingScope,
): scope is LoadableSettingScope {
  return _loadableSettingScopes.includes(scope);
}

export interface CheckpointingSettings {
  enabled?: boolean;
}

export interface SummarizeToolOutputSettings {
  tokenBudget?: number;
}

export type LoadingPhrasesMode = 'tips' | 'witty' | 'all' | 'off';

export interface AccessibilitySettings {
  /** @deprecated Use ui.loadingPhrases instead. */
  enableLoadingPhrases?: boolean;
  screenReader?: boolean;
}

export interface SessionRetentionSettings {
  /** Enable automatic session cleanup */
  enabled?: boolean;

  /** Maximum age of sessions to keep (e.g., "30d", "7d", "24h", "1w") */
  maxAge?: string;

  /** Alternative: Maximum number of sessions to keep (most recent) */
  maxCount?: number;

  /** Minimum retention period (safety limit, defaults to "1d") */
  minRetention?: string;
}

export interface SettingsError {
  message: string;
  path: string;
  severity: 'error' | 'warning';
}

export interface SettingsFile {
  settings: Settings;
  originalSettings: Settings;
  path: string;
  rawJson?: string;
  readOnly?: boolean;
}

function setNestedProperty(
  obj: Record<string, unknown>,
  path: string,
  value: unknown,
) {
  const keys = path.split('.');
  const lastKey = keys.pop();
  if (!lastKey) return;

  let current: Record<string, unknown> = obj;
  for (const key of keys) {
    if (current[key] === undefined) {
      current[key] = {};
    }
    const next = current[key];
    if (typeof next === 'object' && next !== null) {
      // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
      current = next as Record<string, unknown>;
    } else {
      // This path is invalid, so we stop.
      return;
    }
  }
  current[lastKey] = value;
}

export function getDefaultsFromSchema(
  schema: SettingsSchema = getSettingsSchema(),
): Settings {
  const defaults: Record<string, unknown> = {};
  for (const key in schema) {
    const definition = schema[key];
    if (definition.properties) {
      defaults[key] = getDefaultsFromSchema(definition.properties);
    } else if (definition.default !== undefined) {
      defaults[key] = definition.default;
    }
  }
  return defaults as Settings;
}

export function mergeSettings(
  system: Settings,
  systemDefaults: Settings,
  user: Settings,
  workspace: Settings,
  isTrusted: boolean,
): MergedSettings {
  const safeWorkspace = isTrusted ? workspace : ({} as Settings);
  const schemaDefaults = getDefaultsFromSchema();

  // Settings are merged with the following precedence (last one wins for
  // single values):
  // 1. Schema Defaults (Built-in)
  // 2. System Defaults
  // 3. User Settings
  // 4. Workspace Settings
  // 5. System Settings (as overrides)
  // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
  return customDeepMerge(
    getMergeStrategyForPath,
    schemaDefaults,
    systemDefaults,
    user,
    safeWorkspace,
    system,
  ) as MergedSettings;
}

/**
 * Creates a fully populated MergedSettings object for testing purposes.
 * It merges the provided overrides with the default settings from the schema.
 *
 * @param overrides Partial settings to override the defaults.
 * @returns A complete MergedSettings object.
 */
export function createTestMergedSettings(
  overrides: Partial<Settings> = {},
): MergedSettings {
  // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
  return customDeepMerge(
    getMergeStrategyForPath,
    getDefaultsFromSchema(),
    overrides,
  ) as MergedSettings;
}

/**
 * An immutable snapshot of settings state.
 * Used with useSyncExternalStore for reactive updates.
 */
export interface LoadedSettingsSnapshot {
  system: SettingsFile;
  systemDefaults: SettingsFile;
  user: SettingsFile;
  workspace: SettingsFile;
  isTrusted: boolean;
  errors: SettingsError[];
  merged: MergedSettings;
}

export class LoadedSettings {
  constructor(
    system: SettingsFile,
    systemDefaults: SettingsFile,
    user: SettingsFile,
    workspace: SettingsFile,
    isTrusted: boolean,
    errors: SettingsError[] = [],
  ) {
    this.system = system;
    this.systemDefaults = systemDefaults;
    this.user = user;
    this._workspaceFile = workspace;
    this.isTrusted = isTrusted;
    this.workspace = isTrusted
      ? workspace
      : this.createEmptyWorkspace(workspace);
    this.errors = errors;
    this._merged = this.computeMergedSettings();
    this._snapshot = this.computeSnapshot();
  }

  readonly system: SettingsFile;
  readonly systemDefaults: SettingsFile;
  readonly user: SettingsFile;
  workspace: SettingsFile;
  isTrusted: boolean;
  readonly errors: SettingsError[];

  private _workspaceFile: SettingsFile;
  private _merged: MergedSettings;
  private _snapshot: LoadedSettingsSnapshot;
  private _remoteAdminSettings: Partial<Settings> | undefined;

  get merged(): MergedSettings {
    return this._merged;
  }

  setTrusted(isTrusted: boolean): void {
    if (this.isTrusted === isTrusted) {
      return;
    }
    this.isTrusted = isTrusted;
    this.workspace = isTrusted
      ? this._workspaceFile
      : this.createEmptyWorkspace(this._workspaceFile);
    this._merged = this.computeMergedSettings();
    coreEvents.emitSettingsChanged();
  }

  private createEmptyWorkspace(workspace: SettingsFile): SettingsFile {
    return {
      ...workspace,
      settings: {},
      originalSettings: {},
    };
  }

  private computeMergedSettings(): MergedSettings {
    const merged = mergeSettings(
      this.system.settings,
      this.systemDefaults.settings,
      this.user.settings,
      this.workspace.settings,
      this.isTrusted,
    );

    // Remote admin settings always take precedence and file-based admin settings
    // are ignored.
    const adminSettingSchema = getSettingsSchema().admin;
    if (adminSettingSchema?.properties) {
      const adminSchema = adminSettingSchema.properties;
      const adminDefaults = getDefaultsFromSchema(adminSchema);

      // The final admin settings are the defaults overridden by remote settings.
      // Any admin settings from files are ignored.
      // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
      merged.admin = customDeepMerge(
        (path: string[]) => getMergeStrategyForPath(['admin', ...path]),
        adminDefaults,
        this._remoteAdminSettings?.admin ?? {},
      ) as MergedSettings['admin'];
    }
    return merged;
  }

  private computeSnapshot(): LoadedSettingsSnapshot {
    const cloneSettingsFile = (file: SettingsFile): SettingsFile => ({
      path: file.path,
      rawJson: file.rawJson,
      settings: structuredClone(file.settings),
      originalSettings: structuredClone(file.originalSettings),
    });
    return {
      system: cloneSettingsFile(this.system),
      systemDefaults: cloneSettingsFile(this.systemDefaults),
      user: cloneSettingsFile(this.user),
      workspace: cloneSettingsFile(this.workspace),
      isTrusted: this.isTrusted,
      errors: [...this.errors],
      merged: structuredClone(this._merged),
    };
  }

  // Passing this along with getSnapshot to useSyncExternalStore allows for idiomatic reactivity on settings changes
  // React will pass a listener fn into this subscribe fn
  // that listener fn will perform an object identity check on the snapshot and trigger a React re render if the snapshot has changed
  subscribe(listener: () => void): () => void {
    coreEvents.on(CoreEvent.SettingsChanged, listener);
    return () => coreEvents.off(CoreEvent.SettingsChanged, listener);
  }

  getSnapshot(): LoadedSettingsSnapshot {
    return this._snapshot;
  }

  forScope(scope: LoadableSettingScope): SettingsFile {
    switch (scope) {
      case SettingScope.User:
        return this.user;
      case SettingScope.Workspace:
        return this.workspace;
      case SettingScope.System:
        return this.system;
      case SettingScope.SystemDefaults:
        return this.systemDefaults;
      default:
        throw new Error(`Invalid scope: ${scope}`);
    }
  }

  private isPersistable(settingsFile: SettingsFile): boolean {
    return !settingsFile.readOnly;
  }

  setValue(scope: LoadableSettingScope, key: string, value: unknown): void {
    const settingsFile = this.forScope(scope);

    // Clone value to prevent reference sharing
    const valueToSet =
      typeof value === 'object' && value !== null
        ? structuredClone(value)
        : value;

    setNestedProperty(settingsFile.settings, key, valueToSet);

    if (this.isPersistable(settingsFile)) {
      // Use a fresh clone for originalSettings to ensure total independence
      setNestedProperty(
        settingsFile.originalSettings,
        key,
        structuredClone(valueToSet),
      );
      saveSettings(settingsFile);
    }

    this._merged = this.computeMergedSettings();
    this._snapshot = this.computeSnapshot();
    coreEvents.emitSettingsChanged();
  }

  setRemoteAdminSettings(remoteSettings: AdminControlsSettings): void {
    const admin: Settings['admin'] = {};
    const { strictModeDisabled, mcpSetting, cliFeatureSetting } =
      remoteSettings;

    if (Object.keys(remoteSettings).length === 0) {
      this._remoteAdminSettings = { admin };
      this._merged = this.computeMergedSettings();
      return;
    }

    admin.secureModeEnabled = !strictModeDisabled;
    admin.mcp = {
      enabled: mcpSetting?.mcpEnabled,
      config: mcpSetting?.mcpConfig?.mcpServers,
    };
    admin.extensions = {
      enabled: cliFeatureSetting?.extensionsSetting?.extensionsEnabled,
    };
    admin.skills = {
      enabled: cliFeatureSetting?.unmanagedCapabilitiesEnabled,
    };

    this._remoteAdminSettings = { admin };
    this._merged = this.computeMergedSettings();
  }
}

function findEnvFile(startDir: string): string | null {
  let currentDir = path.resolve(startDir);
  while (true) {
    // prefer gemini-specific .env under GEMINI_DIR
    const geminiEnvPath = path.join(currentDir, GEMINI_DIR, '.env');
    if (fs.existsSync(geminiEnvPath)) {
      return geminiEnvPath;
    }
    const envPath = path.join(currentDir, '.env');
    if (fs.existsSync(envPath)) {
      return envPath;
    }
    const parentDir = path.dirname(currentDir);
    if (parentDir === currentDir || !parentDir) {
      // check .env under home as fallback, again preferring gemini-specific .env
      const homeGeminiEnvPath = path.join(homedir(), GEMINI_DIR, '.env');
      if (fs.existsSync(homeGeminiEnvPath)) {
        return homeGeminiEnvPath;
      }
      const homeEnvPath = path.join(homedir(), '.env');
      if (fs.existsSync(homeEnvPath)) {
        return homeEnvPath;
      }
      return null;
    }
    currentDir = parentDir;
  }
}

export function setUpCloudShellEnvironment(
  envFilePath: string | null,
  isTrusted: boolean,
  isSandboxed: boolean,
): void {
  // Special handling for GOOGLE_CLOUD_PROJECT in Cloud Shell:
  // Because GOOGLE_CLOUD_PROJECT in Cloud Shell tracks the project
  // set by the user using "gcloud config set project" we do not want to
  // use its value. So, unless the user overrides GOOGLE_CLOUD_PROJECT in
  // one of the .env files, we set the Cloud Shell-specific default here.
  let value = 'cloudshell-gca';

  if (envFilePath && fs.existsSync(envFilePath)) {
    const envFileContent = fs.readFileSync(envFilePath);
    const parsedEnv = dotenv.parse(envFileContent);
    if (parsedEnv['GOOGLE_CLOUD_PROJECT']) {
      // .env file takes precedence in Cloud Shell
      value = parsedEnv['GOOGLE_CLOUD_PROJECT'];
      if (!isTrusted && isSandboxed) {
        value = sanitizeEnvVar(value);
      }
    }
  }
  process.env['GOOGLE_CLOUD_PROJECT'] = value;
}

export function loadEnvironment(
  settings: Settings,
  workspaceDir: string,
  isWorkspaceTrustedFn = isWorkspaceTrusted,
): void {
  const envFilePath = findEnvFile(workspaceDir);
  const trustResult = isWorkspaceTrustedFn(settings, workspaceDir);

  const isTrusted = trustResult.isTrusted ?? false;
  // Check settings OR check process.argv directly since this might be called
  // before arguments are fully parsed. This is a best-effort sniffing approach
  // that happens early in the CLI lifecycle. It is designed to detect the
  // sandbox flag before the full command-line parser is initialized to ensure
  // security constraints are applied when loading environment variables.
  const args = process.argv.slice(2);
  const doubleDashIndex = args.indexOf('--');
  const relevantArgs =
    doubleDashIndex === -1 ? args : args.slice(0, doubleDashIndex);

  const isSandboxed =
    !!settings.tools?.sandbox ||
    relevantArgs.includes('-s') ||
    relevantArgs.includes('--sandbox');

  // Cloud Shell environment variable handling
  if (process.env['CLOUD_SHELL'] === 'true') {
    setUpCloudShellEnvironment(envFilePath, isTrusted, isSandboxed);
  }

  if (envFilePath) {
    // Manually parse and load environment variables to handle exclusions correctly.
    // This avoids modifying environment variables that were already set from the shell.
    try {
      const envFileContent = fs.readFileSync(envFilePath, 'utf-8');
      const parsedEnv = dotenv.parse(envFileContent);

      const excludedVars =
        settings?.advanced?.excludedEnvVars || DEFAULT_EXCLUDED_ENV_VARS;
      const isProjectEnvFile = !envFilePath.includes(GEMINI_DIR);

      for (const key in parsedEnv) {
        if (Object.hasOwn(parsedEnv, key)) {
          let value = parsedEnv[key];
          // If the workspace is untrusted but we are sandboxed, only allow whitelisted variables.
          if (!isTrusted && isSandboxed) {
            if (!AUTH_ENV_VAR_WHITELIST.includes(key)) {
              continue;
            }
            // Sanitize the value for untrusted sources
            value = sanitizeEnvVar(value);
          }

          // If it's a project .env file, skip loading excluded variables.
          if (isProjectEnvFile && excludedVars.includes(key)) {
            continue;
          }

          // Load variable only if it's not already set in the environment.
          if (!Object.hasOwn(process.env, key)) {
            process.env[key] = value;
          }
        }
      }
    } catch (_e) {
      // Errors are ignored to match the behavior of `dotenv.config({ quiet: true })`.
    }
  }
}

// Cache to store the results of loadSettings to avoid redundant disk I/O.
const settingsCache = createCache<string, LoadedSettings>({
  storage: 'map',
  defaultTtl: 10000, // 10 seconds
});

/**
 * Resets the settings cache. Used exclusively for test isolation.
 * @internal
 */
export function resetSettingsCacheForTesting() {
  settingsCache.clear();
}

/**
 * Loads settings from user and workspace directories.
 * Project settings override user settings.
 */
export function loadSettings(
  workspaceDir: string = process.cwd(),
): LoadedSettings {
  const normalizedWorkspaceDir = path.resolve(workspaceDir);
  return settingsCache.getOrCreate(normalizedWorkspaceDir, () =>
    _doLoadSettings(normalizedWorkspaceDir),
  );
}

/**
 * Internal implementation of the settings loading logic.
 */
function _doLoadSettings(workspaceDir: string): LoadedSettings {
  let systemSettings: Settings = {};
  let systemDefaultSettings: Settings = {};
  let userSettings: Settings = {};
  let workspaceSettings: Settings = {};
  const settingsErrors: SettingsError[] = [];
  const systemSettingsPath = getSystemSettingsPath();
  const systemDefaultsPath = getSystemDefaultsPath();

  const storage = new Storage(workspaceDir);
  const workspaceSettingsPath = storage.getWorkspaceSettingsPath();

  const load = (filePath: string): { settings: Settings; rawJson?: string } => {
    try {
      if (fs.existsSync(filePath)) {
        const content = fs.readFileSync(filePath, 'utf-8');
        const rawSettings: unknown = JSON.parse(stripJsonComments(content));

        if (
          typeof rawSettings !== 'object' ||
          rawSettings === null ||
          Array.isArray(rawSettings)
        ) {
          settingsErrors.push({
            message: 'Settings file is not a valid JSON object.',
            path: filePath,
            severity: 'error',
          });
          return { settings: {} };
        }

        // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
        const settingsObject = rawSettings as Record<string, unknown>;

        // Validate settings structure with Zod
        const validationResult = validateSettings(settingsObject);
        if (!validationResult.success && validationResult.error) {
          const errorMessage = formatValidationError(
            validationResult.error,
            filePath,
          );
          settingsErrors.push({
            message: errorMessage,
            path: filePath,
            severity: 'warning',
          });
        }

        return { settings: settingsObject as Settings, rawJson: content };
      }
    } catch (error: unknown) {
      settingsErrors.push({
        message: getErrorMessage(error),
        path: filePath,
        severity: 'error',
      });
    }
    return { settings: {} };
  };

  const systemResult = load(systemSettingsPath);
  const systemDefaultsResult = load(systemDefaultsPath);
  const userResult = load(USER_SETTINGS_PATH);

  let workspaceResult: { settings: Settings; rawJson?: string } = {
    settings: {} as Settings,
    rawJson: undefined,
  };
  if (!storage.isWorkspaceHomeDir()) {
    workspaceResult = load(workspaceSettingsPath);
  }

  const systemOriginalSettings = structuredClone(systemResult.settings);
  const systemDefaultsOriginalSettings = structuredClone(
    systemDefaultsResult.settings,
  );
  const userOriginalSettings = structuredClone(userResult.settings);
  const workspaceOriginalSettings = structuredClone(workspaceResult.settings);

  // Environment variables for runtime use
  systemSettings = resolveEnvVarsInObject(systemResult.settings);
  systemDefaultSettings = resolveEnvVarsInObject(systemDefaultsResult.settings);
  userSettings = resolveEnvVarsInObject(userResult.settings);
  workspaceSettings = resolveEnvVarsInObject(workspaceResult.settings);

  // Support legacy theme names
  if (userSettings.ui?.theme === 'VS') {
    userSettings.ui.theme = DefaultLight.name;
  } else if (userSettings.ui?.theme === 'VS2015') {
    userSettings.ui.theme = DefaultDark.name;
  }
  if (workspaceSettings.ui?.theme === 'VS') {
    workspaceSettings.ui.theme = DefaultLight.name;
  } else if (workspaceSettings.ui?.theme === 'VS2015') {
    workspaceSettings.ui.theme = DefaultDark.name;
  }

  // For the initial trust check, we can only use user and system settings.
  const initialTrustCheckSettings = customDeepMerge(
    getMergeStrategyForPath,
    getDefaultsFromSchema(),
    systemDefaultSettings,
    userSettings,
    systemSettings,
  );
  const isTrusted =
    isWorkspaceTrusted(initialTrustCheckSettings as Settings, workspaceDir)
      .isTrusted ?? false;

  // Create a temporary merged settings object to pass to loadEnvironment.
  const tempMergedSettings = mergeSettings(
    systemSettings,
    systemDefaultSettings,
    userSettings,
    workspaceSettings,
    isTrusted,
  );

  // loadEnvironment depends on settings so we have to create a temp version of
  // the settings to avoid a cycle
  loadEnvironment(tempMergedSettings, workspaceDir);

  // Check for any fatal errors before proceeding
  const fatalErrors = settingsErrors.filter((e) => e.severity === 'error');
  if (fatalErrors.length > 0) {
    const errorMessages = fatalErrors.map(
      (error) => `Error in ${error.path}: ${error.message}`,
    );
    throw new FatalConfigError(
      `${errorMessages.join('\n')}\nPlease fix the configuration file(s) and try again.`,
    );
  }

  const loadedSettings = new LoadedSettings(
    {
      path: systemSettingsPath,
      settings: systemSettings,
      originalSettings: systemOriginalSettings,
      rawJson: systemResult.rawJson,
      readOnly: true,
    },
    {
      path: systemDefaultsPath,
      settings: systemDefaultSettings,
      originalSettings: systemDefaultsOriginalSettings,
      rawJson: systemDefaultsResult.rawJson,
      readOnly: true,
    },
    {
      path: USER_SETTINGS_PATH,
      settings: userSettings,
      originalSettings: userOriginalSettings,
      rawJson: userResult.rawJson,
      readOnly: false,
    },
    {
      path: storage.isWorkspaceHomeDir() ? '' : workspaceSettingsPath,
      settings: workspaceSettings,
      originalSettings: workspaceOriginalSettings,
      rawJson: workspaceResult.rawJson,
      readOnly: storage.isWorkspaceHomeDir(),
    },
    isTrusted,
    settingsErrors,
  );

  // Automatically migrate deprecated settings when loading.
  migrateDeprecatedSettings(loadedSettings);

  return loadedSettings;
}

/**
 * Migrates deprecated settings to their new counterparts.
 *
 * Deprecated settings are removed from settings files by default.
 *
 * @returns true if any changes were made and need to be saved.
 */
export function migrateDeprecatedSettings(
  loadedSettings: LoadedSettings,
  removeDeprecated = true,
): boolean {
  let anyModified = false;
  const systemWarnings: Map<LoadableSettingScope, string[]> = new Map();

  /**
   * Helper to migrate a boolean setting and track it if it's deprecated.
   */
  const migrateBoolean = (
    settings: Record<string, unknown>,
    oldKey: string,
    newKey: string,
    prefix: string,
    foundDeprecated?: string[],
  ): boolean => {
    let modified = false;
    const oldValue = settings[oldKey];
    const newValue = settings[newKey];

    if (typeof oldValue === 'boolean') {
      if (foundDeprecated) {
        foundDeprecated.push(prefix ? `${prefix}.${oldKey}` : oldKey);
      }
      if (typeof newValue === 'boolean') {
        // Both exist, trust the new one
        if (removeDeprecated) {
          delete settings[oldKey];
          modified = true;
        }
      } else {
        // Only old exists, migrate to new (inverted)
        settings[newKey] = !oldValue;
        if (removeDeprecated) {
          delete settings[oldKey];
        }
        modified = true;
      }
    }
    return modified;
  };

  const processScope = (scope: LoadableSettingScope) => {
    const settingsFile = loadedSettings.forScope(scope);
    const settings = settingsFile.settings;
    const foundDeprecated: string[] = [];

    // Migrate general settings
    const generalSettings = settings.general as
      | Record<string, unknown>
      | undefined;
    if (generalSettings) {
      const newGeneral = { ...generalSettings };
      let modified = false;

      modified =
        migrateBoolean(
          newGeneral,
          'disableAutoUpdate',
          'enableAutoUpdate',
          'general',
          foundDeprecated,
        ) || modified;
      modified =
        migrateBoolean(
          newGeneral,
          'disableUpdateNag',
          'enableAutoUpdateNotification',
          'general',
          foundDeprecated,
        ) || modified;

      if (modified) {
        loadedSettings.setValue(scope, 'general', newGeneral);
        if (!settingsFile.readOnly) {
          anyModified = true;
        }
      }
    }

    // Migrate ui settings
    const uiSettings = settings.ui as Record<string, unknown> | undefined;
    if (uiSettings) {
      const newUi = { ...uiSettings };
      // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
      const accessibilitySettings = newUi['accessibility'] as
        | Record<string, unknown>
        | undefined;

      if (accessibilitySettings) {
        const newAccessibility = { ...accessibilitySettings };
        if (
          migrateBoolean(
            newAccessibility,
            'disableLoadingPhrases',
            'enableLoadingPhrases',
            'ui.accessibility',
            foundDeprecated,
          )
        ) {
          newUi['accessibility'] = newAccessibility;
          loadedSettings.setValue(scope, 'ui', newUi);
          if (!settingsFile.readOnly) {
            anyModified = true;
          }
        }

        // Migrate enableLoadingPhrases: false → loadingPhrases: 'off'
        const enableLP = newAccessibility['enableLoadingPhrases'];
        if (
          typeof enableLP === 'boolean' &&
          newUi['loadingPhrases'] === undefined
        ) {
          if (!enableLP) {
            newUi['loadingPhrases'] = 'off';
            loadedSettings.setValue(scope, 'ui', newUi);
            if (!settingsFile.readOnly) {
              anyModified = true;
            }
          }
          foundDeprecated.push('ui.accessibility.enableLoadingPhrases');
        }
      }
    }

    // Migrate context settings
    const contextSettings = settings.context as
      | Record<string, unknown>
      | undefined;
    if (contextSettings) {
      const newContext = { ...contextSettings };
      // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
      const fileFilteringSettings = newContext['fileFiltering'] as
        | Record<string, unknown>
        | undefined;

      if (fileFilteringSettings) {
        const newFileFiltering = { ...fileFilteringSettings };
        if (
          migrateBoolean(
            newFileFiltering,
            'disableFuzzySearch',
            'enableFuzzySearch',
            'context.fileFiltering',
            foundDeprecated,
          )
        ) {
          newContext['fileFiltering'] = newFileFiltering;
          loadedSettings.setValue(scope, 'context', newContext);
          if (!settingsFile.readOnly) {
            anyModified = true;
          }
        }
      }
    }

    // Migrate tools settings
    const toolsSettings = settings.tools as Record<string, unknown> | undefined;
    if (toolsSettings) {
      if (toolsSettings['approvalMode'] !== undefined) {
        foundDeprecated.push('tools.approvalMode');

        const generalSettings =
          (settings.general as Record<string, unknown> | undefined) || {};
        const newGeneral = { ...generalSettings };

        // Only set defaultApprovalMode if it's not already set
        if (newGeneral['defaultApprovalMode'] === undefined) {
          newGeneral['defaultApprovalMode'] = toolsSettings['approvalMode'];
          loadedSettings.setValue(scope, 'general', newGeneral);
          if (!settingsFile.readOnly) {
            anyModified = true;
          }
        }

        if (removeDeprecated) {
          const newTools = { ...toolsSettings };
          delete newTools['approvalMode'];
          loadedSettings.setValue(scope, 'tools', newTools);
          if (!settingsFile.readOnly) {
            anyModified = true;
          }
        }
      }
    }

    // Migrate experimental agent settings
    const experimentalModified = migrateExperimentalSettings(
      settings,
      loadedSettings,
      scope,
      removeDeprecated,
      foundDeprecated,
    );

    if (experimentalModified) {
      if (!settingsFile.readOnly) {
        anyModified = true;
      }
    }

    if (settingsFile.readOnly && foundDeprecated.length > 0) {
      systemWarnings.set(scope, foundDeprecated);
    }
  };

  processScope(SettingScope.User);
  processScope(SettingScope.Workspace);
  processScope(SettingScope.System);
  processScope(SettingScope.SystemDefaults);

  if (systemWarnings.size > 0) {
    for (const [scope, flags] of systemWarnings) {
      const scopeName =
        scope === SettingScope.SystemDefaults
          ? 'system default'
          : scope.toLowerCase();
      coreEvents.emitFeedback(
        'warning',
        `The ${scopeName} configuration contains deprecated settings: [${flags.join(', ')}]. These could not be migrated automatically as system settings are read-only. Please update the system configuration manually.`,
      );
    }
  }

  return anyModified;
}

export function saveSettings(settingsFile: SettingsFile): void {
  // Clear the entire cache on any save.
  settingsCache.clear();

  try {
    // Ensure the directory exists
    const dirPath = path.dirname(settingsFile.path);
    if (!fs.existsSync(dirPath)) {
      fs.mkdirSync(dirPath, { recursive: true });
    }

    const settingsToSave = settingsFile.originalSettings;

    // Use the format-preserving update function
    updateSettingsFilePreservingFormat(
      settingsFile.path,
      settingsToSave as Record<string, unknown>,
    );
  } catch (error) {
    coreEvents.emitFeedback(
      'error',
      'There was an error saving your latest settings changes.',
      error,
    );
  }
}

export function saveModelChange(
  loadedSettings: LoadedSettings,
  model: string,
): void {
  try {
    loadedSettings.setValue(SettingScope.User, 'model.name', model);
  } catch (error) {
    coreEvents.emitFeedback(
      'error',
      'There was an error saving your preferred model.',
      error,
    );
  }
}

function migrateExperimentalSettings(
  settings: Settings,
  loadedSettings: LoadedSettings,
  scope: LoadableSettingScope,
  removeDeprecated: boolean,
  foundDeprecated?: string[],
): boolean {
  const experimentalSettings = settings.experimental as
    | Record<string, unknown>
    | undefined;

  if (experimentalSettings) {
    const agentsSettings = {
      ...(settings.agents as Record<string, unknown> | undefined),
    };
    const agentsOverrides = {
      // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
      ...((agentsSettings['overrides'] as Record<string, unknown>) || {}),
    };
    let modified = false;

    const migrateExperimental = (
      oldKey: string,
      migrateFn: (oldValue: Record<string, unknown>) => void,
    ) => {
      const old = experimentalSettings[oldKey];
      if (old) {
        foundDeprecated?.push(`experimental.${oldKey}`);
        // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
        migrateFn(old as Record<string, unknown>);
        modified = true;
      }
    };

    // Migrate codebaseInvestigatorSettings -> agents.overrides.codebase_investigator
    migrateExperimental('codebaseInvestigatorSettings', (old) => {
      const override = {
        // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
        ...(agentsOverrides['codebase_investigator'] as
          | Record<string, unknown>
          | undefined),
      };

      if (old['enabled'] !== undefined) override['enabled'] = old['enabled'];

      const runConfig = {
        // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
        ...(override['runConfig'] as Record<string, unknown> | undefined),
      };
      if (old['maxNumTurns'] !== undefined)
        runConfig['maxTurns'] = old['maxNumTurns'];
      if (old['maxTimeMinutes'] !== undefined)
        runConfig['maxTimeMinutes'] = old['maxTimeMinutes'];
      if (Object.keys(runConfig).length > 0) override['runConfig'] = runConfig;

      if (old['model'] !== undefined || old['thinkingBudget'] !== undefined) {
        const modelConfig = {
          // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
          ...(override['modelConfig'] as Record<string, unknown> | undefined),
        };
        if (old['model'] !== undefined) modelConfig['model'] = old['model'];
        if (old['thinkingBudget'] !== undefined) {
          const generateContentConfig = {
            // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
            ...(modelConfig['generateContentConfig'] as
              | Record<string, unknown>
              | undefined),
          };
          const thinkingConfig = {
            // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
            ...(generateContentConfig['thinkingConfig'] as
              | Record<string, unknown>
              | undefined),
          };
          thinkingConfig['thinkingBudget'] = old['thinkingBudget'];
          generateContentConfig['thinkingConfig'] = thinkingConfig;
          modelConfig['generateContentConfig'] = generateContentConfig;
        }
        override['modelConfig'] = modelConfig;
      }

      agentsOverrides['codebase_investigator'] = override;
    });

    // Migrate cliHelpAgentSettings -> agents.overrides.cli_help
    migrateExperimental('cliHelpAgentSettings', (old) => {
      const override = {
        // eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
        ...(agentsOverrides['cli_help'] as Record<string, unknown> | undefined),
      };
      if (old['enabled'] !== undefined) override['enabled'] = old['enabled'];
      agentsOverrides['cli_help'] = override;
    });

    if (modified) {
      agentsSettings['overrides'] = agentsOverrides;
      loadedSettings.setValue(scope, 'agents', agentsSettings);

      if (removeDeprecated) {
        const newExperimental = { ...experimentalSettings };
        delete newExperimental['codebaseInvestigatorSettings'];
        delete newExperimental['cliHelpAgentSettings'];
        loadedSettings.setValue(scope, 'experimental', newExperimental);
      }
      return true;
    }
  }
  return false;
}