universal-dev-standards 4.2.0 → 5.0.0-beta.11

package/src/commands/config.js

@@ -0,0 +1,1316 @@
+import chalk from 'chalk';
+import inquirer from 'inquirer';
+import ora from 'ora';
+import { unlinkSync, existsSync } from 'fs';
+import { join, basename } from 'path';
+import { config } from '../utils/config-manager.js';
+import { msg, t as getMessages, setLanguage, isLanguageExplicitlySet } from '../i18n/messages.js';
+import {
+  getOptionSource,
+  findOption,
+  getAllStandards,
+  getStandardsByLevel,
+  getStandardSource
+} from '../utils/registry.js';
+import {
+  copyStandard,
+  readManifest,
+  writeManifest,
+  isInitialized
+} from '../utils/copier.js';
+import {
+  promptFormat,
+  promptGitWorkflow,
+  promptMergeStrategy,
+  promptCommitLanguage,
+  promptTestLevels,
+  promptConfirm,
+  promptManageAITools,
+  promptAdoptionLevel,
+  promptContentModeChange,
+  handleAgentsMdSharing,
+  promptMethodology,
+  promptSkillsInstallLocation,
+  promptCommandsInstallation,
+  promptDisplayLanguage
+} from '../prompts/init.js';
+import {
+  installSkillsToMultipleAgents,
+  installCommandsToMultipleAgents,
+  getInstalledSkillsInfoForAgent,
+  getInstalledCommandsForAgent
+} from '../utils/skills-installer.js';
+import {
+  getAgentConfig,
+  getAgentDisplayName
+} from '../config/ai-agent-paths.js';
+import {
+  writeIntegrationFile,
+  getToolFilePath
+} from '../utils/integration-generator.js';
+import { getMarketplaceSkillsInfo } from '../utils/github.js';
+import { regenerateIntegrations } from './update.js';
+
+/**
+ * Get localized message with fallback (for config-specific keys)
+ */
+function t(key, fallback) {
+  return msg(key) || fallback;
+}
+
+/**
+ * Vibe mode presets for different development styles
+ */
+const VIBE_PRESETS = {
+  relaxed: {
+    name: 'Relaxed (Prototype/Hackathon)',
+    description: 'Maximum speed, minimal interrupts. Good for rapid prototyping.',
+    settings: {
+      'hitl.threshold': 4,
+      'vibe-coding.enabled': true,
+      'vibe-coding.micro-specs.require-confirmation': false,
+      'vibe-coding.auto-sweep.enabled': true,
+      'vibe-coding.auto-sweep.trigger': 'session-end',
+      'vibe-coding.standards-injection.mode': 'soft'
+    }
+  },
+  balanced: {
+    name: 'Balanced (Recommended)',
+    description: 'Good balance between speed and safety. Confirms critical actions.',
+    settings: {
+      'hitl.threshold': 2,
+      'vibe-coding.enabled': true,
+      'vibe-coding.micro-specs.require-confirmation': true,
+      'vibe-coding.auto-sweep.enabled': true,
+      'vibe-coding.auto-sweep.trigger': 'session-end',
+      'vibe-coding.standards-injection.mode': 'soft'
+    }
+  },
+  strict: {
+    name: 'Strict (Production)',
+    description: 'Maximum safety. Confirms most actions. Good for production code.',
+    settings: {
+      'hitl.threshold': 1,
+      'vibe-coding.enabled': true,
+      'vibe-coding.micro-specs.require-confirmation': true,
+      'vibe-coding.auto-sweep.enabled': true,
+      'vibe-coding.auto-sweep.trigger': 'commit-hook',
+      'vibe-coding.standards-injection.mode': 'strict'
+    }
+  }
+};
+
+/**
+ * Handle config command — unified entry point
+ * @param {string} action - list, get, set, init
+ * @param {string} key - Config key
+ * @param {string} value - Config value
+ * @param {Object} options - Command options
+ */
+export async function configCommand(action, key, value, options) {
+  // Initialize config manager
+  const currentConfig = config.init();
+
+  // Handle 'list' action explicitly
+  if (action === 'list') {
+    console.log(chalk.bold('Current Configuration:'));
+    console.log(JSON.stringify(currentConfig, null, 2));
+    return;
+  }
+
+  // Handle 'get' action
+  if (action === 'get') {
+    if (!key) {
+      console.error(chalk.red('Error: Key is required for get command'));
+      return;
+    }
+    const val = config.get(key);
+    console.log(val !== undefined ? val : chalk.gray('undefined'));
+    return;
+  }
+
+  // Handle 'set' action
+  if (action === 'set') {
+    if (!key || value === undefined) {
+      console.error(chalk.red('Error: Key and value are required for set command'));
+      return;
+    }
+
+    // Type inference
+    let typedValue = value;
+    if (value === 'true') typedValue = true;
+    if (value === 'false') typedValue = false;
+    if (!isNaN(Number(value))) typedValue = Number(value);
+
+    const scope = options.global ? 'global' : 'project';
+    config.set(key, typedValue, scope);
+
+    console.log(chalk.green(`Configuration updated (${scope}): ${key} = ${typedValue}`));
+    return;
+  }
+
+  // Handle 'init' action
+  if (action === 'init') {
+    await handleConfigInit(options);
+    return;
+  }
+
+  // No action: check for --type (direct project configuration) or show interactive menu
+  if (!action) {
+    // --type provided: go directly to project configuration
+    if (options.type) {
+      return runProjectConfiguration(options);
+    }
+
+    // --yes flag with no action: non-interactive mode, show JSON config
+    if (options.yes) {
+      console.log(chalk.bold('Current Configuration:'));
+      console.log(JSON.stringify(currentConfig, null, 2));
+      return;
+    }
+
+    // No arguments at all: show unified interactive menu
+    const projectPath = process.cwd();
+    const initialized = isInitialized(projectPath);
+
+    // Set language from manifest (same pattern as runProjectConfiguration)
+    if (initialized && !isLanguageExplicitlySet()) {
+      const manifest = readManifest(projectPath);
+      if (manifest) {
+        const uiLang = manifest.options?.display_language || 'en';
+        setLanguage(uiLang);
+      }
+    }
+
+    const menuChoices = [];
+
+    if (initialized) {
+      menuChoices.push({
+        name: t('config.menuProjectSettings', 'Project settings (level, AI tools, Skills, format, workflow...)'),
+        value: 'project'
+      });
+    }
+
+    menuChoices.push({
+      name: t('config.menuPreferences', 'Preferences (UI language, HITL threshold, Vibe Coding)'),
+      value: 'preferences'
+    });
+
+    menuChoices.push({
+      name: t('config.menuShowConfig', 'Show current configuration (JSON)'),
+      value: 'show'
+    });
+
+    const { menuChoice } = await inquirer.prompt([
+      {
+        type: 'list',
+        name: 'menuChoice',
+        message: t('config.menuQuestion', 'What would you like to configure?'),
+        choices: menuChoices
+      }
+    ]);
+
+    if (menuChoice === 'project') {
+      return runProjectConfiguration(options);
+    } else if (menuChoice === 'preferences') {
+      await handleConfigInit(options);
+      return;
+    } else if (menuChoice === 'show') {
+      console.log(chalk.bold('Current Configuration:'));
+      console.log(JSON.stringify(currentConfig, null, 2));
+      return;
+    }
+
+    return;
+  }
+
+  console.error(chalk.red(`Unknown action: ${action}`));
+}
+
+/**
+ * Handle config init with optional --vibe-mode
+ * @param {Object} options - Command options
+ */
+async function handleConfigInit(options) {
+  console.log('');
+  console.log(chalk.bold(t('config.initTitle', 'UDS Configuration Setup')));
+  console.log('');
+
+  // Check for --vibe-mode flag
+  if (options.vibeMode) {
+    await initVibeMode(options);
+    return;
+  }
+
+  // Default init: show menu
+  const { initType } = await inquirer.prompt([
+    {
+      type: 'list',
+      name: 'initType',
+      message: t('config.initQuestion', 'What would you like to configure?'),
+      choices: [
+        {
+          name: t('config.displayLanguageOption', 'Display Language - Change UI language'),
+          value: 'display_language'
+        },
+        {
+          name: t('config.vibeMode', 'Vibe Coding Mode - For AI-assisted development'),
+          value: 'vibe'
+        },
+        {
+          name: t('config.missionMode', 'Mission Mode - For goal-oriented development'),
+          value: 'mission'
+        },
+        {
+          name: t('config.customMode', 'Custom - Set individual options'),
+          value: 'custom'
+        }
+      ]
+    }
+  ]);
+
+  if (initType === 'display_language') {
+    await handleDisplayLanguageChange();
+    return;
+  } else if (initType === 'vibe') {
+    await initVibeMode(options);
+  } else if (initType === 'mission') {
+    console.log(chalk.yellow(t('config.missionComingSoon', 'Mission mode setup coming soon!')));
+    console.log(chalk.gray(t('config.useStartCommand', 'For now, use: uds start <mission-type> <intent>')));
+  } else {
+    console.log(chalk.gray(t('config.customHint', 'Use: uds config set <key> <value>')));
+  }
+}
+
+/**
+ * Handle display language change
+ */
+async function handleDisplayLanguageChange() {
+  const projectPath = process.cwd();
+  const initialized = isInitialized(projectPath);
+  let currentLang = config.get('ui.language') || 'en';
+
+  if (initialized) {
+    const manifest = readManifest(projectPath);
+    if (manifest?.options?.display_language) {
+      currentLang = manifest.options.display_language;
+    }
+  }
+
+  const langNames = { en: 'English', 'zh-tw': '繁體中文', 'zh-cn': '简体中文' };
+  console.log(chalk.gray(`  ${t('config.currentLanguage', 'Current language')}: ${langNames[currentLang] || currentLang}`));
+
+  const newLang = await promptDisplayLanguage();
+
+  if (newLang === currentLang) {
+    console.log(chalk.gray(t('config.noLanguageChange', 'Language unchanged.')));
+    return;
+  }
+
+  if (!initialized) {
+    const common = getMessages().commands.common;
+    console.log(chalk.red(common.notInitialized));
+    console.log(chalk.gray(`  ${common.runInit}`));
+    return;
+  }
+
+  const manifest = readManifest(projectPath);
+  if (manifest) {
+    manifest.options = manifest.options || {};
+    manifest.options.display_language = newLang;
+    writeManifest(manifest, projectPath);
+    console.log(chalk.green(t('config.languageUpdated', 'Display language updated!')));
+
+    // Offer to regenerate integrations if AI tools are configured
+    if (manifest.aiTools?.length > 0) {
+      const { confirm } = await inquirer.prompt([{
+        type: 'confirm',
+        name: 'confirm',
+        message: t('config.regenerateForLanguage', 'Regenerate AI tool integrations with new language?'),
+        default: true
+      }]);
+
+      if (confirm) {
+        const spinner = (await import('ora')).default(t('config.applyingPreset', 'Applying...')).start();
+        regenerateIntegrations(projectPath, manifest);
+        writeManifest(manifest, projectPath);
+        spinner.succeed(t('config.languageUpdated', 'Display language updated!'));
+      }
+    }
+  }
+}
+
+/**
+ * Initialize Vibe Coding mode
+ * @param {Object} options - Command options
+ */
+async function initVibeMode(options) {
+  console.log(chalk.bold(t('config.vibeModeTitle', 'Vibe Coding Configuration')));
+  console.log(chalk.gray(t('config.vibeModeDesc', 'Configure UDS for natural language-driven development')));
+  console.log('');
+
+  // Select preset
+  let preset;
+  if (options.yes) {
+    preset = 'balanced';
+  } else {
+    const { selectedPreset } = await inquirer.prompt([
+      {
+        type: 'list',
+        name: 'selectedPreset',
+        message: t('config.selectPreset', 'Select a preset:'),
+        choices: Object.entries(VIBE_PRESETS).map(([key, value]) => ({
+          name: `${t(`config.presets.${key}.name`, value.name)}\n     ${chalk.gray(t(`config.presets.${key}.description`, value.description))}`,
+          value: key,
+          short: t(`config.presets.${key}.name`, value.name)
+        }))
+      }
+    ]);
+    preset = selectedPreset;
+  }
+
+  const presetConfig = VIBE_PRESETS[preset];
+  const scope = options.global ? 'global' : 'project';
+
+  // Show what will be set
+  console.log('');
+  const presetName = t(`config.presets.${preset}.name`, presetConfig.name);
+  console.log(chalk.cyan(`${t('config.applyingPreset', 'Applying preset:')} ${presetName}`));
+  console.log(chalk.gray('─'.repeat(50)));
+
+  for (const [key, value] of Object.entries(presetConfig.settings)) {
+    console.log(`  ${key}: ${chalk.yellow(value)}`);
+  }
+  console.log(chalk.gray('─'.repeat(50)));
+
+  // Confirm unless --yes
+  if (!options.yes) {
+    const { confirm } = await inquirer.prompt([
+      {
+        type: 'confirm',
+        name: 'confirm',
+        message: t('config.confirmApply', 'Apply these settings?'),
+        default: true
+      }
+    ]);
+
+    if (!confirm) {
+      console.log(chalk.gray(t('config.cancelled', 'Configuration cancelled.')));
+      return;
+    }
+  }
+
+  // Apply settings
+  for (const [key, value] of Object.entries(presetConfig.settings)) {
+    config.set(key, value, scope);
+  }
+
+  console.log('');
+  console.log(chalk.green(t('config.vibeEnabled', 'Vibe Coding mode enabled!')));
+  console.log('');
+  console.log(chalk.gray(t('config.nextSteps', 'Next steps:')));
+  console.log(chalk.gray(`  • ${t('config.useSpec', 'Generate specs:')} uds spec create "your idea"`));
+  console.log(chalk.gray(`  • ${t('config.useSweep', 'Clean up code:')} uds sweep`));
+  console.log(chalk.gray(`  • ${t('config.useStart', 'Start a mission:')} uds start greenfield "MyApp"`));
+}
+
+/**
+ * Run project configuration (formerly configureCommand)
+ * @param {Object} options - Command options
+ */
+export async function runProjectConfiguration(options) {
+  const projectPath = process.cwd();
+
+  // Check if initialized first
+  if (!isInitialized(projectPath)) {
+    const common = getMessages().commands.common;
+    console.log(chalk.red(common.notInitialized));
+    console.log(chalk.gray(`  ${common.runInit}`));
+    return;
+  }
+
+  // Read manifest and set language before using getMessages()
+  const manifest = readManifest(projectPath);
+  if (!manifest) {
+    const common = getMessages().commands.common;
+    console.log(chalk.red(common.couldNotReadManifest));
+    return;
+  }
+
+  // Set UI language based on display_language setting
+  // Only override if user didn't explicitly set --ui-lang flag
+  if (!isLanguageExplicitlySet()) {
+    const uiLang = manifest.options?.display_language || 'en';
+    setLanguage(uiLang);
+  }
+
+  // Now get localized messages
+  const msgObj = getMessages().commands.configure;
+  const common = getMessages().commands.common;
+
+  console.log();
+  console.log(chalk.bold(msgObj.title));
+  console.log(chalk.gray('─'.repeat(50)));
+
+  console.log();
+  console.log(chalk.cyan(msgObj.currentConfig));
+  console.log(chalk.gray(`  ${common.level}: ${manifest.level || 2}`));
+  console.log(chalk.gray(`  ${common.format}: ${manifest.format || 'human'}`));
+  console.log(chalk.gray(`  ${common.contentMode}: ${manifest.contentMode || 'minimal'}`));
+  console.log(chalk.gray(`  ${common.aiTools}: ${manifest.aiTools?.length > 0 ? manifest.aiTools.join(', ') : common.none}`));
+  // Only show methodology with -E flag (completely hidden otherwise)
+  if (options.experimental && manifest.methodology?.active) {
+    console.log(chalk.gray(`  ${common.methodology}: ${manifest.methodology.active.toUpperCase()}`) + chalk.yellow(` ${msgObj.experimental}`));
+  }
+  if (manifest.options) {
+    if (manifest.options.workflow) {
+      console.log(chalk.gray(`  ${msgObj.gitWorkflow}: ${manifest.options.workflow}`));
+    }
+    if (manifest.options.merge_strategy) {
+      console.log(chalk.gray(`  ${msgObj.mergeStrategy}: ${manifest.options.merge_strategy}`));
+    }
+    if (manifest.options.commit_language) {
+      console.log(chalk.gray(`  ${msgObj.commitLanguage}: ${manifest.options.commit_language}`));
+    }
+    if (manifest.options.test_levels && manifest.options.test_levels.length > 0) {
+      console.log(chalk.gray(`  ${msgObj.testLevels}: ${manifest.options.test_levels.join(', ')}`));
+    }
+  }
+  console.log();
+
+  // Determine what to configure based on options or interactive mode
+  let configType = options.type || null;
+
+  if (!configType) {
+    const inq = await import('inquirer');
+
+    // Build choices array - methodology only shown with -E flag
+    const baseChoices = [
+      { name: msgObj.optionFormat, value: 'format' },
+      { name: msgObj.optionWorkflow, value: 'workflow' },
+      { name: msgObj.optionMergeStrategy, value: 'merge_strategy' },
+      { name: msgObj.optionCommitLanguage, value: 'commit_language' },
+      { name: msgObj.optionTestLevels, value: 'test_levels' },
+      new inq.default.Separator(),
+      { name: chalk.cyan(msgObj.optionAITools), value: 'ai_tools' },
+      { name: chalk.cyan(msgObj.optionSkills || 'Manage Skills installations'), value: 'skills' },
+      { name: chalk.cyan(msgObj.optionCommands || 'Manage Commands installations'), value: 'commands' },
+      new inq.default.Separator(),
+      { name: chalk.cyan(msgObj.optionLevel), value: 'level' },
+      { name: chalk.cyan(msgObj.optionContentMode), value: 'content_mode' }
+    ];
+
+    // Only add methodology option when -E flag is used
+    if (options.experimental) {
+      baseChoices.push(
+        { name: `${chalk.cyan(msgObj.optionMethodology)} ${chalk.yellow(msgObj.experimental)}`, value: 'methodology' }
+      );
+    }
+
+    baseChoices.push(
+      new inq.default.Separator(),
+      { name: msgObj.optionAll, value: 'all' }
+    );
+
+    const { type } = await inq.default.prompt([
+      {
+        type: 'list',
+        name: 'type',
+        message: msgObj.selectOption,
+        choices: baseChoices
+      }
+    ]);
+    configType = type;
+  }
+
+  // Collect new options
+  const newOptions = { ...manifest.options };
+  let newFormat = manifest.format;
+  let newLevel = manifest.level || 2;
+  let newContentMode = manifest.contentMode || 'minimal';
+  let newAITools = [...(manifest.aiTools || [])];
+  let needsIntegrationRegeneration = false;
+
+  // Handle AI Tools configuration
+  if (configType === 'ai_tools') {
+    const result = await promptManageAITools(manifest.aiTools || []);
+
+    if (result.action === 'add' && result.tools.length > 0) {
+      // Handle AGENTS.md sharing
+      const toolsWithSharing = handleAgentsMdSharing(result.tools);
+      newAITools = [...new Set([...newAITools, ...toolsWithSharing])];
+      needsIntegrationRegeneration = true;
+    } else if (result.action === 'remove' && result.tools.length > 0) {
+      newAITools = newAITools.filter(tool => !result.tools.includes(tool));
+
+      // Remove integration files for removed tools
+      const spinner = ora(msgObj.removingIntegrations).start();
+      for (const tool of result.tools) {
+        const filePath = join(projectPath, getToolFilePath(tool));
+        if (existsSync(filePath)) {
+          try {
+            unlinkSync(filePath);
+            console.log(chalk.gray(`  ${msgObj.removed}: ${getToolFilePath(tool)}`));
+          } catch (err) {
+            console.log(chalk.yellow(`  ${msgObj.couldNotRemove}: ${getToolFilePath(tool)}`));
+          }
+        }
+      }
+      spinner.succeed(msgObj.integrationsRemoved);
+    } else if (result.action === 'view' || result.action === 'cancel') {
+      console.log(chalk.gray(msgObj.noChanges));
+      process.exit(0);
+    }
+  }
+
+  // Handle Skills configuration
+  if (configType === 'skills') {
+    await handleSkillsConfiguration(manifest, projectPath, msgObj, common, options.aiTool, options.skillsLocation);
+    process.exit(0);
+  }
+
+  // Handle Commands configuration
+  if (configType === 'commands') {
+    await handleCommandsConfiguration(manifest, projectPath, msgObj, common, options.aiTool);
+    process.exit(0);
+  }
+
+  // Handle Level configuration
+  if (configType === 'level') {
+    newLevel = await promptAdoptionLevel(manifest.level || 2);
+    if (newLevel !== manifest.level) {
+      needsIntegrationRegeneration = true;
+    }
+  }
+
+  // Handle Content Mode configuration
+  if (configType === 'content_mode') {
+    newContentMode = await promptContentModeChange(manifest.contentMode || 'minimal');
+    if (newContentMode !== manifest.contentMode) {
+      needsIntegrationRegeneration = true;
+    }
+  }
+
+  // Handle Methodology configuration
+  let newMethodology = manifest.methodology?.active || null;
+  if (configType === 'methodology') {
+    newMethodology = await promptMethodology();
+  }
+
+  // Handle traditional options
+  if (configType === 'all' || configType === 'format') {
+    newFormat = await promptFormat();
+  }
+
+  if (configType === 'all' || configType === 'workflow') {
+    newOptions.workflow = await promptGitWorkflow();
+  }
+
+  if (configType === 'all' || configType === 'merge_strategy') {
+    newOptions.merge_strategy = await promptMergeStrategy();
+  }
+
+  if (configType === 'all' || configType === 'commit_language') {
+    newOptions.commit_language = await promptCommitLanguage();
+  }
+
+  if (configType === 'all' || configType === 'test_levels') {
+    newOptions.test_levels = await promptTestLevels();
+  }
+
+  // Show changes
+  console.log();
+  console.log(chalk.cyan(msgObj.newConfig));
+  console.log(chalk.gray(`  ${common.level}: ${newLevel}`));
+  console.log(chalk.gray(`  ${common.format}: ${newFormat}`));
+  console.log(chalk.gray(`  ${common.contentMode}: ${newContentMode}`));
+  console.log(chalk.gray(`  ${common.aiTools}: ${newAITools.length > 0 ? newAITools.join(', ') : common.none}`));
+  if (newMethodology) {
+    console.log(chalk.gray(`  ${common.methodology}: ${newMethodology.toUpperCase()}`));
+  }
+  if (newOptions.workflow) {
+    console.log(chalk.gray(`  ${msgObj.gitWorkflow}: ${newOptions.workflow}`));
+  }
+  if (newOptions.merge_strategy) {
+    console.log(chalk.gray(`  ${msgObj.mergeStrategy}: ${newOptions.merge_strategy}`));
+  }
+  if (newOptions.commit_language) {
+    console.log(chalk.gray(`  ${msgObj.commitLanguage}: ${newOptions.commit_language}`));
+  }
+  if (newOptions.test_levels && newOptions.test_levels.length > 0) {
+    console.log(chalk.gray(`  ${msgObj.testLevels}: ${newOptions.test_levels.join(', ')}`));
+  }
+  console.log();
+
+  // Confirm (skip if --yes flag is provided)
+  if (!options.yes) {
+    const confirmed = await promptConfirm(msgObj.applyChanges);
+    if (!confirmed) {
+      console.log(chalk.yellow(msgObj.configCancelled));
+      process.exit(0);
+    }
+  }
+
+  // Apply changes
+  const spinner = ora(msgObj.updatingConfig).start();
+
+  const results = {
+    copied: [],
+    generated: [],
+    errors: []
+  };
+
+  const standards = getAllStandards();
+  const formatsToUse = newFormat === 'both' ? ['ai', 'human'] : [newFormat];
+
+  // Helper to copy option files
+  const copyOptionFile = async (std, optionCategory, optionId, targetFormat) => {
+    const option = findOption(std, optionCategory, optionId);
+    if (option) {
+      const sourcePath = getOptionSource(option, targetFormat);
+      const result = await copyStandard(sourcePath, '.standards/options', projectPath);
+      if (result.success) {
+        results.copied.push(sourcePath);
+      } else {
+        results.errors.push(`${sourcePath}: ${result.error}`);
+      }
+    }
+  };
+
+  // Copy new option files
+  for (const std of standards) {
+    if (!std.options) continue;
+
+    for (const targetFormat of formatsToUse) {
+      // Git workflow
+      if (std.id === 'git-workflow') {
+        if (newOptions.workflow && newOptions.workflow !== manifest.options?.workflow) {
+          await copyOptionFile(std, 'workflow', newOptions.workflow, targetFormat);
+        }
+        if (newOptions.merge_strategy && newOptions.merge_strategy !== manifest.options?.merge_strategy) {
+          await copyOptionFile(std, 'merge_strategy', newOptions.merge_strategy, targetFormat);
+        }
+      }
+
+      // Commit message
+      if (std.id === 'commit-message') {
+        if (newOptions.commit_language && newOptions.commit_language !== manifest.options?.commit_language) {
+          await copyOptionFile(std, 'commit_language', newOptions.commit_language, targetFormat);
+        }
+      }
+
+      // Testing
+      if (std.id === 'testing' && newOptions.test_levels) {
+        for (const level of newOptions.test_levels) {
+          if (!manifest.options?.test_levels?.includes(level)) {
+            await copyOptionFile(std, 'test_level', level, targetFormat);
+          }
+        }
+      }
+    }
+  }
+
+  // Handle level change - copy new standards if upgrading
+  if (newLevel > (manifest.level || 2)) {
+    const levelSpinner = ora(msgObj.addingStandards).start();
+    const newStandards = getStandardsByLevel(newLevel);
+    const existingStandards = new Set(manifest.standards?.map(s => basename(s)) || []);
+
+    for (const std of newStandards) {
+      for (const targetFormat of formatsToUse) {
+        const sourcePath = getStandardSource(std, targetFormat);
+        const fileName = basename(sourcePath);
+        if (!existingStandards.has(fileName)) {
+          const result = await copyStandard(sourcePath, '.standards', projectPath);
+          if (result.success) {
+            results.copied.push(sourcePath);
+          }
+        }
+      }
+    }
+    levelSpinner.succeed(msgObj.standardsAdded);
+  }
+
+  // Regenerate integration files if needed
+  if (needsIntegrationRegeneration && newAITools.length > 0) {
+    const intSpinner = ora(msgObj.regeneratingIntegrations).start();
+
+    // Build installed standards list
+    const installedStandardsList = manifest.standards?.map(s => basename(s)) || [];
+
+    // Determine language setting
+    let commonLanguage = 'en';
+    if (newOptions.commit_language === 'bilingual') {
+      commonLanguage = 'bilingual';
+    } else if (newOptions.commit_language === 'traditional-chinese') {
+      commonLanguage = 'zh-tw';
+    }
+
+    // Track generated files to handle AGENTS.md sharing
+    const generatedFiles = new Set();
+
+    for (const tool of newAITools) {
+      const targetFile = getToolFilePath(tool);
+      if (generatedFiles.has(targetFile)) {
+        continue; // Skip if already generated (AGENTS.md sharing)
+      }
+
+      const toolConfig = {
+        tool,
+        categories: ['anti-hallucination', 'commit-standards', 'code-review'],
+        language: commonLanguage,
+        installedStandards: installedStandardsList,
+        contentMode: newContentMode,
+        level: newLevel,
+        // Pass commit_language for dynamic commit standards generation
+        commitLanguage: newOptions.commit_language || 'english'
+      };
+
+      const result = writeIntegrationFile(tool, toolConfig, projectPath);
+      if (result.success) {
+        results.generated.push(result.path);
+        generatedFiles.add(targetFile);
+      } else {
+        results.errors.push(`${tool}: ${result.error}`);
+      }
+    }
+    intSpinner.succeed(msgObj.regeneratedIntegrations.replace('{count}', results.generated.length));
+  }
+
+  // Update manifest
+  manifest.format = newFormat;
+  manifest.options = newOptions;
+  manifest.level = newLevel;
+  manifest.contentMode = newContentMode;
+  manifest.aiTools = newAITools;
+  manifest.version = '3.2.0';
+
+  // Update methodology
+  if (newMethodology) {
+    manifest.methodology = {
+      active: newMethodology,
+      available: ['tdd', 'bdd', 'sdd', 'atdd'],
+      config: {
+        checkpointsEnabled: true,
+        reminderIntensity: 'suggest',
+        skipLimit: 3
+      }
+    };
+  } else if (configType === 'methodology' && !newMethodology) {
+    // User explicitly chose "None"
+    manifest.methodology = null;
+  }
+
+  writeManifest(manifest, projectPath);
+
+  spinner.succeed(msgObj.configUpdated);
+
+  // Summary
+  console.log();
+  console.log(chalk.green(msgObj.configSuccess));
+  if (results.copied.length > 0) {
+    console.log(chalk.gray(`  ${msgObj.newOptionsCopied.replace('{count}', results.copied.length)}`));
+  }
+  if (results.generated.length > 0) {
+    console.log(chalk.gray(`  ${msgObj.integrationsRegenerated.replace('{count}', results.generated.length)}`));
+  }
+
+  if (results.errors.length > 0) {
+    console.log();
+    console.log(chalk.yellow(msgObj.errorsOccurred.replace('{count}', results.errors.length)));
+    for (const err of results.errors) {
+      console.log(chalk.gray(`    ${err}`));
+    }
+  }
+
+  // Smart apply: offer to regenerate integrations if config changed but not already regenerated
+  // Skip for types that have their own flow or don't affect integrations
+  const skipApplyTypes = ['skills', 'commands', 'methodology'];
+  const alreadyRegenerated = results.generated.length > 0;
+  const shouldOfferApply = !skipApplyTypes.includes(configType) &&
+                           newAITools.length > 0 &&
+                           !alreadyRegenerated;
+
+  if (shouldOfferApply) {
+    console.log();
+
+    if (options.yes) {
+      // --yes flag: auto-apply without prompting
+      const applySpinner = ora(msgObj.applyingChanges).start();
+      const applyResults = regenerateIntegrations(projectPath, manifest);
+      applySpinner.succeed(msgObj.changesApplied || msgObj.regeneratedIntegrations.replace('{count}', applyResults.updated.length));
+
+      // Update manifest with new file hashes
+      writeManifest(manifest, projectPath);
+
+      if (applyResults.errors.length > 0) {
+        console.log(chalk.yellow(msgObj.errorsOccurred.replace('{count}', applyResults.errors.length)));
+        for (const err of applyResults.errors) {
+          console.log(chalk.gray(`    ${err}`));
+        }
+      }
+    } else {
+      // Interactive mode: prompt user
+      const inq = await import('inquirer');
+      const { apply } = await inq.default.prompt([{
+        type: 'confirm',
+        name: 'apply',
+        message: msgObj.applyChangesNow,
+        default: true
+      }]);
+
+      if (apply) {
+        const applySpinner = ora(msgObj.applyingChanges).start();
+        const applyResults = regenerateIntegrations(projectPath, manifest);
+        applySpinner.succeed(msgObj.changesApplied || msgObj.regeneratedIntegrations.replace('{count}', applyResults.updated.length));
+
+        // Update manifest with new file hashes
+        writeManifest(manifest, projectPath);
+
+        if (applyResults.errors.length > 0) {
+          console.log(chalk.yellow(msgObj.errorsOccurred.replace('{count}', applyResults.errors.length)));
+          for (const err of applyResults.errors) {
+            console.log(chalk.gray(`    ${err}`));
+          }
+        }
+      } else {
+        console.log(chalk.gray(msgObj.runUpdateLater));
+      }
+    }
+  }
+
+  console.log();
+
+  // Exit explicitly to prevent hanging due to inquirer's readline interface
+  process.exit(0);
+}
+
+/**
+ * Handle Skills configuration
+ * @param {Object} manifest - Project manifest
+ * @param {string} projectPath - Project path
+ * @param {Object} msgObj - i18n messages
+ * @param {Object} common - Common i18n messages
+ * @param {string} [specificTool] - Specific AI tool to install (non-interactive mode)
+ * @param {string} [skillsLocation] - Skills installation location (project, user) for non-interactive mode
+ */
+async function handleSkillsConfiguration(manifest, projectPath, msgObj, common, specificTool, skillsLocation) {
+  const inq = await import('inquirer');
+  const aiTools = manifest.aiTools || [];
+
+  // Non-interactive mode: install for specific tool
+  if (specificTool) {
+    const agentCfg = getAgentConfig(specificTool);
+    if (!agentCfg) {
+      console.log(chalk.red(`Unknown AI tool: ${specificTool}`));
+      console.log(chalk.gray('  Available tools: claude-code, opencode, copilot, gemini-cli, roo-code, cursor, windsurf, cline, codex'));
+      return;
+    }
+    if (!agentCfg.supportsSkills) {
+      console.log(chalk.yellow(`${getAgentDisplayName(specificTool)} does not support Skills`));
+      return;
+    }
+
+    // Validate skillsLocation if provided
+    const validLocations = ['project', 'user'];
+    const level = skillsLocation && validLocations.includes(skillsLocation) ? skillsLocation : 'project';
+
+    // Install to specified level (defaults to project)
+    const installations = [{ agent: specificTool, level }];
+    const spinner = ora(`Installing Skills for ${getAgentDisplayName(specificTool)} (${level} level)...`).start();
+    const result = await installSkillsToMultipleAgents(installations, null, projectPath);
+    spinner.stop();
+
+    if (result.success) {
+      console.log(chalk.green(`Skills installed for ${getAgentDisplayName(specificTool)}`));
+    } else {
+      console.log(chalk.yellow('Skills installation completed with issues'));
+    }
+
+    // Update manifest
+    manifest.skills = manifest.skills || {};
+    manifest.skills.installations = manifest.skills.installations || [];
+    const existing = manifest.skills.installations.findIndex(i => i.agent === specificTool);
+    if (existing >= 0) {
+      manifest.skills.installations[existing] = installations[0];
+    } else {
+      manifest.skills.installations.push(installations[0]);
+    }
+    writeManifest(manifest, projectPath);
+    return;
+  }
+
+  // Interactive mode
+  if (aiTools.length === 0) {
+    console.log(chalk.yellow(msgObj.noAiToolsConfigured || 'No AI tools configured'));
+    console.log(chalk.gray(`  ${msgObj.addAiToolsFirst || 'Add AI tools first with: uds config --type ai_tools'}`));
+    return;
+  }
+
+  // Get declined skills from manifest
+  const declinedSkills = manifest.declinedFeatures?.skills || [];
+
+  // Check if Skills are installed via marketplace (Claude Code only)
+  const marketplaceInfo = getMarketplaceSkillsInfo();
+  const hasMarketplaceSkills = marketplaceInfo?.installed;
+
+  // Show current Skills status
+  console.log(chalk.cyan(msgObj.currentSkillsStatus || 'Current Skills status:'));
+
+  // Show marketplace status if applicable
+  if (hasMarketplaceSkills && aiTools.includes('claude-code')) {
+    console.log(chalk.green(`  ✓ ${msgObj.viaMarketplace || 'Via Marketplace'}: ${marketplaceInfo.version || 'installed'}`));
+  }
+
+  for (const tool of aiTools) {
+    const agentCfg = getAgentConfig(tool);
+    if (!agentCfg?.supportsSkills) continue;
+
+    const displayName = getAgentDisplayName(tool);
+    const projectInfo = getInstalledSkillsInfoForAgent(tool, 'project', projectPath);
+    const userInfo = getInstalledSkillsInfoForAgent(tool, 'user', projectPath);
+
+    if (projectInfo?.installed || userInfo?.installed) {
+      console.log(chalk.green(`  ✓ ${displayName}:`));
+      if (userInfo?.installed) {
+        console.log(chalk.gray(`    - User: ${userInfo.version || 'installed'}`));
+      }
+      if (projectInfo?.installed) {
+        console.log(chalk.gray(`    - Project: ${projectInfo.version || 'installed'}`));
+      }
+    } else if (declinedSkills.includes(tool)) {
+      console.log(chalk.yellow(`  ⊘ ${displayName}: ${msgObj.previouslyDeclined || 'Previously declined'}`));
+    } else if (hasMarketplaceSkills && tool === 'claude-code') {
+      // Claude Code has marketplace skills but no file-based installation
+      console.log(chalk.cyan(`  ◎ ${displayName}: ${msgObj.marketplaceOnly || 'Marketplace only (no local files)'}`));
+    } else {
+      console.log(chalk.gray(`  ○ ${displayName}: ${msgObj.notInstalled || 'Not installed'}`));
+    }
+  }
+
+  // Show marketplace coexistence note if user might want to install local files
+  if (hasMarketplaceSkills && aiTools.includes('claude-code')) {
+    console.log();
+    console.log(chalk.cyan(`  ℹ ${msgObj.marketplaceCoexistNote || 'Note: File-based installation will coexist with Marketplace version'}`));
+  }
+  console.log();
+
+  // Build menu choices
+  const menuChoices = [
+    { name: msgObj.installSkills || 'Install/Update Skills', value: 'install' }
+  ];
+
+  // Add reinstall declined option if there are declined skills
+  if (declinedSkills.length > 0) {
+    menuChoices.push({
+      name: msgObj.reinstallDeclinedSkills || 'Reinstall declined Skills',
+      value: 'reinstall_declined'
+    });
+  }
+
+  menuChoices.push(
+    { name: msgObj.viewStatus || 'View status only', value: 'view' },
+    { name: common.cancelled || 'Cancel', value: 'cancel' }
+  );
+
+  // Ask what action to take
+  const { action } = await inq.default.prompt([
+    {
+      type: 'list',
+      name: 'action',
+      message: msgObj.skillsAction || 'What would you like to do?',
+      choices: menuChoices
+    }
+  ]);
+
+  if (action === 'cancel' || action === 'view') {
+    console.log(chalk.gray(msgObj.noChanges || 'No changes made'));
+    return;
+  }
+
+  // Handle reinstall declined action
+  if (action === 'reinstall_declined') {
+    // Get only the declined tools that support skills
+    const declinedToolsWithSupport = declinedSkills.filter(tool => {
+      const agentCfg = getAgentConfig(tool);
+      return agentCfg?.supportsSkills;
+    });
+
+    if (declinedToolsWithSupport.length === 0) {
+      console.log(chalk.gray(msgObj.noChanges || 'No changes made'));
+      return;
+    }
+
+    // Prompt for installation level
+    const { skillsLevel } = await inq.default.prompt([{
+      type: 'list',
+      name: 'skillsLevel',
+      message: msgObj.skillsLevelQuestion || 'Where should Skills be installed?',
+      choices: [
+        { name: `${msgObj.projectLevel || 'Project level'} (.claude/skills/, etc.)`, value: 'project' },
+        { name: `${msgObj.userLevel || 'User level'} (~/.claude/skills/, etc.)`, value: 'user' }
+      ],
+      default: 'project'
+    }]);
+
+    const installations = declinedToolsWithSupport.map(agent => ({
+      agent,
+      location: skillsLevel
+    }));
+
+    // Install Skills
+    const spinner = ora(msgObj.installingSkills || 'Installing Skills...').start();
+    const result = await installSkillsToMultipleAgents(installations, null, projectPath);
+    spinner.stop();
+
+    if (result.success) {
+      console.log(chalk.green(msgObj.skillsInstallSuccess || 'Skills installed successfully'));
+      console.log(chalk.gray(`  ${msgObj.totalInstalled || 'Total installed'}: ${result.totalInstalled}`));
+    } else {
+      console.log(chalk.yellow(msgObj.skillsInstallPartial || 'Skills installed with some issues'));
+      if (result.totalErrors > 0) {
+        console.log(chalk.red(`  ${msgObj.errors || 'Errors'}: ${result.totalErrors}`));
+      }
+    }
+
+    // Update manifest - clear declined status for installed tools
+    manifest.skills = manifest.skills || {};
+    manifest.skills.installations = installations;
+    if (manifest.declinedFeatures?.skills) {
+      manifest.declinedFeatures.skills = manifest.declinedFeatures.skills.filter(
+        tool => !declinedToolsWithSupport.includes(tool)
+      );
+    }
+    writeManifest(manifest, projectPath);
+    return;
+  }
+
+  // Use unified installation prompt
+  const installations = await promptSkillsInstallLocation(aiTools);
+  if (installations.length === 0) {
+    console.log(chalk.gray(msgObj.noChanges || 'No changes made'));
+    return;
+  }
+
+  // Install Skills
+  const spinner = ora(msgObj.installingSkills || 'Installing Skills...').start();
+  const result = await installSkillsToMultipleAgents(installations, null, projectPath);
+  spinner.stop();
+
+  if (result.success) {
+    console.log(chalk.green(msgObj.skillsInstallSuccess || 'Skills installed successfully'));
+    console.log(chalk.gray(`  ${msgObj.totalInstalled || 'Total installed'}: ${result.totalInstalled}`));
+  } else {
+    console.log(chalk.yellow(msgObj.skillsInstallPartial || 'Skills installed with some issues'));
+    if (result.totalErrors > 0) {
+      console.log(chalk.red(`  ${msgObj.errors || 'Errors'}: ${result.totalErrors}`));
+    }
+  }
+
+  // Update manifest
+  manifest.skills = manifest.skills || {};
+  manifest.skills.installations = installations;
+  writeManifest(manifest, projectPath);
+}
+
+/**
+ * Handle Commands configuration
+ * @param {Object} manifest - Project manifest
+ * @param {string} projectPath - Project path
+ * @param {Object} msgObj - i18n messages
+ * @param {Object} common - Common i18n messages
+ * @param {string} [specificTool] - Specific AI tool to install (triggers interactive prompt for level)
+ */
+async function handleCommandsConfiguration(manifest, projectPath, msgObj, common, specificTool) {
+  const inq = await import('inquirer');
+  const aiTools = manifest.aiTools || [];
+
+  // Semi-interactive mode: install for specific tool (prompt for level)
+  if (specificTool) {
+    const agentCfg = getAgentConfig(specificTool);
+    if (!agentCfg) {
+      console.log(chalk.red(`Unknown AI tool: ${specificTool}`));
+      console.log(chalk.gray('  Available tools: claude-code, opencode, copilot, gemini-cli, roo-code'));
+      return;
+    }
+    if (agentCfg.commands === null) {
+      console.log(chalk.yellow(`${getAgentDisplayName(specificTool)} does not support Commands`));
+      console.log(chalk.gray('  Tools that support commands: OpenCode, Copilot, Roo Code, Gemini CLI'));
+      return;
+    }
+
+    // Prompt for installation level
+    const { commandsLevel } = await inq.default.prompt([{
+      type: 'list',
+      name: 'commandsLevel',
+      message: msgObj.commandsLevelQuestion || 'Where should Commands be installed?',
+      choices: [
+        { name: `${msgObj.projectLevel || 'Project level'} (${agentCfg.commands.project}) (${msgObj.recommended || 'Recommended'})`, value: 'project' },
+        { name: `${msgObj.userLevel || 'User level'} (${agentCfg.commands.user})`, value: 'user' }
+      ],
+      default: 'project'
+    }]);
+
+    // Install to selected level
+    const installations = [{ agent: specificTool, level: commandsLevel }];
+    const spinner = ora(`Installing Commands for ${getAgentDisplayName(specificTool)} (${commandsLevel} level)...`).start();
+    const result = await installCommandsToMultipleAgents(installations, null, projectPath);
+    spinner.stop();
+
+    if (result.success) {
+      console.log(chalk.green(`Commands installed for ${getAgentDisplayName(specificTool)}`));
+    } else {
+      console.log(chalk.yellow('Commands installation completed with issues'));
+    }
+
+    // Update manifest
+    manifest.commands = manifest.commands || {};
+    manifest.commands.installations = manifest.commands.installations || [];
+    const existing = manifest.commands.installations.findIndex(i =>
+      typeof i === 'string' ? i === specificTool : i.agent === specificTool
+    );
+    if (existing >= 0) {
+      manifest.commands.installations[existing] = installations[0];
+    } else {
+      manifest.commands.installations.push(installations[0]);
+    }
+    writeManifest(manifest, projectPath);
+    return;
+  }
+
+  // Interactive mode
+  // Filter tools that support commands (commands !== null means support)
+  const commandSupportedTools = aiTools.filter(tool => {
+    const agentCfg = getAgentConfig(tool);
+    return agentCfg?.commands !== null;
+  });
+
+  if (commandSupportedTools.length === 0) {
+    console.log(chalk.yellow(msgObj.noCommandSupportedTools || 'No AI tools with command support configured'));
+    console.log(chalk.gray(`  ${msgObj.commandSupportedList || 'Tools that support commands: OpenCode, Copilot, Roo Code, Gemini CLI'}`));
+    return;
+  }
+
+  // Get declined commands from manifest
+  const declinedCommands = manifest.declinedFeatures?.commands || [];
+
+  // Show current Commands status (check both project and user levels)
+  console.log(chalk.cyan(msgObj.currentCommandsStatus || 'Current Commands status:'));
+  for (const tool of commandSupportedTools) {
+    const displayName = getAgentDisplayName(tool);
+    const projectCmdInfo = getInstalledCommandsForAgent(tool, 'project', projectPath);
+    const userCmdInfo = getInstalledCommandsForAgent(tool, 'user');
+
+    if (projectCmdInfo?.installed || userCmdInfo?.installed) {
+      console.log(chalk.green(`  ✓ ${displayName}:`));
+      if (userCmdInfo?.installed) {
+        console.log(chalk.gray(`    - User: ${userCmdInfo.count} commands`));
+      }
+      if (projectCmdInfo?.installed) {
+        console.log(chalk.gray(`    - Project: ${projectCmdInfo.count} commands`));
+      }
+    } else if (declinedCommands.includes(tool)) {
+      console.log(chalk.yellow(`  ⊘ ${displayName}: ${msgObj.previouslyDeclined || 'Previously declined'}`));
+    } else {
+      console.log(chalk.gray(`  ○ ${displayName}: ${msgObj.notInstalled || 'Not installed'}`));
+    }
+  }
+  console.log();
+
+  // Build menu choices
+  const menuChoices = [
+    { name: msgObj.installCommands || 'Install/Update Commands', value: 'install' }
+  ];
+
+  // Add reinstall declined option if there are declined commands
+  const declinedCommandsWithSupport = declinedCommands.filter(tool =>
+    commandSupportedTools.includes(tool)
+  );
+  if (declinedCommandsWithSupport.length > 0) {
+    menuChoices.push({
+      name: msgObj.reinstallDeclinedCommands || 'Reinstall declined Commands',
+      value: 'reinstall_declined'
+    });
+  }
+
+  menuChoices.push(
+    { name: msgObj.viewStatus || 'View status only', value: 'view' },
+    { name: common.cancelled || 'Cancel', value: 'cancel' }
+  );
+
+  // Ask what action to take
+  const { action } = await inq.default.prompt([
+    {
+      type: 'list',
+      name: 'action',
+      message: msgObj.commandsAction || 'What would you like to do?',
+      choices: menuChoices
+    }
+  ]);
+
+  if (action === 'cancel' || action === 'view') {
+    console.log(chalk.gray(msgObj.noChanges || 'No changes made'));
+    return;
+  }
+
+  // Handle reinstall declined action
+  if (action === 'reinstall_declined') {
+    if (declinedCommandsWithSupport.length === 0) {
+      console.log(chalk.gray(msgObj.noChanges || 'No changes made'));
+      return;
+    }
+
+    // Install Commands
+    const spinner = ora(msgObj.installingCommands || 'Installing Commands...').start();
+    const result = await installCommandsToMultipleAgents(declinedCommandsWithSupport, null, projectPath);
+    spinner.stop();
+
+    if (result.success) {
+      console.log(chalk.green(msgObj.commandsInstallSuccess || 'Commands installed successfully'));
+      console.log(chalk.gray(`  ${msgObj.totalInstalled || 'Total installed'}: ${result.totalInstalled}`));
+    } else {
+      console.log(chalk.yellow(msgObj.commandsInstallPartial || 'Commands installed with some issues'));
+      if (result.totalErrors > 0) {
+        console.log(chalk.red(`  ${msgObj.errors || 'Errors'}: ${result.totalErrors}`));
+      }
+    }
+
+    // Update manifest - clear declined status for installed tools
+    manifest.commands = manifest.commands || {};
+    manifest.commands.installations = declinedCommandsWithSupport;
+    if (manifest.declinedFeatures?.commands) {
+      manifest.declinedFeatures.commands = manifest.declinedFeatures.commands.filter(
+        tool => !declinedCommandsWithSupport.includes(tool)
+      );
+    }
+    writeManifest(manifest, projectPath);
+    return;
+  }
+
+  // Use unified installation prompt
+  const selectedAgents = await promptCommandsInstallation(commandSupportedTools);
+  if (selectedAgents.length === 0) {
+    console.log(chalk.gray(msgObj.noChanges || 'No changes made'));
+    return;
+  }
+
+  // Install Commands
+  const spinner = ora(msgObj.installingCommands || 'Installing Commands...').start();
+  const result = await installCommandsToMultipleAgents(selectedAgents, null, projectPath);
+  spinner.stop();
+
+  if (result.success) {
+    console.log(chalk.green(msgObj.commandsInstallSuccess || 'Commands installed successfully'));
+    console.log(chalk.gray(`  ${msgObj.totalInstalled || 'Total installed'}: ${result.totalInstalled}`));
+  } else {
+    console.log(chalk.yellow(msgObj.commandsInstallPartial || 'Commands installed with some issues'));
+    if (result.totalErrors > 0) {
+      console.log(chalk.red(`  ${msgObj.errors || 'Errors'}: ${result.totalErrors}`));
+    }
+  }
+
+  // Update manifest
+  manifest.commands = manifest.commands || {};
+  manifest.commands.installations = selectedAgents;
+  writeManifest(manifest, projectPath);
+}