@polymorphism-tech/morph-spec 7.4.0 → 7.6.0

package/src/commands/project/update.js

@@ -1,368 +1,415 @@
-import { join, dirname } from 'path';
-import { fileURLToPath } from 'url';
-import { spawnSync } from 'child_process';
-import { existsSync } from 'fs';
-
-const __dirname = dirname(fileURLToPath(import.meta.url));
-import fs from 'fs-extra';
-import ora from 'ora';
-import chalk from 'chalk';
-import { logger } from '../../utils/logger.js';
-import {
-  getContentDir,
-  copyDirectory,
-  copyFile,
-  pathExists,
-  ensureDir,
-  readJson,
-  writeJson,
-  updateGitignore
-} from '../../utils/file-copier.js';
-import {
-  checkCLIOutdated,
-  checkProjectOutdated,
-  saveProjectMorphVersion,
-  getUpdateInstructions,
-  detectInstallMethod
-} from '../../utils/version-checker.js';
-import { installClaudeHooks, installGlobalStatusline } from '../../utils/claude-settings-manager.js';
-import { installSkills } from '../../utils/skills-installer.js';
-import { installAgents, installDomainAgents } from '../../utils/agents-installer.js';
-import { injectMorphImport } from '../../utils/claude-md-injector.js';
-import { getProjectTags } from '../../lib/stack-filter.js';
-
-/**
- * Backup user's config.json before cleaning
- * @param {string} morphPath - Path to .morph directory
- * @returns {Promise<object|null>} Backup of config.json or null
- */
-async function backupUserConfig(morphPath) {
-  try {
-    const configPath = join(morphPath, 'config', 'config.json');
-    if (await pathExists(configPath)) {
-      const config = await readJson(configPath);
-      return config;
-    }
-  } catch (error) {
-    // If backup fails, return null and continue
-  }
-  return null;
-}
-
-/**
- * Clean framework directories but preserve .morph/project/
- * @param {string} morphPath - Path to .morph directory
- * @param {string} targetPath - Project root path
- */
-async function cleanFrameworkDirs(morphPath, targetPath) {
-  const claudeDir = join(targetPath, '.claude');
-  const dirsToClean = [
-    join(morphPath, 'framework', 'templates'),
-    join(morphPath, 'framework', 'standards'),
-    join(morphPath, 'framework', 'hooks'),
-    join(morphPath, 'config'),
-    join(claudeDir, 'commands'),
-    join(claudeDir, 'rules'),
-    join(claudeDir, 'skills'),
-    join(claudeDir, 'agents'),
-  ];
-
-  for (const dir of dirsToClean) {
-    try {
-      if (await pathExists(dir)) {
-        await fs.remove(dir);
-      }
-    } catch (error) {
-      // Continue even if cleanup fails for one directory
-    }
-  }
-}
-
-/**
- * Restore user's config.json after reinstallation
- * @param {string} morphPath - Path to .morph directory
- * @param {string} targetPath - Project root path
- * @param {object|null} configBackup - Backup of config.json
- * @param {string} currentVersion - Current CLI version
- */
-async function restoreUserConfig(morphPath, targetPath, configBackup, currentVersion) {
-  const configDir = join(morphPath, 'config');
-  await ensureDir(configDir);
-  const configPath = join(configDir, 'config.json');
-
-  if (configBackup) {
-    // Preserve user data but update framework version
-    configBackup.frameworkVersion = currentVersion;
-    await writeJson(configPath, configBackup);
-  } else {
-    // Create basic config if none existed
-    const dirName = targetPath.split(/[\\/]/).pop();
-    const defaultConfig = {
-      framework: 'global',
-      frameworkVersion: currentVersion,
-      project: {
-        name: dirName,
-        architecture: 'unknown'
-      }
-    };
-    await writeJson(configPath, defaultConfig);
-  }
-}
-
-export async function updateCommand(options) {
-  const targetPath = process.cwd();
-  const contentDir = getContentDir();
-  const morphPath = join(targetPath, '.morph');
-
-  logger.header('MORPH-SPEC Update');
-
-  // Check if MORPH is initialized
-  let needsInitialization = false;
-  if (!(await pathExists(morphPath))) {
-    logger.warn('MORPH not fully initialized. Creating basic structure...');
-    needsInitialization = true;
-
-    // Create basic .morph structure
-    await ensureDir(join(morphPath, 'context'));
-    await ensureDir(join(morphPath, 'features'));
-    await ensureDir(join(morphPath, 'framework'));
-    await ensureDir(join(morphPath, 'config'));
-    logger.dim('  ✓ Created .morph directory structure');
-  }
-
-  // Check CLI version
-  const spinner = ora('Checking versions...').start();
-  const cliCheck = await checkCLIOutdated();
-  const projectCheck = await checkProjectOutdated(targetPath);
-
-  spinner.stop();
-
-  // Display version info
-  logger.blank();
-  logger.info('Version Status:');
-  logger.dim(`  CLI version: ${cliCheck.current}`);
-
-  if (projectCheck.current) {
-    logger.dim(`  Project MORPH version: ${projectCheck.current}`);
-  } else {
-    logger.dim('  Project MORPH version: not found (legacy installation)');
-  }
-
-  if (cliCheck.latest) {
-    const latestColor = cliCheck.isOutdated ? chalk.yellow : chalk.green;
-    logger.dim(`  Latest available: ${latestColor(cliCheck.latest)}`);
-  }
-  logger.blank();
-
-  // If CLI is outdated, stop and instruct user
-  if (cliCheck.isOutdated && cliCheck.latest) {
-    logger.warn(`Your CLI is outdated (${cliCheck.current} → ${cliCheck.latest})`);
-    logger.blank();
-    logger.info('Please update the CLI first:');
-    logger.blank();
-
-    const method = detectInstallMethod();
-    const instructions = getUpdateInstructions(method);
-
-    instructions.forEach(line => {
-      if (line === '') {
-        logger.blank();
-      } else if (line.startsWith('Or ')) {
-        logger.dim(line);
-      } else {
-        logger.box([line]);
-      }
-    });
-
-    logger.blank();
-    logger.dim('Then run "morph-spec update" again.');
-    process.exit(0);
-  }
-
-  // Proceed with update
-  const updateSpinner = ora('Updating MORPH-SPEC...').start();
-
-  try {
-    // Backup user config before cleaning
-    updateSpinner.text = 'Backing up user configuration...';
-    const configBackup = await backupUserConfig(morphPath);
-    if (configBackup) {
-      logger.dim('  ✓ User config backed up');
-    }
-
-    // Clean framework directories (preserve .morph/project/)
-    updateSpinner.text = 'Cleaning old framework files...';
-    await cleanFrameworkDirs(morphPath, targetPath);
-    logger.dim('  ✓ Old framework files removed');
-
-    const updateTemplates = !options.standards || options.templates;
-    const updateStandards = !options.templates || options.standards;
-
-    // Update templates
-    if (updateTemplates) {
-      updateSpinner.text = 'Updating templates...';
-      const templatesSrc = join(contentDir, 'framework', 'templates');
-      const templatesDest = join(morphPath, 'framework', 'templates');
-      await copyDirectory(templatesSrc, templatesDest);
-    }
-
-    // Update standards
-    if (updateStandards) {
-      updateSpinner.text = 'Updating standards...';
-      const standardsSrc = join(contentDir, 'framework', 'standards');
-      const standardsDest = join(morphPath, 'framework', 'standards');
-      await copyDirectory(standardsSrc, standardsDest);
-    }
-
-    // Update hooks (runtime hook scripts under .morph/framework/hooks/)
-    updateSpinner.text = 'Updating hooks...';
-    const hooksSrc = join(__dirname, '..', '..', '..', 'framework', 'hooks');
-    const hooksDest = join(morphPath, 'framework', 'hooks');
-    if (await pathExists(hooksSrc)) {
-      await copyDirectory(hooksSrc, hooksDest);
-    }
-
-    // Update agents.json (sourced from framework/ — canonical single source of truth)
-    updateSpinner.text = 'Updating agents configuration...';
-    const agentsSrc = join(__dirname, '..', '..', '..', 'framework', 'agents.json');
-    const agentsDest = join(morphPath, 'framework', 'agents.json');
-    if (await pathExists(agentsSrc)) {
-      await copyFile(agentsSrc, agentsDest);
-    }
-
-    // Regenerate derived files (phase-utils.js, skill output tables) from output-schema.js
-    // Only runs when the generator script is present (framework dev installs via npm link)
-    updateSpinner.text = 'Syncing generated refs...';
-    try {
-      const generateScript = join(__dirname, '..', '..', '..', 'scripts', 'generate-refs.js');
-      if (existsSync(generateScript)) {
-        const result = spawnSync(process.execPath, [generateScript], { encoding: 'utf8' });
-        if (result.status === 0) {
-          logger.dim('  ✓ Generated refs synced (phase-utils.js, skill outputs)');
-        }
-      }
-    } catch {
-      // Non-fatal: generator unavailable or files already in sync
-    }
-
-    // Update .claude commands and skills
-    // Source: framework/ (canonical for all stacks)
-    updateSpinner.text = 'Setting up Claude Code integration...';
-    const frameworkDir = join(__dirname, '..', '..', '..', 'framework');
-    const claudeDest = join(targetPath, '.claude');
-
-    let commandsCopied = false;
-
-    // Copy commands directory (slash commands): framework/commands/ → .claude/commands/
-    const commandsSrc = join(frameworkDir, 'commands');
-    const commandsDest = join(claudeDest, 'commands');
-    if (await pathExists(commandsSrc)) {
-      await copyDirectory(commandsSrc, commandsDest);
-      commandsCopied = true;
-    } else {
-      logger.warn('  ⚠ framework/commands/ source missing — commands not updated');
-    }
-
-    // Compute project tags for stack-aware installation of skills, agents, and rules
-    let projectTags = [];
-    try {
-      const cfg = await readJson(join(morphPath, 'config', 'config.json'));
-      projectTags = getProjectTags(cfg);
-    } catch { /* ignore — config may not exist yet */ }
-
-    // Sync morph skills to .claude/skills/ for native Claude Code discovery
-    updateSpinner.text = 'Syncing morph skills to .claude/skills/...';
-    await installSkills(targetPath, { projectTags });
-
-    // Sync native subagents to .claude/agents/
-    updateSpinner.text = 'Syncing agents to .claude/agents/...';
-    await installAgents(targetPath, frameworkDir, { projectTags });
-    await installDomainAgents(targetPath, frameworkDir, { projectTags });
-
-    // Sync path-scoped rules to .claude/rules/
-    updateSpinner.text = 'Syncing rules to .claude/rules/...';
-    const rulesSrc = join(frameworkDir, 'rules');
-    const rulesDest = join(claudeDest, 'rules');
-    if (await pathExists(rulesSrc)) {
-      await copyDirectory(rulesSrc, rulesDest);
-    }
-
-    // Sync runtime CLAUDE.md to .claude/CLAUDE.md
-    updateSpinner.text = 'Syncing .claude/CLAUDE.md...';
-    const runtimeSrc = join(frameworkDir, 'CLAUDE.md');
-    const runtimeDest = join(claudeDest, 'CLAUDE.md');
-    if (await pathExists(runtimeSrc)) {
-      await copyFile(runtimeSrc, runtimeDest);
-    }
-
-    // Sync statusline globally to ~/.claude/
-    updateSpinner.text = 'Syncing statusline to ~/.claude/...';
-    const HOOKS_SRC = join(__dirname, '..', '..', '..', 'framework', 'hooks', 'claude-code');
-    try {
-      await installGlobalStatusline(HOOKS_SRC);
-    } catch {
-      // Non-critical: global dir may not be writable in all environments
-      logger.dim('  ⚠ Could not install statusline globally (non-critical)');
-    }
-
-    // Update Claude Code hooks in .claude/settings.local.json
-    updateSpinner.text = 'Updating Claude Code hooks...';
-    const hooksResult = await installClaudeHooks(targetPath);
-
-    // Ensure root CLAUDE.md has morph-spec @import (preserves user content)
-    updateSpinner.text = 'Checking CLAUDE.md import...';
-    const claudeMdDest = join(targetPath, 'CLAUDE.md');
-    await injectMorphImport(claudeMdDest);
-
-    // Restore user config after framework reinstallation
-    updateSpinner.text = 'Restoring user configuration...';
-    await restoreUserConfig(morphPath, targetPath, configBackup, cliCheck.current);
-    logger.dim('  ✓ User config restored with updated framework version');
-
-    // Update .gitignore with current morph rules
-    updateSpinner.text = 'Updating .gitignore...';
-    await updateGitignore(targetPath);
-
-    // Update .morphversion
-    updateSpinner.text = 'Saving version info...';
-    await saveProjectMorphVersion(targetPath, cliCheck.current);
-
-    updateSpinner.succeed('MORPH-SPEC updated successfully!');
-    logger.blank();
-
-    // Show version change
-    if (projectCheck.current && projectCheck.current !== cliCheck.current) {
-      logger.success(`Updated: ${projectCheck.current} → ${cliCheck.current}`);
-    } else if (!projectCheck.current) {
-      logger.success(`Updated to v${cliCheck.current}`);
-    } else {
-      logger.success(`Already up to date (v${cliCheck.current})`);
-    }
-
-    logger.blank();
-    logger.info('Updated files:');
-    if (updateTemplates) logger.dim('  ✓ .morph/framework/templates/');
-    if (updateStandards) logger.dim('  ✓ .morph/framework/standards/');
-    logger.dim('  ✓ .morph/framework/hooks/');
-    logger.dim('  ✓ .morph/framework/agents.json');
-    if (commandsCopied) logger.dim('  ✓ .claude/commands/');
-
-    logger.dim(`  ✓ .claude/settings.local.json (${hooksResult.installed} hooks installed)`);
-    logger.dim('  ✓ .claude/skills/ (skills installed as directories)');
-    logger.dim('  ✓ .claude/agents/ (native subagents refreshed)');
-    logger.dim('  ✓ .claude/rules/ (path-scoped rules synced)');
-    logger.dim('  ✓ .claude/CLAUDE.md (runtime quick reference)');
-    logger.dim('  ✓ ~/.claude/statusline.sh (global statusline synced)');
-    logger.dim('  ✓ CLAUDE.md');
-    logger.dim('  ✓ .gitignore (morph rules updated)');
-    logger.blank();
-    logger.info('Your config.json was preserved.');
-    logger.dim('Review the updated files for any new features.');
-    logger.blank();
-
-  } catch (error) {
-    updateSpinner.fail('Update failed');
-    logger.error(error.message);
-    process.exit(1);
-  }
-}
+import { join, dirname } from 'path';
+import { fileURLToPath } from 'url';
+import { spawnSync } from 'child_process';
+import { existsSync } from 'fs';
+
+const __dirname = dirname(fileURLToPath(import.meta.url));
+import fs from 'fs-extra';
+import ora from 'ora';
+import chalk from 'chalk';
+import { logger } from '../../utils/logger.js';
+import {
+  getContentDir,
+  copyDirectory,
+  copyFile,
+  pathExists,
+  ensureDir,
+  readJson,
+  writeJson,
+  updateGitignore
+} from '../../utils/file-copier.js';
+import {
+  checkCLIOutdated,
+  checkProjectOutdated,
+  saveProjectMorphVersion,
+  getUpdateInstructions,
+  detectInstallMethod
+} from '../../utils/version-checker.js';
+import { installClaudeHooks, installGlobalStatusline } from '../../utils/claude-settings-manager.js';
+import { installSkills } from '../../utils/skills-installer.js';
+import { installAgents, installDomainAgents } from '../../utils/agents-installer.js';
+import { injectMorphImport } from '../../utils/claude-md-injector.js';
+import { getProjectTags } from '../../lib/stack-filter.js';
+
+/**
+ * Backup user's config.json before cleaning
+ * @param {string} morphPath - Path to .morph directory
+ * @returns {Promise<object|null>} Backup of config.json or null
+ */
+async function backupUserConfig(morphPath) {
+  try {
+    const configPath = join(morphPath, 'config', 'config.json');
+    if (await pathExists(configPath)) {
+      const config = await readJson(configPath);
+      return config;
+    }
+  } catch (error) {
+    // If backup fails, return null and continue
+  }
+  return null;
+}
+
+/**
+ * Clean framework directories but preserve .morph/project/
+ * @param {string} morphPath - Path to .morph directory
+ * @param {string} targetPath - Project root path
+ */
+async function cleanFrameworkDirs(morphPath, targetPath) {
+  const claudeDir = join(targetPath, '.claude');
+  const dirsToClean = [
+    join(morphPath, 'framework', 'templates'),
+    join(morphPath, 'framework', 'standards'),
+    join(morphPath, 'framework', 'hooks'),
+    join(morphPath, 'config'),
+    join(claudeDir, 'commands'),
+    join(claudeDir, 'rules'),
+    join(claudeDir, 'skills'),
+    join(claudeDir, 'agents'),
+  ];
+
+  for (const dir of dirsToClean) {
+    try {
+      if (await pathExists(dir)) {
+        await fs.remove(dir);
+      }
+    } catch (error) {
+      // Continue even if cleanup fails for one directory
+    }
+  }
+}
+
+/**
+ * Restore user's config.json after reinstallation
+ * @param {string} morphPath - Path to .morph directory
+ * @param {string} targetPath - Project root path
+ * @param {object|null} configBackup - Backup of config.json
+ * @param {string} currentVersion - Current CLI version
+ */
+async function restoreUserConfig(morphPath, targetPath, configBackup, currentVersion) {
+  const configDir = join(morphPath, 'config');
+  await ensureDir(configDir);
+  const configPath = join(configDir, 'config.json');
+
+  if (configBackup) {
+    // Preserve user data but update framework version
+    configBackup.frameworkVersion = currentVersion;
+    await writeJson(configPath, configBackup);
+  } else {
+    // Create basic config if none existed
+    const dirName = targetPath.split(/[\\/]/).pop();
+    const defaultConfig = {
+      framework: 'global',
+      frameworkVersion: currentVersion,
+      project: {
+        name: dirName,
+        architecture: 'unknown'
+      }
+    };
+    await writeJson(configPath, defaultConfig);
+  }
+}
+
+/**
+ * Untrack an already-committed `.morph/state.json` from git.
+ *
+ * Before v5's per-feature model, `.morph/state.json` was committed. Adding it to
+ * `.gitignore` does NOT stop git from tracking a file already in the index — so on
+ * exactly the repos that had the P1 sweep problem, `git commit -a` would keep
+ * staging state.json. This runs `git rm --cached` once so the next commit drops it.
+ * The working-tree file is left in place (it's rebuilt from feature.json on load).
+ *
+ * Mildly destructive (mutates the git index), but no data is lost: state.json is a
+ * derivable index. Fail-open — a non-git project or any git error is a silent no-op.
+ *
+ * @param {string} targetPath - Project root
+ * @returns {boolean} true if state.json was untracked, false otherwise
+ */
+export function untrackCommittedStateJson(targetPath) {
+  try {
+    const isRepo = spawnSync('git', ['rev-parse', '--is-inside-work-tree'], {
+      cwd: targetPath, encoding: 'utf-8', stdio: ['ignore', 'pipe', 'ignore']
+    });
+    if (isRepo.status !== 0) return false;
+
+    // Is .morph/state.json currently tracked?
+    const tracked = spawnSync('git', ['ls-files', '--error-unmatch', '.morph/state.json'], {
+      cwd: targetPath, encoding: 'utf-8', stdio: ['ignore', 'pipe', 'ignore']
+    });
+    if (tracked.status !== 0) return false; // not tracked — nothing to migrate
+
+    const rm = spawnSync('git', ['rm', '--cached', '--quiet', '.morph/state.json'], {
+      cwd: targetPath, encoding: 'utf-8', stdio: ['ignore', 'pipe', 'ignore']
+    });
+    return rm.status === 0;
+  } catch {
+    return false;
+  }
+}
+
+export async function updateCommand(options) {
+  const targetPath = process.cwd();
+  const contentDir = getContentDir();
+  const morphPath = join(targetPath, '.morph');
+
+  logger.header('MORPH-SPEC Update');
+
+  // Check if MORPH is initialized
+  let needsInitialization = false;
+  if (!(await pathExists(morphPath))) {
+    logger.warn('MORPH not fully initialized. Creating basic structure...');
+    needsInitialization = true;
+
+    // Create basic .morph structure
+    await ensureDir(join(morphPath, 'context'));
+    await ensureDir(join(morphPath, 'features'));
+    await ensureDir(join(morphPath, 'framework'));
+    await ensureDir(join(morphPath, 'config'));
+    logger.dim('  ✓ Created .morph directory structure');
+  }
+
+  // Check CLI version
+  const spinner = ora('Checking versions...').start();
+  const cliCheck = await checkCLIOutdated();
+  const projectCheck = await checkProjectOutdated(targetPath);
+
+  spinner.stop();
+
+  // Display version info
+  logger.blank();
+  logger.info('Version Status:');
+  logger.dim(`  CLI version: ${cliCheck.current}`);
+
+  if (projectCheck.current) {
+    logger.dim(`  Project MORPH version: ${projectCheck.current}`);
+  } else {
+    logger.dim('  Project MORPH version: not found (legacy installation)');
+  }
+
+  if (cliCheck.latest) {
+    const latestColor = cliCheck.isOutdated ? chalk.yellow : chalk.green;
+    logger.dim(`  Latest available: ${latestColor(cliCheck.latest)}`);
+  }
+  logger.blank();
+
+  // If CLI is outdated, stop and instruct user
+  if (cliCheck.isOutdated && cliCheck.latest) {
+    logger.warn(`Your CLI is outdated (${cliCheck.current} → ${cliCheck.latest})`);
+    logger.blank();
+    logger.info('Please update the CLI first:');
+    logger.blank();
+
+    const method = detectInstallMethod();
+    const instructions = getUpdateInstructions(method);
+
+    instructions.forEach(line => {
+      if (line === '') {
+        logger.blank();
+      } else if (line.startsWith('Or ')) {
+        logger.dim(line);
+      } else {
+        logger.box([line]);
+      }
+    });
+
+    logger.blank();
+    logger.dim('Then run "morph-spec update" again.');
+    process.exit(0);
+  }
+
+  // Proceed with update
+  const updateSpinner = ora('Updating MORPH-SPEC...').start();
+
+  try {
+    // Backup user config before cleaning
+    updateSpinner.text = 'Backing up user configuration...';
+    const configBackup = await backupUserConfig(morphPath);
+    if (configBackup) {
+      logger.dim('  ✓ User config backed up');
+    }
+
+    // Clean framework directories (preserve .morph/project/)
+    updateSpinner.text = 'Cleaning old framework files...';
+    await cleanFrameworkDirs(morphPath, targetPath);
+    logger.dim('  ✓ Old framework files removed');
+
+    const updateTemplates = !options.standards || options.templates;
+    const updateStandards = !options.templates || options.standards;
+
+    // Update templates
+    if (updateTemplates) {
+      updateSpinner.text = 'Updating templates...';
+      const templatesSrc = join(contentDir, 'framework', 'templates');
+      const templatesDest = join(morphPath, 'framework', 'templates');
+      await copyDirectory(templatesSrc, templatesDest);
+    }
+
+    // Update standards
+    if (updateStandards) {
+      updateSpinner.text = 'Updating standards...';
+      const standardsSrc = join(contentDir, 'framework', 'standards');
+      const standardsDest = join(morphPath, 'framework', 'standards');
+      await copyDirectory(standardsSrc, standardsDest);
+    }
+
+    // Update hooks (runtime hook scripts under .morph/framework/hooks/)
+    updateSpinner.text = 'Updating hooks...';
+    const hooksSrc = join(__dirname, '..', '..', '..', 'framework', 'hooks');
+    const hooksDest = join(morphPath, 'framework', 'hooks');
+    if (await pathExists(hooksSrc)) {
+      await copyDirectory(hooksSrc, hooksDest);
+    }
+
+    // Update agents.json (sourced from framework/ — canonical single source of truth)
+    updateSpinner.text = 'Updating agents configuration...';
+    const agentsSrc = join(__dirname, '..', '..', '..', 'framework', 'agents.json');
+    const agentsDest = join(morphPath, 'framework', 'agents.json');
+    if (await pathExists(agentsSrc)) {
+      await copyFile(agentsSrc, agentsDest);
+    }
+
+    // Regenerate derived files (phase-utils.js, skill output tables) from output-schema.js
+    // Only runs when the generator script is present (framework dev installs via npm link)
+    updateSpinner.text = 'Syncing generated refs...';
+    try {
+      const generateScript = join(__dirname, '..', '..', '..', 'scripts', 'generate-refs.js');
+      if (existsSync(generateScript)) {
+        const result = spawnSync(process.execPath, [generateScript], { encoding: 'utf8' });
+        if (result.status === 0) {
+          logger.dim('  ✓ Generated refs synced (phase-utils.js, skill outputs)');
+        }
+      }
+    } catch {
+      // Non-fatal: generator unavailable or files already in sync
+    }
+
+    // Update .claude commands and skills
+    // Source: framework/ (canonical for all stacks)
+    updateSpinner.text = 'Setting up Claude Code integration...';
+    const frameworkDir = join(__dirname, '..', '..', '..', 'framework');
+    const claudeDest = join(targetPath, '.claude');
+
+    let commandsCopied = false;
+
+    // Copy commands directory (slash commands): framework/commands/ → .claude/commands/
+    const commandsSrc = join(frameworkDir, 'commands');
+    const commandsDest = join(claudeDest, 'commands');
+    if (await pathExists(commandsSrc)) {
+      await copyDirectory(commandsSrc, commandsDest);
+      commandsCopied = true;
+    } else {
+      logger.warn('  ⚠ framework/commands/ source missing — commands not updated');
+    }
+
+    // Compute project tags for stack-aware installation of skills, agents, and rules
+    let projectTags = [];
+    try {
+      const cfg = await readJson(join(morphPath, 'config', 'config.json'));
+      projectTags = getProjectTags(cfg);
+    } catch { /* ignore — config may not exist yet */ }
+
+    // Sync morph skills to .claude/skills/ for native Claude Code discovery
+    updateSpinner.text = 'Syncing morph skills to .claude/skills/...';
+    await installSkills(targetPath, { projectTags });
+
+    // Sync native subagents to .claude/agents/
+    updateSpinner.text = 'Syncing agents to .claude/agents/...';
+    await installAgents(targetPath, frameworkDir, { projectTags });
+    await installDomainAgents(targetPath, frameworkDir, { projectTags });
+
+    // Sync path-scoped rules to .claude/rules/
+    updateSpinner.text = 'Syncing rules to .claude/rules/...';
+    const rulesSrc = join(frameworkDir, 'rules');
+    const rulesDest = join(claudeDest, 'rules');
+    if (await pathExists(rulesSrc)) {
+      await copyDirectory(rulesSrc, rulesDest);
+    }
+
+    // Sync runtime CLAUDE.md to .claude/CLAUDE.md
+    updateSpinner.text = 'Syncing .claude/CLAUDE.md...';
+    const runtimeSrc = join(frameworkDir, 'CLAUDE.md');
+    const runtimeDest = join(claudeDest, 'CLAUDE.md');
+    if (await pathExists(runtimeSrc)) {
+      await copyFile(runtimeSrc, runtimeDest);
+    }
+
+    // Sync statusline globally to ~/.claude/
+    updateSpinner.text = 'Syncing statusline to ~/.claude/...';
+    const HOOKS_SRC = join(__dirname, '..', '..', '..', 'framework', 'hooks', 'claude-code');
+    try {
+      await installGlobalStatusline(HOOKS_SRC);
+    } catch {
+      // Non-critical: global dir may not be writable in all environments
+      logger.dim('  ⚠ Could not install statusline globally (non-critical)');
+    }
+
+    // Update Claude Code hooks in .claude/settings.local.json
+    updateSpinner.text = 'Updating Claude Code hooks...';
+    const hooksResult = await installClaudeHooks(targetPath);
+
+    // Ensure root CLAUDE.md has morph-spec @import (preserves user content)
+    updateSpinner.text = 'Checking CLAUDE.md import...';
+    const claudeMdDest = join(targetPath, 'CLAUDE.md');
+    await injectMorphImport(claudeMdDest);
+
+    // Restore user config after framework reinstallation
+    updateSpinner.text = 'Restoring user configuration...';
+    await restoreUserConfig(morphPath, targetPath, configBackup, cliCheck.current);
+    logger.dim('  ✓ User config restored with updated framework version');
+
+    // Update .gitignore with current morph rules
+    updateSpinner.text = 'Updating .gitignore...';
+    await updateGitignore(targetPath);
+
+    // Migration: untrack a pre-v5 committed state.json so it stops being swept
+    // into feature commits. Gitignore alone can't do this for an already-tracked file.
+    const untracked = untrackCommittedStateJson(targetPath);
+
+    // Update .morphversion
+    updateSpinner.text = 'Saving version info...';
+    await saveProjectMorphVersion(targetPath, cliCheck.current);
+
+    updateSpinner.succeed('MORPH-SPEC updated successfully!');
+    logger.blank();
+
+    // Show version change
+    if (projectCheck.current && projectCheck.current !== cliCheck.current) {
+      logger.success(`Updated: ${projectCheck.current} → ${cliCheck.current}`);
+    } else if (!projectCheck.current) {
+      logger.success(`Updated to v${cliCheck.current}`);
+    } else {
+      logger.success(`Already up to date (v${cliCheck.current})`);
+    }
+
+    logger.blank();
+    logger.info('Updated files:');
+    if (updateTemplates) logger.dim('  ✓ .morph/framework/templates/');
+    if (updateStandards) logger.dim('  ✓ .morph/framework/standards/');
+    logger.dim('  ✓ .morph/framework/hooks/');
+    logger.dim('  ✓ .morph/framework/agents.json');
+    if (commandsCopied) logger.dim('  ✓ .claude/commands/');
+
+    logger.dim(`  ✓ .claude/settings.local.json (${hooksResult.installed} hooks installed)`);
+    logger.dim('  ✓ .claude/skills/ (skills installed as directories)');
+    logger.dim('  ✓ .claude/agents/ (native subagents refreshed)');
+    logger.dim('  ✓ .claude/rules/ (path-scoped rules synced)');
+    logger.dim('  ✓ .claude/CLAUDE.md (runtime quick reference)');
+    logger.dim('  ✓ ~/.claude/statusline.sh (global statusline synced)');
+    logger.dim('  ✓ CLAUDE.md');
+    logger.dim('  ✓ .gitignore (morph rules updated)');
+    if (untracked) {
+      logger.dim('  ✓ .morph/state.json untracked (git rm --cached) — commit to finalize');
+      logger.warn('Migration: .morph/state.json was removed from git tracking. The');
+      logger.dim('  working file stays (rebuilt from feature.json); commit the deletion');
+      logger.dim('  so it stops being swept into per-feature commits.');
+    }
+    logger.blank();
+    logger.info('Your config.json was preserved.');
+    logger.dim('Review the updated files for any new features.');
+    logger.blank();
+
+  } catch (error) {
+    updateSpinner.fail('Update failed');
+    logger.error(error.message);
+    process.exit(1);
+  }
+}