bmad-enhanced 1.3.8 → 1.4.1

package/scripts/install-emma.js

@@ -2,6 +2,7 @@
 
 const fs = require('fs-extra');
 const path = require('path');
+const { findProjectRoot } = require('./update/lib/utils');
 
 const BOLD = '\x1b[1m';
 const RESET = '\x1b[0m';
@@ -20,11 +21,10 @@ function printBanner() {
   console.log('');
 }
 
-function checkPrerequisites() {
+function checkPrerequisites(projectRoot) {
   console.log(`${CYAN}[1/4]${RESET} Checking prerequisites...`);
 
-  const targetDir = process.cwd();
-  const bmadDir = path.join(targetDir, '_bmad');
+  const bmadDir = path.join(projectRoot, '_bmad');
 
   // Check if BMAD Method is installed
   if (!fs.existsSync(bmadDir)) {
@@ -45,11 +45,11 @@ function checkPrerequisites() {
   console.log(`${GREEN}  ✓${RESET} Prerequisites met`);
 }
 
-function copyAgentFiles() {
+function copyAgentFiles(projectRoot) {
   console.log(`${CYAN}[2/4]${RESET} Installing Emma agent files...`);
 
   const sourceDir = path.join(__dirname, '..', '_bmad', 'bme', '_vortex');
-  const targetDir = path.join(process.cwd(), '_bmad', 'bme', '_vortex');
+  const targetDir = path.join(projectRoot, '_bmad', 'bme', '_vortex');
 
   // Create target directory structure
   fs.mkdirSync(path.join(targetDir, 'agents'), { recursive: true });
@@ -83,11 +83,11 @@ function copyAgentFiles() {
   console.log(`${GREEN}  ✓${RESET} Agent files installed`);
 }
 
-function updateConfig() {
+function updateConfig(projectRoot) {
   console.log(`${CYAN}[3/4]${RESET} Configuring Emma...`);
 
-  const configPath = path.join(process.cwd(), '_bmad', 'bme', '_vortex', 'config.yaml');
-  const manifestPath = path.join(process.cwd(), '_bmad', '_config', 'agent-manifest.csv');
+  const configPath = path.join(projectRoot, '_bmad', 'bme', '_vortex', 'config.yaml');
+  const manifestPath = path.join(projectRoot, '_bmad', '_config', 'agent-manifest.csv');
 
   // Create config if doesn't exist
   if (!fs.existsSync(configPath)) {
@@ -135,10 +135,10 @@ core_module: bme
   console.log(`${GREEN}  ✓${RESET} Configuration complete`);
 }
 
-function createOutputDirectory() {
+function createOutputDirectory(projectRoot) {
   console.log(`${CYAN}[4/4]${RESET} Setting up output directory...`);
 
-  const outputDir = path.join(process.cwd(), '_bmad-output', 'vortex-artifacts');
+  const outputDir = path.join(projectRoot, '_bmad-output', 'vortex-artifacts');
   fs.mkdirSync(outputDir, { recursive: true });
 
   console.log(`${GREEN}  ✓${RESET} Output directory ready`);
@@ -166,11 +166,14 @@ function printSuccess() {
 
 async function main() {
   try {
+    // Use findProjectRoot for existing projects, fall back to cwd for fresh installs
+    const projectRoot = findProjectRoot() || process.cwd();
+
     printBanner();
-    checkPrerequisites();
-    copyAgentFiles();
-    updateConfig();
-    createOutputDirectory();
+    checkPrerequisites(projectRoot);
+    copyAgentFiles(projectRoot);
+    updateConfig(projectRoot);
+    createOutputDirectory(projectRoot);
     printSuccess();
   } catch (error) {
     console.error(`${RED}✗ Installation failed:${RESET}`, error.message);

package/scripts/install-wade.js

@@ -2,6 +2,7 @@
 
 const fs = require('fs-extra');
 const path = require('path');
+const { findProjectRoot } = require('./update/lib/utils');
 
 const BOLD = '\x1b[1m';
 const RESET = '\x1b[0m';
@@ -20,11 +21,10 @@ function printBanner() {
   console.log('');
 }
 
-function checkPrerequisites() {
+function checkPrerequisites(projectRoot) {
   console.log(`${CYAN}[1/4]${RESET} Checking prerequisites...`);
 
-  const targetDir = process.cwd();
-  const bmadDir = path.join(targetDir, '_bmad');
+  const bmadDir = path.join(projectRoot, '_bmad');
 
   // Check if BMAD Method is installed
   if (!fs.existsSync(bmadDir)) {
@@ -45,11 +45,11 @@ function checkPrerequisites() {
   console.log(`${GREEN}  ✓${RESET} Prerequisites met`);
 }
 
-function copyAgentFiles() {
+function copyAgentFiles(projectRoot) {
   console.log(`${CYAN}[2/4]${RESET} Installing Wade agent files...`);
 
   const sourceDir = path.join(__dirname, '..', '_bmad', 'bme', '_vortex');
-  const targetDir = path.join(process.cwd(), '_bmad', 'bme', '_vortex');
+  const targetDir = path.join(projectRoot, '_bmad', 'bme', '_vortex');
 
   // Create target directory structure
   fs.mkdirSync(path.join(targetDir, 'agents'), { recursive: true });
@@ -83,11 +83,11 @@ function copyAgentFiles() {
   console.log(`${GREEN}  ✓${RESET} Agent files installed`);
 }
 
-function updateConfig() {
+function updateConfig(projectRoot) {
   console.log(`${CYAN}[3/4]${RESET} Configuring Wade...`);
 
-  const configPath = path.join(process.cwd(), '_bmad', 'bme', '_vortex', 'config.yaml');
-  const manifestPath = path.join(process.cwd(), '_bmad', '_config', 'agent-manifest.csv');
+  const configPath = path.join(projectRoot, '_bmad', 'bme', '_vortex', 'config.yaml');
+  const manifestPath = path.join(projectRoot, '_bmad', '_config', 'agent-manifest.csv');
 
   // Update or create config
   if (!fs.existsSync(configPath)) {
@@ -145,10 +145,10 @@ core_module: bme
   console.log(`${GREEN}  ✓${RESET} Configuration complete`);
 }
 
-function createOutputDirectory() {
+function createOutputDirectory(projectRoot) {
   console.log(`${CYAN}[4/4]${RESET} Setting up output directory...`);
 
-  const outputDir = path.join(process.cwd(), '_bmad-output', 'vortex-artifacts');
+  const outputDir = path.join(projectRoot, '_bmad-output', 'vortex-artifacts');
   fs.mkdirSync(outputDir, { recursive: true });
 
   console.log(`${GREEN}  ✓${RESET} Output directory ready`);
@@ -176,11 +176,14 @@ function printSuccess() {
 
 async function main() {
   try {
+    // Use findProjectRoot for existing projects, fall back to cwd for fresh installs
+    const projectRoot = findProjectRoot() || process.cwd();
+
     printBanner();
-    checkPrerequisites();
-    copyAgentFiles();
-    updateConfig();
-    createOutputDirectory();
+    checkPrerequisites(projectRoot);
+    copyAgentFiles(projectRoot);
+    updateConfig(projectRoot);
+    createOutputDirectory(projectRoot);
     printSuccess();
   } catch (error) {
     console.error(`${RED}✗ Installation failed:${RESET}`, error.message);

package/scripts/postinstall.js

@@ -27,9 +27,12 @@ async function main() {
     const versionDetector = require('./update/lib/version-detector');
     const registry = require('./update/migrations/registry');
 
-    const currentVersion = versionDetector.getCurrentVersion();
+    const { findProjectRoot, compareVersions } = require('./update/lib/utils');
+    const projectRoot = findProjectRoot();
+
+    const currentVersion = versionDetector.getCurrentVersion(projectRoot);
     const targetVersion = versionDetector.getTargetVersion();
-    const scenario = versionDetector.detectInstallationScenario();
+    const scenario = versionDetector.detectInstallationScenario(projectRoot);
 
     // Fresh install
     if (scenario === 'fresh' || !currentVersion) {
@@ -52,7 +55,7 @@ async function main() {
     }
 
     // Upgrade detected
-    if (versionDetector.compareVersions(currentVersion, targetVersion) < 0) {
+    if (compareVersions(currentVersion, targetVersion) < 0) {
       console.log(`${YELLOW}${BOLD}⚠ UPGRADE DETECTED${RESET}`);
       console.log('');
       console.log(`  Current version: ${RED}${currentVersion}${RESET}`);
@@ -60,7 +63,7 @@ async function main() {
       console.log('');
 
       // Check for breaking changes
-      const breakingChanges = registry.getBreakingChanges(currentVersion, targetVersion);
+      const breakingChanges = registry.getBreakingChanges(currentVersion);
       if (breakingChanges.length > 0) {
         console.log(`${RED}${BOLD}  ⚠ Breaking changes detected!${RESET}`);
         console.log('');
@@ -83,7 +86,7 @@ async function main() {
     }
 
     // Downgrade (shouldn't happen normally)
-    if (versionDetector.compareVersions(currentVersion, targetVersion) > 0) {
+    if (compareVersions(currentVersion, targetVersion) > 0) {
       console.log(`${YELLOW}Note: Package version (${targetVersion}) is older than installed version (${currentVersion})${RESET}`);
       console.log('');
       return;
@@ -95,8 +98,8 @@ async function main() {
     console.log(`  ${CYAN}npx bmad-install-agents${RESET}  - Install all agents (Emma + Wade)`);
     console.log('');
     console.log('Or install individually:');
-    console.log(`  ${CYAN}npx bmad-install-emma${RESET}    - Install Emma (empathy-mapper)`);
-    console.log(`  ${CYAN}npx bmad-install-wade${RESET}    - Install Wade (wireframe-designer)`);
+    console.log(`  ${CYAN}npx bmad-install-emma${RESET}    - Install Emma (contextualization-expert)`);
+    console.log(`  ${CYAN}npx bmad-install-wade${RESET}    - Install Wade (lean-experiments-specialist)`);
     console.log('');
   }
 }

package/scripts/update/bmad-migrate.js

@@ -2,6 +2,9 @@
 
 const chalk = require('chalk');
 const registry = require('./migrations/registry');
+const backupManager = require('./lib/backup-manager');
+const { refreshInstallation } = require('./lib/refresh-installation');
+const { findProjectRoot } = require('./lib/utils');
 
 /**
  * BMAD-Enhanced Migrate CLI
@@ -11,6 +14,15 @@ const registry = require('./migrations/registry');
 async function main() {
   const args = process.argv.slice(2);
 
+  // Validate project root
+  const projectRoot = findProjectRoot();
+  if (!projectRoot) {
+    console.error('');
+    console.error(chalk.red('Not in a BMAD project. Could not find _bmad/ directory.'));
+    console.error('');
+    process.exit(1);
+  }
+
   // No args - show available migrations
   if (args.length === 0) {
     showAvailableMigrations();
@@ -32,6 +44,15 @@ async function main() {
     process.exit(1);
   }
 
+  // Check if already applied
+  const configPath = require('path').join(projectRoot, '_bmad/bme/_vortex/config.yaml');
+  if (registry.hasMigrationBeenApplied(migrationName, configPath)) {
+    console.log('');
+    console.log(chalk.yellow(`Migration '${migrationName}' has already been applied.`));
+    console.log('');
+    process.exit(0);
+  }
+
   // Load migration module
   if (!migration.module) {
     try {
@@ -44,29 +65,61 @@ async function main() {
     }
   }
 
-  // Run migration
+  // Run migration with backup and refresh
   console.log('');
   console.log(chalk.cyan.bold(`Running migration: ${migration.name}`));
   console.log(chalk.gray(migration.description));
   console.log('');
 
+  let backupMetadata = null;
+
   try {
-    const changes = await migration.module.apply();
+    // Create backup before running delta
+    console.log(chalk.cyan('Creating backup...'));
+    backupMetadata = await backupManager.createBackup('manual', projectRoot);
+    console.log(chalk.green(`✓ Backup created: ${require('path').basename(backupMetadata.backup_dir)}`));
+    console.log('');
+
+    // Run the delta
+    const changes = await migration.module.apply(projectRoot);
 
     console.log('');
-    console.log(chalk.green.bold('✓ Migration completed'));
+    console.log(chalk.green.bold('✓ Migration delta completed'));
     console.log('');
-    console.log(chalk.cyan('Changes:'));
+    console.log(chalk.cyan('Delta changes:'));
     changes.forEach(change => {
       console.log(chalk.gray(`  - ${change}`));
     });
     console.log('');
 
+    // Refresh installation after delta
+    console.log(chalk.cyan('Refreshing installation files...'));
+    await refreshInstallation(projectRoot);
+    console.log(chalk.green('✓ Installation refreshed'));
+    console.log('');
+
   } catch (error) {
     console.error('');
     console.error(chalk.red.bold('✗ Migration failed'));
     console.error(chalk.red(error.message));
     console.error('');
+
+    // Rollback if we have a backup
+    if (backupMetadata) {
+      console.log(chalk.yellow('Restoring from backup...'));
+      try {
+        await backupManager.restoreBackup(backupMetadata, projectRoot);
+        console.log(chalk.green('✓ Installation restored from backup'));
+        console.log('');
+      } catch (restoreError) {
+        console.error(chalk.red('✗ Restore failed!'));
+        console.error(chalk.red(restoreError.message));
+        console.error('');
+        console.error(chalk.yellow(`Manual restore may be needed from: ${backupMetadata.backup_dir}`));
+        console.error('');
+      }
+    }
+
     if (error.stack) {
       console.error(chalk.gray(error.stack));
       console.error('');
@@ -95,7 +148,7 @@ function showAvailableMigrations() {
     const breaking = m.breaking ? chalk.red('[BREAKING]') : chalk.green('[SAFE]');
     console.log(`  ${index + 1}. ${chalk.cyan(m.name)} ${breaking}`);
     console.log(`     ${chalk.gray(m.description)}`);
-    console.log(`     ${chalk.gray(`${m.fromVersion} → ${m.toVersion}`)}`);
+    console.log(`     ${chalk.gray(`From: ${m.fromVersion}`)}`);
     console.log('');
   });
 

package/scripts/update/bmad-update.js

@@ -5,6 +5,7 @@ const chalk = require('chalk');
 const versionDetector = require('./lib/version-detector');
 const migrationRunner = require('./lib/migration-runner');
 const registry = require('./migrations/registry');
+const { findProjectRoot } = require('./lib/utils');
 
 /**
  * BMAD-Enhanced Update CLI
@@ -15,7 +16,6 @@ async function main() {
   const args = process.argv.slice(2);
   const dryRun = args.includes('--dry-run');
   const yes = args.includes('--yes') || args.includes('-y');
-  const force = args.includes('--force');
   const verbose = args.includes('--verbose') || args.includes('-v');
 
   // Header
@@ -25,10 +25,20 @@ async function main() {
   console.log(chalk.bold.magenta('╚════════════════════════════════════════╝'));
   console.log('');
 
+  // Validate project root
+  const projectRoot = findProjectRoot();
+  if (!projectRoot) {
+    console.log(chalk.red('Not in a BMAD project. Could not find _bmad/ directory.'));
+    console.log('');
+    console.log('Run: ' + chalk.cyan('npx bmad-install-agents'));
+    console.log('');
+    process.exit(1);
+  }
+
   // 1. Detect current state
-  const currentVersion = versionDetector.getCurrentVersion();
+  const currentVersion = versionDetector.getCurrentVersion(projectRoot);
   const targetVersion = versionDetector.getTargetVersion();
-  const scenario = versionDetector.detectInstallationScenario();
+  const scenario = versionDetector.detectInstallationScenario(projectRoot);
 
   // Handle different scenarios
   if (scenario === 'fresh') {
@@ -88,7 +98,7 @@ async function main() {
   console.log(`  To:   ${chalk.green(targetVersion)}`);
   console.log('');
 
-  const migrations = registry.getMigrationsFor(currentVersion, targetVersion);
+  const migrations = registry.getMigrationsFor(currentVersion);
 
   if (migrations.length === 0) {
     console.log(chalk.yellow('No migrations needed (versions compatible)'));
@@ -104,7 +114,7 @@ async function main() {
   console.log('');
 
   // 3. Show breaking changes warning
-  const breakingChanges = registry.getBreakingChanges(currentVersion, targetVersion);
+  const breakingChanges = registry.getBreakingChanges(currentVersion);
   if (breakingChanges.length > 0) {
     console.log(chalk.red.bold('⚠ BREAKING CHANGES:'));
     breakingChanges.forEach(change => {
@@ -119,7 +129,7 @@ async function main() {
     console.log('');
 
     try {
-      await migrationRunner.runMigrations(currentVersion, targetVersion, { dryRun: true, verbose });
+      await migrationRunner.runMigrations(currentVersion, { dryRun: true, verbose });
     } catch (error) {
       console.error(chalk.red('Error during preview:'), error.message);
       process.exit(1);
@@ -148,7 +158,7 @@ async function main() {
   console.log(chalk.cyan.bold('Starting migration...'));
 
   try {
-    const result = await migrationRunner.runMigrations(currentVersion, targetVersion, { verbose });
+    const result = await migrationRunner.runMigrations(currentVersion, { verbose });
 
     // 7. Show success report
     console.log('');
@@ -167,7 +177,7 @@ async function main() {
     console.log(chalk.gray(`Backup location: ${result.backupMetadata.backup_dir}`));
     console.log('');
 
-  } catch (error) {
+  } catch (_error) {
     // Error already logged by migration-runner
     process.exit(1);
   }

package/scripts/update/bmad-version.js

@@ -5,6 +5,7 @@ const path = require('path');
 const chalk = require('chalk');
 const yaml = require('js-yaml');
 const versionDetector = require('./lib/version-detector');
+const { findProjectRoot, compareVersions } = require('./lib/utils');
 
 /**
  * BMAD-Enhanced Version CLI
@@ -12,14 +13,26 @@ const versionDetector = require('./lib/version-detector');
  */
 
 async function main() {
-  const currentVersion = versionDetector.getCurrentVersion();
+  const projectRoot = findProjectRoot();
   const targetVersion = versionDetector.getTargetVersion();
-  const scenario = versionDetector.detectInstallationScenario();
 
   console.log('');
   console.log(chalk.bold('BMAD-Enhanced Version Information'));
   console.log('');
 
+  // Not in a BMAD project
+  if (!projectRoot) {
+    console.log(chalk.yellow('Status:           Not in a BMAD project'));
+    console.log(`Package version:  ${chalk.cyan(targetVersion)}`);
+    console.log('');
+    console.log('Run: ' + chalk.cyan('npx bmad-install-agents'));
+    console.log('');
+    return;
+  }
+
+  const currentVersion = versionDetector.getCurrentVersion(projectRoot);
+  const scenario = versionDetector.detectInstallationScenario(projectRoot);
+
   // Fresh install - not installed yet
   if (scenario === 'fresh') {
     console.log(chalk.yellow('Status:           Not installed'));
@@ -64,7 +77,7 @@ async function main() {
   // Status
   if (currentVersion === targetVersion) {
     console.log(chalk.green('Status: ✓ Up to date'));
-  } else if (versionDetector.compareVersions(currentVersion, targetVersion) < 0) {
+  } else if (compareVersions(currentVersion, targetVersion) < 0) {
     console.log(chalk.yellow('Status: ⚠ Update available'));
     console.log('');
     console.log('Run: ' + chalk.cyan('npx bmad-update --dry-run') + ' (to preview)');
@@ -74,7 +87,7 @@ async function main() {
   }
 
   // Show migration history
-  const migrationHistory = await getMigrationHistory();
+  const migrationHistory = await getMigrationHistory(projectRoot);
   if (migrationHistory && migrationHistory.length > 0) {
     console.log('');
     console.log(chalk.cyan('Migration History:'));
@@ -94,10 +107,11 @@ async function main() {
 
 /**
  * Get migration history from config.yaml
+ * @param {string} projectRoot - Project root
  * @returns {Promise<Array|null>} Migration history or null
  */
-async function getMigrationHistory() {
-  const configPath = path.join(process.cwd(), '_bmad/bme/_vortex/config.yaml');
+async function getMigrationHistory(projectRoot) {
+  const configPath = path.join(projectRoot, '_bmad/bme/_vortex/config.yaml');
 
   if (!fs.existsSync(configPath)) {
     return null;
@@ -108,7 +122,7 @@ async function getMigrationHistory() {
     const config = yaml.load(configContent);
 
     return config.migration_history || null;
-  } catch (error) {
+  } catch (_error) {
     return null;
   }
 }

package/scripts/update/lib/backup-manager.js

@@ -2,6 +2,7 @@
 
 const fs = require('fs-extra');
 const path = require('path');
+const { countUserDataFiles } = require('./utils');
 
 /**
  * Backup Manager for BMAD-Enhanced
@@ -11,12 +12,13 @@ const path = require('path');
 /**
  * Create a backup of critical installation files
  * @param {string} version - Current version being backed up
+ * @param {string} projectRoot - Absolute path to project root
  * @returns {Promise<object>} Backup metadata
  */
-async function createBackup(version) {
+async function createBackup(version, projectRoot) {
   const timestamp = Date.now();
   const backupDir = path.join(
-    process.cwd(),
+    projectRoot,
     '_bmad-output/.backups',
     `backup-${version}-${timestamp}`
   );
@@ -24,7 +26,7 @@ async function createBackup(version) {
   console.log(`Creating backup in: ${backupDir}`);
 
   // Ensure backup directory exists
-  await ensureBackupDirectory();
+  await ensureBackupDirectory(projectRoot);
 
   // Create backup directory
   await fs.ensureDir(backupDir);
@@ -34,7 +36,7 @@ async function createBackup(version) {
 
   // Copy each file/directory to backup
   for (const file of filesToBackup) {
-    const sourcePath = path.join(process.cwd(), file.path);
+    const sourcePath = path.join(projectRoot, file.path);
 
     if (!fs.existsSync(sourcePath)) {
       console.log(`  Skipping ${file.path} (does not exist)`);
@@ -44,12 +46,7 @@ async function createBackup(version) {
     const destPath = path.join(backupDir, file.name);
 
     try {
-      if (file.type === 'file') {
-        await fs.copy(sourcePath, destPath);
-      } else if (file.type === 'directory') {
-        await fs.copy(sourcePath, destPath);
-      }
-
+      await fs.copy(sourcePath, destPath);
       backedUpFiles.push(file.path);
       console.log(`  ✓ Backed up: ${file.path}`);
     } catch (error) {
@@ -59,7 +56,7 @@ async function createBackup(version) {
   }
 
   // Count user data files (for integrity check)
-  const userDataCount = await countUserDataFiles();
+  const userDataCount = await countUserDataFiles(projectRoot);
 
   // Create backup manifest
   const manifest = {
@@ -82,9 +79,10 @@ async function createBackup(version) {
 /**
  * Restore from backup after migration failure
  * @param {object} backupMetadata - Metadata from createBackup
+ * @param {string} projectRoot - Absolute path to project root
  * @returns {Promise<void>}
  */
-async function restoreBackup(backupMetadata) {
+async function restoreBackup(backupMetadata, projectRoot) {
   const backupDir = backupMetadata.backup_dir;
 
   console.log('');
@@ -104,7 +102,7 @@ async function restoreBackup(backupMetadata) {
       continue;
     }
 
-    const destPath = path.join(process.cwd(), file.path);
+    const destPath = path.join(projectRoot, file.path);
 
     try {
       // Remove existing file/directory first
@@ -126,10 +124,11 @@ async function restoreBackup(backupMetadata) {
 
 /**
  * List available backups
+ * @param {string} projectRoot - Absolute path to project root
  * @returns {Promise<Array>} List of backup metadata
  */
-async function listBackups() {
-  const backupsDir = path.join(process.cwd(), '_bmad-output/.backups');
+async function listBackups(projectRoot) {
+  const backupsDir = path.join(projectRoot, '_bmad-output/.backups');
 
   if (!fs.existsSync(backupsDir)) {
     return [];
@@ -161,10 +160,11 @@ async function listBackups() {
 /**
  * Clean up old backups, keeping only the most recent N
  * @param {number} keepCount - Number of backups to keep
+ * @param {string} projectRoot - Absolute path to project root
  * @returns {Promise<number>} Number of backups deleted
  */
-async function cleanupOldBackups(keepCount = 5) {
-  const backups = await listBackups();
+async function cleanupOldBackups(keepCount = 5, projectRoot) {
+  const backups = await listBackups(projectRoot);
 
   if (backups.length <= keepCount) {
     return 0; // Nothing to clean up
@@ -188,13 +188,14 @@ async function cleanupOldBackups(keepCount = 5) {
 
 /**
  * Ensure backup directory exists
+ * @param {string} projectRoot - Absolute path to project root
  * @returns {Promise<void>}
  */
-async function ensureBackupDirectory() {
-  const backupDir = path.join(process.cwd(), '_bmad-output/.backups');
+async function ensureBackupDirectory(projectRoot) {
+  const backupDir = path.join(projectRoot, '_bmad-output/.backups');
 
   if (!fs.existsSync(backupDir)) {
-    const outputDir = path.join(process.cwd(), '_bmad-output');
+    const outputDir = path.join(projectRoot, '_bmad-output');
 
     if (!fs.existsSync(outputDir)) {
       throw new Error('_bmad-output directory not found. Is BMAD Method installed?');
@@ -233,47 +234,10 @@ function getFilesToBackup() {
   ];
 }
 
-/**
- * Count user data files in _bmad-output (for integrity check)
- * @returns {Promise<number>} Number of user files
- */
-async function countUserDataFiles() {
-  const outputDir = path.join(process.cwd(), '_bmad-output');
-
-  if (!fs.existsSync(outputDir)) {
-    return 0;
-  }
-
-  let count = 0;
-
-  async function countRecursive(dir) {
-    const entries = await fs.readdir(dir, { withFileTypes: true });
-
-    for (const entry of entries) {
-      const fullPath = path.join(dir, entry.name);
-
-      // Skip .backups and .logs directories
-      if (entry.name === '.backups' || entry.name === '.logs') {
-        continue;
-      }
-
-      if (entry.isDirectory()) {
-        await countRecursive(fullPath);
-      } else if (entry.isFile()) {
-        count++;
-      }
-    }
-  }
-
-  await countRecursive(outputDir);
-  return count;
-}
-
 module.exports = {
   createBackup,
   restoreBackup,
   listBackups,
   cleanupOldBackups,
-  ensureBackupDirectory,
-  countUserDataFiles
+  ensureBackupDirectory
 };