claude-flow-novice 2.0.3 → 2.0.4

package/dist/src/cli/simple-commands/init/index.js

@@ -1,1271 +1,1084 @@
 // init/index.js - Initialize Claude Code integration files
-import { printSuccess, printError, printWarning, exit } from '../../utils.js';
-import { existsSync } from 'fs';
-import { promises as fs } from 'fs';
-import { fileURLToPath } from 'url';
-import { dirname, join } from 'path';
-import process from 'process';
-import { spawn, execSync } from 'child_process';
-import { promisify } from 'util';
-
+import { printSuccess, printError, printWarning } from "../../utils.js";
+import { existsSync } from "fs";
+import { promises as fs } from "fs";
+import { fileURLToPath } from "url";
+import { dirname, join } from "path";
+import process from "process";
+import { spawn, execSync } from "child_process";
 // Helper to replace Deno.Command
 function runCommand(command, args, options = {}) {
-  return new Promise((resolve, reject) => {
-    const child = spawn(command, args, {
-      cwd: options.cwd,
-      env: { ...process.env, ...options.env },
-      stdio: options.stdout === 'inherit' ? 'inherit' : 'pipe',
-    });
-
-    let stdout = '';
-    let stderr = '';
-
-    if (options.stdout !== 'inherit') {
-      child.stdout.on('data', (data) => {
-        stdout += data;
-      });
-      child.stderr.on('data', (data) => {
-        stderr += data;
-      });
-    }
-
-    child.on('close', (code) => {
-      if (code === 0) {
-        resolve({ success: true, code, stdout, stderr });
-      } else {
-        reject(new Error(`Command failed with exit code ${code}`));
-      }
+    return new Promise((resolve, reject)=>{
+        const child = spawn(command, args, {
+            cwd: options.cwd,
+            env: {
+                ...process.env,
+                ...options.env
+            },
+            stdio: options.stdout === 'inherit' ? 'inherit' : 'pipe'
+        });
+        let stdout = '';
+        let stderr = '';
+        if (options.stdout !== 'inherit') {
+            child.stdout.on('data', (data)=>{
+                stdout += data;
+            });
+            child.stderr.on('data', (data)=>{
+                stderr += data;
+            });
+        }
+        child.on('close', (code)=>{
+            if (code === 0) {
+                resolve({
+                    success: true,
+                    code,
+                    stdout,
+                    stderr
+                });
+            } else {
+                reject(new Error(`Command failed with exit code ${code}`));
+            }
+        });
+        child.on('error', reject);
     });
-
-    child.on('error', reject);
-  });
 }
-import { createLocalExecutable } from './executable-wrapper.js';
-import { createSparcStructureManually } from './sparc-structure.js';
-import { createClaudeSlashCommands } from './claude-commands/slash-commands.js';
-import { createOptimizedClaudeSlashCommands } from './claude-commands/optimized-slash-commands.js';
-import { copyTemplates } from './template-copier.js';
-import { copyRevisedTemplates, validateTemplatesExist } from './copy-revised-templates.js';
-import {
-  copyAgentFiles,
-  createAgentDirectories,
-  validateAgentSystem,
-  copyCommandFiles,
-} from './agent-copier.js';
-import { showInitHelp } from './help.js';
-import { batchInitCommand, batchInitFromConfig, validateBatchOptions } from './batch-init.js';
-import { ValidationSystem, runFullValidation } from './validation/index.js';
-import { RollbackSystem, createAtomicOperation } from './rollback/index.js';
-import {
-  createEnhancedClaudeMd,
-  createEnhancedSettingsJson,
-  createWrapperScript,
-  createCommandDoc,
-  createHelperScript,
-  COMMAND_STRUCTURE,
-} from './templates/enhanced-templates.js';
-import { getIsolatedNpxEnv } from '../../../utils/npx-isolated-cache.js';
-import { updateGitignore, needsGitignoreUpdate } from './gitignore-updater.js';
-import {
-  createVerificationClaudeMd,
-  createVerificationSettingsJson,
-} from './templates/verification-claude-md.js';
-import { createFullMemoryBankMd, createMinimalMemoryBankMd } from './templates/memory-bank-md.js';
-import {
-  createFullCoordinationMd,
-  createMinimalCoordinationMd,
-} from './templates/coordination-md.js';
-import { createAgentsReadme, createSessionsReadme } from './templates/readme-files.js';
-import { initializeHiveMind, getHiveMindStatus, rollbackHiveMindInit } from './hive-mind-init.js';
-
+import { createLocalExecutable } from "./executable-wrapper.js";
+import { createSparcStructureManually } from "./sparc-structure.js";
+import { createClaudeSlashCommands } from "./claude-commands/slash-commands.js";
+import { createOptimizedClaudeSlashCommands } from "./claude-commands/optimized-slash-commands.js";
+import { copyTemplates } from "./template-copier.js";
+import { copyRevisedTemplates, validateTemplatesExist } from "./copy-revised-templates.js";
+import { copyAgentFiles, createAgentDirectories, validateAgentSystem, copyCommandFiles } from "./agent-copier.js";
+import { showInitHelp } from "./help.js";
+import { batchInitCommand, batchInitFromConfig, validateBatchOptions } from "./batch-init.js";
+import { ValidationSystem, runFullValidation } from "./validation/index.js";
+import { RollbackSystem, createAtomicOperation } from "./rollback/index.js";
+import { createEnhancedSettingsJson, createWrapperScript, createCommandDoc, createHelperScript, COMMAND_STRUCTURE } from "./templates/enhanced-templates.js";
+import { getIsolatedNpxEnv } from "../../../utils/npx-isolated-cache.js";
+import { updateGitignore } from "./gitignore-updater.js";
+import { createFullMemoryBankMd, createMinimalMemoryBankMd } from "./templates/memory-bank-md.js";
+import { createFullCoordinationMd, createMinimalCoordinationMd } from "./templates/coordination-md.js";
+import { createAgentsReadme, createSessionsReadme } from "./templates/readme-files.js";
+import { initializeHiveMind, getHiveMindStatus, rollbackHiveMindInit } from "./hive-mind-init.js";
 // Get the directory path of this module for resolving template files
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = dirname(__filename);
-
 /**
  * Read the CLAUDE.md template file
  * @returns {Promise<string>} The template content
- */
-async function readClaudeMdTemplate() {
-  // In source: templates/CLAUDE.md
-  // In dist: the files are copied directly to init/ directory (not templates/)
-  const possiblePaths = [
-    join(__dirname, 'templates', 'CLAUDE.md'),  // Source location
-    join(__dirname, 'CLAUDE.md'),               // Dist location (files copied directly)
-  ];
-
-  for (const templatePath of possiblePaths) {
-    try {
-      const content = await fs.readFile(templatePath, 'utf8');
-      console.log(`✅ Using CLAUDE.md template from: ${templatePath}`);
-      return content;
-    } catch (error) {
-      // Try next path
-      continue;
+ */ async function readClaudeMdTemplate() {
+    // In source: templates/CLAUDE.md
+    // In dist: the files are copied directly to init/ directory (not templates/)
+    const possiblePaths = [
+        join(__dirname, 'templates', 'CLAUDE.md'),
+        join(__dirname, 'CLAUDE.md')
+    ];
+    for (const templatePath of possiblePaths){
+        try {
+            const content = await fs.readFile(templatePath, 'utf8');
+            console.log(`✅ Using CLAUDE.md template from: ${templatePath}`);
+            return content;
+        } catch (error) {
+            continue;
+        }
     }
-  }
-
-  // If template not found, throw error instead of falling back
-  throw new Error('CLAUDE.md template file not found! Please ensure templates are included in the build.');
+    // If template not found, throw error instead of falling back
+    throw new Error('CLAUDE.md template file not found! Please ensure templates are included in the build.');
 }
-
 /**
  * Check if Claude Code CLI is installed
- */
-function isClaudeCodeInstalled() {
-  try {
-    execSync('which claude', { stdio: 'ignore' });
-    return true;
-  } catch {
-    return false;
-  }
+ */ function isClaudeCodeInstalled() {
+    try {
+        execSync('which claude', {
+            stdio: 'ignore'
+        });
+        return true;
+    } catch  {
+        return false;
+    }
 }
-
 /**
  * Set up MCP servers in Claude Code (Legacy - replaced by bulletproof system)
- */
-async function setupMcpServers(dryRun = false) {
-  console.log('\n🔌 Setting up MCP servers for Claude Code...');
-
-  const servers = [
-    {
-      name: 'claude-flow-novice',
-      command: 'node dist/mcp/mcp-server-sdk.js',
-      description: 'Claude Flow Novice MCP server with 30 essential tools',
-    },
-  ];
-
-  for (const server of servers) {
-    try {
-      if (!dryRun) {
-        console.log(`  🔄 Adding ${server.name}...`);
-        execSync(`claude mcp add ${server.name} ${server.command}`, { stdio: 'inherit' });
-        console.log(`  ✅ Added ${server.name} - ${server.description}`);
-      } else {
-        console.log(`  [DRY RUN] Would add ${server.name} - ${server.description}`);
-      }
-    } catch (err) {
-      console.log(`  ⚠️  Failed to add ${server.name}: ${err.message}`);
-      console.log(
-        `     You can add it manually with: claude mcp add ${server.name} ${server.command}`,
-      );
+ */ async function setupMcpServers(dryRun1 = false) {
+    console.log('\n🔌 Setting up MCP servers for Claude Code...');
+    const servers = [
+        {
+            name: 'claude-flow-novice',
+            command: 'node dist/mcp/mcp-server-sdk.js',
+            description: 'Claude Flow Novice MCP server with 30 essential tools'
+        }
+    ];
+    for (const server of servers){
+        try {
+            if (!dryRun1) {
+                console.log(`  🔄 Adding ${server.name}...`);
+                execSync(`claude mcp add ${server.name} ${server.command}`, {
+                    stdio: 'inherit'
+                });
+                console.log(`  ✅ Added ${server.name} - ${server.description}`);
+            } else {
+                console.log(`  [DRY RUN] Would add ${server.name} - ${server.description}`);
+            }
+        } catch (err) {
+            console.log(`  ⚠️  Failed to add ${server.name}: ${err.message}`);
+            console.log(`     You can add it manually with: claude mcp add ${server.name} ${server.command}`);
+        }
     }
-  }
-
-  if (!dryRun) {
-    console.log('\n  📋 Verifying MCP servers...');
-    try {
-      execSync('claude mcp list', { stdio: 'inherit' });
-    } catch (err) {
-      console.log('  ⚠️  Could not verify MCP servers');
+    if (!dryRun1) {
+        console.log('\n  📋 Verifying MCP servers...');
+        try {
+            execSync('claude mcp list', {
+                stdio: 'inherit'
+            });
+        } catch (err) {
+            console.log('  ⚠️  Could not verify MCP servers');
+        }
     }
-  }
 }
-
 /**
  * Bulletproof MCP setup using the new configuration manager
- */
-async function setupBulletproofMcp(options = {}) {
-  console.log('\n🛡️  Setting up bulletproof MCP configuration...');
-
-  try {
-    // Import the MCP configuration manager
-    const { enhancedMcpInit } = await import('../../mcp/mcp-config-manager.js');
-
-    const result = await enhancedMcpInit({
-      verbose: options.verbose || false,
-      autoFix: options.autoFix !== false, // Default to true
-      dryRun: options.dryRun || false,
-      enhancedUx: true, // Enable enhanced user experience
-      showEducation: options.showEducation || false // Show educational content for first-time users
-    });
-
-    if (result.success) {
-      console.log('✅ Bulletproof MCP configuration completed successfully');
-
-      // Display additional success information
-      if (result.details) {
-        console.log(`   • Issues Fixed: ${result.details.issuesFixed || 0}`);
-        console.log(`   • Health Score: ${result.details.healthScore || 'N/A'}/100`);
-        console.log(`   • Duration: ${result.duration || 'N/A'}ms`);
-      }
-
-      return true;
-    } else {
-      console.log(`⚠️  MCP configuration had issues: ${result.error}`);
-
-      // Display recovery information if available
-      if (result.rollbackAvailable) {
-        console.log('   🔄 Automatic rollback was performed');
-      }
-
-      if (result.recovery && result.recovery.recommendedActions) {
-        console.log('\n   🛠️ Recommended actions:');
-        result.recovery.recommendedActions.slice(0, 3).forEach((action, i) => {
-          console.log(`     ${i + 1}. ${action}`);
+ */ async function setupBulletproofMcp(options = {}) {
+    console.log('\n🛡️  Setting up bulletproof MCP configuration...');
+    try {
+        // Import the MCP configuration manager
+        const { enhancedMcpInit } = await import("../../mcp/mcp-config-manager.js");
+        const result = await enhancedMcpInit({
+            verbose: options.verbose || false,
+            autoFix: options.autoFix !== false,
+            dryRun: options.dryRun || false,
+            enhancedUx: true,
+            showEducation: options.showEducation || false // Show educational content for first-time users
         });
-      }
-
-      return false;
-    }
-  } catch (error) {
-    console.log(`⚠️  Bulletproof MCP setup failed: ${error.message}`);
-    console.log('     This may be due to missing dependencies or system configuration.');
-
-    // Check if it's a dependency issue
-    if (error.message.includes('Cannot find module') || error.message.includes('import')) {
-      console.log('     💡 Try installing dependencies: npm install');
+        if (result.success) {
+            console.log('✅ Bulletproof MCP configuration completed successfully');
+            // Display additional success information
+            if (result.details) {
+                console.log(`   • Issues Fixed: ${result.details.issuesFixed || 0}`);
+                console.log(`   • Health Score: ${result.details.healthScore || 'N/A'}/100`);
+                console.log(`   • Duration: ${result.duration || 'N/A'}ms`);
+            }
+            return true;
+        } else {
+            console.log(`⚠️  MCP configuration had issues: ${result.error}`);
+            // Display recovery information if available
+            if (result.rollbackAvailable) {
+                console.log('   🔄 Automatic rollback was performed');
+            }
+            if (result.recovery && result.recovery.recommendedActions) {
+                console.log('\n   🛠️ Recommended actions:');
+                result.recovery.recommendedActions.slice(0, 3).forEach((action, i)=>{
+                    console.log(`     ${i + 1}. ${action}`);
+                });
+            }
+            return false;
+        }
+    } catch (error) {
+        console.log(`⚠️  Bulletproof MCP setup failed: ${error.message}`);
+        console.log('     This may be due to missing dependencies or system configuration.');
+        // Check if it's a dependency issue
+        if (error.message.includes('Cannot find module') || error.message.includes('import')) {
+            console.log('     💡 Try installing dependencies: npm install');
+        }
+        console.log('     📞 Falling back to legacy MCP setup...');
+        // Fallback to legacy setup
+        await setupMcpServers(options.dryRun);
+        return false;
     }
-
-    console.log('     📞 Falling back to legacy MCP setup...');
-
-    // Fallback to legacy setup
-    await setupMcpServers(options.dryRun);
-    return false;
-  }
 }
-
 export async function initCommand(subArgs, flags) {
-  // Show help if requested
-  if (flags.help || flags.h || subArgs.includes('--help') || subArgs.includes('-h')) {
-    showInitHelp();
-    return;
-  }
-
-  // Check for verification flags first
-  const hasVerificationFlags =
-    subArgs.includes('--verify') || subArgs.includes('--pair') || flags.verify || flags.pair;
-
-  // Flow-nexus mode removed
-
-  // Default to enhanced Claude Flow v2 init unless other modes are specified
-  // Use --basic flag for old behavior, or verification flags for verification mode
-  if (!flags.basic && !flags.minimal && !flags.sparc && !hasVerificationFlags) {
-    return await enhancedClaudeFlowInit(flags, subArgs);
-  }
-
-  // Check for validation and rollback commands
-  if (subArgs.includes('--validate') || subArgs.includes('--validate-only')) {
-    return handleValidationCommand(subArgs, flags);
-  }
-
-  if (subArgs.includes('--rollback')) {
-    return handleRollbackCommand(subArgs, flags);
-  }
-
-  if (subArgs.includes('--list-backups')) {
-    return handleListBackups(subArgs, flags);
-  }
-
-  // Check for batch operations
-  const batchInitFlag = flags['batch-init'] || subArgs.includes('--batch-init');
-  const configFlag = flags.config || subArgs.includes('--config');
-
-  if (batchInitFlag || configFlag) {
-    return handleBatchInit(subArgs, flags);
-  }
-
-  // Parse init options
-  const initForce = subArgs.includes('--force') || subArgs.includes('-f') || flags.force;
-  const initMinimal = subArgs.includes('--minimal') || subArgs.includes('-m') || flags.minimal;
-  const initSparc = flags.roo || (subArgs && subArgs.includes('--roo')); // SPARC only with --roo flag
-  const initDryRun = subArgs.includes('--dry-run') || subArgs.includes('-d') || flags.dryRun;
-  const initOptimized = initSparc && initForce; // Use optimized templates when both flags are present
-  const selectedModes = flags.modes ? flags.modes.split(',') : null; // Support selective mode initialization
-
-  // Check for verification and pair programming flags
-  const initVerify = subArgs.includes('--verify') || flags.verify;
-  const initPair = subArgs.includes('--pair') || flags.pair;
-
-  // Get the actual working directory (where the command was run from)
-  // Use PWD environment variable which preserves the original directory
-  const workingDir = process.env.PWD || cwd();
-  console.log(`📁 Initializing in: ${workingDir}`);
-
-  // Change to the working directory to ensure all file operations happen there
-  try {
-    process.chdir(workingDir);
-  } catch (err) {
-    printWarning(`Could not change to directory ${workingDir}: ${err.message}`);
-  }
-
-  try {
-    printSuccess('Initializing Claude Code integration files...');
-
-    // Check if files already exist in the working directory
-    const files = ['CLAUDE.md', 'memory-bank.md', 'coordination.md'];
-    const existingFiles = [];
-
-    for (const file of files) {
-      try {
-        await fs.stat(`${workingDir}/${file}`);
-        existingFiles.push(file);
-      } catch {
-        // File doesn't exist, which is what we want
-      }
+    // Show help if requested
+    if (flags.help || flags.h || subArgs.includes('--help') || subArgs.includes('-h')) {
+        showInitHelp();
+        return;
     }
-
-    if (existingFiles.length > 0 && !initForce) {
-      printWarning(`The following files already exist: ${existingFiles.join(', ')}`);
-      console.log('Use --force to overwrite existing files');
-      return;
+    // Check for verification flags first
+    const hasVerificationFlags = subArgs.includes('--verify') || subArgs.includes('--pair') || flags.verify || flags.pair;
+    // Flow-nexus mode removed
+    // Default to enhanced Claude Flow v2 init unless other modes are specified
+    // Use --basic flag for old behavior, or verification flags for verification mode
+    if (!flags.basic && !flags.minimal && !flags.sparc && !hasVerificationFlags) {
+        return await enhancedClaudeFlowInit(flags, subArgs);
     }
-
-    // Use template copier to copy all template files
-    const templateOptions = {
-      sparc: initSparc,
-      minimal: initMinimal,
-      optimized: initOptimized,
-      dryRun: initDryRun,
-      force: initForce,
-      selectedModes: selectedModes,
-      verify: initVerify,
-      pair: initPair,
-    };
-
-    // If verification flags are set, always use generated templates for CLAUDE.md and settings.json
-    if (initVerify || initPair) {
-      console.log('  📁 Creating verification-focused configuration...');
-
-      // Create verification CLAUDE.md
-      if (!initDryRun) {
-        const { createVerificationClaudeMd, createVerificationSettingsJson } = await import(
-          './templates/verification-claude-md.js'
-        );
-        await fs.writeFile(`${workingDir}/CLAUDE.md`, createVerificationClaudeMd(), 'utf8');
-
-        // Create .claude directory and settings
-        await fs.mkdir(`${workingDir}/.claude`, { recursive: true });
-        await fs.writeFile(
-          `${workingDir}/.claude/settings.json`,
-          createVerificationSettingsJson(),
-          'utf8',
-        );
-        console.log('  ✅ Created verification-focused CLAUDE.md and settings.json');
-      } else {
-        console.log('  [DRY RUN] Would create verification-focused CLAUDE.md and settings.json');
-      }
-
-      // Copy other template files from repository if available
-      const validation = validateTemplatesExist();
-      if (validation.valid) {
-        const revisedResults = await copyRevisedTemplates(workingDir, {
-          force: initForce,
-          dryRun: initDryRun,
-          verbose: false,
-          sparc: initSparc,
-        });
-      }
-
-      // Also create standard memory and coordination files
-      const copyResults = await copyTemplates(workingDir, {
-        ...templateOptions,
-        skipClaudeMd: true, // Don't overwrite the verification CLAUDE.md
-        skipSettings: true, // Don't overwrite the verification settings.json
-      });
-    } else {
-      // Standard template copying logic
-      const validation = validateTemplatesExist();
-      if (validation.valid) {
-        console.log('  📁 Copying revised template files...');
-        const revisedResults = await copyRevisedTemplates(workingDir, {
-          force: initForce,
-          dryRun: initDryRun,
-          verbose: true,
-          sparc: initSparc,
-        });
-
-        if (revisedResults.success) {
-          console.log(`  ✅ Copied ${revisedResults.copiedFiles.length} template files`);
-          if (revisedResults.skippedFiles.length > 0) {
-            console.log(`  ⏭️  Skipped ${revisedResults.skippedFiles.length} existing files`);
-          }
-        } else {
-          console.log('  ⚠️  Some template files could not be copied:');
-          revisedResults.errors.forEach((err) => console.log(`    - ${err}`));
-        }
-      } else {
-        // Fall back to generated templates
-        console.log('  ⚠️  Revised templates not available, using generated templates');
-        const copyResults = await copyTemplates(workingDir, templateOptions);
-
-        if (!copyResults.success) {
-          printError('Failed to copy templates:');
-          copyResults.errors.forEach((err) => console.log(`  ❌ ${err}`));
-          return;
-        }
-      }
+    // Check for validation and rollback commands
+    if (subArgs.includes('--validate') || subArgs.includes('--validate-only')) {
+        return handleValidationCommand(subArgs, flags);
     }
-
-    // Agent setup moved to end of function where execution is guaranteed
-
-    // Directory structure is created by template copier
-
-    // SPARC files are created by template copier when --sparc flag is used
-
-    // Memory README files and persistence database are created by template copier
-
-    // Create local claude-flow-novice executable wrapper
-    if (!initDryRun) {
-      await createLocalExecutable(workingDir);
-    } else {
-      console.log('  [DRY RUN] Would create local claude-flow-novice executable wrapper');
+    if (subArgs.includes('--rollback')) {
+        return handleRollbackCommand(subArgs, flags);
     }
-
-    // SPARC initialization
-    if (initSparc) {
-      console.log('\n🚀 Initializing SPARC development environment...');
-
-      if (initDryRun) {
-        console.log('  [DRY RUN] Would run: npx -y create-sparc init --force');
-        console.log('  [DRY RUN] Would create SPARC environment with all modes');
-        console.log(
-          '  [DRY RUN] Would create Claude slash commands' +
-            (initOptimized ? ' (Batchtools-optimized)' : ''),
-        );
-        if (selectedModes) {
-          console.log(
-            `  [DRY RUN] Would create commands for selected modes: ${selectedModes.join(', ')}`,
-          );
+    if (subArgs.includes('--list-backups')) {
+        return handleListBackups(subArgs, flags);
+    }
+    // Check for batch operations
+    const batchInitFlag = flags['batch-init'] || subArgs.includes('--batch-init');
+    const configFlag = flags.config || subArgs.includes('--config');
+    if (batchInitFlag || configFlag) {
+        return handleBatchInit(subArgs, flags);
+    }
+    // Parse init options
+    const initForce = subArgs.includes('--force') || subArgs.includes('-f') || flags.force;
+    const initMinimal = subArgs.includes('--minimal') || subArgs.includes('-m') || flags.minimal;
+    const initSparc = flags.roo || subArgs && subArgs.includes('--roo'); // SPARC only with --roo flag
+    const initDryRun = subArgs.includes('--dry-run') || subArgs.includes('-d') || flags.dryRun;
+    const initOptimized = initSparc && initForce; // Use optimized templates when both flags are present
+    const selectedModes = flags.modes ? flags.modes.split(',') : null; // Support selective mode initialization
+    // Check for verification and pair programming flags
+    const initVerify = subArgs.includes('--verify') || flags.verify;
+    const initPair = subArgs.includes('--pair') || flags.pair;
+    // Get the actual working directory (where the command was run from)
+    // Use PWD environment variable which preserves the original directory
+    const workingDir = process.env.PWD || cwd();
+    console.log(`📁 Initializing in: ${workingDir}`);
+    // Change to the working directory to ensure all file operations happen there
+    try {
+        process.chdir(workingDir);
+    } catch (err) {
+        printWarning(`Could not change to directory ${workingDir}: ${err.message}`);
+    }
+    try {
+        printSuccess('Initializing Claude Code integration files...');
+        // Check if files already exist in the working directory
+        const files = [
+            'CLAUDE.md',
+            'memory-bank.md',
+            'coordination.md'
+        ];
+        const existingFiles = [];
+        for (const file of files){
+            try {
+                await fs.stat(`${workingDir}/${file}`);
+                existingFiles.push(file);
+            } catch  {
+            // File doesn't exist, which is what we want
+            }
         }
-      } else {
-        // Check if create-sparc exists and run it
-        let sparcInitialized = false;
-        try {
-          // Use isolated NPX cache to prevent concurrent conflicts
-          console.log('  🔄 Running: npx -y create-sparc init --force');
-          const createSparcResult = await runCommand(
-            'npx',
-            ['-y', 'create-sparc', 'init', '--force'],
-            {
-              cwd: workingDir,
-              stdout: 'inherit',
-              stderr: 'inherit',
-              env: getIsolatedNpxEnv({
-                PWD: workingDir,
-              }),
-            },
-          );
-
-          if (createSparcResult.success) {
-            console.log('  ✅ SPARC environment initialized successfully');
-            sparcInitialized = true;
-          } else {
-            printWarning('create-sparc failed, creating basic SPARC structure manually...');
-
-            // Fallback: create basic SPARC structure manually
-            await createSparcStructureManually();
-            sparcInitialized = true; // Manual creation still counts as initialized
-          }
-        } catch (err) {
-          printWarning('create-sparc not available, creating basic SPARC structure manually...');
-
-          // Fallback: create basic SPARC structure manually
-          await createSparcStructureManually();
-          sparcInitialized = true; // Manual creation still counts as initialized
+        if (existingFiles.length > 0 && !initForce) {
+            printWarning(`The following files already exist: ${existingFiles.join(', ')}`);
+            console.log('Use --force to overwrite existing files');
+            return;
         }
-
-        // Always create Claude slash commands after SPARC initialization
-        if (sparcInitialized) {
-          try {
-            if (initOptimized) {
-              await createOptimizedClaudeSlashCommands(workingDir, selectedModes);
+        // Use template copier to copy all template files
+        const templateOptions = {
+            sparc: initSparc,
+            minimal: initMinimal,
+            optimized: initOptimized,
+            dryRun: initDryRun,
+            force: initForce,
+            selectedModes: selectedModes,
+            verify: initVerify,
+            pair: initPair
+        };
+        // If verification flags are set, always use generated templates for CLAUDE.md and settings.json
+        if (initVerify || initPair) {
+            console.log('  📁 Creating verification-focused configuration...');
+            // Create verification CLAUDE.md
+            if (!initDryRun) {
+                const { createVerificationClaudeMd, createVerificationSettingsJson } = await import("./templates/verification-claude-md.js");
+                await fs.writeFile(`${workingDir}/CLAUDE.md`, createVerificationClaudeMd(), 'utf8');
+                // Create .claude directory and settings
+                await fs.mkdir(`${workingDir}/.claude`, {
+                    recursive: true
+                });
+                await fs.writeFile(`${workingDir}/.claude/settings.json`, createVerificationSettingsJson(), 'utf8');
+                console.log('  ✅ Created verification-focused CLAUDE.md and settings.json');
             } else {
-              await createClaudeSlashCommands(workingDir);
+                console.log('  [DRY RUN] Would create verification-focused CLAUDE.md and settings.json');
+            }
+            // Copy other template files from repository if available
+            const validation = validateTemplatesExist();
+            if (validation.valid) {
+                const revisedResults = await copyRevisedTemplates(workingDir, {
+                    force: initForce,
+                    dryRun: initDryRun,
+                    verbose: false,
+                    sparc: initSparc
+                });
+            }
+            // Also create standard memory and coordination files
+            const copyResults = await copyTemplates(workingDir, {
+                ...templateOptions,
+                skipClaudeMd: true,
+                skipSettings: true
+            });
+        } else {
+            // Standard template copying logic
+            const validation = validateTemplatesExist();
+            if (validation.valid) {
+                console.log('  📁 Copying revised template files...');
+                const revisedResults = await copyRevisedTemplates(workingDir, {
+                    force: initForce,
+                    dryRun: initDryRun,
+                    verbose: true,
+                    sparc: initSparc
+                });
+                if (revisedResults.success) {
+                    console.log(`  ✅ Copied ${revisedResults.copiedFiles.length} template files`);
+                    if (revisedResults.skippedFiles.length > 0) {
+                        console.log(`  ⏭️  Skipped ${revisedResults.skippedFiles.length} existing files`);
+                    }
+                } else {
+                    console.log('  ⚠️  Some template files could not be copied:');
+                    revisedResults.errors.forEach((err)=>console.log(`    - ${err}`));
+                }
+            } else {
+                // Fall back to generated templates
+                console.log('  ⚠️  Revised templates not available, using generated templates');
+                const copyResults = await copyTemplates(workingDir, templateOptions);
+                if (!copyResults.success) {
+                    printError('Failed to copy templates:');
+                    copyResults.errors.forEach((err)=>console.log(`  ❌ ${err}`));
+                    return;
+                }
             }
-          } catch (err) {
-            // Legacy slash command creation - silently skip if it fails
-            // SPARC slash commands are already created successfully above
-          }
-        }
-      }
-    }
-
-    if (initDryRun) {
-      printSuccess("🔍 Dry run completed! Here's what would be created:");
-      console.log('\n📋 Summary of planned initialization:');
-      console.log(
-        `  • Configuration: ${initOptimized ? 'Batchtools-optimized SPARC' : initSparc ? 'SPARC-enhanced' : 'Standard'}`,
-      );
-      console.log(
-        `  • Template type: ${initOptimized ? 'Optimized for parallel processing' : 'Standard'}`,
-      );
-      console.log('  • Core files: CLAUDE.md, memory-bank.md, coordination.md');
-      console.log('  • Directory structure: memory/, coordination/, .claude/');
-      console.log('  • Local executable: ./claude-flow');
-      if (initSparc) {
-        console.log(
-          `  • Claude Code slash commands: ${selectedModes ? selectedModes.length : 'All'} SPARC mode commands`,
-        );
-        console.log('  • SPARC environment with all development modes');
-      }
-      if (initOptimized) {
-        console.log('  • Batchtools optimization: Enabled for parallel processing');
-        console.log('  • Performance enhancements: Smart batching, concurrent operations');
-      }
-      console.log('\n🚀 To proceed with initialization, run the same command without --dry-run');
-    } else {
-      printSuccess('🎉 Claude Code integration files initialized successfully!');
-
-      if (initOptimized) {
-        console.log('\n⚡ Batchtools Optimization Enabled!');
-        console.log('  • Parallel processing capabilities activated');
-        console.log('  • Performance improvements: 250-500% faster operations');
-        console.log('  • Smart batching and concurrent operations available');
-      }
-
-      console.log('\n📋 What was created:');
-      console.log(
-        `  ✅ CLAUDE.md (${initOptimized ? 'Batchtools-optimized' : initSparc ? 'SPARC-enhanced' : 'Standard configuration'})`,
-      );
-      console.log(
-        `  ✅ memory-bank.md (${initOptimized ? 'With parallel processing' : 'Standard memory system'})`,
-      );
-      console.log(
-        `  ✅ coordination.md (${initOptimized ? 'Enhanced with batchtools' : 'Standard coordination'})`,
-      );
-      console.log('  ✅ Directory structure with memory/ and coordination/');
-      console.log('  ✅ Local executable at ./claude-flow');
-      console.log('  ✅ Persistence database at memory/claude-flow-data.json');
-      console.log('  ✅ Agent system with 64 specialized agents in .claude/agents/');
-
-      if (initSparc) {
-        const modeCount = selectedModes ? selectedModes.length : '20+';
-        console.log(`  ✅ Claude Code slash commands (${modeCount} SPARC modes)`);
-        console.log('  ✅ Complete SPARC development environment');
-      }
-
-      console.log('\n🚀 Next steps:');
-      console.log('1. Review and customize the generated files for your project');
-      console.log("2. Run './claude-flow-novice start' to begin the orchestration system");
-      console.log("3. Use './claude-flow' instead of 'npx claude-flow' for all commands");
-      console.log("4. Use 'claude --dangerously-skip-permissions' for unattended operation");
-
-      if (initSparc) {
-        console.log(
-          '5. Use Claude Code slash commands: /sparc, /sparc-architect, /sparc-tdd, etc.',
-        );
-        console.log("6. Explore SPARC modes with './claude-flow-novice sparc modes'");
-        console.log('7. Try TDD workflow with \'./claude-flow-novice sparc tdd "your task"\'');
-
-        if (initOptimized) {
-          console.log('8. Use batchtools commands: /batchtools, /performance for optimization');
-          console.log('9. Enable parallel processing with --parallel flags');
-          console.log("10. Monitor performance with './claude-flow-novice performance monitor'");
         }
-      }
-
-      // Update .gitignore
-      const gitignoreResult = await updateGitignore(workingDir, initForce, initDryRun);
-      if (gitignoreResult.success) {
+        // Agent setup moved to end of function where execution is guaranteed
+        // Directory structure is created by template copier
+        // SPARC files are created by template copier when --sparc flag is used
+        // Memory README files and persistence database are created by template copier
+        // Create local claude-flow-novice executable wrapper
         if (!initDryRun) {
-          console.log(`  ✅ ${gitignoreResult.message}`);
+            await createLocalExecutable(workingDir);
         } else {
-          console.log(`  ${gitignoreResult.message}`);
+            console.log('  [DRY RUN] Would create local claude-flow-novice executable wrapper');
         }
-      } else {
-        console.log(`  ⚠️  ${gitignoreResult.message}`);
-      }
-
-      console.log('\n💡 Tips:');
-      console.log("  • Type '/' in Claude Code to see all available slash commands");
-      console.log("  • Use './claude-flow-novice status' to check system health");
-      console.log("  • Store important context with './claude-flow-novice memory store'");
-
-      if (initOptimized) {
-        console.log('  • Use --parallel flags for concurrent operations');
-        console.log('  • Enable batch processing for multiple related tasks');
-        console.log('  • Monitor performance with real-time metrics');
-      }
-
-      // Initialize hive-mind system for standard init
-      console.log('\n🧠 Initializing basic hive-mind system...');
-      try {
-        const hiveMindOptions = {
-          config: {
-            integration: {
-              claudeCode: { enabled: isClaudeCodeInstalled() },
-              mcpTools: { enabled: true },
-            },
-            monitoring: { enabled: false }, // Basic setup for standard init
-          },
-        };
-
-        const hiveMindResult = await initializeHiveMind(workingDir, hiveMindOptions, false);
-
-        if (hiveMindResult.success) {
-          console.log('  ✅ Basic hive-mind system initialized');
-          console.log('  💡 Use "npx claude-flow-novice hive-mind" for advanced features');
-        } else {
-          console.log(`  ⚠️  Hive-mind setup skipped: ${hiveMindResult.error}`);
+        // SPARC initialization
+        if (initSparc) {
+            console.log('\n🚀 Initializing SPARC development environment...');
+            if (initDryRun) {
+                console.log('  [DRY RUN] Would run: npx -y create-sparc init --force');
+                console.log('  [DRY RUN] Would create SPARC environment with all modes');
+                console.log('  [DRY RUN] Would create Claude slash commands' + (initOptimized ? ' (Batchtools-optimized)' : ''));
+                if (selectedModes) {
+                    console.log(`  [DRY RUN] Would create commands for selected modes: ${selectedModes.join(', ')}`);
+                }
+            } else {
+                // Check if create-sparc exists and run it
+                let sparcInitialized = false;
+                try {
+                    // Use isolated NPX cache to prevent concurrent conflicts
+                    console.log('  🔄 Running: npx -y create-sparc init --force');
+                    const createSparcResult = await runCommand('npx', [
+                        '-y',
+                        'create-sparc',
+                        'init',
+                        '--force'
+                    ], {
+                        cwd: workingDir,
+                        stdout: 'inherit',
+                        stderr: 'inherit',
+                        env: getIsolatedNpxEnv({
+                            PWD: workingDir
+                        })
+                    });
+                    if (createSparcResult.success) {
+                        console.log('  ✅ SPARC environment initialized successfully');
+                        sparcInitialized = true;
+                    } else {
+                        printWarning('create-sparc failed, creating basic SPARC structure manually...');
+                        // Fallback: create basic SPARC structure manually
+                        await createSparcStructureManually();
+                        sparcInitialized = true; // Manual creation still counts as initialized
+                    }
+                } catch (err) {
+                    printWarning('create-sparc not available, creating basic SPARC structure manually...');
+                    // Fallback: create basic SPARC structure manually
+                    await createSparcStructureManually();
+                    sparcInitialized = true; // Manual creation still counts as initialized
+                }
+                // Always create Claude slash commands after SPARC initialization
+                if (sparcInitialized) {
+                    try {
+                        if (initOptimized) {
+                            await createOptimizedClaudeSlashCommands(workingDir, selectedModes);
+                        } else {
+                            await createClaudeSlashCommands(workingDir);
+                        }
+                    } catch (err) {
+                    // Legacy slash command creation - silently skip if it fails
+                    // SPARC slash commands are already created successfully above
+                    }
+                }
+            }
         }
-      } catch (err) {
-        console.log(`  ⚠️  Hive-mind setup skipped: ${err.message}`);
-      }
-
-      // Check for Claude Code and set up MCP servers (always enabled by default)
-      if (!initDryRun && isClaudeCodeInstalled()) {
-        console.log('\n🔍 Claude Code CLI detected!');
-        const skipMcp = subArgs && subArgs.includes && subArgs.includes('--skip-mcp');
-
-        if (!skipMcp) {
-          // Use bulletproof MCP setup instead of legacy
-          const mcpSuccess = await setupBulletproofMcp({
-            verbose: false,
-            autoFix: true,
-            dryRun: initDryRun
-          });
-
-          if (!mcpSuccess) {
-            console.log('  💡 If you encounter issues, run: claude mcp remove claude-flow-novice -s local');
-          }
+        if (initDryRun) {
+            printSuccess("🔍 Dry run completed! Here's what would be created:");
+            console.log('\n📋 Summary of planned initialization:');
+            console.log(`  • Configuration: ${initOptimized ? 'Batchtools-optimized SPARC' : initSparc ? 'SPARC-enhanced' : 'Standard'}`);
+            console.log(`  • Template type: ${initOptimized ? 'Optimized for parallel processing' : 'Standard'}`);
+            console.log('  • Core files: CLAUDE.md, memory-bank.md, coordination.md');
+            console.log('  • Directory structure: memory/, coordination/, .claude/');
+            console.log('  • Local executable: ./claude-flow');
+            if (initSparc) {
+                console.log(`  • Claude Code slash commands: ${selectedModes ? selectedModes.length : 'All'} SPARC mode commands`);
+                console.log('  • SPARC environment with all development modes');
+            }
+            if (initOptimized) {
+                console.log('  • Batchtools optimization: Enabled for parallel processing');
+                console.log('  • Performance enhancements: Smart batching, concurrent operations');
+            }
+            console.log('\n🚀 To proceed with initialization, run the same command without --dry-run');
         } else {
-          console.log('  ℹ️  Skipping MCP setup (--skip-mcp flag used)');
+            printSuccess('🎉 Claude Code integration files initialized successfully!');
+            if (initOptimized) {
+                console.log('\n⚡ Batchtools Optimization Enabled!');
+                console.log('  • Parallel processing capabilities activated');
+                console.log('  • Performance improvements: 250-500% faster operations');
+                console.log('  • Smart batching and concurrent operations available');
+            }
+            console.log('\n📋 What was created:');
+            console.log(`  ✅ CLAUDE.md (${initOptimized ? 'Batchtools-optimized' : initSparc ? 'SPARC-enhanced' : 'Standard configuration'})`);
+            console.log(`  ✅ memory-bank.md (${initOptimized ? 'With parallel processing' : 'Standard memory system'})`);
+            console.log(`  ✅ coordination.md (${initOptimized ? 'Enhanced with batchtools' : 'Standard coordination'})`);
+            console.log('  ✅ Directory structure with memory/ and coordination/');
+            console.log('  ✅ Local executable at ./claude-flow');
+            console.log('  ✅ Persistence database at memory/claude-flow-data.json');
+            console.log('  ✅ Agent system with 64 specialized agents in .claude/agents/');
+            if (initSparc) {
+                const modeCount = selectedModes ? selectedModes.length : '20+';
+                console.log(`  ✅ Claude Code slash commands (${modeCount} SPARC modes)`);
+                console.log('  ✅ Complete SPARC development environment');
+            }
+            console.log('\n🚀 Next steps:');
+            console.log('1. Review and customize the generated files for your project');
+            console.log("2. Run './claude-flow-novice start' to begin the orchestration system");
+            console.log("3. Use './claude-flow' instead of 'npx claude-flow' for all commands");
+            console.log("4. Use 'claude --dangerously-skip-permissions' for unattended operation");
+            if (initSparc) {
+                console.log('5. Use Claude Code slash commands: /sparc, /sparc-architect, /sparc-tdd, etc.');
+                console.log("6. Explore SPARC modes with './claude-flow-novice sparc modes'");
+                console.log('7. Try TDD workflow with \'./claude-flow-novice sparc tdd "your task"\'');
+                if (initOptimized) {
+                    console.log('8. Use batchtools commands: /batchtools, /performance for optimization');
+                    console.log('9. Enable parallel processing with --parallel flags');
+                    console.log("10. Monitor performance with './claude-flow-novice performance monitor'");
+                }
+            }
+            // Update .gitignore
+            const gitignoreResult = await updateGitignore(workingDir, initForce, initDryRun);
+            if (gitignoreResult.success) {
+                if (!initDryRun) {
+                    console.log(`  ✅ ${gitignoreResult.message}`);
+                } else {
+                    console.log(`  ${gitignoreResult.message}`);
+                }
+            } else {
+                console.log(`  ⚠️  ${gitignoreResult.message}`);
+            }
+            console.log('\n💡 Tips:');
+            console.log("  • Type '/' in Claude Code to see all available slash commands");
+            console.log("  • Use './claude-flow-novice status' to check system health");
+            console.log("  • Store important context with './claude-flow-novice memory store'");
+            if (initOptimized) {
+                console.log('  • Use --parallel flags for concurrent operations');
+                console.log('  • Enable batch processing for multiple related tasks');
+                console.log('  • Monitor performance with real-time metrics');
+            }
+            // Initialize hive-mind system for standard init
+            console.log('\n🧠 Initializing basic hive-mind system...');
+            try {
+                const hiveMindOptions = {
+                    config: {
+                        integration: {
+                            claudeCode: {
+                                enabled: isClaudeCodeInstalled()
+                            },
+                            mcpTools: {
+                                enabled: true
+                            }
+                        },
+                        monitoring: {
+                            enabled: false
+                        }
+                    }
+                };
+                const hiveMindResult = await initializeHiveMind(workingDir, hiveMindOptions, false);
+                if (hiveMindResult.success) {
+                    console.log('  ✅ Basic hive-mind system initialized');
+                    console.log('  💡 Use "npx claude-flow-novice hive-mind" for advanced features');
+                } else {
+                    console.log(`  ⚠️  Hive-mind setup skipped: ${hiveMindResult.error}`);
+                }
+            } catch (err) {
+                console.log(`  ⚠️  Hive-mind setup skipped: ${err.message}`);
+            }
+            // Check for Claude Code and set up MCP servers (always enabled by default)
+            if (!initDryRun && isClaudeCodeInstalled()) {
+                console.log('\n🔍 Claude Code CLI detected!');
+                const skipMcp = subArgs && subArgs.includes && subArgs.includes('--skip-mcp');
+                if (!skipMcp) {
+                    // Use bulletproof MCP setup instead of legacy
+                    const mcpSuccess = await setupBulletproofMcp({
+                        verbose: false,
+                        autoFix: true,
+                        dryRun: initDryRun
+                    });
+                    if (!mcpSuccess) {
+                        console.log('  💡 If you encounter issues, run: claude mcp remove claude-flow-novice -s local');
+                    }
+                } else {
+                    console.log('  ℹ️  Skipping MCP setup (--skip-mcp flag used)');
+                }
+            } else if (!initDryRun && !isClaudeCodeInstalled()) {
+                console.log('\n⚠️  Claude Code CLI not detected!');
+                console.log('  📥 Install with: npm install -g @anthropic-ai/claude-code');
+                console.log('  📋 Then add MCP servers manually with:');
+                console.log('     claude mcp add claude-flow-novice claude-flow-novice mcp start');
+                console.log('     claude mcp add ruv-swarm npx ruv-swarm mcp start');
+            // Flow-nexus integration removed
+            }
         }
-      } else if (!initDryRun && !isClaudeCodeInstalled()) {
-        console.log('\n⚠️  Claude Code CLI not detected!');
-        console.log('  📥 Install with: npm install -g @anthropic-ai/claude-code');
-        console.log('  📋 Then add MCP servers manually with:');
-        console.log('     claude mcp add claude-flow-novice claude-flow-novice mcp start');
-        console.log('     claude mcp add ruv-swarm npx ruv-swarm mcp start');
-        // Flow-nexus integration removed
-      }
+    } catch (err) {
+        printError(`Failed to initialize files: ${err.message}`);
     }
-  } catch (err) {
-    printError(`Failed to initialize files: ${err.message}`);
-  }
 }
-
 // Handle batch initialization
 async function handleBatchInit(subArgs, flags) {
-  try {
-    // Options parsing from flags and subArgs
-    const options = {
-      parallel: !flags['no-parallel'] && flags.parallel !== false,
-      sparc: flags.sparc || flags.s,
-      minimal: flags.minimal || flags.m,
-      force: flags.force || flags.f,
-      maxConcurrency: flags['max-concurrent'] || 5,
-      progressTracking: true,
-      template: flags.template,
-      environments: flags.environments
-        ? flags.environments.split(',').map((env) => env.trim())
-        : ['dev'],
-    };
-
-    // Validate options
-    const validationErrors = validateBatchOptions(options);
-    if (validationErrors.length > 0) {
-      printError('Batch options validation failed:');
-      validationErrors.forEach((error) => console.error(`  - ${error}`));
-      return;
-    }
-
-    // Config file mode
-    if (flags.config) {
-      const configFile = flags.config;
-      printSuccess(`Loading batch configuration from: ${configFile}`);
-      const results = await batchInitFromConfig(configFile, options);
-      if (results) {
-        printSuccess('Batch initialization from config completed');
-      }
-      return;
-    }
-
-    // Batch init mode
-    if (flags['batch-init']) {
-      const projectsString = flags['batch-init'];
-      const projects = projectsString.split(',').map((project) => project.trim());
-
-      if (projects.length === 0) {
-        printError('No projects specified for batch initialization');
-        return;
-      }
-
-      printSuccess(`Initializing ${projects.length} projects in batch mode`);
-      const results = await batchInitCommand(projects, options);
-
-      if (results) {
-        const successful = results.filter((r) => r.success).length;
-        const failed = results.filter((r) => !r.success).length;
-
-        if (failed === 0) {
-          printSuccess(`All ${successful} projects initialized successfully`);
-        } else {
-          printWarning(`${successful} projects succeeded, ${failed} failed`);
+    try {
+        // Options parsing from flags and subArgs
+        const options = {
+            parallel: !flags['no-parallel'] && flags.parallel !== false,
+            sparc: flags.sparc || flags.s,
+            minimal: flags.minimal || flags.m,
+            force: flags.force || flags.f,
+            maxConcurrency: flags['max-concurrent'] || 5,
+            progressTracking: true,
+            template: flags.template,
+            environments: flags.environments ? flags.environments.split(',').map((env)=>env.trim()) : [
+                'dev'
+            ]
+        };
+        // Validate options
+        const validationErrors = validateBatchOptions(options);
+        if (validationErrors.length > 0) {
+            printError('Batch options validation failed:');
+            validationErrors.forEach((error)=>console.error(`  - ${error}`));
+            return;
+        }
+        // Config file mode
+        if (flags.config) {
+            const configFile = flags.config;
+            printSuccess(`Loading batch configuration from: ${configFile}`);
+            const results = await batchInitFromConfig(configFile, options);
+            if (results) {
+                printSuccess('Batch initialization from config completed');
+            }
+            return;
         }
-      }
-      return;
+        // Batch init mode
+        if (flags['batch-init']) {
+            const projectsString = flags['batch-init'];
+            const projects = projectsString.split(',').map((project)=>project.trim());
+            if (projects.length === 0) {
+                printError('No projects specified for batch initialization');
+                return;
+            }
+            printSuccess(`Initializing ${projects.length} projects in batch mode`);
+            const results = await batchInitCommand(projects, options);
+            if (results) {
+                const successful = results.filter((r)=>r.success).length;
+                const failed = results.filter((r)=>!r.success).length;
+                if (failed === 0) {
+                    printSuccess(`All ${successful} projects initialized successfully`);
+                } else {
+                    printWarning(`${successful} projects succeeded, ${failed} failed`);
+                }
+            }
+            return;
+        }
+        printError('No batch operation specified. Use --batch-init <projects> or --config <file>');
+    } catch (err) {
+        printError(`Batch initialization failed: ${err.message}`);
     }
-
-    printError('No batch operation specified. Use --batch-init <projects> or --config <file>');
-  } catch (err) {
-    printError(`Batch initialization failed: ${err.message}`);
-  }
 }
-
 /**
  * Enhanced initialization command with validation and rollback
- */
-async function enhancedInitCommand(subArgs, flags) {
-  console.log('🛡️  Starting enhanced initialization with validation and rollback...');
-
-  // Store parameters to avoid scope issues in async context
-  const args = subArgs || [];
-  const options = flags || {};
-
-  // Get the working directory
-  const workingDir = process.env.PWD || process.cwd();
-
-  // Initialize systems
-  const rollbackSystem = new RollbackSystem(workingDir);
-  const validationSystem = new ValidationSystem(workingDir);
-
-  let atomicOp = null;
-
-  try {
-    // Parse options
-    const initOptions = {
-      force: args.includes('--force') || args.includes('-f') || options.force,
-      minimal: args.includes('--minimal') || args.includes('-m') || options.minimal,
-      sparc: args.includes('--sparc') || args.includes('-s') || options.sparc,
-      skipPreValidation: args.includes('--skip-pre-validation'),
-      skipBackup: args.includes('--skip-backup'),
-      validateOnly: args.includes('--validate-only'),
-    };
-
-    // Phase 1: Pre-initialization validation
-    if (!initOptions.skipPreValidation) {
-      console.log('\n🔍 Phase 1: Pre-initialization validation...');
-      const preValidation = await validationSystem.validatePreInit(initOptions);
-
-      if (!preValidation.success) {
-        printError('Pre-initialization validation failed:');
-        preValidation.errors.forEach((error) => console.error(`  ❌ ${error}`));
-        return;
-      }
-
-      if (preValidation.warnings.length > 0) {
-        printWarning('Pre-initialization warnings:');
-        preValidation.warnings.forEach((warning) => console.warn(`  ⚠️  ${warning}`));
-      }
-
-      printSuccess('Pre-initialization validation passed');
-    }
-
-    // Stop here if validation-only mode
-    if (options.validateOnly) {
-      console.log('\n✅ Validation-only mode completed');
-      return;
-    }
-
-    // Phase 2: Create backup
-    if (!options.skipBackup) {
-      console.log('\n💾 Phase 2: Creating backup...');
-      const backupResult = await rollbackSystem.createPreInitBackup();
-
-      if (!backupResult.success) {
-        printError('Backup creation failed:');
-        backupResult.errors.forEach((error) => console.error(`  ❌ ${error}`));
-        return;
-      }
-    }
-
-    // Phase 3: Initialize with atomic operations
-    console.log('\n🔧 Phase 3: Atomic initialization...');
-    atomicOp = createAtomicOperation(rollbackSystem, 'enhanced-init');
-
-    const atomicBegin = await atomicOp.begin();
-    if (!atomicBegin) {
-      printError('Failed to begin atomic operation');
-      return;
-    }
-
-    // Perform initialization steps with checkpoints
-    await performInitializationWithCheckpoints(rollbackSystem, options, workingDir, dryRun);
-
-    // Phase 4: Post-initialization validation
-    console.log('\n✅ Phase 4: Post-initialization validation...');
-    const postValidation = await validationSystem.validatePostInit();
-
-    if (!postValidation.success) {
-      printError('Post-initialization validation failed:');
-      postValidation.errors.forEach((error) => console.error(`  ❌ ${error}`));
-
-      // Attempt automatic rollback
-      console.log('\n🔄 Attempting automatic rollback...');
-      await atomicOp.rollback();
-      printWarning('Initialization rolled back due to validation failure');
-      return;
-    }
-
-    // Phase 5: Configuration validation
-    console.log('\n🔧 Phase 5: Configuration validation...');
-    const configValidation = await validationSystem.validateConfiguration();
-
-    if (configValidation.warnings.length > 0) {
-      printWarning('Configuration warnings:');
-      configValidation.warnings.forEach((warning) => console.warn(`  ⚠️  ${warning}`));
-    }
-
-    // Phase 6: Health checks
-    console.log('\n🏥 Phase 6: System health checks...');
-    const healthChecks = await validationSystem.runHealthChecks();
-
-    if (healthChecks.warnings.length > 0) {
-      printWarning('Health check warnings:');
-      healthChecks.warnings.forEach((warning) => console.warn(`  ⚠️  ${warning}`));
-    }
-
-    // Commit atomic operation
-    await atomicOp.commit();
-
-    // Generate and display validation report
-    const fullValidation = await runFullValidation(workingDir, {
-      postInit: true,
-      skipPreInit: options.skipPreValidation,
-    });
-
-    console.log('\n📊 Validation Report:');
-    console.log(fullValidation.report);
-
-    printSuccess('🎉 Enhanced initialization completed successfully!');
-    console.log('\n✨ Your SPARC environment is fully validated and ready to use');
-  } catch (error) {
-    printError(`Enhanced initialization failed: ${error.message}`);
-
-    // Attempt rollback if atomic operation is active
-    if (atomicOp && !atomicOp.completed) {
-      console.log('\n🔄 Performing emergency rollback...');
-      try {
-        await atomicOp.rollback();
-        printWarning('Emergency rollback completed');
-      } catch (rollbackError) {
-        printError(`Rollback also failed: ${rollbackError.message}`);
-      }
+ */ async function enhancedInitCommand(subArgs, flags) {
+    console.log('🛡️  Starting enhanced initialization with validation and rollback...');
+    // Store parameters to avoid scope issues in async context
+    const args = subArgs || [];
+    const options = flags || {};
+    // Get the working directory
+    const workingDir = process.env.PWD || process.cwd();
+    // Initialize systems
+    const rollbackSystem = new RollbackSystem(workingDir);
+    const validationSystem = new ValidationSystem(workingDir);
+    let atomicOp = null;
+    try {
+        // Parse options
+        const initOptions = {
+            force: args.includes('--force') || args.includes('-f') || options.force,
+            minimal: args.includes('--minimal') || args.includes('-m') || options.minimal,
+            sparc: args.includes('--sparc') || args.includes('-s') || options.sparc,
+            skipPreValidation: args.includes('--skip-pre-validation'),
+            skipBackup: args.includes('--skip-backup'),
+            validateOnly: args.includes('--validate-only')
+        };
+        // Phase 1: Pre-initialization validation
+        if (!initOptions.skipPreValidation) {
+            console.log('\n🔍 Phase 1: Pre-initialization validation...');
+            const preValidation = await validationSystem.validatePreInit(initOptions);
+            if (!preValidation.success) {
+                printError('Pre-initialization validation failed:');
+                preValidation.errors.forEach((error)=>console.error(`  ❌ ${error}`));
+                return;
+            }
+            if (preValidation.warnings.length > 0) {
+                printWarning('Pre-initialization warnings:');
+                preValidation.warnings.forEach((warning)=>console.warn(`  ⚠️  ${warning}`));
+            }
+            printSuccess('Pre-initialization validation passed');
+        }
+        // Stop here if validation-only mode
+        if (options.validateOnly) {
+            console.log('\n✅ Validation-only mode completed');
+            return;
+        }
+        // Phase 2: Create backup
+        if (!options.skipBackup) {
+            console.log('\n💾 Phase 2: Creating backup...');
+            const backupResult = await rollbackSystem.createPreInitBackup();
+            if (!backupResult.success) {
+                printError('Backup creation failed:');
+                backupResult.errors.forEach((error)=>console.error(`  ❌ ${error}`));
+                return;
+            }
+        }
+        // Phase 3: Initialize with atomic operations
+        console.log('\n🔧 Phase 3: Atomic initialization...');
+        atomicOp = createAtomicOperation(rollbackSystem, 'enhanced-init');
+        const atomicBegin = await atomicOp.begin();
+        if (!atomicBegin) {
+            printError('Failed to begin atomic operation');
+            return;
+        }
+        // Perform initialization steps with checkpoints
+        await performInitializationWithCheckpoints(rollbackSystem, options, workingDir, dryRun);
+        // Phase 4: Post-initialization validation
+        console.log('\n✅ Phase 4: Post-initialization validation...');
+        const postValidation = await validationSystem.validatePostInit();
+        if (!postValidation.success) {
+            printError('Post-initialization validation failed:');
+            postValidation.errors.forEach((error)=>console.error(`  ❌ ${error}`));
+            // Attempt automatic rollback
+            console.log('\n🔄 Attempting automatic rollback...');
+            await atomicOp.rollback();
+            printWarning('Initialization rolled back due to validation failure');
+            return;
+        }
+        // Phase 5: Configuration validation
+        console.log('\n🔧 Phase 5: Configuration validation...');
+        const configValidation = await validationSystem.validateConfiguration();
+        if (configValidation.warnings.length > 0) {
+            printWarning('Configuration warnings:');
+            configValidation.warnings.forEach((warning)=>console.warn(`  ⚠️  ${warning}`));
+        }
+        // Phase 6: Health checks
+        console.log('\n🏥 Phase 6: System health checks...');
+        const healthChecks = await validationSystem.runHealthChecks();
+        if (healthChecks.warnings.length > 0) {
+            printWarning('Health check warnings:');
+            healthChecks.warnings.forEach((warning)=>console.warn(`  ⚠️  ${warning}`));
+        }
+        // Commit atomic operation
+        await atomicOp.commit();
+        // Generate and display validation report
+        const fullValidation = await runFullValidation(workingDir, {
+            postInit: true,
+            skipPreInit: options.skipPreValidation
+        });
+        console.log('\n📊 Validation Report:');
+        console.log(fullValidation.report);
+        printSuccess('🎉 Enhanced initialization completed successfully!');
+        console.log('\n✨ Your SPARC environment is fully validated and ready to use');
+    } catch (error) {
+        printError(`Enhanced initialization failed: ${error.message}`);
+        // Attempt rollback if atomic operation is active
+        if (atomicOp && !atomicOp.completed) {
+            console.log('\n🔄 Performing emergency rollback...');
+            try {
+                await atomicOp.rollback();
+                printWarning('Emergency rollback completed');
+            } catch (rollbackError) {
+                printError(`Rollback also failed: ${rollbackError.message}`);
+            }
+        }
     }
-  }
 }
-
 /**
  * Handle validation commands
- */
-async function handleValidationCommand(subArgs, flags) {
-  const workingDir = process.env.PWD || process.cwd();
-
-  console.log('🔍 Running validation checks...');
-
-  const options = {
-    skipPreInit: subArgs.includes('--skip-pre-init'),
-    skipConfig: subArgs.includes('--skip-config'),
-    skipModeTest: subArgs.includes('--skip-mode-test'),
-    postInit: !subArgs.includes('--pre-init-only'),
-  };
-
-  try {
-    const validationResults = await runFullValidation(workingDir, options);
-
-    console.log('\n📊 Validation Results:');
-    console.log(validationResults.report);
-
-    if (validationResults.success) {
-      printSuccess('✅ All validation checks passed');
-    } else {
-      printError('❌ Some validation checks failed');
-      process.exit(1);
+ */ async function handleValidationCommand(subArgs, flags) {
+    const workingDir = process.env.PWD || process.cwd();
+    console.log('🔍 Running validation checks...');
+    const options = {
+        skipPreInit: subArgs.includes('--skip-pre-init'),
+        skipConfig: subArgs.includes('--skip-config'),
+        skipModeTest: subArgs.includes('--skip-mode-test'),
+        postInit: !subArgs.includes('--pre-init-only')
+    };
+    try {
+        const validationResults = await runFullValidation(workingDir, options);
+        console.log('\n📊 Validation Results:');
+        console.log(validationResults.report);
+        if (validationResults.success) {
+            printSuccess('✅ All validation checks passed');
+        } else {
+            printError('❌ Some validation checks failed');
+            process.exit(1);
+        }
+    } catch (error) {
+        printError(`Validation failed: ${error.message}`);
+        process.exit(1);
     }
-  } catch (error) {
-    printError(`Validation failed: ${error.message}`);
-    process.exit(1);
-  }
 }
-
 /**
  * Handle rollback commands
- */
-async function handleRollbackCommand(subArgs, flags) {
-  const workingDir = process.env.PWD || process.cwd();
-  const rollbackSystem = new RollbackSystem(workingDir);
-
-  try {
-    // Check for specific rollback options
-    if (subArgs.includes('--full')) {
-      console.log('🔄 Performing full rollback...');
-      const result = await rollbackSystem.performFullRollback();
-
-      if (result.success) {
-        printSuccess('Full rollback completed successfully');
-      } else {
-        printError('Full rollback failed:');
-        result.errors.forEach((error) => console.error(`  ❌ ${error}`));
-      }
-    } else if (subArgs.includes('--partial')) {
-      const phaseIndex = subArgs.findIndex((arg) => arg === '--phase');
-      if (phaseIndex !== -1 && subArgs[phaseIndex + 1]) {
-        const phase = subArgs[phaseIndex + 1];
-        console.log(`🔄 Performing partial rollback for phase: ${phase}`);
-
-        const result = await rollbackSystem.performPartialRollback(phase);
-
-        if (result.success) {
-          printSuccess(`Partial rollback completed for phase: ${phase}`);
-        } else {
-          printError(`Partial rollback failed for phase: ${phase}`);
-          result.errors.forEach((error) => console.error(`  ❌ ${error}`));
-        }
-      } else {
-        printError('Partial rollback requires --phase <phase-name>');
-      }
-    } else {
-      // Interactive rollback point selection
-      const rollbackPoints = await rollbackSystem.listRollbackPoints();
-
-      if (rollbackPoints.rollbackPoints.length === 0) {
-        printWarning('No rollback points available');
-        return;
-      }
-
-      console.log('\n📋 Available rollback points:');
-      rollbackPoints.rollbackPoints.forEach((point, index) => {
-        const date = new Date(point.timestamp).toLocaleString();
-        console.log(`  ${index + 1}. ${point.type} - ${date}`);
-      });
-
-      // For now, rollback to the most recent point
-      const latest = rollbackPoints.rollbackPoints[0];
-      if (latest) {
-        console.log(
-          `\n🔄 Rolling back to: ${latest.type} (${new Date(latest.timestamp).toLocaleString()})`,
-        );
-        const result = await rollbackSystem.performFullRollback(latest.backupId);
-
-        if (result.success) {
-          printSuccess('Rollback completed successfully');
+ */ async function handleRollbackCommand(subArgs, flags) {
+    const workingDir = process.env.PWD || process.cwd();
+    const rollbackSystem = new RollbackSystem(workingDir);
+    try {
+        // Check for specific rollback options
+        if (subArgs.includes('--full')) {
+            console.log('🔄 Performing full rollback...');
+            const result = await rollbackSystem.performFullRollback();
+            if (result.success) {
+                printSuccess('Full rollback completed successfully');
+            } else {
+                printError('Full rollback failed:');
+                result.errors.forEach((error)=>console.error(`  ❌ ${error}`));
+            }
+        } else if (subArgs.includes('--partial')) {
+            const phaseIndex = subArgs.findIndex((arg)=>arg === '--phase');
+            if (phaseIndex !== -1 && subArgs[phaseIndex + 1]) {
+                const phase = subArgs[phaseIndex + 1];
+                console.log(`🔄 Performing partial rollback for phase: ${phase}`);
+                const result = await rollbackSystem.performPartialRollback(phase);
+                if (result.success) {
+                    printSuccess(`Partial rollback completed for phase: ${phase}`);
+                } else {
+                    printError(`Partial rollback failed for phase: ${phase}`);
+                    result.errors.forEach((error)=>console.error(`  ❌ ${error}`));
+                }
+            } else {
+                printError('Partial rollback requires --phase <phase-name>');
+            }
         } else {
-          printError('Rollback failed');
+            // Interactive rollback point selection
+            const rollbackPoints = await rollbackSystem.listRollbackPoints();
+            if (rollbackPoints.rollbackPoints.length === 0) {
+                printWarning('No rollback points available');
+                return;
+            }
+            console.log('\n📋 Available rollback points:');
+            rollbackPoints.rollbackPoints.forEach((point, index)=>{
+                const date = new Date(point.timestamp).toLocaleString();
+                console.log(`  ${index + 1}. ${point.type} - ${date}`);
+            });
+            // For now, rollback to the most recent point
+            const latest = rollbackPoints.rollbackPoints[0];
+            if (latest) {
+                console.log(`\n🔄 Rolling back to: ${latest.type} (${new Date(latest.timestamp).toLocaleString()})`);
+                const result = await rollbackSystem.performFullRollback(latest.backupId);
+                if (result.success) {
+                    printSuccess('Rollback completed successfully');
+                } else {
+                    printError('Rollback failed');
+                }
+            }
         }
-      }
+    } catch (error) {
+        printError(`Rollback operation failed: ${error.message}`);
     }
-  } catch (error) {
-    printError(`Rollback operation failed: ${error.message}`);
-  }
 }
-
 /**
  * Handle list backups command
- */
-async function handleListBackups(subArgs, flags) {
-  const workingDir = process.env.PWD || process.cwd();
-  const rollbackSystem = new RollbackSystem(workingDir);
-
-  try {
-    const rollbackPoints = await rollbackSystem.listRollbackPoints();
-
-    console.log('\n📋 Rollback Points and Backups:');
-
-    if (rollbackPoints.rollbackPoints.length === 0) {
-      console.log('  No rollback points available');
-    } else {
-      console.log('\n🔄 Rollback Points:');
-      rollbackPoints.rollbackPoints.forEach((point, index) => {
-        const date = new Date(point.timestamp).toLocaleString();
-        console.log(`  ${index + 1}. ${point.type} - ${date} (${point.backupId || 'No backup'})`);
-      });
-    }
-
-    if (rollbackPoints.checkpoints.length > 0) {
-      console.log('\n📍 Checkpoints:');
-      rollbackPoints.checkpoints.slice(-5).forEach((checkpoint, index) => {
-        const date = new Date(checkpoint.timestamp).toLocaleString();
-        console.log(`  ${index + 1}. ${checkpoint.phase} - ${date} (${checkpoint.status})`);
-      });
+ */ async function handleListBackups(subArgs, flags) {
+    const workingDir = process.env.PWD || process.cwd();
+    const rollbackSystem = new RollbackSystem(workingDir);
+    try {
+        const rollbackPoints = await rollbackSystem.listRollbackPoints();
+        console.log('\n📋 Rollback Points and Backups:');
+        if (rollbackPoints.rollbackPoints.length === 0) {
+            console.log('  No rollback points available');
+        } else {
+            console.log('\n🔄 Rollback Points:');
+            rollbackPoints.rollbackPoints.forEach((point, index)=>{
+                const date = new Date(point.timestamp).toLocaleString();
+                console.log(`  ${index + 1}. ${point.type} - ${date} (${point.backupId || 'No backup'})`);
+            });
+        }
+        if (rollbackPoints.checkpoints.length > 0) {
+            console.log('\n📍 Checkpoints:');
+            rollbackPoints.checkpoints.slice(-5).forEach((checkpoint, index)=>{
+                const date = new Date(checkpoint.timestamp).toLocaleString();
+                console.log(`  ${index + 1}. ${checkpoint.phase} - ${date} (${checkpoint.status})`);
+            });
+        }
+    } catch (error) {
+        printError(`Failed to list backups: ${error.message}`);
     }
-  } catch (error) {
-    printError(`Failed to list backups: ${error.message}`);
-  }
 }
-
 /**
  * Perform initialization with checkpoints
- */
-async function performInitializationWithCheckpoints(
-  rollbackSystem,
-  options,
-  workingDir,
-  dryRun = false,
-) {
-  const phases = [
-    { name: 'file-creation', action: () => createInitialFiles(options, workingDir, dryRun) },
-    { name: 'directory-structure', action: () => createDirectoryStructure(workingDir, dryRun) },
-    { name: 'memory-setup', action: () => setupMemorySystem(workingDir, dryRun) },
-    { name: 'agent-system', action: () => setupAgentSystem(workingDir, dryRun, options) },
-    { name: 'mcp-config', action: () => setupMcpConfiguration(workingDir, dryRun) },
-    { name: 'hooks-system', action: () => setupHooksSystem(workingDir, dryRun) },
-    { name: 'coordination-setup', action: () => setupCoordinationSystem(workingDir, dryRun) },
-    { name: 'executable-creation', action: () => createLocalExecutable(workingDir, dryRun) },
-  ];
-
-  if (options.sparc) {
-    phases.push(
-      { name: 'sparc-init', action: () => createSparcStructureManually() },
-      { name: 'claude-commands', action: () => createClaudeSlashCommands(workingDir) },
-    );
-  }
-
-  for (const phase of phases) {
-    console.log(`  🔧 ${phase.name}...`);
-
-    // Create checkpoint before phase
-    await rollbackSystem.createCheckpoint(phase.name, {
-      timestamp: Date.now(),
-      phase: phase.name,
-    });
-
-    try {
-      await phase.action();
-      console.log(`  ✅ ${phase.name} completed`);
-    } catch (error) {
-      console.error(`  ❌ ${phase.name} failed: ${error.message}`);
-      throw error;
+ */ async function performInitializationWithCheckpoints(rollbackSystem, options, workingDir, dryRun1 = false) {
+    const phases = [
+        {
+            name: 'file-creation',
+            action: ()=>createInitialFiles(options, workingDir, dryRun1)
+        },
+        {
+            name: 'directory-structure',
+            action: ()=>createDirectoryStructure(workingDir, dryRun1)
+        },
+        {
+            name: 'memory-setup',
+            action: ()=>setupMemorySystem(workingDir, dryRun1)
+        },
+        {
+            name: 'agent-system',
+            action: ()=>setupAgentSystem(workingDir, dryRun1, options)
+        },
+        {
+            name: 'mcp-config',
+            action: ()=>setupMcpConfiguration(workingDir, dryRun1)
+        },
+        {
+            name: 'hooks-system',
+            action: ()=>setupHooksSystem(workingDir, dryRun1)
+        },
+        {
+            name: 'coordination-setup',
+            action: ()=>setupCoordinationSystem(workingDir, dryRun1)
+        },
+        {
+            name: 'executable-creation',
+            action: ()=>createLocalExecutable(workingDir, dryRun1)
+        }
+    ];
+    if (options.sparc) {
+        phases.push({
+            name: 'sparc-init',
+            action: ()=>createSparcStructureManually()
+        }, {
+            name: 'claude-commands',
+            action: ()=>createClaudeSlashCommands(workingDir)
+        });
+    }
+    for (const phase of phases){
+        console.log(`  🔧 ${phase.name}...`);
+        // Create checkpoint before phase
+        await rollbackSystem.createCheckpoint(phase.name, {
+            timestamp: Date.now(),
+            phase: phase.name
+        });
+        try {
+            await phase.action();
+            console.log(`  ✅ ${phase.name} completed`);
+        } catch (error) {
+            console.error(`  ❌ ${phase.name} failed: ${error.message}`);
+            throw error;
+        }
     }
-  }
 }
-
 // Helper functions for atomic initialization
-async function createInitialFiles(options, workingDir, dryRun = false) {
-  if (!dryRun) {
-    // Use template file instead of generation
-    const claudeMd = await readClaudeMdTemplate();
-    await fs.writeFile(`${workingDir}/CLAUDE.md`, claudeMd, 'utf8');
-
-    const memoryBankMd = options.minimal ? createMinimalMemoryBankMd() : createFullMemoryBankMd();
-    await fs.writeFile(`${workingDir}/memory-bank.md`, memoryBankMd, 'utf8');
-
-    const coordinationMd = options.minimal
-      ? createMinimalCoordinationMd()
-      : createFullCoordinationMd();
-    await fs.writeFile(`${workingDir}/coordination.md`, coordinationMd, 'utf8');
-  }
-}
-
-async function createDirectoryStructure(workingDir, dryRun = false) {
-  const directories = [
-    'memory',
-    'memory/agents',
-    'memory/sessions',
-    'coordination',
-    'coordination/memory_bank',
-    'coordination/subtasks',
-    'coordination/orchestration',
-    '.claude',
-    '.claude/commands',
-    '.claude/logs',
-  ];
-
-  if (!dryRun) {
-    for (const dir of directories) {
-      await fs.mkdir(`${workingDir}/${dir}`, { recursive: true });
+async function createInitialFiles(options, workingDir, dryRun1 = false) {
+    if (!dryRun1) {
+        // Use template file instead of generation
+        const claudeMd = await readClaudeMdTemplate();
+        await fs.writeFile(`${workingDir}/CLAUDE.md`, claudeMd, 'utf8');
+        const memoryBankMd = options.minimal ? createMinimalMemoryBankMd() : createFullMemoryBankMd();
+        await fs.writeFile(`${workingDir}/memory-bank.md`, memoryBankMd, 'utf8');
+        const coordinationMd = options.minimal ? createMinimalCoordinationMd() : createFullCoordinationMd();
+        await fs.writeFile(`${workingDir}/coordination.md`, coordinationMd, 'utf8');
     }
-  }
 }
-
-async function setupMemorySystem(workingDir, dryRun = false) {
-  if (!dryRun) {
-    const initialData = { agents: [], tasks: [], lastUpdated: Date.now() };
-    await fs.writeFile(
-      `${workingDir}/memory/claude-flow-data.json`,
-      JSON.stringify(initialData, null, 2),
-      'utf8',
-    );
-
-    await fs.writeFile(`${workingDir}/memory/agents/README.md`, createAgentsReadme(), 'utf8');
-    await fs.writeFile(`${workingDir}/memory/sessions/README.md`, createSessionsReadme(), 'utf8');
-  }
+async function createDirectoryStructure(workingDir, dryRun1 = false) {
+    const directories = [
+        'memory',
+        'memory/agents',
+        'memory/sessions',
+        'coordination',
+        'coordination/memory_bank',
+        'coordination/subtasks',
+        'coordination/orchestration',
+        '.claude',
+        '.claude/commands',
+        '.claude/logs'
+    ];
+    if (!dryRun1) {
+        for (const dir of directories){
+            await fs.mkdir(`${workingDir}/${dir}`, {
+                recursive: true
+            });
+        }
+    }
 }
-
-async function setupAgentSystem(workingDir, dryRun = false, options = {}) {
-  if (!dryRun) {
-    console.log('🤖 Setting up agent system...');
-
-    // Create agent directories
-    await createAgentDirectories(workingDir, dryRun);
-
-    // Copy all agent files (80+ agents)
-    const agentResult = await copyAgentFiles(workingDir, {
-      force: options.force || false,
-      dryRun: dryRun,
-    });
-
-    if (agentResult.success) {
-      await validateAgentSystem(workingDir);
-
-      // Copy command files
-      const commandResult = await copyCommandFiles(workingDir, {
-        force: options.force || false,
-        dryRun: dryRun,
-      });
-
-      if (commandResult.success) {
-        console.log('  ✅ Agent system setup complete with 80+ specialized agents');
-      } else {
-        console.log('  ⚠️ Command system setup failed:', commandResult.error);
-      }
-    } else {
-      console.log('  ⚠️ Agent system setup failed:', agentResult.error);
+async function setupMemorySystem(workingDir, dryRun1 = false) {
+    if (!dryRun1) {
+        const initialData = {
+            agents: [],
+            tasks: [],
+            lastUpdated: Date.now()
+        };
+        await fs.writeFile(`${workingDir}/memory/claude-flow-data.json`, JSON.stringify(initialData, null, 2), 'utf8');
+        await fs.writeFile(`${workingDir}/memory/agents/README.md`, createAgentsReadme(), 'utf8');
+        await fs.writeFile(`${workingDir}/memory/sessions/README.md`, createSessionsReadme(), 'utf8');
     }
-  }
 }
-
-async function setupMcpConfiguration(workingDir, dryRun = false) {
-  if (!dryRun) {
-    console.log('🔌 Setting up MCP configuration...');
-
-    const mcpConfig = {
-      "mcpServers": {
-        "claude-flow-novice": {
-          "command": "npx",
-          "args": ["claude-flow-novice", "mcp", "start"],
-          "env": {
-            "CLAUDE_FLOW_NOVICE_MODE": "novice",
-            "CLAUDE_FLOW_NOVICE_SIMPLIFIED": "true"
-          }
+async function setupAgentSystem(workingDir, dryRun1 = false, options = {}) {
+    if (!dryRun1) {
+        console.log('🤖 Setting up agent system...');
+        // Create agent directories
+        await createAgentDirectories(workingDir, dryRun1);
+        // Copy all agent files (80+ agents)
+        const agentResult = await copyAgentFiles(workingDir, {
+            force: options.force || false,
+            dryRun: dryRun1
+        });
+        if (agentResult.success) {
+            await validateAgentSystem(workingDir);
+            // Copy command files
+            const commandResult = await copyCommandFiles(workingDir, {
+                force: options.force || false,
+                dryRun: dryRun1
+            });
+            if (commandResult.success) {
+                console.log('  ✅ Agent system setup complete with 80+ specialized agents');
+            } else {
+                console.log('  ⚠️ Command system setup failed:', commandResult.error);
+            }
+        } else {
+            console.log('  ⚠️ Agent system setup failed:', agentResult.error);
         }
-      }
-    };
-
-    await fs.writeFile(
-      `${workingDir}/.mcp.json`,
-      JSON.stringify(mcpConfig, null, 2),
-      'utf8'
-    );
-    console.log('  ✅ Created .mcp.json configuration');
-  }
+    }
 }
-
-async function setupHooksSystem(workingDir, dryRun = false) {
-  if (!dryRun) {
-    console.log('🪝 Setting up hooks system...');
-
-    // Create .claude/settings.json with hooks configuration
-    const settingsConfig = {
-      "hooks": {
-        "pre-tool": {
-          "command": "npx claude-flow-novice hooks pre-task --description \"{{description}}\"",
-          "enabled": true
-        },
-        "post-tool": {
-          "command": "npx claude-flow-novice hooks post-task --task-id \"{{taskId}}\"",
-          "enabled": true
-        },
-        "pre-edit": {
-          "command": "npx claude-flow-novice hooks pre-edit --file \"{{file}}\"",
-          "enabled": true
-        },
-        "post-edit": {
-          "command": "npx claude-flow-novice hooks post-edit --file \"{{file}}\" --memory-key \"swarm/{{agent}}/{{step}}\"",
-          "enabled": true
-        }
-      },
-      "coordination": {
-        "autoSpawn": true,
-        "memoryPersistence": true,
-        "swarmOrchestration": true
-      }
-    };
-
-    await fs.writeFile(
-      `${workingDir}/.claude/settings.json`,
-      JSON.stringify(settingsConfig, null, 2),
-      'utf8'
-    );
-    console.log('  ✅ Created hooks configuration');
-  }
+async function setupMcpConfiguration(workingDir, dryRun1 = false) {
+    if (!dryRun1) {
+        console.log('🔌 Setting up MCP configuration...');
+        const mcpConfig = {
+            "mcpServers": {
+                "claude-flow-novice": {
+                    "command": "npx",
+                    "args": [
+                        "claude-flow-novice",
+                        "mcp",
+                        "start"
+                    ],
+                    "env": {
+                        "CLAUDE_FLOW_NOVICE_MODE": "novice",
+                        "CLAUDE_FLOW_NOVICE_SIMPLIFIED": "true"
+                    }
+                }
+            }
+        };
+        await fs.writeFile(`${workingDir}/.mcp.json`, JSON.stringify(mcpConfig, null, 2), 'utf8');
+        console.log('  ✅ Created .mcp.json configuration');
+    }
 }
-
-async function setupCoordinationSystem(workingDir, dryRun = false) {
-  // Coordination system is already set up by createDirectoryStructure
-  // This is a placeholder for future coordination setup logic
+async function setupHooksSystem(workingDir, dryRun1 = false) {
+    if (!dryRun1) {
+        console.log('🪝 Setting up hooks system...');
+        // Create .claude/settings.json with hooks configuration
+        const settingsConfig = {
+            "hooks": {
+                "pre-tool": {
+                    "command": "npx claude-flow-novice hooks pre-task --description \"{{description}}\"",
+                    "enabled": true
+                },
+                "post-tool": {
+                    "command": "npx claude-flow-novice hooks post-task --task-id \"{{taskId}}\"",
+                    "enabled": true
+                },
+                "pre-edit": {
+                    "command": "npx claude-flow-novice hooks pre-edit --file \"{{file}}\"",
+                    "enabled": true
+                },
+                "post-edit": {
+                    "command": "npx claude-flow-novice hooks post-edit --file \"{{file}}\" --memory-key \"swarm/{{agent}}/{{step}}\"",
+                    "enabled": true
+                }
+            },
+            "coordination": {
+                "autoSpawn": true,
+                "memoryPersistence": true,
+                "swarmOrchestration": true
+            }
+        };
+        await fs.writeFile(`${workingDir}/.claude/settings.json`, JSON.stringify(settingsConfig, null, 2), 'utf8');
+        console.log('  ✅ Created hooks configuration');
+    }
+}
+async function setupCoordinationSystem(workingDir, dryRun1 = false) {
+// Coordination system is already set up by createDirectoryStructure
+// This is a placeholder for future coordination setup logic
 }
-
 /**
  * Setup monitoring and telemetry for token tracking
- */
-async function setupMonitoring(workingDir) {
-  console.log('  📈 Configuring token usage tracking...');
-
-  const fs = await import('fs/promises');
-  const path = await import('path');
-
-  try {
-    // Create .claude-flow-novice directory for tracking data
-    const trackingDir = path.join(workingDir, '.claude-flow');
-    await fs.mkdir(trackingDir, { recursive: true });
-
-    // Create initial token usage file
-    const tokenUsageFile = path.join(trackingDir, 'token-usage.json');
-    const initialData = {
-      total: 0,
-      input: 0,
-      output: 0,
-      byAgent: {},
-      lastUpdated: new Date().toISOString(),
-    };
-
-    await fs.writeFile(tokenUsageFile, JSON.stringify(initialData, null, 2));
-    printSuccess('  ✓ Created token usage tracking file');
-
-    // Add telemetry configuration to .claude/settings.json if it exists
-    const settingsPath = path.join(workingDir, '.claude', 'settings.json');
+ */ async function setupMonitoring(workingDir) {
+    console.log('  📈 Configuring token usage tracking...');
+    const fs = await import("node:fs/promises");
+    const path = await import("path");
     try {
-      const settingsContent = await fs.readFile(settingsPath, 'utf8');
-      const settings = JSON.parse(settingsContent);
-
-      // Add telemetry hook
-      if (!settings.hooks) settings.hooks = {};
-      if (!settings.hooks['post-task']) settings.hooks['post-task'] = [];
-
-      // Add token tracking hook
-      const tokenTrackingHook =
-        'npx claude-flow-novice internal track-tokens --session-id {{session_id}} --tokens {{token_usage}}';
-      if (!settings.hooks['post-task'].includes(tokenTrackingHook)) {
-        settings.hooks['post-task'].push(tokenTrackingHook);
-      }
-
-      await fs.writeFile(settingsPath, JSON.stringify(settings, null, 2));
-      printSuccess('  ✓ Added token tracking hooks to settings');
-    } catch (err) {
-      console.log('  ⚠️  Could not update settings.json:', err.message);
-    }
-
-    // Create monitoring configuration
-    const monitoringConfig = {
-      enabled: true,
-      telemetry: {
-        claudeCode: {
-          env: 'CLAUDE_CODE_ENABLE_TELEMETRY',
-          value: '1',
-          description: 'Enable Claude Code OpenTelemetry metrics',
-        },
-      },
-      tracking: {
-        tokens: true,
-        costs: true,
-        agents: true,
-        sessions: true,
-      },
-      storage: {
-        location: '.claude-flow/token-usage.json',
-        format: 'json',
-        rotation: 'monthly',
-      },
-    };
-
-    const configPath = path.join(trackingDir, 'monitoring.config.json');
-    await fs.writeFile(configPath, JSON.stringify(monitoringConfig, null, 2));
-    printSuccess('  ✓ Created monitoring configuration');
-
-    // Create shell profile snippet for environment variable
-    const envSnippet = `
+        // Create .claude-flow-novice directory for tracking data
+        const trackingDir = path.join(workingDir, '.claude-flow');
+        await fs.mkdir(trackingDir, {
+            recursive: true
+        });
+        // Create initial token usage file
+        const tokenUsageFile = path.join(trackingDir, 'token-usage.json');
+        const initialData = {
+            total: 0,
+            input: 0,
+            output: 0,
+            byAgent: {},
+            lastUpdated: new Date().toISOString()
+        };
+        await fs.writeFile(tokenUsageFile, JSON.stringify(initialData, null, 2));
+        printSuccess('  ✓ Created token usage tracking file');
+        // Add telemetry configuration to .claude/settings.json if it exists
+        const settingsPath = path.join(workingDir, '.claude', 'settings.json');
+        try {
+            const settingsContent = await fs.readFile(settingsPath, 'utf8');
+            const settings = JSON.parse(settingsContent);
+            // Add telemetry hook
+            if (!settings.hooks) settings.hooks = {};
+            if (!settings.hooks['post-task']) settings.hooks['post-task'] = [];
+            // Add token tracking hook
+            const tokenTrackingHook = 'npx claude-flow-novice internal track-tokens --session-id {{session_id}} --tokens {{token_usage}}';
+            if (!settings.hooks['post-task'].includes(tokenTrackingHook)) {
+                settings.hooks['post-task'].push(tokenTrackingHook);
+            }
+            await fs.writeFile(settingsPath, JSON.stringify(settings, null, 2));
+            printSuccess('  ✓ Added token tracking hooks to settings');
+        } catch (err) {
+            console.log('  ⚠️  Could not update settings.json:', err.message);
+        }
+        // Create monitoring configuration
+        const monitoringConfig = {
+            enabled: true,
+            telemetry: {
+                claudeCode: {
+                    env: 'CLAUDE_CODE_ENABLE_TELEMETRY',
+                    value: '1',
+                    description: 'Enable Claude Code OpenTelemetry metrics'
+                }
+            },
+            tracking: {
+                tokens: true,
+                costs: true,
+                agents: true,
+                sessions: true
+            },
+            storage: {
+                location: '.claude-flow/token-usage.json',
+                format: 'json',
+                rotation: 'monthly'
+            }
+        };
+        const configPath = path.join(trackingDir, 'monitoring.config.json');
+        await fs.writeFile(configPath, JSON.stringify(monitoringConfig, null, 2));
+        printSuccess('  ✓ Created monitoring configuration');
+        // Create shell profile snippet for environment variable
+        const envSnippet = `
 # Claude Flow Token Tracking
 # Add this to your shell profile (.bashrc, .zshrc, etc.)
 export CLAUDE_CODE_ENABLE_TELEMETRY=1
@@ -1273,606 +1086,544 @@ export CLAUDE_CODE_ENABLE_TELEMETRY=1
 # Optional: Set custom metrics path
 # export CLAUDE_METRICS_PATH="$HOME/.claude/metrics"
 `;
-
-    const envPath = path.join(trackingDir, 'env-setup.sh');
-    await fs.writeFile(envPath, envSnippet.trim());
-    printSuccess('  ✓ Created environment setup script');
-
-    console.log('\n  📋 To enable Claude Code telemetry:');
-    console.log('     1. Add to your shell profile: export CLAUDE_CODE_ENABLE_TELEMETRY=1');
-    console.log('     2. Or run: source .claude-flow/env-setup.sh');
-    console.log('\n  💡 Token usage will be tracked in .claude-flow/token-usage.json');
-    console.log('     Run: claude-flow-novice analysis token-usage --breakdown --cost-analysis');
-  } catch (err) {
-    printError(`  Failed to setup monitoring: ${err.message}`);
-  }
+        const envPath = path.join(trackingDir, 'env-setup.sh');
+        await fs.writeFile(envPath, envSnippet.trim());
+        printSuccess('  ✓ Created environment setup script');
+        console.log('\n  📋 To enable Claude Code telemetry:');
+        console.log('     1. Add to your shell profile: export CLAUDE_CODE_ENABLE_TELEMETRY=1');
+        console.log('     2. Or run: source .claude-flow/env-setup.sh');
+        console.log('\n  💡 Token usage will be tracked in .claude-flow/token-usage.json');
+        console.log('     Run: claude-flow-novice analysis token-usage --breakdown --cost-analysis');
+    } catch (err) {
+        printError(`  Failed to setup monitoring: ${err.message}`);
+    }
 }
-
 /**
  * Enhanced Claude Flow v2.0.0 initialization
- */
-async function enhancedClaudeFlowInit(flags, subArgs = []) {
-  console.log('🚀 Initializing Claude Flow v2.0.0 with enhanced features...');
-
-  const workingDir = process.cwd();
-  const force = flags.force || flags.f;
-  const dryRun = flags.dryRun || flags['dry-run'] || flags.d;
-  const initSparc = flags.roo || (subArgs && subArgs.includes('--roo')); // SPARC only with --roo flag
-
-  // Store parameters to avoid scope issues in async context
-  const args = subArgs || [];
-  const options = flags || {};
-
-  // Import fs module for Node.js
-  const fs = await import('fs/promises');
-  const { chmod } = fs;
-
-  try {
-    // Check existing files
-    const existingFiles = [];
-    const filesToCheck = [
-      'CLAUDE.md',
-      '.claude/settings.json',
-      '.mcp.json',
-      'claude-flow.config.json',
-    ];
-
-    for (const file of filesToCheck) {
-      if (existsSync(`${workingDir}/${file}`)) {
-        existingFiles.push(file);
-      }
-    }
-
-    if (existingFiles.length > 0 && !force) {
-      printWarning(`The following files already exist: ${existingFiles.join(', ')}`);
-      console.log('Use --force to overwrite existing files');
-      return;
-    }
-
-    // Create CLAUDE.md from template
-    if (!dryRun) {
-      const claudeMdContent = await readClaudeMdTemplate();
-      await fs.writeFile(`${workingDir}/CLAUDE.md`, claudeMdContent, 'utf8');
-      printSuccess('✓ Created CLAUDE.md (Claude Flow v2.0.0 - Optimized Template)');
-    } else {
-      console.log('[DRY RUN] Would create CLAUDE.md (Claude Flow v2.0.0 - Optimized Template)');
-    }
-
-    // Create .claude directory structure
-    const claudeDir = `${workingDir}/.claude`;
-    if (!dryRun) {
-      await fs.mkdir(claudeDir, { recursive: true });
-      await fs.mkdir(`${claudeDir}/commands`, { recursive: true });
-      await fs.mkdir(`${claudeDir}/helpers`, { recursive: true });
-      printSuccess('✓ Created .claude directory structure');
-    } else {
-      console.log('[DRY RUN] Would create .claude directory structure');
-    }
-
-    // Create settings.json
-    if (!dryRun) {
-      await fs.writeFile(`${claudeDir}/settings.json`, createEnhancedSettingsJson(), 'utf8');
-      printSuccess('✓ Created .claude/settings.json with hooks and MCP configuration');
-    } else {
-      console.log('[DRY RUN] Would create .claude/settings.json');
-    }
-
-    // Create settings.local.json with default MCP permissions
-    const settingsLocal = {
-      permissions: {
-        allow: ['mcp__ruv-swarm', 'mcp__claude-flow'],
-        deny: [],
-      },
-    };
-
-    if (!dryRun) {
-      await fs.writeFile(
-        `${claudeDir}/settings.local.json`,
-        JSON.stringify(settingsLocal, null, 2, 'utf8'),
-      );
-      printSuccess('✓ Created .claude/settings.local.json with default MCP permissions');
-    } else {
-      console.log(
-        '[DRY RUN] Would create .claude/settings.local.json with default MCP permissions',
-      );
-    }
-
-    // Setup bulletproof MCP configuration instead of legacy approach
-    console.log('\n🛡️  Setting up bulletproof MCP configuration...');
-
-    const mcpOptions = {
-      verbose: flags.verbose || false,
-      autoFix: flags['auto-fix'] !== false && !flags['no-auto-fix'], // Default true unless explicitly disabled
-      dryRun: dryRun,
-      enhancedUx: true, // Enable enhanced user experience
-      showEducation: flags['show-education'] || false,
-      serverConfig: {
-        mcpServers: {
-          'claude-flow-novice': {
-            command: 'npx',
-            args: ['claude-flow-novice', 'mcp', 'start'],
-            env: {
-              NODE_ENV: 'production',
-              CLAUDE_FLOW_NOVICE_MODE: 'novice'
+ */ async function enhancedClaudeFlowInit(flags, subArgs = []) {
+    console.log('🚀 Initializing Claude Flow v2.0.0 with enhanced features...');
+    const workingDir = process.cwd();
+    const force = flags.force || flags.f;
+    const dryRun1 = flags.dryRun || flags['dry-run'] || flags.d;
+    const initSparc = flags.roo || subArgs && subArgs.includes('--roo'); // SPARC only with --roo flag
+    // Store parameters to avoid scope issues in async context
+    const args = subArgs || [];
+    const options = flags || {};
+    // Import fs module for Node.js
+    const fs = await import("node:fs/promises");
+    const { chmod } = fs;
+    try {
+        // Check existing files
+        const existingFiles = [];
+        const filesToCheck = [
+            'CLAUDE.md',
+            '.claude/settings.json',
+            '.mcp.json',
+            'claude-flow.config.json'
+        ];
+        for (const file of filesToCheck){
+            if (existsSync(`${workingDir}/${file}`)) {
+                existingFiles.push(file);
             }
-          }
         }
-      }
-    };
-
-    let mcpSuccess = false;
-    try {
-      const { enhancedMcpInit } = await import('../../mcp/mcp-config-manager.js');
-      const result = await enhancedMcpInit(mcpOptions);
-
-      if (result.success) {
-        printSuccess('✓ Bulletproof MCP configuration completed successfully');
-        if (result.details) {
-          console.log(`   • Issues Fixed: ${result.details.issuesFixed || 0}`);
-          console.log(`   • Health Score: ${result.details.healthScore || 'N/A'}/100`);
+        if (existingFiles.length > 0 && !force) {
+            printWarning(`The following files already exist: ${existingFiles.join(', ')}`);
+            console.log('Use --force to overwrite existing files');
+            return;
         }
-        mcpSuccess = true;
-      } else {
-        printWarning(`⚠️  MCP configuration had issues: ${result.error || 'Unknown error'}`);
-        if (result.rollbackAvailable) {
-          console.log('   🔄 Automatic rollback was performed');
+        // Create CLAUDE.md from template
+        if (!dryRun1) {
+            const claudeMdContent = await readClaudeMdTemplate();
+            await fs.writeFile(`${workingDir}/CLAUDE.md`, claudeMdContent, 'utf8');
+            printSuccess('✓ Created CLAUDE.md (Claude Flow v2.0.0 - Optimized Template)');
+        } else {
+            console.log('[DRY RUN] Would create CLAUDE.md (Claude Flow v2.0.0 - Optimized Template)');
         }
-      }
-    } catch (error) {
-      printWarning(`⚠️  Bulletproof MCP setup failed: ${error.message}`);
-      printWarning('   📞 Falling back to legacy MCP configuration...');
-
-      // Fallback to legacy config creation
-      const mcpConfig = {
-        mcpServers: {
-          'claude-flow-novice': {
-            command: 'npx',
-            args: ['claude-flow-novice', 'mcp', 'start'],
-            env: {
-              NODE_ENV: 'production',
-              CLAUDE_FLOW_NOVICE_MODE: 'novice'
+        // Create .claude directory structure
+        const claudeDir = `${workingDir}/.claude`;
+        if (!dryRun1) {
+            await fs.mkdir(claudeDir, {
+                recursive: true
+            });
+            await fs.mkdir(`${claudeDir}/commands`, {
+                recursive: true
+            });
+            await fs.mkdir(`${claudeDir}/helpers`, {
+                recursive: true
+            });
+            printSuccess('✓ Created .claude directory structure');
+        } else {
+            console.log('[DRY RUN] Would create .claude directory structure');
+        }
+        // Create settings.json
+        if (!dryRun1) {
+            await fs.writeFile(`${claudeDir}/settings.json`, createEnhancedSettingsJson(), 'utf8');
+            printSuccess('✓ Created .claude/settings.json with hooks and MCP configuration');
+        } else {
+            console.log('[DRY RUN] Would create .claude/settings.json');
+        }
+        // Create settings.local.json with default MCP permissions
+        const settingsLocal = {
+            permissions: {
+                allow: [
+                    'mcp__ruv-swarm',
+                    'mcp__claude-flow'
+                ],
+                deny: []
             }
-          }
+        };
+        if (!dryRun1) {
+            await fs.writeFile(`${claudeDir}/settings.local.json`, JSON.stringify(settingsLocal, null, 2, 'utf8'));
+            printSuccess('✓ Created .claude/settings.local.json with default MCP permissions');
+        } else {
+            console.log('[DRY RUN] Would create .claude/settings.local.json with default MCP permissions');
         }
-      };
-
-      if (!dryRun) {
-        await fs.writeFile(`${workingDir}/.mcp.json`, JSON.stringify(mcpConfig, null, 2), 'utf8');
-        printSuccess('✓ Created .mcp.json with legacy configuration');
-      } else {
-        console.log('[DRY RUN] Would create .mcp.json with legacy configuration');
-      }
-      mcpSuccess = true; // Consider legacy success for continuation
-    }
-
-    // Create claude-flow.config.json for Claude Flow specific settings
-    const claudeFlowConfig = {
-      features: {
-        autoTopologySelection: true,
-        parallelExecution: true,
-        neuralTraining: true,
-        bottleneckAnalysis: true,
-        smartAutoSpawning: true,
-        selfHealingWorkflows: true,
-        crossSessionMemory: true,
-        githubIntegration: true,
-      },
-      performance: {
-        maxAgents: 10,
-        defaultTopology: 'hierarchical',
-        executionStrategy: 'parallel',
-        tokenOptimization: true,
-        cacheEnabled: true,
-        telemetryLevel: 'detailed',
-      },
-    };
-
-    if (!dryRun) {
-      await fs.writeFile(
-        `${workingDir}/claude-flow.config.json`,
-        JSON.stringify(claudeFlowConfig, null, 2, 'utf8'),
-      );
-      printSuccess('✓ Created claude-flow.config.json for Claude Flow settings');
-    } else {
-      console.log('[DRY RUN] Would create claude-flow.config.json for Claude Flow settings');
-    }
-
-    // Create command documentation
-    for (const [category, commands] of Object.entries(COMMAND_STRUCTURE)) {
-      const categoryDir = `${claudeDir}/commands/${category}`;
-
-      if (!dryRun) {
-        await fs.mkdir(categoryDir, { recursive: true });
-
-        // Create category README
-        const categoryReadme = `# ${category.charAt(0).toUpperCase() + category.slice(1)} Commands
+        // Setup bulletproof MCP configuration instead of legacy approach
+        console.log('\n🛡️  Setting up bulletproof MCP configuration...');
+        const mcpOptions = {
+            verbose: flags.verbose || false,
+            autoFix: flags['auto-fix'] !== false && !flags['no-auto-fix'],
+            dryRun: dryRun1,
+            enhancedUx: true,
+            showEducation: flags['show-education'] || false,
+            serverConfig: {
+                mcpServers: {
+                    'claude-flow-novice': {
+                        command: 'npx',
+                        args: [
+                            'claude-flow-novice',
+                            'mcp',
+                            'start'
+                        ],
+                        env: {
+                            NODE_ENV: 'production',
+                            CLAUDE_FLOW_NOVICE_MODE: 'novice'
+                        }
+                    }
+                }
+            }
+        };
+        let mcpSuccess = false;
+        try {
+            const { enhancedMcpInit } = await import("../../mcp/mcp-config-manager.js");
+            const result = await enhancedMcpInit(mcpOptions);
+            if (result.success) {
+                printSuccess('✓ Bulletproof MCP configuration completed successfully');
+                if (result.details) {
+                    console.log(`   • Issues Fixed: ${result.details.issuesFixed || 0}`);
+                    console.log(`   • Health Score: ${result.details.healthScore || 'N/A'}/100`);
+                }
+                mcpSuccess = true;
+            } else {
+                printWarning(`⚠️  MCP configuration had issues: ${result.error || 'Unknown error'}`);
+                if (result.rollbackAvailable) {
+                    console.log('   🔄 Automatic rollback was performed');
+                }
+            }
+        } catch (error) {
+            printWarning(`⚠️  Bulletproof MCP setup failed: ${error.message}`);
+            printWarning('   📞 Falling back to legacy MCP configuration...');
+            // Fallback to legacy config creation
+            const mcpConfig = {
+                mcpServers: {
+                    'claude-flow-novice': {
+                        command: 'npx',
+                        args: [
+                            'claude-flow-novice',
+                            'mcp',
+                            'start'
+                        ],
+                        env: {
+                            NODE_ENV: 'production',
+                            CLAUDE_FLOW_NOVICE_MODE: 'novice'
+                        }
+                    }
+                }
+            };
+            if (!dryRun1) {
+                await fs.writeFile(`${workingDir}/.mcp.json`, JSON.stringify(mcpConfig, null, 2), 'utf8');
+                printSuccess('✓ Created .mcp.json with legacy configuration');
+            } else {
+                console.log('[DRY RUN] Would create .mcp.json with legacy configuration');
+            }
+            mcpSuccess = true; // Consider legacy success for continuation
+        }
+        // Create claude-flow.config.json for Claude Flow specific settings
+        const claudeFlowConfig = {
+            features: {
+                autoTopologySelection: true,
+                parallelExecution: true,
+                neuralTraining: true,
+                bottleneckAnalysis: true,
+                smartAutoSpawning: true,
+                selfHealingWorkflows: true,
+                crossSessionMemory: true,
+                githubIntegration: true
+            },
+            performance: {
+                maxAgents: 10,
+                defaultTopology: 'hierarchical',
+                executionStrategy: 'parallel',
+                tokenOptimization: true,
+                cacheEnabled: true,
+                telemetryLevel: 'detailed'
+            }
+        };
+        if (!dryRun1) {
+            await fs.writeFile(`${workingDir}/claude-flow.config.json`, JSON.stringify(claudeFlowConfig, null, 2, 'utf8'));
+            printSuccess('✓ Created claude-flow.config.json for Claude Flow settings');
+        } else {
+            console.log('[DRY RUN] Would create claude-flow.config.json for Claude Flow settings');
+        }
+        // Create command documentation
+        for (const [category, commands] of Object.entries(COMMAND_STRUCTURE)){
+            const categoryDir = `${claudeDir}/commands/${category}`;
+            if (!dryRun1) {
+                await fs.mkdir(categoryDir, {
+                    recursive: true
+                });
+                // Create category README
+                const categoryReadme = `# ${category.charAt(0).toUpperCase() + category.slice(1)} Commands
 
 Commands for ${category} operations in Claude Flow.
 
 ## Available Commands
 
-${commands.map((cmd) => `- [${cmd}](./${cmd}.md)`).join('\n')}
+${commands.map((cmd)=>`- [${cmd}](./${cmd}.md)`).join('\n')}
 `;
-        await fs.writeFile(`${categoryDir}/README.md`, categoryReadme, 'utf8');
-
-        // Create individual command docs
-        for (const command of commands) {
-          const doc = createCommandDoc(category, command);
-          if (doc) {
-            await fs.writeFile(`${categoryDir}/${command}.md`, doc, 'utf8');
-          }
+                await fs.writeFile(`${categoryDir}/README.md`, categoryReadme, 'utf8');
+                // Create individual command docs
+                for (const command of commands){
+                    const doc = createCommandDoc(category, command);
+                    if (doc) {
+                        await fs.writeFile(`${categoryDir}/${command}.md`, doc, 'utf8');
+                    }
+                }
+                console.log(`  ✓ Created ${commands.length} ${category} command docs`);
+            } else {
+                console.log(`[DRY RUN] Would create ${commands.length} ${category} command docs`);
+            }
         }
-
-        console.log(`  ✓ Created ${commands.length} ${category} command docs`);
-      } else {
-        console.log(`[DRY RUN] Would create ${commands.length} ${category} command docs`);
-      }
-    }
-
-    // Create wrapper scripts
-    if (!dryRun) {
-      // Unix wrapper - now uses universal ES module compatible wrapper
-      const unixWrapper = createWrapperScript('unix');
-      await fs.writeFile(`${workingDir}/claude-flow`, unixWrapper, 'utf8');
-      await fs.chmod(`${workingDir}/claude-flow`, 0o755);
-
-      // Windows wrapper
-      await fs.writeFile(`${workingDir}/claude-flow.bat`, createWrapperScript('windows', 'utf8'));
-
-      // PowerShell wrapper
-      await fs.writeFile(
-        `${workingDir}/claude-flow.ps1`,
-        createWrapperScript('powershell', 'utf8'),
-      );
-
-      printSuccess('✓ Created platform-specific wrapper scripts');
-    } else {
-      console.log('[DRY RUN] Would create wrapper scripts');
-    }
-
-    // Create helper scripts
-    const helpers = [
-      'setup-mcp.sh',
-      'quick-start.sh',
-      'github-setup.sh',
-      'github-safe.js',
-      'standard-checkpoint-hooks.sh',
-      'checkpoint-manager.sh',
-    ];
-    for (const helper of helpers) {
-      if (!dryRun) {
-        const content = createHelperScript(helper);
-        if (content) {
-          await fs.writeFile(`${claudeDir}/helpers/${helper}`, content, 'utf8');
-          await fs.chmod(`${claudeDir}/helpers/${helper}`, 0o755);
+        // Create wrapper scripts
+        if (!dryRun1) {
+            // Unix wrapper - now uses universal ES module compatible wrapper
+            const unixWrapper = createWrapperScript('unix');
+            await fs.writeFile(`${workingDir}/claude-flow`, unixWrapper, 'utf8');
+            await fs.chmod(`${workingDir}/claude-flow`, 0o755);
+            // Windows wrapper
+            await fs.writeFile(`${workingDir}/claude-flow.bat`, createWrapperScript('windows', 'utf8'));
+            // PowerShell wrapper
+            await fs.writeFile(`${workingDir}/claude-flow.ps1`, createWrapperScript('powershell', 'utf8'));
+            printSuccess('✓ Created platform-specific wrapper scripts');
+        } else {
+            console.log('[DRY RUN] Would create wrapper scripts');
         }
-      }
-    }
-
-    if (!dryRun) {
-      printSuccess(`✓ Created ${helpers.length} helper scripts`);
-    } else {
-      console.log(`[DRY RUN] Would create ${helpers.length} helper scripts`);
-    }
-
-    // Create standard directories from original init
-    const standardDirs = [
-      'memory',
-      'memory/agents',
-      'memory/sessions',
-      'coordination',
-      'coordination/memory_bank',
-      'coordination/subtasks',
-      'coordination/orchestration',
-      '.swarm', // Add .swarm directory for shared memory
-      '.hive-mind', // Add .hive-mind directory for hive-mind system
-      '.claude/checkpoints', // Add checkpoints directory for Git checkpoint system
-    ];
-
-    for (const dir of standardDirs) {
-      if (!dryRun) {
-        await fs.mkdir(`${workingDir}/${dir}`, { recursive: true });
-      }
-    }
-
-    if (!dryRun) {
-      printSuccess('✓ Created standard directory structure');
-
-      // Initialize memory system
-      const initialData = { agents: [], tasks: [], lastUpdated: Date.now() };
-      await fs.writeFile(
-        `${workingDir}/memory/claude-flow-data.json`,
-        JSON.stringify(initialData, null, 2, 'utf8'),
-      );
-
-      // Create README files
-      await fs.writeFile(`${workingDir}/memory/agents/README.md`, createAgentsReadme(), 'utf8');
-      await fs.writeFile(`${workingDir}/memory/sessions/README.md`, createSessionsReadme(), 'utf8');
-
-      printSuccess('✓ Initialized memory system');
-
-      // Initialize memory database with fallback support
-      try {
-        // Import and initialize FallbackMemoryStore to create the database
-        const { FallbackMemoryStore } = await import('../../../memory/fallback-store.js');
-        const memoryStore = new FallbackMemoryStore();
-        await memoryStore.initialize();
-
-        if (memoryStore.isUsingFallback()) {
-          printSuccess('✓ Initialized memory system (in-memory fallback for npx compatibility)');
-          console.log(
-            '  💡 For persistent storage, install locally: npm install claude-flow@alpha',
-          );
+        // Create helper scripts
+        const helpers = [
+            'setup-mcp.sh',
+            'quick-start.sh',
+            'github-setup.sh',
+            'github-safe.js',
+            'standard-checkpoint-hooks.sh',
+            'checkpoint-manager.sh'
+        ];
+        for (const helper of helpers){
+            if (!dryRun1) {
+                const content = createHelperScript(helper);
+                if (content) {
+                    await fs.writeFile(`${claudeDir}/helpers/${helper}`, content, 'utf8');
+                    await fs.chmod(`${claudeDir}/helpers/${helper}`, 0o755);
+                }
+            }
+        }
+        if (!dryRun1) {
+            printSuccess(`✓ Created ${helpers.length} helper scripts`);
         } else {
-          printSuccess('✓ Initialized memory database (.swarm/memory.db)');
+            console.log(`[DRY RUN] Would create ${helpers.length} helper scripts`);
         }
-
-        memoryStore.close();
-      } catch (err) {
-        console.log(`  ⚠️  Could not initialize memory system: ${err.message}`);
-        console.log('     Memory will be initialized on first use');
-      }
-
-      // Initialize comprehensive hive-mind system
-      console.log('\n🧠 Initializing Hive Mind System...');
-      try {
-        const hiveMindOptions = {
-          config: {
-            integration: {
-              claudeCode: { enabled: isClaudeCodeInstalled() },
-              mcpTools: { enabled: true },
-            },
-            monitoring: { enabled: flags.monitoring || false },
-          },
-        };
-
-        const hiveMindResult = await initializeHiveMind(workingDir, hiveMindOptions, dryRun);
-
-        if (hiveMindResult.success) {
-          printSuccess(
-            `✓ Hive Mind System initialized with ${hiveMindResult.features.length} features`,
-          );
-
-          // Log individual features
-          hiveMindResult.features.forEach((feature) => {
-            console.log(`    • ${feature}`);
-          });
+        // Create standard directories from original init
+        const standardDirs = [
+            'memory',
+            'memory/agents',
+            'memory/sessions',
+            'coordination',
+            'coordination/memory_bank',
+            'coordination/subtasks',
+            'coordination/orchestration',
+            '.swarm',
+            '.hive-mind',
+            '.claude/checkpoints'
+        ];
+        for (const dir of standardDirs){
+            if (!dryRun1) {
+                await fs.mkdir(`${workingDir}/${dir}`, {
+                    recursive: true
+                });
+            }
+        }
+        if (!dryRun1) {
+            printSuccess('✓ Created standard directory structure');
+            // Initialize memory system
+            const initialData = {
+                agents: [],
+                tasks: [],
+                lastUpdated: Date.now()
+            };
+            await fs.writeFile(`${workingDir}/memory/claude-flow-data.json`, JSON.stringify(initialData, null, 2, 'utf8'));
+            // Create README files
+            await fs.writeFile(`${workingDir}/memory/agents/README.md`, createAgentsReadme(), 'utf8');
+            await fs.writeFile(`${workingDir}/memory/sessions/README.md`, createSessionsReadme(), 'utf8');
+            printSuccess('✓ Initialized memory system');
+            // Initialize memory database with fallback support
+            try {
+                // Import and initialize FallbackMemoryStore to create the database
+                const { FallbackMemoryStore } = await import("../../../memory/fallback-store.js");
+                const memoryStore = new FallbackMemoryStore();
+                await memoryStore.initialize();
+                if (memoryStore.isUsingFallback()) {
+                    printSuccess('✓ Initialized memory system (in-memory fallback for npx compatibility)');
+                    console.log('  💡 For persistent storage, install locally: npm install claude-flow@alpha');
+                } else {
+                    printSuccess('✓ Initialized memory database (.swarm/memory.db)');
+                }
+                memoryStore.close();
+            } catch (err) {
+                console.log(`  ⚠️  Could not initialize memory system: ${err.message}`);
+                console.log('     Memory will be initialized on first use');
+            }
+            // Initialize comprehensive hive-mind system
+            console.log('\n🧠 Initializing Hive Mind System...');
+            try {
+                const hiveMindOptions = {
+                    config: {
+                        integration: {
+                            claudeCode: {
+                                enabled: isClaudeCodeInstalled()
+                            },
+                            mcpTools: {
+                                enabled: true
+                            }
+                        },
+                        monitoring: {
+                            enabled: flags.monitoring || false
+                        }
+                    }
+                };
+                const hiveMindResult = await initializeHiveMind(workingDir, hiveMindOptions, dryRun1);
+                if (hiveMindResult.success) {
+                    printSuccess(`✓ Hive Mind System initialized with ${hiveMindResult.features.length} features`);
+                    // Log individual features
+                    hiveMindResult.features.forEach((feature)=>{
+                        console.log(`    • ${feature}`);
+                    });
+                } else {
+                    console.log(`  ⚠️  Hive Mind initialization failed: ${hiveMindResult.error}`);
+                    if (hiveMindResult.rollbackRequired) {
+                        console.log('  🔄 Automatic rollback may be required');
+                    }
+                }
+            } catch (err) {
+                console.log(`  ⚠️  Could not initialize hive-mind system: ${err.message}`);
+            }
+        }
+        // Update .gitignore with Claude Flow entries
+        const gitignoreResult = await updateGitignore(workingDir, force, dryRun1);
+        if (gitignoreResult.success) {
+            if (!dryRun1) {
+                printSuccess(`✓ ${gitignoreResult.message}`);
+            } else {
+                console.log(gitignoreResult.message);
+            }
         } else {
-          console.log(`  ⚠️  Hive Mind initialization failed: ${hiveMindResult.error}`);
-          if (hiveMindResult.rollbackRequired) {
-            console.log('  🔄 Automatic rollback may be required');
-          }
+            console.log(`  ⚠️  ${gitignoreResult.message}`);
         }
-      } catch (err) {
-        console.log(`  ⚠️  Could not initialize hive-mind system: ${err.message}`);
-      }
-    }
-
-    // Update .gitignore with Claude Flow entries
-    const gitignoreResult = await updateGitignore(workingDir, force, dryRun);
-    if (gitignoreResult.success) {
-      if (!dryRun) {
-        printSuccess(`✓ ${gitignoreResult.message}`);
-      } else {
-        console.log(gitignoreResult.message);
-      }
-    } else {
-      console.log(`  ⚠️  ${gitignoreResult.message}`);
-    }
-
-    // SPARC initialization (only with --roo flag)
-    let sparcInitialized = false;
-    if (initSparc) {
-      console.log('\n🚀 Initializing SPARC development environment...');
-      try {
-        // Run create-sparc
-        console.log('  🔄 Running: npx -y create-sparc init --force');
-        execSync('npx -y create-sparc init --force', {
-          cwd: workingDir,
-          stdio: 'inherit',
-        });
-        sparcInitialized = true;
-        printSuccess('✅ SPARC environment initialized successfully');
-      } catch (err) {
-        console.log(`  ⚠️  Could not run create-sparc: ${err.message}`);
-        console.log('     SPARC features will be limited to basic functionality');
-      }
-    }
-
-    // Create Claude slash commands for SPARC
-    if (sparcInitialized && !dryRun) {
-      console.log('\n📝 Creating Claude Code slash commands...');
-      await createClaudeSlashCommands(workingDir);
-    }
-
-    // Check for Claude Code and set up MCP servers (always enabled by default)
-    if (!dryRun && isClaudeCodeInstalled()) {
-      console.log('\n🔍 Claude Code CLI detected!');
-      const skipMcp =
-        (options && options['skip-mcp']) ||
-        (subArgs && subArgs.includes && subArgs.includes('--skip-mcp'));
-
-      if (!skipMcp) {
-        // Use bulletproof MCP setup for enhanced init
-        const mcpSuccess = await setupBulletproofMcp({
-          verbose: true,
-          autoFix: true,
-          dryRun: dryRun
-        });
-
-        if (!mcpSuccess) {
-          console.log('  💡 If you encounter issues, run: claude mcp remove claude-flow-novice -s local');
+        // SPARC initialization (only with --roo flag)
+        let sparcInitialized = false;
+        if (initSparc) {
+            console.log('\n🚀 Initializing SPARC development environment...');
+            try {
+                // Run create-sparc
+                console.log('  🔄 Running: npx -y create-sparc init --force');
+                execSync('npx -y create-sparc init --force', {
+                    cwd: workingDir,
+                    stdio: 'inherit'
+                });
+                sparcInitialized = true;
+                printSuccess('✅ SPARC environment initialized successfully');
+            } catch (err) {
+                console.log(`  ⚠️  Could not run create-sparc: ${err.message}`);
+                console.log('     SPARC features will be limited to basic functionality');
+            }
         }
-      } else {
-        console.log('  ℹ️  Skipping MCP setup (--skip-mcp flag used)');
-        console.log('\n  📋 To add MCP servers manually:');
-        console.log('     claude mcp add claude-flow-novice npx claude-flow-novice mcp start');
-        console.log('     claude mcp add ruv-swarm npx ruv-swarm@latest mcp start');
-        // Flow-nexus integration removed
-        console.log('\n  💡 MCP servers are defined in .mcp.json (project scope)');
-      }
-    } else if (!dryRun && !isClaudeCodeInstalled()) {
-      console.log('\n⚠️  Claude Code CLI not detected!');
-      console.log('\n  📥 To install Claude Code:');
-      console.log('     npm install -g @anthropic-ai/claude-code');
-      console.log('\n  📋 After installing, add MCP servers:');
-      console.log('     claude mcp add claude-flow-novice npx claude-flow-novice mcp start');
-      console.log('     claude mcp add ruv-swarm npx ruv-swarm@latest mcp start');
-      // Flow-nexus integration removed
-      console.log('\n  💡 MCP servers are defined in .mcp.json (project scope)');
-    }
-
-    // Create agent directories and copy all agent files
-    console.log('\n🤖 Setting up agent system...');
-    if (!dryRun) {
-      await createAgentDirectories(workingDir, dryRun);
-      const agentResult = await copyAgentFiles(workingDir, {
-        force: force,
-        dryRun: dryRun,
-      });
-
-      if (agentResult.success) {
-        await validateAgentSystem(workingDir);
-
-        // Copy command files including Flow Nexus commands
-        console.log('\n📚 Setting up command system...');
-        const commandResult = await copyCommandFiles(workingDir, {
-          force: force,
-          dryRun: dryRun,
-        });
-
-        if (commandResult.success) {
-          console.log('✅ ✓ Command system setup complete with Flow Nexus integration');
+        // Create Claude slash commands for SPARC
+        if (sparcInitialized && !dryRun1) {
+            console.log('\n📝 Creating Claude Code slash commands...');
+            await createClaudeSlashCommands(workingDir);
+        }
+        // Check for Claude Code and set up MCP servers (always enabled by default)
+        if (!dryRun1 && isClaudeCodeInstalled()) {
+            console.log('\n🔍 Claude Code CLI detected!');
+            const skipMcp = options && options['skip-mcp'] || subArgs && subArgs.includes && subArgs.includes('--skip-mcp');
+            if (!skipMcp) {
+                // Use bulletproof MCP setup for enhanced init
+                const mcpSuccess = await setupBulletproofMcp({
+                    verbose: true,
+                    autoFix: true,
+                    dryRun: dryRun1
+                });
+                if (!mcpSuccess) {
+                    console.log('  💡 If you encounter issues, run: claude mcp remove claude-flow-novice -s local');
+                }
+            } else {
+                console.log('  ℹ️  Skipping MCP setup (--skip-mcp flag used)');
+                console.log('\n  📋 To add MCP servers manually:');
+                console.log('     claude mcp add claude-flow-novice npx claude-flow-novice mcp start');
+                console.log('     claude mcp add ruv-swarm npx ruv-swarm@latest mcp start');
+                // Flow-nexus integration removed
+                console.log('\n  💡 MCP servers are defined in .mcp.json (project scope)');
+            }
+        } else if (!dryRun1 && !isClaudeCodeInstalled()) {
+            console.log('\n⚠️  Claude Code CLI not detected!');
+            console.log('\n  📥 To install Claude Code:');
+            console.log('     npm install -g @anthropic-ai/claude-code');
+            console.log('\n  📋 After installing, add MCP servers:');
+            console.log('     claude mcp add claude-flow-novice npx claude-flow-novice mcp start');
+            console.log('     claude mcp add ruv-swarm npx ruv-swarm@latest mcp start');
+            // Flow-nexus integration removed
+            console.log('\n  💡 MCP servers are defined in .mcp.json (project scope)');
+        }
+        // Create agent directories and copy all agent files
+        console.log('\n🤖 Setting up agent system...');
+        if (!dryRun1) {
+            await createAgentDirectories(workingDir, dryRun1);
+            const agentResult = await copyAgentFiles(workingDir, {
+                force: force,
+                dryRun: dryRun1
+            });
+            if (agentResult.success) {
+                await validateAgentSystem(workingDir);
+                // Copy command files including Flow Nexus commands
+                console.log('\n📚 Setting up command system...');
+                const commandResult = await copyCommandFiles(workingDir, {
+                    force: force,
+                    dryRun: dryRun1
+                });
+                if (commandResult.success) {
+                    console.log('✅ ✓ Command system setup complete with Flow Nexus integration');
+                } else {
+                    console.log('⚠️  Command system setup failed:', commandResult.error);
+                }
+                console.log('✅ ✓ Agent system setup complete with 64 specialized agents');
+            } else {
+                console.log('⚠️  Agent system setup failed:', agentResult.error);
+            }
+            // Setup hooks system for novice users
+            console.log('\n🪝 Setting up hooks system...');
+            const hooksConfig = {
+                hooks: {
+                    pre_task: {
+                        enabled: true,
+                        command: "npx claude-flow-novice hooks pre-task --description \"$TASK_DESCRIPTION\"",
+                        description: "Pre-task coordination hook"
+                    },
+                    post_edit: {
+                        enabled: true,
+                        command: "npx claude-flow-novice hooks post-edit --file \"$FILE_PATH\" --memory-key \"swarm/$AGENT_ID/$STEP\"",
+                        description: "Post-edit memory storage hook"
+                    },
+                    post_task: {
+                        enabled: true,
+                        command: "npx claude-flow-novice hooks post-task --task-id \"$TASK_ID\"",
+                        description: "Post-task completion hook"
+                    }
+                },
+                memory: {
+                    enabled: true,
+                    persistence: "local",
+                    namespace: "claude-flow-novice"
+                }
+            };
+            const hooksConfigPath = `${claudeDir}/hooks.json`;
+            await fs.writeFile(hooksConfigPath, JSON.stringify(hooksConfig, null, 2), 'utf8');
+            console.log('✅ ✓ Hooks system setup complete with automated coordination');
         } else {
-          console.log('⚠️  Command system setup failed:', commandResult.error);
+            console.log('  [DRY RUN] Would create agent system with 64 specialized agents');
+            console.log('  [DRY RUN] Would create hooks system with automated coordination');
         }
-
-        console.log('✅ ✓ Agent system setup complete with 64 specialized agents');
-      } else {
-        console.log('⚠️  Agent system setup failed:', agentResult.error);
-      }
-
-      // Setup hooks system for novice users
-      console.log('\n🪝 Setting up hooks system...');
-      const hooksConfig = {
-        hooks: {
-          pre_task: {
-            enabled: true,
-            command: "npx claude-flow-novice hooks pre-task --description \"$TASK_DESCRIPTION\"",
-            description: "Pre-task coordination hook"
-          },
-          post_edit: {
-            enabled: true,
-            command: "npx claude-flow-novice hooks post-edit --file \"$FILE_PATH\" --memory-key \"swarm/$AGENT_ID/$STEP\"",
-            description: "Post-edit memory storage hook"
-          },
-          post_task: {
-            enabled: true,
-            command: "npx claude-flow-novice hooks post-task --task-id \"$TASK_ID\"",
-            description: "Post-task completion hook"
-          }
-        },
-        memory: {
-          enabled: true,
-          persistence: "local",
-          namespace: "claude-flow-novice"
+        // Optional: Setup monitoring and telemetry
+        const enableMonitoring = flags.monitoring || flags['enable-monitoring'];
+        if (enableMonitoring && !dryRun1) {
+            console.log('\n📊 Setting up monitoring and telemetry...');
+            await setupMonitoring(workingDir);
         }
-      };
-
-      const hooksConfigPath = `${claudeDir}/hooks.json`;
-      await fs.writeFile(hooksConfigPath, JSON.stringify(hooksConfig, null, 2), 'utf8');
-      console.log('✅ ✓ Hooks system setup complete with automated coordination');
-
-    } else {
-      console.log('  [DRY RUN] Would create agent system with 64 specialized agents');
-      console.log('  [DRY RUN] Would create hooks system with automated coordination');
-    }
-
-    // Optional: Setup monitoring and telemetry
-    const enableMonitoring = flags.monitoring || flags['enable-monitoring'];
-    if (enableMonitoring && !dryRun) {
-      console.log('\n📊 Setting up monitoring and telemetry...');
-      await setupMonitoring(workingDir);
-    }
-
-    // Final instructions with hive-mind status
-    console.log('\n🎉 Claude Flow v2.0.0 initialization complete!');
-
-    // Display MCP setup status prominently
-    if (mcpSuccess) {
-      console.log('\n🛡️  Bulletproof MCP Configuration Status:');
-      console.log('  ✅ MCP server successfully configured with auto-recovery');
-      console.log('  ✅ Conflict detection and resolution enabled');
-      console.log('  ✅ Automatic backup and rollback capability active');
-      console.log('  ✅ Project-specific configuration created (.mcp.json)');
-    } else {
-      console.log('\n⚠️  MCP Configuration Status:');
-      console.log('  ⚠️  MCP setup completed with fallback configuration');
-      console.log('  💡 Run health check: npx claude-flow-novice mcp health');
-    }
-
-    // Display hive-mind status
-    const hiveMindStatus = getHiveMindStatus(workingDir);
-    console.log('\n🧠 Hive Mind System Status:');
-    console.log(`  Configuration: ${hiveMindStatus.configured ? '✅ Ready' : '❌ Missing'}`);
-    console.log(
-      `  Database: ${hiveMindStatus.database === 'sqlite' ? '✅ SQLite' : hiveMindStatus.database === 'fallback' ? '⚠️ JSON Fallback' : '❌ Not initialized'}`,
-    );
-    console.log(
-      `  Directory Structure: ${hiveMindStatus.directories ? '✅ Created' : '❌ Missing'}`,
-    );
-
-    console.log('\n📚 Quick Start:');
-    if (isClaudeCodeInstalled()) {
-      console.log('1. Verify MCP setup: claude mcp list');
-      console.log('2. View available commands: ls .claude/commands/');
-      console.log('3. Start a swarm: npx claude-flow-novice swarm "your objective" --claude');
-      console.log('4. Use hive-mind: npx claude-flow-novice hive-mind spawn "command" --claude');
-      console.log('5. Use enhanced MCP tools in Claude Code for bulletproof coordination');
-      if (hiveMindStatus.configured) {
-        console.log('5. Initialize first swarm: npx claude-flow-novice hive-mind init');
-      }
-    } else {
-      console.log('1. Install Claude Code: npm install -g @anthropic-ai/claude-code');
-      console.log('2. Add MCP servers (see instructions above)');
-      console.log('3. View available commands: ls .claude/commands/');
-      console.log('4. Start a swarm: npx claude-flow-novice swarm "your objective" --claude');
-      console.log('5. Use hive-mind: npx claude-flow-novice hive-mind spawn "command" --claude');
-      if (hiveMindStatus.configured) {
-        console.log('6. Initialize first swarm: npx claude-flow-novice hive-mind init');
-      }
-    }
-    console.log('\n💡 Tips:');
-    console.log('• Check .claude/commands/ for detailed documentation');
-    console.log('• Use --help with any command for options');
-    console.log('• Run commands with --claude flag for best Claude Code integration');
-    if (mcpSuccess) {
-      console.log('• MCP health check: npx claude-flow-novice mcp health');
-      console.log('• Configuration backups are automatically created for safety');
-      console.log('• Project-specific .mcp.json prevents conflicts with other projects');
-    }
-    console.log('• Enable GitHub integration with .claude/helpers/github-setup.sh');
-    console.log('• Git checkpoints are automatically enabled in settings.json');
-    console.log('• Use .claude/helpers/checkpoint-manager.sh for easy rollback');
-  } catch (err) {
-    printError(`Failed to initialize Claude Flow v2.0.0: ${err.message}`);
-
-    // Attempt hive-mind rollback if it was partially initialized
-    try {
-      const hiveMindStatus = getHiveMindStatus(workingDir);
-      if (hiveMindStatus.directories || hiveMindStatus.configured) {
-        console.log('\n🔄 Attempting hive-mind system rollback...');
-        const rollbackResult = await rollbackHiveMindInit(workingDir);
-        if (rollbackResult.success) {
-          console.log('  ✅ Hive-mind rollback completed');
+        // Final instructions with hive-mind status
+        console.log('\n🎉 Claude Flow v2.0.0 initialization complete!');
+        // Display MCP setup status prominently
+        if (mcpSuccess) {
+            console.log('\n🛡️  Bulletproof MCP Configuration Status:');
+            console.log('  ✅ MCP server successfully configured with auto-recovery');
+            console.log('  ✅ Conflict detection and resolution enabled');
+            console.log('  ✅ Automatic backup and rollback capability active');
+            console.log('  ✅ Project-specific configuration created (.mcp.json)');
+        } else {
+            console.log('\n⚠️  MCP Configuration Status:');
+            console.log('  ⚠️  MCP setup completed with fallback configuration');
+            console.log('  💡 Run health check: npx claude-flow-novice mcp health');
+        }
+        // Display hive-mind status
+        const hiveMindStatus = getHiveMindStatus(workingDir);
+        console.log('\n🧠 Hive Mind System Status:');
+        console.log(`  Configuration: ${hiveMindStatus.configured ? '✅ Ready' : '❌ Missing'}`);
+        console.log(`  Database: ${hiveMindStatus.database === 'sqlite' ? '✅ SQLite' : hiveMindStatus.database === 'fallback' ? '⚠️ JSON Fallback' : '❌ Not initialized'}`);
+        console.log(`  Directory Structure: ${hiveMindStatus.directories ? '✅ Created' : '❌ Missing'}`);
+        console.log('\n📚 Quick Start:');
+        if (isClaudeCodeInstalled()) {
+            console.log('1. Verify MCP setup: claude mcp list');
+            console.log('2. View available commands: ls .claude/commands/');
+            console.log('3. Start a swarm: npx claude-flow-novice swarm "your objective" --claude');
+            console.log('4. Use hive-mind: npx claude-flow-novice hive-mind spawn "command" --claude');
+            console.log('5. Use enhanced MCP tools in Claude Code for bulletproof coordination');
+            if (hiveMindStatus.configured) {
+                console.log('5. Initialize first swarm: npx claude-flow-novice hive-mind init');
+            }
         } else {
-          console.log(`  ⚠️  Hive-mind rollback failed: ${rollbackResult.error}`);
+            console.log('1. Install Claude Code: npm install -g @anthropic-ai/claude-code');
+            console.log('2. Add MCP servers (see instructions above)');
+            console.log('3. View available commands: ls .claude/commands/');
+            console.log('4. Start a swarm: npx claude-flow-novice swarm "your objective" --claude');
+            console.log('5. Use hive-mind: npx claude-flow-novice hive-mind spawn "command" --claude');
+            if (hiveMindStatus.configured) {
+                console.log('6. Initialize first swarm: npx claude-flow-novice hive-mind init');
+            }
+        }
+        console.log('\n💡 Tips:');
+        console.log('• Check .claude/commands/ for detailed documentation');
+        console.log('• Use --help with any command for options');
+        console.log('• Run commands with --claude flag for best Claude Code integration');
+        if (mcpSuccess) {
+            console.log('• MCP health check: npx claude-flow-novice mcp health');
+            console.log('• Configuration backups are automatically created for safety');
+            console.log('• Project-specific .mcp.json prevents conflicts with other projects');
+        }
+        console.log('• Enable GitHub integration with .claude/helpers/github-setup.sh');
+        console.log('• Git checkpoints are automatically enabled in settings.json');
+        console.log('• Use .claude/helpers/checkpoint-manager.sh for easy rollback');
+    } catch (err) {
+        printError(`Failed to initialize Claude Flow v2.0.0: ${err.message}`);
+        // Attempt hive-mind rollback if it was partially initialized
+        try {
+            const hiveMindStatus = getHiveMindStatus(workingDir);
+            if (hiveMindStatus.directories || hiveMindStatus.configured) {
+                console.log('\n🔄 Attempting hive-mind system rollback...');
+                const rollbackResult = await rollbackHiveMindInit(workingDir);
+                if (rollbackResult.success) {
+                    console.log('  ✅ Hive-mind rollback completed');
+                } else {
+                    console.log(`  ⚠️  Hive-mind rollback failed: ${rollbackResult.error}`);
+                }
+            }
+        } catch (rollbackErr) {
+            console.log(`  ⚠️  Rollback error: ${rollbackErr.message}`);
         }
-      }
-    } catch (rollbackErr) {
-      console.log(`  ⚠️  Rollback error: ${rollbackErr.message}`);
     }
-  }
-}
-
-// Flow Nexus initialization removed
+} // Flow Nexus initialization removed