claude-flow/src/cli/simple-commands/init/index.js

Enterprise-grade AI agent orchestration with ruv-swarm integration (Alpha Release)

// init/index.js - Initialize Claude Code integration files
import { printSuccess, printError, printWarning } from '../../utils.js';
import { Deno, cwd, exit, existsSync } from '../../node-compat.js';
import process from 'process';
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 { execSync } from 'child_process';
import { promises as fs } from 'fs';
import { 
  createSparcClaudeMd, 
  createFullClaudeMd, 
  createMinimalClaudeMd,
  createOptimizedSparcClaudeMd 
} from './templates/claude-md.js';
import { 
  createFullMemoryBankMd, 
  createMinimalMemoryBankMd,
  createOptimizedMemoryBankMd 
} from './templates/memory-bank-md.js';
import { 
  createFullCoordinationMd, 
  createMinimalCoordinationMd,
  createOptimizedCoordinationMd 
} from './templates/coordination-md.js';
import { 
  createAgentsReadme, 
  createSessionsReadme 
} from './templates/readme-files.js';
import { 
  createSparcModeTemplates, 
  createSparcModesOverview,
  createSwarmStrategyTemplates 
} from './templates/sparc-modes.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';

/**
 * Check if Claude Code CLI is installed
 */
function isClaudeCodeInstalled() {
  try {
    execSync('which claude', { stdio: 'ignore' });
    return true;
  } catch {
    return false;
  }
}

/**
 * Set up MCP servers in Claude Code
 */
async function setupMcpServers(dryRun = false) {
  console.log('\n🔌 Setting up MCP servers for Claude Code...');
  
  const servers = [
    {
      name: 'claude-flow',
      command: 'npx claude-flow@alpha mcp start',
      description: 'Claude Flow MCP server with swarm orchestration (alpha)'
    },
    {
      name: 'ruv-swarm',
      command: 'npx ruv-swarm mcp start',
      description: 'ruv-swarm MCP server for enhanced coordination'
    }
  ];
  
  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}`);
    }
  }
  
  if (!dryRun) {
    console.log('\n  📋 Verifying MCP servers...');
    try {
      execSync('claude mcp list', { stdio: 'inherit' });
    } catch (err) {
      console.log('  ⚠️  Could not verify MCP servers');
    }
  }
}

export async function initCommand(subArgs, flags) {
  // Show help if requested
  if (flags.help || flags.h || subArgs.includes('--help') || subArgs.includes('-h')) {
    showInitHelp();
    return;
  }
  
  // Default to enhanced Claude Flow v2 init
  // Use --basic flag for old behavior
  if (!flags.basic && !flags.minimal && !flags.sparc) {
    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);
  }
  
  // Check if enhanced initialization is requested
  const useEnhanced = subArgs.includes('--enhanced') || subArgs.includes('--safe');
  
  if (useEnhanced) {
    return enhancedInitCommand(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 = subArgs.includes('--sparc') || subArgs.includes('-s') || flags.sparc;
  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
  
  // 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 Deno.stat(`${workingDir}/${file}`);
        existingFiles.push(file);
      } catch {
        // File doesn't exist, which is what we want
      }
    }
    
    if (existingFiles.length > 0 && !initForce) {
      printWarning(`The following files already exist: ${existingFiles.join(', ')}`);
      console.log('Use --force to overwrite existing files');
      return;
    }
    
    // Create CLAUDE.md
    const claudeMd = initOptimized ? await createOptimizedSparcClaudeMd() :
                     initSparc ? createSparcClaudeMd() : 
                     initMinimal ? createMinimalClaudeMd() : createFullClaudeMd();
    
    if (!initDryRun) {
      await Deno.writeTextFile('CLAUDE.md', claudeMd);
      console.log(`  ✓ Created CLAUDE.md${initOptimized ? ' (Batchtools-optimized SPARC)' : initSparc ? ' (SPARC-enhanced)' : ''}`);
    } else {
      console.log(`  [DRY RUN] Would create CLAUDE.md${initOptimized ? ' (Batchtools-optimized SPARC)' : initSparc ? ' (SPARC-enhanced)' : ''}`);
    }
    
    // Create memory-bank.md
    const memoryBankMd = initOptimized ? await createOptimizedMemoryBankMd() :
                         initMinimal ? createMinimalMemoryBankMd() : createFullMemoryBankMd();
    if (!initDryRun) {
      await Deno.writeTextFile('memory-bank.md', memoryBankMd);
      console.log('  ✓ Created memory-bank.md' + (initOptimized ? ' (Optimized for parallel operations)' : ''));
    } else {
      console.log('  [DRY RUN] Would create memory-bank.md' + (initOptimized ? ' (Optimized for parallel operations)' : ''));
    }
    
    // Create coordination.md
    const coordinationMd = initOptimized ? await createOptimizedCoordinationMd() :
                           initMinimal ? createMinimalCoordinationMd() : createFullCoordinationMd();
    if (!initDryRun) {
      await Deno.writeTextFile('coordination.md', coordinationMd);
      console.log('  ✓ Created coordination.md' + (initOptimized ? ' (Enhanced with batchtools)' : ''));
    } else {
      console.log('  [DRY RUN] Would create coordination.md' + (initOptimized ? ' (Enhanced with batchtools)' : ''));
    }
    
    // Create directory structure
    const directories = [
      'memory',
      'memory/agents',
      'memory/sessions',
      'coordination',
      'coordination/memory_bank',
      'coordination/subtasks',
      'coordination/orchestration',
      '.claude',
      '.claude/commands',
      '.claude/commands/sparc',
      '.claude/commands/swarm',
      '.claude/logs',
      '.swarm'  // Add .swarm directory for memory persistence (matching hive-mind pattern)
    ];
    
    for (const dir of directories) {
      try {
        if (!initDryRun) {
          await Deno.mkdir(dir, { recursive: true });
          console.log(`  ✓ Created ${dir}/ directory`);
        } else {
          console.log(`  [DRY RUN] Would create ${dir}/ directory`);
        }
      } catch (err) {
        if (err.code !== 'EEXIST') {
          throw err;
        }
      }
    }
    
    // Create SPARC command files if --sparc flag is used
    if (initSparc && !initDryRun) {
      try {
        const sparcTargetDir = `${workingDir}/.claude/commands/sparc`;
        
        // Get SPARC mode templates
        const sparcTemplates = createSparcModeTemplates();
        
        console.log('  📁 Creating SPARC command files...');
        
        for (const [filename, content] of Object.entries(sparcTemplates)) {
          try {
            await Deno.writeTextFile(`${sparcTargetDir}/${filename}`, content);
            console.log(`    ✓ Created ${filename}`);
          } catch (err) {
            console.log(`    ⚠️  Could not create ${filename}: ${err.message}`);
          }
        }
        
        // Also create sparc-modes.md overview file
        const sparcModesOverview = createSparcModesOverview();
        await Deno.writeTextFile(`${sparcTargetDir}/sparc-modes.md`, sparcModesOverview);
        console.log(`    ✓ Created sparc-modes.md`);
        
        console.log('  ✅ SPARC command files created successfully');
      } catch (err) {
        console.log(`  ⚠️  Could not create SPARC files: ${err.message}`);
      }
      
      // Also create swarm strategy files
      try {
        const swarmTargetDir = `${workingDir}/.claude/commands/swarm`;
        
        // Get swarm strategy templates
        const swarmTemplates = createSwarmStrategyTemplates();
        
        console.log('  📁 Creating swarm strategy files...');
        
        for (const [filename, content] of Object.entries(swarmTemplates)) {
          try {
            await Deno.writeTextFile(`${swarmTargetDir}/${filename}`, content);
            console.log(`    ✓ Created ${filename}`);
          } catch (err) {
            console.log(`    ⚠️  Could not create ${filename}: ${err.message}`);
          }
        }
        
        console.log('  ✅ Swarm strategy files created successfully');
      } catch (err) {
        console.log(`  ⚠️  Could not create swarm files: ${err.message}`);
      }
      
      // Create .claude/config.json
      try {
        const configContent = {
          "version": "1.0",
          "sparc": {
            "enabled": true,
            "modes": ["orchestrator", "coder", "researcher", "tdd", "architect", "reviewer", "debugger", "tester", "analyzer", "optimizer", "documenter", "designer", "innovator", "swarm-coordinator", "memory-manager", "batch-executor", "workflow-manager"]
          },
          "swarm": {
            "enabled": true,
            "strategies": ["research", "development", "analysis", "testing", "optimization", "maintenance"]
          }
        };
        
        await Deno.writeTextFile(`${workingDir}/.claude/config.json`, JSON.stringify(configContent, null, 2));
        console.log('  ✓ Created .claude/config.json');
      } catch (err) {
        console.log(`  ⚠️  Could not create config.json: ${err.message}`);
      }
    }
    
    // Create placeholder files for memory directories
    const agentsReadme = createAgentsReadme();
    if (!initDryRun) {
      await Deno.writeTextFile('memory/agents/README.md', agentsReadme);
      console.log('  ✓ Created memory/agents/README.md');
    } else {
      console.log('  [DRY RUN] Would create memory/agents/README.md');
    }
    
    const sessionsReadme = createSessionsReadme();
    if (!initDryRun) {
      await Deno.writeTextFile('memory/sessions/README.md', sessionsReadme);
      console.log('  ✓ Created memory/sessions/README.md');
    } else {
      console.log('  [DRY RUN] Would create memory/sessions/README.md');
    }
    
    // Initialize persistence database
    const initialData = {
      agents: [],
      tasks: [],
      lastUpdated: Date.now()
    };
    if (!initDryRun) {
      await Deno.writeTextFile('memory/claude-flow-data.json', JSON.stringify(initialData, null, 2));
      console.log('  ✓ Created memory/claude-flow-data.json (persistence database)');
    } else {
      console.log('  [DRY RUN] Would create memory/claude-flow-data.json (persistence database)');
    }
    
    // Create local claude-flow executable wrapper
    if (!initDryRun) {
      await createLocalExecutable(workingDir);
    } else {
      console.log('  [DRY RUN] Would create local claude-flow executable wrapper');
    }
    
    // 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
          const createSparcCommand = new Deno.Command('npx', {
            args: ['-y', 'create-sparc', 'init', '--force'],
            cwd: workingDir, // Use the original working directory
            stdout: 'inherit',
            stderr: 'inherit',
            env: getIsolatedNpxEnv({
              PWD: workingDir, // Ensure PWD is set correctly
            }),
          });
          
          console.log('  🔄 Running: npx -y create-sparc init --force');
          const createSparcResult = await createSparcCommand.output();
          
          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) {
            printWarning(`Could not create Claude Code slash commands: ${err.message}`);
          }
        }
      }
    }
    
    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');
      
      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 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 sparc modes\'');
        console.log('7. Try TDD workflow with \'./claude-flow 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 performance monitor\'');
        }
      }
      
      console.log('\n💡 Tips:');
      console.log('  • Type \'/\' in Claude Code to see all available slash commands');
      console.log('  • Use \'./claude-flow status\' to check system health');
      console.log('  • Store important context with \'./claude-flow 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');
      }
      
      // 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) {
          await setupMcpServers(initDryRun);
        } 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 claude-flow mcp start');
        console.log('     claude mcp add ruv-swarm npx ruv-swarm mcp start');
      }
    }
    
  } 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`);
        }
      }
      return;
    }
    
    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 = Deno.env.get('PWD') || Deno.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 = Deno.env.get('PWD') || Deno.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);
  }
}

/**
 * Handle rollback commands
 */
async function handleRollbackCommand(subArgs, flags) {
  const workingDir = Deno.env.get('PWD') || Deno.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');
        } else {
          printError('Rollback failed');
        }
      }
    }
    
  } catch (error) {
    printError(`Rollback operation failed: ${error.message}`);
  }
}

/**
 * Handle list backups command
 */
async function handleListBackups(subArgs, flags) {
  const workingDir = Deno.env.get('PWD') || Deno.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}`);
  }
}

/**
 * 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: '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;
    }
  }
}

// Helper functions for atomic initialization
async function createInitialFiles(options, workingDir, dryRun = false) {
  if (!dryRun) {
    const claudeMd = options.sparc ? createSparcClaudeMd() : 
                     options.minimal ? createMinimalClaudeMd() : createFullClaudeMd();
    await Deno.writeTextFile(`${workingDir}/CLAUDE.md`, claudeMd);

    const memoryBankMd = options.minimal ? createMinimalMemoryBankMd() : createFullMemoryBankMd();
    await Deno.writeTextFile(`${workingDir}/memory-bank.md`, memoryBankMd);

    const coordinationMd = options.minimal ? createMinimalCoordinationMd() : createFullCoordinationMd();
    await Deno.writeTextFile(`${workingDir}/coordination.md`, coordinationMd);
  }
}

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 Deno.mkdir(`${workingDir}/${dir}`, { recursive: true });
    }
  }
}

async function setupMemorySystem(workingDir, dryRun = false) {
  if (!dryRun) {
    const initialData = { agents: [], tasks: [], lastUpdated: Date.now() };
    await Deno.writeTextFile(`${workingDir}/memory/claude-flow-data.json`, JSON.stringify(initialData, null, 2));
    
    await Deno.writeTextFile(`${workingDir}/memory/agents/README.md`, createAgentsReadme());
    await Deno.writeTextFile(`${workingDir}/memory/sessions/README.md`, createSessionsReadme());
  }
}

async function setupCoordinationSystem(workingDir, dryRun = false) {
  // Coordination system is already set up by createDirectoryStructure
  // This is a placeholder for future coordination setup logic
}

/**
 * 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;
  
  // 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'];
    
    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
    if (!dryRun) {
      await Deno.writeTextFile(`${workingDir}/CLAUDE.md`, createEnhancedClaudeMd());
      printSuccess('✓ Created CLAUDE.md (Claude Flow v2.0.0)');
    } else {
      console.log('[DRY RUN] Would create CLAUDE.md (Claude Flow v2.0.0)');
    }
    
    // Create .claude directory structure
    const claudeDir = `${workingDir}/.claude`;
    if (!dryRun) {
      await Deno.mkdir(claudeDir, { recursive: true });
      await Deno.mkdir(`${claudeDir}/commands`, { recursive: true });
      await Deno.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 Deno.writeTextFile(`${claudeDir}/settings.json`, createEnhancedSettingsJson());
      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 Deno.writeTextFile(`${claudeDir}/settings.local.json`, JSON.stringify(settingsLocal, null, 2));
      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');
    }
    
    // Create command documentation
    for (const [category, commands] of Object.entries(COMMAND_STRUCTURE)) {
      const categoryDir = `${claudeDir}/commands/${category}`;
      
      if (!dryRun) {
        await Deno.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}](./${cmd}.md)`).join('\n')}
`;
        await Deno.writeTextFile(`${categoryDir}/README.md`, categoryReadme);
        
        // Create individual command docs
        for (const command of commands) {
          const doc = createCommandDoc(category, command);
          if (doc) {
            await Deno.writeTextFile(`${categoryDir}/${command}.md`, doc);
          }
        }
        
        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 Deno.writeTextFile(`${workingDir}/claude-flow`, unixWrapper);
      await fs.chmod(`${workingDir}/claude-flow`, 0o755);
      
      // Windows wrapper
      await Deno.writeTextFile(`${workingDir}/claude-flow.bat`, createWrapperScript('windows'));
      
      // PowerShell wrapper
      await Deno.writeTextFile(`${workingDir}/claude-flow.ps1`, createWrapperScript('powershell'));
      
      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'];
    for (const helper of helpers) {
      if (!dryRun) {
        const content = createHelperScript(helper);
        if (content) {
          await Deno.writeTextFile(`${claudeDir}/helpers/${helper}`, content);
          await fs.chmod(`${claudeDir}/helpers/${helper}`, 0o755);
        }
      }
    }
    
    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
    ];
    
    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));
      
      // Create README files
      await fs.writeFile(`${workingDir}/memory/agents/README.md`, createAgentsReadme());
      await fs.writeFile(`${workingDir}/memory/sessions/README.md`, createSessionsReadme());
      
      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');
      }
    }
    
    // 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) {
        await setupMcpServers(dryRun);
      } 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 claude-flow mcp start');
        console.log('     claude mcp add ruv-swarm npx ruv-swarm mcp start');
      }
    } 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 claude-flow mcp start');
      console.log('     claude mcp add ruv-swarm npx ruv-swarm mcp start');
    }
    
    // Final instructions
    console.log('\n🎉 Claude Flow v2.0.0 initialization complete!');
    console.log('\n📚 Quick Start:');
    if (isClaudeCodeInstalled()) {
      console.log('1. View available commands: ls .claude/commands/');
      console.log('2. Start a swarm: npx claude-flow swarm init');
      console.log('3. Use MCP tools in Claude Code for enhanced coordination');
    } 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 swarm init');
    }
    console.log('\n💡 Tips:');
    console.log('• Check .claude/commands/ for detailed documentation');
    console.log('• Use --help with any command for options');
    console.log('• Enable GitHub integration with .claude/helpers/github-setup.sh');
    
  } catch (err) {
    printError(`Failed to initialize Claude Flow v2.0.0: ${err.message}`);
  }
}