@sparkleideas/claude-flow 3.5.2-patch.1

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

@@ -0,0 +1,2002 @@
+// init/index.js - Initialize Claude Code integration files
+import { printSuccess, printError, printWarning, exit } from '../../utils.js';
+import { existsSync } from 'fs';
+import process from 'process';
+import os from 'os';
+import { spawn, execSync } from 'child_process';
+import { promisify } from 'util';
+
+// 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}`));
+      }
+    });
+    
+    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';
+// execSync imported above as execSyncOriginal\nconst execSync = execSyncOriginal;
+import { promises as fs } from 'fs';
+import { copyTemplates } from './template-copier.js';
+import { copyRevisedTemplates, validateTemplatesExist } from './copy-revised-templates.js';
+import { copyAgentFiles, createAgentDirectories, validateAgentSystem, copyCommandFiles } from './agent-copier.js';
+import { copySkillFiles, createSkillDirectories, validateSkillSystem } from './skills-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 { createOptimizedSparcClaudeMd } from './templates/claude-md.js';
+import { getIsolatedNpxEnv } from '../../../utils/npx-isolated-cache.js';
+import { updateGitignore, needsGitignoreUpdate } from './gitignore-updater.js';
+import {
+  createFullClaudeMd,
+  createSparcClaudeMd,
+  createMinimalClaudeMd,
+} from './templates/claude-md.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';
+
+/**
+ * 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: '@sparkleideas/claude-flow',
+      command: 'npx @sparkleideas/claude-flow@alpha mcp start',
+      description: 'Claude Flow MCP server with swarm orchestration (alpha)',
+    },
+    {
+      name: '@sparkleideas/ruv-swarm',
+      command: 'npx @sparkleideas/ruv-swarm mcp start',
+      description: '@sparkleideas/ruv-swarm MCP server for enhanced coordination',
+    },
+    {
+      name: 'flow-nexus',
+      command: 'npx flow-nexus@latest mcp start',
+      description: 'Flow Nexus Complete MCP server for advanced AI orchestration',
+    },
+  ];
+
+  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} ${server.command}`,
+      );
+    }
+  }
+
+  if (!dryRun) {
+    console.log('\n  📋 Verifying MCP servers...');
+    try {
+      execSync('claude mcp list', { stdio: 'inherit' });
+    } catch (err) {
+      console.log('  ⚠️  Could not verify MCP servers');
+    }
+  }
+}
+
+/**
+ * Create statusline script content (embedded fallback for binary builds)
+ */
+function createStatuslineScript() {
+  return `
+#!/bin/bash
+
+# Read JSON input from stdin
+INPUT=$(cat)
+MODEL=$(echo "$INPUT" | jq -r \'.model.display_name // "Claude"\')
+CWD=$(echo "$INPUT" | jq -r \'.workspace.current_dir // .cwd\')
+DIR=$(basename "$CWD")
+
+# Replace claude-code-flow with branded name
+if [ "$DIR" = "claude-code-flow" ]; then
+  DIR="🌊 Claude Flow"
+fi
+
+# Get git branch
+BRANCH=$(cd "$CWD" 2>/dev/null && git branch --show-current 2>/dev/null)
+
+# Start building statusline
+printf "\\033[1m$MODEL\\033[0m in \\033[36m$DIR\\033[0m"
+[ -n "$BRANCH" ] && printf " on \\033[33m⎇ $BRANCH\\033[0m"
+
+# Claude-Flow integration
+FLOW_DIR="$CWD/.@sparkleideas/claude-flow"
+
+if [ -d "$FLOW_DIR" ]; then
+  printf " │"
+
+  # 1. Swarm Configuration & Topology
+  if [ -f "$FLOW_DIR/swarm-config.json" ]; then
+    STRATEGY=$(jq -r \'.defaultStrategy // empty\' "$FLOW_DIR/swarm-config.json" 2>/dev/null)
+    if [ -n "$STRATEGY" ]; then
+      # Map strategy to topology icon
+      case "$STRATEGY" in
+        "balanced") TOPO_ICON="⚡mesh" ;;
+        "conservative") TOPO_ICON="⚡hier" ;;
+        "aggressive") TOPO_ICON="⚡ring" ;;
+        *) TOPO_ICON="⚡$STRATEGY" ;;
+      esac
+      printf " \\033[35m$TOPO_ICON\\033[0m"
+
+      # Count agent profiles as "configured agents"
+      AGENT_COUNT=$(jq -r \'.agentProfiles | length\' "$FLOW_DIR/swarm-config.json" 2>/dev/null)
+      if [ -n "$AGENT_COUNT" ] && [ "$AGENT_COUNT" != "null" ] && [ "$AGENT_COUNT" -gt 0 ]; then
+        printf "  \\033[35m🤖 $AGENT_COUNT\\033[0m"
+      fi
+    fi
+  fi
+
+  # 2. Real-time System Metrics
+  if [ -f "$FLOW_DIR/metrics/system-metrics.json" ]; then
+    # Get latest metrics (last entry in array)
+    LATEST=$(jq -r \'.[-1]\' "$FLOW_DIR/metrics/system-metrics.json" 2>/dev/null)
+
+    if [ -n "$LATEST" ] && [ "$LATEST" != "null" ]; then
+      # Memory usage
+      MEM_PERCENT=$(echo "$LATEST" | jq -r \'.memoryUsagePercent // 0\' | awk \'{printf "%.0f", $1}\')
+      if [ -n "$MEM_PERCENT" ] && [ "$MEM_PERCENT" != "null" ]; then
+        # Color-coded memory (green <60%, yellow 60-80%, red >80%)
+        if [ "$MEM_PERCENT" -lt 60 ]; then
+          MEM_COLOR="\\033[32m"  # Green
+        elif [ "$MEM_PERCENT" -lt 80 ]; then
+          MEM_COLOR="\\033[33m"  # Yellow
+        else
+          MEM_COLOR="\\033[31m"  # Red
+        fi
+        printf "  \${MEM_COLOR}💾 \${MEM_PERCENT}%\\033[0m"
+      fi
+
+      # CPU load
+      CPU_LOAD=$(echo "$LATEST" | jq -r \'.cpuLoad // 0\' | awk \'{printf "%.0f", $1 * 100}\')
+      if [ -n "$CPU_LOAD" ] && [ "$CPU_LOAD" != "null" ]; then
+        # Color-coded CPU (green <50%, yellow 50-75%, red >75%)
+        if [ "$CPU_LOAD" -lt 50 ]; then
+          CPU_COLOR="\\033[32m"  # Green
+        elif [ "$CPU_LOAD" -lt 75 ]; then
+          CPU_COLOR="\\033[33m"  # Yellow
+        else
+          CPU_COLOR="\\033[31m"  # Red
+        fi
+        printf "  \${CPU_COLOR}⚙ \${CPU_LOAD}%\\033[0m"
+      fi
+    fi
+  fi
+
+  # 3. Session State
+  if [ -f "$FLOW_DIR/session-state.json" ]; then
+    SESSION_ID=$(jq -r \'.sessionId // empty\' "$FLOW_DIR/session-state.json" 2>/dev/null)
+    ACTIVE=$(jq -r \'.active // false\' "$FLOW_DIR/session-state.json" 2>/dev/null)
+
+    if [ "$ACTIVE" = "true" ] && [ -n "$SESSION_ID" ]; then
+      # Show abbreviated session ID
+      SHORT_ID=$(echo "$SESSION_ID" | cut -d\'-\' -f1)
+      printf "  \\033[34m🔄 $SHORT_ID\\033[0m"
+    fi
+  fi
+
+  # 4. Performance Metrics from task-metrics.json
+  if [ -f "$FLOW_DIR/metrics/task-metrics.json" ]; then
+    # Parse task metrics for success rate, avg time, and streak
+    METRICS=$(jq -r \'
+      # Calculate metrics
+      (map(select(.success == true)) | length) as $successful |
+      (length) as $total |
+      (if $total > 0 then ($successful / $total * 100) else 0 end) as $success_rate |
+      (map(.duration // 0) | add / length) as $avg_duration |
+      # Calculate streak (consecutive successes from end)
+      (reverse |
+        reduce .[] as $task (0;
+          if $task.success == true then . + 1 else 0 end
+        )
+      ) as $streak |
+      {
+        success_rate: $success_rate,
+        avg_duration: $avg_duration,
+        streak: $streak,
+        total: $total
+      } | @json
+    \' "$FLOW_DIR/metrics/task-metrics.json" 2>/dev/null)
+
+    if [ -n "$METRICS" ] && [ "$METRICS" != "null" ]; then
+      # Success Rate
+      SUCCESS_RATE=$(echo "$METRICS" | jq -r \'.success_rate // 0\' | awk \'{printf "%.0f", $1}\')
+      TOTAL_TASKS=$(echo "$METRICS" | jq -r \'.total // 0\')
+
+      if [ -n "$SUCCESS_RATE" ] && [ "$TOTAL_TASKS" -gt 0 ]; then
+        # Color-code: Green (>80%), Yellow (60-80%), Red (<60%)
+        if [ "$SUCCESS_RATE" -gt 80 ]; then
+          SUCCESS_COLOR="\\033[32m"  # Green
+        elif [ "$SUCCESS_RATE" -ge 60 ]; then
+          SUCCESS_COLOR="\\033[33m"  # Yellow
+        else
+          SUCCESS_COLOR="\\033[31m"  # Red
+        fi
+        printf "  \${SUCCESS_COLOR}🎯 \${SUCCESS_RATE}%\\033[0m"
+      fi
+
+      # Average Time
+      AVG_TIME=$(echo "$METRICS" | jq -r \'.avg_duration // 0\')
+      if [ -n "$AVG_TIME" ] && [ "$TOTAL_TASKS" -gt 0 ]; then
+        # Format smartly: seconds, minutes, or hours
+        if [ $(echo "$AVG_TIME < 60" | bc -l 2>/dev/null || echo 0) -eq 1 ]; then
+          TIME_STR=$(echo "$AVG_TIME" | awk \'{printf "%.1fs", $1}\')
+        elif [ $(echo "$AVG_TIME < 3600" | bc -l 2>/dev/null || echo 0) -eq 1 ]; then
+          TIME_STR=$(echo "$AVG_TIME" | awk \'{printf "%.1fm", $1/60}\')
+        else
+          TIME_STR=$(echo "$AVG_TIME" | awk \'{printf "%.1fh", $1/3600}\')
+        fi
+        printf "  \\033[36m⏱️  $TIME_STR\\033[0m"
+      fi
+
+      # Streak (only show if > 0)
+      STREAK=$(echo "$METRICS" | jq -r \'.streak // 0\')
+      if [ -n "$STREAK" ] && [ "$STREAK" -gt 0 ]; then
+        printf "  \\033[91m🔥 $STREAK\\033[0m"
+      fi
+    fi
+  fi
+
+  # 5. Active Tasks (check for task files)
+  if [ -d "$FLOW_DIR/tasks" ]; then
+    TASK_COUNT=$(find "$FLOW_DIR/tasks" -name "*.json" -type f 2>/dev/null | wc -l)
+    if [ "$TASK_COUNT" -gt 0 ]; then
+      printf "  \\033[36m📋 $TASK_COUNT\\033[0m"
+    fi
+  fi
+
+  # 6. Check for hooks activity
+  if [ -f "$FLOW_DIR/hooks-state.json" ]; then
+    HOOKS_ACTIVE=$(jq -r \'.enabled // false\' "$FLOW_DIR/hooks-state.json" 2>/dev/null)
+    if [ "$HOOKS_ACTIVE" = "true" ]; then
+      printf " \\033[35m🔗\\033[0m"
+    fi
+  fi
+fi
+
+echo
+`;
+}
+
+export async function initCommand(subArgs, flags) {
+  // Show help if requested
+  if (flags.help || flags.h || subArgs.includes('--help') || subArgs.includes('-h')) {
+    showInitHelp();
+    return;
+  }
+
+  // Handle --env flag for .env template generation
+  if (flags.env || subArgs.includes('--env')) {
+    const { generateEnvTemplate } = await import('../env-template.js');
+    const workingDir = process.env.PWD || process.cwd();
+    const force = flags.force || flags.f;
+
+    console.log('📋 Generating .env template file...\n');
+    const result = await generateEnvTemplate(workingDir, force);
+
+    if (result.created) {
+      console.log('\n📚 Next steps:');
+      console.log('1. Open .env file and add your API keys');
+      console.log('2. Get keys from:');
+      console.log('   • Anthropic: https://console.anthropic.com/settings/keys');
+      console.log('   • OpenRouter: https://openrouter.ai/keys');
+      console.log('3. Enable memory: @sparkleideas/claude-flow agent run coder "task" --enable-memory\n');
+      console.log('💡 See docs/REASONINGBANK-COST-OPTIMIZATION.md for cost savings tips');
+    } else if (result.exists) {
+      console.log('💡 To overwrite: @sparkleideas/claude-flow init --env --force');
+    }
+
+    return;
+  }
+
+  // Check for verification flags first
+  const hasVerificationFlags = subArgs.includes('--verify') || subArgs.includes('--pair') ||
+                               flags.verify || flags.pair;
+
+  // Handle Flow Nexus minimal init
+  if (flags['flow-nexus']) {
+    return await flowNexusMinimalInit(flags, subArgs);
+  }
+
+  // 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);
+  }
+
+  // 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 = 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
+      }
+    }
+
+    if (existingFiles.length > 0 && !initForce) {
+      printWarning(`The following files already exist: ${existingFiles.join(', ')}`);
+      console.log('Use --force to overwrite existing files');
+      return;
+    }
+
+    // Use template copier to copy all template files
+    const templateOptions = {
+      sparc: initSparc,
+      minimal: initMinimal,
+      optimized: initOptimized,
+      dryRun: initDryRun,
+      force: initForce,
+      selectedModes: selectedModes,
+      verify: initVerify,
+      pair: initPair,
+    };
+
+    // If verification flags are set, always use generated templates for CLAUDE.md and settings.json
+    if (initVerify || initPair) {
+      console.log('  📁 Creating verification-focused configuration...');
+      
+      // Create verification CLAUDE.md
+      if (!initDryRun) {
+        const { createVerificationClaudeMd, createVerificationSettingsJson } = await import('./templates/verification-claude-md.js');
+        await fs.writeFile(`${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;
+        }
+      }
+    }
+
+    // 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 @sparkleideas/claude-flow@alpha executable wrapper
+    if (!initDryRun) {
+      await createLocalExecutable(workingDir);
+    } else {
+      console.log('  [DRY RUN] Would create local @sparkleideas/claude-flow@alpha 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
+          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
+          }
+        }
+      }
+    }
+
+    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@alpha');
+      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@alpha');
+      console.log('  ✅ Persistence database at memory/claude-flow@alpha-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@alpha start' to begin the orchestration system");
+      console.log("3. Use './claude-flow@alpha' instead of 'npx @sparkleideas/claude-flow@alpha' 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@alpha sparc modes'");
+        console.log('7. Try TDD workflow with \'./claude-flow@alpha 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@alpha 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@alpha status' to check system health");
+      console.log("  • Store important context with './claude-flow@alpha 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 @sparkleideas/claude-flow@alpha 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) {
+          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 @sparkleideas/claude-flow npx @sparkleideas/claude-flow@alpha mcp start');
+        console.log('     claude mcp add @sparkleideas/ruv-swarm npx @sparkleideas/ruv-swarm mcp start');
+        console.log('     claude mcp add flow-nexus npx flow-nexus@latest 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 = 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);
+    }
+  } 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');
+        } else {
+          printError('Rollback failed');
+        }
+      }
+    }
+  } 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})`);
+      });
+    }
+  } 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: ${error.message}`);
+      throw error;
+    }
+  }
+}
+
+// Helper functions for atomic initialization
+async function createInitialFiles(options, workingDir, dryRun = false) {
+  if (!dryRun) {
+    const claudeMd = options.sparc
+      ? createSparcClaudeMd()
+      : options.minimal
+        ? createMinimalClaudeMd()
+        : createFullClaudeMd();
+    await fs.writeFile(`${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 setupMemorySystem(workingDir, dryRun = false) {
+  if (!dryRun) {
+    const initialData = { agents: [], tasks: [], lastUpdated: Date.now() };
+    await fs.writeFile(
+      `${workingDir}/memory/claude-flow@alpha-data.json`, JSON.stringify(initialData, null, 2), 'utf8'
+    );
+
+    await fs.writeFile(`${workingDir}/memory/agents/README.md`, createAgentsReadme(), 'utf8');
+    await fs.writeFile(`${workingDir}/memory/sessions/README.md`, createSessionsReadme(), 'utf8');
+  }
+}
+
+async function setupCoordinationSystem(workingDir, dryRun = 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 .@sparkleideas/claude-flow@alpha directory for tracking data
+    const trackingDir = path.join(workingDir, '.@sparkleideas/claude-flow@alpha');
+    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 @sparkleideas/claude-flow@alpha 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: '.@sparkleideas/claude-flow@alpha/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
+
+# 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 .@sparkleideas/claude-flow@alpha/env-setup.sh');
+    console.log('\n  💡 Token usage will be tracked in .@sparkleideas/claude-flow@alpha/token-usage.json');
+    console.log('     Run: @sparkleideas/claude-flow@alpha analysis token-usage --breakdown --cost-analysis');
+    
+  } catch (err) {
+    printError(`  Failed to setup monitoring: ${err.message}`);
+  }
+}
+
+/**
+ * Enhanced Claude Flow v2.0.0 initialization
+ */
+async function enhancedClaudeFlowInit(flags, subArgs = []) {
+  console.log('🚀 Initializing Claude Flow v2.0.0 with enhanced features...');
+
+  const workingDir = process.cwd();
+  const force = flags.force || flags.f;
+  const dryRun = flags.dryRun || flags['dry-run'] || flags.d;
+  const initSparc = flags.roo || (subArgs && subArgs.includes('--roo')); // SPARC only with --roo flag
+
+  // Parse --agent flag for specialized agent setup
+  const agentType = flags.agent || (subArgs && subArgs.find(arg => arg.startsWith('--agent='))?.split('=')[1]);
+  const initReasoning = agentType === 'reasoning' || (subArgs && subArgs.includes('--agent') && subArgs.includes('reasoning'));
+
+  // Store parameters to avoid scope issues in async context
+  const args = subArgs || [];
+  const options = flags || {};
+
+  // Import fs, path, and os modules for Node.js
+  const fs = await import('fs/promises');
+  const { chmod } = fs;
+  const path = await import('path');
+  const os = await import('os');
+
+  try {
+    // Check existing files
+    const existingFiles = [];
+    const filesToCheck = [
+      'CLAUDE.md',
+      '.claude/settings.json',
+      '.mcp.json',
+      // Removed @sparkleideas/claude-flow@alpha.config.json per user request
+    ];
+
+    for (const file of filesToCheck) {
+      if (existsSync(`${workingDir}/${file}`)) {
+        existingFiles.push(file);
+      }
+    }
+
+    if (existingFiles.length > 0 && !force) {
+      printWarning(`The following files already exist: ${existingFiles.join(', ')}`);
+      console.log('Use --force to overwrite existing files');
+      return;
+    }
+
+    // Create CLAUDE.md
+    if (!dryRun) {
+      await fs.writeFile(`${workingDir}/CLAUDE.md`, createOptimizedSparcClaudeMd(), 'utf8');
+      printSuccess('✓ Created CLAUDE.md (Claude Flow v2.0.0 - Optimized)');
+    } else {
+      console.log('[DRY RUN] Would create CLAUDE.md (Claude Flow v2.0.0 - Optimized)');
+    }
+
+    // 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');
+    }
+
+    // Copy statusline script
+    try {
+      let statuslineTemplate;
+      try {
+        // Try to read from templates directory first
+        statuslineTemplate = await fs.readFile(
+          path.join(__dirname, 'templates', 'statusline-command.sh'),
+          'utf8'
+        );
+      } catch {
+        // Fallback to embedded content (for binary builds)
+        statuslineTemplate = createStatuslineScript();
+      }
+
+      if (!dryRun) {
+        // Write to project .claude directory
+        await fs.writeFile(`${claudeDir}/statusline-command.sh`, statuslineTemplate, 'utf8');
+        await fs.chmod(`${claudeDir}/statusline-command.sh`, 0o755);
+
+        // Also write to home ~/.claude directory for global use
+        const homeClaudeDir = path.join(os.homedir(), '.claude');
+        await fs.mkdir(homeClaudeDir, { recursive: true });
+        await fs.writeFile(path.join(homeClaudeDir, 'statusline-command.sh'), statuslineTemplate, 'utf8');
+        await fs.chmod(path.join(homeClaudeDir, 'statusline-command.sh'), 0o755);
+
+        printSuccess('✓ Created statusline-command.sh in both .claude/ and ~/.claude/');
+      } else {
+        console.log('[DRY RUN] Would create .claude/statusline-command.sh and ~/.claude/statusline-command.sh');
+      }
+    } catch (err) {
+      // Not critical, just skip
+      if (!dryRun) {
+        console.log('  ⚠️  Could not create statusline script, skipping...');
+        console.log(`  ℹ️  Error: ${err.message}`);
+      }
+    }
+
+    // Create settings.local.json with default MCP permissions
+    const settingsLocal = {
+      permissions: {
+        allow: ['mcp__ruv-swarm', 'mcp__claude-flow@alpha', 'mcp__flow-nexus'],
+        deny: [],
+      },
+    };
+
+    if (!dryRun) {
+      await fs.writeFile(
+        `${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',
+      );
+    }
+
+    // Create .mcp.json at project root for MCP server configuration
+    const mcpConfig = {
+      mcpServers: {
+        '@sparkleideas/claude-flow@alpha': {
+          command: 'npx',
+          args: ['@sparkleideas/claude-flow@alpha', 'mcp', 'start'],
+          type: 'stdio',
+        },
+        '@sparkleideas/ruv-swarm': {
+          command: 'npx',
+          args: ['@sparkleideas/ruv-swarm@latest', 'mcp', 'start'],
+          type: 'stdio',
+        },
+        'flow-nexus': {
+          command: 'npx',
+          args: ['flow-nexus@latest', 'mcp', 'start'],
+          type: 'stdio',
+        },
+      },
+    };
+
+    if (!dryRun) {
+      await fs.writeFile(`${workingDir}/.mcp.json`, JSON.stringify(mcpConfig, null, 2, 'utf8'));
+      printSuccess('✓ Created .mcp.json at project root for MCP server configuration');
+    } else {
+      console.log('[DRY RUN] Would create .mcp.json at project root for MCP server configuration');
+    }
+
+    // Removed @sparkleideas/claude-flow@alpha.config.json creation per user request
+
+    // Create command documentation
+    for (const [category, commands] of Object.entries(COMMAND_STRUCTURE)) {
+      const categoryDir = `${claudeDir}/commands/${category}`;
+
+      if (!dryRun) {
+        await fs.mkdir(categoryDir, { recursive: true });
+
+        // Create category README
+        const categoryReadme = `# ${category.charAt(0).toUpperCase() + category.slice(1)} Commands
+
+Commands for ${category} operations in Claude Flow.
+
+## Available Commands
+
+${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');
+          }
+        }
+
+        console.log(`  ✓ Created ${commands.length} ${category} command docs`);
+      } else {
+        console.log(`[DRY RUN] Would create ${commands.length} ${category} command docs`);
+      }
+    }
+
+    // Create wrapper scripts using the dedicated function
+    if (!dryRun) {
+      await createLocalExecutable(workingDir, dryRun);
+    } else {
+      console.log('[DRY RUN] Would create wrapper scripts');
+    }
+
+    // Create helper scripts
+    const helpers = ['setup-mcp.sh', 'quick-start.sh', 'github-setup.sh', 'github-safe.js', 'standard-checkpoint-hooks.sh', 'checkpoint-manager.sh'];
+    for (const helper of helpers) {
+      if (!dryRun) {
+        const content = createHelperScript(helper);
+        if (content) {
+          await fs.writeFile(`${claudeDir}/helpers/${helper}`, content, 'utf8');
+          await fs.chmod(`${claudeDir}/helpers/${helper}`, 0o755);
+        }
+      }
+    }
+
+    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@alpha-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 {
+        // Check if database exists BEFORE creating it
+        const dbPath = '.swarm/memory.db';
+        const { existsSync } = await import('fs');
+        const dbExistedBefore = existsSync(dbPath);
+
+        // Handle ReasoningBank migration BEFORE FallbackMemoryStore initialization
+        // This prevents schema conflicts with old databases
+        if (dbExistedBefore) {
+          console.log('  🔍 Checking existing database for ReasoningBank schema...');
+
+          try {
+            const {
+              initializeReasoningBank,
+              checkReasoningBankTables,
+              migrateReasoningBank
+            } = await import('../../../reasoningbank/reasoningbank-adapter.js');
+
+            // Set the database path for ReasoningBank
+            process.env.CLAUDE_FLOW_DB_PATH = dbPath;
+
+            const tableCheck = await checkReasoningBankTables();
+
+            if (tableCheck.exists) {
+              console.log('  ✅ ReasoningBank schema already complete');
+            } else if (force) {
+              // User used --force flag, migrate the database
+              console.log(`  🔄 Migrating database: ${tableCheck.missingTables.length} tables missing`);
+              console.log(`     Missing: ${tableCheck.missingTables.join(', ')}`);
+
+              const migrationResult = await migrateReasoningBank();
+
+              if (migrationResult.success) {
+                printSuccess(`  ✓ Migration complete: added ${migrationResult.addedTables?.length || 0} tables`);
+                console.log('     Use --reasoningbank flag to enable AI-powered memory features');
+              } else {
+                console.log(`  ⚠️  Migration failed: ${migrationResult.message}`);
+                console.log('     Basic memory will work, use: memory init --reasoningbank to retry');
+              }
+            } else {
+              // Database exists with missing tables but no --force flag
+              console.log(`  ℹ️  Database has ${tableCheck.missingTables.length} missing ReasoningBank tables`);
+              console.log(`     Missing: ${tableCheck.missingTables.join(', ')}`);
+              console.log('     Use --force to migrate existing database');
+              console.log('     Or use: memory init --reasoningbank');
+            }
+          } catch (rbErr) {
+            console.log(`  ⚠️  ReasoningBank check failed: ${rbErr.message}`);
+            console.log('     Will attempt normal initialization...');
+          }
+        }
+
+        // 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 @sparkleideas/claude-flow@alpha',
+          );
+        } else {
+          printSuccess('✓ Initialized memory database (.swarm/memory.db)');
+
+          // Initialize ReasoningBank schema for fresh databases
+          if (!dbExistedBefore) {
+            try {
+              const {
+                initializeReasoningBank
+              } = await import('../../../reasoningbank/reasoningbank-adapter.js');
+
+              // Set the database path for ReasoningBank
+              process.env.CLAUDE_FLOW_DB_PATH = dbPath;
+
+              console.log('  🧠 Initializing ReasoningBank schema...');
+              await initializeReasoningBank();
+              printSuccess('  ✓ ReasoningBank schema initialized (use --reasoningbank flag for AI-powered memory)');
+            } catch (rbErr) {
+              console.log(`  ⚠️  ReasoningBank initialization failed: ${rbErr.message}`);
+              console.log('     Basic memory will work, use: memory init --reasoningbank to retry');
+            }
+          }
+        }
+
+        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
+      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}`);
+          });
+        } 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, 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) {
+        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 @sparkleideas/claude-flow npx @sparkleideas/claude-flow@alpha mcp start');
+        console.log('     claude mcp add @sparkleideas/ruv-swarm npx @sparkleideas/ruv-swarm@latest mcp start');
+        console.log('     claude mcp add flow-nexus npx flow-nexus@latest mcp start');
+        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 @sparkleideas/claude-flow@alpha npx @sparkleideas/claude-flow@alpha mcp start');
+      console.log('     claude mcp add @sparkleideas/ruv-swarm npx @sparkleideas/ruv-swarm@latest mcp start');
+      console.log('     claude mcp add flow-nexus npx flow-nexus@latest mcp start');
+      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');
+        } else {
+          console.log('⚠️  Command system setup failed:', commandResult.error);
+        }
+
+        // Copy skill files including skill-builder
+        console.log('\n🎯 Setting up skill system...');
+        const skillResult = await copySkillFiles(workingDir, {
+          force: force,
+          dryRun: dryRun
+        });
+
+        if (skillResult.success) {
+          await validateSkillSystem(workingDir);
+          console.log('✅ ✓ Skill system setup complete with skill-builder');
+        } else {
+          console.log('⚠️  Skill system setup failed:', skillResult.error);
+        }
+
+        console.log('✅ ✓ Agent system setup complete with 64 specialized agents');
+      } else {
+        console.log('⚠️  Agent system setup failed:', agentResult.error);
+      }
+
+      // Setup reasoning agents if --agent reasoning flag is used
+      if (initReasoning) {
+        console.log('\n🧠 Setting up reasoning agents with ReasoningBank integration...');
+        try {
+          const reasoningAgentsDir = `${workingDir}/.claude/agents/reasoning`;
+          await fs.mkdir(reasoningAgentsDir, { recursive: true });
+
+          // Import path module
+          const path = await import('path');
+          const { fileURLToPath } = await import('url');
+          const { dirname, join } = path.default;
+
+          // Get the source reasoning agents directory
+          const __filename = fileURLToPath(import.meta.url);
+          const __dirname = dirname(__filename);
+          const sourceReasoningDir = join(__dirname, '../../../../.claude/agents/reasoning');
+
+          // Copy reasoning agent files
+          try {
+            const reasoningFiles = await fs.readdir(sourceReasoningDir);
+            let copiedReasoningAgents = 0;
+
+            for (const file of reasoningFiles) {
+              if (file.endsWith('.md')) {
+                const sourcePath = join(sourceReasoningDir, file);
+                const destPath = join(reasoningAgentsDir, file);
+                const content = await fs.readFile(sourcePath, 'utf8');
+                await fs.writeFile(destPath, content);
+                copiedReasoningAgents++;
+              }
+            }
+
+            printSuccess(`✓ Copied ${copiedReasoningAgents} reasoning agent files`);
+            console.log('  📚 Reasoning agents available:');
+            console.log('    • goal-planner - Goal-Oriented Action Planning specialist');
+            console.log('    • sublinear-goal-planner - Sub-linear complexity goal planning');
+            console.log('  💡 Use: npx @sparkleideas/agentic-flow --agent goal-planner --task "your task"');
+            console.log('  📖 Documentation: .claude/agents/reasoning/README.md');
+          } catch (err) {
+            console.log(`  ⚠️  Could not copy reasoning agents: ${err.message}`);
+            console.log('     Reasoning agents may not be available yet');
+          }
+        } catch (err) {
+          console.log(`  ⚠️  Reasoning agent setup failed: ${err.message}`);
+        }
+      }
+    } else {
+      console.log('  [DRY RUN] Would create agent system with 64 specialized agents');
+      if (initReasoning) {
+        console.log('  [DRY RUN] Would also setup reasoning agents with ReasoningBank integration');
+      }
+    }
+
+    // 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 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. View available commands: ls .claude/commands/');
+      console.log('2. Start a swarm: npx @sparkleideas/claude-flow@alpha swarm "your objective" --claude');
+      console.log('3. Use hive-mind: npx @sparkleideas/claude-flow@alpha hive-mind spawn "command" --claude');
+      console.log('4. Use MCP tools in Claude Code for enhanced coordination');
+      if (hiveMindStatus.configured) {
+        console.log('5. Initialize first swarm: npx @sparkleideas/claude-flow@alpha 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 @sparkleideas/claude-flow@alpha swarm "your objective" --claude');
+      console.log('5. Use hive-mind: npx @sparkleideas/claude-flow@alpha hive-mind spawn "command" --claude');
+      if (hiveMindStatus.configured) {
+        console.log('6. Initialize first swarm: npx @sparkleideas/claude-flow@alpha 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');
+    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: ${rollbackErr.message}`);
+    }
+  }
+}
+
+/**
+ * Flow Nexus minimal initialization - only creates Flow Nexus CLAUDE.md, commands, and agents
+ */
+async function flowNexusMinimalInit(flags, subArgs) {
+  console.log('🌐 Flow Nexus: Initializing minimal setup...');
+  
+  try {
+    const force = flags.force || flags.f;
+    
+    // Import functions we need
+    const { createFlowNexusClaudeMd } = await import('./templates/claude-md.js');
+    const { promises: fs } = await import('fs');
+    
+    // Create Flow Nexus CLAUDE.md
+    console.log('📝 Creating Flow Nexus CLAUDE.md...');
+    const flowNexusClaudeMd = createFlowNexusClaudeMd();
+    await fs.writeFile('CLAUDE.md', flowNexusClaudeMd);
+    console.log('  ✅ Created CLAUDE.md with Flow Nexus integration');
+    
+    // Create .claude/commands/flow-nexus directory and copy commands
+    console.log('📁 Setting up Flow Nexus commands...');
+    await fs.mkdir('.claude/commands/flow-nexus', { recursive: true });
+    
+    // Copy Flow Nexus command files
+    const { fileURLToPath } = await import('url');
+    const { dirname, join } = await import('path');
+    const __filename = fileURLToPath(import.meta.url);
+    const __dirname = dirname(__filename);
+    const sourceCommandsDir = join(__dirname, '../../../../.claude/commands/flow-nexus');
+    try {
+      const commandFiles = await fs.readdir(sourceCommandsDir);
+      let copiedCommands = 0;
+      
+      for (const file of commandFiles) {
+        if (file.endsWith('.md')) {
+          const sourcePath = `${sourceCommandsDir}/${file}`;
+          const destPath = `.claude/commands/flow-nexus/${file}`;
+          const content = await fs.readFile(sourcePath, 'utf8');
+          await fs.writeFile(destPath, content);
+          copiedCommands++;
+        }
+      }
+      
+      console.log(`  ✅ Copied ${copiedCommands} Flow Nexus command files`);
+    } catch (err) {
+      console.log('  ⚠️  Could not copy Flow Nexus commands:', err.message);
+    }
+    
+    // Create .claude/agents/flow-nexus directory and copy agents
+    console.log('🤖 Setting up Flow Nexus agents...');
+    await fs.mkdir('.claude/agents/flow-nexus', { recursive: true });
+    
+    // Copy Flow Nexus agent files
+    const sourceAgentsDir = join(__dirname, '../../../../.claude/agents/flow-nexus');
+    try {
+      const agentFiles = await fs.readdir(sourceAgentsDir);
+      let copiedAgents = 0;
+      
+      for (const file of agentFiles) {
+        if (file.endsWith('.md')) {
+          const sourcePath = `${sourceAgentsDir}/${file}`;
+          const destPath = `.claude/agents/flow-nexus/${file}`;
+          const content = await fs.readFile(sourcePath, 'utf8');
+          await fs.writeFile(destPath, content);
+          copiedAgents++;
+        }
+      }
+      
+      console.log(`  ✅ Copied ${copiedAgents} Flow Nexus agent files`);
+    } catch (err) {
+      console.log('  ⚠️  Could not copy Flow Nexus agents:', err.message);
+    }
+    
+    console.log('\n🎉 Flow Nexus minimal initialization complete!');
+    console.log('📚 Created: CLAUDE.md with Flow Nexus documentation');
+    console.log('📁 Created: .claude/commands/flow-nexus/ directory with command documentation');
+    console.log('🤖 Created: .claude/agents/flow-nexus/ directory with specialized agents');
+    console.log('');
+    console.log('💡 Quick Start:');
+    console.log('  1. Register: mcp__flow-nexus__user_register({ email, password })');
+    console.log('  2. Login: mcp__flow-nexus__user_login({ email, password })');
+    console.log('  3. Deploy: mcp__flow-nexus__swarm_init({ topology: "mesh", maxAgents: 5 })');
+    console.log('');
+    console.log('🔗 Use Flow Nexus MCP tools in Claude Code for full functionality');
+    
+  } catch (err) {
+    console.log(`❌ Flow Nexus initialization failed: ${err.message}`);
+    console.log('Stack trace:', err.stack);
+    process.exit(1);
+  }
+}