@sparkleideas/cli 3.1.0-alpha.17 → 3.1.0-alpha.18

package/dist/src/init/executor.js

@@ -1,1612 +0,0 @@
-/**
- * Init Executor
- * Main execution logic for V3 initialization
- */
-import * as fs from 'fs';
-import * as path from 'path';
-import { fileURLToPath } from 'url';
-import { dirname } from 'path';
-// ESM-compatible __dirname
-const __filename = fileURLToPath(import.meta.url);
-const __dirname = dirname(__filename);
-import { detectPlatform, DEFAULT_INIT_OPTIONS } from './types.js';
-import { generateSettingsJson, generateSettings } from './settings-generator.js';
-import { generateMCPJson } from './mcp-generator.js';
-import { generateStatuslineScript, generateStatuslineHook } from './statusline-generator.js';
-import { generatePreCommitHook, generatePostCommitHook, generateSessionManager, generateAgentRouter, generateMemoryHelper, } from './helpers-generator.js';
-import { generateClaudeMd } from './claudemd-generator.js';
-/**
- * Skills to copy based on configuration
- */
-const SKILLS_MAP = {
-    core: [
-        'swarm-orchestration',
-        'swarm-advanced',
-        'sparc-methodology',
-        'hooks-automation',
-        'pair-programming',
-        'verification-quality',
-        'stream-chain',
-        'skill-builder',
-    ],
-    browser: ['browser'], // agent-browser integration
-    dualMode: ['dual-mode'], // Claude Code + Codex hybrid execution
-    agentdb: [
-        'agentdb-advanced',
-        'agentdb-learning',
-        'agentdb-memory-patterns',
-        'agentdb-optimization',
-        'agentdb-vector-search',
-        'reasoningbank-agentdb',
-        'reasoningbank-intelligence',
-    ],
-    github: [
-        'github-code-review',
-        'github-multi-repo',
-        'github-project-management',
-        'github-release-management',
-        'github-workflow-automation',
-    ],
-    flowNexus: [
-        'flow-nexus-neural',
-        'flow-nexus-platform',
-        'flow-nexus-swarm',
-    ],
-    v3: [
-        'v3-cli-modernization',
-        'v3-core-implementation',
-        'v3-ddd-architecture',
-        'v3-integration-deep',
-        'v3-mcp-optimization',
-        'v3-memory-unification',
-        'v3-performance-optimization',
-        'v3-security-overhaul',
-        'v3-swarm-coordination',
-    ],
-};
-/**
- * Commands to copy based on configuration
- */
-const COMMANDS_MAP = {
-    core: ['claude-flow-help.md', 'claude-flow-swarm.md', 'claude-flow-memory.md'],
-    analysis: ['analysis'],
-    automation: ['automation'],
-    github: ['github'],
-    hooks: ['hooks'],
-    monitoring: ['monitoring'],
-    optimization: ['optimization'],
-    sparc: ['sparc'],
-};
-/**
- * Agents to copy based on configuration
- */
-const AGENTS_MAP = {
-    core: ['core'],
-    consensus: ['consensus'],
-    github: ['github'],
-    hiveMind: ['hive-mind'],
-    sparc: ['sparc'],
-    swarm: ['swarm'],
-    browser: ['browser'], // agent-browser integration
-    dualMode: ['dual-mode'], // Claude Code + Codex hybrid execution
-    // V3-specific agents
-    v3: ['v3'],
-    optimization: ['optimization'],
-    templates: ['templates'],
-    testing: ['testing'],
-    sublinear: ['sublinear'],
-    flowNexus: ['flow-nexus'],
-    analysis: ['analysis'],
-    architecture: ['architecture'],
-    development: ['development'],
-    devops: ['devops'],
-    documentation: ['documentation'],
-    specialized: ['specialized'],
-    goal: ['goal'],
-    sona: ['sona'],
-    payments: ['payments'],
-    data: ['data'],
-    custom: ['custom'],
-};
-/**
- * Directory structure to create
- */
-const DIRECTORIES = {
-    claude: [
-        '.claude',
-        '.claude/skills',
-        '.claude/commands',
-        '.claude/agents',
-        '.claude/helpers',
-    ],
-    runtime: [
-        '.claude-flow',
-        '.claude-flow/data',
-        '.claude-flow/logs',
-        '.claude-flow/sessions',
-        '.claude-flow/hooks',
-        '.claude-flow/agents',
-        '.claude-flow/workflows',
-    ],
-};
-/**
- * Execute initialization
- */
-export async function executeInit(options) {
-    // Detect platform
-    const platform = detectPlatform();
-    const result = {
-        success: true,
-        platform,
-        created: {
-            directories: [],
-            files: [],
-        },
-        skipped: [],
-        errors: [],
-        summary: {
-            skillsCount: 0,
-            commandsCount: 0,
-            agentsCount: 0,
-            hooksEnabled: 0,
-        },
-    };
-    const targetDir = options.targetDir;
-    try {
-        // Create directory structure
-        await createDirectories(targetDir, options, result);
-        // Generate and write settings.json
-        if (options.components.settings) {
-            await writeSettings(targetDir, options, result);
-        }
-        // Generate and write .mcp.json
-        if (options.components.mcp) {
-            await writeMCPConfig(targetDir, options, result);
-        }
-        // Copy skills
-        if (options.components.skills) {
-            await copySkills(targetDir, options, result);
-        }
-        // Copy commands
-        if (options.components.commands) {
-            await copyCommands(targetDir, options, result);
-        }
-        // Copy agents
-        if (options.components.agents) {
-            await copyAgents(targetDir, options, result);
-        }
-        // Generate helpers
-        if (options.components.helpers) {
-            await writeHelpers(targetDir, options, result);
-        }
-        // Generate statusline
-        if (options.components.statusline) {
-            await writeStatusline(targetDir, options, result);
-        }
-        // Generate runtime config
-        if (options.components.runtime) {
-            await writeRuntimeConfig(targetDir, options, result);
-        }
-        // Create initial metrics for statusline (prevents "all zeros" display)
-        if (options.components.statusline) {
-            await writeInitialMetrics(targetDir, options, result);
-        }
-        // Generate CLAUDE.md
-        if (options.components.claudeMd) {
-            await writeClaudeMd(targetDir, options, result);
-        }
-        // Count enabled hooks
-        result.summary.hooksEnabled = countEnabledHooks(options);
-    }
-    catch (error) {
-        result.success = false;
-        result.errors.push(error instanceof Error ? error.message : String(error));
-    }
-    return result;
-}
-/**
- * Merge new settings into existing settings.json
- * Preserves user customizations while adding new features like Agent Teams
- * Uses platform-specific commands for Mac, Linux, and Windows
- */
-function mergeSettingsForUpgrade(existing) {
-    const merged = { ...existing };
-    const platform = detectPlatform();
-    const isWindows = platform.os === 'windows';
-    // Platform-specific command wrappers
-    // Windows: Use PowerShell-compatible commands
-    // Mac/Linux: Use bash-compatible commands with 2>/dev/null
-    const teammateIdleCmd = isWindows
-        ? 'npx @sparkleideas/cli@latest hooks teammate-idle --auto-assign true 2>$null; exit 0'
-        : 'npx @sparkleideas/cli@latest hooks teammate-idle --auto-assign true 2>/dev/null || true';
-    const taskCompletedCmd = isWindows
-        ? 'if ($env:TASK_ID) { npx @sparkleideas/cli@latest hooks task-completed --task-id $env:TASK_ID --train-patterns true 2>$null }; exit 0'
-        : '[ -n "$TASK_ID" ] && npx @sparkleideas/cli@latest hooks task-completed --task-id "$TASK_ID" --train-patterns true 2>/dev/null || true';
-    // 1. Merge env vars (preserve existing, add new)
-    const existingEnv = existing.env || {};
-    merged.env = {
-        ...existingEnv,
-        CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS: '1',
-        CLAUDE_FLOW_V3_ENABLED: existingEnv.CLAUDE_FLOW_V3_ENABLED || 'true',
-        CLAUDE_FLOW_HOOKS_ENABLED: existingEnv.CLAUDE_FLOW_HOOKS_ENABLED || 'true',
-    };
-    // 2. Merge hooks (preserve existing, add new Agent Teams hooks)
-    const existingHooks = existing.hooks || {};
-    merged.hooks = { ...existingHooks };
-    // Add TeammateIdle hook if not present
-    if (!existingHooks.TeammateIdle) {
-        merged.hooks.TeammateIdle = [
-            {
-                hooks: [
-                    {
-                        type: 'command',
-                        command: teammateIdleCmd,
-                        timeout: 5000,
-                        continueOnError: true,
-                    },
-                ],
-            },
-        ];
-    }
-    // Add TaskCompleted hook if not present
-    if (!existingHooks.TaskCompleted) {
-        merged.hooks.TaskCompleted = [
-            {
-                hooks: [
-                    {
-                        type: 'command',
-                        command: taskCompletedCmd,
-                        timeout: 5000,
-                        continueOnError: true,
-                    },
-                ],
-            },
-        ];
-    }
-    // 3. Merge claudeFlow settings (preserve existing, add agentTeams)
-    const existingClaudeFlow = existing.claudeFlow || {};
-    merged.claudeFlow = {
-        ...existingClaudeFlow,
-        version: existingClaudeFlow.version || '3.0.0',
-        enabled: existingClaudeFlow.enabled !== false,
-        agentTeams: {
-            enabled: true,
-            teammateMode: 'auto',
-            taskListEnabled: true,
-            mailboxEnabled: true,
-            coordination: {
-                autoAssignOnIdle: true,
-                trainPatternsOnComplete: true,
-                notifyLeadOnComplete: true,
-                sharedMemoryNamespace: 'agent-teams',
-            },
-            hooks: {
-                teammateIdle: { enabled: true, autoAssign: true, checkTaskList: true },
-                taskCompleted: { enabled: true, trainPatterns: true, notifyLead: true },
-            },
-        },
-    };
-    return merged;
-}
-/**
- * Execute upgrade - updates helpers and creates missing metrics without losing data
- * This is safe for existing users who want the latest statusline fixes
- * @param targetDir - Target directory
- * @param upgradeSettings - If true, merge new settings into existing settings.json
- */
-export async function executeUpgrade(targetDir, upgradeSettings = false) {
-    const result = {
-        success: true,
-        updated: [],
-        created: [],
-        preserved: [],
-        errors: [],
-        settingsUpdated: [],
-    };
-    try {
-        // Ensure required directories exist
-        const dirs = [
-            '.claude/helpers',
-            '.claude-flow/metrics',
-            '.claude-flow/security',
-            '.claude-flow/learning',
-        ];
-        for (const dir of dirs) {
-            const fullPath = path.join(targetDir, dir);
-            if (!fs.existsSync(fullPath)) {
-                fs.mkdirSync(fullPath, { recursive: true });
-            }
-        }
-        // 1. ALWAYS update statusline helper (force overwrite)
-        const statuslinePath = path.join(targetDir, '.claude', 'helpers', 'statusline.cjs');
-        // Use default options with statusline config
-        const upgradeOptions = {
-            ...DEFAULT_INIT_OPTIONS,
-            targetDir,
-            force: true,
-            statusline: {
-                ...DEFAULT_INIT_OPTIONS.statusline,
-                refreshInterval: 5000,
-            },
-        };
-        const statuslineContent = generateStatuslineScript(upgradeOptions);
-        if (fs.existsSync(statuslinePath)) {
-            result.updated.push('.claude/helpers/statusline.cjs');
-        }
-        else {
-            result.created.push('.claude/helpers/statusline.cjs');
-        }
-        fs.writeFileSync(statuslinePath, statuslineContent, 'utf-8');
-        // 2. Create MISSING metrics files only (preserve existing data)
-        const metricsDir = path.join(targetDir, '.claude-flow', 'metrics');
-        const securityDir = path.join(targetDir, '.claude-flow', 'security');
-        // v3-progress.json
-        const progressPath = path.join(metricsDir, 'v3-progress.json');
-        if (!fs.existsSync(progressPath)) {
-            const progress = {
-                version: '3.0.0',
-                initialized: new Date().toISOString(),
-                domains: { completed: 0, total: 5, status: 'INITIALIZING' },
-                ddd: { progress: 0, modules: 0, totalFiles: 0, totalLines: 0 },
-                swarm: { activeAgents: 0, maxAgents: 15, topology: 'hierarchical-mesh' },
-                learning: { status: 'READY', patternsLearned: 0, sessionsCompleted: 0 },
-                _note: 'Metrics will update as you use Claude Flow'
-            };
-            fs.writeFileSync(progressPath, JSON.stringify(progress, null, 2), 'utf-8');
-            result.created.push('.claude-flow/metrics/v3-progress.json');
-        }
-        else {
-            result.preserved.push('.claude-flow/metrics/v3-progress.json');
-        }
-        // swarm-activity.json
-        const activityPath = path.join(metricsDir, 'swarm-activity.json');
-        if (!fs.existsSync(activityPath)) {
-            const activity = {
-                timestamp: new Date().toISOString(),
-                processes: { agentic_flow: 0, mcp_server: 0, estimated_agents: 0 },
-                swarm: { active: false, agent_count: 0, coordination_active: false },
-                integration: { agentic_flow_active: false, mcp_active: false },
-                _initialized: true
-            };
-            fs.writeFileSync(activityPath, JSON.stringify(activity, null, 2), 'utf-8');
-            result.created.push('.claude-flow/metrics/swarm-activity.json');
-        }
-        else {
-            result.preserved.push('.claude-flow/metrics/swarm-activity.json');
-        }
-        // learning.json
-        const learningPath = path.join(metricsDir, 'learning.json');
-        if (!fs.existsSync(learningPath)) {
-            const learning = {
-                initialized: new Date().toISOString(),
-                routing: { accuracy: 0, decisions: 0 },
-                patterns: { shortTerm: 0, longTerm: 0, quality: 0 },
-                sessions: { total: 0, current: null },
-                _note: 'Intelligence grows as you use Claude Flow'
-            };
-            fs.writeFileSync(learningPath, JSON.stringify(learning, null, 2), 'utf-8');
-            result.created.push('.claude-flow/metrics/learning.json');
-        }
-        else {
-            result.preserved.push('.claude-flow/metrics/learning.json');
-        }
-        // audit-status.json
-        const auditPath = path.join(securityDir, 'audit-status.json');
-        if (!fs.existsSync(auditPath)) {
-            const audit = {
-                initialized: new Date().toISOString(),
-                status: 'PENDING',
-                cvesFixed: 0,
-                totalCves: 3,
-                lastScan: null,
-                _note: 'Run: npx @sparkleideas/cli@latest security scan'
-            };
-            fs.writeFileSync(auditPath, JSON.stringify(audit, null, 2), 'utf-8');
-            result.created.push('.claude-flow/security/audit-status.json');
-        }
-        else {
-            result.preserved.push('.claude-flow/security/audit-status.json');
-        }
-        // 3. Merge settings if requested
-        if (upgradeSettings) {
-            const settingsPath = path.join(targetDir, '.claude', 'settings.json');
-            if (fs.existsSync(settingsPath)) {
-                try {
-                    const existingSettings = JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
-                    const mergedSettings = mergeSettingsForUpgrade(existingSettings);
-                    fs.writeFileSync(settingsPath, JSON.stringify(mergedSettings, null, 2), 'utf-8');
-                    result.updated.push('.claude/settings.json');
-                    result.settingsUpdated = [
-                        'env.CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS',
-                        'hooks.TeammateIdle',
-                        'hooks.TaskCompleted',
-                        'claudeFlow.agentTeams',
-                    ];
-                }
-                catch (settingsError) {
-                    result.errors.push(`Settings merge failed: ${settingsError instanceof Error ? settingsError.message : String(settingsError)}`);
-                }
-            }
-            else {
-                // Create new settings.json with defaults
-                const defaultSettings = generateSettings(DEFAULT_INIT_OPTIONS);
-                fs.writeFileSync(settingsPath, JSON.stringify(defaultSettings, null, 2), 'utf-8');
-                result.created.push('.claude/settings.json');
-                result.settingsUpdated = ['Created new settings.json with Agent Teams'];
-            }
-        }
-    }
-    catch (error) {
-        result.success = false;
-        result.errors.push(error instanceof Error ? error.message : String(error));
-    }
-    return result;
-}
-/**
- * Execute upgrade with --add-missing flag
- * Adds any new skills, agents, and commands that don't exist yet
- * @param targetDir - Target directory
- * @param upgradeSettings - If true, merge new settings into existing settings.json
- */
-export async function executeUpgradeWithMissing(targetDir, upgradeSettings = false) {
-    // First do the normal upgrade (pass through upgradeSettings)
-    const result = await executeUpgrade(targetDir, upgradeSettings);
-    if (!result.success) {
-        return result;
-    }
-    // Initialize tracking arrays
-    result.addedSkills = [];
-    result.addedAgents = [];
-    result.addedCommands = [];
-    try {
-        // Ensure target directories exist
-        const skillsDir = path.join(targetDir, '.claude', 'skills');
-        const agentsDir = path.join(targetDir, '.claude', 'agents');
-        const commandsDir = path.join(targetDir, '.claude', 'commands');
-        for (const dir of [skillsDir, agentsDir, commandsDir]) {
-            if (!fs.existsSync(dir)) {
-                fs.mkdirSync(dir, { recursive: true });
-            }
-        }
-        // Find source directories
-        const sourceSkillsDir = findSourceDir('skills');
-        const sourceAgentsDir = findSourceDir('agents');
-        const sourceCommandsDir = findSourceDir('commands');
-        // Debug: Log source directories found
-        if (process.env.DEBUG || process.env.CLAUDE_FLOW_DEBUG) {
-            console.log('[DEBUG] Source directories:');
-            console.log(`  Skills: ${sourceSkillsDir || 'NOT FOUND'}`);
-            console.log(`  Agents: ${sourceAgentsDir || 'NOT FOUND'}`);
-            console.log(`  Commands: ${sourceCommandsDir || 'NOT FOUND'}`);
-        }
-        // Add missing skills
-        if (sourceSkillsDir) {
-            const allSkills = Object.values(SKILLS_MAP).flat();
-            const debugMode = process.env.DEBUG || process.env.CLAUDE_FLOW_DEBUG;
-            if (debugMode) {
-                console.log(`[DEBUG] Checking ${allSkills.length} skills from SKILLS_MAP`);
-            }
-            for (const skillName of [...new Set(allSkills)]) {
-                const sourcePath = path.join(sourceSkillsDir, skillName);
-                const targetPath = path.join(skillsDir, skillName);
-                const sourceExists = fs.existsSync(sourcePath);
-                const targetExists = fs.existsSync(targetPath);
-                if (debugMode) {
-                    console.log(`[DEBUG] Skill '${skillName}': source=${sourceExists}, target=${targetExists}`);
-                }
-                if (sourceExists && !targetExists) {
-                    copyDirRecursive(sourcePath, targetPath);
-                    result.addedSkills.push(skillName);
-                    result.created.push(`.claude/skills/${skillName}`);
-                }
-            }
-        }
-        // Add missing agents
-        if (sourceAgentsDir) {
-            const allAgents = Object.values(AGENTS_MAP).flat();
-            for (const agentCategory of [...new Set(allAgents)]) {
-                const sourcePath = path.join(sourceAgentsDir, agentCategory);
-                const targetPath = path.join(agentsDir, agentCategory);
-                if (fs.existsSync(sourcePath) && !fs.existsSync(targetPath)) {
-                    copyDirRecursive(sourcePath, targetPath);
-                    result.addedAgents.push(agentCategory);
-                    result.created.push(`.claude/agents/${agentCategory}`);
-                }
-            }
-        }
-        // Add missing commands
-        if (sourceCommandsDir) {
-            const allCommands = Object.values(COMMANDS_MAP).flat();
-            for (const cmdName of [...new Set(allCommands)]) {
-                const sourcePath = path.join(sourceCommandsDir, cmdName);
-                const targetPath = path.join(commandsDir, cmdName);
-                if (fs.existsSync(sourcePath) && !fs.existsSync(targetPath)) {
-                    if (fs.statSync(sourcePath).isDirectory()) {
-                        copyDirRecursive(sourcePath, targetPath);
-                    }
-                    else {
-                        fs.copyFileSync(sourcePath, targetPath);
-                    }
-                    result.addedCommands.push(cmdName);
-                    result.created.push(`.claude/commands/${cmdName}`);
-                }
-            }
-        }
-    }
-    catch (error) {
-        result.errors.push(`Add missing failed: ${error instanceof Error ? error.message : String(error)}`);
-    }
-    return result;
-}
-/**
- * Create directory structure
- */
-async function createDirectories(targetDir, options, result) {
-    const dirs = [
-        ...DIRECTORIES.claude,
-        ...(options.components.runtime ? DIRECTORIES.runtime : []),
-    ];
-    for (const dir of dirs) {
-        const fullPath = path.join(targetDir, dir);
-        if (!fs.existsSync(fullPath)) {
-            fs.mkdirSync(fullPath, { recursive: true });
-            result.created.directories.push(dir);
-        }
-    }
-}
-/**
- * Write settings.json
- */
-async function writeSettings(targetDir, options, result) {
-    const settingsPath = path.join(targetDir, '.claude', 'settings.json');
-    if (fs.existsSync(settingsPath) && !options.force) {
-        result.skipped.push('.claude/settings.json');
-        return;
-    }
-    const content = generateSettingsJson(options);
-    fs.writeFileSync(settingsPath, content, 'utf-8');
-    result.created.files.push('.claude/settings.json');
-}
-/**
- * Write .mcp.json
- */
-async function writeMCPConfig(targetDir, options, result) {
-    const mcpPath = path.join(targetDir, '.mcp.json');
-    if (fs.existsSync(mcpPath) && !options.force) {
-        result.skipped.push('.mcp.json');
-        return;
-    }
-    const content = generateMCPJson(options);
-    fs.writeFileSync(mcpPath, content, 'utf-8');
-    result.created.files.push('.mcp.json');
-}
-/**
- * Copy skills from source
- */
-async function copySkills(targetDir, options, result) {
-    const skillsConfig = options.skills;
-    const targetSkillsDir = path.join(targetDir, '.claude', 'skills');
-    // Determine which skills to copy
-    const skillsToCopy = [];
-    if (skillsConfig.all) {
-        // Copy all available skills
-        Object.values(SKILLS_MAP).forEach(skills => skillsToCopy.push(...skills));
-    }
-    else {
-        if (skillsConfig.core)
-            skillsToCopy.push(...SKILLS_MAP.core);
-        if (skillsConfig.agentdb)
-            skillsToCopy.push(...SKILLS_MAP.agentdb);
-        if (skillsConfig.github)
-            skillsToCopy.push(...SKILLS_MAP.github);
-        if (skillsConfig.flowNexus)
-            skillsToCopy.push(...SKILLS_MAP.flowNexus);
-        if (skillsConfig.browser)
-            skillsToCopy.push(...SKILLS_MAP.browser);
-        if (skillsConfig.v3)
-            skillsToCopy.push(...SKILLS_MAP.v3);
-        if (skillsConfig.dualMode)
-            skillsToCopy.push(...SKILLS_MAP.dualMode);
-    }
-    // Find source skills directory
-    const sourceSkillsDir = findSourceDir('skills', options.sourceBaseDir);
-    if (!sourceSkillsDir) {
-        result.errors.push('Could not find source skills directory');
-        return;
-    }
-    // Copy each skill
-    for (const skillName of [...new Set(skillsToCopy)]) {
-        const sourcePath = path.join(sourceSkillsDir, skillName);
-        const targetPath = path.join(targetSkillsDir, skillName);
-        if (fs.existsSync(sourcePath)) {
-            if (!fs.existsSync(targetPath) || options.force) {
-                copyDirRecursive(sourcePath, targetPath);
-                result.created.files.push(`.claude/skills/${skillName}`);
-                result.summary.skillsCount++;
-            }
-            else {
-                result.skipped.push(`.claude/skills/${skillName}`);
-            }
-        }
-    }
-}
-/**
- * Copy commands from source
- */
-async function copyCommands(targetDir, options, result) {
-    const commandsConfig = options.commands;
-    const targetCommandsDir = path.join(targetDir, '.claude', 'commands');
-    // Determine which commands to copy
-    const commandsToCopy = [];
-    if (commandsConfig.all) {
-        Object.values(COMMANDS_MAP).forEach(cmds => commandsToCopy.push(...cmds));
-    }
-    else {
-        if (commandsConfig.core)
-            commandsToCopy.push(...COMMANDS_MAP.core);
-        if (commandsConfig.analysis)
-            commandsToCopy.push(...COMMANDS_MAP.analysis);
-        if (commandsConfig.automation)
-            commandsToCopy.push(...COMMANDS_MAP.automation);
-        if (commandsConfig.github)
-            commandsToCopy.push(...COMMANDS_MAP.github);
-        if (commandsConfig.hooks)
-            commandsToCopy.push(...COMMANDS_MAP.hooks);
-        if (commandsConfig.monitoring)
-            commandsToCopy.push(...COMMANDS_MAP.monitoring);
-        if (commandsConfig.optimization)
-            commandsToCopy.push(...COMMANDS_MAP.optimization);
-        if (commandsConfig.sparc)
-            commandsToCopy.push(...COMMANDS_MAP.sparc);
-    }
-    // Find source commands directory
-    const sourceCommandsDir = findSourceDir('commands', options.sourceBaseDir);
-    if (!sourceCommandsDir) {
-        result.errors.push('Could not find source commands directory');
-        return;
-    }
-    // Copy each command/directory
-    for (const cmdName of [...new Set(commandsToCopy)]) {
-        const sourcePath = path.join(sourceCommandsDir, cmdName);
-        const targetPath = path.join(targetCommandsDir, cmdName);
-        if (fs.existsSync(sourcePath)) {
-            if (!fs.existsSync(targetPath) || options.force) {
-                if (fs.statSync(sourcePath).isDirectory()) {
-                    copyDirRecursive(sourcePath, targetPath);
-                }
-                else {
-                    fs.copyFileSync(sourcePath, targetPath);
-                }
-                result.created.files.push(`.claude/commands/${cmdName}`);
-                result.summary.commandsCount++;
-            }
-            else {
-                result.skipped.push(`.claude/commands/${cmdName}`);
-            }
-        }
-    }
-}
-/**
- * Copy agents from source
- */
-async function copyAgents(targetDir, options, result) {
-    const agentsConfig = options.agents;
-    const targetAgentsDir = path.join(targetDir, '.claude', 'agents');
-    // Determine which agents to copy
-    const agentsToCopy = [];
-    if (agentsConfig.all) {
-        Object.values(AGENTS_MAP).forEach(agents => agentsToCopy.push(...agents));
-    }
-    else {
-        if (agentsConfig.core)
-            agentsToCopy.push(...AGENTS_MAP.core);
-        if (agentsConfig.consensus)
-            agentsToCopy.push(...AGENTS_MAP.consensus);
-        if (agentsConfig.github)
-            agentsToCopy.push(...AGENTS_MAP.github);
-        if (agentsConfig.hiveMind)
-            agentsToCopy.push(...AGENTS_MAP.hiveMind);
-        if (agentsConfig.sparc)
-            agentsToCopy.push(...AGENTS_MAP.sparc);
-        if (agentsConfig.swarm)
-            agentsToCopy.push(...AGENTS_MAP.swarm);
-        if (agentsConfig.browser)
-            agentsToCopy.push(...AGENTS_MAP.browser);
-        // V3-specific agent categories
-        if (agentsConfig.v3)
-            agentsToCopy.push(...(AGENTS_MAP.v3 || []));
-        if (agentsConfig.optimization)
-            agentsToCopy.push(...(AGENTS_MAP.optimization || []));
-        if (agentsConfig.testing)
-            agentsToCopy.push(...(AGENTS_MAP.testing || []));
-        // Dual-mode agents (Claude Code + Codex hybrid)
-        if (agentsConfig.dualMode)
-            agentsToCopy.push(...(AGENTS_MAP.dualMode || []));
-    }
-    // Find source agents directory
-    const sourceAgentsDir = findSourceDir('agents', options.sourceBaseDir);
-    if (!sourceAgentsDir) {
-        result.errors.push('Could not find source agents directory');
-        return;
-    }
-    // Copy each agent category
-    for (const agentCategory of [...new Set(agentsToCopy)]) {
-        const sourcePath = path.join(sourceAgentsDir, agentCategory);
-        const targetPath = path.join(targetAgentsDir, agentCategory);
-        if (fs.existsSync(sourcePath)) {
-            if (!fs.existsSync(targetPath) || options.force) {
-                copyDirRecursive(sourcePath, targetPath);
-                // Count agent files (.yaml and .md)
-                const yamlFiles = countFiles(sourcePath, '.yaml');
-                const mdFiles = countFiles(sourcePath, '.md');
-                result.summary.agentsCount += yamlFiles + mdFiles;
-                result.created.files.push(`.claude/agents/${agentCategory}`);
-            }
-            else {
-                result.skipped.push(`.claude/agents/${agentCategory}`);
-            }
-        }
-    }
-}
-/**
- * Find source helpers directory
- */
-function findSourceHelpersDir(sourceBaseDir) {
-    const possiblePaths = [];
-    // If explicit source base directory is provided, check it first
-    if (sourceBaseDir) {
-        possiblePaths.push(path.join(sourceBaseDir, '.claude', 'helpers'));
-    }
-    // IMPORTANT: Check the package's own .claude/helpers directory
-    // This is the primary path when running as an npm package
-    // __dirname is typically /path/to/node_modules/@sparkleideas/cli/dist/src/init
-    // We need to go up 3 levels to reach the package root (dist/src/init -> dist/src -> dist -> root)
-    const packageRoot = path.resolve(__dirname, '..', '..', '..');
-    const packageHelpers = path.join(packageRoot, '.claude', 'helpers');
-    if (fs.existsSync(packageHelpers)) {
-        possiblePaths.unshift(packageHelpers); // Add to beginning (highest priority)
-    }
-    // From dist/src/init -> go up to project root
-    let currentDir = __dirname;
-    for (let i = 0; i < 10; i++) {
-        const parentDir = path.dirname(currentDir);
-        const helpersPath = path.join(parentDir, '.claude', 'helpers');
-        if (fs.existsSync(helpersPath)) {
-            possiblePaths.push(helpersPath);
-        }
-        currentDir = parentDir;
-    }
-    // Also check relative to process.cwd() for development
-    const cwdBased = [
-        path.join(process.cwd(), '.claude', 'helpers'),
-        path.join(process.cwd(), '..', '.claude', 'helpers'),
-        path.join(process.cwd(), '..', '..', '.claude', 'helpers'),
-    ];
-    possiblePaths.push(...cwdBased);
-    for (const p of possiblePaths) {
-        if (fs.existsSync(p)) {
-            return p;
-        }
-    }
-    return null;
-}
-/**
- * Write helper scripts
- */
-async function writeHelpers(targetDir, options, result) {
-    const helpersDir = path.join(targetDir, '.claude', 'helpers');
-    // Find source helpers directory (works for npm package and local dev)
-    const sourceHelpersDir = findSourceHelpersDir(options.sourceBaseDir);
-    // Try to copy existing helpers from source first
-    if (sourceHelpersDir && fs.existsSync(sourceHelpersDir)) {
-        const helperFiles = fs.readdirSync(sourceHelpersDir);
-        let copiedCount = 0;
-        for (const file of helperFiles) {
-            const sourcePath = path.join(sourceHelpersDir, file);
-            const destPath = path.join(helpersDir, file);
-            // Skip directories and only copy files
-            if (!fs.statSync(sourcePath).isFile())
-                continue;
-            if (!fs.existsSync(destPath) || options.force) {
-                fs.copyFileSync(sourcePath, destPath);
-                // Make shell scripts and mjs files executable
-                if (file.endsWith('.sh') || file.endsWith('.mjs')) {
-                    fs.chmodSync(destPath, '755');
-                }
-                result.created.files.push(`.claude/helpers/${file}`);
-                copiedCount++;
-            }
-            else {
-                result.skipped.push(`.claude/helpers/${file}`);
-            }
-        }
-        if (copiedCount > 0) {
-            return; // Skip generating if we copied from source
-        }
-    }
-    // Fall back to generating helpers if source not available
-    const helpers = {
-        'pre-commit': generatePreCommitHook(),
-        'post-commit': generatePostCommitHook(),
-        'session.js': generateSessionManager(),
-        'router.js': generateAgentRouter(),
-        'memory.js': generateMemoryHelper(),
-    };
-    for (const [name, content] of Object.entries(helpers)) {
-        const filePath = path.join(helpersDir, name);
-        if (!fs.existsSync(filePath) || options.force) {
-            fs.writeFileSync(filePath, content, 'utf-8');
-            // Make shell scripts executable
-            if (!name.endsWith('.js')) {
-                fs.chmodSync(filePath, '755');
-            }
-            result.created.files.push(`.claude/helpers/${name}`);
-        }
-        else {
-            result.skipped.push(`.claude/helpers/${name}`);
-        }
-    }
-}
-/**
- * Find source .claude directory for statusline files
- */
-function findSourceClaudeDir(sourceBaseDir) {
-    const possiblePaths = [];
-    // If explicit source base directory is provided, check it first
-    if (sourceBaseDir) {
-        possiblePaths.push(path.join(sourceBaseDir, '.claude'));
-    }
-    // IMPORTANT: Check the package's own .claude directory
-    // Go up 3 levels: dist/src/init -> dist/src -> dist -> root
-    const packageRoot = path.resolve(__dirname, '..', '..', '..');
-    const packageClaude = path.join(packageRoot, '.claude');
-    if (fs.existsSync(packageClaude)) {
-        possiblePaths.unshift(packageClaude); // Add to beginning (highest priority)
-    }
-    // From dist/src/init -> go up to project root
-    let currentDir = __dirname;
-    for (let i = 0; i < 10; i++) {
-        const parentDir = path.dirname(currentDir);
-        const claudePath = path.join(parentDir, '.claude');
-        if (fs.existsSync(claudePath)) {
-            possiblePaths.push(claudePath);
-        }
-        currentDir = parentDir;
-    }
-    for (const p of possiblePaths) {
-        if (fs.existsSync(p)) {
-            return p;
-        }
-    }
-    return null;
-}
-/**
- * Write statusline configuration
- */
-async function writeStatusline(targetDir, options, result) {
-    const claudeDir = path.join(targetDir, '.claude');
-    const helpersDir = path.join(targetDir, '.claude', 'helpers');
-    // Find source .claude directory (works for npm package and local dev)
-    const sourceClaudeDir = findSourceClaudeDir(options.sourceBaseDir);
-    // Try to copy existing advanced statusline files from source
-    const advancedStatuslineFiles = [
-        { src: 'statusline.sh', dest: 'statusline.sh', dir: claudeDir },
-        { src: 'statusline.mjs', dest: 'statusline.mjs', dir: claudeDir },
-    ];
-    let copiedAdvanced = false;
-    if (sourceClaudeDir) {
-        for (const file of advancedStatuslineFiles) {
-            const sourcePath = path.join(sourceClaudeDir, file.src);
-            const destPath = path.join(file.dir, file.dest);
-            if (fs.existsSync(sourcePath)) {
-                if (!fs.existsSync(destPath) || options.force) {
-                    fs.copyFileSync(sourcePath, destPath);
-                    // Make shell scripts and mjs executable
-                    if (file.src.endsWith('.sh') || file.src.endsWith('.mjs')) {
-                        fs.chmodSync(destPath, '755');
-                    }
-                    result.created.files.push(`.claude/${file.dest}`);
-                    copiedAdvanced = true;
-                }
-                else {
-                    result.skipped.push(`.claude/${file.dest}`);
-                }
-            }
-        }
-    }
-    // Fall back to generating simple statusline if advanced files not available
-    if (!copiedAdvanced) {
-        const statuslineScript = generateStatuslineScript(options);
-        const statuslineHook = generateStatuslineHook(options);
-        const files = {
-            'statusline.cjs': statuslineScript, // .cjs for ES module project compatibility
-            'statusline-hook.sh': statuslineHook,
-        };
-        for (const [name, content] of Object.entries(files)) {
-            const filePath = path.join(helpersDir, name);
-            if (!fs.existsSync(filePath) || options.force) {
-                fs.writeFileSync(filePath, content, 'utf-8');
-                result.created.files.push(`.claude/helpers/${name}`);
-            }
-            else {
-                result.skipped.push(`.claude/helpers/${name}`);
-            }
-        }
-    }
-}
-/**
- * Write runtime configuration (.claude-flow/)
- */
-async function writeRuntimeConfig(targetDir, options, result) {
-    const configPath = path.join(targetDir, '.claude-flow', 'config.yaml');
-    if (fs.existsSync(configPath) && !options.force) {
-        result.skipped.push('.claude-flow/config.yaml');
-        return;
-    }
-    const config = `# Claude Flow V3 Runtime Configuration
-# Generated: ${new Date().toISOString()}
-
-version: "3.0.0"
-
-swarm:
-  topology: ${options.runtime.topology}
-  maxAgents: ${options.runtime.maxAgents}
-  autoScale: true
-  coordinationStrategy: consensus
-
-memory:
-  backend: ${options.runtime.memoryBackend}
-  enableHNSW: ${options.runtime.enableHNSW}
-  persistPath: .claude-flow/data
-  cacheSize: 100
-
-neural:
-  enabled: ${options.runtime.enableNeural}
-  modelPath: .claude-flow/neural
-
-hooks:
-  enabled: true
-  autoExecute: true
-
-mcp:
-  autoStart: ${options.mcp.autoStart}
-  port: ${options.mcp.port}
-`;
-    fs.writeFileSync(configPath, config, 'utf-8');
-    result.created.files.push('.claude-flow/config.yaml');
-    // Write .gitignore
-    const gitignorePath = path.join(targetDir, '.claude-flow', '.gitignore');
-    const gitignore = `# Claude Flow runtime files
-data/
-logs/
-sessions/
-neural/
-*.log
-*.tmp
-`;
-    if (!fs.existsSync(gitignorePath) || options.force) {
-        fs.writeFileSync(gitignorePath, gitignore, 'utf-8');
-        result.created.files.push('.claude-flow/.gitignore');
-    }
-    // Write CAPABILITIES.md with full system overview
-    await writeCapabilitiesDoc(targetDir, options, result);
-}
-/**
- * Write initial metrics files for statusline
- * Creates baseline data so statusline shows meaningful state instead of all zeros
- */
-async function writeInitialMetrics(targetDir, options, result) {
-    const metricsDir = path.join(targetDir, '.claude-flow', 'metrics');
-    const learningDir = path.join(targetDir, '.claude-flow', 'learning');
-    const securityDir = path.join(targetDir, '.claude-flow', 'security');
-    // Ensure directories exist
-    for (const dir of [metricsDir, learningDir, securityDir]) {
-        if (!fs.existsSync(dir)) {
-            fs.mkdirSync(dir, { recursive: true });
-        }
-    }
-    // Create initial v3-progress.json
-    const progressPath = path.join(metricsDir, 'v3-progress.json');
-    if (!fs.existsSync(progressPath) || options.force) {
-        const progress = {
-            version: '3.0.0',
-            initialized: new Date().toISOString(),
-            domains: {
-                completed: 0,
-                total: 5,
-                status: 'INITIALIZING'
-            },
-            ddd: {
-                progress: 0,
-                modules: 0,
-                totalFiles: 0,
-                totalLines: 0
-            },
-            swarm: {
-                activeAgents: 0,
-                maxAgents: options.runtime.maxAgents,
-                topology: options.runtime.topology
-            },
-            learning: {
-                status: 'READY',
-                patternsLearned: 0,
-                sessionsCompleted: 0
-            },
-            _note: 'Metrics will update as you use Claude Flow. Run: npx @sparkleideas/cli@latest daemon start'
-        };
-        fs.writeFileSync(progressPath, JSON.stringify(progress, null, 2), 'utf-8');
-        result.created.files.push('.claude-flow/metrics/v3-progress.json');
-    }
-    // Create initial swarm-activity.json
-    const activityPath = path.join(metricsDir, 'swarm-activity.json');
-    if (!fs.existsSync(activityPath) || options.force) {
-        const activity = {
-            timestamp: new Date().toISOString(),
-            processes: {
-                agentic_flow: 0,
-                mcp_server: 0,
-                estimated_agents: 0
-            },
-            swarm: {
-                active: false,
-                agent_count: 0,
-                coordination_active: false
-            },
-            integration: {
-                agentic_flow_active: false,
-                mcp_active: false
-            },
-            _initialized: true
-        };
-        fs.writeFileSync(activityPath, JSON.stringify(activity, null, 2), 'utf-8');
-        result.created.files.push('.claude-flow/metrics/swarm-activity.json');
-    }
-    // Create initial learning.json
-    const learningPath = path.join(metricsDir, 'learning.json');
-    if (!fs.existsSync(learningPath) || options.force) {
-        const learning = {
-            initialized: new Date().toISOString(),
-            routing: {
-                accuracy: 0,
-                decisions: 0
-            },
-            patterns: {
-                shortTerm: 0,
-                longTerm: 0,
-                quality: 0
-            },
-            sessions: {
-                total: 0,
-                current: null
-            },
-            _note: 'Intelligence grows as you use Claude Flow'
-        };
-        fs.writeFileSync(learningPath, JSON.stringify(learning, null, 2), 'utf-8');
-        result.created.files.push('.claude-flow/metrics/learning.json');
-    }
-    // Create initial audit-status.json
-    const auditPath = path.join(securityDir, 'audit-status.json');
-    if (!fs.existsSync(auditPath) || options.force) {
-        const audit = {
-            initialized: new Date().toISOString(),
-            status: 'PENDING',
-            cvesFixed: 0,
-            totalCves: 3,
-            lastScan: null,
-            _note: 'Run: npx @sparkleideas/cli@latest security scan'
-        };
-        fs.writeFileSync(auditPath, JSON.stringify(audit, null, 2), 'utf-8');
-        result.created.files.push('.claude-flow/security/audit-status.json');
-    }
-}
-/**
- * Write CAPABILITIES.md - comprehensive overview of all Claude Flow features
- */
-async function writeCapabilitiesDoc(targetDir, options, result) {
-    const capabilitiesPath = path.join(targetDir, '.claude-flow', 'CAPABILITIES.md');
-    if (fs.existsSync(capabilitiesPath) && !options.force) {
-        result.skipped.push('.claude-flow/CAPABILITIES.md');
-        return;
-    }
-    const capabilities = `# Claude Flow V3 - Complete Capabilities Reference
-> Generated: ${new Date().toISOString()}
-> Full documentation: https://github.com/ruvnet/claude-flow
-
-## 📋 Table of Contents
-
-1. [Overview](#overview)
-2. [Swarm Orchestration](#swarm-orchestration)
-3. [Available Agents (60+)](#available-agents)
-4. [CLI Commands (26 Commands, 140+ Subcommands)](#cli-commands)
-5. [Hooks System (27 Hooks + 12 Workers)](#hooks-system)
-6. [Memory & Intelligence (RuVector)](#memory--intelligence)
-7. [Hive-Mind Consensus](#hive-mind-consensus)
-8. [Performance Targets](#performance-targets)
-9. [Integration Ecosystem](#integration-ecosystem)
-
----
-
-## Overview
-
-Claude Flow V3 is a domain-driven design architecture for multi-agent AI coordination with:
-
-- **15-Agent Swarm Coordination** with hierarchical and mesh topologies
-- **HNSW Vector Search** - 150x-12,500x faster pattern retrieval
-- **SONA Neural Learning** - Self-optimizing with <0.05ms adaptation
-- **Byzantine Fault Tolerance** - Queen-led consensus mechanisms
-- **MCP Server Integration** - Model Context Protocol support
-
-### Current Configuration
-| Setting | Value |
-|---------|-------|
-| Topology | ${options.runtime.topology} |
-| Max Agents | ${options.runtime.maxAgents} |
-| Memory Backend | ${options.runtime.memoryBackend} |
-| HNSW Indexing | ${options.runtime.enableHNSW ? 'Enabled' : 'Disabled'} |
-| Neural Learning | ${options.runtime.enableNeural ? 'Enabled' : 'Disabled'} |
-
----
-
-## Swarm Orchestration
-
-### Topologies
-| Topology | Description | Best For |
-|----------|-------------|----------|
-| \`hierarchical\` | Queen controls workers directly | Anti-drift, tight control |
-| \`mesh\` | Fully connected peer network | Distributed tasks |
-| \`hierarchical-mesh\` | V3 hybrid (recommended) | 10+ agents |
-| \`ring\` | Circular communication | Sequential workflows |
-| \`star\` | Central coordinator | Simple coordination |
-| \`adaptive\` | Dynamic based on load | Variable workloads |
-
-### Strategies
-- \`balanced\` - Even distribution across agents
-- \`specialized\` - Clear roles, no overlap (anti-drift)
-- \`adaptive\` - Dynamic task routing
-
-### Quick Commands
-\`\`\`bash
-# Initialize swarm
-npx @sparkleideas/cli@latest swarm init --topology hierarchical --max-agents 8 --strategy specialized
-
-# Check status
-npx @sparkleideas/cli@latest swarm status
-
-# Monitor activity
-npx @sparkleideas/cli@latest swarm monitor
-\`\`\`
-
----
-
-## Available Agents
-
-### Core Development (5)
-\`coder\`, \`reviewer\`, \`tester\`, \`planner\`, \`researcher\`
-
-### V3 Specialized (4)
-\`security-architect\`, \`security-auditor\`, \`memory-specialist\`, \`performance-engineer\`
-
-### Swarm Coordination (5)
-\`hierarchical-coordinator\`, \`mesh-coordinator\`, \`adaptive-coordinator\`, \`collective-intelligence-coordinator\`, \`swarm-memory-manager\`
-
-### Consensus & Distributed (7)
-\`byzantine-coordinator\`, \`raft-manager\`, \`gossip-coordinator\`, \`consensus-builder\`, \`crdt-synchronizer\`, \`quorum-manager\`, \`security-manager\`
-
-### Performance & Optimization (5)
-\`perf-analyzer\`, \`performance-benchmarker\`, \`task-orchestrator\`, \`memory-coordinator\`, \`smart-agent\`
-
-### GitHub & Repository (9)
-\`github-modes\`, \`pr-manager\`, \`code-review-swarm\`, \`issue-tracker\`, \`release-manager\`, \`workflow-automation\`, \`project-board-sync\`, \`repo-architect\`, \`multi-repo-swarm\`
-
-### SPARC Methodology (6)
-\`sparc-coord\`, \`sparc-coder\`, \`specification\`, \`pseudocode\`, \`architecture\`, \`refinement\`
-
-### Specialized Development (8)
-\`backend-dev\`, \`mobile-dev\`, \`ml-developer\`, \`cicd-engineer\`, \`api-docs\`, \`system-architect\`, \`code-analyzer\`, \`base-template-generator\`
-
-### Testing & Validation (2)
-\`tdd-london-swarm\`, \`production-validator\`
-
-### Agent Routing by Task
-| Task Type | Recommended Agents | Topology |
-|-----------|-------------------|----------|
-| Bug Fix | researcher, coder, tester | mesh |
-| New Feature | coordinator, architect, coder, tester, reviewer | hierarchical |
-| Refactoring | architect, coder, reviewer | mesh |
-| Performance | researcher, perf-engineer, coder | hierarchical |
-| Security | security-architect, auditor, reviewer | hierarchical |
-| Docs | researcher, api-docs | mesh |
-
----
-
-## CLI Commands
-
-### Core Commands (12)
-| Command | Subcommands | Description |
-|---------|-------------|-------------|
-| \`init\` | 4 | Project initialization |
-| \`agent\` | 8 | Agent lifecycle management |
-| \`swarm\` | 6 | Multi-agent coordination |
-| \`memory\` | 11 | AgentDB with HNSW search |
-| \`mcp\` | 9 | MCP server management |
-| \`task\` | 6 | Task assignment |
-| \`session\` | 7 | Session persistence |
-| \`config\` | 7 | Configuration |
-| \`status\` | 3 | System monitoring |
-| \`workflow\` | 6 | Workflow templates |
-| \`hooks\` | 17 | Self-learning hooks |
-| \`hive-mind\` | 6 | Consensus coordination |
-
-### Advanced Commands (14)
-| Command | Subcommands | Description |
-|---------|-------------|-------------|
-| \`daemon\` | 5 | Background workers |
-| \`neural\` | 5 | Pattern training |
-| \`security\` | 6 | Security scanning |
-| \`performance\` | 5 | Profiling & benchmarks |
-| \`providers\` | 5 | AI provider config |
-| \`plugins\` | 5 | Plugin management |
-| \`deployment\` | 5 | Deploy management |
-| \`embeddings\` | 4 | Vector embeddings |
-| \`claims\` | 4 | Authorization |
-| \`migrate\` | 5 | V2→V3 migration |
-| \`process\` | 4 | Process management |
-| \`doctor\` | 1 | Health diagnostics |
-| \`completions\` | 4 | Shell completions |
-
-### Example Commands
-\`\`\`bash
-# Initialize
-npx @sparkleideas/cli@latest init --wizard
-
-# Spawn agent
-npx @sparkleideas/cli@latest agent spawn -t coder --name my-coder
-
-# Memory operations
-npx @sparkleideas/cli@latest memory store --key "pattern" --value "data" --namespace patterns
-npx @sparkleideas/cli@latest memory search --query "authentication"
-
-# Diagnostics
-npx @sparkleideas/cli@latest doctor --fix
-\`\`\`
-
----
-
-## Hooks System
-
-### 27 Available Hooks
-
-#### Core Hooks (6)
-| Hook | Description |
-|------|-------------|
-| \`pre-edit\` | Context before file edits |
-| \`post-edit\` | Record edit outcomes |
-| \`pre-command\` | Risk assessment |
-| \`post-command\` | Command metrics |
-| \`pre-task\` | Task start + agent suggestions |
-| \`post-task\` | Task completion learning |
-
-#### Session Hooks (4)
-| Hook | Description |
-|------|-------------|
-| \`session-start\` | Start/restore session |
-| \`session-end\` | Persist state |
-| \`session-restore\` | Restore previous |
-| \`notify\` | Cross-agent notifications |
-
-#### Intelligence Hooks (5)
-| Hook | Description |
-|------|-------------|
-| \`route\` | Optimal agent routing |
-| \`explain\` | Routing decisions |
-| \`pretrain\` | Bootstrap intelligence |
-| \`build-agents\` | Generate configs |
-| \`transfer\` | Pattern transfer |
-
-#### Coverage Hooks (3)
-| Hook | Description |
-|------|-------------|
-| \`coverage-route\` | Coverage-based routing |
-| \`coverage-suggest\` | Improvement suggestions |
-| \`coverage-gaps\` | Gap analysis |
-
-### 12 Background Workers
-| Worker | Priority | Purpose |
-|--------|----------|---------|
-| \`ultralearn\` | normal | Deep knowledge |
-| \`optimize\` | high | Performance |
-| \`consolidate\` | low | Memory consolidation |
-| \`predict\` | normal | Predictive preload |
-| \`audit\` | critical | Security |
-| \`map\` | normal | Codebase mapping |
-| \`preload\` | low | Resource preload |
-| \`deepdive\` | normal | Deep analysis |
-| \`document\` | normal | Auto-docs |
-| \`refactor\` | normal | Suggestions |
-| \`benchmark\` | normal | Benchmarking |
-| \`testgaps\` | normal | Coverage gaps |
-
----
-
-## Memory & Intelligence
-
-### RuVector Intelligence System
-- **SONA**: Self-Optimizing Neural Architecture (<0.05ms)
-- **MoE**: Mixture of Experts routing
-- **HNSW**: 150x-12,500x faster search
-- **EWC++**: Prevents catastrophic forgetting
-- **Flash Attention**: 2.49x-7.47x speedup
-- **Int8 Quantization**: 3.92x memory reduction
-
-### 4-Step Intelligence Pipeline
-1. **RETRIEVE** - HNSW pattern search
-2. **JUDGE** - Success/failure verdicts
-3. **DISTILL** - LoRA learning extraction
-4. **CONSOLIDATE** - EWC++ preservation
-
-### Memory Commands
-\`\`\`bash
-# Store pattern
-npx @sparkleideas/cli@latest memory store --key "name" --value "data" --namespace patterns
-
-# Semantic search
-npx @sparkleideas/cli@latest memory search --query "authentication"
-
-# List entries
-npx @sparkleideas/cli@latest memory list --namespace patterns
-
-# Initialize database
-npx @sparkleideas/cli@latest memory init --force
-\`\`\`
-
----
-
-## Hive-Mind Consensus
-
-### Queen Types
-| Type | Role |
-|------|------|
-| Strategic Queen | Long-term planning |
-| Tactical Queen | Execution coordination |
-| Adaptive Queen | Dynamic optimization |
-
-### Worker Types (8)
-\`researcher\`, \`coder\`, \`analyst\`, \`tester\`, \`architect\`, \`reviewer\`, \`optimizer\`, \`documenter\`
-
-### Consensus Mechanisms
-| Mechanism | Fault Tolerance | Use Case |
-|-----------|-----------------|----------|
-| \`byzantine\` | f < n/3 faulty | Adversarial |
-| \`raft\` | f < n/2 failed | Leader-based |
-| \`gossip\` | Eventually consistent | Large scale |
-| \`crdt\` | Conflict-free | Distributed |
-| \`quorum\` | Configurable | Flexible |
-
-### Hive-Mind Commands
-\`\`\`bash
-# Initialize
-npx @sparkleideas/cli@latest hive-mind init --queen-type strategic
-
-# Status
-npx @sparkleideas/cli@latest hive-mind status
-
-# Spawn workers
-npx @sparkleideas/cli@latest hive-mind spawn --count 5 --type worker
-
-# Consensus
-npx @sparkleideas/cli@latest hive-mind consensus --propose "task"
-\`\`\`
-
----
-
-## Performance Targets
-
-| Metric | Target | Status |
-|--------|--------|--------|
-| HNSW Search | 150x-12,500x faster | ✅ Implemented |
-| Memory Reduction | 50-75% | ✅ Implemented (3.92x) |
-| SONA Integration | Pattern learning | ✅ Implemented |
-| Flash Attention | 2.49x-7.47x | 🔄 In Progress |
-| MCP Response | <100ms | ✅ Achieved |
-| CLI Startup | <500ms | ✅ Achieved |
-| SONA Adaptation | <0.05ms | 🔄 In Progress |
-
----
-
-## Integration Ecosystem
-
-### Integrated Packages
-| Package | Version | Purpose |
-|---------|---------|---------|
-| agentic-flow | 2.0.1-alpha | Core coordination |
-| agentdb | 2.0.0-alpha.3.4 | Vector database |
-| @ruvector/attention | 0.1.3 | Flash attention |
-| @ruvector/sona | 0.1.5 | Neural learning |
-
-### Optional Integrations
-| Package | Command |
-|---------|---------|
-| ruv-swarm | \`npx ruv-swarm mcp start\` |
-| flow-nexus | \`npx flow-nexus@latest mcp start\` |
-| agentic-jujutsu | \`npx agentic-jujutsu@latest\` |
-
-### MCP Server Setup
-\`\`\`bash
-# Add Claude Flow MCP
-claude mcp add claude-flow -- npx -y @sparkleideas/cli@latest
-
-# Optional servers
-claude mcp add ruv-swarm -- npx -y ruv-swarm mcp start
-claude mcp add flow-nexus -- npx -y flow-nexus@latest mcp start
-\`\`\`
-
----
-
-## Quick Reference
-
-### Essential Commands
-\`\`\`bash
-# Setup
-npx @sparkleideas/cli@latest init --wizard
-npx @sparkleideas/cli@latest daemon start
-npx @sparkleideas/cli@latest doctor --fix
-
-# Swarm
-npx @sparkleideas/cli@latest swarm init --topology hierarchical --max-agents 8
-npx @sparkleideas/cli@latest swarm status
-
-# Agents
-npx @sparkleideas/cli@latest agent spawn -t coder
-npx @sparkleideas/cli@latest agent list
-
-# Memory
-npx @sparkleideas/cli@latest memory search --query "patterns"
-
-# Hooks
-npx @sparkleideas/cli@latest hooks pre-task --description "task"
-npx @sparkleideas/cli@latest hooks worker dispatch --trigger optimize
-\`\`\`
-
-### File Structure
-\`\`\`
-.claude-flow/
-├── config.yaml      # Runtime configuration
-├── CAPABILITIES.md  # This file
-├── data/            # Memory storage
-├── logs/            # Operation logs
-├── sessions/        # Session state
-├── hooks/           # Custom hooks
-├── agents/          # Agent configs
-└── workflows/       # Workflow templates
-\`\`\`
-
----
-
-**Full Documentation**: https://github.com/ruvnet/claude-flow
-**Issues**: https://github.com/ruvnet/claude-flow/issues
-`;
-    fs.writeFileSync(capabilitiesPath, capabilities, 'utf-8');
-    result.created.files.push('.claude-flow/CAPABILITIES.md');
-}
-/**
- * Write CLAUDE.md with swarm guidance
- */
-async function writeClaudeMd(targetDir, options, result) {
-    const claudeMdPath = path.join(targetDir, 'CLAUDE.md');
-    if (fs.existsSync(claudeMdPath) && !options.force) {
-        result.skipped.push('CLAUDE.md');
-        return;
-    }
-    // Determine template: explicit option > infer from components > 'standard'
-    const inferredTemplate = (!options.components.commands && !options.components.agents) ? 'minimal' : undefined;
-    const content = generateClaudeMd(options, inferredTemplate);
-    fs.writeFileSync(claudeMdPath, content, 'utf-8');
-    result.created.files.push('CLAUDE.md');
-}
-/**
- * Find source directory for skills/commands/agents
- */
-function findSourceDir(type, sourceBaseDir) {
-    // Build list of possible paths to check
-    const possiblePaths = [];
-    // If explicit source base directory is provided, use it first
-    if (sourceBaseDir) {
-        possiblePaths.push(path.join(sourceBaseDir, '.claude', type));
-    }
-    // IMPORTANT: Check the package's own .claude directory first
-    // This is the primary path when running as an npm package
-    // __dirname is typically /path/to/node_modules/@sparkleideas/cli/dist/src/init
-    // We need to go up 3 levels to reach the package root (dist/src/init -> dist/src -> dist -> root)
-    const packageRoot = path.resolve(__dirname, '..', '..', '..');
-    const packageDotClaude = path.join(packageRoot, '.claude', type);
-    if (fs.existsSync(packageDotClaude)) {
-        possiblePaths.unshift(packageDotClaude); // Add to beginning (highest priority)
-    }
-    // From dist/src/init -> go up to project root
-    const distPath = __dirname;
-    // Try to find the project root by looking for .claude directory
-    let currentDir = distPath;
-    for (let i = 0; i < 10; i++) {
-        const parentDir = path.dirname(currentDir);
-        const dotClaudePath = path.join(parentDir, '.claude', type);
-        if (fs.existsSync(dotClaudePath)) {
-            possiblePaths.push(dotClaudePath);
-        }
-        currentDir = parentDir;
-    }
-    // Also check relative to process.cwd() for development
-    const cwdBased = [
-        path.join(process.cwd(), '.claude', type),
-        path.join(process.cwd(), '..', '.claude', type),
-        path.join(process.cwd(), '..', '..', '.claude', type),
-    ];
-    possiblePaths.push(...cwdBased);
-    // Check v2 directory for agents
-    if (type === 'agents') {
-        possiblePaths.push(path.join(process.cwd(), 'v2', '.claude', type), path.join(process.cwd(), '..', 'v2', '.claude', type));
-    }
-    // Plugin directory
-    possiblePaths.push(path.join(process.cwd(), 'plugin', type), path.join(process.cwd(), '..', 'plugin', type));
-    for (const p of possiblePaths) {
-        if (fs.existsSync(p)) {
-            return p;
-        }
-    }
-    return null;
-}
-/**
- * Copy directory recursively
- */
-function copyDirRecursive(src, dest) {
-    fs.mkdirSync(dest, { recursive: true });
-    const entries = fs.readdirSync(src, { withFileTypes: true });
-    for (const entry of entries) {
-        const srcPath = path.join(src, entry.name);
-        const destPath = path.join(dest, entry.name);
-        if (entry.isDirectory()) {
-            copyDirRecursive(srcPath, destPath);
-        }
-        else {
-            fs.copyFileSync(srcPath, destPath);
-        }
-    }
-}
-/**
- * Count files with extension in directory
- */
-function countFiles(dir, ext) {
-    let count = 0;
-    const entries = fs.readdirSync(dir, { withFileTypes: true });
-    for (const entry of entries) {
-        const fullPath = path.join(dir, entry.name);
-        if (entry.isDirectory()) {
-            count += countFiles(fullPath, ext);
-        }
-        else if (entry.name.endsWith(ext)) {
-            count++;
-        }
-    }
-    return count;
-}
-/**
- * Count enabled hooks
- */
-function countEnabledHooks(options) {
-    const hooks = options.hooks;
-    let count = 0;
-    if (hooks.preToolUse)
-        count++;
-    if (hooks.postToolUse)
-        count++;
-    if (hooks.userPromptSubmit)
-        count++;
-    if (hooks.sessionStart)
-        count++;
-    if (hooks.stop)
-        count++;
-    if (hooks.notification)
-        count++;
-    return count;
-}
-export default executeInit;
-//# sourceMappingURL=executor.js.map