kynjal-cli 4.0.0 → 4.0.1

package/dist/src/init/executor.js

@@ -2,70 +2,14 @@
  * Init Executor
  * Main execution logic for V3 initialization
  */
-var __assign = (this && this.__assign) || function () {
-    __assign = Object.assign || function(t) {
-        for (var s, i = 1, n = arguments.length; i < n; i++) {
-            s = arguments[i];
-            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
-                t[p] = s[p];
-        }
-        return t;
-    };
-    return __assign.apply(this, arguments);
-};
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
-    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
-        if (ar || !(i in from)) {
-            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
-            ar[i] = from[i];
-        }
-    }
-    return to.concat(ar || Array.prototype.slice.call(from));
-};
 import * as fs from 'fs';
 import * as path from 'path';
 import { fileURLToPath } from 'url';
 import { createRequire } from 'module';
 import { dirname } from 'path';
 // ESM-compatible __dirname
-var __filename = fileURLToPath(import.meta.url);
-var __dirname = dirname(__filename);
+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';
@@ -75,7 +19,7 @@ import { generateClaudeMd } from './claudemd-generator.js';
 /**
  * Skills to copy based on configuration
  */
-var SKILLS_MAP = {
+const SKILLS_MAP = {
     core: [
         'swarm-orchestration',
         'swarm-advanced',
@@ -86,8 +30,8 @@ var SKILLS_MAP = {
         'stream-chain',
         'skill-builder',
     ],
-    browser: ['browser'],
-    dualMode: ['dual-mode'],
+    browser: ['browser'], // agent-browser integration
+    dualMode: ['dual-mode'], // Claude Code + Codex hybrid execution
     agentdb: [
         'agentdb-advanced',
         'agentdb-learning',
@@ -120,12 +64,12 @@ var SKILLS_MAP = {
         'v3-performance-optimization',
         'v3-security-overhaul',
         'v3-swarm-coordination',
-    ]
+    ],
 };
 /**
  * Commands to copy based on configuration
  */
-var COMMANDS_MAP = {
+const COMMANDS_MAP = {
     core: ['claude-flow-help.md', 'claude-flow-swarm.md', 'claude-flow-memory.md'],
     analysis: ['analysis'],
     automation: ['automation'],
@@ -133,20 +77,20 @@ var COMMANDS_MAP = {
     hooks: ['hooks'],
     monitoring: ['monitoring'],
     optimization: ['optimization'],
-    sparc: ['sparc']
+    sparc: ['sparc'],
 };
 /**
  * Agents to copy based on configuration
  */
-var AGENTS_MAP = {
+const AGENTS_MAP = {
     core: ['core'],
     consensus: ['consensus'],
     github: ['github'],
     hiveMind: ['hive-mind'],
     sparc: ['sparc'],
     swarm: ['swarm'],
-    browser: ['browser'],
-    dualMode: ['dual-mode'],
+    browser: ['browser'], // agent-browser integration
+    dualMode: ['dual-mode'], // Claude Code + Codex hybrid execution
     // V3-specific agents
     v3: ['v3'],
     optimization: ['optimization'],
@@ -165,12 +109,12 @@ var AGENTS_MAP = {
     payments: ['payments'],
     data: ['data'],
     design: ['design'],
-    custom: ['custom']
+    custom: ['custom'],
 };
 /**
  * Directory structure to create
  */
-var DIRECTORIES = {
+const DIRECTORIES = {
     claude: [
         '.claude',
         '.claude/skills',
@@ -186,115 +130,82 @@ var DIRECTORIES = {
         '.claude-flow/hooks',
         '.claude-flow/agents',
         '.claude-flow/workflows',
-    ]
+    ],
 };
 /**
  * Execute initialization
  */
-export function executeInit(options) {
-    return __awaiter(this, void 0, Promise, function () {
-        var platform, result, targetDir, error_1;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    platform = detectPlatform();
-                    result = {
-                        success: true,
-                        platform: platform,
-                        created: {
-                            directories: [],
-                            files: []
-                        },
-                        skipped: [],
-                        errors: [],
-                        summary: {
-                            skillsCount: 0,
-                            commandsCount: 0,
-                            agentsCount: 0,
-                            hooksEnabled: 0
-                        }
-                    };
-                    targetDir = options.targetDir;
-                    _a.label = 1;
-                case 1:
-                    _a.trys.push([1, 23, , 24]);
-                    // Create directory structure
-                    return [4 /*yield*/, createDirectories(targetDir, options, result)];
-                case 2:
-                    // Create directory structure
-                    _a.sent();
-                    if (!options.components.settings) return [3 /*break*/, 4];
-                    return [4 /*yield*/, writeSettings(targetDir, options, result)];
-                case 3:
-                    _a.sent();
-                    _a.label = 4;
-                case 4:
-                    if (!options.components.mcp) return [3 /*break*/, 6];
-                    return [4 /*yield*/, writeMCPConfig(targetDir, options, result)];
-                case 5:
-                    _a.sent();
-                    _a.label = 6;
-                case 6:
-                    if (!options.components.skills) return [3 /*break*/, 8];
-                    return [4 /*yield*/, copySkills(targetDir, options, result)];
-                case 7:
-                    _a.sent();
-                    _a.label = 8;
-                case 8:
-                    if (!options.components.commands) return [3 /*break*/, 10];
-                    return [4 /*yield*/, copyCommands(targetDir, options, result)];
-                case 9:
-                    _a.sent();
-                    _a.label = 10;
-                case 10:
-                    if (!options.components.agents) return [3 /*break*/, 12];
-                    return [4 /*yield*/, copyAgents(targetDir, options, result)];
-                case 11:
-                    _a.sent();
-                    _a.label = 12;
-                case 12:
-                    if (!options.components.helpers) return [3 /*break*/, 14];
-                    return [4 /*yield*/, writeHelpers(targetDir, options, result)];
-                case 13:
-                    _a.sent();
-                    _a.label = 14;
-                case 14:
-                    if (!options.components.statusline) return [3 /*break*/, 16];
-                    return [4 /*yield*/, writeStatusline(targetDir, options, result)];
-                case 15:
-                    _a.sent();
-                    _a.label = 16;
-                case 16:
-                    if (!options.components.runtime) return [3 /*break*/, 18];
-                    return [4 /*yield*/, writeRuntimeConfig(targetDir, options, result)];
-                case 17:
-                    _a.sent();
-                    _a.label = 18;
-                case 18:
-                    if (!options.components.statusline) return [3 /*break*/, 20];
-                    return [4 /*yield*/, writeInitialMetrics(targetDir, options, result)];
-                case 19:
-                    _a.sent();
-                    _a.label = 20;
-                case 20:
-                    if (!options.components.claudeMd) return [3 /*break*/, 22];
-                    return [4 /*yield*/, writeClaudeMd(targetDir, options, result)];
-                case 21:
-                    _a.sent();
-                    _a.label = 22;
-                case 22:
-                    // Count enabled hooks
-                    result.summary.hooksEnabled = countEnabledHooks(options);
-                    return [3 /*break*/, 24];
-                case 23:
-                    error_1 = _a.sent();
-                    result.success = false;
-                    result.errors.push(error_1 instanceof Error ? error_1.message : String(error_1));
-                    return [3 /*break*/, 24];
-                case 24: return [2 /*return*/, result];
-            }
-        });
-    });
+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
@@ -302,10 +213,9 @@ export function executeInit(options) {
  * Uses platform-specific commands for Mac, Linux, and Windows
  */
 function mergeSettingsForUpgrade(existing) {
-    var _a, _b, _c;
-    var merged = __assign({}, existing);
-    var platform = detectPlatform();
-    var isWindows = platform.os === 'windows';
+    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
@@ -313,46 +223,51 @@ function mergeSettingsForUpgrade(existing) {
     // TeammateIdle/TaskCompleted are not valid Claude Code hook events and caused warnings.
     // Agent Teams hook config lives in claudeFlow.agentTeams.hooks instead.
     // 1. Merge env vars (preserve existing, add new)
-    var existingEnv = existing.env || {};
-    merged.env = __assign(__assign({}, 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' });
+    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 + auto-memory hooks)
-    var existingHooks = existing.hooks || {};
-    merged.hooks = __assign({}, existingHooks);
+    const existingHooks = existing.hooks || {};
+    merged.hooks = { ...existingHooks };
     // Cross-platform auto-memory hook commands that resolve paths via git root.
     // Uses node -e with git rev-parse so hooks work regardless of CWD (#1259, #1284).
-    var gitRootResolver = "var c=require('child_process'),p=require('path'),u=require('url'),r;"
+    const gitRootResolver = "var c=require('child_process'),p=require('path'),u=require('url'),r;"
         + "try{r=c.execSync('git rev-parse --show-toplevel',{encoding:'utf8'}).trim()}"
         + 'catch(e){r=process.cwd()}';
-    var autoMemoryScript = '.claude/helpers/auto-memory-hook.mjs';
-    var autoMemoryImportCmd = "node -e \"" + gitRootResolver + "var f=p.join(r,'" + autoMemoryScript + "');import(u.pathToFileURL(f).href)\" import";
-    var autoMemorySyncCmd = "node -e \"" + gitRootResolver + "var f=p.join(r,'" + autoMemoryScript + "');import(u.pathToFileURL(f).href)\" sync";
+    const autoMemoryScript = '.claude/helpers/auto-memory-hook.mjs';
+    const autoMemoryImportCmd = `node -e "${gitRootResolver}var f=p.join(r,'${autoMemoryScript}');import(u.pathToFileURL(f).href)" import`;
+    const autoMemorySyncCmd = `node -e "${gitRootResolver}var f=p.join(r,'${autoMemoryScript}');import(u.pathToFileURL(f).href)" sync`;
     // Add auto-memory import to SessionStart (if not already present)
-    var sessionStartHooks = existingHooks.SessionStart;
-    var hasAutoMemoryImport = sessionStartHooks === null || sessionStartHooks === void 0 ? void 0 : sessionStartHooks.some(function (group) { var _a; return (_a = group.hooks) === null || _a === void 0 ? void 0 : _a.some(function (h) { var _a; return (_a = h.command) === null || _a === void 0 ? void 0 : _a.includes('auto-memory-hook'); }); });
+    const sessionStartHooks = existingHooks.SessionStart;
+    const hasAutoMemoryImport = sessionStartHooks?.some(group => group.hooks?.some(h => h.command?.includes('auto-memory-hook')));
     if (!hasAutoMemoryImport) {
-        var startHooks = merged.hooks;
+        const startHooks = merged.hooks;
         if (!startHooks.SessionStart) {
             startHooks.SessionStart = [{ hooks: [] }];
         }
-        var startGroup = startHooks.SessionStart[0];
+        const startGroup = startHooks.SessionStart[0];
         if (!startGroup.hooks)
             startGroup.hooks = [];
         startGroup.hooks.push({
             type: 'command',
             command: autoMemoryImportCmd,
             timeout: 6000,
-            continueOnError: true
+            continueOnError: true,
         });
     }
     // Add auto-memory sync to SessionEnd (if not already present)
-    var sessionEndHooks = existingHooks.SessionEnd;
-    var hasAutoMemorySync = sessionEndHooks === null || sessionEndHooks === void 0 ? void 0 : sessionEndHooks.some(function (group) { var _a; return (_a = group.hooks) === null || _a === void 0 ? void 0 : _a.some(function (h) { var _a; return (_a = h.command) === null || _a === void 0 ? void 0 : _a.includes('auto-memory-hook'); }); });
+    const sessionEndHooks = existingHooks.SessionEnd;
+    const hasAutoMemorySync = sessionEndHooks?.some(group => group.hooks?.some(h => h.command?.includes('auto-memory-hook')));
     if (!hasAutoMemorySync) {
-        var endHooks = merged.hooks;
+        const endHooks = merged.hooks;
         if (!endHooks.SessionEnd) {
             endHooks.SessionEnd = [{ hooks: [] }];
         }
-        var endGroup = endHooks.SessionEnd[0];
+        const endGroup = endHooks.SessionEnd[0];
         if (!endGroup.hooks)
             endGroup.hooks = [];
         // Insert at beginning so sync runs before other cleanup
@@ -360,7 +275,7 @@ function mergeSettingsForUpgrade(existing) {
             type: 'command',
             command: autoMemorySyncCmd,
             timeout: 8000,
-            continueOnError: true
+            continueOnError: true,
         });
     }
     // NOTE: TeammateIdle and TaskCompleted are NOT valid Claude Code hook events.
@@ -371,17 +286,22 @@ function mergeSettingsForUpgrade(existing) {
     // Their configuration lives in claudeFlow.agentTeams.hooks instead.
     // 3. Fix statusLine config (remove invalid fields, ensure correct format)
     // Claude Code only supports: type, command, padding
-    var existingStatusLine = existing.statusLine;
+    const existingStatusLine = existing.statusLine;
     if (existingStatusLine) {
         merged.statusLine = {
             type: 'command',
-            command: existingStatusLine.command || "node -e \"var c=require('child_process'),p=require('path'),r;try{r=c.execSync('git rev-parse --show-toplevel',{encoding:'utf8'}).trim()}catch(e){r=process.cwd()}var s=p.join(r,'.claude/helpers/statusline.cjs');process.argv.splice(1,0,s);require(s)\""
+            command: existingStatusLine.command || `node -e "var c=require('child_process'),p=require('path'),r;try{r=c.execSync('git rev-parse --show-toplevel',{encoding:'utf8'}).trim()}catch(e){r=process.cwd()}var s=p.join(r,'.claude/helpers/statusline.cjs');process.argv.splice(1,0,s);require(s)"`,
+            // Remove invalid fields: refreshMs, enabled (not supported by Claude Code)
         };
     }
     // 4. Merge claudeFlow settings (preserve existing, add agentTeams + memory)
-    var existingClaudeFlow = existing.claudeFlow || {};
-    var existingMemory = existingClaudeFlow.memory || {};
-    merged.claudeFlow = __assign(__assign({}, existingClaudeFlow), { version: existingClaudeFlow.version || '3.0.0', enabled: existingClaudeFlow.enabled !== false, agentTeams: {
+    const existingClaudeFlow = existing.claudeFlow || {};
+    const existingMemory = existingClaudeFlow.memory || {};
+    merged.claudeFlow = {
+        ...existingClaudeFlow,
+        version: existingClaudeFlow.version || '3.0.0',
+        enabled: existingClaudeFlow.enabled !== false,
+        agentTeams: {
             enabled: true,
             teammateMode: 'auto',
             taskListEnabled: true,
@@ -390,13 +310,20 @@ function mergeSettingsForUpgrade(existing) {
                 autoAssignOnIdle: true,
                 trainPatternsOnComplete: true,
                 notifyLeadOnComplete: true,
-                sharedMemoryNamespace: 'agent-teams'
+                sharedMemoryNamespace: 'agent-teams',
             },
             hooks: {
                 teammateIdle: { enabled: true, autoAssign: true, checkTaskList: true },
-                taskCompleted: { enabled: true, trainPatterns: true, notifyLead: true }
-            }
-        }, memory: __assign(__assign({}, existingMemory), { learningBridge: (_a = existingMemory.learningBridge) !== null && _a !== void 0 ? _a : { enabled: true }, memoryGraph: (_b = existingMemory.memoryGraph) !== null && _b !== void 0 ? _b : { enabled: true }, agentScopes: (_c = existingMemory.agentScopes) !== null && _c !== void 0 ? _c : { enabled: true } }) });
+                taskCompleted: { enabled: true, trainPatterns: true, notifyLead: true },
+            },
+        },
+        memory: {
+            ...existingMemory,
+            learningBridge: existingMemory.learningBridge ?? { enabled: true },
+            memoryGraph: existingMemory.memoryGraph ?? { enabled: true },
+            agentScopes: existingMemory.agentScopes ?? { enabled: true },
+        },
+    };
     return merged;
 }
 /**
@@ -405,190 +332,200 @@ function mergeSettingsForUpgrade(existing) {
  * @param targetDir - Target directory
  * @param upgradeSettings - If true, merge new settings into existing settings.json
  */
-export function executeUpgrade(targetDir, upgradeSettings) {
-    if (upgradeSettings === void 0) { upgradeSettings = false; }
-    return __awaiter(this, void 0, Promise, function () {
-        var result, dirs, _i, dirs_1, dir, fullPath, sourceHelpersForUpgrade, criticalHelpers, _a, criticalHelpers_1, helperName, targetPath, sourcePath, generatedCritical, _b, _c, _d, helperName, content, targetPath, statuslinePath, upgradeOptions, statuslineContent, metricsDir, securityDir, progressPath, progress, activityPath, activity, learningPath, learning, auditPath, audit, settingsPath, existingSettings, mergedSettings, defaultSettings;
-        return __generator(this, function (_e) {
-            result = {
-                success: true,
-                updated: [],
-                created: [],
-                preserved: [],
-                errors: [],
-                settingsUpdated: []
-            };
-            try {
-                dirs = [
-                    '.claude/helpers',
-                    '.claude-flow/metrics',
-                    '.claude-flow/security',
-                    '.claude-flow/learning',
-                ];
-                for (_i = 0, dirs_1 = dirs; _i < dirs_1.length; _i++) {
-                    dir = dirs_1[_i];
-                    fullPath = path.join(targetDir, dir);
-                    if (!fs.existsSync(fullPath)) {
-                        fs.mkdirSync(fullPath, { recursive: true });
+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 });
+            }
+        }
+        // 0. ALWAYS update critical helpers (force overwrite)
+        const sourceHelpersForUpgrade = findSourceHelpersDir();
+        if (sourceHelpersForUpgrade) {
+            const criticalHelpers = ['auto-memory-hook.mjs', 'hook-handler.cjs', 'intelligence.cjs'];
+            for (const helperName of criticalHelpers) {
+                const targetPath = path.join(targetDir, '.claude', 'helpers', helperName);
+                const sourcePath = path.join(sourceHelpersForUpgrade, helperName);
+                if (fs.existsSync(sourcePath)) {
+                    if (fs.existsSync(targetPath)) {
+                        result.updated.push(`.claude/helpers/${helperName}`);
                     }
-                }
-                sourceHelpersForUpgrade = findSourceHelpersDir();
-                if (sourceHelpersForUpgrade) {
-                    criticalHelpers = ['auto-memory-hook.mjs', 'hook-handler.cjs', 'intelligence.cjs'];
-                    for (_a = 0, criticalHelpers_1 = criticalHelpers; _a < criticalHelpers_1.length; _a++) {
-                        helperName = criticalHelpers_1[_a];
-                        targetPath = path.join(targetDir, '.claude', 'helpers', helperName);
-                        sourcePath = path.join(sourceHelpersForUpgrade, helperName);
-                        if (fs.existsSync(sourcePath)) {
-                            if (fs.existsSync(targetPath)) {
-                                result.updated.push(".claude/helpers/" + helperName);
-                            }
-                            else {
-                                result.created.push(".claude/helpers/" + helperName);
-                            }
-                            fs.copyFileSync(sourcePath, targetPath);
-                            try {
-                                fs.chmodSync(targetPath, '755');
-                            }
-                            catch (_f) { }
-                        }
+                    else {
+                        result.created.push(`.claude/helpers/${helperName}`);
                     }
-                }
-                else {
-                    generatedCritical = {
-                        'hook-handler.cjs': generateHookHandler(),
-                        'intelligence.cjs': generateIntelligenceStub(),
-                        'auto-memory-hook.mjs': generateAutoMemoryHook()
-                    };
-                    for (_b = 0, _c = Object.entries(generatedCritical); _b < _c.length; _b++) {
-                        _d = _c[_b], helperName = _d[0], content = _d[1];
-                        targetPath = path.join(targetDir, '.claude', 'helpers', helperName);
-                        if (fs.existsSync(targetPath)) {
-                            result.updated.push(".claude/helpers/" + helperName);
-                        }
-                        else {
-                            result.created.push(".claude/helpers/" + helperName);
-                        }
-                        fs.writeFileSync(targetPath, content, 'utf-8');
-                        try {
-                            fs.chmodSync(targetPath, '755');
-                        }
-                        catch (_g) { }
+                    fs.copyFileSync(sourcePath, targetPath);
+                    try {
+                        fs.chmodSync(targetPath, '755');
                     }
+                    catch { }
                 }
-                statuslinePath = path.join(targetDir, '.claude', 'helpers', 'statusline.cjs');
-                upgradeOptions = __assign(__assign({}, DEFAULT_INIT_OPTIONS), { targetDir: targetDir, force: true, statusline: __assign(__assign({}, DEFAULT_INIT_OPTIONS.statusline), { refreshInterval: 5000 }) });
-                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');
-                metricsDir = path.join(targetDir, '.claude-flow', 'metrics');
-                securityDir = path.join(targetDir, '.claude-flow', 'security');
-                progressPath = path.join(metricsDir, 'v3-progress.json');
-                if (!fs.existsSync(progressPath)) {
-                    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 Ruflo'
-                    };
-                    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');
-                }
-                activityPath = path.join(metricsDir, 'swarm-activity.json');
-                if (!fs.existsSync(activityPath)) {
-                    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');
-                }
-                learningPath = path.join(metricsDir, 'learning.json');
-                if (!fs.existsSync(learningPath)) {
-                    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 Ruflo'
-                    };
-                    fs.writeFileSync(learningPath, JSON.stringify(learning, null, 2), 'utf-8');
-                    result.created.push('.claude-flow/metrics/learning.json');
+            }
+        }
+        else {
+            // Source not found (npx with broken paths) — use generated fallbacks
+            const generatedCritical = {
+                'hook-handler.cjs': generateHookHandler(),
+                'intelligence.cjs': generateIntelligenceStub(),
+                'auto-memory-hook.mjs': generateAutoMemoryHook(),
+            };
+            for (const [helperName, content] of Object.entries(generatedCritical)) {
+                const targetPath = path.join(targetDir, '.claude', 'helpers', helperName);
+                if (fs.existsSync(targetPath)) {
+                    result.updated.push(`.claude/helpers/${helperName}`);
                 }
                 else {
-                    result.preserved.push('.claude-flow/metrics/learning.json');
+                    result.created.push(`.claude/helpers/${helperName}`);
                 }
-                auditPath = path.join(securityDir, 'audit-status.json');
-                if (!fs.existsSync(auditPath)) {
-                    audit = {
-                        initialized: new Date().toISOString(),
-                        status: 'PENDING',
-                        cvesFixed: 0,
-                        totalCves: 3,
-                        lastScan: null,
-                        _note: 'Run: npx @claude-flow/cli@latest security scan'
-                    };
-                    fs.writeFileSync(auditPath, JSON.stringify(audit, null, 2), 'utf-8');
-                    result.created.push('.claude-flow/security/audit-status.json');
+                fs.writeFileSync(targetPath, content, 'utf-8');
+                try {
+                    fs.chmodSync(targetPath, '755');
                 }
-                else {
-                    result.preserved.push('.claude-flow/security/audit-status.json');
+                catch { }
+            }
+        }
+        // 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 Ruflo'
+            };
+            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 Ruflo'
+            };
+            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 @claude-flow/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.SessionStart (auto-memory import)',
+                        'hooks.SessionEnd (auto-memory sync)',
+                        'hooks.TeammateIdle (removed — not a valid Claude Code hook)',
+                        'hooks.TaskCompleted (removed — not a valid Claude Code hook)',
+                        'claudeFlow.agentTeams',
+                        'claudeFlow.memory (learningBridge, memoryGraph, agentScopes)',
+                    ];
                 }
-                // 3. Merge settings if requested
-                if (upgradeSettings) {
-                    settingsPath = path.join(targetDir, '.claude', 'settings.json');
-                    if (fs.existsSync(settingsPath)) {
-                        try {
-                            existingSettings = JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
-                            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.SessionStart (auto-memory import)',
-                                'hooks.SessionEnd (auto-memory sync)',
-                                'hooks.TeammateIdle (removed — not a valid Claude Code hook)',
-                                'hooks.TaskCompleted (removed — not a valid Claude Code hook)',
-                                'claudeFlow.agentTeams',
-                                'claudeFlow.memory (learningBridge, memoryGraph, agentScopes)',
-                            ];
-                        }
-                        catch (settingsError) {
-                            result.errors.push("Settings merge failed: " + (settingsError instanceof Error ? settingsError.message : String(settingsError)));
-                        }
-                    }
-                    else {
-                        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 (settingsError) {
+                    result.errors.push(`Settings merge failed: ${settingsError instanceof Error ? settingsError.message : String(settingsError)}`);
                 }
             }
-            catch (error) {
-                result.success = false;
-                result.errors.push(error instanceof Error ? error.message : String(error));
+            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'];
             }
-            return [2 /*return*/, result];
-        });
-    });
+        }
+    }
+    catch (error) {
+        result.success = false;
+        result.errors.push(error instanceof Error ? error.message : String(error));
+    }
+    return result;
 }
 /**
  * Execute upgrade with --add-missing flag
@@ -596,351 +533,310 @@ export function executeUpgrade(targetDir, upgradeSettings) {
  * @param targetDir - Target directory
  * @param upgradeSettings - If true, merge new settings into existing settings.json
  */
-export function executeUpgradeWithMissing(targetDir, upgradeSettings) {
-    if (upgradeSettings === void 0) { upgradeSettings = false; }
-    return __awaiter(this, void 0, Promise, function () {
-        var result, skillsDir, agentsDir, commandsDir, _i, _a, dir, sourceSkillsDir, sourceAgentsDir, sourceCommandsDir, allSkills, debugMode, _b, _c, skillName, sourcePath, targetPath, sourceExists, targetExists, allAgents, _d, _e, agentCategory, sourcePath, targetPath, allCommands, _f, _g, cmdName, sourcePath, targetPath;
-        return __generator(this, function (_h) {
-            switch (_h.label) {
-                case 0: return [4 /*yield*/, executeUpgrade(targetDir, upgradeSettings)];
-                case 1:
-                    result = _h.sent();
-                    if (!result.success) {
-                        return [2 /*return*/, result];
-                    }
-                    // Initialize tracking arrays
-                    result.addedSkills = [];
-                    result.addedAgents = [];
-                    result.addedCommands = [];
-                    try {
-                        skillsDir = path.join(targetDir, '.claude', 'skills');
-                        agentsDir = path.join(targetDir, '.claude', 'agents');
-                        commandsDir = path.join(targetDir, '.claude', 'commands');
-                        for (_i = 0, _a = [skillsDir, agentsDir, commandsDir]; _i < _a.length; _i++) {
-                            dir = _a[_i];
-                            if (!fs.existsSync(dir)) {
-                                fs.mkdirSync(dir, { recursive: true });
-                            }
-                        }
-                        sourceSkillsDir = findSourceDir('skills');
-                        sourceAgentsDir = findSourceDir('agents');
-                        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) {
-                            allSkills = Object.values(SKILLS_MAP).flat();
-                            debugMode = process.env.DEBUG || process.env.CLAUDE_FLOW_DEBUG;
-                            if (debugMode) {
-                                console.log("[DEBUG] Checking " + allSkills.length + " skills from SKILLS_MAP");
-                            }
-                            for (_b = 0, _c = __spreadArray([], new Set(allSkills), true); _b < _c.length; _b++) {
-                                skillName = _c[_b];
-                                sourcePath = path.join(sourceSkillsDir, skillName);
-                                targetPath = path.join(skillsDir, skillName);
-                                sourceExists = fs.existsSync(sourcePath);
-                                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) {
-                            allAgents = Object.values(AGENTS_MAP).flat();
-                            for (_d = 0, _e = __spreadArray([], new Set(allAgents), true); _d < _e.length; _d++) {
-                                agentCategory = _e[_d];
-                                sourcePath = path.join(sourceAgentsDir, agentCategory);
-                                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) {
-                            allCommands = Object.values(COMMANDS_MAP).flat();
-                            for (_f = 0, _g = __spreadArray([], new Set(allCommands), true); _f < _g.length; _f++) {
-                                cmdName = _g[_f];
-                                sourcePath = path.join(sourceCommandsDir, cmdName);
-                                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);
-                                }
-                            }
-                        }
+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);
                     }
-                    catch (error) {
-                        result.errors.push("Add missing failed: " + (error instanceof Error ? error.message : String(error)));
+                    else {
+                        fs.copyFileSync(sourcePath, targetPath);
                     }
-                    return [2 /*return*/, result];
+                    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
  */
-function createDirectories(targetDir, options, result) {
-    return __awaiter(this, void 0, Promise, function () {
-        var dirs, _i, dirs_2, dir, fullPath;
-        return __generator(this, function (_a) {
-            dirs = __spreadArray(__spreadArray([], DIRECTORIES.claude, true), (options.components.runtime ? DIRECTORIES.runtime : []), true);
-            for (_i = 0, dirs_2 = dirs; _i < dirs_2.length; _i++) {
-                dir = dirs_2[_i];
-                fullPath = path.join(targetDir, dir);
-                if (!fs.existsSync(fullPath)) {
-                    fs.mkdirSync(fullPath, { recursive: true });
-                    result.created.directories.push(dir);
-                }
-            }
-            return [2 /*return*/];
-        });
-    });
+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
  */
-function writeSettings(targetDir, options, result) {
-    return __awaiter(this, void 0, Promise, function () {
-        var settingsPath, content;
-        return __generator(this, function (_a) {
-            settingsPath = path.join(targetDir, '.claude', 'settings.json');
-            if (fs.existsSync(settingsPath) && !options.force) {
-                result.skipped.push('.claude/settings.json');
-                return [2 /*return*/];
-            }
-            content = generateSettingsJson(options);
-            fs.writeFileSync(settingsPath, content, 'utf-8');
-            result.created.files.push('.claude/settings.json');
-            return [2 /*return*/];
-        });
-    });
+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
  */
-function writeMCPConfig(targetDir, options, result) {
-    return __awaiter(this, void 0, Promise, function () {
-        var mcpPath, content;
-        return __generator(this, function (_a) {
-            mcpPath = path.join(targetDir, '.mcp.json');
-            if (fs.existsSync(mcpPath) && !options.force) {
-                result.skipped.push('.mcp.json');
-                return [2 /*return*/];
-            }
-            content = generateMCPJson(options);
-            fs.writeFileSync(mcpPath, content, 'utf-8');
-            result.created.files.push('.mcp.json');
-            return [2 /*return*/];
-        });
-    });
+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
  */
-function copySkills(targetDir, options, result) {
-    return __awaiter(this, void 0, Promise, function () {
-        var skillsConfig, targetSkillsDir, skillsToCopy, sourceSkillsDir, _i, _a, skillName, sourcePath, targetPath;
-        return __generator(this, function (_b) {
-            skillsConfig = options.skills;
-            targetSkillsDir = path.join(targetDir, '.claude', 'skills');
-            skillsToCopy = [];
-            if (skillsConfig.all) {
-                // Copy all available skills
-                Object.values(SKILLS_MAP).forEach(function (skills) { return skillsToCopy.push.apply(skillsToCopy, skills); });
+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);
+        if (skillsConfig.design)
+            skillsToCopy.push(...(SKILLS_MAP.design || []));
+    }
+    // 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 {
-                if (skillsConfig.core)
-                    skillsToCopy.push.apply(skillsToCopy, SKILLS_MAP.core);
-                if (skillsConfig.agentdb)
-                    skillsToCopy.push.apply(skillsToCopy, SKILLS_MAP.agentdb);
-                if (skillsConfig.github)
-                    skillsToCopy.push.apply(skillsToCopy, SKILLS_MAP.github);
-                if (skillsConfig.flowNexus)
-                    skillsToCopy.push.apply(skillsToCopy, SKILLS_MAP.flowNexus);
-                if (skillsConfig.browser)
-                    skillsToCopy.push.apply(skillsToCopy, SKILLS_MAP.browser);
-                if (skillsConfig.v3)
-                    skillsToCopy.push.apply(skillsToCopy, SKILLS_MAP.v3);
-                if (skillsConfig.dualMode)
-                    skillsToCopy.push.apply(skillsToCopy, SKILLS_MAP.dualMode);
-                if (skillsConfig.design)
-                    skillsToCopy.push.apply(skillsToCopy, (SKILLS_MAP.design || []));
-            }
-            sourceSkillsDir = findSourceDir('skills', options.sourceBaseDir);
-            if (!sourceSkillsDir) {
-                result.errors.push('Could not find source skills directory');
-                return [2 /*return*/];
-            }
-            // Copy each skill
-            for (_i = 0, _a = __spreadArray([], new Set(skillsToCopy), true); _i < _a.length; _i++) {
-                skillName = _a[_i];
-                sourcePath = path.join(sourceSkillsDir, skillName);
-                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);
-                    }
-                }
+                result.skipped.push(`.claude/skills/${skillName}`);
             }
-            return [2 /*return*/];
-        });
-    });
+        }
+    }
 }
 /**
  * Copy commands from source
  */
-function copyCommands(targetDir, options, result) {
-    return __awaiter(this, void 0, Promise, function () {
-        var commandsConfig, targetCommandsDir, commandsToCopy, sourceCommandsDir, _i, _a, cmdName, sourcePath, targetPath;
-        return __generator(this, function (_b) {
-            commandsConfig = options.commands;
-            targetCommandsDir = path.join(targetDir, '.claude', 'commands');
-            commandsToCopy = [];
-            if (commandsConfig.all) {
-                Object.values(COMMANDS_MAP).forEach(function (cmds) { return commandsToCopy.push.apply(commandsToCopy, cmds); });
+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 {
-                if (commandsConfig.core)
-                    commandsToCopy.push.apply(commandsToCopy, COMMANDS_MAP.core);
-                if (commandsConfig.analysis)
-                    commandsToCopy.push.apply(commandsToCopy, COMMANDS_MAP.analysis);
-                if (commandsConfig.automation)
-                    commandsToCopy.push.apply(commandsToCopy, COMMANDS_MAP.automation);
-                if (commandsConfig.github)
-                    commandsToCopy.push.apply(commandsToCopy, COMMANDS_MAP.github);
-                if (commandsConfig.hooks)
-                    commandsToCopy.push.apply(commandsToCopy, COMMANDS_MAP.hooks);
-                if (commandsConfig.monitoring)
-                    commandsToCopy.push.apply(commandsToCopy, COMMANDS_MAP.monitoring);
-                if (commandsConfig.optimization)
-                    commandsToCopy.push.apply(commandsToCopy, COMMANDS_MAP.optimization);
-                if (commandsConfig.sparc)
-                    commandsToCopy.push.apply(commandsToCopy, COMMANDS_MAP.sparc);
+                result.skipped.push(`.claude/commands/${cmdName}`);
             }
-            sourceCommandsDir = findSourceDir('commands', options.sourceBaseDir);
-            if (!sourceCommandsDir) {
-                result.errors.push('Could not find source commands directory');
-                return [2 /*return*/];
-            }
-            // Copy each command/directory
-            for (_i = 0, _a = __spreadArray([], new Set(commandsToCopy), true); _i < _a.length; _i++) {
-                cmdName = _a[_i];
-                sourcePath = path.join(sourceCommandsDir, cmdName);
-                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);
-                    }
-                }
-            }
-            return [2 /*return*/];
-        });
-    });
+        }
+    }
 }
 /**
  * Copy agents from source
  */
-function copyAgents(targetDir, options, result) {
-    return __awaiter(this, void 0, Promise, function () {
-        var agentsConfig, targetAgentsDir, agentsToCopy, sourceAgentsDir, _i, _a, agentCategory, sourcePath, targetPath, yamlFiles, mdFiles;
-        return __generator(this, function (_b) {
-            agentsConfig = options.agents;
-            targetAgentsDir = path.join(targetDir, '.claude', 'agents');
-            agentsToCopy = [];
-            if (agentsConfig.all) {
-                Object.values(AGENTS_MAP).forEach(function (agents) { return agentsToCopy.push.apply(agentsToCopy, agents); });
+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 || []));
+        // Design agents (design-architect, ux-researcher, ui-developer, accessibility-auditor)
+        if (agentsConfig.design)
+            agentsToCopy.push(...(AGENTS_MAP.design || []));
+        // 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 {
-                if (agentsConfig.core)
-                    agentsToCopy.push.apply(agentsToCopy, AGENTS_MAP.core);
-                if (agentsConfig.consensus)
-                    agentsToCopy.push.apply(agentsToCopy, AGENTS_MAP.consensus);
-                if (agentsConfig.github)
-                    agentsToCopy.push.apply(agentsToCopy, AGENTS_MAP.github);
-                if (agentsConfig.hiveMind)
-                    agentsToCopy.push.apply(agentsToCopy, AGENTS_MAP.hiveMind);
-                if (agentsConfig.sparc)
-                    agentsToCopy.push.apply(agentsToCopy, AGENTS_MAP.sparc);
-                if (agentsConfig.swarm)
-                    agentsToCopy.push.apply(agentsToCopy, AGENTS_MAP.swarm);
-                if (agentsConfig.browser)
-                    agentsToCopy.push.apply(agentsToCopy, AGENTS_MAP.browser);
-                // V3-specific agent categories
-                if (agentsConfig.v3)
-                    agentsToCopy.push.apply(agentsToCopy, (AGENTS_MAP.v3 || []));
-                if (agentsConfig.optimization)
-                    agentsToCopy.push.apply(agentsToCopy, (AGENTS_MAP.optimization || []));
-                if (agentsConfig.testing)
-                    agentsToCopy.push.apply(agentsToCopy, (AGENTS_MAP.testing || []));
-                // Design agents (design-architect, ux-researcher, ui-developer, accessibility-auditor)
-                if (agentsConfig.design)
-                    agentsToCopy.push.apply(agentsToCopy, (AGENTS_MAP.design || []));
-                // Dual-mode agents (Claude Code + Codex hybrid)
-                if (agentsConfig.dualMode)
-                    agentsToCopy.push.apply(agentsToCopy, (AGENTS_MAP.dualMode || []));
+                result.skipped.push(`.claude/agents/${agentCategory}`);
             }
-            sourceAgentsDir = findSourceDir('agents', options.sourceBaseDir);
-            if (!sourceAgentsDir) {
-                result.errors.push('Could not find source agents directory');
-                return [2 /*return*/];
-            }
-            // Copy each agent category
-            for (_i = 0, _a = __spreadArray([], new Set(agentsToCopy), true); _i < _a.length; _i++) {
-                agentCategory = _a[_i];
-                sourcePath = path.join(sourceAgentsDir, agentCategory);
-                targetPath = path.join(targetAgentsDir, agentCategory);
-                if (fs.existsSync(sourcePath)) {
-                    if (!fs.existsSync(targetPath) || options.force) {
-                        copyDirRecursive(sourcePath, targetPath);
-                        yamlFiles = countFiles(sourcePath, '.yaml');
-                        mdFiles = countFiles(sourcePath, '.md');
-                        result.summary.agentsCount += yamlFiles + mdFiles;
-                        result.created.files.push(".claude/agents/" + agentCategory);
-                    }
-                    else {
-                        result.skipped.push(".claude/agents/" + agentCategory);
-                    }
-                }
-            }
-            return [2 /*return*/];
-        });
-    });
+        }
+    }
 }
 /**
  * Find source helpers directory.
@@ -948,46 +844,45 @@ function copyAgents(targetDir, options, result) {
  * returning the target directory or an incomplete source.
  */
 function findSourceHelpersDir(sourceBaseDir) {
-    var possiblePaths = [];
-    var SENTINEL_FILE = 'hook-handler.cjs'; // Must exist in valid source
+    const possiblePaths = [];
+    const SENTINEL_FILE = 'hook-handler.cjs'; // Must exist in valid source
     // If explicit source base directory is provided, check it first
     if (sourceBaseDir) {
         possiblePaths.push(path.join(sourceBaseDir, '.claude', 'helpers'));
     }
     // Strategy 1: require.resolve to find package root (most reliable for npx)
     try {
-        var esmRequire = createRequire(import.meta.url);
-        var pkgJsonPath = esmRequire.resolve('@claude-flow/cli/package.json');
-        var pkgRoot = path.dirname(pkgJsonPath);
+        const esmRequire = createRequire(import.meta.url);
+        const pkgJsonPath = esmRequire.resolve('@claude-flow/cli/package.json');
+        const pkgRoot = path.dirname(pkgJsonPath);
         possiblePaths.push(path.join(pkgRoot, '.claude', 'helpers'));
     }
-    catch (_a) {
+    catch {
         // Not installed as a package — skip
     }
     // Strategy 2: __dirname-based (dist/src/init -> package root)
-    var packageRoot = path.resolve(__dirname, '..', '..', '..');
-    var packageHelpers = path.join(packageRoot, '.claude', 'helpers');
+    const packageRoot = path.resolve(__dirname, '..', '..', '..');
+    const packageHelpers = path.join(packageRoot, '.claude', 'helpers');
     possiblePaths.push(packageHelpers);
     // Strategy 3: Walk up from __dirname looking for package root
-    var currentDir = __dirname;
-    for (var i = 0; i < 10; i++) {
-        var parentDir = path.dirname(currentDir);
+    let currentDir = __dirname;
+    for (let i = 0; i < 10; i++) {
+        const parentDir = path.dirname(currentDir);
         if (parentDir === currentDir)
             break; // hit filesystem root
-        var helpersPath = path.join(parentDir, '.claude', 'helpers');
+        const helpersPath = path.join(parentDir, '.claude', 'helpers');
         possiblePaths.push(helpersPath);
         currentDir = parentDir;
     }
     // Strategy 4: Check cwd-relative paths (for local dev)
-    var cwdBased = [
+    const cwdBased = [
         path.join(process.cwd(), '.claude', 'helpers'),
         path.join(process.cwd(), '..', '.claude', 'helpers'),
         path.join(process.cwd(), '..', '..', '.claude', 'helpers'),
     ];
-    possiblePaths.push.apply(possiblePaths, cwdBased);
+    possiblePaths.push(...cwdBased);
     // Return first path that exists AND contains the sentinel file
-    for (var _i = 0, possiblePaths_1 = possiblePaths; _i < possiblePaths_1.length; _i++) {
-        var p = possiblePaths_1[_i];
+    for (const p of possiblePaths) {
         if (fs.existsSync(p) && fs.existsSync(path.join(p, SENTINEL_FILE))) {
             return p;
         }
@@ -997,97 +892,90 @@ function findSourceHelpersDir(sourceBaseDir) {
 /**
  * Write helper scripts
  */
-function writeHelpers(targetDir, options, result) {
-    return __awaiter(this, void 0, Promise, function () {
-        var helpersDir, sourceHelpersDir, helperFiles, copiedCount, _i, helperFiles_1, file, sourcePath, destPath, helpers, _a, _b, _c, name, content, filePath;
-        return __generator(this, function (_d) {
-            helpersDir = path.join(targetDir, '.claude', 'helpers');
-            sourceHelpersDir = findSourceHelpersDir(options.sourceBaseDir);
-            // Try to copy existing helpers from source first
-            if (sourceHelpersDir && fs.existsSync(sourceHelpersDir)) {
-                helperFiles = fs.readdirSync(sourceHelpersDir);
-                copiedCount = 0;
-                for (_i = 0, helperFiles_1 = helperFiles; _i < helperFiles_1.length; _i++) {
-                    file = helperFiles_1[_i];
-                    sourcePath = path.join(sourceHelpersDir, file);
-                    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 [2 /*return*/]; // Skip generating if we copied from source
+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++;
             }
-            helpers = {
-                'pre-commit': generatePreCommitHook(),
-                'post-commit': generatePostCommitHook(),
-                'session.js': generateSessionManager(),
-                'router.js': generateAgentRouter(),
-                'memory.js': generateMemoryHelper(),
-                'hook-handler.cjs': generateHookHandler(),
-                'intelligence.cjs': generateIntelligenceStub(),
-                'auto-memory-hook.mjs': generateAutoMemoryHook()
-            };
-            for (_a = 0, _b = Object.entries(helpers); _a < _b.length; _a++) {
-                _c = _b[_a], name = _c[0], content = _c[1];
-                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);
-                }
+            else {
+                result.skipped.push(`.claude/helpers/${file}`);
             }
-            return [2 /*return*/];
-        });
-    });
+        }
+        if (copiedCount > 0) {
+            return; // Skip generating if we copied from source
+        }
+    }
+    // Fall back to generating helpers if source not available
+    const helpers = {
+        'pre-commit': generatePreCommitHook(),
+        'post-commit': generatePostCommitHook(),
+        'session.js': generateSessionManager(),
+        'router.js': generateAgentRouter(),
+        'memory.js': generateMemoryHelper(),
+        'hook-handler.cjs': generateHookHandler(),
+        'intelligence.cjs': generateIntelligenceStub(),
+        'auto-memory-hook.mjs': generateAutoMemoryHook(),
+    };
+    for (const [name, content] of Object.entries(helpers)) {
+        const filePath = path.join(helpersDir, name);
+        if (!fs.existsSync(filePath) || options.force) {
+            fs.writeFileSync(filePath, content, 'utf-8');
+            // Make shell scripts executable
+            if (!name.endsWith('.js')) {
+                fs.chmodSync(filePath, '755');
+            }
+            result.created.files.push(`.claude/helpers/${name}`);
+        }
+        else {
+            result.skipped.push(`.claude/helpers/${name}`);
+        }
+    }
 }
 /**
  * Find source .claude directory for statusline files
  */
 function findSourceClaudeDir(sourceBaseDir) {
-    var possiblePaths = [];
+    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
-    var packageRoot = path.resolve(__dirname, '..', '..', '..');
-    var packageClaude = path.join(packageRoot, '.claude');
+    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
-    var currentDir = __dirname;
-    for (var i = 0; i < 10; i++) {
-        var parentDir = path.dirname(currentDir);
-        var claudePath = path.join(parentDir, '.claude');
+    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 (var _i = 0, possiblePaths_2 = possiblePaths; _i < possiblePaths_2.length; _i++) {
-        var p = possiblePaths_2[_i];
+    for (const p of possiblePaths) {
         if (fs.existsSync(p)) {
             return p;
         }
@@ -1097,235 +985,661 @@ function findSourceClaudeDir(sourceBaseDir) {
 /**
  * Write statusline configuration
  */
-function writeStatusline(targetDir, options, result) {
-    return __awaiter(this, void 0, Promise, function () {
-        var claudeDir, helpersDir, sourceClaudeDir, advancedStatuslineFiles, _i, advancedStatuslineFiles_1, file, sourcePath, destPath, statuslineScript, statuslinePath;
-        return __generator(this, function (_a) {
-            claudeDir = path.join(targetDir, '.claude');
-            helpersDir = path.join(targetDir, '.claude', 'helpers');
-            sourceClaudeDir = findSourceClaudeDir(options.sourceBaseDir);
-            advancedStatuslineFiles = [
-                { src: 'statusline.sh', dest: 'statusline.sh', dir: claudeDir },
-                { src: 'statusline.mjs', dest: 'statusline.mjs', dir: claudeDir },
-            ];
-            if (sourceClaudeDir) {
-                for (_i = 0, advancedStatuslineFiles_1 = advancedStatuslineFiles; _i < advancedStatuslineFiles_1.length; _i++) {
-                    file = advancedStatuslineFiles_1[_i];
-                    sourcePath = path.join(sourceClaudeDir, file.src);
-                    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);
-                        }
-                        else {
-                            result.skipped.push(".claude/" + file.dest);
-                        }
+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 },
+    ];
+    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}`);
+                }
+                else {
+                    result.skipped.push(`.claude/${file.dest}`);
                 }
             }
-            statuslineScript = generateStatuslineScript(options);
-            statuslinePath = path.join(helpersDir, 'statusline.cjs');
-            fs.writeFileSync(statuslinePath, statuslineScript, 'utf-8');
-            result.created.files.push('.claude/helpers/statusline.cjs');
-            return [2 /*return*/];
-        });
-    });
+        }
+    }
+    // ALWAYS generate statusline.cjs — the generated version includes AgentDB
+    // vectors/size, tests, ADRs, hooks, and integration stats that the
+    // pre-installed static copy in the npm package lacks.
+    // This must overwrite any copy from writeHelpers() which copies the legacy file.
+    const statuslineScript = generateStatuslineScript(options);
+    const statuslinePath = path.join(helpersDir, 'statusline.cjs');
+    fs.writeFileSync(statuslinePath, statuslineScript, 'utf-8');
+    result.created.files.push('.claude/helpers/statusline.cjs');
 }
 /**
  * Write runtime configuration (.claude-flow/)
  */
-function writeRuntimeConfig(targetDir, options, result) {
-    var _a, _b, _c;
-    return __awaiter(this, void 0, Promise, function () {
-        var configPath, config, gitignorePath, gitignore;
-        return __generator(this, function (_d) {
-            switch (_d.label) {
-                case 0:
-                    configPath = path.join(targetDir, '.claude-flow', 'config.yaml');
-                    if (fs.existsSync(configPath) && !options.force) {
-                        result.skipped.push('.claude-flow/config.yaml');
-                        return [2 /*return*/];
-                    }
-                    config = "# RuFlo V3 Runtime Configuration\n# Generated: " + new Date().toISOString() + "\n\nversion: \"3.0.0\"\n\nswarm:\n  topology: " + options.runtime.topology + "\n  maxAgents: " + options.runtime.maxAgents + "\n  autoScale: true\n  coordinationStrategy: consensus\n\nmemory:\n  backend: " + options.runtime.memoryBackend + "\n  enableHNSW: " + options.runtime.enableHNSW + "\n  persistPath: .claude-flow/data\n  cacheSize: 100\n  # ADR-049: Self-Learning Memory\n  learningBridge:\n    enabled: " + ((_a = options.runtime.enableLearningBridge) !== null && _a !== void 0 ? _a : options.runtime.enableNeural) + "\n    sonaMode: balanced\n    confidenceDecayRate: 0.005\n    accessBoostAmount: 0.03\n    consolidationThreshold: 10\n  memoryGraph:\n    enabled: " + ((_b = options.runtime.enableMemoryGraph) !== null && _b !== void 0 ? _b : true) + "\n    pageRankDamping: 0.85\n    maxNodes: 5000\n    similarityThreshold: 0.8\n  agentScopes:\n    enabled: " + ((_c = options.runtime.enableAgentScopes) !== null && _c !== void 0 ? _c : true) + "\n    defaultScope: project\n\nneural:\n  enabled: " + options.runtime.enableNeural + "\n  modelPath: .claude-flow/neural\n\nhooks:\n  enabled: true\n  autoExecute: true\n\nmcp:\n  autoStart: " + options.mcp.autoStart + "\n  port: " + options.mcp.port + "\n";
-                    fs.writeFileSync(configPath, config, 'utf-8');
-                    result.created.files.push('.claude-flow/config.yaml');
-                    gitignorePath = path.join(targetDir, '.claude-flow', '.gitignore');
-                    gitignore = "# Claude Flow runtime files\ndata/\nlogs/\nsessions/\nneural/\n*.log\n*.tmp\n";
-                    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
-                    return [4 /*yield*/, writeCapabilitiesDoc(targetDir, options, result)];
-                case 1:
-                    // Write CAPABILITIES.md with full system overview
-                    _d.sent();
-                    return [2 /*return*/];
-            }
-        });
-    });
+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 = `# RuFlo 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
+  # ADR-049: Self-Learning Memory
+  learningBridge:
+    enabled: ${options.runtime.enableLearningBridge ?? options.runtime.enableNeural}
+    sonaMode: balanced
+    confidenceDecayRate: 0.005
+    accessBoostAmount: 0.03
+    consolidationThreshold: 10
+  memoryGraph:
+    enabled: ${options.runtime.enableMemoryGraph ?? true}
+    pageRankDamping: 0.85
+    maxNodes: 5000
+    similarityThreshold: 0.8
+  agentScopes:
+    enabled: ${options.runtime.enableAgentScopes ?? true}
+    defaultScope: project
+
+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
  */
-function writeInitialMetrics(targetDir, options, result) {
-    return __awaiter(this, void 0, Promise, function () {
-        var metricsDir, learningDir, securityDir, _i, _a, dir, progressPath, progress, activityPath, activity, learningPath, learning, auditPath, audit;
-        return __generator(this, function (_b) {
-            metricsDir = path.join(targetDir, '.claude-flow', 'metrics');
-            learningDir = path.join(targetDir, '.claude-flow', 'learning');
-            securityDir = path.join(targetDir, '.claude-flow', 'security');
-            // Ensure directories exist
-            for (_i = 0, _a = [metricsDir, learningDir, securityDir]; _i < _a.length; _i++) {
-                dir = _a[_i];
-                if (!fs.existsSync(dir)) {
-                    fs.mkdirSync(dir, { recursive: true });
-                }
-            }
-            progressPath = path.join(metricsDir, 'v3-progress.json');
-            if (!fs.existsSync(progressPath) || options.force) {
-                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 Ruflo. Run: npx ruflo@latest daemon start'
-                };
-                fs.writeFileSync(progressPath, JSON.stringify(progress, null, 2), 'utf-8');
-                result.created.files.push('.claude-flow/metrics/v3-progress.json');
-            }
-            activityPath = path.join(metricsDir, 'swarm-activity.json');
-            if (!fs.existsSync(activityPath) || options.force) {
-                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');
-            }
-            learningPath = path.join(metricsDir, 'learning.json');
-            if (!fs.existsSync(learningPath) || options.force) {
-                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 Ruflo'
-                };
-                fs.writeFileSync(learningPath, JSON.stringify(learning, null, 2), 'utf-8');
-                result.created.files.push('.claude-flow/metrics/learning.json');
-            }
-            auditPath = path.join(securityDir, 'audit-status.json');
-            if (!fs.existsSync(auditPath) || options.force) {
-                audit = {
-                    initialized: new Date().toISOString(),
-                    status: 'PENDING',
-                    cvesFixed: 0,
-                    totalCves: 3,
-                    lastScan: null,
-                    _note: 'Run: npx @claude-flow/cli@latest security scan'
-                };
-                fs.writeFileSync(auditPath, JSON.stringify(audit, null, 2), 'utf-8');
-                result.created.files.push('.claude-flow/security/audit-status.json');
-            }
-            return [2 /*return*/];
-        });
-    });
+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 Ruflo. Run: npx ruflo@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 Ruflo'
+        };
+        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 @claude-flow/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 Ruflo features
  */
-function writeCapabilitiesDoc(targetDir, options, result) {
-    return __awaiter(this, void 0, Promise, function () {
-        var capabilitiesPath, capabilities;
-        return __generator(this, function (_a) {
-            capabilitiesPath = path.join(targetDir, '.claude-flow', 'CAPABILITIES.md');
-            if (fs.existsSync(capabilitiesPath) && !options.force) {
-                result.skipped.push('.claude-flow/CAPABILITIES.md');
-                return [2 /*return*/];
-            }
-            capabilities = "# RuFlo V3 - Complete Capabilities Reference\n> Generated: " + new Date().toISOString() + "\n> Full documentation: https://github.com/ruvnet/claude-flow\n\n## \uD83D\uDCCB Table of Contents\n\n1. [Overview](#overview)\n2. [Swarm Orchestration](#swarm-orchestration)\n3. [Available Agents (60+)](#available-agents)\n4. [CLI Commands (26 Commands, 140+ Subcommands)](#cli-commands)\n5. [Hooks System (27 Hooks + 12 Workers)](#hooks-system)\n6. [Memory & Intelligence (RuVector)](#memory--intelligence)\n7. [Hive-Mind Consensus](#hive-mind-consensus)\n8. [Performance Targets](#performance-targets)\n9. [Integration Ecosystem](#integration-ecosystem)\n\n---\n\n## Overview\n\nRuFlo V3 is a domain-driven design architecture for multi-agent AI coordination with:\n\n- **15-Agent Swarm Coordination** with hierarchical and mesh topologies\n- **HNSW Vector Search** - 150x-12,500x faster pattern retrieval\n- **SONA Neural Learning** - Self-optimizing with <0.05ms adaptation\n- **Byzantine Fault Tolerance** - Queen-led consensus mechanisms\n- **MCP Server Integration** - Model Context Protocol support\n\n### Current Configuration\n| Setting | Value |\n|---------|-------|\n| Topology | " + options.runtime.topology + " |\n| Max Agents | " + options.runtime.maxAgents + " |\n| Memory Backend | " + options.runtime.memoryBackend + " |\n| HNSW Indexing | " + (options.runtime.enableHNSW ? 'Enabled' : 'Disabled') + " |\n| Neural Learning | " + (options.runtime.enableNeural ? 'Enabled' : 'Disabled') + " |\n| LearningBridge | " + (options.runtime.enableLearningBridge ? 'Enabled (SONA + ReasoningBank)' : 'Disabled') + " |\n| Knowledge Graph | " + (options.runtime.enableMemoryGraph ? 'Enabled (PageRank + Communities)' : 'Disabled') + " |\n| Agent Scopes | " + (options.runtime.enableAgentScopes ? 'Enabled (project/local/user)' : 'Disabled') + " |\n\n---\n\n## Swarm Orchestration\n\n### Topologies\n| Topology | Description | Best For |\n|----------|-------------|----------|\n| `hierarchical` | Queen controls workers directly | Anti-drift, tight control |\n| `mesh` | Fully connected peer network | Distributed tasks |\n| `hierarchical-mesh` | V3 hybrid (recommended) | 10+ agents |\n| `ring` | Circular communication | Sequential workflows |\n| `star` | Central coordinator | Simple coordination |\n| `adaptive` | Dynamic based on load | Variable workloads |\n\n### Strategies\n- `balanced` - Even distribution across agents\n- `specialized` - Clear roles, no overlap (anti-drift)\n- `adaptive` - Dynamic task routing\n\n### Quick Commands\n```bash\n# Initialize swarm\nnpx @claude-flow/cli@latest swarm init --topology hierarchical --max-agents 8 --strategy specialized\n\n# Check status\nnpx @claude-flow/cli@latest swarm status\n\n# Monitor activity\nnpx @claude-flow/cli@latest swarm monitor\n```\n\n---\n\n## Available Agents\n\n### Core Development (5)\n`coder`, `reviewer`, `tester`, `planner`, `researcher`\n\n### V3 Specialized (4)\n`security-architect`, `security-auditor`, `memory-specialist`, `performance-engineer`\n\n### Swarm Coordination (5)\n`hierarchical-coordinator`, `mesh-coordinator`, `adaptive-coordinator`, `collective-intelligence-coordinator`, `swarm-memory-manager`\n\n### Consensus & Distributed (7)\n`byzantine-coordinator`, `raft-manager`, `gossip-coordinator`, `consensus-builder`, `crdt-synchronizer`, `quorum-manager`, `security-manager`\n\n### Performance & Optimization (5)\n`perf-analyzer`, `performance-benchmarker`, `task-orchestrator`, `memory-coordinator`, `smart-agent`\n\n### GitHub & Repository (9)\n`github-modes`, `pr-manager`, `code-review-swarm`, `issue-tracker`, `release-manager`, `workflow-automation`, `project-board-sync`, `repo-architect`, `multi-repo-swarm`\n\n### SPARC Methodology (6)\n`sparc-coord`, `sparc-coder`, `specification`, `pseudocode`, `architecture`, `refinement`\n\n### Specialized Development (8)\n`backend-dev`, `mobile-dev`, `ml-developer`, `cicd-engineer`, `api-docs`, `system-architect`, `code-analyzer`, `base-template-generator`\n\n### Testing & Validation (2)\n`tdd-london-swarm`, `production-validator`\n\n### Agent Routing by Task\n| Task Type | Recommended Agents | Topology |\n|-----------|-------------------|----------|\n| Bug Fix | researcher, coder, tester | mesh |\n| New Feature | coordinator, architect, coder, tester, reviewer | hierarchical |\n| Refactoring | architect, coder, reviewer | mesh |\n| Performance | researcher, perf-engineer, coder | hierarchical |\n| Security | security-architect, auditor, reviewer | hierarchical |\n| Docs | researcher, api-docs | mesh |\n\n---\n\n## CLI Commands\n\n### Core Commands (12)\n| Command | Subcommands | Description |\n|---------|-------------|-------------|\n| `init` | 4 | Project initialization |\n| `agent` | 8 | Agent lifecycle management |\n| `swarm` | 6 | Multi-agent coordination |\n| `memory` | 11 | AgentDB with HNSW search |\n| `mcp` | 9 | MCP server management |\n| `task` | 6 | Task assignment |\n| `session` | 7 | Session persistence |\n| `config` | 7 | Configuration |\n| `status` | 3 | System monitoring |\n| `workflow` | 6 | Workflow templates |\n| `hooks` | 17 | Self-learning hooks |\n| `hive-mind` | 6 | Consensus coordination |\n\n### Advanced Commands (14)\n| Command | Subcommands | Description |\n|---------|-------------|-------------|\n| `daemon` | 5 | Background workers |\n| `neural` | 5 | Pattern training |\n| `security` | 6 | Security scanning |\n| `performance` | 5 | Profiling & benchmarks |\n| `providers` | 5 | AI provider config |\n| `plugins` | 5 | Plugin management |\n| `deployment` | 5 | Deploy management |\n| `embeddings` | 4 | Vector embeddings |\n| `claims` | 4 | Authorization |\n| `migrate` | 5 | V2\u2192V3 migration |\n| `process` | 4 | Process management |\n| `doctor` | 1 | Health diagnostics |\n| `completions` | 4 | Shell completions |\n\n### Example Commands\n```bash\n# Initialize\nnpx @claude-flow/cli@latest init --wizard\n\n# Spawn agent\nnpx @claude-flow/cli@latest agent spawn -t coder --name my-coder\n\n# Memory operations\nnpx @claude-flow/cli@latest memory store --key \"pattern\" --value \"data\" --namespace patterns\nnpx @claude-flow/cli@latest memory search --query \"authentication\"\n\n# Diagnostics\nnpx @claude-flow/cli@latest doctor --fix\n```\n\n---\n\n## Hooks System\n\n### 27 Available Hooks\n\n#### Core Hooks (6)\n| Hook | Description |\n|------|-------------|\n| `pre-edit` | Context before file edits |\n| `post-edit` | Record edit outcomes |\n| `pre-command` | Risk assessment |\n| `post-command` | Command metrics |\n| `pre-task` | Task start + agent suggestions |\n| `post-task` | Task completion learning |\n\n#### Session Hooks (4)\n| Hook | Description |\n|------|-------------|\n| `session-start` | Start/restore session |\n| `session-end` | Persist state |\n| `session-restore` | Restore previous |\n| `notify` | Cross-agent notifications |\n\n#### Intelligence Hooks (5)\n| Hook | Description |\n|------|-------------|\n| `route` | Optimal agent routing |\n| `explain` | Routing decisions |\n| `pretrain` | Bootstrap intelligence |\n| `build-agents` | Generate configs |\n| `transfer` | Pattern transfer |\n\n#### Coverage Hooks (3)\n| Hook | Description |\n|------|-------------|\n| `coverage-route` | Coverage-based routing |\n| `coverage-suggest` | Improvement suggestions |\n| `coverage-gaps` | Gap analysis |\n\n### 12 Background Workers\n| Worker | Priority | Purpose |\n|--------|----------|---------|\n| `ultralearn` | normal | Deep knowledge |\n| `optimize` | high | Performance |\n| `consolidate` | low | Memory consolidation |\n| `predict` | normal | Predictive preload |\n| `audit` | critical | Security |\n| `map` | normal | Codebase mapping |\n| `preload` | low | Resource preload |\n| `deepdive` | normal | Deep analysis |\n| `document` | normal | Auto-docs |\n| `refactor` | normal | Suggestions |\n| `benchmark` | normal | Benchmarking |\n| `testgaps` | normal | Coverage gaps |\n\n---\n\n## Memory & Intelligence\n\n### RuVector Intelligence System\n- **SONA**: Self-Optimizing Neural Architecture (<0.05ms)\n- **MoE**: Mixture of Experts routing\n- **HNSW**: 150x-12,500x faster search\n- **EWC++**: Prevents catastrophic forgetting\n- **Flash Attention**: 2.49x-7.47x speedup\n- **Int8 Quantization**: 3.92x memory reduction\n\n### 4-Step Intelligence Pipeline\n1. **RETRIEVE** - HNSW pattern search\n2. **JUDGE** - Success/failure verdicts\n3. **DISTILL** - LoRA learning extraction\n4. **CONSOLIDATE** - EWC++ preservation\n\n### Self-Learning Memory (ADR-049)\n\n| Component | Status | Description |\n|-----------|--------|-------------|\n| **LearningBridge** | " + (options.runtime.enableLearningBridge ? '✅ Enabled' : '⏸ Disabled') + " | Connects insights to SONA/ReasoningBank neural pipeline |\n| **MemoryGraph** | " + (options.runtime.enableMemoryGraph ? '✅ Enabled' : '⏸ Disabled') + " | PageRank knowledge graph + community detection |\n| **AgentMemoryScope** | " + (options.runtime.enableAgentScopes ? '✅ Enabled' : '⏸ Disabled') + " | 3-scope agent memory (project/local/user) |\n\n**LearningBridge** - Insights trigger learning trajectories. Confidence evolves: +0.03 on access, -0.005/hour decay. Consolidation runs the JUDGE/DISTILL/CONSOLIDATE pipeline.\n\n**MemoryGraph** - Builds a knowledge graph from entry references. PageRank identifies influential insights. Communities group related knowledge. Graph-aware ranking blends vector + structural scores.\n\n**AgentMemoryScope** - Maps Claude Code 3-scope directories:\n- `project`: `<gitRoot>/.claude/agent-memory/<agent>/`\n- `local`: `<gitRoot>/.claude/agent-memory-local/<agent>/`\n- `user`: `~/.claude/agent-memory/<agent>/`\n\nHigh-confidence insights (>0.8) can transfer between agents.\n\n### Memory Commands\n```bash\n# Store pattern\nnpx @claude-flow/cli@latest memory store --key \"name\" --value \"data\" --namespace patterns\n\n# Semantic search\nnpx @claude-flow/cli@latest memory search --query \"authentication\"\n\n# List entries\nnpx @claude-flow/cli@latest memory list --namespace patterns\n\n# Initialize database\nnpx @claude-flow/cli@latest memory init --force\n```\n\n---\n\n## Hive-Mind Consensus\n\n### Queen Types\n| Type | Role |\n|------|------|\n| Strategic Queen | Long-term planning |\n| Tactical Queen | Execution coordination |\n| Adaptive Queen | Dynamic optimization |\n\n### Worker Types (8)\n`researcher`, `coder`, `analyst`, `tester`, `architect`, `reviewer`, `optimizer`, `documenter`\n\n### Consensus Mechanisms\n| Mechanism | Fault Tolerance | Use Case |\n|-----------|-----------------|----------|\n| `byzantine` | f < n/3 faulty | Adversarial |\n| `raft` | f < n/2 failed | Leader-based |\n| `gossip` | Eventually consistent | Large scale |\n| `crdt` | Conflict-free | Distributed |\n| `quorum` | Configurable | Flexible |\n\n### Hive-Mind Commands\n```bash\n# Initialize\nnpx @claude-flow/cli@latest hive-mind init --queen-type strategic\n\n# Status\nnpx @claude-flow/cli@latest hive-mind status\n\n# Spawn workers\nnpx @claude-flow/cli@latest hive-mind spawn --count 5 --type worker\n\n# Consensus\nnpx @claude-flow/cli@latest hive-mind consensus --propose \"task\"\n```\n\n---\n\n## Performance Targets\n\n| Metric | Target | Status |\n|--------|--------|--------|\n| HNSW Search | 150x-12,500x faster | \u2705 Implemented |\n| Memory Reduction | 50-75% | \u2705 Implemented (3.92x) |\n| SONA Integration | Pattern learning | \u2705 Implemented |\n| Flash Attention | 2.49x-7.47x | \uD83D\uDD04 In Progress |\n| MCP Response | <100ms | \u2705 Achieved |\n| CLI Startup | <500ms | \u2705 Achieved |\n| SONA Adaptation | <0.05ms | \uD83D\uDD04 In Progress |\n| Graph Build (1k) | <200ms | \u2705 2.78ms (71.9x headroom) |\n| PageRank (1k) | <100ms | \u2705 12.21ms (8.2x headroom) |\n| Insight Recording | <5ms/each | \u2705 0.12ms (41x headroom) |\n| Consolidation | <500ms | \u2705 0.26ms (1,955x headroom) |\n| Knowledge Transfer | <100ms | \u2705 1.25ms (80x headroom) |\n\n---\n\n## Integration Ecosystem\n\n### Integrated Packages\n| Package | Version | Purpose |\n|---------|---------|---------|\n| agentic-flow | 3.0.0-alpha.1 | Core coordination + ReasoningBank + Router |\n| agentdb | 3.0.0-alpha.10 | Vector database + 8 controllers |\n| @ruvector/attention | 0.1.3 | Flash attention |\n| @ruvector/sona | 0.1.5 | Neural learning |\n\n### Optional Integrations\n| Package | Command |\n|---------|---------|\n| ruv-swarm | `npx ruv-swarm mcp start` |\n| flow-nexus | `npx flow-nexus@latest mcp start` |\n| agentic-jujutsu | `npx agentic-jujutsu@latest` |\n\n### MCP Server Setup\n```bash\n# Add Ruflo MCP\nclaude mcp add ruflo -- npx -y ruflo@latest\n\n# Optional servers\nclaude mcp add ruv-swarm -- npx -y ruv-swarm mcp start\nclaude mcp add flow-nexus -- npx -y flow-nexus@latest mcp start\n```\n\n---\n\n## Quick Reference\n\n### Essential Commands\n```bash\n# Setup\nnpx ruflo@latest init --wizard\nnpx ruflo@latest daemon start\nnpx ruflo@latest doctor --fix\n\n# Swarm\nnpx ruflo@latest swarm init --topology hierarchical --max-agents 8\nnpx ruflo@latest swarm status\n\n# Agents\nnpx ruflo@latest agent spawn -t coder\nnpx ruflo@latest agent list\n\n# Memory\nnpx ruflo@latest memory search --query \"patterns\"\n\n# Hooks\nnpx ruflo@latest hooks pre-task --description \"task\"\nnpx ruflo@latest hooks worker dispatch --trigger optimize\n```\n\n### File Structure\n```\n.claude-flow/\n\u251C\u2500\u2500 config.yaml      # Runtime configuration\n\u251C\u2500\u2500 CAPABILITIES.md  # This file\n\u251C\u2500\u2500 data/            # Memory storage\n\u251C\u2500\u2500 logs/            # Operation logs\n\u251C\u2500\u2500 sessions/        # Session state\n\u251C\u2500\u2500 hooks/           # Custom hooks\n\u251C\u2500\u2500 agents/          # Agent configs\n\u2514\u2500\u2500 workflows/       # Workflow templates\n```\n\n---\n\n**Full Documentation**: https://github.com/ruvnet/claude-flow\n**Issues**: https://github.com/ruvnet/claude-flow/issues\n";
-            fs.writeFileSync(capabilitiesPath, capabilities, 'utf-8');
-            result.created.files.push('.claude-flow/CAPABILITIES.md');
-            return [2 /*return*/];
-        });
-    });
+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 = `# RuFlo 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
+
+RuFlo 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'} |
+| LearningBridge | ${options.runtime.enableLearningBridge ? 'Enabled (SONA + ReasoningBank)' : 'Disabled'} |
+| Knowledge Graph | ${options.runtime.enableMemoryGraph ? 'Enabled (PageRank + Communities)' : 'Disabled'} |
+| Agent Scopes | ${options.runtime.enableAgentScopes ? 'Enabled (project/local/user)' : '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 @claude-flow/cli@latest swarm init --topology hierarchical --max-agents 8 --strategy specialized
+
+# Check status
+npx @claude-flow/cli@latest swarm status
+
+# Monitor activity
+npx @claude-flow/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 @claude-flow/cli@latest init --wizard
+
+# Spawn agent
+npx @claude-flow/cli@latest agent spawn -t coder --name my-coder
+
+# Memory operations
+npx @claude-flow/cli@latest memory store --key "pattern" --value "data" --namespace patterns
+npx @claude-flow/cli@latest memory search --query "authentication"
+
+# Diagnostics
+npx @claude-flow/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
+
+### Self-Learning Memory (ADR-049)
+
+| Component | Status | Description |
+|-----------|--------|-------------|
+| **LearningBridge** | ${options.runtime.enableLearningBridge ? '✅ Enabled' : '⏸ Disabled'} | Connects insights to SONA/ReasoningBank neural pipeline |
+| **MemoryGraph** | ${options.runtime.enableMemoryGraph ? '✅ Enabled' : '⏸ Disabled'} | PageRank knowledge graph + community detection |
+| **AgentMemoryScope** | ${options.runtime.enableAgentScopes ? '✅ Enabled' : '⏸ Disabled'} | 3-scope agent memory (project/local/user) |
+
+**LearningBridge** - Insights trigger learning trajectories. Confidence evolves: +0.03 on access, -0.005/hour decay. Consolidation runs the JUDGE/DISTILL/CONSOLIDATE pipeline.
+
+**MemoryGraph** - Builds a knowledge graph from entry references. PageRank identifies influential insights. Communities group related knowledge. Graph-aware ranking blends vector + structural scores.
+
+**AgentMemoryScope** - Maps Claude Code 3-scope directories:
+- \`project\`: \`<gitRoot>/.claude/agent-memory/<agent>/\`
+- \`local\`: \`<gitRoot>/.claude/agent-memory-local/<agent>/\`
+- \`user\`: \`~/.claude/agent-memory/<agent>/\`
+
+High-confidence insights (>0.8) can transfer between agents.
+
+### Memory Commands
+\`\`\`bash
+# Store pattern
+npx @claude-flow/cli@latest memory store --key "name" --value "data" --namespace patterns
+
+# Semantic search
+npx @claude-flow/cli@latest memory search --query "authentication"
+
+# List entries
+npx @claude-flow/cli@latest memory list --namespace patterns
+
+# Initialize database
+npx @claude-flow/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 @claude-flow/cli@latest hive-mind init --queen-type strategic
+
+# Status
+npx @claude-flow/cli@latest hive-mind status
+
+# Spawn workers
+npx @claude-flow/cli@latest hive-mind spawn --count 5 --type worker
+
+# Consensus
+npx @claude-flow/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 |
+| Graph Build (1k) | <200ms | ✅ 2.78ms (71.9x headroom) |
+| PageRank (1k) | <100ms | ✅ 12.21ms (8.2x headroom) |
+| Insight Recording | <5ms/each | ✅ 0.12ms (41x headroom) |
+| Consolidation | <500ms | ✅ 0.26ms (1,955x headroom) |
+| Knowledge Transfer | <100ms | ✅ 1.25ms (80x headroom) |
+
+---
+
+## Integration Ecosystem
+
+### Integrated Packages
+| Package | Version | Purpose |
+|---------|---------|---------|
+| agentic-flow | 3.0.0-alpha.1 | Core coordination + ReasoningBank + Router |
+| agentdb | 3.0.0-alpha.10 | Vector database + 8 controllers |
+| @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 Ruflo MCP
+claude mcp add ruflo -- npx -y ruflo@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 ruflo@latest init --wizard
+npx ruflo@latest daemon start
+npx ruflo@latest doctor --fix
+
+# Swarm
+npx ruflo@latest swarm init --topology hierarchical --max-agents 8
+npx ruflo@latest swarm status
+
+# Agents
+npx ruflo@latest agent spawn -t coder
+npx ruflo@latest agent list
+
+# Memory
+npx ruflo@latest memory search --query "patterns"
+
+# Hooks
+npx ruflo@latest hooks pre-task --description "task"
+npx ruflo@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
  */
-function writeClaudeMd(targetDir, options, result) {
-    return __awaiter(this, void 0, Promise, function () {
-        var claudeMdPath, inferredTemplate, content;
-        return __generator(this, function (_a) {
-            claudeMdPath = path.join(targetDir, 'CLAUDE.md');
-            if (fs.existsSync(claudeMdPath) && !options.force) {
-                result.skipped.push('CLAUDE.md');
-                return [2 /*return*/];
-            }
-            inferredTemplate = (!options.components.commands && !options.components.agents) ? 'minimal' : undefined;
-            content = generateClaudeMd(options, inferredTemplate);
-            fs.writeFileSync(claudeMdPath, content, 'utf-8');
-            result.created.files.push('CLAUDE.md');
-            return [2 /*return*/];
-        });
-    });
+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
-    var possiblePaths = [];
+    const possiblePaths = [];
     // If explicit source base directory is provided, use it first
     if (sourceBaseDir) {
         possiblePaths.push(path.join(sourceBaseDir, '.claude', type));
@@ -1334,38 +1648,37 @@ function findSourceDir(type, sourceBaseDir) {
     // This is the primary path when running as an npm package
     // __dirname is typically /path/to/node_modules/@claude-flow/cli/dist/src/init
     // We need to go up 3 levels to reach the package root (dist/src/init -> dist/src -> dist -> root)
-    var packageRoot = path.resolve(__dirname, '..', '..', '..');
-    var packageDotClaude = path.join(packageRoot, '.claude', type);
+    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
-    var distPath = __dirname;
+    const distPath = __dirname;
     // Try to find the project root by looking for .claude directory
-    var currentDir = distPath;
-    for (var i = 0; i < 10; i++) {
-        var parentDir = path.dirname(currentDir);
-        var dotClaudePath = path.join(parentDir, '.claude', type);
+    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
-    var cwdBased = [
+    const cwdBased = [
         path.join(process.cwd(), '.claude', type),
         path.join(process.cwd(), '..', '.claude', type),
         path.join(process.cwd(), '..', '..', '.claude', type),
     ];
-    possiblePaths.push.apply(possiblePaths, cwdBased);
+    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 (var _i = 0, possiblePaths_3 = possiblePaths; _i < possiblePaths_3.length; _i++) {
-        var p = possiblePaths_3[_i];
+    for (const p of possiblePaths) {
         if (fs.existsSync(p)) {
             return p;
         }
@@ -1377,11 +1690,10 @@ function findSourceDir(type, sourceBaseDir) {
  */
 function copyDirRecursive(src, dest) {
     fs.mkdirSync(dest, { recursive: true });
-    var entries = fs.readdirSync(src, { withFileTypes: true });
-    for (var _i = 0, entries_1 = entries; _i < entries_1.length; _i++) {
-        var entry = entries_1[_i];
-        var srcPath = path.join(src, entry.name);
-        var destPath = path.join(dest, entry.name);
+    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);
         }
@@ -1394,11 +1706,10 @@ function copyDirRecursive(src, dest) {
  * Count files with extension in directory
  */
 function countFiles(dir, ext) {
-    var count = 0;
-    var entries = fs.readdirSync(dir, { withFileTypes: true });
-    for (var _i = 0, entries_2 = entries; _i < entries_2.length; _i++) {
-        var entry = entries_2[_i];
-        var fullPath = path.join(dir, entry.name);
+    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);
         }
@@ -1412,8 +1723,8 @@ function countFiles(dir, ext) {
  * Count enabled hooks
  */
 function countEnabledHooks(options) {
-    var hooks = options.hooks;
-    var count = 0;
+    const hooks = options.hooks;
+    let count = 0;
     if (hooks.preToolUse)
         count++;
     if (hooks.postToolUse)