@claude-flow/cli 3.32.1 → 3.32.3

package/dist/src/init/executor.js

@@ -1,2142 +0,0 @@
-/**
- * Init Executor
- * Main execution logic for V3 initialization
- */
-import * as fs from 'fs';
-import * as path from 'path';
-import { fileURLToPath } from 'url';
-import { createRequire } from 'module';
-import { dirname } from 'path';
-// ESM-compatible __dirname
-const __filename = fileURLToPath(import.meta.url);
-const __dirname = dirname(__filename);
-import { detectPlatform, DEFAULT_INIT_OPTIONS } from './types.js';
-import { generateSettingsJson, generateSettings } from './settings-generator.js';
-import { generateMCPJson } from './mcp-generator.js';
-import { generateStatuslineScript } from './statusline-generator.js';
-import { generatePreCommitHook, generatePostCommitHook, generateSessionManager, generateAgentRouter, generateMemoryHelper, generateHookHandler, generateIntelligenceStub, generateAutoMemoryHook, generateRufloHookCjs, } from './helpers-generator.js';
-import { getInstalledCliVersion, HELPERS_STAMP_FILE } from './helper-refresh.js';
-import { generateClaudeMd } from './claudemd-generator.js';
-import { recordMemoryPackagePath } from './memory-package-resolver.js';
-/**
- * Skills to copy based on configuration
- */
-const SKILLS_MAP = {
-    core: [
-        'swarm-orchestration',
-        'swarm-advanced',
-        'sparc-methodology',
-        'hooks-automation',
-        'pair-programming',
-        'verification-quality',
-        'stream-chain',
-        'skill-builder',
-    ],
-    browser: ['browser'], // agent-browser integration
-    dualMode: ['dual-mode'], // Claude Code + Codex hybrid execution
-    agentdb: [
-        'agentdb-advanced',
-        'agentdb-learning',
-        'agentdb-memory-patterns',
-        'agentdb-optimization',
-        'agentdb-vector-search',
-        'reasoningbank-agentdb',
-        'reasoningbank-intelligence',
-    ],
-    github: [
-        'github-code-review',
-        'github-multi-repo',
-        'github-project-management',
-        'github-release-management',
-        'github-workflow-automation',
-    ],
-    flowNexus: [
-        'flow-nexus-neural',
-        'flow-nexus-platform',
-        'flow-nexus-swarm',
-    ],
-    v3: [
-        'v3-cli-modernization',
-        'v3-core-implementation',
-        'v3-ddd-architecture',
-        'v3-integration-deep',
-        'v3-mcp-optimization',
-        'v3-memory-unification',
-        'v3-performance-optimization',
-        'v3-security-overhaul',
-        'v3-swarm-coordination',
-    ],
-};
-/**
- * Commands to copy based on configuration
- * ADR-128 Phase 4: every subdirectory under .claude/commands/ now has a
- * corresponding key. The flow-nexus/ dir was deleted (belongs to the plugin).
- * New substrate keys default true; opt-in keys (pair, training, stream-chain,
- * truth, verify) default false per ADR-128 §Phase 3 opt-in rationale.
- */
-const COMMANDS_MAP = {
-    core: ['claude-flow-help.md', 'claude-flow-swarm.md', 'claude-flow-memory.md'],
-    analysis: ['analysis'],
-    automation: ['automation'],
-    github: ['github'],
-    hooks: ['hooks'],
-    monitoring: ['monitoring'],
-    optimization: ['optimization'],
-    sparc: ['sparc'],
-    // ADR-128 Phase 4 promotions (previously orphaned)
-    agents: ['agents'],
-    coordination: ['coordination'],
-    hiveMind: ['hive-mind'],
-    memory: ['memory'],
-    swarm: ['swarm'],
-    workflows: ['workflows'],
-    // Opt-in categories (non-universal; default false in CommandsConfig)
-    pair: ['pair'],
-    training: ['training'],
-    streamChain: ['stream-chain'],
-    truth: ['truth'],
-    verify: ['verify'],
-};
-/**
- * Agents to copy based on configuration
- */
-const AGENTS_MAP = {
-    core: ['core'],
-    consensus: ['consensus'],
-    github: ['github'],
-    hiveMind: ['hive-mind'],
-    sparc: ['sparc'],
-    swarm: ['swarm'],
-    browser: ['browser'], // agent-browser integration
-    dualMode: ['dual-mode'], // Claude Code + Codex hybrid execution
-    // V3-specific agents
-    v3: ['v3'],
-    optimization: ['optimization'],
-    templates: ['templates'],
-    testing: ['testing'],
-    sublinear: ['sublinear'],
-    flowNexus: ['flow-nexus'],
-    analysis: ['analysis'],
-    architecture: ['architecture'],
-    development: ['development'],
-    devops: ['devops'],
-    documentation: ['documentation'],
-    specialized: ['specialized'],
-    goal: ['goal'],
-    sona: ['sona'],
-    payments: ['payments'],
-    data: ['data'],
-    custom: ['custom'],
-};
-/**
- * Directory structure to create
- */
-const DIRECTORIES = {
-    claude: [
-        '.claude',
-        '.claude/skills',
-        '.claude/commands',
-        '.claude/agents',
-        '.claude/helpers',
-    ],
-    runtime: [
-        '.claude-flow',
-        '.claude-flow/data',
-        '.claude-flow/logs',
-        '.claude-flow/sessions',
-        '.claude-flow/hooks',
-        '.claude-flow/agents',
-        '.claude-flow/workflows',
-    ],
-};
-/**
- * Execute initialization
- */
-export async function executeInit(options) {
-    // Detect platform
-    const platform = detectPlatform();
-    const result = {
-        success: true,
-        platform,
-        created: {
-            directories: [],
-            files: [],
-        },
-        skipped: [],
-        errors: [],
-        summary: {
-            skillsCount: 0,
-            commandsCount: 0,
-            agentsCount: 0,
-            hooksEnabled: 0,
-        },
-    };
-    const targetDir = options.targetDir;
-    try {
-        // Create directory structure
-        await createDirectories(targetDir, options, result);
-        // Generate and write settings.json
-        if (options.components.settings) {
-            await writeSettings(targetDir, options, result);
-        }
-        // Generate and write .mcp.json
-        if (options.components.mcp) {
-            await writeMCPConfig(targetDir, options, result);
-        }
-        // Copy skills
-        if (options.components.skills) {
-            await copySkills(targetDir, options, result);
-        }
-        // Copy commands
-        if (options.components.commands) {
-            await copyCommands(targetDir, options, result);
-        }
-        // Copy agents
-        if (options.components.agents) {
-            await copyAgents(targetDir, options, result);
-        }
-        // Generate helpers
-        if (options.components.helpers) {
-            await writeHelpers(targetDir, options, result);
-            // #2545: The auto-memory hook needs @claude-flow/memory, which is an
-            // optionalDependency of the CLI and lands in the npx cache — unreachable
-            // by a node_modules walk-up from the user's project. Resolve it from the
-            // CLI's own context now (where it IS present) and record the absolute
-            // path in a machine-local sidecar the hook reads first. Best-effort:
-            // when the optional dep is absent the hook fails loud and doctor flags it.
-            const memRecord = recordMemoryPackagePath(targetDir, 'init');
-            if (memRecord) {
-                result.created.files.push('.claude-flow/memory-package.json');
-            }
-            // #2568-followup: if this project already has a memory DB that predates
-            // the `vector_indexes` table (older CLI / agentdb-written), self-heal it
-            // so the statusline vector count + namespace routing work. Best-effort,
-            // dynamically imported so a WASM-only host without better-sqlite3 just
-            // skips it.
-            //
-            // Persistent memory ON BY DEFAULT: `runtime.memoryBackend` already
-            // defaults to 'hybrid' in DEFAULT_INIT_OPTIONS, but that only ever
-            // configured the DECLARED backend — the actual .swarm/memory.db file
-            // was never created until something eventually called `memory store`
-            // or the user ran `memory init --force` by hand (both the generated
-            // CLAUDE.md and the quickstart docs told users to do this as a
-            // separate step). A fresh project could sit for days looking
-            // "configured for AgentDB" while genuinely capturing nothing, with no
-            // signal that the config and the on-disk reality had diverged. Fresh
-            // projects now get the DB eagerly created here, matching what
-            // `memoryBackend` already promised; MINIMAL_INIT_OPTIONS
-            // (memoryBackend: 'memory') opts out, matching its non-persistent intent.
-            try {
-                const memDbPath = path.join(targetDir, '.swarm', 'memory.db');
-                if (fs.existsSync(memDbPath)) {
-                    const { repairVectorIndexes } = await import('../memory/memory-initializer.js');
-                    await repairVectorIndexes(memDbPath, { autoRecover: true });
-                }
-                else if (options.runtime.memoryBackend !== 'memory') {
-                    const { initializeMemoryDatabase } = await import('../memory/memory-initializer.js');
-                    const initResult = await initializeMemoryDatabase({
-                        backend: options.runtime.memoryBackend,
-                        dbPath: memDbPath,
-                        verbose: false,
-                    });
-                    if (initResult.success) {
-                        result.created.files.push('.swarm/memory.db');
-                    }
-                }
-            }
-            catch { /* best-effort — never block init on memory setup */ }
-        }
-        // Generate statusline
-        if (options.components.statusline) {
-            await writeStatusline(targetDir, options, result);
-        }
-        // Generate runtime config
-        if (options.components.runtime) {
-            await writeRuntimeConfig(targetDir, options, result);
-        }
-        // Create initial metrics for statusline (prevents "all zeros" display)
-        if (options.components.statusline) {
-            await writeInitialMetrics(targetDir, options, result);
-        }
-        // Generate CLAUDE.md
-        if (options.components.claudeMd) {
-            await writeClaudeMd(targetDir, options, result);
-        }
-        // Count enabled hooks
-        result.summary.hooksEnabled = countEnabledHooks(options);
-    }
-    catch (error) {
-        result.success = false;
-        result.errors.push(error instanceof Error ? error.message : String(error));
-    }
-    return result;
-}
-/**
- * Merge new settings into existing settings.json
- * Preserves user customizations while adding new features like Agent Teams
- * Uses platform-specific commands for Mac, Linux, and Windows
- */
-function mergeSettingsForUpgrade(existing) {
-    const merged = { ...existing };
-    const platform = detectPlatform();
-    const isWindows = platform.os === 'windows';
-    // Platform-specific command wrappers
-    // Windows: Use PowerShell-compatible commands
-    // Mac/Linux: Use bash-compatible commands with 2>/dev/null
-    // NOTE: teammateIdleCmd and taskCompletedCmd were removed.
-    // 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)
-    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)
-    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).
-    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()}';
-    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)
-    const sessionStartHooks = existingHooks.SessionStart;
-    const hasAutoMemoryImport = sessionStartHooks?.some(group => group.hooks?.some(h => h.command?.includes('auto-memory-hook')));
-    if (!hasAutoMemoryImport) {
-        const startHooks = merged.hooks;
-        if (!startHooks.SessionStart) {
-            startHooks.SessionStart = [{ hooks: [] }];
-        }
-        const startGroup = startHooks.SessionStart[0];
-        if (!startGroup.hooks)
-            startGroup.hooks = [];
-        startGroup.hooks.push({
-            type: 'command',
-            command: autoMemoryImportCmd,
-            timeout: 6000,
-            continueOnError: true,
-        });
-    }
-    // Add auto-memory sync to SessionEnd (if not already present)
-    const sessionEndHooks = existingHooks.SessionEnd;
-    const hasAutoMemorySync = sessionEndHooks?.some(group => group.hooks?.some(h => h.command?.includes('auto-memory-hook')));
-    if (!hasAutoMemorySync) {
-        const endHooks = merged.hooks;
-        if (!endHooks.SessionEnd) {
-            endHooks.SessionEnd = [{ hooks: [] }];
-        }
-        const endGroup = endHooks.SessionEnd[0];
-        if (!endGroup.hooks)
-            endGroup.hooks = [];
-        // Insert at beginning so sync runs before other cleanup
-        endGroup.hooks.unshift({
-            type: 'command',
-            command: autoMemorySyncCmd,
-            timeout: 8000,
-            continueOnError: true,
-        });
-    }
-    // NOTE: TeammateIdle and TaskCompleted are NOT valid Claude Code hook events.
-    // They cause warnings when present in settings.json hooks.
-    // Remove them if they exist from a previous init.
-    delete merged.hooks.TeammateIdle;
-    delete merged.hooks.TaskCompleted;
-    // 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
-    //
-    // #2448 — Detect and REGENERATE the runaway `npx @claude-flow/cli@latest`
-    // statusline form. Pre-#2337 init wrote this to settings.json; it spawns
-    // a cold Node process + npm registry round-trip on every fire (statusline
-    // refires every few hundred ms), which on macOS produced load average 49
-    // / jetsam / kernel panic. Preserving the user's existing command (the
-    // old behavior here) means anyone who installed pre-#2337 and upgraded
-    // never gets the fix. Now we detect the broken form and overwrite.
-    const NEW_STATUSLINE_CMD = `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)"`;
-    // Matches any invocation of `claude-flow hooks statusline` — either via npx
-    // (`npx [--prefer-offline] [@]claude-flow[/cli][@<tag>] hooks statusline …`)
-    // or as a bare command (`claude-flow hooks statusline …`). Both forms cold-
-    // load the ONNX model on every fire (~1s); Claude Code times out and hides
-    // the status bar (#2450). The migration replaces the whole command with
-    // NEW_STATUSLINE_CMD which invokes the local helper directly via `node -e`.
-    // Flag-list repetition bounded at 10 (real invocations never carry more) —
-    // an unbounded `*` here is exponential-backtracking-prone (CodeQL
-    // js/redos): a crafted settings.json command string with dozens of
-    // dash-token repetitions can hang this check for minutes.
-    const BROKEN_STATUSLINE_RE = /(?:npx\s+(?:--?\S+\s+){0,10})?@?claude-flow(?:\/cli)?(?:@\S+)?\s+hooks\s+statusline/;
-    const existingStatusLine = existing.statusLine;
-    if (existingStatusLine) {
-        const existingCmd = typeof existingStatusLine.command === 'string' ? existingStatusLine.command : '';
-        const isBroken = BROKEN_STATUSLINE_RE.test(existingCmd);
-        merged.statusLine = {
-            type: 'command',
-            command: isBroken || !existingCmd ? NEW_STATUSLINE_CMD : existingCmd,
-            // Remove invalid fields: refreshMs, enabled (not supported by Claude Code)
-        };
-    }
-    // #2448 — Detect and REGENERATE per-action hook commands that still use
-    // the runaway `npx @claude-flow/cli@latest hooks <sub>` form. These fire
-    // on every PreToolUse/PostToolUse/UserPromptSubmit, each spawning ~130 MB
-    // of cold Node + npm registry resolution; the storm is what kernel-paniced
-    // the reporter's machine in #2448.
-    //
-    // We walk each hook event's `hooks[]` and swap any command matching the
-    // broken pattern for the local-helper form. Idempotent: re-running this
-    // migration on already-correct settings is a no-op.
-    // Bounded for the same reason as BROKEN_STATUSLINE_RE above (CodeQL js/redos).
-    const BROKEN_HOOK_RE = /npx\s+(?:--?\S+\s+){0,10}@?claude-flow\/cli@latest\s+hooks\s+(\S+)/;
-    const localHookCmd = (sub) => {
-        // POSIX form mirrors settings-generator.ts::hookCmd() exactly.
-        // Windows users hit a separate code path (cmd /c …) — Claude Code on
-        // Windows is rarer and the migration there is left to a follow-up.
-        if (process.platform === 'win32') {
-            return `cmd /c "IF EXIST \"%CLAUDE_PROJECT_DIR%\\.claude\\helpers\\hook-handler.cjs\" (node \"%CLAUDE_PROJECT_DIR%\\.claude\\helpers\\hook-handler.cjs\" ${sub}) ELSE (node \"%USERPROFILE%\\.claude\\helpers\\hook-handler.cjs\" ${sub})"`;
-        }
-        return `sh -c 'D="\${CLAUDE_PROJECT_DIR:-.}"; [ -f "$D/.claude/helpers/hook-handler.cjs" ] || D="\${HOME}"; exec node "$D/.claude/helpers/hook-handler.cjs" ${sub}'`;
-    };
-    const mergedHooks = merged.hooks;
-    if (mergedHooks) {
-        for (const eventName of Object.keys(mergedHooks)) {
-            const groups = mergedHooks[eventName];
-            if (!Array.isArray(groups))
-                continue;
-            for (const group of groups) {
-                if (!Array.isArray(group.hooks))
-                    continue;
-                for (const h of group.hooks) {
-                    if (typeof h?.command !== 'string')
-                        continue;
-                    const m = BROKEN_HOOK_RE.exec(h.command);
-                    if (!m)
-                        continue;
-                    // Subcommand captured (e.g. "pre-bash", "post-edit", "route") — keep it.
-                    h.command = localHookCmd(m[1]);
-                }
-            }
-        }
-    }
-    // 4. Merge claudeFlow settings (preserve existing, add agentTeams + memory)
-    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,
-            mailboxEnabled: true,
-            coordination: {
-                autoAssignOnIdle: true,
-                trainPatternsOnComplete: true,
-                notifyLeadOnComplete: true,
-                sharedMemoryNamespace: 'agent-teams',
-            },
-            hooks: {
-                teammateIdle: { enabled: true, autoAssign: true, checkTaskList: true },
-                taskCompleted: { enabled: true, trainPatterns: true, notifyLead: true },
-            },
-        },
-        memory: {
-            ...existingMemory,
-            learningBridge: existingMemory.learningBridge ?? { enabled: true },
-            memoryGraph: existingMemory.memoryGraph ?? { enabled: true },
-            agentScopes: existingMemory.agentScopes ?? { enabled: true },
-        },
-    };
-    return merged;
-}
-/**
- * Execute upgrade - updates helpers and creates missing metrics without losing data
- * This is safe for existing users who want the latest statusline fixes
- * @param targetDir - Target directory
- * @param upgradeSettings - If true, merge new settings into existing settings.json
- */
-export async function executeUpgrade(targetDir, upgradeSettings = false) {
-    const result = {
-        success: true,
-        updated: [],
-        created: [],
-        preserved: [],
-        errors: [],
-        settingsUpdated: [],
-    };
-    try {
-        // Ensure required directories exist
-        const dirs = [
-            '.claude/helpers',
-            '.claude-flow/metrics',
-            '.claude-flow/security',
-            '.claude-flow/learning',
-        ];
-        for (const dir of dirs) {
-            const fullPath = path.join(targetDir, dir);
-            if (!fs.existsSync(fullPath)) {
-                fs.mkdirSync(fullPath, { recursive: true });
-            }
-        }
-        // 0. ALWAYS update critical helpers (force overwrite)
-        const sourceHelpersForUpgrade = findSourceHelpersDir();
-        if (sourceHelpersForUpgrade) {
-            // Keep in sync with helper-refresh.ts:CRITICAL_HELPERS.
-            const criticalHelpers = ['auto-memory-hook.mjs', 'hook-handler.cjs', 'intelligence.cjs', 'statusline.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}`);
-                    }
-                    else {
-                        result.created.push(`.claude/helpers/${helperName}`);
-                    }
-                    fs.copyFileSync(sourcePath, targetPath);
-                    try {
-                        fs.chmodSync(targetPath, '755');
-                    }
-                    catch { }
-                }
-            }
-        }
-        else {
-            // Source not found (npx with broken paths) — use generated fallbacks
-            const generatedCritical = {
-                'hook-handler.cjs': generateHookHandler(),
-                'intelligence.cjs': generateIntelligenceStub(),
-                'auto-memory-hook.mjs': generateAutoMemoryHook(),
-            };
-            for (const [helperName, content] of Object.entries(generatedCritical)) {
-                const targetPath = path.join(targetDir, '.claude', 'helpers', helperName);
-                if (fs.existsSync(targetPath)) {
-                    result.updated.push(`.claude/helpers/${helperName}`);
-                }
-                else {
-                    result.created.push(`.claude/helpers/${helperName}`);
-                }
-                fs.writeFileSync(targetPath, content, 'utf-8');
-                try {
-                    fs.chmodSync(targetPath, '755');
-                }
-                catch { }
-            }
-        }
-        // Stamp the installed version so the startup auto-refresh treats these as
-        // current (no redundant re-copy on the next command).
-        try {
-            fs.writeFileSync(path.join(targetDir, '.claude', 'helpers', HELPERS_STAMP_FILE), getInstalledCliVersion(), 'utf-8');
-        }
-        catch { /* non-fatal */ }
-        // #2545: (re)record the resolved @claude-flow/memory path so the auto-memory
-        // hook can find it on the npx install path. Best-effort — see executeInit.
-        const memRecord = recordMemoryPackagePath(targetDir, 'upgrade');
-        if (memRecord) {
-            result.updated.push('.claude-flow/memory-package.json');
-        }
-        // 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)',
-                    ];
-                }
-                catch (settingsError) {
-                    result.errors.push(`Settings merge failed: ${settingsError instanceof Error ? settingsError.message : String(settingsError)}`);
-                }
-            }
-            else {
-                // Create new settings.json with defaults
-                const defaultSettings = generateSettings(DEFAULT_INIT_OPTIONS);
-                fs.writeFileSync(settingsPath, JSON.stringify(defaultSettings, null, 2), 'utf-8');
-                result.created.push('.claude/settings.json');
-                result.settingsUpdated = ['Created new settings.json with Agent Teams'];
-            }
-        }
-    }
-    catch (error) {
-        result.success = false;
-        result.errors.push(error instanceof Error ? error.message : String(error));
-    }
-    return result;
-}
-/**
- * Execute upgrade with --add-missing flag
- * Adds any new skills, agents, and commands that don't exist yet
- * @param targetDir - Target directory
- * @param upgradeSettings - If true, merge new settings into existing settings.json
- */
-export async function executeUpgradeWithMissing(targetDir, upgradeSettings = false) {
-    // First do the normal upgrade (pass through upgradeSettings)
-    const result = await executeUpgrade(targetDir, upgradeSettings);
-    if (!result.success) {
-        return result;
-    }
-    // Initialize tracking arrays
-    result.addedSkills = [];
-    result.addedAgents = [];
-    result.addedCommands = [];
-    try {
-        // Ensure target directories exist
-        const skillsDir = path.join(targetDir, '.claude', 'skills');
-        const agentsDir = path.join(targetDir, '.claude', 'agents');
-        const commandsDir = path.join(targetDir, '.claude', 'commands');
-        for (const dir of [skillsDir, agentsDir, commandsDir]) {
-            if (!fs.existsSync(dir)) {
-                fs.mkdirSync(dir, { recursive: true });
-            }
-        }
-        // Find source directories
-        const sourceSkillsDir = findSourceDir('skills');
-        const sourceAgentsDir = findSourceDir('agents');
-        const sourceCommandsDir = findSourceDir('commands');
-        // Debug: Log source directories found
-        if (process.env.DEBUG || process.env.CLAUDE_FLOW_DEBUG) {
-            console.log('[DEBUG] Source directories:');
-            console.log(`  Skills: ${sourceSkillsDir || 'NOT FOUND'}`);
-            console.log(`  Agents: ${sourceAgentsDir || 'NOT FOUND'}`);
-            console.log(`  Commands: ${sourceCommandsDir || 'NOT FOUND'}`);
-        }
-        // Add missing skills
-        if (sourceSkillsDir) {
-            const allSkills = Object.values(SKILLS_MAP).flat();
-            const debugMode = process.env.DEBUG || process.env.CLAUDE_FLOW_DEBUG;
-            if (debugMode) {
-                console.log(`[DEBUG] Checking ${allSkills.length} skills from SKILLS_MAP`);
-            }
-            for (const skillName of [...new Set(allSkills)]) {
-                const sourcePath = path.join(sourceSkillsDir, skillName);
-                const targetPath = path.join(skillsDir, skillName);
-                const sourceExists = fs.existsSync(sourcePath);
-                const targetExists = fs.existsSync(targetPath);
-                if (debugMode) {
-                    console.log(`[DEBUG] Skill '${skillName}': source=${sourceExists}, target=${targetExists}`);
-                }
-                if (sourceExists && !targetExists) {
-                    copyDirRecursive(sourcePath, targetPath);
-                    result.addedSkills.push(skillName);
-                    result.created.push(`.claude/skills/${skillName}`);
-                }
-            }
-        }
-        // Add missing agents
-        if (sourceAgentsDir) {
-            const allAgents = Object.values(AGENTS_MAP).flat();
-            for (const agentCategory of [...new Set(allAgents)]) {
-                const sourcePath = path.join(sourceAgentsDir, agentCategory);
-                const targetPath = path.join(agentsDir, agentCategory);
-                if (fs.existsSync(sourcePath) && !fs.existsSync(targetPath)) {
-                    copyDirRecursive(sourcePath, targetPath);
-                    result.addedAgents.push(agentCategory);
-                    result.created.push(`.claude/agents/${agentCategory}`);
-                }
-            }
-        }
-        // Add missing commands
-        if (sourceCommandsDir) {
-            const allCommands = Object.values(COMMANDS_MAP).flat();
-            for (const cmdName of [...new Set(allCommands)]) {
-                const sourcePath = path.join(sourceCommandsDir, cmdName);
-                const targetPath = path.join(commandsDir, cmdName);
-                if (fs.existsSync(sourcePath) && !fs.existsSync(targetPath)) {
-                    if (fs.statSync(sourcePath).isDirectory()) {
-                        copyDirRecursive(sourcePath, targetPath);
-                    }
-                    else {
-                        fs.copyFileSync(sourcePath, targetPath);
-                    }
-                    result.addedCommands.push(cmdName);
-                    result.created.push(`.claude/commands/${cmdName}`);
-                }
-            }
-        }
-    }
-    catch (error) {
-        result.errors.push(`Add missing failed: ${error instanceof Error ? error.message : String(error)}`);
-    }
-    return result;
-}
-/**
- * Create directory structure
- */
-async function createDirectories(targetDir, options, result) {
-    const dirs = [
-        ...DIRECTORIES.claude,
-        ...(options.components.runtime ? DIRECTORIES.runtime : []),
-    ];
-    for (const dir of dirs) {
-        const fullPath = path.join(targetDir, dir);
-        if (!fs.existsSync(fullPath)) {
-            fs.mkdirSync(fullPath, { recursive: true });
-            result.created.directories.push(dir);
-        }
-    }
-}
-/**
- * Write settings.json
- */
-async function writeSettings(targetDir, options, result) {
-    const settingsPath = path.join(targetDir, '.claude', 'settings.json');
-    const generated = JSON.parse(generateSettingsJson(options));
-    if (fs.existsSync(settingsPath) && !options.force) {
-        // Merge hooks/env/permissions into existing settings instead of skipping
-        try {
-            const existing = JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
-            let merged = false;
-            // Merge hooks (the critical missing piece — #1484)
-            if (generated.hooks && !existing.hooks) {
-                existing.hooks = generated.hooks;
-                merged = true;
-            }
-            // Merge env vars (for CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS etc.)
-            if (generated.env) {
-                existing.env = { ...(existing.env || {}), ...generated.env };
-                merged = true;
-            }
-            // Merge permissions (add ruflo allow rules)
-            if (generated.permissions?.allow) {
-                const existingAllow = existing.permissions?.allow || [];
-                const newRules = generated.permissions.allow.filter((r) => !existingAllow.includes(r));
-                if (newRules.length > 0) {
-                    existing.permissions = existing.permissions || {};
-                    existing.permissions.allow = [...existingAllow, ...newRules];
-                    merged = true;
-                }
-            }
-            if (merged) {
-                fs.writeFileSync(settingsPath, JSON.stringify(existing, null, 2), 'utf-8');
-                result.created.files.push('.claude/settings.json (merged hooks)');
-            }
-            else {
-                result.skipped.push('.claude/settings.json');
-            }
-        }
-        catch {
-            // Existing file is corrupt — overwrite
-            fs.writeFileSync(settingsPath, JSON.stringify(generated, null, 2), 'utf-8');
-            result.created.files.push('.claude/settings.json');
-        }
-        return;
-    }
-    fs.writeFileSync(settingsPath, JSON.stringify(generated, null, 2), 'utf-8');
-    result.created.files.push('.claude/settings.json');
-}
-/**
- * #1779 — Walk parents of `targetDir` plus the user-global Claude Code
- * config locations, looking for any `.mcp.json` (or `~/.claude.json`)
- * that already declares a `ruflo`-keyed MCP server. We use this to skip
- * writing our own `claude-flow`-keyed entry when the user has already
- * registered the same binary under the new name — that's exactly the
- * "same MCP server twice under two different prefixes" duplication the
- * issue describes.
- *
- * Returns the path of the file that already declares `ruflo`/`claude-flow` (so we can
- * surface it in the skipped-message), or null if none found.
- */
-function detectExistingRufloMCP(targetDir) {
-    const home = (process.env.HOME ?? process.env.USERPROFILE) ?? '';
-    const candidates = new Set();
-    // User-global Claude Code config locations
-    if (home) {
-        candidates.add(path.join(home, '.claude.json'));
-        candidates.add(path.join(home, '.claude', 'mcp.json'));
-    }
-    // Walk parents of targetDir up to root, checking for .mcp.json at each
-    const targetResolved = path.resolve(targetDir);
-    let dir = targetResolved;
-    const targetAncestors = new Set();
-    while (true) {
-        candidates.add(path.join(dir, '.mcp.json'));
-        targetAncestors.add(normalizeProjectKey(dir));
-        const parent = path.dirname(dir);
-        if (parent === dir)
-            break;
-        dir = parent;
-    }
-    // Skip the targetDir itself — that's the one we're about to write
-    candidates.delete(path.join(targetResolved, '.mcp.json'));
-    for (const candidate of candidates) {
-        if (!fs.existsSync(candidate))
-            continue;
-        try {
-            const parsed = JSON.parse(fs.readFileSync(candidate, 'utf-8'));
-            if (!parsed || typeof parsed !== 'object')
-                continue;
-            // (a) Top-level mcpServers (legacy / global form).
-            // Accept BOTH names so init does not add a second server for the same
-            // binary when a project carries a pre-rename `claude-flow` registration
-            // and the current generator would write `ruflo` (#2612).
-            if (parsed.mcpServers && typeof parsed.mcpServers === 'object') {
-                const servers = parsed.mcpServers;
-                // #2369: also recognise the legacy dist-tag keys generated by
-                // pre-rename installs (claude-flow ≤ 2.x). Without these the
-                // detection walks parent dirs, doesn't match, and writes a NEW
-                // claude-flow-keyed config — both servers then run under
-                // different prefixes producing duplicate-tool noise.
-                if ('claude-flow' in servers ||
-                    'ruflo' in servers ||
-                    'claude-flow@alpha' in servers ||
-                    'claude-flow@v3alpha' in servers)
-                    return candidate;
-            }
-            // (b) #1840: Claude Code project-scoped registrations under
-            //     parsed.projects[<projectPath>].mcpServers. Match by
-            //     normalized path against targetDir or any of its ancestors so an
-            //     existing `claude-flow` or `ruflo` registration in this repo is
-            //     detected even when Claude stored the key with different casing/slash style.
-            if (parsed.projects && typeof parsed.projects === 'object') {
-                for (const [projectKey, projectVal] of Object.entries(parsed.projects)) {
-                    if (!projectVal || typeof projectVal !== 'object')
-                        continue;
-                    const projectMcp = projectVal.mcpServers;
-                    if (!projectMcp || typeof projectMcp !== 'object')
-                        continue;
-                    const mcp = projectMcp;
-                    // #2369: legacy dist-tag keys also count as already-registered.
-                    if (!('claude-flow' in mcp) &&
-                        !('ruflo' in mcp) &&
-                        !('claude-flow@alpha' in mcp) &&
-                        !('claude-flow@v3alpha' in mcp))
-                        continue;
-                    if (targetAncestors.has(normalizeProjectKey(projectKey))) {
-                        return `${candidate} (projects[${projectKey}])`;
-                    }
-                }
-            }
-        }
-        catch { /* malformed JSON — ignore */ }
-    }
-    return null;
-}
-/**
- * Normalize a project path key for cross-platform comparison.
- * Claude Code stores Windows paths like "C:/Users/.../Project" while
- * Node's `path.resolve()` may emit "C:\Users\...\Project". Lowercase +
- * forward-slash gives a stable comparison key on both platforms.
- */
-function normalizeProjectKey(p) {
-    return path.resolve(p).replace(/\\/g, '/').toLowerCase();
-}
-/**
- * Write .mcp.json
- */
-async function writeMCPConfig(targetDir, options, result) {
-    const mcpPath = path.join(targetDir, '.mcp.json');
-    if (fs.existsSync(mcpPath) && !options.force) {
-        // #2369: an existing .mcp.json from a pre-rename install is the most
-        // common cause of "autopilot tools missing after init" reports. Parse
-        // the existing file and surface a loud, specific message naming the
-        // stale key so users know to either delete the file or re-run with
-        // --force. Without this they get a silent skip and no warning.
-        try {
-            const parsed = JSON.parse(fs.readFileSync(mcpPath, 'utf-8'));
-            const servers = parsed?.mcpServers;
-            if (servers && typeof servers === 'object') {
-                const staleKeys = ['claude-flow@alpha', 'claude-flow@v3alpha'].filter(k => k in servers);
-                if (staleKeys.length > 0) {
-                    result.skipped.push(`.mcp.json (existing file uses deprecated key '${staleKeys[0]}' — autopilot/browser/wasm-agent tools will be missing; ` +
-                        `delete .mcp.json and re-run, or re-run with --force to overwrite)`);
-                    return;
-                }
-            }
-        }
-        catch {
-            // Existing file isn't valid JSON — fall through to the generic skip.
-        }
-        result.skipped.push('.mcp.json');
-        return;
-    }
-    // #1779/#2612 — Skip writing if the user already has this MCP server
-    // registered elsewhere (parent .mcp.json, ~/.claude.json, etc). The
-    // canonical key is `claude-flow` (per #2206 — matches mcp__claude-flow__*
-    // plugin tool refs); a stray `ruflo`-keyed entry pointing at the same
-    // binary is the legacy-duplicate form that #2612 healed. Writing our
-    // fresh `claude-flow` entry on top of either variant starts the same
-    // binary twice under two tool namespaces. Force-mode (`--force`)
-    // bypasses this guard for users who actually want both registrations.
-    if (!options.force) {
-        const existingRufloPath = detectExistingRufloMCP(targetDir);
-        if (existingRufloPath) {
-            result.skipped.push(`.mcp.json (existing ruflo/claude-flow MCP registration found at ${existingRufloPath} — would create duplicate; pass --force to write anyway)`);
-            return;
-        }
-    }
-    const content = generateMCPJson(options);
-    fs.writeFileSync(mcpPath, content, 'utf-8');
-    result.created.files.push('.mcp.json');
-}
-/**
- * Copy skills from source
- */
-async function copySkills(targetDir, options, result) {
-    const skillsConfig = options.skills;
-    const targetSkillsDir = path.join(targetDir, '.claude', 'skills');
-    // Determine which skills to copy
-    const skillsToCopy = [];
-    if (skillsConfig.all) {
-        // Copy all available skills
-        Object.values(SKILLS_MAP).forEach(skills => skillsToCopy.push(...skills));
-    }
-    else {
-        if (skillsConfig.core)
-            skillsToCopy.push(...SKILLS_MAP.core);
-        if (skillsConfig.agentdb)
-            skillsToCopy.push(...SKILLS_MAP.agentdb);
-        if (skillsConfig.github)
-            skillsToCopy.push(...SKILLS_MAP.github);
-        if (skillsConfig.flowNexus)
-            skillsToCopy.push(...SKILLS_MAP.flowNexus);
-        if (skillsConfig.browser)
-            skillsToCopy.push(...SKILLS_MAP.browser);
-        if (skillsConfig.v3)
-            skillsToCopy.push(...SKILLS_MAP.v3);
-        if (skillsConfig.dualMode)
-            skillsToCopy.push(...SKILLS_MAP.dualMode);
-    }
-    // Find source skills directory
-    const sourceSkillsDir = findSourceDir('skills', options.sourceBaseDir);
-    if (!sourceSkillsDir) {
-        result.errors.push('Could not find source skills directory');
-        return;
-    }
-    // Copy each skill
-    for (const skillName of [...new Set(skillsToCopy)]) {
-        const sourcePath = path.join(sourceSkillsDir, skillName);
-        const targetPath = path.join(targetSkillsDir, skillName);
-        if (fs.existsSync(sourcePath)) {
-            if (!fs.existsSync(targetPath) || options.force) {
-                copyDirRecursive(sourcePath, targetPath);
-                result.created.files.push(`.claude/skills/${skillName}`);
-                result.summary.skillsCount++;
-            }
-            else {
-                result.skipped.push(`.claude/skills/${skillName}`);
-            }
-        }
-    }
-}
-/**
- * Copy commands from source
- */
-async function copyCommands(targetDir, options, result) {
-    const commandsConfig = options.commands;
-    const targetCommandsDir = path.join(targetDir, '.claude', 'commands');
-    // Determine which commands to copy
-    const commandsToCopy = [];
-    if (commandsConfig.all) {
-        Object.values(COMMANDS_MAP).forEach(cmds => commandsToCopy.push(...cmds));
-    }
-    else {
-        if (commandsConfig.core)
-            commandsToCopy.push(...COMMANDS_MAP.core);
-        if (commandsConfig.analysis)
-            commandsToCopy.push(...COMMANDS_MAP.analysis);
-        if (commandsConfig.automation)
-            commandsToCopy.push(...COMMANDS_MAP.automation);
-        if (commandsConfig.github)
-            commandsToCopy.push(...COMMANDS_MAP.github);
-        if (commandsConfig.hooks)
-            commandsToCopy.push(...COMMANDS_MAP.hooks);
-        if (commandsConfig.monitoring)
-            commandsToCopy.push(...COMMANDS_MAP.monitoring);
-        if (commandsConfig.optimization)
-            commandsToCopy.push(...COMMANDS_MAP.optimization);
-        if (commandsConfig.sparc)
-            commandsToCopy.push(...COMMANDS_MAP.sparc);
-        // ADR-128 Phase 4 substrate promotions
-        if (commandsConfig.agents)
-            commandsToCopy.push(...(COMMANDS_MAP.agents || []));
-        if (commandsConfig.coordination)
-            commandsToCopy.push(...(COMMANDS_MAP.coordination || []));
-        if (commandsConfig.hiveMind)
-            commandsToCopy.push(...(COMMANDS_MAP.hiveMind || []));
-        if (commandsConfig.memory)
-            commandsToCopy.push(...(COMMANDS_MAP.memory || []));
-        if (commandsConfig.swarm)
-            commandsToCopy.push(...(COMMANDS_MAP.swarm || []));
-        if (commandsConfig.workflows)
-            commandsToCopy.push(...(COMMANDS_MAP.workflows || []));
-        // ADR-128 Phase 4 opt-in categories
-        if (commandsConfig.pair)
-            commandsToCopy.push(...(COMMANDS_MAP.pair || []));
-        if (commandsConfig.training)
-            commandsToCopy.push(...(COMMANDS_MAP.training || []));
-        if (commandsConfig.streamChain)
-            commandsToCopy.push(...(COMMANDS_MAP.streamChain || []));
-        if (commandsConfig.truth)
-            commandsToCopy.push(...(COMMANDS_MAP.truth || []));
-        if (commandsConfig.verify)
-            commandsToCopy.push(...(COMMANDS_MAP.verify || []));
-    }
-    // Find source commands directory
-    const sourceCommandsDir = findSourceDir('commands', options.sourceBaseDir);
-    if (!sourceCommandsDir) {
-        result.errors.push('Could not find source commands directory');
-        return;
-    }
-    // Copy each command/directory
-    for (const cmdName of [...new Set(commandsToCopy)]) {
-        const sourcePath = path.join(sourceCommandsDir, cmdName);
-        const targetPath = path.join(targetCommandsDir, cmdName);
-        if (fs.existsSync(sourcePath)) {
-            if (!fs.existsSync(targetPath) || options.force) {
-                if (fs.statSync(sourcePath).isDirectory()) {
-                    copyDirRecursive(sourcePath, targetPath);
-                }
-                else {
-                    fs.copyFileSync(sourcePath, targetPath);
-                }
-                result.created.files.push(`.claude/commands/${cmdName}`);
-                result.summary.commandsCount++;
-            }
-            else {
-                result.skipped.push(`.claude/commands/${cmdName}`);
-            }
-        }
-    }
-}
-/**
- * Copy agents from source
- */
-async function copyAgents(targetDir, options, result) {
-    const agentsConfig = options.agents;
-    const targetAgentsDir = path.join(targetDir, '.claude', 'agents');
-    // Determine which agents to copy
-    const agentsToCopy = [];
-    if (agentsConfig.all) {
-        Object.values(AGENTS_MAP).forEach(agents => agentsToCopy.push(...agents));
-    }
-    else {
-        if (agentsConfig.core)
-            agentsToCopy.push(...AGENTS_MAP.core);
-        if (agentsConfig.consensus)
-            agentsToCopy.push(...AGENTS_MAP.consensus);
-        if (agentsConfig.github)
-            agentsToCopy.push(...AGENTS_MAP.github);
-        if (agentsConfig.hiveMind)
-            agentsToCopy.push(...AGENTS_MAP.hiveMind);
-        if (agentsConfig.sparc)
-            agentsToCopy.push(...AGENTS_MAP.sparc);
-        if (agentsConfig.swarm)
-            agentsToCopy.push(...AGENTS_MAP.swarm);
-        if (agentsConfig.browser)
-            agentsToCopy.push(...AGENTS_MAP.browser);
-        // V3-specific agent categories
-        if (agentsConfig.v3)
-            agentsToCopy.push(...(AGENTS_MAP.v3 || []));
-        if (agentsConfig.optimization)
-            agentsToCopy.push(...(AGENTS_MAP.optimization || []));
-        if (agentsConfig.testing)
-            agentsToCopy.push(...(AGENTS_MAP.testing || []));
-        // Dual-mode agents (Claude Code + Codex hybrid)
-        if (agentsConfig.dualMode)
-            agentsToCopy.push(...(AGENTS_MAP.dualMode || []));
-    }
-    // Find source agents directory
-    const sourceAgentsDir = findSourceDir('agents', options.sourceBaseDir);
-    if (!sourceAgentsDir) {
-        result.errors.push('Could not find source agents directory');
-        return;
-    }
-    // Copy each agent category
-    for (const agentCategory of [...new Set(agentsToCopy)]) {
-        const sourcePath = path.join(sourceAgentsDir, agentCategory);
-        const targetPath = path.join(targetAgentsDir, agentCategory);
-        if (fs.existsSync(sourcePath)) {
-            if (!fs.existsSync(targetPath) || options.force) {
-                copyDirRecursive(sourcePath, targetPath);
-                // Count agent files (.md only — .yaml agents were migrated to .md)
-                const mdFiles = countFiles(sourcePath, '.md');
-                result.summary.agentsCount += mdFiles;
-                result.created.files.push(`.claude/agents/${agentCategory}`);
-            }
-            else {
-                result.skipped.push(`.claude/agents/${agentCategory}`);
-            }
-        }
-    }
-}
-/**
- * Find source helpers directory.
- * Validates that the directory contains hook-handler.cjs to avoid
- * returning the target directory or an incomplete source.
- */
-function findSourceHelpersDir(sourceBaseDir) {
-    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 {
-        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 {
-        // Not installed as a package — skip
-    }
-    // Strategy 2: __dirname-based (dist/src/init -> package root)
-    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
-    let currentDir = __dirname;
-    for (let i = 0; i < 10; i++) {
-        const parentDir = path.dirname(currentDir);
-        if (parentDir === currentDir)
-            break; // hit filesystem root
-        const helpersPath = path.join(parentDir, '.claude', 'helpers');
-        possiblePaths.push(helpersPath);
-        currentDir = parentDir;
-    }
-    // Strategy 4: Check cwd-relative paths (for local dev)
-    const cwdBased = [
-        path.join(process.cwd(), '.claude', 'helpers'),
-        path.join(process.cwd(), '..', '.claude', 'helpers'),
-        path.join(process.cwd(), '..', '..', '.claude', 'helpers'),
-    ];
-    possiblePaths.push(...cwdBased);
-    // Return first path that exists AND contains the sentinel file
-    for (const p of possiblePaths) {
-        if (fs.existsSync(p) && fs.existsSync(path.join(p, SENTINEL_FILE))) {
-            return p;
-        }
-    }
-    return null;
-}
-/**
- * Write helper scripts
- */
-async function writeHelpers(targetDir, options, result) {
-    const helpersDir = path.join(targetDir, '.claude', 'helpers');
-    // Find source helpers directory (works for npm package and local dev)
-    const sourceHelpersDir = findSourceHelpersDir(options.sourceBaseDir);
-    // On Windows: emit a notice before writing helpers — the settings.json
-    // hooks will use node-based commands instead of bash shims (#2132).
-    if (process.platform === 'win32') {
-        console.log('Detected Windows — adding cross-platform hook overrides to .claude/settings.json (#2132)');
-    }
-    // Try to copy existing helpers from source first
-    if (sourceHelpersDir && fs.existsSync(sourceHelpersDir)) {
-        const helperFiles = fs.readdirSync(sourceHelpersDir);
-        let copiedCount = 0;
-        for (const file of helperFiles) {
-            const sourcePath = path.join(sourceHelpersDir, file);
-            const destPath = path.join(helpersDir, file);
-            // Skip directories and only copy files
-            if (!fs.statSync(sourcePath).isFile())
-                continue;
-            if (!fs.existsSync(destPath) || options.force) {
-                fs.copyFileSync(sourcePath, destPath);
-                // Make shell scripts and mjs files executable
-                if (file.endsWith('.sh') || file.endsWith('.mjs')) {
-                    fs.chmodSync(destPath, '755');
-                }
-                result.created.files.push(`.claude/helpers/${file}`);
-                copiedCount++;
-            }
-            else {
-                result.skipped.push(`.claude/helpers/${file}`);
-            }
-        }
-        // #2132: Always generate ruflo-hook.cjs regardless of source copy path.
-        // The source helpers dir may not contain this file (it lives in
-        // plugins/ruflo-core/scripts/, not .claude/helpers/), but it must
-        // always be present so Windows users can use the node-based shim.
-        const rufloHookDest = path.join(helpersDir, 'ruflo-hook.cjs');
-        if (!fs.existsSync(rufloHookDest) || options.force) {
-            fs.writeFileSync(rufloHookDest, generateRufloHookCjs(), 'utf-8');
-            result.created.files.push('.claude/helpers/ruflo-hook.cjs');
-        }
-        else {
-            result.skipped.push('.claude/helpers/ruflo-hook.cjs');
-        }
-        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(),
-        // #2132: cross-platform Node.js port of ruflo-hook.sh — always deployed so
-        // Windows users have a working shim even if the plugin's hooks.json bash
-        // commands are overridden via settings.json.
-        'ruflo-hook.cjs': generateRufloHookCjs(),
-    };
-    for (const [name, content] of Object.entries(helpers)) {
-        const filePath = path.join(helpersDir, name);
-        if (!fs.existsSync(filePath) || options.force) {
-            fs.writeFileSync(filePath, content, 'utf-8');
-            // Make shell scripts executable
-            if (!name.endsWith('.js')) {
-                fs.chmodSync(filePath, '755');
-            }
-            result.created.files.push(`.claude/helpers/${name}`);
-        }
-        else {
-            result.skipped.push(`.claude/helpers/${name}`);
-        }
-    }
-}
-/**
- * Find source .claude directory for statusline files
- */
-function findSourceClaudeDir(sourceBaseDir) {
-    const possiblePaths = [];
-    // If explicit source base directory is provided, check it first
-    if (sourceBaseDir) {
-        possiblePaths.push(path.join(sourceBaseDir, '.claude'));
-    }
-    // IMPORTANT: Check the package's own .claude directory
-    // Go up 3 levels: dist/src/init -> dist/src -> dist -> root
-    const packageRoot = path.resolve(__dirname, '..', '..', '..');
-    const packageClaude = path.join(packageRoot, '.claude');
-    if (fs.existsSync(packageClaude)) {
-        possiblePaths.unshift(packageClaude); // Add to beginning (highest priority)
-    }
-    // From dist/src/init -> go up to project root
-    let currentDir = __dirname;
-    for (let i = 0; i < 10; i++) {
-        const parentDir = path.dirname(currentDir);
-        const claudePath = path.join(parentDir, '.claude');
-        if (fs.existsSync(claudePath)) {
-            possiblePaths.push(claudePath);
-        }
-        currentDir = parentDir;
-    }
-    for (const p of possiblePaths) {
-        if (fs.existsSync(p)) {
-            return p;
-        }
-    }
-    return null;
-}
-/**
- * Write statusline configuration
- */
-async function writeStatusline(targetDir, options, result) {
-    const claudeDir = path.join(targetDir, '.claude');
-    const helpersDir = path.join(targetDir, '.claude', 'helpers');
-    // Find source .claude directory (works for npm package and local dev)
-    const sourceClaudeDir = findSourceClaudeDir(options.sourceBaseDir);
-    // Try to copy existing advanced statusline files from source
-    const advancedStatuslineFiles = [
-        { src: 'statusline.sh', dest: 'statusline.sh', dir: claudeDir },
-        { src: 'statusline.mjs', dest: 'statusline.mjs', dir: claudeDir },
-    ];
-    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}`);
-                }
-            }
-        }
-    }
-    // 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/)
- */
-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
- */
-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
- */
-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 mcp start
-
-# 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
- */
-async function writeClaudeMd(targetDir, options, result) {
-    const claudeMdPath = path.join(targetDir, 'CLAUDE.md');
-    if (fs.existsSync(claudeMdPath) && !options.force) {
-        result.skipped.push('CLAUDE.md');
-    }
-    else {
-        // #2208: if overwriting an existing CLAUDE.md (force mode), back it up first so
-        // users don't silently lose curated project context.
-        if (fs.existsSync(claudeMdPath)) {
-            const backupBase = `${claudeMdPath}.pre-ruflo`;
-            // Don't clobber an existing backup — append a timestamp if one already exists.
-            const backupPath = fs.existsSync(backupBase)
-                ? `${backupBase}.${Date.now()}`
-                : backupBase;
-            fs.copyFileSync(claudeMdPath, backupPath);
-            result.created.files.push(path.basename(backupPath));
-            console.warn(`[ruflo init] Existing CLAUDE.md backed up to ${path.basename(backupPath)} before overwrite`);
-        }
-        // 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');
-    }
-    // Also write/append global ~/.claude/CLAUDE.md so ruflo tools are used automatically (#1497).
-    // Opt-out via --no-global / options.skipGlobalClaudeMd (#1744 — keeps global rules file pristine
-    // for users who don't want a per-machine pointer block).
-    const homeDir = process.env.HOME || process.env.USERPROFILE || '';
-    if (homeDir && !options.skipGlobalClaudeMd) {
-        const globalClaudeDir = path.join(homeDir, '.claude');
-        const globalClaudeMd = path.join(globalClaudeDir, 'CLAUDE.md');
-        const rufloBlock = [
-            '',
-            '# Ruflo Integration (auto-generated by ruflo init)',
-            'When working on multi-file tasks or complex features, use ToolSearch to find and invoke ruflo MCP tools.',
-            'Key tools: memory_store, memory_search, hooks_route, swarm_init, agent_spawn.',
-            'Check system-reminder tags for [INTELLIGENCE] pattern suggestions before starting work.',
-            '',
-        ].join('\n');
-        try {
-            if (!fs.existsSync(globalClaudeDir)) {
-                fs.mkdirSync(globalClaudeDir, { recursive: true });
-            }
-            if (fs.existsSync(globalClaudeMd)) {
-                const existing = fs.readFileSync(globalClaudeMd, 'utf-8');
-                if (!existing.includes('Ruflo Integration')) {
-                    fs.appendFileSync(globalClaudeMd, rufloBlock);
-                    result.created.files.push('~/.claude/CLAUDE.md (appended ruflo block)');
-                }
-            }
-            else {
-                fs.writeFileSync(globalClaudeMd, rufloBlock.trimStart(), 'utf-8');
-                result.created.files.push('~/.claude/CLAUDE.md');
-            }
-        }
-        catch {
-            // Non-critical — global CLAUDE.md is best-effort
-        }
-    }
-    else if (options.skipGlobalClaudeMd) {
-        result.skipped.push('~/.claude/CLAUDE.md (--no-global)');
-    }
-}
-/**
- * Find source directory for skills/commands/agents
- */
-function findSourceDir(type, sourceBaseDir) {
-    // Build list of possible paths to check
-    const possiblePaths = [];
-    // If explicit source base directory is provided, use it first
-    if (sourceBaseDir) {
-        possiblePaths.push(path.join(sourceBaseDir, '.claude', type));
-    }
-    // IMPORTANT: Check the package's own .claude directory first
-    // This is the primary path when running as an npm package
-    // __dirname is typically /path/to/node_modules/@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)
-    const packageRoot = path.resolve(__dirname, '..', '..', '..');
-    const packageDotClaude = path.join(packageRoot, '.claude', type);
-    if (fs.existsSync(packageDotClaude)) {
-        possiblePaths.unshift(packageDotClaude); // Add to beginning (highest priority)
-    }
-    // From dist/src/init -> go up to project root
-    const distPath = __dirname;
-    // Try to find the project root by looking for .claude directory
-    let currentDir = distPath;
-    for (let i = 0; i < 10; i++) {
-        const parentDir = path.dirname(currentDir);
-        const dotClaudePath = path.join(parentDir, '.claude', type);
-        if (fs.existsSync(dotClaudePath)) {
-            possiblePaths.push(dotClaudePath);
-        }
-        currentDir = parentDir;
-    }
-    // Also check relative to process.cwd() for development
-    const cwdBased = [
-        path.join(process.cwd(), '.claude', type),
-        path.join(process.cwd(), '..', '.claude', type),
-        path.join(process.cwd(), '..', '..', '.claude', type),
-    ];
-    possiblePaths.push(...cwdBased);
-    // Check v2 directory for agents
-    if (type === 'agents') {
-        possiblePaths.push(path.join(process.cwd(), 'v2', '.claude', type), path.join(process.cwd(), '..', 'v2', '.claude', type));
-    }
-    // Plugin directory
-    possiblePaths.push(path.join(process.cwd(), 'plugin', type), path.join(process.cwd(), '..', 'plugin', type));
-    for (const p of possiblePaths) {
-        if (fs.existsSync(p)) {
-            return p;
-        }
-    }
-    return null;
-}
-/**
- * Copy directory recursively
- */
-function copyDirRecursive(src, dest) {
-    fs.mkdirSync(dest, { recursive: true });
-    const entries = fs.readdirSync(src, { withFileTypes: true });
-    for (const entry of entries) {
-        const srcPath = path.join(src, entry.name);
-        const destPath = path.join(dest, entry.name);
-        if (entry.isDirectory()) {
-            copyDirRecursive(srcPath, destPath);
-        }
-        else {
-            fs.copyFileSync(srcPath, destPath);
-        }
-    }
-}
-/**
- * Count files with extension in directory
- */
-function countFiles(dir, ext) {
-    let count = 0;
-    const entries = fs.readdirSync(dir, { withFileTypes: true });
-    for (const entry of entries) {
-        const fullPath = path.join(dir, entry.name);
-        if (entry.isDirectory()) {
-            count += countFiles(fullPath, ext);
-        }
-        else if (entry.name.endsWith(ext)) {
-            count++;
-        }
-    }
-    return count;
-}
-/**
- * Count enabled hooks
- */
-function countEnabledHooks(options) {
-    const hooks = options.hooks;
-    let count = 0;
-    if (hooks.preToolUse)
-        count++;
-    if (hooks.postToolUse)
-        count++;
-    if (hooks.userPromptSubmit)
-        count++;
-    if (hooks.sessionStart)
-        count++;
-    if (hooks.stop)
-        count++;
-    if (hooks.preCompact)
-        count++;
-    if (hooks.notification)
-        count++;
-    return count;
-}
-export default executeInit;
-//# sourceMappingURL=executor.js.map