monomind 1.10.1 → 1.10.2

package/packages/@monomind/cli/dist/src/init/executor.js

@@ -0,0 +1,2172 @@
+/**
+ * Init Executor
+ * Main execution logic for V1 initialization
+ */
+import * as fs from 'fs';
+import * as path from 'path';
+import { fileURLToPath, pathToFileURL } from 'url';
+import { createRequire } from 'module';
+import { dirname } from 'path';
+// ESM-compatible __dirname
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = dirname(__filename);
+/**
+ * Atomic write helper — writes to a sibling .tmp file then renames into place.
+ * SIGINT or crash during a partial write would otherwise corrupt user-critical
+ * files (.claude/settings.json, .mcp.json, helper scripts that Claude Code
+ * executes on every hook). Without atomicity a half-written settings.json or
+ * a zero-byte hook-handler.cjs disables Claude Code's protections silently.
+ */
+function atomicWriteFile(target, content, encoding) {
+    const tmp = `${target}.${process.pid}.tmp`;
+    if (encoding && typeof content === 'string') {
+        fs.writeFileSync(tmp, content, encoding);
+    }
+    else if (typeof content === 'string') {
+        fs.writeFileSync(tmp, content, 'utf-8');
+    }
+    else {
+        fs.writeFileSync(tmp, content);
+    }
+    fs.renameSync(tmp, target);
+}
+import { detectPlatform, DEFAULT_INIT_OPTIONS } from './types.js';
+import { writeSharedInstructions } from './shared-instructions-generator.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, } from './helpers-generator.js';
+import { generateClaudeMd } from './claudemd-generator.js';
+/**
+ * Skills to copy based on configuration
+ */
+const SKILLS_MAP = {
+    core: [
+        'swarm-orchestration',
+        'swarm-advanced',
+        'swarm-coordination',
+        'sparc-methodology',
+        'hooks-automation',
+        'pair-programming',
+        'verification-quality',
+        'stream-chain',
+        'skill-builder',
+        'specialagent',
+        'mastermind',
+        'monodesign',
+        'monomotion',
+        'hive-mind-advanced',
+    ],
+    browser: ['agent-browser-testing'],
+    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',
+    ],
+    advanced: [
+        'agentic-integration',
+        'agentic-jujutsu',
+        'cli-modernization',
+        'core-implementation',
+        'ddd-architecture',
+        'mcp-optimization',
+        'memory-unification',
+        'performance-analysis',
+        'performance-optimization',
+        'security-hardening',
+    ],
+};
+/**
+ * Commands to copy based on configuration
+ */
+const COMMANDS_MAP = {
+    core: [
+        'mastermind.md', 'tokens.md', 'browse.md', 'sparc.md', 'ts.md',
+    ],
+    agents: ['agents'],
+    analysis: ['analysis'],
+    automation: ['automation'],
+    coordination: ['coordination'],
+    github: ['github'],
+    hiveMind: ['hive-mind'],
+    hooks: ['hooks'],
+    mastermind: ['mastermind'],
+    memory: ['memory'],
+    monitoring: ['monitoring'],
+    monograph: ['monograph'],
+    monomind: ['monomind'],
+    optimization: ['optimization'],
+    pair: ['pair'],
+    sparc: ['sparc'],
+    streamChain: ['stream-chain'],
+    swarm: ['swarm'],
+    training: ['training'],
+    truth: ['truth'],
+    verify: ['verify'],
+    workflows: ['workflows'],
+};
+/**
+ * Agents to copy based on configuration
+ */
+const AGENTS_MAP = {
+    academic: ['academic'],
+    analysis: ['analysis'],
+    architecture: ['architecture'],
+    consensus: ['consensus'],
+    core: ['core'],
+    data: ['data'],
+    design: ['design'],
+    development: ['development'],
+    devops: ['devops'],
+    documentation: ['documentation'],
+    engineering: ['engineering'],
+    gameDevelopment: ['game-development'],
+    github: ['github'],
+    goal: ['goal'],
+    hiveMind: ['hive-mind'],
+    marketing: ['marketing'],
+    neural: ['neural'],
+    optimization: ['optimization'],
+    paidMedia: ['paid-media'],
+    payments: ['payments'],
+    product: ['product'],
+    projectManagement: ['project-management'],
+    reasoning: ['reasoning'],
+    sales: ['sales'],
+    schemas: ['schemas'],
+    sona: ['sona'],
+    sparc: ['sparc'],
+    spatialComputing: ['spatial-computing'],
+    specialists: ['specialists'],
+    specialized: ['specialized'],
+    sublinear: ['sublinear'],
+    support: ['support'],
+    swarm: ['swarm'],
+    templates: ['templates'],
+    testing: ['testing'],
+};
+/**
+ * Directory structure to create
+ */
+const DIRECTORIES = {
+    claude: [
+        '.claude',
+        '.claude/skills',
+        '.claude/commands',
+        '.claude/agents',
+        '.claude/helpers',
+    ],
+    runtime: [
+        '.monomind',
+        '.monomind/data',
+        '.monomind/logs',
+        '.monomind/sessions',
+        '.monomind/hooks',
+        '.monomind/agents',
+        '.monomind/workflows',
+    ],
+};
+/**
+ * Execute initialization
+ */
+/**
+ * Remove legacy ruv-swarm configuration from existing project files.
+ * Safe to call even if no legacy config exists.
+ */
+function cleanupLegacyTools(targetDir) {
+    const cleaned = [];
+    // Helper to fix MCP server args: replace @monomind/cli@latest with monomind@latest
+    function fixMcpArgs(servers) {
+        let changed = false;
+        for (const name of Object.keys(servers)) {
+            const srv = servers[name];
+            if (Array.isArray(srv.args)) {
+                srv.args = srv.args.map((a) => {
+                    if (typeof a === 'string' && a.includes('@monomind/cli@')) {
+                        changed = true;
+                        return a.replace(/@monomind\/cli@[^\s]*/g, 'monomind@latest');
+                    }
+                    return a;
+                });
+            }
+        }
+        return changed;
+    }
+    // Clean ruv-swarm from .mcp.json and fix old MCP package name
+    const mcpJsonPath = path.join(targetDir, '.mcp.json');
+    if (fs.existsSync(mcpJsonPath)) {
+        try {
+            const mcp = JSON.parse(fs.readFileSync(mcpJsonPath, 'utf-8'));
+            let mcpChanged = false;
+            if (mcp.mcpServers && mcp.mcpServers['ruv-swarm']) {
+                delete mcp.mcpServers['ruv-swarm'];
+                mcpChanged = true;
+                cleaned.push('.mcp.json: removed ruv-swarm entry');
+            }
+            if (mcp.mcpServers && fixMcpArgs(mcp.mcpServers)) {
+                mcpChanged = true;
+                cleaned.push('.mcp.json: updated MCP package name to monomind@latest');
+            }
+            if (mcpChanged) {
+                atomicWriteFile(mcpJsonPath, JSON.stringify(mcp, null, 2));
+            }
+        }
+        catch { /* non-fatal */ }
+    }
+    // Clean ruv-swarm from .claude/settings.json hooks and fix MCP package name
+    const settingsPath = path.join(targetDir, '.claude', 'settings.json');
+    if (fs.existsSync(settingsPath)) {
+        try {
+            const raw = fs.readFileSync(settingsPath, 'utf-8');
+            const settings = JSON.parse(raw);
+            let settingsChanged = false;
+            if (raw.includes('ruv-swarm')) {
+                // Remove legacy ruv-swarm hook entries from all hook arrays
+                const hookKeys = ['PreToolUse', 'PostToolUse', 'UserPromptSubmit', 'SessionStart', 'SessionEnd', 'Stop', 'SubagentStart', 'SubagentStop', 'PreCompact'];
+                for (const key of hookKeys) {
+                    if (Array.isArray(settings.hooks?.[key])) {
+                        const before = settings.hooks[key].length;
+                        settings.hooks[key] = settings.hooks[key].filter((entry) => {
+                            const str = JSON.stringify(entry);
+                            return !str.includes('ruv-swarm');
+                        });
+                        if (settings.hooks[key].length !== before)
+                            settingsChanged = true;
+                    }
+                }
+                if (settingsChanged) {
+                    cleaned.push('.claude/settings.json: removed ruv-swarm hooks');
+                }
+            }
+            // Fix wrong MCP package name in mcpServers
+            if (settings.mcpServers && fixMcpArgs(settings.mcpServers)) {
+                settingsChanged = true;
+                cleaned.push('.claude/settings.json: updated MCP package name to monomind@latest');
+            }
+            if (settingsChanged) {
+                atomicWriteFile(settingsPath, JSON.stringify(settings, null, 2));
+            }
+        }
+        catch { /* non-fatal */ }
+    }
+    return cleaned;
+}
+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 {
+        // Remove legacy ruv-swarm configs before writing new ones
+        const legacyCleaned = cleanupLegacyTools(targetDir);
+        for (const msg of legacyCleaned) {
+            result.created.files.push(`[cleaned] ${msg}`);
+        }
+        // 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);
+        }
+        // Generate .agents/shared_instructions.md + seed project memory
+        writeSharedInstructions(targetDir, options.force, result);
+        // Count enabled hooks
+        result.summary.hooksEnabled = countEnabledHooks(options);
+        // Build knowledge graph in background (non-blocking)
+        if (options.components.graphify) {
+            await initKnowledgeGraph(targetDir, result);
+        }
+        // Start daemon with background workers (non-blocking)
+        await startDaemonBackground(targetDir, result);
+        // Run doctor auto-fix (non-blocking, best-effort)
+        await runDoctorFix(targetDir, result);
+    }
+    catch (error) {
+        result.success = false;
+        result.errors.push(error instanceof Error ? error.message : String(error));
+    }
+    return result;
+}
+/**
+ * Initialize the Monograph knowledge graph.
+ * Spawns buildAsync as a detached child process to avoid SQLite lock contention.
+ * Uses the same build.lock file as graphify-freshen.cjs — if a session-start
+ * hook build is already running, we skip to avoid SQLITE_BUSY.
+ */
+async function initKnowledgeGraph(targetDir, result) {
+    const outputDir = path.join(targetDir, '.monomind', 'graph');
+    fs.mkdirSync(outputDir, { recursive: true });
+    const lockPath = path.join(outputDir, 'build.lock');
+    const now = Date.now();
+    // If graphify-freshen.cjs (session-start hook) already holds a fresh lock, skip.
+    try {
+        const stat = fs.statSync(lockPath);
+        if (now - stat.mtimeMs < 5 * 60 * 1000) {
+            result.skipped.push('knowledge graph build: already in progress (session-start hook running)');
+            return;
+        }
+        fs.unlinkSync(lockPath);
+    }
+    catch { /* no lock — proceed */ }
+    // Resolve @monoes/monograph from the CLI package's own node_modules first
+    // (correct for npm/npx installs), then fall back to user project node_modules.
+    let entryPoint = null;
+    try {
+        const cliRequire = createRequire(import.meta.url);
+        entryPoint = cliRequire.resolve('@monoes/monograph/dist/src/index.js');
+    }
+    catch {
+        const fallback = path.join(targetDir, 'node_modules', '@monoes', 'monograph', 'dist', 'src', 'index.js');
+        if (fs.existsSync(fallback))
+            entryPoint = fallback;
+    }
+    if (!entryPoint) {
+        // Auto-install @monoes/monograph and retry before giving up
+        try {
+            const { execSync } = await import('child_process');
+            execSync('npm install @monoes/monograph', { cwd: targetDir, stdio: 'ignore', timeout: 60000 });
+            try {
+                const cliRequire2 = createRequire(import.meta.url);
+                entryPoint = cliRequire2.resolve('@monoes/monograph/dist/src/index.js');
+            }
+            catch {
+                const fallback2 = path.join(targetDir, 'node_modules', '@monoes', 'monograph', 'dist', 'src', 'index.js');
+                if (fs.existsSync(fallback2))
+                    entryPoint = fallback2;
+            }
+        }
+        catch { /* install failed, fall through */ }
+        if (!entryPoint) {
+            result.skipped.push('knowledge graph: @monoes/monograph not found (auto-install failed)');
+            return;
+        }
+        result.created.files.push('@monoes/monograph (auto-installed for knowledge graph)');
+    }
+    // Acquire lock before spawning so graphify-freshen.cjs sees it and skips
+    try {
+        fs.writeFileSync(lockPath, String(process.pid));
+    }
+    catch { /* non-fatal */ }
+    const { spawn } = await import('child_process');
+    const logPath = path.join(outputDir, 'build.log');
+    let logFd = 'ignore';
+    try {
+        logFd = fs.openSync(logPath, 'a');
+    }
+    catch { /* non-fatal */ }
+    const script = `
+import { buildAsync } from ${JSON.stringify(pathToFileURL(entryPoint).href)};
+import { unlinkSync } from 'fs';
+try { await buildAsync(${JSON.stringify(targetDir)}); } finally {
+  try { unlinkSync(${JSON.stringify(lockPath)}); } catch {}
+}`;
+    const child = spawn(process.execPath, ['--input-type=module', '--eval', script], {
+        detached: true,
+        stdio: ['ignore', logFd, logFd],
+        cwd: targetDir,
+    });
+    child.unref();
+    // Close the parent's copy of the fd — the child has its own inherited copy
+    if (typeof logFd === 'number') {
+        try {
+            fs.closeSync(logFd);
+        }
+        catch { /* non-fatal */ }
+    }
+    result.created.files.push('.monomind/graph/ (knowledge graph building in background)');
+}
+/**
+ * Start the monomind daemon with background workers.
+ * Non-fatal: if daemon fails to start, init continues.
+ */
+async function startDaemonBackground(targetDir, result) {
+    try {
+        const { execSync } = await import('child_process');
+        // Check if daemon is already running
+        const pidFile = path.join(targetDir, '.monomind', 'daemon.pid');
+        const { existsSync, readFileSync } = await import('fs');
+        if (existsSync(pidFile)) {
+            const pid = parseInt(readFileSync(pidFile, 'utf8').trim(), 10);
+            try {
+                process.kill(pid, 0);
+                result.skipped.push('daemon: already running (PID ' + pid + ')');
+                return;
+            }
+            catch { /* stale PID, continue */ }
+        }
+        execSync('npx monomind@latest daemon start --background', {
+            cwd: targetDir,
+            stdio: 'ignore',
+            timeout: 15000,
+        });
+        result.created.files.push('monomind daemon (background workers started)');
+    }
+    catch {
+        result.skipped.push('daemon: could not auto-start (run: monomind daemon start)');
+    }
+}
+/**
+ * Run doctor --install to auto-fix any remaining issues.
+ * Non-fatal: best-effort health check and auto-install.
+ */
+async function runDoctorFix(targetDir, result) {
+    try {
+        const { execSync } = await import('child_process');
+        execSync('npx monomind@latest doctor --install', {
+            cwd: targetDir,
+            stdio: 'ignore',
+            timeout: 120000,
+        });
+        result.created.files.push('doctor --install (health check + auto-fix)');
+    }
+    catch {
+        result.skipped.push('doctor: auto-fix skipped (run: monomind doctor --install)');
+    }
+}
+/**
+ * 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 monomind.agentTeams.hooks instead.
+    // 1. Merge env vars (preserve existing, add new)
+    const existingEnv = existing.env || {};
+    merged.env = {
+        ...existingEnv,
+        CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS: '1',
+        MONOMIND_V1_ENABLED: existingEnv.MONOMIND_V1_ENABLED || 'true',
+        MONOMIND_HOOKS_ENABLED: existingEnv.MONOMIND_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 monomind.agentTeams.hooks instead.
+    // 3. Fix statusLine config (remove invalid fields, ensure correct format)
+    // Claude Code only supports: type, command, padding
+    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)"`,
+            // Remove invalid fields: refreshMs, enabled (not supported by Claude Code)
+        };
+    }
+    // 4. Merge monomind settings (preserve existing, add agentTeams + memory)
+    const existingMonomind = existing.monomind || {};
+    const existingMemory = existingMonomind.memory || {};
+    merged.monomind = {
+        ...existingMonomind,
+        version: existingMonomind.version || '3.0.0',
+        enabled: existingMonomind.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 {
+        // Fix legacy ruv-swarm configs and old MCP package names
+        const legacyCleaned = cleanupLegacyTools(targetDir);
+        for (const msg of legacyCleaned) {
+            result.updated.push(`[cleaned] ${msg}`);
+        }
+        // Ensure required directories exist
+        const dirs = [
+            '.claude/helpers',
+            '.monomind/metrics',
+            '.monomind/security',
+            '.monomind/learning',
+        ];
+        for (const dir of dirs) {
+            const fullPath = path.join(targetDir, dir);
+            if (!fs.existsSync(fullPath)) {
+                fs.mkdirSync(fullPath, { recursive: true });
+            }
+        }
+        // 0. ALWAYS update critical helpers (force overwrite)
+        const sourceHelpersForUpgrade = findSourceHelpersDir();
+        if (sourceHelpersForUpgrade) {
+            const criticalHelpers = ['auto-memory-hook.mjs', 'hook-handler.cjs', 'intelligence.cjs'];
+            for (const helperName of criticalHelpers) {
+                const targetPath = path.join(targetDir, '.claude', 'helpers', helperName);
+                const sourcePath = path.join(sourceHelpersForUpgrade, helperName);
+                if (fs.existsSync(sourcePath)) {
+                    if (fs.existsSync(targetPath)) {
+                        result.updated.push(`.claude/helpers/${helperName}`);
+                    }
+                    else {
+                        result.created.push(`.claude/helpers/${helperName}`);
+                    }
+                    // Atomic copy-via-rename: a SIGINT/crash during copy would leave a
+                    // half-written hook-handler.cjs which Claude Code executes on every
+                    // hook event — partial JS could disable security checks silently.
+                    {
+                        const tmp = targetPath + '.tmp';
+                        fs.copyFileSync(sourcePath, tmp);
+                        try {
+                            fs.chmodSync(tmp, 0o755);
+                        }
+                        catch { }
+                        fs.renameSync(tmp, targetPath);
+                    }
+                }
+            }
+        }
+        else {
+            // Source not found (npx with broken paths) — use generated fallbacks
+            const generatedCritical = {
+                'hook-handler.cjs': generateHookHandler(),
+                'intelligence.cjs': generateIntelligenceStub(),
+                'auto-memory-hook.mjs': generateAutoMemoryHook(),
+            };
+            for (const [helperName, content] of Object.entries(generatedCritical)) {
+                const targetPath = path.join(targetDir, '.claude', 'helpers', helperName);
+                if (fs.existsSync(targetPath)) {
+                    result.updated.push(`.claude/helpers/${helperName}`);
+                }
+                else {
+                    result.created.push(`.claude/helpers/${helperName}`);
+                }
+                // Atomic write (PID-suffixed) so a partial hook-handler.cjs cannot
+                // ship if init is interrupted, and concurrent inits don't collide on
+                // the same .tmp filename.
+                const tmp = `${targetPath}.${process.pid}.tmp`;
+                fs.writeFileSync(tmp, content, 'utf-8');
+                try {
+                    fs.chmodSync(tmp, 0o755);
+                }
+                catch { }
+                fs.renameSync(tmp, targetPath);
+            }
+        }
+        // 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');
+        }
+        atomicWriteFile(statuslinePath, statuslineContent);
+        // 2. Create MISSING metrics files only (preserve existing data)
+        const metricsDir = path.join(targetDir, '.monomind', 'metrics');
+        const securityDir = path.join(targetDir, '.monomind', 'security');
+        // v1-progress.json
+        const progressPath = path.join(metricsDir, 'v1-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 Monomind'
+            };
+            atomicWriteFile(progressPath, JSON.stringify(progress, null, 2));
+            result.created.push('.monomind/metrics/v1-progress.json');
+        }
+        else {
+            result.preserved.push('.monomind/metrics/v1-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
+            };
+            atomicWriteFile(activityPath, JSON.stringify(activity, null, 2));
+            result.created.push('.monomind/metrics/swarm-activity.json');
+        }
+        else {
+            result.preserved.push('.monomind/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 Monomind'
+            };
+            atomicWriteFile(learningPath, JSON.stringify(learning, null, 2));
+            result.created.push('.monomind/metrics/learning.json');
+        }
+        else {
+            result.preserved.push('.monomind/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 monomind@latest security scan'
+            };
+            atomicWriteFile(auditPath, JSON.stringify(audit, null, 2));
+            result.created.push('.monomind/security/audit-status.json');
+        }
+        else {
+            result.preserved.push('.monomind/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);
+                    atomicWriteFile(settingsPath, JSON.stringify(mergedSettings, null, 2));
+                    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)',
+                        'monomind.agentTeams',
+                        'monomind.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);
+                atomicWriteFile(settingsPath, JSON.stringify(defaultSettings, null, 2));
+                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.MONOMIND_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.MONOMIND_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 monomind 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) {
+                atomicWriteFile(settingsPath, JSON.stringify(existing, null, 2));
+                result.created.files.push('.claude/settings.json (merged hooks)');
+            }
+            else {
+                result.skipped.push('.claude/settings.json');
+            }
+        }
+        catch {
+            // Existing file is corrupt — overwrite
+            atomicWriteFile(settingsPath, JSON.stringify(generated, null, 2));
+            result.created.files.push('.claude/settings.json');
+        }
+        return;
+    }
+    atomicWriteFile(settingsPath, JSON.stringify(generated, null, 2));
+    result.created.files.push('.claude/settings.json');
+}
+/**
+ * Write .mcp.json
+ */
+async function writeMCPConfig(targetDir, options, result) {
+    const mcpPath = path.join(targetDir, '.mcp.json');
+    if (fs.existsSync(mcpPath) && !options.force) {
+        result.skipped.push('.mcp.json');
+        return;
+    }
+    const content = generateMCPJson(options);
+    atomicWriteFile(mcpPath, content);
+    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.browser)
+            skillsToCopy.push(...SKILLS_MAP.browser);
+        if (skillsConfig.advanced)
+            skillsToCopy.push(...SKILLS_MAP.advanced);
+    }
+    // Find source skills directory
+    const sourceSkillsDir = findSourceDir('skills', options.sourceBaseDir);
+    if (!sourceSkillsDir) {
+        result.errors.push('Could not find source skills directory');
+        return;
+    }
+    // Remove stale skill directories no longer in the current version's map
+    const knownSkills = new Set([...new Set(skillsToCopy)]);
+    if (fs.existsSync(targetSkillsDir)) {
+        for (const existing of fs.readdirSync(targetSkillsDir)) {
+            if (!knownSkills.has(existing)) {
+                const stalePath = path.join(targetSkillsDir, existing);
+                fs.rmSync(stalePath, { recursive: true, force: true });
+                result.created.files.push(`[cleaned] .claude/skills/${existing} (stale)`);
+            }
+        }
+    }
+    // Always copy/overwrite skills (never skip — ensures new version content lands)
+    for (const skillName of knownSkills) {
+        const sourcePath = path.join(sourceSkillsDir, skillName);
+        const targetPath = path.join(targetSkillsDir, skillName);
+        if (fs.existsSync(sourcePath)) {
+            if (fs.existsSync(targetPath)) {
+                fs.rmSync(targetPath, { recursive: true, force: true });
+            }
+            copyDirRecursive(sourcePath, targetPath);
+            result.created.files.push(`.claude/skills/${skillName}`);
+            result.summary.skillsCount++;
+        }
+    }
+}
+/**
+ * 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.agents)
+            commandsToCopy.push(...(COMMANDS_MAP.agents || []));
+        if (commandsConfig.analysis)
+            commandsToCopy.push(...COMMANDS_MAP.analysis);
+        if (commandsConfig.automation)
+            commandsToCopy.push(...COMMANDS_MAP.automation);
+        if (commandsConfig.coordination)
+            commandsToCopy.push(...(COMMANDS_MAP.coordination || []));
+        if (commandsConfig.github)
+            commandsToCopy.push(...COMMANDS_MAP.github);
+        if (commandsConfig.hiveMind)
+            commandsToCopy.push(...(COMMANDS_MAP.hiveMind || []));
+        if (commandsConfig.hooks)
+            commandsToCopy.push(...COMMANDS_MAP.hooks);
+        if (commandsConfig.mastermind)
+            commandsToCopy.push(...(COMMANDS_MAP.mastermind || []));
+        if (commandsConfig.memory)
+            commandsToCopy.push(...(COMMANDS_MAP.memory || []));
+        if (commandsConfig.monitoring)
+            commandsToCopy.push(...COMMANDS_MAP.monitoring);
+        if (commandsConfig.monograph)
+            commandsToCopy.push(...(COMMANDS_MAP.monograph || []));
+        if (commandsConfig.monomind)
+            commandsToCopy.push(...(COMMANDS_MAP.monomind || []));
+        if (commandsConfig.optimization)
+            commandsToCopy.push(...COMMANDS_MAP.optimization);
+        if (commandsConfig.pair)
+            commandsToCopy.push(...(COMMANDS_MAP.pair || []));
+        if (commandsConfig.sparc)
+            commandsToCopy.push(...COMMANDS_MAP.sparc);
+        if (commandsConfig.streamChain)
+            commandsToCopy.push(...(COMMANDS_MAP.streamChain || []));
+        if (commandsConfig.swarm)
+            commandsToCopy.push(...(COMMANDS_MAP.swarm || []));
+        if (commandsConfig.training)
+            commandsToCopy.push(...(COMMANDS_MAP.training || []));
+        if (commandsConfig.truth)
+            commandsToCopy.push(...(COMMANDS_MAP.truth || []));
+        if (commandsConfig.verify)
+            commandsToCopy.push(...(COMMANDS_MAP.verify || []));
+        if (commandsConfig.workflows)
+            commandsToCopy.push(...(COMMANDS_MAP.workflows || []));
+    }
+    // Find source commands directory
+    const sourceCommandsDir = findSourceDir('commands', options.sourceBaseDir);
+    if (!sourceCommandsDir) {
+        result.errors.push('Could not find source commands directory');
+        return;
+    }
+    // Remove stale command files/directories no longer in the current version's map
+    const knownCommands = new Set([...new Set(commandsToCopy)]);
+    if (fs.existsSync(targetCommandsDir)) {
+        for (const existing of fs.readdirSync(targetCommandsDir)) {
+            if (!knownCommands.has(existing)) {
+                const stalePath = path.join(targetCommandsDir, existing);
+                fs.rmSync(stalePath, { recursive: true, force: true });
+                result.created.files.push(`[cleaned] .claude/commands/${existing} (stale)`);
+            }
+        }
+    }
+    // Always copy/overwrite commands (never skip — ensures new version content lands)
+    for (const cmdName of knownCommands) {
+        const sourcePath = path.join(sourceCommandsDir, cmdName);
+        const targetPath = path.join(targetCommandsDir, cmdName);
+        if (fs.existsSync(sourcePath)) {
+            if (fs.existsSync(targetPath)) {
+                fs.rmSync(targetPath, { recursive: true, force: true });
+            }
+            if (fs.statSync(sourcePath).isDirectory()) {
+                copyDirRecursive(sourcePath, targetPath);
+            }
+            else {
+                fs.copyFileSync(sourcePath, targetPath);
+            }
+            result.created.files.push(`.claude/commands/${cmdName}`);
+            result.summary.commandsCount++;
+        }
+    }
+}
+/**
+ * Copy agents from source
+ */
+async function copyAgents(targetDir, options, result) {
+    const agentsConfig = options.agents;
+    const targetAgentsDir = path.join(targetDir, '.claude', 'agents');
+    // Determine which agents to copy
+    const agentsToCopy = [];
+    if (agentsConfig.all) {
+        Object.values(AGENTS_MAP).forEach(agents => agentsToCopy.push(...agents));
+    }
+    else {
+        if (agentsConfig.core)
+            agentsToCopy.push(...AGENTS_MAP.core);
+        if (agentsConfig.consensus)
+            agentsToCopy.push(...AGENTS_MAP.consensus);
+        if (agentsConfig.github)
+            agentsToCopy.push(...AGENTS_MAP.github);
+        if (agentsConfig.hiveMind)
+            agentsToCopy.push(...AGENTS_MAP.hiveMind);
+        if (agentsConfig.sparc)
+            agentsToCopy.push(...AGENTS_MAP.sparc);
+        if (agentsConfig.swarm)
+            agentsToCopy.push(...AGENTS_MAP.swarm);
+        if (agentsConfig.optimization)
+            agentsToCopy.push(...(AGENTS_MAP.optimization || []));
+        if (agentsConfig.testing)
+            agentsToCopy.push(...(AGENTS_MAP.testing || []));
+    }
+    // Find source agents directory
+    const sourceAgentsDir = findSourceDir('agents', options.sourceBaseDir);
+    if (!sourceAgentsDir) {
+        result.errors.push('Could not find source agents directory');
+        return;
+    }
+    // Remove stale agent category directories no longer in the current version's map
+    const knownAgents = new Set([...new Set(agentsToCopy)]);
+    if (fs.existsSync(targetAgentsDir)) {
+        for (const existing of fs.readdirSync(targetAgentsDir)) {
+            if (!knownAgents.has(existing)) {
+                const stalePath = path.join(targetAgentsDir, existing);
+                fs.rmSync(stalePath, { recursive: true, force: true });
+                result.created.files.push(`[cleaned] .claude/agents/${existing} (stale)`);
+            }
+        }
+    }
+    // Always copy/overwrite agents (never skip — ensures new version content lands)
+    for (const agentCategory of knownAgents) {
+        const sourcePath = path.join(sourceAgentsDir, agentCategory);
+        const targetPath = path.join(targetAgentsDir, agentCategory);
+        if (fs.existsSync(sourcePath)) {
+            if (fs.existsSync(targetPath)) {
+                fs.rmSync(targetPath, { recursive: true, force: true });
+            }
+            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}`);
+        }
+    }
+}
+/**
+ * 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('@monomind/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);
+    // Try to copy existing helpers from source first
+    if (sourceHelpersDir && fs.existsSync(sourceHelpersDir)) {
+        const helperFiles = fs.readdirSync(sourceHelpersDir);
+        let copiedCount = 0;
+        for (const file of helperFiles) {
+            const sourcePath = path.join(sourceHelpersDir, file);
+            const destPath = path.join(helpersDir, file);
+            // Skip directories and only copy files
+            if (!fs.statSync(sourcePath).isFile())
+                continue;
+            if (!fs.existsSync(destPath) || options.force) {
+                fs.copyFileSync(sourcePath, destPath);
+                // Make shell scripts and mjs files executable
+                if (file.endsWith('.sh') || file.endsWith('.mjs')) {
+                    fs.chmodSync(destPath, '755');
+                }
+                result.created.files.push(`.claude/helpers/${file}`);
+                copiedCount++;
+            }
+            else {
+                result.skipped.push(`.claude/helpers/${file}`);
+            }
+        }
+        if (copiedCount > 0) {
+            return; // Skip generating if we copied from source
+        }
+    }
+    // Fall back to generating helpers if source not available
+    const helpers = {
+        'pre-commit': generatePreCommitHook(),
+        'post-commit': generatePostCommitHook(),
+        'session.js': generateSessionManager(),
+        'router.js': generateAgentRouter(),
+        'memory.js': generateMemoryHelper(),
+        'hook-handler.cjs': generateHookHandler(),
+        'intelligence.cjs': generateIntelligenceStub(),
+        'auto-memory-hook.mjs': generateAutoMemoryHook(),
+    };
+    for (const [name, content] of Object.entries(helpers)) {
+        const filePath = path.join(helpersDir, name);
+        if (!fs.existsSync(filePath) || options.force) {
+            atomicWriteFile(filePath, content);
+            // Make shell scripts executable
+            if (!name.endsWith('.js')) {
+                fs.chmodSync(filePath, '755');
+            }
+            result.created.files.push(`.claude/helpers/${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');
+    atomicWriteFile(statuslinePath, statuslineScript);
+    result.created.files.push('.claude/helpers/statusline.cjs');
+}
+/**
+ * Write runtime configuration (.monomind/)
+ */
+async function writeRuntimeConfig(targetDir, options, result) {
+    const configPath = path.join(targetDir, '.monomind', 'config.yaml');
+    if (fs.existsSync(configPath) && !options.force) {
+        result.skipped.push('.monomind/config.yaml');
+        return;
+    }
+    const config = `# Monomind 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: .monomind/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: .monomind/neural
+
+hooks:
+  enabled: true
+  autoExecute: true
+
+mcp:
+  autoStart: ${options.mcp.autoStart}
+  port: ${options.mcp.port}
+`;
+    atomicWriteFile(configPath, config);
+    result.created.files.push('.monomind/config.yaml');
+    // Write .gitignore
+    const gitignorePath = path.join(targetDir, '.monomind', '.gitignore');
+    const gitignore = `# Monomind runtime files
+data/
+logs/
+sessions/
+neural/
+*.log
+*.tmp
+`;
+    if (!fs.existsSync(gitignorePath) || options.force) {
+        atomicWriteFile(gitignorePath, gitignore);
+        result.created.files.push('.monomind/.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, '.monomind', 'metrics');
+    const learningDir = path.join(targetDir, '.monomind', 'learning');
+    const securityDir = path.join(targetDir, '.monomind', 'security');
+    // Ensure directories exist
+    for (const dir of [metricsDir, learningDir, securityDir]) {
+        if (!fs.existsSync(dir)) {
+            fs.mkdirSync(dir, { recursive: true });
+        }
+    }
+    // Create initial v1-progress.json
+    const progressPath = path.join(metricsDir, 'v1-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 Monomind. Run: npx monomind@latest daemon start'
+        };
+        atomicWriteFile(progressPath, JSON.stringify(progress, null, 2));
+        result.created.files.push('.monomind/metrics/v1-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
+        };
+        atomicWriteFile(activityPath, JSON.stringify(activity, null, 2));
+        result.created.files.push('.monomind/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 Monomind'
+        };
+        atomicWriteFile(learningPath, JSON.stringify(learning, null, 2));
+        result.created.files.push('.monomind/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 monomind@latest security scan'
+        };
+        atomicWriteFile(auditPath, JSON.stringify(audit, null, 2));
+        result.created.files.push('.monomind/security/audit-status.json');
+    }
+}
+/**
+ * Write CAPABILITIES.md - comprehensive overview of all Monomind features
+ */
+async function writeCapabilitiesDoc(targetDir, options, result) {
+    const capabilitiesPath = path.join(targetDir, '.monomind', 'CAPABILITIES.md');
+    if (fs.existsSync(capabilitiesPath) && !options.force) {
+        result.skipped.push('.monomind/CAPABILITIES.md');
+        return;
+    }
+    const capabilities = `# Monomind - Complete Capabilities Reference
+> Generated: ${new Date().toISOString()}
+> Full documentation: https://github.com/nokhodian/monomind
+
+## 📋 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
+
+Monomind 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\` | V1 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 monomind@latest swarm init --topology hierarchical --max-agents 8 --strategy specialized
+
+# Check status
+npx monomind@latest swarm status
+
+# Monitor activity
+npx monomind@latest swarm monitor
+\`\`\`
+
+---
+
+## Available Agents
+
+### Core Development (5)
+\`coder\`, \`reviewer\`, \`tester\`, \`planner\`, \`researcher\`
+
+### V1 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→V1 migration |
+| \`process\` | 4 | Process management |
+| \`doctor\` | 1 | Health diagnostics |
+| \`completions\` | 4 | Shell completions |
+
+### Example Commands
+\`\`\`bash
+# Initialize
+npx monomind@latest init --wizard
+
+# Spawn agent
+npx monomind@latest agent spawn -t coder --name my-coder
+
+# Memory operations
+npx monomind@latest memory store --key "pattern" --value "data" --namespace patterns
+npx monomind@latest memory search --query "authentication"
+
+# Diagnostics
+npx monomind@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 monomind@latest memory store --key "name" --value "data" --namespace patterns
+
+# Semantic search
+npx monomind@latest memory search --query "authentication"
+
+# List entries
+npx monomind@latest memory list --namespace patterns
+
+# Initialize database
+npx monomind@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 monomind@latest hive-mind init --queen-type strategic
+
+# Status
+npx monomind@latest hive-mind status
+
+# Spawn workers
+npx monomind@latest hive-mind spawn --count 5 --type worker
+
+# Consensus
+npx monomind@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 |
+|---------|---------|
+| agentic-jujutsu | \`npx agentic-jujutsu@latest\` |
+
+### MCP Server Setup
+\`\`\`bash
+# Add Monomind MCP
+claude mcp add monomind -- npx -y monomind@latest mcp start
+\`\`\`
+
+---
+
+## Quick Reference
+
+### Essential Commands
+\`\`\`bash
+# Setup
+npx monomind@latest init --wizard
+npx monomind@latest daemon start
+npx monomind@latest doctor --fix
+
+# Swarm
+npx monomind@latest swarm init --topology hierarchical --max-agents 8
+npx monomind@latest swarm status
+
+# Agents
+npx monomind@latest agent spawn -t coder
+npx monomind@latest agent list
+
+# Memory
+npx monomind@latest memory search --query "patterns"
+
+# Hooks
+npx monomind@latest hooks pre-task --description "task"
+npx monomind@latest hooks worker dispatch --trigger optimize
+\`\`\`
+
+### File Structure
+\`\`\`
+.monomind/
+├── 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/nokhodian/monomind
+**Issues**: https://github.com/nokhodian/monomind/issues
+`;
+    atomicWriteFile(capabilitiesPath, capabilities);
+    result.created.files.push('.monomind/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 {
+        // Determine template: explicit option > infer from components > 'standard'
+        const inferredTemplate = (!options.components.commands && !options.components.agents) ? 'minimal' : undefined;
+        const content = generateClaudeMd(options, inferredTemplate);
+        atomicWriteFile(claudeMdPath, content);
+        result.created.files.push('CLAUDE.md');
+    }
+    // Also write/append global ~/.claude/CLAUDE.md so monomind tools are used automatically (#1497)
+    const homeDir = process.env.HOME || process.env.USERPROFILE || '';
+    if (homeDir) {
+        const globalClaudeDir = path.join(homeDir, '.claude');
+        const globalClaudeMd = path.join(globalClaudeDir, 'CLAUDE.md');
+        const monomindBlock = [
+            '',
+            '# Monomind Integration (auto-generated by monomind init)',
+            'When working on multi-file tasks or complex features, use ToolSearch to find and invoke monomind 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('Monomind Integration')) {
+                    fs.appendFileSync(globalClaudeMd, monomindBlock);
+                    result.created.files.push('~/.claude/CLAUDE.md (appended monomind block)');
+                }
+            }
+            else {
+                atomicWriteFile(globalClaudeMd, monomindBlock.trimStart());
+                result.created.files.push('~/.claude/CLAUDE.md');
+            }
+        }
+        catch {
+            // Non-critical — global CLAUDE.md is best-effort
+        }
+        // Also inject the token-display hook into ~/.claude/settings.json
+        const globalSettingsPath = path.join(globalClaudeDir, 'settings.json');
+        try {
+            if (!fs.existsSync(globalClaudeDir)) {
+                fs.mkdirSync(globalClaudeDir, { recursive: true });
+            }
+            let globalSettings = {};
+            if (fs.existsSync(globalSettingsPath)) {
+                try {
+                    globalSettings = JSON.parse(fs.readFileSync(globalSettingsPath, 'utf-8'));
+                }
+                catch { /* malformed JSON — start fresh */ }
+            }
+            // Inject SessionStart token hook if not already present
+            const hooks = globalSettings.hooks ?? {};
+            const sessionStartHooks = hooks['SessionStart'] ?? [];
+            const tokenHookCommand = 'npx --yes monomind@latest tokens today';
+            const alreadyPresent = sessionStartHooks.some(entry => Array.isArray(entry.hooks) && entry.hooks.some(h => h.command === tokenHookCommand));
+            if (!alreadyPresent) {
+                sessionStartHooks.push({
+                    hooks: [{ type: 'command', command: tokenHookCommand, timeout: 10000 }],
+                });
+                hooks['SessionStart'] = sessionStartHooks;
+                globalSettings.hooks = hooks;
+                atomicWriteFile(globalSettingsPath, JSON.stringify(globalSettings, null, 2));
+                result.created.files.push('~/.claude/settings.json (added token hook)');
+            }
+        }
+        catch {
+            // Non-critical — global settings hook is best-effort
+        }
+    }
+}
+/**
+ * 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/@monomind/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