@monoes/monomindcli 2.8.4 → 2.9.2

package/dist/src/init/executor.js

@@ -10,185 +10,18 @@ import { dirname } from 'path';
 // ESM-compatible __dirname
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = dirname(__filename);
-const MAX_EXEC_FILE_BYTES = 10 * 1024 * 1024; // 10 MB
-/**
- * Probe whether an optionalDependency actually resolved in this install
- * (npm silently skips optionalDependencies it can't satisfy — see
- * docs/AUDIT-BACKLOG.md P1-1/P1-23). Used to caveat generated docs instead
- * of presenting these features as unconditionally working.
- */
-function _isOptionalPackageResolvable(pkg) {
-    try {
-        const req = createRequire(import.meta.url);
-        req.resolve(pkg);
-        return true;
-    }
-    catch {
-        return false;
-    }
-}
-/**
- * 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 { detectPlatform } 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 { FORCE_SYNC_HELPERS, FORCE_SYNC_GENERATORS, INIT_FALLBACK_HELPERS, } from './helpers-generator.js';
-import { generateClaudeMd } from './claudemd-generator.js';
-import { generateOpencodeJson, generateAgentsMd, generateHooksPlugin, generateStatusCommand, convertAgentMd, convertCommandMd, convertSkillMd, opencodeCommandFilename } from './opencode-generator.js';
-import { generateKimiMcpJson, mergeKimiMcpJson, generateKimiAgentsMd, generateKimiGateScript, generateKimiPluginManifest, generateKimiStatuslineSh, mergeKimiTuiTomlStatusline, convertKimiAgentMd, convertKimiSkillMd, convertKimiCommandToFlowSkill, convertKimiPluginCommandMd, kimiCommandFilename } from './kimi-generator.js';
-import { generateGeminiMd, generateGeminiRulesMd, generateStatuslineSh, } from './geminimd-generator.js';
-/**
- * Skills to copy based on configuration
- */
-const SKILLS_MAP = {
-    core: [
-        'swarm-orchestration',
-        'swarm-advanced',
-        'hooks-automation',
-        'pair-programming',
-        'verification-quality',
-        'skill-builder',
-        'specialagent',
-        'monodesign',
-        'monomotion',
-        'monolean',
-        'monolean-review',
-        'monolean-audit',
-        'monolean-debt',
-        'monolean-help',
-        'hive-mind-advanced',
-        // The mastermind command files installed by init invoke
-        // Skill("mastermind-<name>") at runtime — one top-level
-        // mastermind-<name>/SKILL.md directory per skill. The glob expands in
-        // copySkills against the source tree, so newly added mastermind skills
-        // ship automatically; without them those references break in user projects.
-        'mastermind-*',
-    ],
-    browser: ['agent-browser-testing'],
-    // NOTE: memory-toolkit and github-toolkit are single consolidated skills
-    // (not one skill per capability) — see .claude/skills/memory-toolkit and
-    // .claude/skills/github-toolkit. The finer-grained names previously listed
-    // here (memory-advanced, github-code-review, etc.) never had matching
-    // source directories and silently copied nothing.
-    memory: ['memory-toolkit'],
-    github: ['github-toolkit'],
-    advanced: [
-        'agentic-jujutsu',
-        'performance-analysis',
-    ],
-};
-/**
- * Commands to copy based on configuration
- */
-const COMMANDS_MAP = {
-    core: [
-        'mastermind.md', 'tokens.md', 'monobrowse.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: ['mastermind'],
-    optimization: ['optimization'],
-    pair: ['pair'],
-    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'],
-    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',
-        '.gemini',
-        '.gemini/skills',
-        '.gemini/rules',
-        '.gemini/helpers',
-    ],
-    runtime: [
-        '.monomind',
-        '.monomind/data',
-        '.monomind/logs',
-        '.monomind/sessions',
-        '.monomind/hooks',
-        '.monomind/agents',
-        '.monomind/workflows',
-    ],
-};
+// Split modules
+import { DIRECTORIES, MAX_EXEC_FILE_BYTES } from './shared.js';
+import { writeSettings, writeMCPConfig, writeHelpers, writeStatusline, writeClaudeMd } from './write-claude.js';
+import { writeRuntimeConfig, writeInitialMetrics } from './write-runtime-config.js';
+import { writeGeminiFiles } from './write-antigravity.js';
+import { writeOpencodeFiles } from './write-opencode.js';
+import { writeKimiFiles } from './write-kimicode.js';
+import { copySkills, copyCommands, copyAgents } from './copy-assets.js';
+// Re-export upgrade functions so index.ts barrel still works via './executor.js'
+export { executeUpgrade, executeUpgradeWithMissing } from './upgrade.js';
 /**
  * Execute initialization
  */
@@ -238,11 +71,15 @@ export async function executeInit(options) {
             for (const cap of capMgr.getActive()) {
                 console.log(`  ✓ ${cap.name}`);
             }
-            // Second Brain: if documents capability is active, index documents
+            // Second Brain: if documents capability is active, index the full tree.
+            // Even when it is NOT active (code-only projects), ingest common
+            // documentation files so the Second Brain is seeded with project context
+            // that would otherwise cause zero-hits on every prompt.
             const activeNames = capMgr.getActive().map((c) => c.name);
-            if (activeNames.includes('documents')) {
-                try {
-                    const { ingestDirectory } = await import('../knowledge/document-pipeline.js');
+            try {
+                const { ingestDirectory, ingestDocument } = await import('../knowledge/document-pipeline.js');
+                const fs = await import('node:fs');
+                if (activeNames.includes('documents')) {
                     console.log('\nIndexing documents for Second Brain...');
                     const docResult = await ingestDirectory(targetDir, 'shared', { rootDir: targetDir });
                     if (docResult.filesProcessed > 0) {
@@ -251,11 +88,44 @@ export async function executeInit(options) {
                     else {
                         console.log('  ✓ Knowledge base initialized (no new documents to index)');
                     }
-                    result.created.files.push('.monomind/knowledge/');
                 }
-                catch (docErr) {
-                    result.skipped.push(`knowledge indexing: ${docErr instanceof Error ? docErr.message : String(docErr)}`);
+                else {
+                    // Code-only project: ingest common doc directories and root files
+                    // so the Second Brain is not empty. Skip silently when nothing exists.
+                    console.log('\nSeeding Second Brain with project docs...');
+                    let seeded = 0;
+                    let seededChunks = 0;
+                    // Ingest doc directories (doc/, docs/) if present
+                    for (const docDir of ['doc', 'docs']) {
+                        const dirPath = path.join(targetDir, docDir);
+                        if (fs.existsSync(dirPath) && fs.statSync(dirPath).isDirectory()) {
+                            const dirResult = await ingestDirectory(dirPath, 'shared', { rootDir: targetDir });
+                            seeded += dirResult.filesProcessed;
+                            seededChunks += dirResult.totalChunks;
+                        }
+                    }
+                    // Ingest common root markdown files
+                    for (const rootDoc of ['README.md', 'CONTRIBUTING.md', 'CHANGELOG.md', 'CLAUDE.md']) {
+                        const filePath = path.join(targetDir, rootDoc);
+                        if (fs.existsSync(filePath)) {
+                            const fileResult = await ingestDocument(filePath, 'shared', targetDir);
+                            if (!fileResult.skipped) {
+                                seeded++;
+                                seededChunks += fileResult.chunksIndexed;
+                            }
+                        }
+                    }
+                    if (seeded > 0) {
+                        console.log(`  ✓ ${seededChunks} chunks from ${seeded} documents`);
+                    }
+                    else {
+                        console.log('  ✓ Knowledge base initialized (no project docs found)');
+                    }
                 }
+                result.created.files.push('.monomind/knowledge/');
+            }
+            catch (docErr) {
+                result.skipped.push(`knowledge indexing: ${docErr instanceof Error ? docErr.message : String(docErr)}`);
             }
         }
         catch (scanError) {
@@ -429,15 +299,6 @@ try { await buildAsync(${JSON.stringify(targetDir)}); } finally {
  * Non-fatal: best-effort health check and auto-install.
  */
 async function runDoctorFix(targetDir, result) {
-    // Run the doctor THIS binary ships, in-process.
-    //
-    // This used to be `execSync('npx monomind@latest doctor --install')`, which
-    // was wrong in three ways at once: it downloaded and ran a DIFFERENT version
-    // than the one the user deliberately invoked (so `monomind@2.7.0 init` was
-    // finished by whatever `latest` happened to be), it silently required network
-    // — on a machine without it, the 120s timeout elapsed and init reported
-    // "skipped" with no explanation — and `stdio: 'ignore'` discarded everything
-    // it said, so a failed health check looked identical to a passing one.
     try {
         const { doctorCommand } = await import('../commands/doctor.js');
         if (!doctorCommand.action) {
@@ -449,7 +310,6 @@ async function runDoctorFix(targetDir, result) {
             flags: { install: true },
             cwd: targetDir,
         });
-        // Report what actually happened rather than asserting success either way.
         if (res && res.success === false) {
             result.skipped.push('doctor: reported issues (run: monomind doctor for details)');
         }
@@ -462,456 +322,6 @@ async function runDoctorFix(targetDir, result) {
         result.skipped.push(`doctor: auto-fix failed (${detail}) — run: monomind doctor --install`);
     }
 }
-/**
- * Merge new settings into existing settings.json
- * Preserves user customizations while adding new features like Agent Teams
- * Uses platform-specific commands for Mac, Linux, and Windows
- */
-function mergeSettingsForUpgrade(existing) {
-    const merged = { ...existing };
-    const platform = detectPlatform();
-    const isWindows = platform.os === 'windows';
-    // Platform-specific command wrappers
-    // Windows: Use PowerShell-compatible commands
-    // Mac/Linux: Use bash-compatible commands with 2>/dev/null
-    // NOTE: teammateIdleCmd and taskCompletedCmd were removed.
-    // TeammateIdle/TaskCompleted are not valid Claude Code hook events and caused warnings.
-    // Agent Teams hook config lives in monomind.agentTeams.hooks instead.
-    // 1. Merge env vars (preserve existing, add new)
-    const existingEnv = existing.env || {};
-    merged.env = {
-        ...existingEnv,
-        CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS: '1',
-        MONOMIND_V1_ENABLED: existingEnv.MONOMIND_V1_ENABLED || 'true',
-        MONOMIND_HOOKS_ENABLED: existingEnv.MONOMIND_HOOKS_ENABLED || 'true',
-    };
-    // 2. Merge hooks (preserve existing, add new Agent Teams + auto-memory hooks)
-    const existingHooks = existing.hooks || {};
-    merged.hooks = { ...existingHooks };
-    // Cross-platform auto-memory hook commands that resolve paths via git root.
-    // Uses node -e with git rev-parse so hooks work regardless of CWD (#1259, #1284).
-    const gitRootResolver = "var c=require('child_process'),p=require('path'),u=require('url'),r;"
-        + "try{r=c.execSync('git rev-parse --show-toplevel',{encoding:'utf8'}).trim()}"
-        + 'catch(e){r=process.cwd()}';
-    const autoMemoryScript = '.claude/helpers/auto-memory-hook.mjs';
-    const autoMemoryImportCmd = `node -e "${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 {
-        // 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 + subdirectories (force overwrite)
-        const sourceHelpersForUpgrade = findSourceHelpersDir();
-        if (sourceHelpersForUpgrade) {
-            const destHelpersDir = path.join(targetDir, '.claude', 'helpers');
-            // Copy top-level critical files atomically. Membership and fallback
-            // generators come from the shared HELPER_FILES registry (helpers-generator.ts)
-            // rather than a hardcoded list here — see that file's comment for why.
-            const criticalHelpers = FORCE_SYNC_HELPERS;
-            // Generated fallback for any critical helper missing from the source dir itself
-            // (e.g. the published npm template lacking auto-memory-hook.mjs).
-            const criticalGenerators = FORCE_SYNC_GENERATORS;
-            for (const helperName of criticalHelpers) {
-                const targetPath = path.join(destHelpersDir, 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/${helperName}`);
-                    }
-                    // Atomic copy-via-rename so a partial write can't leave a broken hook
-                    const tmp = targetPath + '.tmp';
-                    fs.copyFileSync(sourcePath, tmp);
-                    try {
-                        fs.chmodSync(tmp, 0o755);
-                    }
-                    catch { }
-                    fs.renameSync(tmp, targetPath);
-                }
-                else if (!fs.existsSync(targetPath) && criticalGenerators[helperName]) {
-                    const content = criticalGenerators[helperName]();
-                    const tmp = `${targetPath}.${process.pid}.tmp`;
-                    fs.writeFileSync(tmp, content, 'utf-8');
-                    try {
-                        fs.chmodSync(tmp, 0o755);
-                    }
-                    catch { }
-                    fs.renameSync(tmp, targetPath);
-                    result.created.push(`.claude/helpers/${helperName}`);
-                }
-            }
-            // Always recursively sync subdirectories (utils/, handlers/) — required by hook-handler.cjs.
-            // Uses recursive copy so any future nested subdirs are also covered.
-            for (const subdir of ['utils', 'handlers']) {
-                const srcSubdir = path.join(sourceHelpersForUpgrade, subdir);
-                const destSubdir = path.join(destHelpersDir, subdir);
-                if (fs.existsSync(srcSubdir)) {
-                    copyDirRecursive(srcSubdir, destSubdir);
-                    result.updated.push(`.claude/helpers/${subdir}/`);
-                }
-            }
-        }
-        else {
-            // Source not found (npx with broken paths) — use generated fallbacks
-            // for every force-synced helper that has one (see HELPER_FILES registry).
-            const generatedCritical = Object.fromEntries(Object.entries(FORCE_SYNC_GENERATORS).map(([name, generate]) => [name, generate()]));
-            for (const [helperName, content] of Object.entries(generatedCritical)) {
-                const targetPath = path.join(targetDir, '.claude', 'helpers', helperName);
-                if (fs.existsSync(targetPath)) {
-                    result.updated.push(`.claude/helpers/${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. Statusline fallback — only generate if source copy above didn't cover it
-        const statuslinePath = path.join(targetDir, '.claude', 'helpers', 'statusline.cjs');
-        if (!sourceHelpersForUpgrade || !fs.existsSync(path.join(sourceHelpersForUpgrade, 'statusline.cjs'))) {
-            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: { mcp_server: 0, estimated_agents: 0 },
-                swarm: { active: false, agent_count: 0, coordination_active: false },
-                integration: { 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) && fs.statSync(settingsPath).size <= MAX_EXEC_FILE_BYTES) {
-                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
  */
@@ -928,1852 +338,6 @@ async function createDirectories(targetDir, options, result) {
         }
     }
 }
-/**
- * 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 && fs.statSync(settingsPath).size <= MAX_EXEC_FILE_BYTES) {
-        // 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 (e) {
-            // Existing file is corrupt — overwrite
-            if (process.env.DEBUG || process.env.MONOMIND_DEBUG)
-                console.error('[writeSettings] existing settings.json unparseable, overwriting with generated defaults:', e);
-            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');
-}
-/**
- * Provenance manifest for generated .claude content.
- *
- * init used to "clean stale" entries by deleting every name under
- * .claude/{skills,commands,agents} that was absent from the current version's
- * SKILLS_MAP/COMMANDS_MAP/AGENTS_MAP. Every user-authored command and skill is
- * absent from those maps, so that pass deleted user content on the very first
- * run — unrecoverable data loss.
- *
- * The manifest records exactly which entries *this tool* wrote, so the stale
- * sweep can be restricted to those. Anything init did not write is never
- * removed. Projects initialised by an older version have no manifest, so their
- * first run under the fix deletes nothing and seeds the manifest instead;
- * stale generated content may survive one extra run, which is the correct
- * trade (preserving stale generated content is recoverable, deleting user
- * content is not).
- */
-const INIT_MANIFEST_REL = path.join('.monomind', 'init-manifest.json');
-/**
- * Read the provenance manifest. Returns null when absent or unreadable —
- * callers must treat that as "provenance unknown", i.e. delete nothing.
- */
-function readInitManifest(targetDir) {
-    const manifestPath = path.join(targetDir, INIT_MANIFEST_REL);
-    try {
-        if (!fs.existsSync(manifestPath))
-            return null;
-        const parsed = JSON.parse(fs.readFileSync(manifestPath, 'utf8'));
-        if (!parsed || typeof parsed !== 'object')
-            return null;
-        return {
-            version: typeof parsed.version === 'number' ? parsed.version : 1,
-            skills: Array.isArray(parsed.skills) ? parsed.skills.filter((s) => typeof s === 'string') : [],
-            commands: Array.isArray(parsed.commands) ? parsed.commands.filter((s) => typeof s === 'string') : [],
-            agents: Array.isArray(parsed.agents) ? parsed.agents.filter((s) => typeof s === 'string') : [],
-        };
-    }
-    catch {
-        return null;
-    }
-}
-/**
- * Names init previously generated in one section. Empty set when no manifest
- * exists — which makes the stale sweep a no-op rather than a delete-everything.
- */
-function previouslyGenerated(targetDir, section) {
-    return new Set(readInitManifest(targetDir)?.[section] ?? []);
-}
-/**
- * Record the entries init just wrote for one section, merging into any
- * existing manifest so a partial run (e.g. --only-claude, or a section whose
- * source dir was missing) never drops provenance for the other sections.
- */
-function recordGenerated(targetDir, section, entries) {
-    const manifestPath = path.join(targetDir, INIT_MANIFEST_REL);
-    const existing = readInitManifest(targetDir);
-    const manifest = existing ?? { version: 1, skills: [], commands: [], agents: [] };
-    manifest.version = 1;
-    manifest[section] = [...new Set(entries)].sort();
-    try {
-        fs.mkdirSync(path.dirname(manifestPath), { recursive: true });
-        atomicWriteFile(manifestPath, JSON.stringify(manifest, null, 2) + '\n');
-    }
-    catch {
-        // Non-fatal: without a manifest the next run simply deletes nothing.
-    }
-}
-/**
- * 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.memory)
-            skillsToCopy.push(...SKILLS_MAP.memory);
-        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;
-    }
-    // Expand glob-style entries ('mastermind-*') against the source tree.
-    // Only directories that actually contain a SKILL.md count — this also
-    // filters exFAT AppleDouble junk (._mastermind-…).
-    for (const entry of skillsToCopy.filter(e => e.endsWith('*'))) {
-        const prefix = entry.slice(0, -1);
-        skillsToCopy.splice(skillsToCopy.indexOf(entry), 1);
-        skillsToCopy.push(...fs.readdirSync(sourceSkillsDir).filter(n => n.startsWith(prefix) &&
-            fs.existsSync(path.join(sourceSkillsDir, n, 'SKILL.md'))));
-    }
-    // Remove stale skill directories that a PREVIOUS init generated and this
-    // version no longer ships. Entries init never wrote (user-authored skills,
-    // skills installed by other tools) are left untouched — see readInitManifest.
-    const knownSkills = new Set([...new Set(skillsToCopy)]);
-    const priorSkills = previouslyGenerated(targetDir, 'skills');
-    if (fs.existsSync(targetSkillsDir)) {
-        for (const existing of fs.readdirSync(targetSkillsDir)) {
-            if (!knownSkills.has(existing) && priorSkills.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)
-    const writtenSkills = [];
-    for (const skillName of knownSkills) {
-        const sourcePath = path.join(sourceSkillsDir, skillName);
-        const targetPath = path.join(targetSkillsDir, skillName);
-        if (fs.existsSync(sourcePath)) {
-            // Deliberately NOT rmSync'd first. copyDirRecursive overwrites every
-            // file it ships, so wiping the directory adds nothing except destroying
-            // anything the user put inside it — notes beside a shipped skill, an
-            // extra command in a shipped folder. `init --force` did exactly that.
-            // The cost of not wiping is that a file removed from a newer version
-            // lingers; the cost of wiping is silent data loss, which is worse.
-            copyDirRecursive(sourcePath, targetPath);
-            writtenSkills.push(skillName);
-            result.created.files.push(`.claude/skills/${skillName}`);
-            result.summary.skillsCount++;
-        }
-        else {
-            // A skill referenced in SKILLS_MAP has no matching source directory —
-            // surface this instead of silently copying nothing, so drift between
-            // SKILLS_MAP and the actual .claude/skills/ tree gets caught.
-            result.errors.push(`Skill '${skillName}' listed in SKILLS_MAP has no source directory at ${sourcePath} — skipped`);
-        }
-    }
-    // Record provenance so the next run can distinguish "we wrote this" from
-    // "the user wrote this". Keep entries this run did not re-write but that a
-    // previous run generated and that still exist, so provenance is not lost
-    // when a section is partially skipped.
-    const retainedSkills = [...priorSkills].filter(n => !writtenSkills.includes(n) && fs.existsSync(path.join(targetSkillsDir, n)));
-    recordGenerated(targetDir, 'skills', [...writtenSkills, ...retainedSkills]);
-}
-/**
- * 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.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 that a PREVIOUS init generated and
-    // this version no longer ships. User-authored commands are never touched.
-    const knownCommands = new Set([...new Set(commandsToCopy)]);
-    const priorCommands = previouslyGenerated(targetDir, 'commands');
-    if (fs.existsSync(targetCommandsDir)) {
-        for (const existing of fs.readdirSync(targetCommandsDir)) {
-            if (!knownCommands.has(existing) && priorCommands.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)
-    const writtenCommands = [];
-    for (const cmdName of knownCommands) {
-        const sourcePath = path.join(sourceCommandsDir, cmdName);
-        const targetPath = path.join(targetCommandsDir, cmdName);
-        if (fs.existsSync(sourcePath)) {
-            // No pre-copy rmSync — see the note in copySkills. Both branches below
-            // overwrite what they ship, so wiping first only destroys files the user
-            // added inside a shipped command directory.
-            if (fs.statSync(sourcePath).isDirectory()) {
-                copyDirRecursive(sourcePath, targetPath);
-            }
-            else {
-                fs.copyFileSync(sourcePath, targetPath);
-            }
-            writtenCommands.push(cmdName);
-            result.created.files.push(`.claude/commands/${cmdName}`);
-            result.summary.commandsCount++;
-        }
-    }
-    const retainedCommands = [...priorCommands].filter(n => !writtenCommands.includes(n) && fs.existsSync(path.join(targetCommandsDir, n)));
-    recordGenerated(targetDir, 'commands', [...writtenCommands, ...retainedCommands]);
-}
-/**
- * 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.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 that a PREVIOUS init generated and
-    // this version no longer ships. User-authored agent dirs are never touched.
-    const knownAgents = new Set([...new Set(agentsToCopy)]);
-    const priorAgents = previouslyGenerated(targetDir, 'agents');
-    if (fs.existsSync(targetAgentsDir)) {
-        for (const existing of fs.readdirSync(targetAgentsDir)) {
-            if (!knownAgents.has(existing) && priorAgents.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)
-    const writtenAgents = [];
-    for (const agentCategory of knownAgents) {
-        const sourcePath = path.join(sourceAgentsDir, agentCategory);
-        const targetPath = path.join(targetAgentsDir, agentCategory);
-        if (fs.existsSync(sourcePath)) {
-            // Deliberately NOT rmSync'd first. copyDirRecursive overwrites every
-            // file it ships, so wiping the directory adds nothing except destroying
-            // anything the user put inside it — notes beside a shipped skill, an
-            // extra command in a shipped folder. `init --force` did exactly that.
-            // The cost of not wiping is that a file removed from a newer version
-            // lingers; the cost of wiping is silent data loss, which is worse.
-            copyDirRecursive(sourcePath, targetPath);
-            // Count agent files (.md only — .yaml agents were migrated to .md)
-            const mdFiles = countFiles(sourcePath, '.md');
-            result.summary.agentsCount += mdFiles;
-            writtenAgents.push(agentCategory);
-            result.created.files.push(`.claude/agents/${agentCategory}`);
-        }
-    }
-    const retainedAgents = [...priorAgents].filter(n => !writtenAgents.includes(n) && fs.existsSync(path.join(targetAgentsDir, n)));
-    recordGenerated(targetDir, 'agents', [...writtenAgents, ...retainedAgents]);
-}
-/**
- * Find source helpers directory.
- * Validates that the directory contains hook-handler.cjs AND its required
- * subdirectory files (utils/telemetry.cjs etc.) to avoid accepting a partial
- * or corrupted source that would reproduce the missing-utils/ bug class.
- */
-function findSourceHelpersDir(sourceBaseDir) {
-    const possiblePaths = [];
-    // All sentinel files must exist — hook-handler.cjs requires these at startup
-    const SENTINEL_FILES = [
-        'hook-handler.cjs',
-        path.join('utils', 'telemetry.cjs'),
-        path.join('utils', 'monograph.cjs'),
-        path.join('utils', 'micro-agents.cjs'),
-    ];
-    // 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 both published package names (@monoes/monomindcli is the scoped CLI package,
-    // monomind is the umbrella — neither is @monomind/cli which is the monorepo name only)
-    for (const pkgName of ['@monoes/monomindcli/package.json', 'monomind/packages/@monomind/cli/package.json', '@monomind/cli/package.json']) {
-        try {
-            const esmRequire = createRequire(import.meta.url);
-            const pkgJsonPath = esmRequire.resolve(pkgName);
-            const pkgRoot = path.dirname(pkgJsonPath);
-            possiblePaths.push(path.join(pkgRoot, '.claude', 'helpers'));
-            break;
-        }
-        catch {
-            // Not installed under this name — try next
-        }
-    }
-    // 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;
-    }
-    // NOTE: deliberately no cwd-ancestor-search fallback here (removed — see
-    // docs/AUDIT-BACKLOG.md P3-25). Searching process.cwd() and its parents for
-    // ".claude/helpers" could pick up an unrelated project's own helper scripts
-    // (stale, customized, or untrusted) when `monomind init` is run from a
-    // nested subdirectory of some other checkout. Helper source resolution is
-    // restricted to the package's own bundled location(s) above; if none of
-    // those are found, callers should treat it as a corrupt install rather than
-    // silently falling back to scanning ancestor directories for someone else's
-    // files.
-    // Return first path that exists AND contains ALL sentinel files
-    for (const p of possiblePaths) {
-        if (fs.existsSync(p) && SENTINEL_FILES.every(f => fs.existsSync(path.join(p, f)))) {
-            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 (recursive — includes utils/ and handlers/)
-    if (sourceHelpersDir && fs.existsSync(sourceHelpersDir)) {
-        const copyRecursive = (srcDir, destDir, relBase) => {
-            fs.mkdirSync(destDir, { recursive: true });
-            for (const entry of fs.readdirSync(srcDir, { withFileTypes: true })) {
-                // Skip exFAT/macOS AppleDouble junk files (e.g. "._foo.cjs").
-                if (entry.name.startsWith('._'))
-                    continue;
-                const srcPath = path.join(srcDir, entry.name);
-                const destPath = path.join(destDir, entry.name);
-                const relPath = relBase ? `${relBase}/${entry.name}` : entry.name;
-                if (entry.isDirectory()) {
-                    copyRecursive(srcPath, destPath, relPath);
-                }
-                else {
-                    if (!fs.existsSync(destPath) || options.force) {
-                        fs.copyFileSync(srcPath, destPath);
-                        if (entry.name.endsWith('.sh') || entry.name.endsWith('.mjs')) {
-                            fs.chmodSync(destPath, '755');
-                        }
-                        result.created.files.push(`.claude/helpers/${relPath}`);
-                    }
-                    else {
-                        result.skipped.push(`.claude/helpers/${relPath}`);
-                    }
-                }
-            }
-        };
-        copyRecursive(sourceHelpersDir, helpersDir, '');
-        const geminiHelpersDir = path.join(targetDir, '.gemini', 'helpers');
-        copyRecursive(sourceHelpersDir, geminiHelpersDir, '');
-    }
-    // Always run the fallback generator too — it only fills in files still missing
-    // after the source copy above (it no-ops on anything the copy already wrote).
-    // Without this, a source dir that's present but incomplete (e.g. missing
-    // auto-memory-hook.mjs) silently ships a project wired to hooks that reference
-    // a file that was never installed.
-    const helpers = Object.fromEntries(Object.entries(INIT_FALLBACK_HELPERS).map(([name, generate]) => [name, generate()]));
-    for (const [name, content] of Object.entries(helpers)) {
-        const filePath = path.join(helpersDir, name);
-        // If the source dir has this file, copyRecursive above already applied
-        // the correct (force-aware) copy — never let this generated fallback
-        // clobber it with a bare-bones stub. Only step in when source truly
-        // doesn't have the file, regardless of `force`.
-        const inSource = !!(sourceHelpersDir && fs.existsSync(path.join(sourceHelpersDir, name)));
-        if (inSource)
-            continue;
-        if (!fs.existsSync(filePath) || options.force) {
-            atomicWriteFile(filePath, content);
-            // Make shell scripts executable
-            if (!name.endsWith('.js')) {
-                fs.chmodSync(filePath, '755');
-            }
-            result.created.files.push(`.claude/helpers/${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
-    // 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}
-    confidenceDecayRate: 0.005
-    accessBoostAmount: 0.03
-    consolidationThreshold: 10
-  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: ${options.mcp.port}
-`;
-    atomicWriteFile(configPath, config);
-    result.created.files.push('.monomind/config.yaml');
-    // Write .monomind/.gitignore — commit config/knowledge/metrics, exclude sensitive data
-    const gitignorePath = path.join(targetDir, '.monomind', '.gitignore');
-    const gitignore = `# Monomind — exclude files that may contain secrets or sensitive prompt data
-# Sessions contain conversation history (prompts, code snippets, user data)
-sessions/
-# Security scan results may expose vulnerability details
-security/
-# Temporary and machine-specific files
-*.tmp
-*.log
-daemon.pid
-# Never commit credentials or keys
-*.key
-*.token
-*.secret
-.env
-`;
-    if (!fs.existsSync(gitignorePath) || options.force) {
-        atomicWriteFile(gitignorePath, gitignore);
-        result.created.files.push('.monomind/.gitignore');
-    }
-    // Ensure the project-level .gitignore does NOT blanket-ignore .monomind/
-    // A blanket ignore prevents config, metrics, and knowledge graph from being committed.
-    // We remove any bare `.monomind/` or `**/.monomind/` lines and add specific excludes instead.
-    const projectGitignorePath = path.join(targetDir, '.gitignore');
-    if (fs.existsSync(projectGitignorePath) && fs.statSync(projectGitignorePath).size <= MAX_EXEC_FILE_BYTES) {
-        const existing = fs.readFileSync(projectGitignorePath, 'utf-8');
-        const blanketPattern = /^(\*\*\/)?\.monomind\/?\s*$/gm;
-        if (blanketPattern.test(existing)) {
-            const fixed = existing
-                .split('\n')
-                .filter(line => !/^(\*\*\/)?\.monomind\/?\s*$/.test(line))
-                .join('\n');
-            const specificExcludes = [
-                '# monomind runtime — exclude sensitive and machine-specific data',
-                '.monomind/sessions/',
-                '.monomind/security/',
-                '.monomind/*.tmp',
-                '.monomind/*.log',
-                '.monomind/daemon.pid',
-                '.monomind/*.db',
-                '.monomind/*.db-wal',
-                '.monomind/*.db-shm',
-            ].join('\n');
-            atomicWriteFile(projectGitignorePath, fixed.trimEnd() + '\n' + specificExcludes + '\n');
-            result.updated.push('.gitignore (replaced blanket .monomind/ ignore with specific excludes)');
-        }
-    }
-    // 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 (workers refresh at session 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: {
-                mcp_server: 0,
-                estimated_agents: 0
-            },
-            swarm: {
-                active: false,
-                agent_count: 0,
-                coordination_active: false
-            },
-            integration: {
-                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 hooksAvailable = _isOptionalPackageResolvable('@monoes/hooks');
-    const capabilities = `# Monomind - Complete Capabilities Reference
-> Generated: ${new Date().toISOString()}
-> Full documentation: https://github.com/monoes/monomind
-
-## 📋 Table of Contents
-
-1. [Overview](#overview)
-2. [Swarm Orchestration](#swarm-orchestration)
-3. [Available Agents (60+)](#available-agents)
-4. [CLI Commands](#cli-commands)
-5. [Hooks System (29 Hook Subcommands + 15 Background Workers)](#hooks-system)
-6. [Memory & Intelligence](#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
-- **ANN Vector Search** - indexed pattern retrieval via SQLite (better-sqlite3, sql.js WASM fallback)
-- **Keyword Routing** - deterministic task→agent routing with outcome measurement
-- **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'} |
-| Learning | ${options.runtime.enableLearningBridge ? 'Enabled' : '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\`
-
-### 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
-| Command | Subcommands | Description |
-|---------|-------------|-------------|
-| \`init\` | 5 | Project initialization |
-| \`agent\` | 7 | Agent lifecycle management |
-| \`swarm\` | 6 | Multi-agent coordination |
-| \`memory\` | 12 | SQLite with ANN vector search |
-| \`mcp\` | 9 | MCP server management |
-| \`task\` | 5 | Task assignment |
-| \`session\` | 6 | Session persistence |
-| \`config\` | 7 | Configuration |
-| \`status\` | 3 | System monitoring |
-| \`hooks\` | 29 | Self-learning hooks + 15 background workers${hooksAvailable ? '' : ' (background workers unavailable in this install)'} |
-
-> Note: there is no \`hive-mind\`, \`workflow\`, \`neural\`, \`embeddings\`, \`claims\`, \`migrate\`, or \`process\` CLI command.
-> Hive-Mind consensus (byzantine/raft/quorum) is available exclusively via MCP tools, not the CLI.
-> Neural pattern learning was merged into \`hooks intelligence\`.
-
-### Advanced Commands
-| Command | Subcommands | Description |
-|---------|-------------|-------------|
-| \`security\` | 6 | Security scanning |
-| \`performance\` | 4 | Profiling & benchmarks |
-| \`providers\` | 4 | AI provider config |
-| \`guidance\` | 1 | Governance gate setup |
-| \`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
-
-### 29 Available Hook Subcommands${hooksAvailable ? '' : ' — background workers unavailable in this install (@monoes/hooks did not resolve)'}
-
-#### 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 |
-
-### 15 Background Workers (@monoes/hooks, run in-process)
-| Worker | Priority | Purpose |
-|--------|----------|---------|
-| \`performance\` | normal | Benchmark performance |
-| \`health\` | high | System health monitoring |
-| \`swarm\` | high | Swarm activity monitoring |
-| \`git\` | normal | Branch/change tracking |
-| \`learning\` | normal | Learning optimization |
-| \`adr\` | low | ADR compliance |
-| \`ddd\` | low | DDD progress |
-| \`security\` | high | Secret/vulnerability scan |
-| \`patterns\` | normal | Pattern consolidation |
-| \`cache\` | background | Cache cleanup |
-| \`progress\` | normal | Progress tracking |
-| \`map\` | normal | Codebase mapping |
-| \`audit\` | high | Security audit metrics |
-| \`optimize\` | normal | Performance snapshot |
-| \`consolidate\` | low | Memory consolidation |
-
-Metrics-producing workers (ddd, map, audit, optimize, consolidate) refresh at
-session start when their output is >6h old; run on demand with
-\`monomind hooks worker run <name>\`.
-
----
-
-## Memory & Intelligence
-
-### Intelligence System
-- **Keyword routing**: Deterministic task→agent routing with outcome measurement
-- **ANN pattern search**: Indexed vector search via SQLite
-- **ReasoningBank**: Stores learned patterns and trajectories for retrieval
-- **Int8 Quantization**: ~4x memory reduction for stored embeddings
-
-Routing and learning are JS-only — no native neural engine is required. Route
-and command outcomes are recorded and scored so routing quality is measured.
-
-### Self-Learning Memory (ADR-049)
-
-| Component | Status | Description |
-|-----------|--------|-------------|
-| **Learning** | ${options.runtime.enableLearningBridge ? '✅ Enabled' : '⏸ Disabled'} | Connects insights to the pattern store |
-| **AgentMemoryScope** | ${options.runtime.enableAgentScopes ? '✅ Enabled' : '⏸ Disabled'} | 3-scope agent memory (project/local/user) |
-
-**Learning** — Insights trigger learning trajectories. Confidence evolves: +0.03 on access, -0.005/hour decay.
-
-**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
-
-> **Experimental, MCP-only.** There is no \`hive-mind\` CLI command — this is
-> single-process vote counting exposed exclusively via MCP tools
-> (\`hive-mind-tools.ts\`), not distributed networking. Reach it through the
-> MCP server (\`npx monomind@latest mcp start\`) once connected to an MCP client.
-
-### 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 | Status |
-|-----------|-----------------|--------|
-| \`byzantine\` / \`bft\` | f < n/3 faulty | Implemented (vote counting) |
-| \`raft\` | f < n/2 failed | Implemented (vote counting) |
-| \`quorum\` | Configurable | Implemented |
-| \`gossip\` | Eventually consistent | Planned — not implemented, rejected by \`hive_mind_init\` |
-| \`crdt\` | Conflict-free | Planned — not implemented, rejected by \`hive_mind_init\` |
-
----
-
-## Performance Targets
-
-| Metric | Target | Status |
-|--------|--------|--------|
-| ANN Search | Indexed vector search | ✅ Implemented (SQLite) |
-| Memory Reduction | 50-75% | ✅ Implemented (~4x via Int8 quantization) |
-| Pattern Learning | Recorded + retrievable | ✅ Implemented (ReasoningBank) |
-| MCP Response | <100ms | ✅ Achieved |
-| CLI Startup | <500ms | ✅ Achieved |
-| 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 |
-|---------|---------|---------|
-| better-sqlite3 (sql.js WASM fallback) | latest | SQLite vector database (ANN search) |
-
-### 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 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 run 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/monoes/monomind
-**Issues**: https://github.com/monoes/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.',
-            '**Code navigation**: ALWAYS call `mcp__monomind__monograph_query` BEFORE grep/rg/find for code exploration — it returns file path + line number from a pre-built knowledge graph. Call `mcp__monomind__monograph_suggest` with a task description for multi-file tasks. Only fall back to grep if monograph returns 0 results or the DB is not built.',
-            'Check system-reminder tags for [INTELLIGENCE] pattern suggestions and [MONOGRAPH] context before starting work.',
-            '',
-        ].join('\n');
-        try {
-            if (!fs.existsSync(globalClaudeDir)) {
-                fs.mkdirSync(globalClaudeDir, { recursive: true });
-            }
-            if (fs.existsSync(globalClaudeMd) && fs.statSync(globalClaudeMd).size <= MAX_EXEC_FILE_BYTES) {
-                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 if (!existing.includes('monograph_query')) {
-                    // Upgrade existing block to include monograph instructions
-                    const updated = existing.replace(/# Monomind Integration[^\n]*\n(?:(?!^#).+\n)*/m, monomindBlock.trimStart() + '\n');
-                    atomicWriteFile(globalClaudeMd, updated);
-                    result.created.files.push('~/.claude/CLAUDE.md (upgraded monomind block)');
-                }
-            }
-            else {
-                atomicWriteFile(globalClaudeMd, monomindBlock.trimStart());
-                result.created.files.push('~/.claude/CLAUDE.md');
-            }
-        }
-        catch (e) {
-            // Non-critical — global CLAUDE.md is best-effort
-            if (process.env.DEBUG || process.env.MONOMIND_DEBUG)
-                console.error('[writeClaudeMd] failed to write/append ~/.claude/CLAUDE.md:', e);
-        }
-        // 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) && fs.statSync(globalSettingsPath).size <= MAX_EXEC_FILE_BYTES) {
-                try {
-                    globalSettings = JSON.parse(fs.readFileSync(globalSettingsPath, 'utf-8'));
-                }
-                catch (e) {
-                    // malformed JSON — start fresh
-                    if (process.env.DEBUG || process.env.MONOMIND_DEBUG)
-                        console.error('[writeClaudeMd] ~/.claude/settings.json unparseable, starting fresh:', e);
-                }
-            }
-            // 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 (e) {
-            // Non-critical — global settings hook is best-effort
-            if (process.env.DEBUG || process.env.MONOMIND_DEBUG)
-                console.error('[writeClaudeMd] failed to inject token hook into ~/.claude/settings.json:', e);
-        }
-    }
-}
-/**
- * Write Antigravity (agy) integration files:
- *   GEMINI.md                       — agent instructions read by agy
- *   .gemini/rules/monomind.md       — workflow rules file
- *   .gemini/helpers/statusline.sh   — shell wrapper for the agy status bar
- *   .gemini/settings.json           — wires the statusline command into agy
- */
-async function writeGeminiFiles(targetDir, options, result) {
-    // GEMINI.md
-    const geminiMdPath = path.join(targetDir, 'GEMINI.md');
-    if (!fs.existsSync(geminiMdPath) || options.force) {
-        atomicWriteFile(geminiMdPath, generateGeminiMd(options));
-        result.created.files.push('GEMINI.md');
-    }
-    else {
-        result.skipped.push('GEMINI.md');
-    }
-    // .gemini/rules/monomind.md
-    const geminiRulesDir = path.join(targetDir, '.gemini', 'rules');
-    fs.mkdirSync(geminiRulesDir, { recursive: true });
-    const rulesPath = path.join(geminiRulesDir, 'monomind.md');
-    if (!fs.existsSync(rulesPath) || options.force) {
-        atomicWriteFile(rulesPath, generateGeminiRulesMd(options));
-        result.created.files.push('.gemini/rules/monomind.md');
-    }
-    else {
-        result.skipped.push('.gemini/rules/monomind.md');
-    }
-    // .gemini/helpers/statusline.sh
-    const geminiHelpersDir = path.join(targetDir, '.gemini', 'helpers');
-    fs.mkdirSync(geminiHelpersDir, { recursive: true });
-    const statuslineShPath = path.join(geminiHelpersDir, 'statusline.sh');
-    if (!fs.existsSync(statuslineShPath) || options.force) {
-        atomicWriteFile(statuslineShPath, generateStatuslineSh());
-        try {
-            fs.chmodSync(statuslineShPath, 0o755);
-        }
-        catch { /* ignore on Windows */ }
-        result.created.files.push('.gemini/helpers/statusline.sh');
-    }
-    else {
-        result.skipped.push('.gemini/helpers/statusline.sh');
-    }
-    // .gemini/settings.json — only write if not already present (user may have
-    // their own agy settings; never clobber on force either — we only add to it)
-    const geminiSettingsPath = path.join(targetDir, '.gemini', 'settings.json');
-    try {
-        let existing = {};
-        if (fs.existsSync(geminiSettingsPath) && fs.statSync(geminiSettingsPath).size <= MAX_EXEC_FILE_BYTES) {
-            existing = JSON.parse(fs.readFileSync(geminiSettingsPath, 'utf-8'));
-        }
-        if (!existing.statusLine) {
-            existing.statusLine = { type: 'command', command: '.gemini/helpers/statusline.sh' };
-            atomicWriteFile(geminiSettingsPath, JSON.stringify(existing, null, 2));
-            result.created.files.push('.gemini/settings.json (statusLine wired)');
-        }
-        else {
-            result.skipped.push('.gemini/settings.json (statusLine already configured)');
-        }
-    }
-    catch (e) {
-        result.errors.push(`writeGeminiFiles: failed to write .gemini/settings.json: ${e instanceof Error ? e.message : String(e)}`);
-    }
-    // Also update the global ~/.gemini/antigravity-cli/settings.json (best-effort)
-    const homeDir = process.env.HOME || process.env.USERPROFILE || '';
-    if (homeDir) {
-        const globalAgyDir = path.join(homeDir, '.gemini', 'antigravity-cli');
-        const globalAgySettings = path.join(globalAgyDir, 'settings.json');
-        const globalStatuslineSh = path.join(globalAgyDir, 'statusline.sh');
-        try {
-            // Only touch the global config when it already exists — i.e. the user
-            // actually runs agy. Creating the directory for non-agy users would be
-            // init mutating state outside the project for no benefit.
-            if (fs.existsSync(globalAgyDir)) {
-                // Write/overwrite the global statusline wrapper
-                if (!fs.existsSync(globalStatuslineSh) || options.force) {
-                    atomicWriteFile(globalStatuslineSh, generateStatuslineSh());
-                    try {
-                        fs.chmodSync(globalStatuslineSh, 0o755);
-                    }
-                    catch { /* ignore */ }
-                    result.created.files.push('~/.gemini/antigravity-cli/statusline.sh');
-                }
-                // Inject statusLine into global agy settings without clobbering existing keys
-                let globalSettings = {};
-                if (fs.existsSync(globalAgySettings) && fs.statSync(globalAgySettings).size <= MAX_EXEC_FILE_BYTES) {
-                    try {
-                        globalSettings = JSON.parse(fs.readFileSync(globalAgySettings, 'utf-8'));
-                    }
-                    catch { /* reset */ }
-                }
-                if (!globalSettings.statusLine) {
-                    globalSettings.statusLine = {
-                        type: 'command',
-                        command: `${globalAgyDir}/statusline.sh`,
-                    };
-                    atomicWriteFile(globalAgySettings, JSON.stringify(globalSettings, null, 2));
-                    result.created.files.push('~/.gemini/antigravity-cli/settings.json (statusLine wired)');
-                }
-            }
-        }
-        catch (e) {
-            // Non-critical — global agy settings is best-effort
-            if (process.env.DEBUG || process.env.MONOMIND_DEBUG) {
-                console.error('[writeGeminiFiles] failed to update global agy settings:', e);
-            }
-        }
-    }
-}
-/**
- * Write opencode artifacts. ADDITIVE — only invoked when
- * `components.opencode` is set. Never touches .claude/ or .gemini/.
- *
- * Tier 1: opencode.json (MCP server + permissions + instructions).
- * Tier 2 (added next): AGENTS.md + .opencode/{agent,command,skills}/ converted
- * from the Claude tree.
- */
-async function writeOpencodeFiles(targetDir, options, result) {
-    // opencode.json — write only if absent (or --force). Never clobber a user's
-    // hand-written config; mirror writeGeminiFiles' skip-if-exists policy.
-    const opencodeJsonPath = path.join(targetDir, 'opencode.json');
-    if (!fs.existsSync(opencodeJsonPath) || options.force) {
-        atomicWriteFile(opencodeJsonPath, generateOpencodeJson(options));
-        result.created.files.push('opencode.json');
-    }
-    else {
-        result.skipped.push('opencode.json');
-    }
-    // AGENTS.md — opencode's instructions file (CLAUDE.md equivalent).
-    const agentsMdPath = path.join(targetDir, 'AGENTS.md');
-    if (!fs.existsSync(agentsMdPath) || options.force) {
-        atomicWriteFile(agentsMdPath, generateAgentsMd());
-        result.created.files.push('AGENTS.md');
-    }
-    else {
-        result.skipped.push('AGENTS.md');
-    }
-    // Hook-shim plugin (Tier 3) — bridges monomind's gate handlers into
-    // opencode's tool.execute.before. .opencode/plugins/ (plural) per opencode docs.
-    const pluginDir = path.join(targetDir, '.opencode', 'plugins');
-    const pluginPath = path.join(pluginDir, 'monomind-hooks.ts');
-    if (!fs.existsSync(pluginPath) || options.force) {
-        fs.mkdirSync(pluginDir, { recursive: true });
-        atomicWriteFile(pluginPath, generateHooksPlugin());
-        result.created.files.push('.opencode/plugins/monomind-hooks.ts');
-    }
-    else {
-        result.skipped.push('.opencode/plugins/monomind-hooks.ts');
-    }
-    // /monomind-status command — the opencode equivalent of the Claude Code
-    // statusline (opencode has no custom statusbar UI). Runs statusline.cjs
-    // unchanged and reports a formatted summary.
-    const statusCmdPath = path.join(targetDir, '.opencode', 'command', 'monomind-status.md');
-    if (!fs.existsSync(statusCmdPath) || options.force) {
-        fs.mkdirSync(path.dirname(statusCmdPath), { recursive: true });
-        atomicWriteFile(statusCmdPath, generateStatusCommand());
-        result.created.files.push('.opencode/command/monomind-status.md');
-    }
-    else {
-        result.skipped.push('.opencode/command/monomind-status.md');
-    }
-    // Convert the .claude/{agents,commands,skills} tree that copyAgents/Skills/
-    // Commands just wrote into opencode shape. Reading from the target .claude/
-    // dir (not the package source) means only the user's selected subset is
-    // converted, and we never re-implement the MAP filtering logic.
-    const claudeDir = path.join(targetDir, '.claude');
-    let agentCount = 0, commandCount = 0, skillCount = 0;
-    const seenAgents = new Set();
-    // Agents → .opencode/agent/<name>.md (flattened, deduped by name)
-    const srcAgents = path.join(claudeDir, 'agents');
-    if (fs.existsSync(srcAgents)) {
-        const destAgents = path.join(targetDir, '.opencode', 'agent');
-        for (const rel of walkMdFiles(srcAgents)) {
-            const abs = path.join(srcAgents, rel);
-            if (!isLikelyUserFile(rel))
-                continue; // skip READMEs etc.
-            const src = fs.readFileSync(abs, 'utf-8');
-            const fallback = path.basename(rel, '.md');
-            const converted = convertAgentMd(src, fallback);
-            const name = extractFmName(converted) || fallback;
-            if (seenAgents.has(name))
-                continue;
-            seenAgents.add(name);
-            fs.mkdirSync(destAgents, { recursive: true });
-            atomicWriteFile(path.join(destAgents, `${name}.md`), converted);
-            agentCount++;
-        }
-    }
-    // Commands → .opencode/command/<category>-<name>.md (namespace preserved)
-    const srcCommands = path.join(claudeDir, 'commands');
-    if (fs.existsSync(srcCommands)) {
-        const destCommands = path.join(targetDir, '.opencode', 'command');
-        for (const rel of walkMdFiles(srcCommands)) {
-            const abs = path.join(srcCommands, rel);
-            if (!isLikelyUserFile(rel))
-                continue;
-            const segs = rel.split(path.sep);
-            const category = segs.length > 1 ? segs[0] : 'monomind';
-            const fileBase = path.basename(rel, '.md');
-            const src = fs.readFileSync(abs, 'utf-8');
-            const converted = convertCommandMd(src, category, fileBase);
-            fs.mkdirSync(destCommands, { recursive: true });
-            atomicWriteFile(path.join(destCommands, opencodeCommandFilename(category, fileBase)), converted);
-            commandCount++;
-        }
-    }
-    // Skills → .opencode/skills/<name>/SKILL.md (same shape)
-    const srcSkills = path.join(claudeDir, 'skills');
-    if (fs.existsSync(srcSkills)) {
-        for (const rel of walkMdFiles(srcSkills)) {
-            // rel looks like "<skillName>/SKILL.md"
-            const segs = rel.split(path.sep);
-            if (segs.length < 2 || segs[segs.length - 1] !== 'SKILL.md')
-                continue;
-            const skillName = segs[0];
-            const abs = path.join(srcSkills, rel);
-            const src = fs.readFileSync(abs, 'utf-8');
-            const converted = convertSkillMd(src, skillName);
-            const destDir = path.join(targetDir, '.opencode', 'skills', skillName);
-            fs.mkdirSync(destDir, { recursive: true });
-            atomicWriteFile(path.join(destDir, 'SKILL.md'), converted);
-            skillCount++;
-        }
-    }
-    if (agentCount)
-        result.created.files.push(`.opencode/agent/ (${agentCount} agents)`);
-    if (commandCount)
-        result.created.files.push(`.opencode/command/ (${commandCount} commands)`);
-    if (skillCount)
-        result.created.files.push(`.opencode/skills/ (${skillCount} skills)`);
-}
-/**
- * Write Kimi Code artifacts. ADDITIVE — only invoked when
- * `components.kimicode` is set. Never touches .claude/, .gemini/, .opencode/.
- *
- * Tier 1: .kimi-code/mcp.json (merged, never clobbered), AGENTS.md (skip-if-exists),
- *         .kimi-code/{agents,skills}/ converted from the Claude tree.
- * Tier 2: .kimi-code/plugin/hooks/monomind-gate.mjs — stdin/exit-code bridge into
- *         the existing .claude/helpers gate handlers (kimi has no project-level
- *         hooks, so enforcement only activates via the Tier 3 plugin).
- * Tier 3: .kimi-code/plugin/kimi.plugin.json + commands/ — installable via
- *         `/plugins install ./.kimi-code/plugin` for /monomind:* slash commands
- *         and auto-wired hooks.
- */
-async function writeKimiFiles(targetDir, options, result) {
-    const kimiDir = path.join(targetDir, '.kimi-code');
-    // .kimi-code/mcp.json — MERGE the monomind server into an existing file;
-    // never clobber the user's other servers. Even --force merges (it refreshes
-    // the monomind entry only) — a full overwrite would destroy unrelated
-    // servers the user configured. Unparseable existing file → skip.
-    const mcpJsonPath = path.join(kimiDir, 'mcp.json');
-    if (!fs.existsSync(mcpJsonPath)) {
-        fs.mkdirSync(kimiDir, { recursive: true });
-        atomicWriteFile(mcpJsonPath, generateKimiMcpJson(options));
-        result.created.files.push('.kimi-code/mcp.json');
-    }
-    else {
-        const current = fs.readFileSync(mcpJsonPath, 'utf-8');
-        const merged = mergeKimiMcpJson(current, options);
-        if (merged === null) {
-            result.skipped.push('.kimi-code/mcp.json (unparseable — not touched)');
-        }
-        else if (merged !== current) {
-            atomicWriteFile(mcpJsonPath, merged);
-            result.updated.push('.kimi-code/mcp.json (merged monomind server)');
-        }
-        else {
-            result.skipped.push('.kimi-code/mcp.json');
-        }
-    }
-    // AGENTS.md — kimi's workspace instructions file. Skip-if-exists, ALWAYS:
-    // the opencode target or a hand-written file may already provide one, and
-    // under --force the two generators would otherwise flip the file depending
-    // on write order. Users who want regeneration delete the file first —
-    // same never-clobber spirit as the mcp.json merge above.
-    const agentsMdPath = path.join(targetDir, 'AGENTS.md');
-    if (!fs.existsSync(agentsMdPath)) {
-        atomicWriteFile(agentsMdPath, generateKimiAgentsMd());
-        result.created.files.push('AGENTS.md');
-    }
-    else {
-        result.skipped.push('AGENTS.md');
-    }
-    // Convert the .claude/{agents,commands,skills} tree that copyAgents/Skills/
-    // Commands just wrote into kimi shape — same approach as writeOpencodeFiles:
-    // reading from the target .claude/ dir means only the user's selected subset
-    // is converted.
-    const claudeDir = path.join(targetDir, '.claude');
-    let agentCount = 0, commandCount = 0, skillCount = 0;
-    const seenAgents = new Set();
-    // Agents → .kimi-code/agents/<name>.md (flattened, deduped by name)
-    const srcAgents = path.join(claudeDir, 'agents');
-    if (fs.existsSync(srcAgents)) {
-        const destAgents = path.join(kimiDir, 'agents');
-        for (const rel of walkMdFiles(srcAgents)) {
-            const abs = path.join(srcAgents, rel);
-            if (!isLikelyUserFile(rel))
-                continue;
-            const src = fs.readFileSync(abs, 'utf-8');
-            const fallback = path.basename(rel, '.md');
-            const converted = convertKimiAgentMd(src, fallback);
-            const name = extractFmName(converted) || fallback;
-            if (seenAgents.has(name))
-                continue;
-            seenAgents.add(name);
-            fs.mkdirSync(destAgents, { recursive: true });
-            atomicWriteFile(path.join(destAgents, `${name}.md`), converted);
-            agentCount++;
-        }
-    }
-    // Skills → .kimi-code/skills/<name>/SKILL.md (same shape).
-    // Track the directory names written here so command flow-skills below never
-    // overwrite a REAL skill that happens to share the <category>-<name> slug
-    // (e.g. a skill dir "mastermind-debug" vs a command "mastermind/debug.md").
-    const writtenSkillDirs = new Set();
-    const srcSkills = path.join(claudeDir, 'skills');
-    if (fs.existsSync(srcSkills)) {
-        for (const rel of walkMdFiles(srcSkills)) {
-            const segs = rel.split(path.sep);
-            if (segs.length < 2 || segs[segs.length - 1] !== 'SKILL.md')
-                continue;
-            const skillName = segs[0];
-            const abs = path.join(srcSkills, rel);
-            const src = fs.readFileSync(abs, 'utf-8');
-            const converted = convertKimiSkillMd(src, skillName);
-            const destDir = path.join(kimiDir, 'skills', skillName);
-            fs.mkdirSync(destDir, { recursive: true });
-            atomicWriteFile(path.join(destDir, 'SKILL.md'), converted);
-            writtenSkillDirs.add(skillName);
-            skillCount++;
-        }
-    }
-    // Commands → TWO outputs from the same source pass:
-    //   (a) .kimi-code/skills/<cat>-<name>/SKILL.md as type:flow skills — the only
-    //       project-level invocable-command mechanism kimi has (/skill:<name>).
-    //   (b) .kimi-code/plugin/commands/<cat>-<name>.md for the Tier 3 plugin
-    //       (/monomind:<name> slash commands once installed).
-    const srcCommands = path.join(claudeDir, 'commands');
-    const pluginDir = path.join(kimiDir, 'plugin');
-    // Always create plugin/commands/ — the manifest declares ./commands/ and a
-    // missing path surfaces as a plugin diagnostic in kimi (e.g. --skip-claude
-    // runs where no commands were converted).
-    const destPluginCommands = path.join(pluginDir, 'commands');
-    fs.mkdirSync(destPluginCommands, { recursive: true });
-    if (fs.existsSync(srcCommands)) {
-        for (const rel of walkMdFiles(srcCommands)) {
-            const abs = path.join(srcCommands, rel);
-            if (!isLikelyUserFile(rel))
-                continue;
-            const segs = rel.split(path.sep);
-            const category = segs.length > 1 ? segs[0] : 'monomind';
-            const fileBase = path.basename(rel, '.md');
-            const src = fs.readFileSync(abs, 'utf-8');
-            // (a) flow skill — skipped when a real skill already owns this directory
-            // name (real skills win; the plugin command below still provides the
-            // command under /monomind:<name>).
-            const flowSkill = convertKimiCommandToFlowSkill(src, category, fileBase);
-            const flowName = extractFmName(flowSkill) || `${category}-${fileBase}`;
-            if (writtenSkillDirs.has(flowName)) {
-                result.skipped.push(`.kimi-code/skills/${flowName}/ (command flow-skill conflicts with a real skill — plugin command kept)`);
-            }
-            else {
-                const flowDir = path.join(kimiDir, 'skills', flowName);
-                fs.mkdirSync(flowDir, { recursive: true });
-                atomicWriteFile(path.join(flowDir, 'SKILL.md'), flowSkill);
-                writtenSkillDirs.add(flowName);
-                skillCount++;
-            }
-            // (b) plugin command
-            const pluginCmd = convertKimiPluginCommandMd(src, category, fileBase);
-            fs.mkdirSync(destPluginCommands, { recursive: true });
-            atomicWriteFile(path.join(destPluginCommands, kimiCommandFilename(category, fileBase)), pluginCmd);
-            commandCount++;
-        }
-    }
-    // Tier 2: hook gate bridge script.
-    const hooksDir = path.join(pluginDir, 'hooks');
-    const gatePath = path.join(hooksDir, 'monomind-gate.mjs');
-    if (!fs.existsSync(gatePath) || options.force) {
-        fs.mkdirSync(hooksDir, { recursive: true });
-        atomicWriteFile(gatePath, generateKimiGateScript());
-        result.created.files.push('.kimi-code/plugin/hooks/monomind-gate.mjs');
-    }
-    else {
-        result.skipped.push('.kimi-code/plugin/hooks/monomind-gate.mjs');
-    }
-    // Tier 3: plugin manifest.
-    const manifestPath = path.join(pluginDir, 'kimi.plugin.json');
-    if (!fs.existsSync(manifestPath) || options.force) {
-        fs.mkdirSync(pluginDir, { recursive: true });
-        atomicWriteFile(manifestPath, generateKimiPluginManifest(options));
-        result.created.files.push('.kimi-code/plugin/kimi.plugin.json');
-    }
-    else {
-        result.skipped.push('.kimi-code/plugin/kimi.plugin.json');
-    }
-    if (agentCount)
-        result.created.files.push(`.kimi-code/agents/ (${agentCount} agents)`);
-    if (skillCount)
-        result.created.files.push(`.kimi-code/skills/ (${skillCount} skills)`);
-    if (commandCount)
-        result.created.files.push(`.kimi-code/plugin/commands/ (${commandCount} commands)`);
-    // Statusline — the footer under kimi's chatbox. Lives in the USER's
-    // ~/.kimi-code/ (kimi has no project-level statusline config), gated on
-    // that directory already existing (i.e. the user actually runs kimi —
-    // init must not create global state for non-kimi users). The tui.toml
-    // merge never clobbers an existing [status_line].command.
-    const homeDir = process.env.HOME || process.env.USERPROFILE || '';
-    if (homeDir) {
-        const kimiHome = path.join(homeDir, '.kimi-code');
-        if (fs.existsSync(kimiHome)) {
-            try {
-                const statuslineShPath = path.join(kimiHome, 'statusline.sh');
-                if (!fs.existsSync(statuslineShPath) || options.force) {
-                    atomicWriteFile(statuslineShPath, generateKimiStatuslineSh());
-                    try {
-                        fs.chmodSync(statuslineShPath, 0o755);
-                    }
-                    catch { /* ignore on Windows */ }
-                    result.created.files.push('~/.kimi-code/statusline.sh');
-                }
-                else {
-                    result.skipped.push('~/.kimi-code/statusline.sh');
-                }
-                const tuiTomlPath = path.join(kimiHome, 'tui.toml');
-                const relCommand = '~/.kimi-code/statusline.sh';
-                const existingToml = fs.existsSync(tuiTomlPath) ? fs.readFileSync(tuiTomlPath, 'utf-8') : '';
-                const mergedToml = mergeKimiTuiTomlStatusline(existingToml, relCommand);
-                if (mergedToml !== existingToml) {
-                    atomicWriteFile(tuiTomlPath, mergedToml);
-                    result.created.files.push('~/.kimi-code/tui.toml ([status_line].command wired)');
-                }
-                else {
-                    result.skipped.push('~/.kimi-code/tui.toml (status_line.command already set)');
-                }
-            }
-            catch (e) {
-                // Best-effort, like the agy global settings — a statusline failure
-                // must never fail init.
-                if (process.env.DEBUG || process.env.MONOMIND_DEBUG) {
-                    console.error('[writeKimiFiles] failed to wire kimi statusline:', e);
-                }
-            }
-        }
-    }
-}
-/** Recursively collect .md files under dir, returned relative to dir. */
-function walkMdFiles(dir) {
-    const out = [];
-    const visit = (d, prefix) => {
-        let entries;
-        try {
-            entries = fs.readdirSync(d, { withFileTypes: true });
-        }
-        catch {
-            return;
-        }
-        for (const e of entries) {
-            const rel = prefix ? `${prefix}${path.sep}${e.name}` : e.name;
-            if (e.isDirectory())
-                visit(path.join(d, e.name), rel);
-            else if (e.isFile() && /\.md$/i.test(e.name))
-                out.push(rel);
-        }
-    };
-    visit(dir, '');
-    return out;
-}
-/** Skip READMEs and other non-definition markdown. */
-function isLikelyUserFile(rel) {
-    const base = path.basename(rel).toLowerCase();
-    if (base === 'readme.md' || base === 'readme')
-        return false;
-    return true;
-}
-/** Pull the `name:` scalar from a frontmatter block (best-effort). */
-function extractFmName(md) {
-    const m = md.match(/^---\r?\n[\s\S]*?\r?\n---/);
-    if (!m)
-        return null;
-    const fm = m[0];
-    const nm = fm.match(/^name\s*:\s*(.+?)\s*$/m);
-    return nm ? nm[1].replace(/^["']|["']$/g, '') : null;
-}
-/**
- * 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) {
-        // Skip exFAT/macOS AppleDouble junk files (e.g. "._foo.js") so they don't
-        // get perpetuated into every newly-initialized project.
-        if (entry.name.startsWith('._'))
-            continue;
-        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
  */
@@ -2813,7 +377,6 @@ function _registerMonomindProject(dir) {
             }
         }
         catch (e) {
-            // Unparseable registry — proceeding with an empty list will overwrite it below, losing previously registered projects
             if (process.env.DEBUG || process.env.MONOMIND_DEBUG)
                 console.error('[_registerMonomindProject] ~/.monomind-projects.json unparseable, resetting:', e);
         }
@@ -2867,7 +430,7 @@ export function findMonomindProjects(maxDepth = 3) {
         if (fs.existsSync(marker)) {
             found.add(dir);
             return;
-        } // don't recurse into a monomind project
+        }
         let entries;
         try {
             entries = fs.readdirSync(dir, { withFileTypes: true });