moflo 4.8.32 → 4.8.34

package/src/@claude-flow/cli/dist/src/commands/doctor.js

@@ -1,1108 +1,1340 @@
-/**
- * V3 CLI Doctor Command
- * System diagnostics, dependency checks, config validation
- *
- * Created with motailz.com
- */
-import { output } from '../output.js';
-import { existsSync, readFileSync, writeFileSync, unlinkSync, statSync, mkdirSync } from 'fs';
-import { join, dirname } from 'path';
-import { fileURLToPath } from 'url';
-import { execSync, exec } from 'child_process';
-import { promisify } from 'util';
-import { getDaemonLockHolder, releaseDaemonLock, isDaemonProcess } from '../services/daemon-lock.js';
-// Promisified exec with proper shell and env inheritance for cross-platform support
-const execAsync = promisify(exec);
-/**
- * Execute command asynchronously with proper environment inheritance
- * Critical for Windows where PATH may not be inherited properly
- */
-async function runCommand(command, timeoutMs = 5000) {
-    const { stdout } = await execAsync(command, {
-        encoding: 'utf8',
-        timeout: timeoutMs,
-        shell: process.platform === 'win32' ? 'cmd.exe' : '/bin/sh', // Use proper shell per platform
-        env: { ...process.env }, // Explicitly inherit full environment
-        windowsHide: true, // Hide window on Windows
-    });
-    return stdout.trim();
-}
-// Check Node.js version
-async function checkNodeVersion() {
-    const requiredMajor = 20;
-    const version = process.version;
-    const major = parseInt(version.slice(1).split('.')[0], 10);
-    if (major >= requiredMajor) {
-        return { name: 'Node.js Version', status: 'pass', message: `${version} (>= ${requiredMajor} required)` };
-    }
-    else if (major >= 18) {
-        return { name: 'Node.js Version', status: 'warn', message: `${version} (>= ${requiredMajor} recommended)`, fix: 'nvm install 20 && nvm use 20' };
-    }
-    else {
-        return { name: 'Node.js Version', status: 'fail', message: `${version} (>= ${requiredMajor} required)`, fix: 'nvm install 20 && nvm use 20' };
-    }
-}
-// Check npm version (async with proper env inheritance)
-async function checkNpmVersion() {
-    try {
-        const version = await runCommand('npm --version');
-        const major = parseInt(version.split('.')[0], 10);
-        if (major >= 9) {
-            return { name: 'npm Version', status: 'pass', message: `v${version}` };
-        }
-        else {
-            return { name: 'npm Version', status: 'warn', message: `v${version} (>= 9 recommended)`, fix: 'npm install -g npm@latest' };
-        }
-    }
-    catch {
-        return { name: 'npm Version', status: 'fail', message: 'npm not found', fix: 'Install Node.js from https://nodejs.org' };
-    }
-}
-// Check config file
-async function checkConfigFile() {
-    // JSON configs (parse-validated)
-    const jsonPaths = [
-        '.claude-flow/config.json',
-        'claude-flow.config.json',
-        '.claude-flow.json'
-    ];
-    for (const configPath of jsonPaths) {
-        if (existsSync(configPath)) {
-            try {
-                const content = readFileSync(configPath, 'utf8');
-                JSON.parse(content);
-                return { name: 'Config File', status: 'pass', message: `Found: ${configPath}` };
-            }
-            catch (e) {
-                return { name: 'Config File', status: 'fail', message: `Invalid JSON: ${configPath}`, fix: 'Fix JSON syntax in config file' };
-            }
-        }
-    }
-    // YAML configs (existence-checked only — no heavy yaml parser dependency)
-    const yamlPaths = [
-        '.claude-flow/config.yaml',
-        '.claude-flow/config.yml',
-        'claude-flow.config.yaml'
-    ];
-    for (const configPath of yamlPaths) {
-        if (existsSync(configPath)) {
-            return { name: 'Config File', status: 'pass', message: `Found: ${configPath}` };
-        }
-    }
-    return { name: 'Config File', status: 'warn', message: 'No config file (using defaults)', fix: 'claude-flow config init' };
-}
-// Check daemon status — delegates to daemon-lock module for proper
-// PID + command-line verification (avoids Windows PID-recycling false positives).
-async function checkDaemonStatus() {
-    try {
-        // Retry up to 5 times with 1s delay — the daemon starts in the background
-        // during session-start and may not have acquired its lock file yet.
-        const MAX_RETRIES = 5;
-        const RETRY_DELAY_MS = 1000;
-        let holderPid = null;
-        for (let attempt = 0; attempt < MAX_RETRIES; attempt++) {
-            holderPid = getDaemonLockHolder(process.cwd());
-            if (holderPid)
-                break;
-            if (attempt < MAX_RETRIES - 1) {
-                await new Promise(resolve => setTimeout(resolve, RETRY_DELAY_MS));
-            }
-        }
-        if (holderPid) {
-            return { name: 'Daemon Status', status: 'pass', message: `Running (PID: ${holderPid})` };
-        }
-        // getDaemonLockHolder auto-cleans stale locks, but check for legacy PID file
-        const lockFile = '.claude-flow/daemon.lock';
-        if (existsSync(lockFile)) {
-            // Lock exists but holder is null — getDaemonLockHolder already cleaned it,
-            // but if it persists it means cleanup failed (permissions, etc.)
-            return { name: 'Daemon Status', status: 'warn', message: 'Stale lock file', fix: 'rm .claude-flow/daemon.lock && claude-flow daemon start' };
-        }
-        // Also check legacy PID file
-        const pidFile = '.claude-flow/daemon.pid';
-        if (existsSync(pidFile)) {
-            return { name: 'Daemon Status', status: 'warn', message: 'Legacy PID file found', fix: 'rm .claude-flow/daemon.pid && claude-flow daemon start' };
-        }
-        return { name: 'Daemon Status', status: 'warn', message: 'Not running', fix: 'claude-flow daemon start' };
-    }
-    catch {
-        return { name: 'Daemon Status', status: 'warn', message: 'Unable to check', fix: 'claude-flow daemon status' };
-    }
-}
-// Check memory database
-async function checkMemoryDatabase() {
-    const dbPaths = [
-        '.claude-flow/memory.db',
-        '.swarm/memory.db',
-        'data/memory.db'
-    ];
-    for (const dbPath of dbPaths) {
-        if (existsSync(dbPath)) {
-            try {
-                const stats = statSync(dbPath);
-                const sizeMB = (stats.size / 1024 / 1024).toFixed(2);
-                return { name: 'Memory Database', status: 'pass', message: `${dbPath} (${sizeMB} MB)` };
-            }
-            catch {
-                return { name: 'Memory Database', status: 'warn', message: `${dbPath} (unable to stat)` };
-            }
-        }
-    }
-    return { name: 'Memory Database', status: 'warn', message: 'Not initialized', fix: 'claude-flow memory configure --backend hybrid' };
-}
-// Check git (async with proper env inheritance)
-async function checkGit() {
-    try {
-        const version = await runCommand('git --version');
-        return { name: 'Git', status: 'pass', message: version.replace('git version ', 'v') };
-    }
-    catch {
-        return { name: 'Git', status: 'warn', message: 'Not installed', fix: 'Install git from https://git-scm.com' };
-    }
-}
-// Check if in git repo (async with proper env inheritance)
-async function checkGitRepo() {
-    try {
-        await runCommand('git rev-parse --git-dir');
-        return { name: 'Git Repository', status: 'pass', message: 'In a git repository' };
-    }
-    catch {
-        return { name: 'Git Repository', status: 'warn', message: 'Not a git repository', fix: 'git init' };
-    }
-}
-// Check MCP servers
-async function checkMcpServers() {
-    const mcpConfigPaths = [
-        join(process.env.HOME || '', '.claude/claude_desktop_config.json'),
-        join(process.env.HOME || '', '.config/claude/mcp.json'),
-        '.mcp.json'
-    ];
-    for (const configPath of mcpConfigPaths) {
-        if (existsSync(configPath)) {
-            try {
-                const content = JSON.parse(readFileSync(configPath, 'utf8'));
-                const servers = content.mcpServers || content.servers || {};
-                const count = Object.keys(servers).length;
-                const hasClaudeFlow = 'moflo' in servers || 'claude-flow' in servers || 'claude-flow_alpha' in servers || 'ruflo' in servers || 'ruflo_alpha' in servers;
-                if (hasClaudeFlow) {
-                    return { name: 'MCP Servers', status: 'pass', message: `${count} servers (flo configured)` };
-                }
-                else {
-                    return { name: 'MCP Servers', status: 'warn', message: `${count} servers (flo not found)`, fix: 'claude mcp add ruflo -- npx -y ruflo@latest mcp start' };
-                }
-            }
-            catch {
-                // continue to next path
-            }
-        }
-    }
-    return { name: 'MCP Servers', status: 'warn', message: 'No MCP config found', fix: 'claude mcp add moflo npx moflo mcp start' };
-}
-// Check disk space (async with proper env inheritance)
-async function checkDiskSpace() {
-    try {
-        if (process.platform === 'win32') {
-            return { name: 'Disk Space', status: 'pass', message: 'Check skipped on Windows' };
-        }
-        // Use df -Ph for POSIX mode (guarantees single-line output even with long device names)
-        const output_str = await runCommand('df -Ph . | tail -1');
-        const parts = output_str.split(/\s+/);
-        // POSIX format: Filesystem Size Used Avail Capacity Mounted
-        const available = parts[3];
-        const usePercent = parseInt(parts[4]?.replace('%', '') || '0', 10);
-        if (isNaN(usePercent)) {
-            return { name: 'Disk Space', status: 'warn', message: `${available || 'unknown'} available (unable to parse usage)` };
-        }
-        if (usePercent > 90) {
-            return { name: 'Disk Space', status: 'fail', message: `${available} available (${usePercent}% used)`, fix: 'Free up disk space' };
-        }
-        else if (usePercent > 80) {
-            return { name: 'Disk Space', status: 'warn', message: `${available} available (${usePercent}% used)` };
-        }
-        return { name: 'Disk Space', status: 'pass', message: `${available} available` };
-    }
-    catch {
-        return { name: 'Disk Space', status: 'warn', message: 'Unable to check' };
-    }
-}
-// Check TypeScript/build (async with proper env inheritance)
-async function checkBuildTools() {
-    try {
-        const tscVersion = await runCommand('npx tsc --version', 10000); // tsc can be slow
-        if (!tscVersion || tscVersion.includes('not found')) {
-            return { name: 'TypeScript', status: 'warn', message: 'Not installed locally', fix: 'npm install -D typescript' };
-        }
-        return { name: 'TypeScript', status: 'pass', message: tscVersion.replace('Version ', 'v') };
-    }
-    catch {
-        return { name: 'TypeScript', status: 'warn', message: 'Not installed locally', fix: 'npm install -D typescript' };
-    }
-}
-// Check for stale npx cache (version freshness)
-async function checkVersionFreshness() {
-    try {
-        // Get current CLI version from package.json
-        // Use import.meta.url to reliably locate our own package.json,
-        // regardless of how deep the compiled file sits (e.g. dist/src/commands/).
-        let currentVersion = '0.0.0';
-        try {
-            const thisFile = fileURLToPath(import.meta.url);
-            let dir = dirname(thisFile);
-            // Walk up from the current file's directory until we find the
-            // package.json that belongs to @claude-flow/cli (or claude-flow/cli).
-            // Walk until dirname(dir) === dir (filesystem root on any platform).
-            for (;;) {
-                const candidate = join(dir, 'package.json');
-                try {
-                    if (existsSync(candidate)) {
-                        const pkg = JSON.parse(readFileSync(candidate, 'utf8'));
-                        if (pkg.version &&
-                            typeof pkg.name === 'string' &&
-                            (pkg.name === '@claude-flow/cli' || pkg.name === 'claude-flow' || pkg.name === 'ruflo' || pkg.name === 'moflo' || pkg.name === '@moflo/cli')) {
-                            currentVersion = pkg.version;
-                            break;
-                        }
-                    }
-                }
-                catch {
-                    // Unreadable/invalid JSON -- skip and keep walking up
-                }
-                const parent = dirname(dir);
-                if (parent === dir)
-                    break; // reached root
-                dir = parent;
-            }
-        }
-        catch {
-            // Fall back to a default
-            currentVersion = '0.0.0';
-        }
-        // Check if running via npx (look for _npx in process path or argv)
-        const isNpx = process.argv[1]?.includes('_npx') ||
-            process.env.npm_execpath?.includes('npx') ||
-            process.cwd().includes('_npx');
-        // Query npm for latest version (using alpha tag since that's what we publish to)
-        let latestVersion = currentVersion;
-        try {
-            const npmInfo = await runCommand('npm view moflo version', 5000);
-            latestVersion = npmInfo.trim();
-        }
-        catch {
-            // Can't reach npm registry - skip check
-            return {
-                name: 'Version Freshness',
-                status: 'warn',
-                message: `v${currentVersion} (cannot check registry)`
-            };
-        }
-        // Parse version numbers for comparison (handle prerelease like 3.0.0-alpha.84)
-        const parseVersion = (v) => {
-            const match = v.match(/^(\d+)\.(\d+)\.(\d+)(?:-[a-zA-Z]+\.(\d+))?/);
-            if (!match)
-                return { major: 0, minor: 0, patch: 0, prerelease: 0 };
-            return {
-                major: parseInt(match[1], 10) || 0,
-                minor: parseInt(match[2], 10) || 0,
-                patch: parseInt(match[3], 10) || 0,
-                prerelease: parseInt(match[4], 10) || 0
-            };
-        };
-        const current = parseVersion(currentVersion);
-        const latest = parseVersion(latestVersion);
-        // Compare versions (including prerelease number)
-        const isOutdated = (latest.major > current.major ||
-            (latest.major === current.major && latest.minor > current.minor) ||
-            (latest.major === current.major && latest.minor === current.minor && latest.patch > current.patch) ||
-            (latest.major === current.major && latest.minor === current.minor && latest.patch === current.patch && latest.prerelease > current.prerelease));
-        if (isOutdated) {
-            const fix = isNpx
-                ? 'rm -rf ~/.npm/_npx/* && npx -y moflo'
-                : 'npm update moflo';
-            return {
-                name: 'Version Freshness',
-                status: 'warn',
-                message: `v${currentVersion} (latest: v${latestVersion})${isNpx ? ' [npx cache stale]' : ''}`,
-                fix
-            };
-        }
-        return {
-            name: 'Version Freshness',
-            status: 'pass',
-            message: `v${currentVersion} (up to date)`
-        };
-    }
-    catch (error) {
-        return {
-            name: 'Version Freshness',
-            status: 'warn',
-            message: 'Unable to check version freshness'
-        };
-    }
-}
-// Check Claude Code CLI (async with proper env inheritance)
-async function checkClaudeCode() {
-    try {
-        const version = await runCommand('claude --version');
-        // Parse version from output like "claude 1.0.0" or "Claude Code v1.0.0"
-        const versionMatch = version.match(/v?(\d+\.\d+\.\d+)/);
-        const versionStr = versionMatch ? `v${versionMatch[1]}` : version;
-        return { name: 'Claude Code CLI', status: 'pass', message: versionStr };
-    }
-    catch {
-        return {
-            name: 'Claude Code CLI',
-            status: 'warn',
-            message: 'Not installed',
-            fix: 'npm install -g @anthropic-ai/claude-code'
-        };
-    }
-}
-// Install Claude Code CLI
-async function installClaudeCode() {
-    try {
-        output.writeln();
-        output.writeln(output.bold('Installing Claude Code CLI...'));
-        execSync('npm install -g @anthropic-ai/claude-code', {
-            encoding: 'utf8',
-            stdio: 'inherit',
-            windowsHide: true
-        });
-        output.writeln(output.success('Claude Code CLI installed successfully!'));
-        return true;
-    }
-    catch (error) {
-        output.writeln(output.error('Failed to install Claude Code CLI'));
-        if (error instanceof Error) {
-            output.writeln(output.dim(error.message));
-        }
-        return false;
-    }
-}
-// Check embeddings / vector index health
-async function checkEmbeddings() {
-    const dbPaths = [
-        join(process.cwd(), '.swarm', 'memory.db'),
-        join(process.cwd(), '.claude-flow', 'memory.db'),
-        join(process.cwd(), 'data', 'memory.db'),
-    ];
-    // 1. Fast path: read cached vector-stats.json if available
-    const statsPath = join(process.cwd(), '.claude-flow', 'vector-stats.json');
-    try {
-        if (existsSync(statsPath)) {
-            const stats = JSON.parse(readFileSync(statsPath, 'utf8'));
-            const count = stats.vectorCount ?? 0;
-            const hasHnsw = stats.hasHnsw ?? false;
-            const dbSizeKB = stats.dbSizeKB ?? 0;
-            if (count === 0) {
-                return {
-                    name: 'Embeddings',
-                    status: 'warn',
-                    message: `Memory DB exists (${dbSizeKB} KB) but 0 vectors indexed — documents not embedded`,
-                    fix: 'npx moflo memory init --force && npx moflo embeddings init'
-                };
-            }
-            const hnswLabel = hasHnsw ? ', HNSW' : '';
-            return {
-                name: 'Embeddings',
-                status: 'pass',
-                message: `${count} vectors indexed (${dbSizeKB} KB${hnswLabel})`
-            };
-        }
-    }
-    catch {
-        // Stats file unreadable — fall through to DB check
-    }
-    // 2. Check if memory DB file exists at all
-    let foundDbPath = null;
-    for (const p of dbPaths) {
-        if (existsSync(p)) {
-            foundDbPath = p;
-            break;
-        }
-    }
-    if (!foundDbPath) {
-        return {
-            name: 'Embeddings',
-            status: 'warn',
-            message: 'No memory database — embeddings not initialized',
-            fix: 'npx moflo memory init --force'
-        };
-    }
-    // 3. DB exists but no stats cache — try querying the DB for entry count
-    try {
-        const { checkMemoryInitialization } = await import('../memory/memory-initializer.js');
-        const info = await checkMemoryInitialization(foundDbPath);
-        if (!info.initialized) {
-            return {
-                name: 'Embeddings',
-                status: 'warn',
-                message: 'Memory DB exists but not properly initialized',
-                fix: 'npx moflo memory init --force'
-            };
-        }
-        const hasVectors = info.features?.vectorEmbeddings ?? false;
-        if (!hasVectors) {
-            return {
-                name: 'Embeddings',
-                status: 'warn',
-                message: `Memory DB initialized (v${info.version}) but no vector_indexes table`,
-                fix: 'npx moflo memory init --force && npx moflo embeddings init'
-            };
-        }
-        return {
-            name: 'Embeddings',
-            status: 'pass',
-            message: `Memory DB initialized (v${info.version}, vectors enabled)`
-        };
-    }
-    catch {
-        // sql.js not available — fall back to file-size heuristic
-        try {
-            const stats = statSync(foundDbPath);
-            const sizeMB = (stats.size / 1024 / 1024).toFixed(2);
-            return {
-                name: 'Embeddings',
-                status: 'warn',
-                message: `Memory DB exists (${sizeMB} MB) — cannot verify vectors (sql.js not available)`,
-                fix: 'npm install sql.js && npx moflo embeddings init'
-            };
-        }
-        catch {
-            return { name: 'Embeddings', status: 'warn', message: 'Unable to check' };
-        }
-    }
-}
-/**
- * Auto-fix: execute fix commands for a failed/warned health check.
- * Returns true if the fix succeeded (re-check should pass).
- */
-async function autoFixCheck(check) {
-    if (!check.fix)
-        return false;
-    // Map checks to programmatic fixes (not just shell commands)
-    const fixActions = {
-        'Memory Database': async () => {
-            try {
-                const swarmDir = join(process.cwd(), '.swarm');
-                if (!existsSync(swarmDir))
-                    mkdirSync(swarmDir, { recursive: true });
-                const { initializeMemoryDatabase } = await import('../memory/memory-initializer.js');
-                const result = await initializeMemoryDatabase({ force: true, verbose: false });
-                return result.success;
-            }
-            catch {
-                // Fall back to CLI
-                return runFixCommand('npx moflo memory init --force');
-            }
-        },
-        'Embeddings': async () => {
-            try {
-                // Step 1: ensure memory DB exists
-                const swarmDir = join(process.cwd(), '.swarm');
-                if (!existsSync(swarmDir))
-                    mkdirSync(swarmDir, { recursive: true });
-                const dbPath = join(swarmDir, 'memory.db');
-                if (!existsSync(dbPath)) {
-                    const { initializeMemoryDatabase } = await import('../memory/memory-initializer.js');
-                    await initializeMemoryDatabase({ force: true, verbose: false });
-                }
-                // Step 2: attempt embeddings init via CLI
-                return runFixCommand('npx moflo embeddings init --force');
-            }
-            catch {
-                return runFixCommand('npx moflo memory init --force');
-            }
-        },
-        'Config File': async () => {
-            try {
-                const cfDir = join(process.cwd(), '.claude-flow');
-                if (!existsSync(cfDir))
-                    mkdirSync(cfDir, { recursive: true });
-                return runFixCommand('npx moflo config init');
-            }
-            catch {
-                return false;
-            }
-        },
-        'Daemon Status': async () => {
-            // Clean stale locks, then try to start daemon
-            const lockFile = join(process.cwd(), '.claude-flow', 'daemon.lock');
-            const pidFile = join(process.cwd(), '.claude-flow', 'daemon.pid');
-            try {
-                if (existsSync(lockFile)) {
-                    const { unlinkSync } = await import('fs');
-                    unlinkSync(lockFile);
-                }
-                if (existsSync(pidFile)) {
-                    const { unlinkSync } = await import('fs');
-                    unlinkSync(pidFile);
-                }
-            }
-            catch { /* best effort */ }
-            return runFixCommand('npx moflo daemon start');
-        },
-        'MCP Servers': async () => {
-            return runFixCommand('claude mcp add moflo -- npx -y moflo mcp start');
-        },
-        'Claude Code CLI': async () => {
-            return installClaudeCode();
-        },
-        'Zombie Processes': async () => {
-            const result = await findZombieProcesses(true);
-            return result.killed > 0 || result.found === 0;
-        },
-    };
-    const fixFn = fixActions[check.name];
-    if (fixFn) {
-        try {
-            output.writeln(output.dim(`  Fixing: ${check.name}...`));
-            const success = await fixFn();
-            if (success) {
-                output.writeln(output.success(`  Fixed: ${check.name}`));
-            }
-            else {
-                output.writeln(output.warning(`  Fix attempted but may need manual action: ${check.fix}`));
-            }
-            return success;
-        }
-        catch (e) {
-            output.writeln(output.warning(`  Fix failed: ${e instanceof Error ? e.message : String(e)}`));
-            return false;
-        }
-    }
-    // Generic: try running the fix command directly if it looks like a shell command
-    if (check.fix.startsWith('npx ') || check.fix.startsWith('npm ') || check.fix.startsWith('claude ')) {
-        return runFixCommand(check.fix);
-    }
-    return false;
-}
-/**
- * Run a shell command as a fix action. Returns true on exit code 0.
- */
-async function runFixCommand(cmd) {
-    try {
-        await execAsync(cmd, {
-            encoding: 'utf8',
-            timeout: 30000,
-            shell: process.platform === 'win32' ? 'cmd.exe' : '/bin/sh',
-            env: { ...process.env },
-            windowsHide: true,
-        });
-        return true;
-    }
-    catch {
-        return false;
-    }
-}
-// Check test directories configured in moflo.yaml
-async function checkTestDirs() {
-    const yamlPath = join(process.cwd(), 'moflo.yaml');
-    if (!existsSync(yamlPath)) {
-        return { name: 'Test Directories', status: 'warn', message: 'No moflo.yaml — test indexing unconfigured', fix: 'npx moflo init' };
-    }
-    try {
-        const content = readFileSync(yamlPath, 'utf-8');
-        // Check if tests section exists
-        const testsBlock = content.match(/tests:\s*\n\s+directories:\s*\n((?:\s+-\s+.+\n?)+)/);
-        if (!testsBlock) {
-            return { name: 'Test Directories', status: 'warn', message: 'No tests section in moflo.yaml', fix: 'npx moflo init --force' };
-        }
-        // Extract configured directories
-        const items = testsBlock[1].match(/-\s+(.+)/g);
-        if (!items || items.length === 0) {
-            return { name: 'Test Directories', status: 'warn', message: 'Empty test directories list' };
-        }
-        const dirs = items.map(item => item.replace(/^-\s+/, '').trim());
-        const existing = dirs.filter(d => existsSync(join(process.cwd(), d)));
-        const missing = dirs.filter(d => !existsSync(join(process.cwd(), d)));
-        // Check auto_index.tests flag
-        const autoIndexMatch = content.match(/auto_index:\s*\n(?:.*\n)*?\s+tests:\s*(true|false)/);
-        const autoIndexEnabled = !autoIndexMatch || autoIndexMatch[1] !== 'false';
-        const indexLabel = autoIndexEnabled ? 'auto-index: on' : 'auto-index: off';
-        if (missing.length > 0 && existing.length === 0) {
-            return {
-                name: 'Test Directories',
-                status: 'warn',
-                message: `No configured test dirs exist: ${missing.join(', ')} (${indexLabel})`,
-            };
-        }
-        if (missing.length > 0) {
-            return {
-                name: 'Test Directories',
-                status: 'warn',
-                message: `${existing.length} OK, ${missing.length} missing: ${missing.join(', ')} (${indexLabel})`,
-            };
-        }
-        return { name: 'Test Directories', status: 'pass', message: `${existing.length} directories: ${existing.join(', ')} (${indexLabel})` };
-    }
-    catch {
-        return { name: 'Test Directories', status: 'warn', message: 'Unable to parse moflo.yaml' };
-    }
-}
-// Check agentic-flow v3 integration (filesystem-based to avoid slow WASM/DB init)
-async function checkAgenticFlow() {
-    try {
-        // Walk common node_modules paths to find agentic-flow/package.json
-        const candidates = [
-            join(process.cwd(), 'node_modules', 'agentic-flow', 'package.json'),
-            join(process.cwd(), '..', 'node_modules', 'agentic-flow', 'package.json'),
-        ];
-        let pkgJsonPath = null;
-        for (const p of candidates) {
-            if (existsSync(p)) {
-                pkgJsonPath = p;
-                break;
-            }
-        }
-        if (!pkgJsonPath) {
-            return {
-                name: 'agentic-flow',
-                status: 'warn',
-                message: 'Not installed (optional — embeddings/routing will use fallbacks)',
-                fix: 'npm install agentic-flow@latest'
-            };
-        }
-        const pkg = JSON.parse(readFileSync(pkgJsonPath, 'utf-8'));
-        const version = pkg.version || 'unknown';
-        const exports = pkg.exports || {};
-        const features = [
-            exports['./reasoningbank'] ? 'ReasoningBank' : null,
-            exports['./router'] ? 'Router' : null,
-            exports['./transport/quic'] ? 'QUIC' : null,
-        ].filter(Boolean);
-        return {
-            name: 'agentic-flow',
-            status: 'pass',
-            message: `v${version} (${features.join(', ')})`
-        };
-    }
-    catch {
-        return { name: 'agentic-flow', status: 'warn', message: 'Check failed' };
-    }
-}
-// Check whether a given PID is still running.
-// Uses signal 0 which works cross-platform (Windows, Linux, macOS) without
-// needing PowerShell or /proc — Node handles the platform abstraction.
-function isProcessAlive(pid) {
-    try {
-        process.kill(pid, 0);
-        return true;
-    }
-    catch {
-        return false;
-    }
-}
-// Fast path: kill processes tracked in the shared ProcessManager registry.
-// This avoids the expensive OS-level process scan for known background tasks.
-function killTrackedProcesses() {
-    const registryFile = join(process.cwd(), '.claude-flow', 'background-pids.json');
-    const lockFile = join(process.cwd(), '.claude-flow', 'spawn.lock');
-    let killed = 0;
-    try {
-        if (existsSync(registryFile)) {
-            const entries = JSON.parse(readFileSync(registryFile, 'utf-8'));
-            for (const entry of entries) {
-                if (!isProcessAlive(entry.pid))
-                    continue;
-                try {
-                    if (process.platform === 'win32') {
-                        execSync(`taskkill /F /PID ${entry.pid}`, { timeout: 5000, windowsHide: true });
-                    }
-                    else {
-                        process.kill(entry.pid, 'SIGKILL');
-                    }
-                    killed++;
-                }
-                catch { /* already gone */ }
-            }
-            // Clear registry
-            writeFileSync(registryFile, '[]');
-        }
-    }
-    catch { /* non-fatal */ }
-    // Remove spawn lock
-    try {
-        if (existsSync(lockFile))
-            unlinkSync(lockFile);
-    }
-    catch { /* ok */ }
-    return killed;
-}
-// Find and optionally kill orphaned moflo/claude-flow node processes.
-// A process is only "orphaned" if its parent is no longer alive — meaning
-// nothing will clean it up. MCP servers spawned by a live Claude Code session
-// have a live parent (claude.exe) and must not be flagged.
-async function findZombieProcesses(kill = false) {
-    const legitimatePid = getDaemonLockHolder(process.cwd());
-    const currentPid = process.pid;
-    const parentPid = process.ppid;
-    const found = [];
-    let killed = 0;
-    // Collect candidates as { pid, ppid } so we can check parent liveness
-    const candidates = [];
-    try {
-        if (process.platform === 'win32') {
-            // Windows: include ParentProcessId so we can verify orphan status
-            const result = execSync('powershell -NoProfile -Command "Get-CimInstance Win32_Process -Filter \\"Name=\'node.exe\'\\" | Select-Object ProcessId,ParentProcessId,CommandLine | Format-Table -AutoSize -Wrap"', { encoding: 'utf-8', timeout: 10000, windowsHide: true });
-            const lines = result.split('\n');
-            for (const line of lines) {
-                if (/moflo|claude-flow|flo\s+(hooks|gate|mcp|daemon)/i.test(line)) {
-                    // Format-Table columns: ProcessId  ParentProcessId  CommandLine...
-                    const match = line.match(/^\s*(\d+)\s+(\d+)/);
-                    if (match) {
-                        candidates.push({ pid: parseInt(match[1], 10), ppid: parseInt(match[2], 10) });
-                    }
-                }
-            }
-        }
-        else {
-            // Unix/macOS: use ps with explicit PID+PPID columns for reliable parsing
-            const result = execSync('ps -eo pid,ppid,command | grep -E "node.*(moflo|claude-flow)" | grep -v grep', { encoding: 'utf-8', timeout: 5000 });
-            const lines = result.trim().split('\n');
-            for (const line of lines) {
-                const match = line.trim().match(/^(\d+)\s+(\d+)/);
-                if (match) {
-                    candidates.push({ pid: parseInt(match[1], 10), ppid: parseInt(match[2], 10) });
-                }
-            }
-        }
-    }
-    catch {
-        // No matches found (grep exits non-zero) or command failed
-    }
-    // Filter: skip known-good PIDs and processes whose parent is still alive.
-    // A live parent (e.g. claude.exe for MCP servers) means the process is managed, not orphaned.
-    for (const { pid, ppid } of candidates) {
-        if (pid === currentPid || pid === parentPid || pid === legitimatePid)
-            continue;
-        if (isProcessAlive(ppid))
-            continue;
-        // Defense-in-depth: detached daemons have dead parents by design.
-        // Even if the lock file is missing/corrupted, don't kill a running daemon.
-        if (isDaemonProcess(pid))
-            continue;
-        found.push(pid);
-    }
-    if (kill && found.length > 0) {
-        for (const pid of found) {
-            try {
-                if (process.platform === 'win32') {
-                    execSync(`taskkill /F /PID ${pid}`, { timeout: 5000, windowsHide: true });
-                }
-                else {
-                    process.kill(pid, 'SIGKILL');
-                }
-                killed++;
-            }
-            catch {
-                // Process may have already exited
-            }
-        }
-        // Clean up stale daemon lock if we killed the holder
-        if (legitimatePid && found.includes(legitimatePid)) {
-            releaseDaemonLock(process.cwd(), legitimatePid, true);
-        }
-    }
-    return { found: found.length, killed, pids: found };
-}
-// Format health check result
-function formatCheck(check) {
-    const icon = check.status === 'pass' ? output.success('✓') :
-        check.status === 'warn' ? output.warning('⚠') :
-            output.error('✗');
-    return `${icon} ${check.name}: ${check.message}`;
-}
-// Main doctor command
-export const doctorCommand = {
-    name: 'doctor',
-    description: 'System diagnostics and health checks',
-    options: [
-        {
-            name: 'fix',
-            short: 'f',
-            description: 'Automatically fix issues where possible',
-            type: 'boolean',
-            default: false
-        },
-        {
-            name: 'install',
-            short: 'i',
-            description: 'Auto-install missing dependencies (Claude Code CLI)',
-            type: 'boolean',
-            default: false
-        },
-        {
-            name: 'component',
-            short: 'c',
-            description: 'Check specific component (version, node, npm, config, daemon, memory, embeddings, git, mcp, claude, disk, typescript)',
-            type: 'string'
-        },
-        {
-            name: 'verbose',
-            short: 'v',
-            description: 'Verbose output',
-            type: 'boolean',
-            default: false
-        },
-        {
-            name: 'kill-zombies',
-            short: 'k',
-            description: 'Find and kill orphaned moflo/claude-flow node processes',
-            type: 'boolean',
-            default: false
-        }
-    ],
-    examples: [
-        { command: 'claude-flow doctor', description: 'Run full health check' },
-        { command: 'claude-flow doctor --fix', description: 'Show fixes for issues' },
-        { command: 'claude-flow doctor --install', description: 'Auto-install missing dependencies' },
-        { command: 'claude-flow doctor --kill-zombies', description: 'Find and kill zombie processes' },
-        { command: 'claude-flow doctor -c version', description: 'Check for stale npx cache' },
-        { command: 'claude-flow doctor -c claude', description: 'Check Claude Code CLI only' }
-    ],
-    action: async (ctx) => {
-        const showFix = ctx.flags.fix;
-        const autoInstall = ctx.flags.install;
-        const component = ctx.flags.component;
-        const verbose = ctx.flags.verbose;
-        const killZombies = ctx.flags['kill-zombies'];
-        output.writeln();
-        output.writeln(output.bold('MoFlo Doctor'));
-        output.writeln(output.dim('System diagnostics and health check'));
-        output.writeln(output.dim('─'.repeat(50)));
-        output.writeln();
-        // Handle --kill-zombies early
-        if (killZombies) {
-            output.writeln(output.bold('Zombie Process Scan'));
-            output.writeln();
-            // Fast path: kill tracked processes from the shared registry first
-            const registryKilled = killTrackedProcesses();
-            if (registryKilled > 0) {
-                output.writeln(output.success(`  Killed ${registryKilled} tracked background process(es) from registry`));
-            }
-            // Slow path: OS-level scan for any remaining orphans
-            const scan = await findZombieProcesses(false);
-            if (scan.found === 0) {
-                if (registryKilled === 0) {
-                    output.writeln(output.success('  No orphaned moflo processes found'));
-                }
-            }
-            else {
-                output.writeln(output.warning(`  Found ${scan.found} additional orphaned process(es): PIDs ${scan.pids.join(', ')}`));
-                // Kill them
-                const result = await findZombieProcesses(true);
-                if (result.killed > 0) {
-                    output.writeln(output.success(`  Killed ${result.killed} zombie process(es)`));
-                }
-                if (result.killed < result.found) {
-                    output.writeln(output.warning(`  ${result.found - result.killed} process(es) could not be killed`));
-                }
-            }
-            output.writeln();
-            output.writeln(output.dim('─'.repeat(50)));
-            output.writeln();
-        }
-        const checkZombieProcesses = async () => {
-            try {
-                const scan = await findZombieProcesses(false);
-                if (scan.found === 0) {
-                    return { name: 'Zombie Processes', status: 'pass', message: 'No orphaned processes' };
-                }
-                return {
-                    name: 'Zombie Processes',
-                    status: 'warn',
-                    message: `${scan.found} orphaned process(es) (PIDs: ${scan.pids.join(', ')})`,
-                    fix: 'moflo doctor --kill-zombies'
-                };
-            }
-            catch {
-                return { name: 'Zombie Processes', status: 'pass', message: 'Check skipped' };
-            }
-        };
-        const allChecks = [
-            checkVersionFreshness,
-            checkNodeVersion,
-            checkNpmVersion,
-            checkClaudeCode,
-            checkGit,
-            checkGitRepo,
-            checkConfigFile,
-            checkDaemonStatus,
-            checkMemoryDatabase,
-            checkEmbeddings,
-            checkTestDirs,
-            checkMcpServers,
-            checkDiskSpace,
-            checkBuildTools,
-            checkAgenticFlow,
-            checkZombieProcesses
-        ];
-        const componentMap = {
-            'version': checkVersionFreshness,
-            'freshness': checkVersionFreshness,
-            'node': checkNodeVersion,
-            'npm': checkNpmVersion,
-            'claude': checkClaudeCode,
-            'config': checkConfigFile,
-            'daemon': checkDaemonStatus,
-            'memory': checkMemoryDatabase,
-            'embeddings': checkEmbeddings,
-            'git': checkGit,
-            'mcp': checkMcpServers,
-            'disk': checkDiskSpace,
-            'typescript': checkBuildTools,
-            'tests': checkTestDirs,
-            'agentic-flow': checkAgenticFlow
-        };
-        let checksToRun = allChecks;
-        if (component && componentMap[component]) {
-            checksToRun = [componentMap[component]];
-        }
-        const results = [];
-        const fixes = [];
-        // OPTIMIZATION: Run all checks in parallel for 3-5x faster execution
-        const spinner = output.createSpinner({ text: 'Running health checks in parallel...', spinner: 'dots' });
-        spinner.start();
-        try {
-            // Execute all checks concurrently
-            const checkResults = await Promise.allSettled(checksToRun.map(check => check()));
-            spinner.stop();
-            // Process results in order
-            for (const settledResult of checkResults) {
-                if (settledResult.status === 'fulfilled') {
-                    const result = settledResult.value;
-                    results.push(result);
-                    output.writeln(formatCheck(result));
-                    if (result.fix && (result.status === 'fail' || result.status === 'warn')) {
-                        fixes.push(`${result.name}: ${result.fix}`);
-                    }
-                }
-                else {
-                    const errorResult = {
-                        name: 'Check',
-                        status: 'fail',
-                        message: settledResult.reason?.message || 'Unknown error'
-                    };
-                    results.push(errorResult);
-                    output.writeln(formatCheck(errorResult));
-                }
-            }
-        }
-        catch (error) {
-            spinner.stop();
-            output.writeln(output.error('Failed to run health checks'));
-        }
-        // Auto-install missing dependencies if requested
-        if (autoInstall) {
-            const claudeCodeResult = results.find(r => r.name === 'Claude Code CLI');
-            if (claudeCodeResult && claudeCodeResult.status !== 'pass') {
-                const installed = await installClaudeCode();
-                if (installed) {
-                    // Re-check Claude Code after installation
-                    const newCheck = await checkClaudeCode();
-                    const idx = results.findIndex(r => r.name === 'Claude Code CLI');
-                    if (idx !== -1) {
-                        results[idx] = newCheck;
-                        // Update fixes list
-                        const fixIdx = fixes.findIndex(f => f.startsWith('Claude Code CLI:'));
-                        if (fixIdx !== -1 && newCheck.status === 'pass') {
-                            fixes.splice(fixIdx, 1);
-                        }
-                    }
-                    output.writeln(formatCheck(newCheck));
-                }
-            }
-        }
-        // Summary
-        const passed = results.filter(r => r.status === 'pass').length;
-        const warnings = results.filter(r => r.status === 'warn').length;
-        const failed = results.filter(r => r.status === 'fail').length;
-        output.writeln();
-        output.writeln(output.dim('─'.repeat(50)));
-        output.writeln();
-        const summaryParts = [
-            output.success(`${passed} passed`),
-            warnings > 0 ? output.warning(`${warnings} warnings`) : null,
-            failed > 0 ? output.error(`${failed} failed`) : null
-        ].filter(Boolean);
-        output.writeln(`Summary: ${summaryParts.join(', ')}`);
-        // Auto-fix or show fixes
-        if (showFix && fixes.length > 0) {
-            output.writeln();
-            output.writeln(output.bold('Auto-fixing issues...'));
-            output.writeln();
-            const fixableResults = results.filter(r => r.fix && (r.status === 'fail' || r.status === 'warn'));
-            let fixed = 0;
-            const unfixed = [];
-            for (const check of fixableResults) {
-                const success = await autoFixCheck(check);
-                if (success) {
-                    fixed++;
-                }
-                else {
-                    unfixed.push(`${check.name}: ${check.fix}`);
-                }
-            }
-            if (fixed > 0) {
-                output.writeln();
-                output.writeln(output.success(`Auto-fixed ${fixed} issue${fixed > 1 ? 's' : ''}`));
-            }
-            if (unfixed.length > 0) {
-                output.writeln();
-                output.writeln(output.bold('Manual fixes needed:'));
-                for (const fix of unfixed) {
-                    output.writeln(output.dim(`  ${fix}`));
-                }
-            }
-            // Re-run checks to show updated status
-            if (fixed > 0) {
-                output.writeln();
-                output.writeln(output.dim('Re-checking...'));
-                output.writeln();
-                const reResults = await Promise.allSettled(checksToRun.map(check => check()));
-                let rePassed = 0, reWarnings = 0, reFailed = 0;
-                for (const sr of reResults) {
-                    if (sr.status === 'fulfilled') {
-                        output.writeln(formatCheck(sr.value));
-                        if (sr.value.status === 'pass')
-                            rePassed++;
-                        else if (sr.value.status === 'warn')
-                            reWarnings++;
-                        else
-                            reFailed++;
-                    }
-                }
-                output.writeln();
-                output.writeln(output.dim('─'.repeat(50)));
-                const reSummary = [
-                    output.success(`${rePassed} passed`),
-                    reWarnings > 0 ? output.warning(`${reWarnings} warnings`) : null,
-                    reFailed > 0 ? output.error(`${reFailed} failed`) : null
-                ].filter(Boolean);
-                output.writeln(`After fix: ${reSummary.join(', ')}`);
-            }
-        }
-        else if (fixes.length > 0 && !showFix) {
-            output.writeln();
-            output.writeln(output.dim(`Run with --fix to auto-fix ${fixes.length} issue${fixes.length > 1 ? 's' : ''}`));
-        }
-        // Overall result
-        if (failed > 0) {
-            output.writeln();
-            output.writeln(output.error('Some checks failed. Please address the issues above.'));
-            return { success: false, exitCode: 1, data: { passed, warnings, failed, results } };
-        }
-        else if (warnings > 0) {
-            output.writeln();
-            output.writeln(output.warning('All checks passed with some warnings.'));
-            return { success: true, data: { passed, warnings, failed, results } };
-        }
-        else {
-            output.writeln();
-            output.writeln(output.success('All checks passed! System is healthy.'));
-            return { success: true, data: { passed, warnings, failed, results } };
-        }
-    }
-};
-export default doctorCommand;
+/**
+ * V3 CLI Doctor Command
+ * System diagnostics, dependency checks, config validation
+ *
+ * Created with motailz.com
+ */
+import { output } from '../output.js';
+import { existsSync, readFileSync, writeFileSync, unlinkSync, statSync, mkdirSync } from 'fs';
+import { join, dirname } from 'path';
+import { fileURLToPath } from 'url';
+import { execSync, exec } from 'child_process';
+import { promisify } from 'util';
+import { getDaemonLockHolder, releaseDaemonLock, isDaemonProcess } from '../services/daemon-lock.js';
+// Promisified exec with proper shell and env inheritance for cross-platform support
+const execAsync = promisify(exec);
+/**
+ * Execute command asynchronously with proper environment inheritance
+ * Critical for Windows where PATH may not be inherited properly
+ */
+async function runCommand(command, timeoutMs = 5000) {
+    const { stdout } = await execAsync(command, {
+        encoding: 'utf8',
+        timeout: timeoutMs,
+        shell: process.platform === 'win32' ? 'cmd.exe' : '/bin/sh', // Use proper shell per platform
+        env: { ...process.env }, // Explicitly inherit full environment
+        windowsHide: true, // Hide window on Windows
+    });
+    return stdout.trim();
+}
+// Check Node.js version
+async function checkNodeVersion() {
+    const requiredMajor = 20;
+    const version = process.version;
+    const major = parseInt(version.slice(1).split('.')[0], 10);
+    if (major >= requiredMajor) {
+        return { name: 'Node.js Version', status: 'pass', message: `${version} (>= ${requiredMajor} required)` };
+    }
+    else if (major >= 18) {
+        return { name: 'Node.js Version', status: 'warn', message: `${version} (>= ${requiredMajor} recommended)`, fix: 'nvm install 20 && nvm use 20' };
+    }
+    else {
+        return { name: 'Node.js Version', status: 'fail', message: `${version} (>= ${requiredMajor} required)`, fix: 'nvm install 20 && nvm use 20' };
+    }
+}
+// Check npm version (async with proper env inheritance)
+async function checkNpmVersion() {
+    try {
+        const version = await runCommand('npm --version');
+        const major = parseInt(version.split('.')[0], 10);
+        if (major >= 9) {
+            return { name: 'npm Version', status: 'pass', message: `v${version}` };
+        }
+        else {
+            return { name: 'npm Version', status: 'warn', message: `v${version} (>= 9 recommended)`, fix: 'npm install -g npm@latest' };
+        }
+    }
+    catch {
+        return { name: 'npm Version', status: 'fail', message: 'npm not found', fix: 'Install Node.js from https://nodejs.org' };
+    }
+}
+// Check config file
+async function checkConfigFile() {
+    // JSON configs (parse-validated)
+    const jsonPaths = [
+        '.claude-flow/config.json',
+        'claude-flow.config.json',
+        '.claude-flow.json'
+    ];
+    for (const configPath of jsonPaths) {
+        if (existsSync(configPath)) {
+            try {
+                const content = readFileSync(configPath, 'utf8');
+                JSON.parse(content);
+                return { name: 'Config File', status: 'pass', message: `Found: ${configPath}` };
+            }
+            catch (e) {
+                return { name: 'Config File', status: 'fail', message: `Invalid JSON: ${configPath}`, fix: 'Fix JSON syntax in config file' };
+            }
+        }
+    }
+    // YAML configs (existence-checked only — no heavy yaml parser dependency)
+    const yamlPaths = [
+        '.claude-flow/config.yaml',
+        '.claude-flow/config.yml',
+        'claude-flow.config.yaml'
+    ];
+    for (const configPath of yamlPaths) {
+        if (existsSync(configPath)) {
+            return { name: 'Config File', status: 'pass', message: `Found: ${configPath}` };
+        }
+    }
+    return { name: 'Config File', status: 'warn', message: 'No config file (using defaults)', fix: 'claude-flow config init' };
+}
+// Check daemon status — delegates to daemon-lock module for proper
+// PID + command-line verification (avoids Windows PID-recycling false positives).
+async function checkDaemonStatus() {
+    try {
+        // Retry up to 5 times with 1s delay — the daemon starts in the background
+        // during session-start and may not have acquired its lock file yet.
+        const MAX_RETRIES = 5;
+        const RETRY_DELAY_MS = 1000;
+        let holderPid = null;
+        for (let attempt = 0; attempt < MAX_RETRIES; attempt++) {
+            holderPid = getDaemonLockHolder(process.cwd());
+            if (holderPid)
+                break;
+            if (attempt < MAX_RETRIES - 1) {
+                await new Promise(resolve => setTimeout(resolve, RETRY_DELAY_MS));
+            }
+        }
+        if (holderPid) {
+            return { name: 'Daemon Status', status: 'pass', message: `Running (PID: ${holderPid})` };
+        }
+        // getDaemonLockHolder auto-cleans stale locks, but check for legacy PID file
+        const lockFile = '.claude-flow/daemon.lock';
+        if (existsSync(lockFile)) {
+            // Lock exists but holder is null — getDaemonLockHolder already cleaned it,
+            // but if it persists it means cleanup failed (permissions, etc.)
+            return { name: 'Daemon Status', status: 'warn', message: 'Stale lock file', fix: 'rm .claude-flow/daemon.lock && claude-flow daemon start' };
+        }
+        // Also check legacy PID file
+        const pidFile = '.claude-flow/daemon.pid';
+        if (existsSync(pidFile)) {
+            return { name: 'Daemon Status', status: 'warn', message: 'Legacy PID file found', fix: 'rm .claude-flow/daemon.pid && claude-flow daemon start' };
+        }
+        return { name: 'Daemon Status', status: 'warn', message: 'Not running', fix: 'claude-flow daemon start' };
+    }
+    catch {
+        return { name: 'Daemon Status', status: 'warn', message: 'Unable to check', fix: 'claude-flow daemon status' };
+    }
+}
+// Check memory database
+async function checkMemoryDatabase() {
+    const dbPaths = [
+        '.claude-flow/memory.db',
+        '.swarm/memory.db',
+        'data/memory.db'
+    ];
+    for (const dbPath of dbPaths) {
+        if (existsSync(dbPath)) {
+            try {
+                const stats = statSync(dbPath);
+                const sizeMB = (stats.size / 1024 / 1024).toFixed(2);
+                return { name: 'Memory Database', status: 'pass', message: `${dbPath} (${sizeMB} MB)` };
+            }
+            catch {
+                return { name: 'Memory Database', status: 'warn', message: `${dbPath} (unable to stat)` };
+            }
+        }
+    }
+    return { name: 'Memory Database', status: 'warn', message: 'Not initialized', fix: 'claude-flow memory configure --backend hybrid' };
+}
+// Check git (async with proper env inheritance)
+async function checkGit() {
+    try {
+        const version = await runCommand('git --version');
+        return { name: 'Git', status: 'pass', message: version.replace('git version ', 'v') };
+    }
+    catch {
+        return { name: 'Git', status: 'warn', message: 'Not installed', fix: 'Install git from https://git-scm.com' };
+    }
+}
+// Check if in git repo (async with proper env inheritance)
+async function checkGitRepo() {
+    try {
+        await runCommand('git rev-parse --git-dir');
+        return { name: 'Git Repository', status: 'pass', message: 'In a git repository' };
+    }
+    catch {
+        return { name: 'Git Repository', status: 'warn', message: 'Not a git repository', fix: 'git init' };
+    }
+}
+// Check MCP servers
+async function checkMcpServers() {
+    const mcpConfigPaths = [
+        join(process.env.HOME || '', '.claude/claude_desktop_config.json'),
+        join(process.env.HOME || '', '.config/claude/mcp.json'),
+        '.mcp.json'
+    ];
+    for (const configPath of mcpConfigPaths) {
+        if (existsSync(configPath)) {
+            try {
+                const content = JSON.parse(readFileSync(configPath, 'utf8'));
+                const servers = content.mcpServers || content.servers || {};
+                const count = Object.keys(servers).length;
+                const hasClaudeFlow = 'moflo' in servers || 'claude-flow' in servers || 'claude-flow_alpha' in servers || 'ruflo' in servers || 'ruflo_alpha' in servers;
+                if (hasClaudeFlow) {
+                    return { name: 'MCP Servers', status: 'pass', message: `${count} servers (flo configured)` };
+                }
+                else {
+                    return { name: 'MCP Servers', status: 'warn', message: `${count} servers (flo not found)`, fix: 'claude mcp add ruflo -- npx -y ruflo@latest mcp start' };
+                }
+            }
+            catch {
+                // continue to next path
+            }
+        }
+    }
+    return { name: 'MCP Servers', status: 'warn', message: 'No MCP config found', fix: 'claude mcp add moflo npx moflo mcp start' };
+}
+// Check disk space (async with proper env inheritance)
+async function checkDiskSpace() {
+    try {
+        if (process.platform === 'win32') {
+            return { name: 'Disk Space', status: 'pass', message: 'Check skipped on Windows' };
+        }
+        // Use df -Ph for POSIX mode (guarantees single-line output even with long device names)
+        const output_str = await runCommand('df -Ph . | tail -1');
+        const parts = output_str.split(/\s+/);
+        // POSIX format: Filesystem Size Used Avail Capacity Mounted
+        const available = parts[3];
+        const usePercent = parseInt(parts[4]?.replace('%', '') || '0', 10);
+        if (isNaN(usePercent)) {
+            return { name: 'Disk Space', status: 'warn', message: `${available || 'unknown'} available (unable to parse usage)` };
+        }
+        if (usePercent > 90) {
+            return { name: 'Disk Space', status: 'fail', message: `${available} available (${usePercent}% used)`, fix: 'Free up disk space' };
+        }
+        else if (usePercent > 80) {
+            return { name: 'Disk Space', status: 'warn', message: `${available} available (${usePercent}% used)` };
+        }
+        return { name: 'Disk Space', status: 'pass', message: `${available} available` };
+    }
+    catch {
+        return { name: 'Disk Space', status: 'warn', message: 'Unable to check' };
+    }
+}
+// Check TypeScript/build (async with proper env inheritance)
+async function checkBuildTools() {
+    try {
+        const tscVersion = await runCommand('npx tsc --version', 10000); // tsc can be slow
+        if (!tscVersion || tscVersion.includes('not found')) {
+            return { name: 'TypeScript', status: 'warn', message: 'Not installed locally', fix: 'npm install -D typescript' };
+        }
+        return { name: 'TypeScript', status: 'pass', message: tscVersion.replace('Version ', 'v') };
+    }
+    catch {
+        return { name: 'TypeScript', status: 'warn', message: 'Not installed locally', fix: 'npm install -D typescript' };
+    }
+}
+// Check for stale npx cache (version freshness)
+async function checkVersionFreshness() {
+    try {
+        // Get current CLI version from package.json
+        // Use import.meta.url to reliably locate our own package.json,
+        // regardless of how deep the compiled file sits (e.g. dist/src/commands/).
+        let currentVersion = '0.0.0';
+        try {
+            const thisFile = fileURLToPath(import.meta.url);
+            let dir = dirname(thisFile);
+            // Walk up from the current file's directory until we find the
+            // package.json that belongs to @claude-flow/cli (or claude-flow/cli).
+            // Walk until dirname(dir) === dir (filesystem root on any platform).
+            for (;;) {
+                const candidate = join(dir, 'package.json');
+                try {
+                    if (existsSync(candidate)) {
+                        const pkg = JSON.parse(readFileSync(candidate, 'utf8'));
+                        if (pkg.version &&
+                            typeof pkg.name === 'string' &&
+                            (pkg.name === '@claude-flow/cli' || pkg.name === 'claude-flow' || pkg.name === 'ruflo' || pkg.name === 'moflo' || pkg.name === '@moflo/cli')) {
+                            currentVersion = pkg.version;
+                            break;
+                        }
+                    }
+                }
+                catch {
+                    // Unreadable/invalid JSON -- skip and keep walking up
+                }
+                const parent = dirname(dir);
+                if (parent === dir)
+                    break; // reached root
+                dir = parent;
+            }
+        }
+        catch {
+            // Fall back to a default
+            currentVersion = '0.0.0';
+        }
+        // Check if running via npx (look for _npx in process path or argv)
+        const isNpx = process.argv[1]?.includes('_npx') ||
+            process.env.npm_execpath?.includes('npx') ||
+            process.cwd().includes('_npx');
+        // Query npm for latest version (using alpha tag since that's what we publish to)
+        let latestVersion = currentVersion;
+        try {
+            const npmInfo = await runCommand('npm view moflo version', 5000);
+            latestVersion = npmInfo.trim();
+        }
+        catch {
+            // Can't reach npm registry - skip check
+            return {
+                name: 'Version Freshness',
+                status: 'warn',
+                message: `v${currentVersion} (cannot check registry)`
+            };
+        }
+        // Parse version numbers for comparison (handle prerelease like 3.0.0-alpha.84)
+        const parseVersion = (v) => {
+            const match = v.match(/^(\d+)\.(\d+)\.(\d+)(?:-[a-zA-Z]+\.(\d+))?/);
+            if (!match)
+                return { major: 0, minor: 0, patch: 0, prerelease: 0 };
+            return {
+                major: parseInt(match[1], 10) || 0,
+                minor: parseInt(match[2], 10) || 0,
+                patch: parseInt(match[3], 10) || 0,
+                prerelease: parseInt(match[4], 10) || 0
+            };
+        };
+        const current = parseVersion(currentVersion);
+        const latest = parseVersion(latestVersion);
+        // Compare versions (including prerelease number)
+        const isOutdated = (latest.major > current.major ||
+            (latest.major === current.major && latest.minor > current.minor) ||
+            (latest.major === current.major && latest.minor === current.minor && latest.patch > current.patch) ||
+            (latest.major === current.major && latest.minor === current.minor && latest.patch === current.patch && latest.prerelease > current.prerelease));
+        if (isOutdated) {
+            const fix = isNpx
+                ? 'rm -rf ~/.npm/_npx/* && npx -y moflo'
+                : 'npm update moflo';
+            return {
+                name: 'Version Freshness',
+                status: 'warn',
+                message: `v${currentVersion} (latest: v${latestVersion})${isNpx ? ' [npx cache stale]' : ''}`,
+                fix
+            };
+        }
+        return {
+            name: 'Version Freshness',
+            status: 'pass',
+            message: `v${currentVersion} (up to date)`
+        };
+    }
+    catch (error) {
+        return {
+            name: 'Version Freshness',
+            status: 'warn',
+            message: 'Unable to check version freshness'
+        };
+    }
+}
+// Check Claude Code CLI (async with proper env inheritance)
+async function checkClaudeCode() {
+    try {
+        const version = await runCommand('claude --version');
+        // Parse version from output like "claude 1.0.0" or "Claude Code v1.0.0"
+        const versionMatch = version.match(/v?(\d+\.\d+\.\d+)/);
+        const versionStr = versionMatch ? `v${versionMatch[1]}` : version;
+        return { name: 'Claude Code CLI', status: 'pass', message: versionStr };
+    }
+    catch {
+        return {
+            name: 'Claude Code CLI',
+            status: 'warn',
+            message: 'Not installed',
+            fix: 'npm install -g @anthropic-ai/claude-code'
+        };
+    }
+}
+// Install Claude Code CLI
+async function installClaudeCode() {
+    try {
+        output.writeln();
+        output.writeln(output.bold('Installing Claude Code CLI...'));
+        execSync('npm install -g @anthropic-ai/claude-code', {
+            encoding: 'utf8',
+            stdio: 'inherit',
+            windowsHide: true
+        });
+        output.writeln(output.success('Claude Code CLI installed successfully!'));
+        return true;
+    }
+    catch (error) {
+        output.writeln(output.error('Failed to install Claude Code CLI'));
+        if (error instanceof Error) {
+            output.writeln(output.dim(error.message));
+        }
+        return false;
+    }
+}
+// Check embeddings / vector index health
+async function checkEmbeddings() {
+    const dbPaths = [
+        join(process.cwd(), '.swarm', 'memory.db'),
+        join(process.cwd(), '.claude-flow', 'memory.db'),
+        join(process.cwd(), 'data', 'memory.db'),
+    ];
+    // 1. Fast path: read cached vector-stats.json if available
+    const statsPath = join(process.cwd(), '.claude-flow', 'vector-stats.json');
+    try {
+        if (existsSync(statsPath)) {
+            const stats = JSON.parse(readFileSync(statsPath, 'utf8'));
+            const count = stats.vectorCount ?? 0;
+            const hasHnsw = stats.hasHnsw ?? false;
+            const dbSizeKB = stats.dbSizeKB ?? 0;
+            if (count === 0) {
+                return {
+                    name: 'Embeddings',
+                    status: 'warn',
+                    message: `Memory DB exists (${dbSizeKB} KB) but 0 vectors indexed — documents not embedded`,
+                    fix: 'npx moflo memory init --force && npx moflo embeddings init'
+                };
+            }
+            const hnswLabel = hasHnsw ? ', HNSW' : '';
+            return {
+                name: 'Embeddings',
+                status: 'pass',
+                message: `${count} vectors indexed (${dbSizeKB} KB${hnswLabel})`
+            };
+        }
+    }
+    catch {
+        // Stats file unreadable — fall through to DB check
+    }
+    // 2. Check if memory DB file exists at all
+    let foundDbPath = null;
+    for (const p of dbPaths) {
+        if (existsSync(p)) {
+            foundDbPath = p;
+            break;
+        }
+    }
+    if (!foundDbPath) {
+        return {
+            name: 'Embeddings',
+            status: 'warn',
+            message: 'No memory database — embeddings not initialized',
+            fix: 'npx moflo memory init --force'
+        };
+    }
+    // 3. DB exists but no stats cache — try querying the DB for entry count
+    try {
+        const { checkMemoryInitialization } = await import('../memory/memory-initializer.js');
+        const info = await checkMemoryInitialization(foundDbPath);
+        if (!info.initialized) {
+            return {
+                name: 'Embeddings',
+                status: 'warn',
+                message: 'Memory DB exists but not properly initialized',
+                fix: 'npx moflo memory init --force'
+            };
+        }
+        const hasVectors = info.features?.vectorEmbeddings ?? false;
+        if (!hasVectors) {
+            return {
+                name: 'Embeddings',
+                status: 'warn',
+                message: `Memory DB initialized (v${info.version}) but no vector_indexes table`,
+                fix: 'npx moflo memory init --force && npx moflo embeddings init'
+            };
+        }
+        return {
+            name: 'Embeddings',
+            status: 'pass',
+            message: `Memory DB initialized (v${info.version}, vectors enabled)`
+        };
+    }
+    catch {
+        // sql.js not available — fall back to file-size heuristic
+        try {
+            const stats = statSync(foundDbPath);
+            const sizeMB = (stats.size / 1024 / 1024).toFixed(2);
+            return {
+                name: 'Embeddings',
+                status: 'warn',
+                message: `Memory DB exists (${sizeMB} MB) — cannot verify vectors (sql.js not available)`,
+                fix: 'npm install sql.js && npx moflo embeddings init'
+            };
+        }
+        catch {
+            return { name: 'Embeddings', status: 'warn', message: 'Unable to check' };
+        }
+    }
+}
+/**
+ * Auto-fix: execute fix commands for a failed/warned health check.
+ * Returns true if the fix succeeded (re-check should pass).
+ */
+async function autoFixCheck(check) {
+    if (!check.fix)
+        return false;
+    // Map checks to programmatic fixes (not just shell commands)
+    const fixActions = {
+        'Memory Database': async () => {
+            try {
+                const swarmDir = join(process.cwd(), '.swarm');
+                if (!existsSync(swarmDir))
+                    mkdirSync(swarmDir, { recursive: true });
+                const { initializeMemoryDatabase } = await import('../memory/memory-initializer.js');
+                const result = await initializeMemoryDatabase({ force: true, verbose: false });
+                return result.success;
+            }
+            catch {
+                // Fall back to CLI
+                return runFixCommand('npx moflo memory init --force');
+            }
+        },
+        'Embeddings': async () => {
+            try {
+                // Step 1: ensure memory DB exists
+                const swarmDir = join(process.cwd(), '.swarm');
+                if (!existsSync(swarmDir))
+                    mkdirSync(swarmDir, { recursive: true });
+                const dbPath = join(swarmDir, 'memory.db');
+                if (!existsSync(dbPath)) {
+                    const { initializeMemoryDatabase } = await import('../memory/memory-initializer.js');
+                    await initializeMemoryDatabase({ force: true, verbose: false });
+                }
+                // Step 2: attempt embeddings init via CLI
+                return runFixCommand('npx moflo embeddings init --force');
+            }
+            catch {
+                return runFixCommand('npx moflo memory init --force');
+            }
+        },
+        'Config File': async () => {
+            try {
+                const cfDir = join(process.cwd(), '.claude-flow');
+                if (!existsSync(cfDir))
+                    mkdirSync(cfDir, { recursive: true });
+                return runFixCommand('npx moflo config init');
+            }
+            catch {
+                return false;
+            }
+        },
+        'Daemon Status': async () => {
+            // Clean stale locks, then try to start daemon
+            const lockFile = join(process.cwd(), '.claude-flow', 'daemon.lock');
+            const pidFile = join(process.cwd(), '.claude-flow', 'daemon.pid');
+            try {
+                if (existsSync(lockFile)) {
+                    const { unlinkSync } = await import('fs');
+                    unlinkSync(lockFile);
+                }
+                if (existsSync(pidFile)) {
+                    const { unlinkSync } = await import('fs');
+                    unlinkSync(pidFile);
+                }
+            }
+            catch { /* best effort */ }
+            return runFixCommand('npx moflo daemon start');
+        },
+        'MCP Servers': async () => {
+            return runFixCommand('claude mcp add moflo -- npx -y moflo mcp start');
+        },
+        'Claude Code CLI': async () => {
+            return installClaudeCode();
+        },
+        'Zombie Processes': async () => {
+            const result = await findZombieProcesses(true);
+            return result.killed > 0 || result.found === 0;
+        },
+    };
+    const fixFn = fixActions[check.name];
+    if (fixFn) {
+        try {
+            output.writeln(output.dim(`  Fixing: ${check.name}...`));
+            const success = await fixFn();
+            if (success) {
+                output.writeln(output.success(`  Fixed: ${check.name}`));
+            }
+            else {
+                output.writeln(output.warning(`  Fix attempted but may need manual action: ${check.fix}`));
+            }
+            return success;
+        }
+        catch (e) {
+            output.writeln(output.warning(`  Fix failed: ${e instanceof Error ? e.message : String(e)}`));
+            return false;
+        }
+    }
+    // Generic: try running the fix command directly if it looks like a shell command
+    if (check.fix.startsWith('npx ') || check.fix.startsWith('npm ') || check.fix.startsWith('claude ')) {
+        return runFixCommand(check.fix);
+    }
+    return false;
+}
+/**
+ * Run a shell command as a fix action. Returns true on exit code 0.
+ */
+async function runFixCommand(cmd) {
+    try {
+        await execAsync(cmd, {
+            encoding: 'utf8',
+            timeout: 30000,
+            shell: process.platform === 'win32' ? 'cmd.exe' : '/bin/sh',
+            env: { ...process.env },
+            windowsHide: true,
+        });
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+// Check test directories configured in moflo.yaml
+async function checkTestDirs() {
+    const yamlPath = join(process.cwd(), 'moflo.yaml');
+    if (!existsSync(yamlPath)) {
+        return { name: 'Test Directories', status: 'warn', message: 'No moflo.yaml — test indexing unconfigured', fix: 'npx moflo init' };
+    }
+    try {
+        const content = readFileSync(yamlPath, 'utf-8');
+        // Check if tests section exists
+        const testsBlock = content.match(/tests:\s*\n\s+directories:\s*\n((?:\s+-\s+.+\n?)+)/);
+        if (!testsBlock) {
+            return { name: 'Test Directories', status: 'warn', message: 'No tests section in moflo.yaml', fix: 'npx moflo init --force' };
+        }
+        // Extract configured directories
+        const items = testsBlock[1].match(/-\s+(.+)/g);
+        if (!items || items.length === 0) {
+            return { name: 'Test Directories', status: 'warn', message: 'Empty test directories list' };
+        }
+        const dirs = items.map(item => item.replace(/^-\s+/, '').trim());
+        const existing = dirs.filter(d => existsSync(join(process.cwd(), d)));
+        const missing = dirs.filter(d => !existsSync(join(process.cwd(), d)));
+        // Check auto_index.tests flag
+        const autoIndexMatch = content.match(/auto_index:\s*\n(?:.*\n)*?\s+tests:\s*(true|false)/);
+        const autoIndexEnabled = !autoIndexMatch || autoIndexMatch[1] !== 'false';
+        const indexLabel = autoIndexEnabled ? 'auto-index: on' : 'auto-index: off';
+        if (missing.length > 0 && existing.length === 0) {
+            return {
+                name: 'Test Directories',
+                status: 'warn',
+                message: `No configured test dirs exist: ${missing.join(', ')} (${indexLabel})`,
+            };
+        }
+        if (missing.length > 0) {
+            return {
+                name: 'Test Directories',
+                status: 'warn',
+                message: `${existing.length} OK, ${missing.length} missing: ${missing.join(', ')} (${indexLabel})`,
+            };
+        }
+        return { name: 'Test Directories', status: 'pass', message: `${existing.length} directories: ${existing.join(', ')} (${indexLabel})` };
+    }
+    catch {
+        return { name: 'Test Directories', status: 'warn', message: 'Unable to parse moflo.yaml' };
+    }
+}
+// Check agentic-flow v3 integration (filesystem-based to avoid slow WASM/DB init)
+async function checkAgenticFlow() {
+    try {
+        // Walk common node_modules paths to find agentic-flow/package.json
+        const candidates = [
+            join(process.cwd(), 'node_modules', 'agentic-flow', 'package.json'),
+            join(process.cwd(), '..', 'node_modules', 'agentic-flow', 'package.json'),
+        ];
+        let pkgJsonPath = null;
+        for (const p of candidates) {
+            if (existsSync(p)) {
+                pkgJsonPath = p;
+                break;
+            }
+        }
+        if (!pkgJsonPath) {
+            return {
+                name: 'agentic-flow',
+                status: 'warn',
+                message: 'Not installed (optional — embeddings/routing will use fallbacks)',
+                fix: 'npm install agentic-flow@latest'
+            };
+        }
+        const pkg = JSON.parse(readFileSync(pkgJsonPath, 'utf-8'));
+        const version = pkg.version || 'unknown';
+        const exports = pkg.exports || {};
+        const features = [
+            exports['./reasoningbank'] ? 'ReasoningBank' : null,
+            exports['./router'] ? 'Router' : null,
+            exports['./transport/quic'] ? 'QUIC' : null,
+        ].filter(Boolean);
+        return {
+            name: 'agentic-flow',
+            status: 'pass',
+            message: `v${version} (${features.join(', ')})`
+        };
+    }
+    catch {
+        return { name: 'agentic-flow', status: 'warn', message: 'Check failed' };
+    }
+}
+// Check semantic search quality — verify no 0.500 keyword fallback scores
+async function checkSemanticQuality() {
+    try {
+        const { searchEntries } = await import('../memory/memory-initializer.js');
+        const result = await searchEntries({
+            query: 'test infrastructure health check',
+            namespace: 'patterns',
+            limit: 5,
+            threshold: 0.1
+        });
+        if (!result.success || result.results.length === 0) {
+            return {
+                name: 'Semantic Quality',
+                status: 'warn',
+                message: 'No search results (empty database or no patterns namespace)',
+            };
+        }
+        const scores = result.results.map((r) => r.score);
+        const allSame = scores.every((s) => s === scores[0]);
+        const hasFallback = scores.some((s) => s === 0.5);
+        if (hasFallback) {
+            return {
+                name: 'Semantic Quality',
+                status: 'fail',
+                message: `${scores.length} results, scores include 0.500 fallback (keyword-only, no embeddings)`,
+                fix: 'Re-index with: npx moflo embeddings build --force'
+            };
+        }
+        if (allSame && scores.length > 1) {
+            return {
+                name: 'Semantic Quality',
+                status: 'warn',
+                message: `${scores.length} results, all scores identical (${scores[0].toFixed(3)}) — degraded search`,
+            };
+        }
+        const topScore = Math.max(...scores);
+        return {
+            name: 'Semantic Quality',
+            status: topScore >= 0.3 ? 'pass' : 'warn',
+            message: `${scores.length} results, top ${topScore.toFixed(3)}, varied (semantic search active)`,
+        };
+    }
+    catch (e) {
+        return {
+            name: 'Semantic Quality',
+            status: 'warn',
+            message: `Check failed: ${e instanceof Error ? e.message.split('\n')[0] : 'error'}`,
+        };
+    }
+}
+// Check memory-backed patterns (populated by pretrain) as a fallback for neural checks
+async function checkMemoryPatterns(namespace) {
+    try {
+        // @ts-ignore — memory is not in tsconfig project references but is available at runtime
+        const memoryMod = await import('../../../../memory/dist/index.js');
+        if (memoryMod.search) {
+            const results = await memoryMod.search({ query: 'pattern', namespace, limit: 1 });
+            return results?.length ?? 0;
+        }
+        // Fallback: try AgentDB route
+        if (memoryMod.getStore) {
+            const store = memoryMod.getStore();
+            const entries = store?.list?.(namespace) ?? [];
+            return entries.length;
+        }
+    }
+    catch {
+        // Memory module not available
+    }
+    return 0;
+}
+// Check intelligence layer: SONA, EWC++, LoRA, Flash Attention, ReasoningBank
+// Exercises each component with a lightweight functional test rather than just checking "loaded".
+async function checkIntelligence() {
+    try {
+        // @ts-ignore — neural is not in tsconfig project references but is available at runtime
+        // Import neural module — path is relative to compiled output at dist/src/commands/
+        const neural = await import('../../../../neural/dist/index.js');
+        const results = [];
+        const failures = [];
+        // 1. SONA — create manager, run trajectory lifecycle
+        try {
+            const sona = neural.createSONAManager('balanced');
+            await sona.initialize();
+            const tid = sona.beginTrajectory('doctor-check', 'general');
+            const embedding = new Float32Array(64).fill(0.1);
+            sona.recordStep(tid, 'test-action', 0.8, embedding);
+            const traj = sona.completeTrajectory(tid, 0.9);
+            if (traj && traj.steps.length > 0) {
+                results.push('SONA');
+            }
+            else {
+                failures.push('SONA (no trajectory output)');
+            }
+            await sona.cleanup();
+        }
+        catch (e) {
+            failures.push(`SONA (${e instanceof Error ? e.message : 'error'})`);
+        }
+        // 2. ReasoningBank — store + retrieve
+        try {
+            const rb = neural.createReasoningBank();
+            const embedding = new Float32Array(64).fill(0.2);
+            rb.storeTrajectory({
+                id: 'doctor-test',
+                context: 'health check',
+                domain: 'general',
+                mode: 'balanced',
+                steps: [{ action: 'test', reward: 1, embedding, timestamp: Date.now() }],
+                startTime: Date.now(),
+                endTime: Date.now(),
+                quality: 1,
+            });
+            const retrieved = rb.retrieve(embedding, 1);
+            if (retrieved.length > 0) {
+                results.push('ReasoningBank');
+            }
+            else {
+                // Fallback: check memory-backed patterns from pretrain
+                const memoryPatterns = await checkMemoryPatterns('patterns');
+                if (memoryPatterns > 0) {
+                    results.push('ReasoningBank(memory)');
+                }
+                else {
+                    failures.push('ReasoningBank (retrieve failed)');
+                }
+            }
+        }
+        catch (e) {
+            failures.push(`ReasoningBank (${e instanceof Error ? e.message : 'error'})`);
+        }
+        // 3. PatternLearner — extract + match
+        try {
+            const pl = neural.createPatternLearner();
+            const embedding = new Float32Array(64).fill(0.3);
+            pl.extractPattern({
+                id: 'doctor-pl', context: 'test', domain: 'general', mode: 'balanced',
+                steps: [{ action: 'test', reward: 1, embedding, timestamp: Date.now() }],
+                startTime: Date.now(), endTime: Date.now(), quality: 1,
+            }, { trajectoryId: 'doctor-pl', keyInsights: ['test'], compressedEmbedding: embedding, timestamp: Date.now() });
+            const matches = pl.findMatches(embedding, 1);
+            if (matches.length > 0) {
+                results.push('PatternLearner');
+            }
+            else {
+                // Fallback: check memory-backed patterns from pretrain
+                const memoryPatterns = await checkMemoryPatterns('patterns');
+                if (memoryPatterns > 0) {
+                    results.push('PatternLearner(memory)');
+                }
+                else {
+                    failures.push('PatternLearner (no matches)');
+                }
+            }
+        }
+        catch (e) {
+            failures.push(`PatternLearner (${e instanceof Error ? e.message : 'error'})`);
+        }
+        // 4. SONALearningEngine (MicroLoRA + EWC++)
+        try {
+            const engine = neural.createSONALearningEngine();
+            const ctx = { domain: 'general', queryEmbedding: new Float32Array(768).fill(0.1) };
+            const adapted = await engine.adapt(ctx);
+            const components = [];
+            if (adapted && adapted.transformedQuery)
+                components.push('LoRA');
+            if (adapted && adapted.patterns !== undefined)
+                components.push('EWC++');
+            if (components.length > 0) {
+                results.push(...components);
+            }
+            else {
+                failures.push('LoRA/EWC++ (adapt returned no data)');
+            }
+        }
+        catch (e) {
+            // Gracefully handle cold/uninitialized state
+            const msg = e instanceof Error ? e.message : 'error';
+            if (msg.includes('undefined') || msg.includes('not initialized')) {
+                results.push('LoRA/EWC++(cold)');
+            }
+            else {
+                failures.push(`LoRA/EWC++ (${msg})`);
+            }
+        }
+        // 5. RL Algorithms — quick instantiation check
+        try {
+            const algNames = [];
+            const ppo = neural.createPPO();
+            if (ppo)
+                algNames.push('PPO');
+            const dqn = neural.createDQN();
+            if (dqn)
+                algNames.push('DQN');
+            const ql = neural.createQLearning();
+            if (ql)
+                algNames.push('Q-Learn');
+            if (algNames.length > 0) {
+                results.push(`RL(${algNames.join('+')})`);
+            }
+        }
+        catch (e) {
+            failures.push(`RL (${e instanceof Error ? e.message : 'error'})`);
+        }
+        if (failures.length > 0) {
+            return {
+                name: 'Intelligence',
+                status: results.length > 0 ? 'warn' : 'fail',
+                message: `${results.join(', ')} OK; FAILED: ${failures.join(', ')}`,
+                fix: 'Check neural module imports and dependencies',
+            };
+        }
+        return {
+            name: 'Intelligence',
+            status: 'pass',
+            message: results.join(', '),
+        };
+    }
+    catch (e) {
+        return {
+            name: 'Intelligence',
+            status: 'warn',
+            message: `Module unavailable: ${e instanceof Error ? e.message.split('\n')[0] : 'import failed'}`,
+            fix: 'Ensure @claude-flow/neural is built (npm run build)',
+        };
+    }
+}
+// Check whether a given PID is still running.
+// Uses signal 0 which works cross-platform (Windows, Linux, macOS) without
+// needing PowerShell or /proc — Node handles the platform abstraction.
+function isProcessAlive(pid) {
+    try {
+        process.kill(pid, 0);
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+// Fast path: kill processes tracked in the shared ProcessManager registry.
+// This avoids the expensive OS-level process scan for known background tasks.
+function killTrackedProcesses() {
+    const registryFile = join(process.cwd(), '.claude-flow', 'background-pids.json');
+    const lockFile = join(process.cwd(), '.claude-flow', 'spawn.lock');
+    let killed = 0;
+    try {
+        if (existsSync(registryFile)) {
+            const entries = JSON.parse(readFileSync(registryFile, 'utf-8'));
+            for (const entry of entries) {
+                if (!isProcessAlive(entry.pid))
+                    continue;
+                try {
+                    if (process.platform === 'win32') {
+                        execSync(`taskkill /F /PID ${entry.pid}`, { timeout: 5000, windowsHide: true });
+                    }
+                    else {
+                        process.kill(entry.pid, 'SIGKILL');
+                    }
+                    killed++;
+                }
+                catch { /* already gone */ }
+            }
+            // Clear registry
+            writeFileSync(registryFile, '[]');
+        }
+    }
+    catch { /* non-fatal */ }
+    // Remove spawn lock
+    try {
+        if (existsSync(lockFile))
+            unlinkSync(lockFile);
+    }
+    catch { /* ok */ }
+    return killed;
+}
+// Find and optionally kill orphaned moflo/claude-flow node processes.
+// A process is only "orphaned" if its parent is no longer alive — meaning
+// nothing will clean it up. MCP servers spawned by a live Claude Code session
+// have a live parent (claude.exe) and must not be flagged.
+async function findZombieProcesses(kill = false) {
+    const legitimatePid = getDaemonLockHolder(process.cwd());
+    const currentPid = process.pid;
+    const parentPid = process.ppid;
+    const found = [];
+    let killed = 0;
+    // Collect candidates as { pid, ppid } so we can check parent liveness
+    const candidates = [];
+    try {
+        if (process.platform === 'win32') {
+            // Windows: include ParentProcessId so we can verify orphan status
+            const result = execSync('powershell -NoProfile -Command "Get-CimInstance Win32_Process -Filter \\"Name=\'node.exe\'\\" | Select-Object ProcessId,ParentProcessId,CommandLine | Format-Table -AutoSize -Wrap"', { encoding: 'utf-8', timeout: 10000, windowsHide: true });
+            const lines = result.split('\n');
+            for (const line of lines) {
+                if (/moflo|claude-flow|flo\s+(hooks|gate|mcp|daemon)/i.test(line)) {
+                    // Format-Table columns: ProcessId  ParentProcessId  CommandLine...
+                    const match = line.match(/^\s*(\d+)\s+(\d+)/);
+                    if (match) {
+                        candidates.push({ pid: parseInt(match[1], 10), ppid: parseInt(match[2], 10) });
+                    }
+                }
+            }
+        }
+        else {
+            // Unix/macOS: use ps with explicit PID+PPID columns for reliable parsing
+            const result = execSync('ps -eo pid,ppid,command | grep -E "node.*(moflo|claude-flow)" | grep -v grep', { encoding: 'utf-8', timeout: 5000 });
+            const lines = result.trim().split('\n');
+            for (const line of lines) {
+                const match = line.trim().match(/^(\d+)\s+(\d+)/);
+                if (match) {
+                    candidates.push({ pid: parseInt(match[1], 10), ppid: parseInt(match[2], 10) });
+                }
+            }
+        }
+    }
+    catch {
+        // No matches found (grep exits non-zero) or command failed
+    }
+    // Filter: skip known-good PIDs and processes whose parent is still alive.
+    // A live parent (e.g. claude.exe for MCP servers) means the process is managed, not orphaned.
+    for (const { pid, ppid } of candidates) {
+        if (pid === currentPid || pid === parentPid || pid === legitimatePid)
+            continue;
+        if (isProcessAlive(ppid))
+            continue;
+        // Defense-in-depth: detached daemons have dead parents by design.
+        // Even if the lock file is missing/corrupted, don't kill a running daemon.
+        if (isDaemonProcess(pid))
+            continue;
+        found.push(pid);
+    }
+    if (kill && found.length > 0) {
+        for (const pid of found) {
+            try {
+                if (process.platform === 'win32') {
+                    execSync(`taskkill /F /PID ${pid}`, { timeout: 5000, windowsHide: true });
+                }
+                else {
+                    process.kill(pid, 'SIGKILL');
+                }
+                killed++;
+            }
+            catch {
+                // Process may have already exited
+            }
+        }
+        // Clean up stale daemon lock if we killed the holder
+        if (legitimatePid && found.includes(legitimatePid)) {
+            releaseDaemonLock(process.cwd(), legitimatePid, true);
+        }
+    }
+    return { found: found.length, killed, pids: found };
+}
+// Format health check result
+function formatCheck(check) {
+    const icon = check.status === 'pass' ? output.success('✓') :
+        check.status === 'warn' ? output.warning('⚠') :
+            output.error('✗');
+    return `${icon} ${check.name}: ${check.message}`;
+}
+// Main doctor command
+export const doctorCommand = {
+    name: 'doctor',
+    description: 'System diagnostics and health checks',
+    options: [
+        {
+            name: 'fix',
+            short: 'f',
+            description: 'Automatically fix issues where possible',
+            type: 'boolean',
+            default: false
+        },
+        {
+            name: 'install',
+            short: 'i',
+            description: 'Auto-install missing dependencies (Claude Code CLI)',
+            type: 'boolean',
+            default: false
+        },
+        {
+            name: 'component',
+            short: 'c',
+            description: 'Check specific component (version, node, npm, config, daemon, memory, embeddings, git, mcp, claude, disk, typescript, semantic, intelligence)',
+            type: 'string'
+        },
+        {
+            name: 'verbose',
+            short: 'v',
+            description: 'Verbose output',
+            type: 'boolean',
+            default: false
+        },
+        {
+            name: 'kill-zombies',
+            short: 'k',
+            description: 'Find and kill orphaned moflo/claude-flow node processes',
+            type: 'boolean',
+            default: false
+        }
+    ],
+    examples: [
+        { command: 'claude-flow doctor', description: 'Run full health check' },
+        { command: 'claude-flow doctor --fix', description: 'Show fixes for issues' },
+        { command: 'claude-flow doctor --install', description: 'Auto-install missing dependencies' },
+        { command: 'claude-flow doctor --kill-zombies', description: 'Find and kill zombie processes' },
+        { command: 'claude-flow doctor -c version', description: 'Check for stale npx cache' },
+        { command: 'claude-flow doctor -c claude', description: 'Check Claude Code CLI only' }
+    ],
+    action: async (ctx) => {
+        const showFix = ctx.flags.fix;
+        const autoInstall = ctx.flags.install;
+        const component = ctx.flags.component;
+        const verbose = ctx.flags.verbose;
+        const killZombies = ctx.flags['kill-zombies'];
+        output.writeln();
+        output.writeln(output.bold('MoFlo Doctor'));
+        output.writeln(output.dim('System diagnostics and health check'));
+        output.writeln(output.dim('─'.repeat(50)));
+        output.writeln();
+        // Handle --kill-zombies early
+        if (killZombies) {
+            output.writeln(output.bold('Zombie Process Scan'));
+            output.writeln();
+            // Fast path: kill tracked processes from the shared registry first
+            const registryKilled = killTrackedProcesses();
+            if (registryKilled > 0) {
+                output.writeln(output.success(`  Killed ${registryKilled} tracked background process(es) from registry`));
+            }
+            // Slow path: OS-level scan for any remaining orphans
+            const scan = await findZombieProcesses(false);
+            if (scan.found === 0) {
+                if (registryKilled === 0) {
+                    output.writeln(output.success('  No orphaned moflo processes found'));
+                }
+            }
+            else {
+                output.writeln(output.warning(`  Found ${scan.found} additional orphaned process(es): PIDs ${scan.pids.join(', ')}`));
+                // Kill them
+                const result = await findZombieProcesses(true);
+                if (result.killed > 0) {
+                    output.writeln(output.success(`  Killed ${result.killed} zombie process(es)`));
+                }
+                if (result.killed < result.found) {
+                    output.writeln(output.warning(`  ${result.found - result.killed} process(es) could not be killed`));
+                }
+            }
+            output.writeln();
+            output.writeln(output.dim('─'.repeat(50)));
+            output.writeln();
+        }
+        const checkZombieProcesses = async () => {
+            try {
+                const scan = await findZombieProcesses(false);
+                if (scan.found === 0) {
+                    return { name: 'Zombie Processes', status: 'pass', message: 'No orphaned processes' };
+                }
+                return {
+                    name: 'Zombie Processes',
+                    status: 'warn',
+                    message: `${scan.found} orphaned process(es) (PIDs: ${scan.pids.join(', ')})`,
+                    fix: 'moflo doctor --kill-zombies'
+                };
+            }
+            catch {
+                return { name: 'Zombie Processes', status: 'pass', message: 'Check skipped' };
+            }
+        };
+        const allChecks = [
+            checkVersionFreshness,
+            checkNodeVersion,
+            checkNpmVersion,
+            checkClaudeCode,
+            checkGit,
+            checkGitRepo,
+            checkConfigFile,
+            checkDaemonStatus,
+            checkMemoryDatabase,
+            checkEmbeddings,
+            checkTestDirs,
+            checkMcpServers,
+            checkDiskSpace,
+            checkBuildTools,
+            checkAgenticFlow,
+            checkSemanticQuality,
+            checkIntelligence,
+            checkZombieProcesses
+        ];
+        const componentMap = {
+            'version': checkVersionFreshness,
+            'freshness': checkVersionFreshness,
+            'node': checkNodeVersion,
+            'npm': checkNpmVersion,
+            'claude': checkClaudeCode,
+            'config': checkConfigFile,
+            'daemon': checkDaemonStatus,
+            'memory': checkMemoryDatabase,
+            'embeddings': checkEmbeddings,
+            'git': checkGit,
+            'mcp': checkMcpServers,
+            'disk': checkDiskSpace,
+            'typescript': checkBuildTools,
+            'tests': checkTestDirs,
+            'agentic-flow': checkAgenticFlow,
+            'semantic': checkSemanticQuality,
+            'quality': checkSemanticQuality,
+            'intelligence': checkIntelligence
+        };
+        let checksToRun = allChecks;
+        if (component && componentMap[component]) {
+            checksToRun = [componentMap[component]];
+        }
+        const results = [];
+        const fixes = [];
+        // OPTIMIZATION: Run all checks in parallel for 3-5x faster execution
+        const spinner = output.createSpinner({ text: 'Running health checks in parallel...', spinner: 'dots' });
+        spinner.start();
+        try {
+            // Execute all checks concurrently
+            const checkResults = await Promise.allSettled(checksToRun.map(check => check()));
+            spinner.stop();
+            // Process results in order
+            for (const settledResult of checkResults) {
+                if (settledResult.status === 'fulfilled') {
+                    const result = settledResult.value;
+                    results.push(result);
+                    output.writeln(formatCheck(result));
+                    if (result.fix && (result.status === 'fail' || result.status === 'warn')) {
+                        fixes.push(`${result.name}: ${result.fix}`);
+                    }
+                }
+                else {
+                    const errorResult = {
+                        name: 'Check',
+                        status: 'fail',
+                        message: settledResult.reason?.message || 'Unknown error'
+                    };
+                    results.push(errorResult);
+                    output.writeln(formatCheck(errorResult));
+                }
+            }
+        }
+        catch (error) {
+            spinner.stop();
+            output.writeln(output.error('Failed to run health checks'));
+        }
+        // Auto-install missing dependencies if requested
+        if (autoInstall) {
+            const claudeCodeResult = results.find(r => r.name === 'Claude Code CLI');
+            if (claudeCodeResult && claudeCodeResult.status !== 'pass') {
+                const installed = await installClaudeCode();
+                if (installed) {
+                    // Re-check Claude Code after installation
+                    const newCheck = await checkClaudeCode();
+                    const idx = results.findIndex(r => r.name === 'Claude Code CLI');
+                    if (idx !== -1) {
+                        results[idx] = newCheck;
+                        // Update fixes list
+                        const fixIdx = fixes.findIndex(f => f.startsWith('Claude Code CLI:'));
+                        if (fixIdx !== -1 && newCheck.status === 'pass') {
+                            fixes.splice(fixIdx, 1);
+                        }
+                    }
+                    output.writeln(formatCheck(newCheck));
+                }
+            }
+        }
+        // Summary
+        const passed = results.filter(r => r.status === 'pass').length;
+        const warnings = results.filter(r => r.status === 'warn').length;
+        const failed = results.filter(r => r.status === 'fail').length;
+        output.writeln();
+        output.writeln(output.dim('─'.repeat(50)));
+        output.writeln();
+        const summaryParts = [
+            output.success(`${passed} passed`),
+            warnings > 0 ? output.warning(`${warnings} warnings`) : null,
+            failed > 0 ? output.error(`${failed} failed`) : null
+        ].filter(Boolean);
+        output.writeln(`Summary: ${summaryParts.join(', ')}`);
+        // Auto-fix or show fixes
+        if (showFix && fixes.length > 0) {
+            output.writeln();
+            output.writeln(output.bold('Auto-fixing issues...'));
+            output.writeln();
+            const fixableResults = results.filter(r => r.fix && (r.status === 'fail' || r.status === 'warn'));
+            let fixed = 0;
+            const unfixed = [];
+            for (const check of fixableResults) {
+                const success = await autoFixCheck(check);
+                if (success) {
+                    fixed++;
+                }
+                else {
+                    unfixed.push(`${check.name}: ${check.fix}`);
+                }
+            }
+            if (fixed > 0) {
+                output.writeln();
+                output.writeln(output.success(`Auto-fixed ${fixed} issue${fixed > 1 ? 's' : ''}`));
+            }
+            if (unfixed.length > 0) {
+                output.writeln();
+                output.writeln(output.bold('Manual fixes needed:'));
+                for (const fix of unfixed) {
+                    output.writeln(output.dim(`  ${fix}`));
+                }
+            }
+            // Re-run checks to show updated status
+            if (fixed > 0) {
+                output.writeln();
+                output.writeln(output.dim('Re-checking...'));
+                output.writeln();
+                const reResults = await Promise.allSettled(checksToRun.map(check => check()));
+                let rePassed = 0, reWarnings = 0, reFailed = 0;
+                for (const sr of reResults) {
+                    if (sr.status === 'fulfilled') {
+                        output.writeln(formatCheck(sr.value));
+                        if (sr.value.status === 'pass')
+                            rePassed++;
+                        else if (sr.value.status === 'warn')
+                            reWarnings++;
+                        else
+                            reFailed++;
+                    }
+                }
+                output.writeln();
+                output.writeln(output.dim('─'.repeat(50)));
+                const reSummary = [
+                    output.success(`${rePassed} passed`),
+                    reWarnings > 0 ? output.warning(`${reWarnings} warnings`) : null,
+                    reFailed > 0 ? output.error(`${reFailed} failed`) : null
+                ].filter(Boolean);
+                output.writeln(`After fix: ${reSummary.join(', ')}`);
+            }
+        }
+        else if (fixes.length > 0 && !showFix) {
+            output.writeln();
+            output.writeln(output.dim(`Run with --fix to auto-fix ${fixes.length} issue${fixes.length > 1 ? 's' : ''}`));
+        }
+        // Overall result
+        if (failed > 0) {
+            output.writeln();
+            output.writeln(output.error('Some checks failed. Please address the issues above.'));
+            return { success: false, exitCode: 1, data: { passed, warnings, failed, results } };
+        }
+        else if (warnings > 0) {
+            output.writeln();
+            output.writeln(output.warning('All checks passed with some warnings.'));
+            return { success: true, data: { passed, warnings, failed, results } };
+        }
+        else {
+            output.writeln();
+            output.writeln(output.success('All checks passed! System is healthy.'));
+            return { success: true, data: { passed, warnings, failed, results } };
+        }
+    }
+};
+export default doctorCommand;
 //# sourceMappingURL=doctor.js.map