@cleocode/core 2026.4.42 → 2026.4.44

package/dist/system/health.js

@@ -1,1206 +0,0 @@
-/**
- * System health checks core module.
- * @task T4783
- * @task T4795
- */
-import { execFileSync } from 'node:child_process';
-import { existsSync, readFileSync, statSync } from 'node:fs';
-import { createRequire } from 'node:module';
-import { join } from 'node:path';
-import { checkGitHooks } from '../hooks.js';
-import { checkInjection } from '../injection.js';
-import { getAgentsHome, isProjectInitialized } from '../paths.js';
-import { getSystemInfo } from '../platform.js';
-import { checkBrainDb, checkCleoStructure, checkConfig, checkGlobalHome, checkGlobalTemplates, checkLogDir, checkMemoryBridge, checkNexusBridge, checkProjectContext, checkProjectInfo, checkSqliteDb, ensureCleoStructure, ensureGlobalScaffold, } from '../scaffold.js';
-import { checkGlobalSchemas } from '../schema-management.js';
-import { getAccessor } from '../store/data-accessor.js';
-import { checkCleoGitignore, checkCoreFilesNotIgnored, checkLegacyAgentOutputs, checkNodeVersion, checkVitalFilesTracked, } from '../validation/doctor/checks.js';
-import { checkAllDependencies } from './dependencies.js';
-import { checkStorageMigration } from './storage-preflight.js';
-// NOTE on storage-migration preflight consolidation (T511):
-// `checkStorageMigration` lives in ./storage-preflight.ts and is the single
-// source of truth. Both `self-update.ts` and `upgrade.ts` import it from
-// `@cleocode/core/internal`.  No duplication exists — this comment documents
-// that the consolidation is already in place.
-const _require = createRequire(import.meta.url);
-const databaseSyncCtor = (() => {
-    try {
-        return _require('node:sqlite').DatabaseSync;
-    }
-    catch {
-        return null;
-    }
-})();
-/** Stale JSON files that should not exist alongside tasks.db (ADR-006). */
-const STALE_JSON_FILES = ['todo.json', 'sessions.json', 'todo-archive.json'];
-function resolveStructuredLogPath(cleoDir) {
-    const defaultPath = join(cleoDir, 'logs', 'cleo.log');
-    const configPath = join(cleoDir, 'config.json');
-    if (!existsSync(configPath))
-        return defaultPath;
-    try {
-        const config = JSON.parse(readFileSync(configPath, 'utf-8'));
-        if (!config.logging?.filePath)
-            return defaultPath;
-        return join(cleoDir, config.logging.filePath);
-    }
-    catch {
-        return defaultPath;
-    }
-}
-function checkAuditLogAvailability(dbPath) {
-    if (!databaseSyncCtor) {
-        return {
-            name: 'audit_log',
-            status: 'warn',
-            message: 'audit_log check unavailable: node:sqlite runtime not found',
-        };
-    }
-    try {
-        const db = new databaseSyncCtor(dbPath, { readOnly: true });
-        try {
-            const tableRow = db
-                .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='audit_log'")
-                .get();
-            if (!tableRow?.name) {
-                return {
-                    name: 'audit_log',
-                    status: 'fail',
-                    message: 'audit_log table missing from tasks.db (run: cleo upgrade)',
-                };
-            }
-            const countRow = db.prepare('SELECT COUNT(1) AS count FROM audit_log').get();
-            return {
-                name: 'audit_log',
-                status: 'pass',
-                message: `audit_log table available (${countRow?.count ?? 0} rows)`,
-            };
-        }
-        finally {
-            db.close();
-        }
-    }
-    catch {
-        return {
-            name: 'audit_log',
-            status: 'warn',
-            message: 'Unable to validate audit_log availability from tasks.db',
-        };
-    }
-}
-/** Run system health checks (SQLite-first per ADR-006). */
-export async function getSystemHealth(projectRoot, opts) {
-    const cleoDir = join(projectRoot, '.cleo');
-    const checks = [];
-    // Check .cleo directory
-    if (existsSync(cleoDir)) {
-        checks.push({ name: 'cleo_dir', status: 'pass', message: '.cleo directory exists' });
-    }
-    else {
-        checks.push({ name: 'cleo_dir', status: 'fail', message: '.cleo directory not found' });
-    }
-    // Check tasks.db (primary data store per ADR-006)
-    const dbPath = join(cleoDir, 'tasks.db');
-    if (existsSync(dbPath)) {
-        try {
-            const dbSize = statSync(dbPath).size;
-            if (dbSize > 0) {
-                checks.push({ name: 'tasks_db', status: 'pass', message: `tasks.db: ${dbSize} bytes` });
-            }
-            else {
-                checks.push({ name: 'tasks_db', status: 'warn', message: 'tasks.db exists but is empty' });
-            }
-        }
-        catch {
-            checks.push({
-                name: 'tasks_db',
-                status: 'fail',
-                message: 'tasks.db exists but is not readable',
-            });
-        }
-    }
-    else {
-        checks.push({ name: 'tasks_db', status: 'fail', message: 'tasks.db not found' });
-    }
-    if (existsSync(dbPath)) {
-        checks.push(checkAuditLogAvailability(dbPath));
-    }
-    // Check signaldock.db with schema health (local agent messaging per T225)
-    const sdDbPath = join(cleoDir, 'signaldock.db');
-    if (existsSync(sdDbPath)) {
-        try {
-            const { DatabaseSync: SdDb } = _require('node:sqlite');
-            const sdDb = new SdDb(sdDbPath);
-            try {
-                const tables = sdDb
-                    .prepare("SELECT COUNT(*) as count FROM sqlite_master WHERE type='table' AND name NOT LIKE 'sqlite_%' AND name NOT LIKE '_signaldock%'")
-                    .get();
-                const journalMode = sdDb.prepare('PRAGMA journal_mode').get();
-                let schemaVersion = 'unknown';
-                try {
-                    const meta = sdDb
-                        .prepare("SELECT value FROM _signaldock_meta WHERE key = 'schema_version'")
-                        .get();
-                    schemaVersion = meta?.value ?? 'unknown';
-                }
-                catch {
-                    /* meta table may not exist */
-                }
-                checks.push({
-                    name: 'signaldock_db',
-                    status: tables.count >= 20 ? 'pass' : 'warn',
-                    message: `signaldock.db: ${tables.count} tables, ${journalMode.journal_mode}, v${schemaVersion}`,
-                });
-            }
-            finally {
-                sdDb.close();
-            }
-        }
-        catch {
-            checks.push({
-                name: 'signaldock_db',
-                status: 'pass',
-                message: `signaldock.db: ${statSync(sdDbPath).size} bytes`,
-            });
-        }
-    }
-    else {
-        checks.push({
-            name: 'signaldock_db',
-            status: 'warn',
-            message: 'signaldock.db not found. Run: cleo init',
-        });
-    }
-    // Check config.json (config remains JSON per ADR-006)
-    const configPath = join(cleoDir, 'config.json');
-    if (existsSync(configPath)) {
-        try {
-            JSON.parse(readFileSync(configPath, 'utf-8'));
-            checks.push({ name: 'config_json', status: 'pass', message: 'config.json is valid JSON' });
-        }
-        catch {
-            checks.push({
-                name: 'config_json',
-                status: 'warn',
-                message: 'config.json is not valid JSON',
-            });
-        }
-    }
-    else {
-        checks.push({ name: 'config_json', status: 'warn', message: 'config.json not found' });
-    }
-    // Check for stale JSON files alongside tasks.db
-    if (existsSync(dbPath)) {
-        const staleFiles = STALE_JSON_FILES.filter((f) => existsSync(join(cleoDir, f)));
-        if (staleFiles.length > 0) {
-            checks.push({
-                name: 'stale_json',
-                status: 'warn',
-                message: `Stale JSON files found alongside tasks.db: ${staleFiles.join(', ')}. Run: cleo upgrade`,
-            });
-        }
-    }
-    if (opts?.detailed) {
-        const logPath = resolveStructuredLogPath(cleoDir);
-        if (existsSync(logPath)) {
-            checks.push({
-                name: 'log_file',
-                status: 'pass',
-                message: `structured log present: ${logPath}`,
-            });
-        }
-        else {
-            checks.push({
-                name: 'log_file',
-                status: 'warn',
-                message: `structured log not found: ${logPath}`,
-            });
-        }
-        const backupDir = join(cleoDir, '.backups');
-        if (existsSync(backupDir)) {
-            checks.push({ name: 'backups_dir', status: 'pass', message: '.backups directory exists' });
-        }
-        else {
-            checks.push({
-                name: 'backups_dir',
-                status: 'pass',
-                message: 'No backups directory (created on first write)',
-            });
-        }
-    }
-    // Get version
-    let version = 'unknown';
-    try {
-        const pkgPath = join(projectRoot, 'package.json');
-        if (existsSync(pkgPath)) {
-            const pkg = JSON.parse(readFileSync(pkgPath, 'utf-8'));
-            version = pkg.version || 'unknown';
-        }
-    }
-    catch {
-        // fallback
-    }
-    const failCount = checks.filter((c) => c.status === 'fail').length;
-    const warnCount = checks.filter((c) => c.status === 'warn').length;
-    const overall = failCount > 0 ? 'error' : warnCount > 0 ? 'warning' : 'healthy';
-    const installation = failCount > 0 ? 'degraded' : 'ok';
-    return { overall, checks, version, installation };
-}
-/** Run extended diagnostics with fix suggestions. */
-export async function getSystemDiagnostics(projectRoot, opts) {
-    const healthResult = await getSystemHealth(projectRoot, { detailed: true });
-    const diagChecks = healthResult.checks.map((c) => ({
-        name: c.name,
-        status: c.status,
-        details: c.message,
-        fix: c.status === 'fail'
-            ? c.name === 'cleo_dir'
-                ? 'Run: cleo init'
-                : c.name === 'tasks_db'
-                    ? 'Run: cleo init (or restore from backup)'
-                    : undefined
-            : undefined,
-    }));
-    // Storage migration pre-flight check
-    const preflight = checkStorageMigration(projectRoot);
-    if (preflight.migrationNeeded) {
-        diagChecks.push({
-            name: 'storage_migration',
-            status: 'fail',
-            details: preflight.summary,
-            fix: preflight.fix ?? undefined,
-        });
-    }
-    else {
-        diagChecks.push({
-            name: 'storage_migration',
-            status: 'pass',
-            details: preflight.summary,
-        });
-    }
-    // Schema version check — read via DataAccessor (per ADR-006)
-    const cleoDir = join(projectRoot, '.cleo');
-    const dbPath = join(cleoDir, 'tasks.db');
-    if (existsSync(dbPath)) {
-        try {
-            const accessor = await getAccessor(projectRoot);
-            const schemaVersion = await accessor.getSchemaVersion();
-            if (schemaVersion) {
-                diagChecks.push({
-                    name: 'schema_version',
-                    status: 'pass',
-                    details: `Schema version: ${schemaVersion}`,
-                });
-            }
-            else {
-                diagChecks.push({
-                    name: 'schema_version',
-                    status: 'warn',
-                    details: 'No schema version in SQLite',
-                    fix: 'Run: cleo upgrade',
-                });
-            }
-        }
-        catch {
-            diagChecks.push({
-                name: 'schema_version',
-                status: 'warn',
-                details: 'Could not read schema version from SQLite',
-                fix: 'Run: cleo upgrade',
-            });
-        }
-    }
-    // Check for stale sessions — read from SQLite accessor
-    if (existsSync(dbPath)) {
-        try {
-            const accessor = await getAccessor(projectRoot);
-            const sessions = await accessor.loadSessions();
-            const activeSessions = sessions.filter((s) => s.status === 'active');
-            if (activeSessions.length > 3) {
-                diagChecks.push({
-                    name: 'stale_sessions',
-                    status: 'warn',
-                    details: `${activeSessions.length} active sessions (may include stale)`,
-                    fix: 'Run: cleo session gc',
-                });
-            }
-            else {
-                diagChecks.push({
-                    name: 'stale_sessions',
-                    status: 'pass',
-                    details: `${activeSessions.length} active session(s)`,
-                });
-            }
-        }
-        catch {
-            // skip
-        }
-    }
-    // Filter checks if specific ones requested
-    let filteredChecks = diagChecks;
-    if (opts?.checks && opts.checks.length > 0) {
-        filteredChecks = diagChecks.filter((c) => opts.checks.includes(c.name));
-    }
-    const passedCount = filteredChecks.filter((c) => c.status === 'pass').length;
-    const warnedCount = filteredChecks.filter((c) => c.status === 'warn').length;
-    const failedCount = filteredChecks.filter((c) => c.status === 'fail').length;
-    return {
-        timestamp: new Date().toISOString(),
-        checks: filteredChecks,
-        summary: {
-            total: filteredChecks.length,
-            passed: passedCount,
-            warned: warnedCount,
-            failed: failedCount,
-        },
-    };
-}
-async function fileSize(path) {
-    try {
-        return statSync(path).size;
-    }
-    catch {
-        return -1;
-    }
-}
-function mapCheckResult(cr) {
-    return {
-        check: cr.id,
-        status: cr.status === 'passed'
-            ? 'ok'
-            : cr.status === 'info'
-                ? 'ok'
-                : cr.status === 'warning'
-                    ? 'warning'
-                    : 'error',
-        message: cr.message,
-        ...(cr.fix ? { fix: cr.fix } : {}),
-    };
-}
-/** Map HookCheckResult[] from hooks.ts into a single DoctorCheck summary. */
-function mapHookResults(results) {
-    const missing = results.filter((r) => !r.installed);
-    const stale = results.filter((r) => r.installed && !r.current);
-    if (missing.length > 0) {
-        return {
-            check: 'git_hooks',
-            status: 'warning',
-            message: `Missing git hooks: ${missing.map((r) => r.hook).join(', ')}`,
-            details: { missing: missing.map((r) => r.hook), fix: 'cleo init --force' },
-        };
-    }
-    if (stale.length > 0) {
-        return {
-            check: 'git_hooks',
-            status: 'warning',
-            message: `Stale git hooks: ${stale.map((r) => r.hook).join(', ')}`,
-            details: { stale: stale.map((r) => r.hook), fix: 'cleo upgrade' },
-        };
-    }
-    return {
-        check: 'git_hooks',
-        status: 'ok',
-        message: `All ${results.length} managed git hooks installed and current`,
-    };
-}
-/** Map schema-management.ts CheckResult into a DoctorCheck. */
-function mapSchemaCheckResult(sr) {
-    if (sr.missing.length > 0) {
-        return {
-            check: 'global_schemas',
-            status: 'warning',
-            message: `Missing global schemas: ${sr.missing.join(', ')}`,
-            details: { missing: sr.missing, fix: 'cleo upgrade' },
-        };
-    }
-    if (sr.stale.length > 0) {
-        return {
-            check: 'global_schemas',
-            status: 'warning',
-            message: `Stale global schemas: ${sr.stale.join(', ')}`,
-            details: { stale: sr.stale, fix: 'cleo upgrade' },
-        };
-    }
-    return {
-        check: 'global_schemas',
-        status: 'ok',
-        message: `All ${sr.installed} global schemas installed and current`,
-    };
-}
-/**
- * Check contributor project dev channel availability and health.
- * No-op for non-contributor projects (ADR-029).
- *
- * Reports whether cleo-dev is on PATH and responsive. Does NOT mandate
- * using cleo-dev — agents should prefer it when healthy, fall back to
- * production cleo when the dev build is broken.
- */
-function checkContributorChannel(projectRoot) {
-    const configPath = join(projectRoot, '.cleo', 'config.json');
-    if (!existsSync(configPath)) {
-        return { check: 'contributor_channel', status: 'ok', message: 'Not a contributor project' };
-    }
-    let isContributor = false;
-    let devCli = 'cleo-dev';
-    try {
-        const config = JSON.parse(readFileSync(configPath, 'utf-8'));
-        isContributor = config.contributor?.isContributorProject === true;
-        devCli = config.contributor?.devCli ?? 'cleo-dev';
-    }
-    catch {
-        return { check: 'contributor_channel', status: 'ok', message: 'Not a contributor project' };
-    }
-    if (!isContributor) {
-        return { check: 'contributor_channel', status: 'ok', message: 'Not a contributor project' };
-    }
-    // Check that cleo-dev is on PATH
-    const pathDirs = (process.env['PATH'] ?? '').split(':').filter(Boolean);
-    const devCliOnPath = pathDirs.some((dir) => existsSync(join(dir, devCli)));
-    if (!devCliOnPath) {
-        return {
-            check: 'contributor_channel',
-            status: 'warning',
-            message: `Contributor project: '${devCli}' not on PATH. Using production cleo. Run ./install.sh --dev to enable dev channel.`,
-            fix: './install.sh --dev',
-        };
-    }
-    // Probe whether the dev CLI actually responds
-    try {
-        const version = execFileSync(devCli, ['--version'], { timeout: 5000 }).toString().trim();
-        return {
-            check: 'contributor_channel',
-            status: 'ok',
-            message: `Contributor project: '${devCli}' healthy (v${version}). Prefer dev channel for unreleased features.`,
-        };
-    }
-    catch {
-        return {
-            check: 'contributor_channel',
-            status: 'warning',
-            message: `Contributor project: '${devCli}' on PATH but not responding. Dev build may need rebuild (npm run build). Production cleo available as fallback.`,
-            fix: 'npm run build',
-        };
-    }
-}
-/**
- * Run adapter health checks for all discovered adapters and return doctor
- * check entries. Returns an empty array when no adapters are initialized
- * (adapters are optional — their absence is not an error).
- *
- * @param projectRoot - Absolute path to the project root
- * @returns Array of DoctorCheck entries, one per adapter (plus a summary if none found)
- */
-async function checkAdapterHealth(projectRoot) {
-    const results = [];
-    try {
-        const { AdapterManager } = await import('../adapters/index.js');
-        const { getPackageRoot } = await import('../scaffold.js');
-        // Prefer the caller-supplied projectRoot; fall back to the package root for
-        // adapter manifest discovery when projectRoot is not a package root itself.
-        const pkgRoot = projectRoot || getPackageRoot();
-        const manager = AdapterManager.getInstance(pkgRoot);
-        // Discover manifests (idempotent if already discovered)
-        manager.discover();
-        // Run health checks on any already-initialized adapters
-        const healthMap = await manager.healthCheckAll();
-        if (healthMap.size === 0) {
-            // No adapters initialized — adapters are optional, report as info
-            results.push({
-                check: 'adapter_health',
-                status: 'ok',
-                message: 'No adapters initialized (adapters are optional)',
-            });
-        }
-        else {
-            for (const [adapterId, status] of healthMap) {
-                results.push({
-                    check: `adapter_${adapterId.replace(/-/g, '_')}`,
-                    status: status.healthy ? 'ok' : 'warning',
-                    message: status.healthy
-                        ? `Adapter ${adapterId} (${status.provider}) healthy`
-                        : `Adapter ${adapterId} (${status.provider}) unhealthy`,
-                    ...(status.details && Object.keys(status.details).length > 0
-                        ? { details: status.details }
-                        : {}),
-                    ...(!status.healthy ? { fix: `cleo adapter health ${adapterId}` } : {}),
-                });
-            }
-        }
-    }
-    catch {
-        // Adapter system is non-critical — never let it block the doctor report
-        results.push({
-            check: 'adapter_health',
-            status: 'warning',
-            message: 'Adapter health check unavailable (adapter system not reachable)',
-        });
-    }
-    return results;
-}
-/**
- * Run comprehensive doctor diagnostics combining dependency checks,
- * directory checks, data file checks, gitignore checks, and environment info.
- * @task T4795
- */
-export async function coreDoctorReport(projectRoot) {
-    const checks = [];
-    // 1. Dependency registry — single source of truth for all external deps (T507)
-    const depReport = await checkAllDependencies();
-    // Wire individual dependency results into the doctor check list so existing
-    // consumers (CLI renderers, tests) see familiar DoctorCheck entries.
-    for (const dep of depReport.results) {
-        const isRequired = dep.category === 'required';
-        const status = dep.healthy
-            ? dep.installed
-                ? 'ok'
-                : 'warning' // optional/feature not installed — warn, not error
-            : isRequired
-                ? 'error'
-                : 'warning';
-        const message = dep.installed
-            ? `${dep.name}${dep.version ? ` ${dep.version}` : ''}${dep.location ? ` (${dep.location})` : ''}`
-            : (dep.error ?? `${dep.name} not found`);
-        checks.push({
-            check: `dep_${dep.name.replace(/-/g, '_')}`,
-            status,
-            message,
-            ...(dep.suggestedFix ? { fix: dep.suggestedFix } : {}),
-        });
-    }
-    // 2. Check CLEO directories
-    const cleoDir = join(projectRoot, '.cleo');
-    const dirExists = existsSync(cleoDir);
-    checks.push({
-        check: 'project_dir',
-        status: dirExists ? 'ok' : 'error',
-        message: dirExists
-            ? `Project dir: ${cleoDir}`
-            : `Project dir not found: ${cleoDir}. Run: cleo init`,
-    });
-    // 3. Check data files — SQLite is the primary store (ADR-006)
-    const dbPath = join(cleoDir, 'tasks.db');
-    const dbExists = existsSync(dbPath);
-    const dbSize = await fileSize(dbPath);
-    checks.push({
-        check: 'tasks_db',
-        status: dbExists ? 'ok' : 'error',
-        message: dbExists ? `tasks.db: ${dbSize} bytes` : `tasks.db not found. Run: cleo init`,
-    });
-    if (dbExists) {
-        try {
-            const accessor = await getAccessor(projectRoot);
-            const taskCount = await accessor.countTasks();
-            const schemaVersion = (await accessor.getMetaValue('schemaVersion')) ?? 'unknown';
-            checks.push({
-                check: 'tasks_db_data',
-                status: 'ok',
-                message: `${taskCount} tasks, schema v${schemaVersion}`,
-                details: { taskCount, schemaVersion },
-            });
-        }
-        catch {
-            checks.push({
-                check: 'tasks_db_data',
-                status: 'error',
-                message: 'Failed to read tasks from SQLite database',
-            });
-        }
-        const auditLogCheck = checkAuditLogAvailability(dbPath);
-        checks.push({
-            check: 'audit_log',
-            status: auditLogCheck.status === 'pass'
-                ? 'ok'
-                : auditLogCheck.status === 'warn'
-                    ? 'warning'
-                    : 'error',
-            message: auditLogCheck.message ?? 'audit_log availability check completed',
-            ...(auditLogCheck.status === 'fail' ? { fix: 'Run: cleo upgrade' } : {}),
-        });
-        // SQLite integrity check
-        try {
-            const { getNativeDb, getDb: getDbInit } = await import('../store/sqlite.js');
-            // Ensure the DB is initialized so getNativeDb() returns a valid handle
-            await getDbInit(projectRoot);
-            const nativeDb = getNativeDb();
-            if (nativeDb) {
-                const result = nativeDb.prepare('PRAGMA integrity_check').get();
-                const integrityOk = result?.integrity_check === 'ok';
-                checks.push({
-                    check: 'sqlite_integrity',
-                    status: integrityOk ? 'ok' : 'warning',
-                    message: integrityOk
-                        ? 'SQLite integrity check passed'
-                        : 'SQLite integrity check reported issues',
-                    ...(integrityOk ? {} : { fix: 'Run: cleo upgrade' }),
-                });
-            }
-        }
-        catch {
-            // SQLite integrity check is best-effort
-        }
-    }
-    const configPath = join(cleoDir, 'config.json');
-    const configExists = existsSync(configPath);
-    checks.push({
-        check: 'config_file',
-        status: configExists ? 'ok' : 'warning',
-        message: configExists ? 'config.json present' : 'config.json not found (using defaults)',
-    });
-    // Check for stale JSON files that should have been cleaned up after migration
-    const staleJsonFiles = STALE_JSON_FILES.filter((f) => existsSync(join(cleoDir, f)));
-    if (dbExists && staleJsonFiles.length > 0) {
-        checks.push({
-            check: 'stale_json',
-            status: 'warning',
-            message: `Stale JSON files found alongside tasks.db: ${staleJsonFiles.join(', ')}. Run: cleo upgrade`,
-            details: { files: staleJsonFiles },
-        });
-    }
-    const logPath = resolveStructuredLogPath(cleoDir);
-    const logExists = existsSync(logPath);
-    checks.push({
-        check: 'log_file',
-        status: logExists ? 'ok' : 'warning',
-        message: logExists
-            ? `structured log present: ${logPath}`
-            : `structured log not found: ${logPath}`,
-    });
-    // 4. Check root .gitignore for .cleo/ blocking
-    const rootGitignorePath = join(projectRoot, '.gitignore');
-    if (existsSync(rootGitignorePath)) {
-        try {
-            const gitignoreContent = readFileSync(rootGitignorePath, 'utf-8');
-            const blockingLines = gitignoreContent.split('\n').filter((line) => {
-                const trimmed = line.trim();
-                if (trimmed.startsWith('#') || trimmed === '')
-                    return false;
-                return /^\/?\.cleo\/?(\*)?$/.test(trimmed);
-            });
-            checks.push({
-                check: 'root_gitignore',
-                status: blockingLines.length > 0 ? 'warning' : 'ok',
-                message: blockingLines.length > 0
-                    ? `.cleo/ is ignored in root .gitignore. Run 'cleo init' to fix.`
-                    : 'Root .gitignore does not block .cleo/',
-                ...(blockingLines.length > 0 ? { details: { blockingLines } } : {}),
-            });
-        }
-        catch {
-            // Ignore read errors for gitignore check
-        }
-    }
-    // 5. Gitignore integrity, vital files, legacy paths (delegated to core checks)
-    checks.push(mapCheckResult(checkCleoGitignore(projectRoot)));
-    checks.push(mapCheckResult(checkVitalFilesTracked(projectRoot)));
-    checks.push(mapCheckResult(checkCoreFilesNotIgnored(projectRoot)));
-    checks.push(mapCheckResult(checkLegacyAgentOutputs(projectRoot)));
-    // 5b. Isolated .cleo/.git checkpoint repo check (T4872)
-    const cleoGitHeadExists = existsSync(join(cleoDir, '.git', 'HEAD'));
-    checks.push({
-        check: 'cleo_git_repo',
-        status: cleoGitHeadExists ? 'ok' : 'warning',
-        message: cleoGitHeadExists
-            ? '.cleo/.git isolated checkpoint repo exists'
-            : '.cleo/.git not found — run: cleo init',
-    });
-    // 5c. Global scaffold checks: home, templates, schemas
-    checks.push(mapCheckResult(checkGlobalHome()));
-    checks.push(mapCheckResult(checkGlobalTemplates()));
-    checks.push(mapSchemaCheckResult(checkGlobalSchemas()));
-    // 5d. Project scaffold checks: log dir, structure, git hooks, project-info, injection
-    checks.push(mapCheckResult(checkLogDir(projectRoot)));
-    const hookResults = await checkGitHooks(projectRoot);
-    checks.push(mapHookResults(hookResults));
-    checks.push(mapCheckResult(checkProjectInfo(projectRoot)));
-    // Project context check
-    checks.push(mapCheckResult(checkProjectContext(projectRoot)));
-    checks.push(mapCheckResult(checkInjection(projectRoot)));
-    // Contributor project channel check (ADR-029)
-    checks.push(checkContributorChannel(projectRoot));
-    // Agent definition presence check
-    const agentDefPath = join(getAgentsHome(), 'agents', 'cleo-subagent');
-    checks.push({
-        check: 'agent_definition',
-        status: existsSync(agentDefPath) ? 'ok' : 'warning',
-        message: existsSync(agentDefPath)
-            ? 'cleo-subagent agent definition installed'
-            : 'cleo-subagent not found — run: cleo init',
-        ...(existsSync(agentDefPath) ? {} : { fix: 'cleo init' }),
-    });
-    // 5e. brain.db and memory-bridge checks (T511 — consolidate startup checks into doctor)
-    // These are checked in startupHealthCheck() as warnings. The doctor report is the
-    // comprehensive view so it must include them too, making startupHealthCheck() a subset.
-    const brainDbCheckResult = checkBrainDb(projectRoot);
-    checks.push({
-        check: 'brain_db',
-        status: brainDbCheckResult.status === 'passed'
-            ? 'ok'
-            : brainDbCheckResult.status === 'warning'
-                ? 'warning'
-                : 'error',
-        message: brainDbCheckResult.message,
-        ...(brainDbCheckResult.fix ? { fix: brainDbCheckResult.fix } : {}),
-    });
-    const memBridgeCheckResult = checkMemoryBridge(projectRoot);
-    checks.push({
-        check: 'memory_bridge',
-        status: memBridgeCheckResult.status === 'passed' ? 'ok' : 'warning',
-        message: memBridgeCheckResult.message,
-        ...(memBridgeCheckResult.fix ? { fix: memBridgeCheckResult.fix } : {}),
-    });
-    const nexusBridgeCheckResult = checkNexusBridge(projectRoot);
-    checks.push({
-        check: 'nexus_bridge',
-        status: nexusBridgeCheckResult.status === 'passed' ? 'ok' : 'warning',
-        message: nexusBridgeCheckResult.message,
-        ...(nexusBridgeCheckResult.fix ? { fix: nexusBridgeCheckResult.fix } : {}),
-    });
-    // 5f. Adapter health checks (T511 — wire adapter health into doctor)
-    // `cleo adapter health` was previously isolated from the doctor report.
-    // The doctor is the comprehensive diagnostic view so adapter health belongs here.
-    const adapterChecks = await checkAdapterHealth(projectRoot);
-    for (const ac of adapterChecks) {
-        checks.push(ac);
-    }
-    // 6a. GitHub templates presence (informational only — non-critical)
-    const gitDir = join(projectRoot, '.git');
-    const gitHubTemplatesDir = join(projectRoot, '.github', 'ISSUE_TEMPLATE');
-    if (existsSync(gitDir)) {
-        // Only check when this is a git repo
-        checks.push({
-            check: 'github_templates',
-            status: existsSync(gitHubTemplatesDir) ? 'ok' : 'warning',
-            message: existsSync(gitHubTemplatesDir)
-                ? '.github/ISSUE_TEMPLATE/ present'
-                : '.github/ISSUE_TEMPLATE/ not found — run: cleo init or cleo upgrade',
-            ...(existsSync(gitHubTemplatesDir) ? {} : { fix: 'cleo init' }),
-        });
-    }
-    // 6. Environment - Node.js version validation
-    checks.push(mapCheckResult(checkNodeVersion()));
-    const sysInfo = getSystemInfo();
-    checks.push({
-        check: 'platform',
-        status: 'ok',
-        message: `${sysInfo.osType} ${sysInfo.osRelease} (${sysInfo.platform}/${sysInfo.arch}), Node ${sysInfo.nodeVersion}`,
-        details: {
-            platform: sysInfo.platform,
-            arch: sysInfo.arch,
-            osType: sysInfo.osType,
-            osRelease: sysInfo.osRelease,
-            nodeVersion: sysInfo.nodeVersion,
-            totalMemory: sysInfo.totalMemory,
-            freeMemory: sysInfo.freeMemory,
-            hostname: sysInfo.hostname,
-        },
-    });
-    // Summary
-    const errorCount = checks.filter((c) => c.status === 'error').length;
-    const warningCount = checks.filter((c) => c.status === 'warning').length;
-    const healthy = errorCount === 0;
-    return { healthy, errors: errorCount, warnings: warningCount, checks, dependencies: depReport };
-}
-/**
- * Run auto-fix for failed doctor checks by calling the corresponding ensure* functions.
- * Returns a list of fix results for each attempted repair.
- */
-export async function runDoctorFixes(projectRoot) {
-    const { ensureCleoStructure, ensureGitignore, ensureConfig, ensureProjectInfo, ensureProjectContext, ensureCleoGitRepo, ensureGlobalHome, ensureGlobalTemplates, } = await import('../scaffold.js');
-    const { ensureGitHooks } = await import('../hooks.js');
-    const { ensureGlobalSchemas } = await import('../schema-management.js');
-    const { ensureInjection } = await import('../injection.js');
-    const report = await coreDoctorReport(projectRoot);
-    const failedChecks = report.checks.filter((c) => c.status !== 'ok');
-    const results = [];
-    // Map check names to their fix functions
-    const fixMap = {
-        project_dir: async () => {
-            const r = await ensureCleoStructure(projectRoot);
-            return {
-                check: 'project_dir',
-                action: r.action === 'skipped' ? 'skipped' : 'fixed',
-                message: r.details ?? r.action,
-            };
-        },
-        cleo_gitignore: async () => {
-            const r = await ensureGitignore(projectRoot);
-            return {
-                check: 'cleo_gitignore',
-                action: r.action === 'skipped' ? 'skipped' : 'fixed',
-                message: r.details ?? r.action,
-            };
-        },
-        config_file: async () => {
-            const r = await ensureConfig(projectRoot);
-            return {
-                check: 'config_file',
-                action: r.action === 'skipped' ? 'skipped' : 'fixed',
-                message: r.details ?? r.action,
-            };
-        },
-        cleo_project_info: async () => {
-            const r = await ensureProjectInfo(projectRoot, { force: true });
-            return {
-                check: 'cleo_project_info',
-                action: r.action === 'skipped' ? 'skipped' : 'fixed',
-                message: r.details ?? r.action,
-            };
-        },
-        cleo_project_context: async () => {
-            const r = await ensureProjectContext(projectRoot, { force: true });
-            return {
-                check: 'cleo_project_context',
-                action: r.action === 'skipped' ? 'skipped' : 'fixed',
-                message: r.details ?? r.action,
-            };
-        },
-        cleo_git_repo: async () => {
-            const r = await ensureCleoGitRepo(projectRoot);
-            return {
-                check: 'cleo_git_repo',
-                action: r.action === 'skipped' ? 'skipped' : 'fixed',
-                message: r.details ?? r.action,
-            };
-        },
-        contributor_channel: async () => {
-            const { ensureContributorMcp: ensureContributorDev } = await import('../scaffold.js');
-            const r = await ensureContributorDev(projectRoot);
-            return {
-                check: 'contributor_channel',
-                action: r.action === 'skipped' ? 'skipped' : 'fixed',
-                message: r.details ?? r.action,
-            };
-        },
-        git_hooks: async () => {
-            const r = await ensureGitHooks(projectRoot, { force: true });
-            return {
-                check: 'git_hooks',
-                action: r.action === 'skipped' ? 'skipped' : 'fixed',
-                message: r.details ?? r.action,
-            };
-        },
-        global_schemas: async () => {
-            const r = ensureGlobalSchemas();
-            const msg = `Installed ${r.installed}, updated ${r.updated} of ${r.total} schemas`;
-            return {
-                check: 'global_schemas',
-                action: r.installed + r.updated > 0 ? 'fixed' : 'skipped',
-                message: msg,
-            };
-        },
-        injection_health: async () => {
-            const r = await ensureInjection(projectRoot);
-            return {
-                check: 'injection_health',
-                action: r.action === 'skipped' ? 'skipped' : 'fixed',
-                message: r.details ?? r.action,
-            };
-        },
-        cleo_structure: async () => {
-            const r = await ensureCleoStructure(projectRoot);
-            return {
-                check: 'cleo_structure',
-                action: r.action === 'skipped' ? 'skipped' : 'fixed',
-                message: r.details ?? r.action,
-            };
-        },
-        global_home: async () => {
-            const r = await ensureGlobalHome();
-            return {
-                check: 'global_home',
-                action: r.action === 'skipped' ? 'skipped' : 'fixed',
-                message: r.details ?? r.action,
-            };
-        },
-        global_templates: async () => {
-            const r = await ensureGlobalTemplates();
-            return {
-                check: 'global_templates',
-                action: r.action === 'skipped' ? 'skipped' : 'fixed',
-                message: r.details ?? r.action,
-            };
-        },
-        log_dir: async () => {
-            // Log dir is part of REQUIRED_CLEO_SUBDIRS, so ensureCleoStructure fixes it
-            const r = await ensureCleoStructure(projectRoot);
-            return {
-                check: 'log_dir',
-                action: r.action === 'skipped' ? 'skipped' : 'fixed',
-                message: r.details ?? r.action,
-            };
-        },
-    };
-    for (const check of failedChecks) {
-        const fixer = fixMap[check.check];
-        if (!fixer)
-            continue;
-        try {
-            const result = await fixer();
-            results.push(result);
-        }
-        catch (err) {
-            results.push({
-                check: check.check,
-                action: 'failed',
-                message: err instanceof Error ? err.message : String(err),
-            });
-        }
-    }
-    return results;
-}
-/**
- * Unified startup health check for CLI entry points.
- *
- * This is the single entry point for startup diagnostics. It follows a
- * three-phase approach:
- *
- * Phase 1: Global scaffold (~/.cleo/) — always auto-repaired.
- *   The global home is CLEO infrastructure, not project data. It is safe
- *   to create/repair unconditionally on every startup.
- *
- * Phase 2: Project detection — determines if this is an initialized project.
- *   Uses isProjectInitialized() from paths.ts as the SSoT for detection.
- *
- * Phase 3: Project health — lightweight checks on the project scaffold.
- *   If the project is initialized, runs check* functions to detect drift.
- *   Auto-repairs safe items (missing subdirs via ensureCleoStructure).
- *   Flags items requiring full upgrade (missing DB, config issues).
- *
- * Design principles:
- *   - SSoT: All checks delegate to scaffold.ts check* functions
- *   - DRY: No duplicated health-check logic
- *   - SRP: This function only diagnoses and does safe auto-repair
- *   - Graceful: Never throws. All errors are captured as check results.
- *   - Logged: Returns structured results for the caller to log via pino
- *
- * @param projectRoot - Absolute path to the project root (defaults to cwd)
- */
-export async function startupHealthCheck(projectRoot) {
-    const root = projectRoot ?? process.cwd();
-    const system = getSystemInfo();
-    const checks = [];
-    const failures = [];
-    let globalHealthy = true;
-    let projectHealthy = true;
-    // ── Phase 1: Global scaffold (~/.cleo/) ──────────────────────────
-    // Always auto-repair. This is infrastructure, not project data.
-    try {
-        // Check current state first (read-only)
-        const globalHomeCheck = checkGlobalHome();
-        const globalTemplateCheck = checkGlobalTemplates();
-        const globalSchemaCheck = checkGlobalSchemas();
-        const globalNeedsRepair = globalHomeCheck.status !== 'passed' ||
-            globalTemplateCheck.status !== 'passed' ||
-            !globalSchemaCheck.ok;
-        if (globalNeedsRepair) {
-            // Auto-repair home and templates via ensureGlobalScaffold (idempotent, safe)
-            const scaffoldResult = await ensureGlobalScaffold();
-            checks.push({
-                check: 'global_home',
-                status: 'pass',
-                message: scaffoldResult.home.action === 'skipped'
-                    ? 'Global home already current'
-                    : `Global home ${scaffoldResult.home.action}: ${scaffoldResult.home.details ?? ''}`,
-                repaired: scaffoldResult.home.action !== 'skipped',
-            });
-            // Schemas are read at runtime from the package path; only copy if stale
-            if (!globalSchemaCheck.ok) {
-                const { ensureGlobalSchemas } = await import('../schema-management.js');
-                const schemaResult = ensureGlobalSchemas();
-                checks.push({
-                    check: 'global_schemas',
-                    status: 'pass',
-                    message: `Schemas: ${schemaResult.installed} installed, ${schemaResult.updated} updated of ${schemaResult.total}`,
-                    repaired: schemaResult.installed > 0 || schemaResult.updated > 0,
-                });
-            }
-            else {
-                checks.push({
-                    check: 'global_schemas',
-                    status: 'pass',
-                    message: `All ${globalSchemaCheck.installed} schemas current`,
-                });
-            }
-            checks.push({
-                check: 'global_templates',
-                status: 'pass',
-                message: scaffoldResult.templates.action === 'skipped'
-                    ? 'Templates already current'
-                    : `Templates ${scaffoldResult.templates.action}: ${scaffoldResult.templates.details ?? ''}`,
-                repaired: scaffoldResult.templates.action !== 'skipped',
-            });
-        }
-        else {
-            checks.push({ check: 'global_home', status: 'pass', message: 'Global home healthy' }, {
-                check: 'global_schemas',
-                status: 'pass',
-                message: `All ${globalSchemaCheck.installed} schemas current`,
-            }, { check: 'global_templates', status: 'pass', message: 'Templates present' });
-        }
-    }
-    catch (err) {
-        // Global scaffold failure is non-fatal but degrades the system
-        globalHealthy = false;
-        const msg = err instanceof Error ? err.message : String(err);
-        const failCheck = {
-            check: 'global_scaffold',
-            status: 'fail',
-            message: `Global scaffold repair failed: ${msg}`,
-        };
-        checks.push(failCheck);
-        failures.push(failCheck);
-    }
-    // ── Phase 2: Project detection ───────────────────────────────────
-    if (!isProjectInitialized(root)) {
-        checks.push({
-            check: 'project_initialized',
-            status: 'fail',
-            message: 'Project not initialized (.cleo/ or tasks.db missing)',
-        });
-        return {
-            state: 'needs_init',
-            globalHealthy,
-            projectHealthy: false,
-            checks,
-            failures,
-            system,
-        };
-    }
-    checks.push({
-        check: 'project_initialized',
-        status: 'pass',
-        message: 'Project initialized',
-    });
-    // ── Phase 3: Lightweight project health checks ───────────────────
-    // Run read-only check* functions to detect drift. Only auto-repair
-    // safe structural items (missing subdirs). Flag everything else.
-    const structureCheck = checkCleoStructure(root);
-    const configCheck = checkConfig(root);
-    const dbCheck = checkSqliteDb(root);
-    const logDirCheck = checkLogDir(root);
-    // Structure: auto-repairable (missing subdirs are safe to create)
-    if (structureCheck.status !== 'passed') {
-        try {
-            await ensureCleoStructure(root);
-            checks.push({
-                check: 'cleo_structure',
-                status: 'pass',
-                message: 'Structure repaired: missing subdirectories created',
-                repaired: true,
-            });
-        }
-        catch (err) {
-            projectHealthy = false;
-            const msg = err instanceof Error ? err.message : String(err);
-            const failCheck = {
-                check: 'cleo_structure',
-                status: 'fail',
-                message: `Structure repair failed: ${msg}`,
-            };
-            checks.push(failCheck);
-            failures.push(failCheck);
-        }
-    }
-    else {
-        checks.push({ check: 'cleo_structure', status: 'pass', message: 'Structure healthy' });
-    }
-    // Config: NOT auto-repairable on startup (requires explicit init/upgrade)
-    if (configCheck.status === 'failed') {
-        projectHealthy = false;
-        const failCheck = {
-            check: 'config',
-            status: 'fail',
-            message: configCheck.message,
-        };
-        checks.push(failCheck);
-        failures.push(failCheck);
-    }
-    else {
-        checks.push({
-            check: 'config',
-            status: configCheck.status === 'warning' ? 'warn' : 'pass',
-            message: configCheck.message,
-        });
-    }
-    // SQLite DB: NOT auto-repairable on startup
-    if (dbCheck.status === 'failed') {
-        projectHealthy = false;
-        const failCheck = {
-            check: 'sqlite_db',
-            status: 'fail',
-            message: dbCheck.message,
-        };
-        checks.push(failCheck);
-        failures.push(failCheck);
-    }
-    else {
-        checks.push({
-            check: 'sqlite_db',
-            status: dbCheck.status === 'warning' ? 'warn' : 'pass',
-            message: dbCheck.message,
-        });
-    }
-    // Log directory: auto-repairable (part of ensureCleoStructure above,
-    // but verify explicitly since it was just added to REQUIRED_CLEO_SUBDIRS)
-    if (logDirCheck.status !== 'passed') {
-        // ensureCleoStructure above should have created it, but check again
-        checks.push({
-            check: 'log_dir',
-            status: 'warn',
-            message: logDirCheck.message,
-        });
-    }
-    else {
-        checks.push({ check: 'log_dir', status: 'pass', message: 'Log directory present' });
-    }
-    // Brain.db: warning-level check (not a startup failure)
-    const brainDbCheck = checkBrainDb(root);
-    checks.push({
-        check: 'brain_db',
-        status: brainDbCheck.status === 'passed' ? 'pass' : 'warn',
-        message: brainDbCheck.message,
-    });
-    // Memory bridge: info-level check
-    const memBridgeCheck = checkMemoryBridge(root);
-    checks.push({
-        check: 'memory_bridge',
-        status: memBridgeCheck.status === 'passed' ? 'pass' : 'warn',
-        message: memBridgeCheck.message,
-    });
-    // Nexus bridge: info-level check (T552)
-    const nexusBridgeCheck = checkNexusBridge(root);
-    checks.push({
-        check: 'nexus_bridge',
-        status: nexusBridgeCheck.status === 'passed' ? 'pass' : 'warn',
-        message: nexusBridgeCheck.message,
-    });
-    // NEXUS auto-registration (best-effort, never blocks startup)
-    try {
-        const { nexusReconcile } = await import('../nexus/registry.js');
-        await nexusReconcile(root);
-        checks.push({
-            check: 'nexus_registration',
-            status: 'pass',
-            message: 'NEXUS registry reconciled',
-        });
-    }
-    catch {
-        checks.push({
-            check: 'nexus_registration',
-            status: 'warn',
-            message: 'NEXUS reconciliation skipped (non-fatal)',
-        });
-    }
-    // Determine overall state
-    const hasFailures = failures.length > 0;
-    const state = hasFailures && !projectHealthy ? 'needs_upgrade' : 'healthy';
-    return {
-        state,
-        globalHealthy,
-        projectHealthy,
-        checks,
-        failures,
-        system,
-    };
-}
-//# sourceMappingURL=health.js.map