@cleocode/core 2026.4.42 → 2026.4.43

package/dist/upgrade.js

@@ -1,1371 +0,0 @@
-/**
- * Core upgrade logic - unified project maintenance.
- *
- * Handles:
- *   1. Storage engine migration (JSON → SQLite)
- *   2. Schema version upgrades
- *   3. Structural repairs (checksums, missing fields)
- *   4. Global ~/.cleo data migration
- *
- * CLI delegates here (shared-core pattern).
- *
- * @task T4699
- * @epic T4454
- */
-import { copyFileSync, existsSync, mkdirSync, readdirSync, readFileSync, writeFileSync, } from 'node:fs';
-import { join } from 'node:path';
-import { ensureGitHooks } from './hooks.js';
-import { initAgentDefinition, initCoreSkills, initNexusRegistration, installGitHubTemplates, } from './init.js';
-import { ensureInjection } from './injection.js';
-import { detectLegacyAgentOutputs, migrateAgentOutputs } from './migration/agent-outputs.js';
-import { getCleoDirAbsolute, getCleoHome, getProjectRoot } from './paths.js';
-import { ensureCleoGitRepo, ensureCleoStructure, ensureConfig, ensureGitignore, ensureProjectContext, ensureProjectInfo, ensureSqliteDb, removeCleoFromRootGitignore, } from './scaffold.js';
-import { cleanProjectSchemas, ensureGlobalSchemas } from './schema-management.js';
-import { acquireLock, forceCheckpointBeforeOperation } from './store/index.js';
-import { checkStorageMigration } from './system/storage-preflight.js';
-/**
- * Run a full upgrade pass on the project .cleo/ directory.
- *
- * Steps:
- *   1. Pre-flight storage check (JSON → SQLite)
- *   2. If migration needed and not dry-run, run auto-migration with backup
- *   3. Schema version checks on JSON files
- *   4. Structural repairs (checksums, missing fields)
- *
- * @param options.dryRun  Preview changes without applying
- * @param options.includeGlobal  Also check global ~/.cleo
- * @param options.autoMigrate  Auto-migrate storage if needed (default: true)
- * @param options.forceDetect  Force re-detection of project type (ignore staleness)
- * @param options.mapCodebase  Run full codebase analysis and store to brain.db
- * @param options.projectName  Update project name in project-info and nexus
- * @param options.cwd  Project directory override
- */
-export async function runUpgrade(options = {}) {
-    const isDryRun = options.dryRun ?? false;
-    const autoMigrate = options.autoMigrate ?? true;
-    const actions = [];
-    const errors = [];
-    let storageMigrationResult;
-    // ── Step 1: Pre-flight storage check ──────────────────────────────
-    let preflight;
-    try {
-        preflight = checkStorageMigration(options.cwd);
-    }
-    catch (err) {
-        actions.push({
-            action: 'storage_preflight',
-            status: 'error',
-            details: `Pre-flight check failed: ${String(err)}`,
-        });
-        return {
-            success: false,
-            upToDate: false,
-            dryRun: isDryRun,
-            actions,
-            applied: 0,
-            errors: [String(err)],
-        };
-    }
-    // Determine what actions are actually needed
-    const cleoDir = getCleoDirAbsolute(options.cwd);
-    const dbPath = join(cleoDir, 'tasks.db');
-    const dbExists = existsSync(dbPath);
-    const legacyRecordCount = preflight.details.todoJsonTaskCount +
-        preflight.details.archiveJsonTaskCount +
-        preflight.details.sessionsJsonCount;
-    // Migration needed only if: no DB exists AND JSON has data
-    const needsMigration = !dbExists && legacyRecordCount > 0;
-    // Cleanup needed if: DB exists AND stale JSON files exist
-    const needsCleanup = dbExists && preflight.migrationNeeded;
-    if (needsMigration) {
-        if (isDryRun) {
-            actions.push({
-                action: 'storage_migration',
-                status: 'preview',
-                details: preflight.summary,
-                fix: preflight.fix ?? undefined,
-            });
-        }
-        else if (autoMigrate) {
-            // Auto-migrate with SAFE backup-first approach.
-            // CRITICAL: Never delete tasks.db without a verified backup.
-            // Previous implementation (pre-2026.2.6) had a destructive bug
-            // that unconditionally deleted tasks.db before migration, causing
-            // total data loss of 4,295 tasks. This fix follows the project's
-            // atomic operation pattern: backup → migrate to temp → validate → rename.
-            let migrationLock = null;
-            try {
-                // CRITICAL: Acquire migration lock before any destructive operations
-                const cleoDir = getCleoDirAbsolute(options.cwd);
-                const dbPath = join(cleoDir, 'tasks.db');
-                try {
-                    migrationLock = await acquireLock(dbPath, { stale: 30_000, retries: 0 });
-                }
-                catch {
-                    // Lock acquisition failed — another migration is in progress
-                    actions.push({
-                        action: 'storage_migration',
-                        status: 'error',
-                        details: 'Cannot acquire migration lock: Another migration is currently in progress',
-                        fix: 'Wait for the other migration to complete, then retry.',
-                    });
-                    errors.push('Cannot acquire migration lock: Another migration is currently in progress');
-                    return { success: false, upToDate: false, dryRun: isDryRun, actions, applied: 0, errors };
-                }
-                // CRITICAL: Force checkpoint before ANY destructive operations
-                await forceCheckpointBeforeOperation('storage-migration', options.cwd);
-                // Initialize migration state tracking
-                const { MigrationLogger } = await import('./migration/logger.js');
-                const { createMigrationState, updateMigrationPhase, updateMigrationProgress, addMigrationWarning, completeMigration, failMigration, } = await import('./migration/state.js');
-                const logger = new MigrationLogger(cleoDir);
-                await createMigrationState(cleoDir, {
-                    todoJson: { path: join(cleoDir, 'todo.json'), checksum: '' },
-                    sessionsJson: { path: join(cleoDir, 'sessions.json'), checksum: '' },
-                    archiveJson: { path: join(cleoDir, 'todo-archive.json'), checksum: '' },
-                });
-                await updateMigrationPhase(cleoDir, 'backup');
-                logger.info('init', 'start', 'Migration state initialized');
-                const dbBackupPath = join(cleoDir, 'backups', 'safety', `tasks.db.pre-migration.${Date.now()}`);
-                const dbTempPath = join(cleoDir, 'tasks.db.migrating');
-                // Step 1: Backup existing tasks.db if it exists (NEVER delete without backup)
-                if (existsSync(dbPath)) {
-                    const backupDir = join(cleoDir, 'backups', 'safety');
-                    if (!existsSync(backupDir)) {
-                        mkdirSync(backupDir, { recursive: true });
-                    }
-                    copyFileSync(dbPath, dbBackupPath);
-                    // Verify backup integrity: SHA-256 checksum + SQLite open check
-                    const { createHash } = await import('node:crypto');
-                    const origChecksum = createHash('sha256').update(readFileSync(dbPath)).digest('hex');
-                    const backupChecksum = createHash('sha256')
-                        .update(readFileSync(dbBackupPath))
-                        .digest('hex');
-                    if (origChecksum !== backupChecksum) {
-                        throw new Error(`Backup verification failed: checksum mismatch. ` +
-                            `Aborting migration to prevent data loss.`);
-                    }
-                    const { validateSqliteDatabase } = await import('./store/atomic.js');
-                    const backupIsValid = await validateSqliteDatabase(dbBackupPath);
-                    if (!backupIsValid) {
-                        throw new Error(`Backup verification failed: backup is not a valid SQLite database. ` +
-                            `Aborting migration to prevent data loss.`);
-                    }
-                    logger.info('backup', 'verified', 'Backup integrity verified', {
-                        checksum: origChecksum,
-                    });
-                }
-                // Step 2: Remove temp DB if leftover from a previous failed attempt
-                if (existsSync(dbTempPath)) {
-                    const { unlinkSync } = await import('node:fs');
-                    unlinkSync(dbTempPath);
-                }
-                // Step 3: Save config backup in case we need to restore after failure
-                const configPath = join(cleoDir, 'config.json');
-                let configBackup = null;
-                if (existsSync(configPath)) {
-                    configBackup = readFileSync(configPath, 'utf-8');
-                }
-                // Step 4: Close any existing DB connection before migration
-                const { resetDbState } = await import('./store/sqlite.js');
-                resetDbState();
-                // Step 5 removed — do not delete original DB; atomic rename preserves it until new DB is verified
-                // Step 6: Migrate JSON → temp DB, then atomically rename into place
-                await updateMigrationPhase(cleoDir, 'import');
-                const { migrateJsonToSqliteAtomic } = await import('./store/migration-sqlite.js');
-                const { atomicDatabaseMigration, validateSqliteDatabase: validateDb } = await import('./store/atomic.js');
-                const result = await migrateJsonToSqliteAtomic(options.cwd, dbTempPath, logger);
-                // Step 6b: Atomically rename temp DB into place (only if migration succeeded)
-                if (result.success) {
-                    const atomicResult = await atomicDatabaseMigration(dbPath, dbTempPath, validateDb);
-                    if (!atomicResult.success) {
-                        throw new Error(`Atomic rename failed: ${atomicResult.error}. Original database preserved.`);
-                    }
-                }
-                // Update progress
-                await updateMigrationProgress(cleoDir, {
-                    tasksImported: result.tasksImported,
-                    archivedImported: result.archivedImported,
-                    sessionsImported: result.sessionsImported,
-                });
-                // Log any warnings
-                for (const warning of result.warnings) {
-                    await addMigrationWarning(cleoDir, warning);
-                    logger.warn('import', 'warning', warning);
-                }
-                // Step 7: Close db connection so config update doesn't conflict
-                resetDbState();
-                // Step 8: Validate migration result before committing
-                if (result.success) {
-                    // Verify the new DB has reasonable data
-                    const totalImported = result.tasksImported + result.archivedImported;
-                    if (totalImported === 0 && existsSync(dbBackupPath)) {
-                        // Migration "succeeded" but imported nothing — likely a bug.
-                        // Restore from backup to prevent silent data loss.
-                        copyFileSync(dbBackupPath, dbPath);
-                        if (configBackup) {
-                            writeFileSync(configPath, configBackup);
-                        }
-                        actions.push({
-                            action: 'storage_migration',
-                            status: 'error',
-                            details: 'Migration imported 0 tasks despite existing data. Restored from backup.',
-                            fix: 'Run `cleo upgrade --dry-run` to diagnose, then retry.',
-                        });
-                        errors.push('Migration imported 0 tasks — restored from backup to prevent data loss');
-                    }
-                    else {
-                        // Migration successful with data — update config to sqlite
-                        let config = {};
-                        if (existsSync(configPath)) {
-                            try {
-                                config = JSON.parse(readFileSync(configPath, 'utf-8'));
-                            }
-                            catch {
-                                // Start fresh config
-                            }
-                        }
-                        if (!config.storage || typeof config.storage !== 'object') {
-                            config.storage = {};
-                        }
-                        config.storage.engine = 'sqlite';
-                        writeFileSync(configPath, JSON.stringify(config, null, 2));
-                        actions.push({
-                            action: 'storage_migration',
-                            status: 'applied',
-                            details: `Migrated to SQLite: ${result.tasksImported} tasks, ` +
-                                `${result.archivedImported} archived, ${result.sessionsImported} sessions`,
-                        });
-                        storageMigrationResult = {
-                            migrated: true,
-                            tasksImported: result.tasksImported,
-                            archivedImported: result.archivedImported,
-                            sessionsImported: result.sessionsImported,
-                            warnings: result.warnings,
-                        };
-                        // Mark migration as complete
-                        await updateMigrationPhase(cleoDir, 'complete');
-                        await completeMigration(cleoDir);
-                        logger.info('complete', 'finish', 'Migration completed successfully');
-                    }
-                }
-                else {
-                    // Migration had errors — restore DB and config from backup
-                    if (existsSync(dbBackupPath)) {
-                        copyFileSync(dbBackupPath, dbPath);
-                    }
-                    if (configBackup) {
-                        writeFileSync(configPath, configBackup);
-                    }
-                    // Mark migration as failed
-                    await updateMigrationPhase(cleoDir, 'failed');
-                    for (const error of result.errors) {
-                        await addMigrationWarning(cleoDir, `ERROR: ${error}`);
-                    }
-                    await failMigration(cleoDir, result.errors.join('; '));
-                    logger.error('failed', 'error', 'Migration failed', { errors: result.errors });
-                    actions.push({
-                        action: 'storage_migration',
-                        status: 'error',
-                        details: `Migration failed: ${result.errors.join('; ')}. Restored from backup.`,
-                        fix: preflight.fix ?? undefined,
-                    });
-                    errors.push(...result.errors);
-                }
-            }
-            catch (err) {
-                // Catastrophic error — attempt to restore from backup
-                try {
-                    const cleoDir = getCleoDirAbsolute(options.cwd);
-                    const dbPath = join(cleoDir, 'tasks.db');
-                    const safetyDir = join(cleoDir, 'backups', 'safety');
-                    if (existsSync(safetyDir)) {
-                        // Find most recent pre-migration backup
-                        const backups = readdirSync(safetyDir)
-                            .filter((f) => f.startsWith('tasks.db.pre-migration.'))
-                            .sort()
-                            .reverse();
-                        if (backups.length > 0 && !existsSync(dbPath)) {
-                            copyFileSync(join(safetyDir, backups[0]), dbPath);
-                        }
-                    }
-                }
-                catch {
-                    // Best-effort recovery — don't mask original error
-                }
-                actions.push({
-                    action: 'storage_migration',
-                    status: 'error',
-                    details: `Migration error: ${String(err)}`,
-                    fix: preflight.fix ?? undefined,
-                });
-                errors.push(String(err));
-            }
-            finally {
-                // Always release the migration lock
-                if (migrationLock) {
-                    try {
-                        await migrationLock();
-                    }
-                    catch {
-                        // Best-effort lock release
-                    }
-                }
-            }
-        }
-        else {
-            // autoMigrate=false: just report
-            actions.push({
-                action: 'storage_migration',
-                status: 'skipped',
-                details: preflight.summary,
-                fix: preflight.fix ?? undefined,
-            });
-        }
-    }
-    else {
-        actions.push({
-            action: 'storage_preflight',
-            status: 'skipped',
-            details: preflight.summary,
-            reason: dbExists
-                ? 'SQLite DB exists and is accessible — no migration needed. Use --diagnose for column/migration validation.'
-                : 'No legacy JSON data found and no DB exists — nothing to migrate.',
-        });
-    }
-    // ── Step 2: SQLite structural repairs ────────────────────────────
-    // Direct Drizzle SQL updates — no TaskFile loading required.
-    if (existsSync(dbPath)) {
-        try {
-            const { runAllRepairs } = await import('./repair.js');
-            const repairActions = await runAllRepairs(options.cwd, isDryRun);
-            for (const ra of repairActions) {
-                actions.push({ ...ra, status: ra.status });
-            }
-        }
-        catch {
-            // DB may not exist yet. Not an error.
-        }
-    }
-    // ── Step 2a: Sequence state migration (.sequence/.sequence.json -> SQLite) ──
-    if (existsSync(dbPath)) {
-        const legacySequenceFiles = ['.sequence', '.sequence.json'].filter((f) => existsSync(join(cleoDir, f)));
-        if (legacySequenceFiles.length > 0) {
-            if (isDryRun) {
-                actions.push({
-                    action: 'sequence_migration',
-                    status: 'preview',
-                    details: `Would migrate legacy sequence file(s) to SQLite metadata: ${legacySequenceFiles.join(', ')}`,
-                });
-            }
-            else {
-                try {
-                    const { showSequence } = await import('./sequence/index.js');
-                    const sequence = await showSequence(options.cwd);
-                    actions.push({
-                        action: 'sequence_migration',
-                        status: 'applied',
-                        details: `Migrated legacy sequence state to SQLite (counter=${String(sequence.counter ?? 0)}).`,
-                    });
-                }
-                catch (err) {
-                    actions.push({
-                        action: 'sequence_migration',
-                        status: 'error',
-                        details: `Failed to migrate sequence state: ${String(err)}`,
-                    });
-                }
-            }
-        }
-    }
-    // ── Step 2b: Stale JSON file cleanup (post-migration) ────────────
-    // If tasks.db exists and there are stale legacy files, safely backup and delete them
-    // so they don't trigger false positives or cause confusion.
-    if (needsCleanup) {
-        const staleJsonFiles = [
-            'todo.json',
-            'sessions.json',
-            'todo-archive.json',
-            '.sequence',
-            '.sequence.json',
-        ];
-        const foundStale = staleJsonFiles.filter((f) => existsSync(join(cleoDir, f)));
-        if (foundStale.length > 0) {
-            if (isDryRun) {
-                actions.push({
-                    action: 'stale_json_cleanup',
-                    status: 'preview',
-                    details: `Would backup and delete ${foundStale.length} legacy JSON file(s): ${foundStale.join(', ')}`,
-                });
-            }
-            else {
-                try {
-                    // Backup stale files first
-                    const backupDir = join(cleoDir, '.backups', `legacy-json-${Date.now()}`);
-                    mkdirSync(backupDir, { recursive: true });
-                    for (const f of foundStale) {
-                        const src = join(cleoDir, f);
-                        copyFileSync(src, join(backupDir, f));
-                    }
-                    // Delete the originals
-                    const { unlinkSync } = await import('node:fs');
-                    for (const f of foundStale) {
-                        unlinkSync(join(cleoDir, f));
-                    }
-                    actions.push({
-                        action: 'stale_json_cleanup',
-                        status: 'applied',
-                        details: `Deleted ${foundStale.length} legacy JSON file(s) (backed up to ${backupDir})`,
-                    });
-                }
-                catch (err) {
-                    actions.push({
-                        action: 'stale_json_cleanup',
-                        status: 'error',
-                        details: `Failed to clean up legacy JSON files: ${String(err)}`,
-                    });
-                }
-            }
-        }
-    }
-    // ── Step 3: Global ~/.cleo check ──────────────────────────────────
-    if (options.includeGlobal) {
-        try {
-            const globalDir = getCleoHome();
-            const globalPreflight = checkStorageMigration(join(globalDir, '..'));
-            if (globalPreflight.migrationNeeded) {
-                actions.push({
-                    action: 'global_storage_check',
-                    status: isDryRun ? 'preview' : 'skipped',
-                    details: `Global (~/.cleo): ${globalPreflight.summary}`,
-                    fix: globalPreflight.fix ?? undefined,
-                });
-            }
-            else {
-                actions.push({
-                    action: 'global_storage_check',
-                    status: 'skipped',
-                    details: `Global (~/.cleo): ${globalPreflight.summary}`,
-                });
-            }
-        }
-        catch {
-            // Global check is best-effort
-        }
-    }
-    // ── Step 4: Gitignore integrity repair ───────────────────────────
-    try {
-        const projectRoot = getProjectRoot(options.cwd);
-        if (isDryRun) {
-            // Check current state for dry-run reporting
-            const gitignorePath = join(cleoDir, '.gitignore');
-            if (!existsSync(gitignorePath)) {
-                actions.push({
-                    action: 'gitignore_integrity',
-                    status: 'preview',
-                    details: 'Would create .cleo/.gitignore from template',
-                });
-            }
-            else {
-                actions.push({
-                    action: 'gitignore_integrity',
-                    status: 'preview',
-                    details: 'Would verify .cleo/.gitignore matches template',
-                });
-            }
-        }
-        else {
-            const gitignoreResult = await ensureGitignore(projectRoot);
-            actions.push({
-                action: 'gitignore_integrity',
-                status: gitignoreResult.action === 'skipped' ? 'skipped' : 'applied',
-                details: gitignoreResult.details ?? gitignoreResult.action,
-            });
-        }
-    }
-    catch {
-        // Gitignore repair is best-effort
-    }
-    // ── Step 5: Agent-outputs migration (delegated to migration utility)
-    try {
-        const projectRoot = getProjectRoot(options.cwd);
-        const detection = detectLegacyAgentOutputs(projectRoot, cleoDir);
-        if (!detection.hasLegacy) {
-            actions.push({
-                action: 'agent_outputs_migration',
-                status: 'skipped',
-                details: 'No legacy output directories found',
-            });
-        }
-        else if (isDryRun) {
-            actions.push({
-                action: 'agent_outputs_migration',
-                status: 'preview',
-                details: `Would migrate ${detection.legacyPaths.join(' + ')} → .cleo/agent-outputs/${detection.hasCanonical ? ' (merging with existing)' : ''}`,
-            });
-        }
-        else {
-            const result = migrateAgentOutputs(projectRoot, cleoDir);
-            actions.push({
-                action: 'agent_outputs_migration',
-                status: result.migrated ? 'applied' : 'skipped',
-                details: result.summary,
-            });
-        }
-    }
-    catch {
-        // Agent outputs migration is best-effort
-    }
-    // ── Step 6: Project context re-detection ────────────────────────
-    try {
-        const projectRootForContext = getProjectRoot(options.cwd);
-        if (isDryRun) {
-            const contextPath = join(cleoDir, 'project-context.json');
-            if (!existsSync(contextPath)) {
-                actions.push({
-                    action: 'project_context_detection',
-                    status: 'preview',
-                    details: 'Would detect and create project-context.json',
-                });
-            }
-            else {
-                try {
-                    const context = JSON.parse(readFileSync(contextPath, 'utf-8'));
-                    if (context.detectedAt) {
-                        const daysSince = (Date.now() - new Date(context.detectedAt).getTime()) / (1000 * 60 * 60 * 24);
-                        if (daysSince > 30) {
-                            actions.push({
-                                action: 'project_context_detection',
-                                status: 'preview',
-                                details: `Would refresh project-context.json (${Math.round(daysSince)} days old)`,
-                            });
-                        }
-                        else {
-                            actions.push({
-                                action: 'project_context_detection',
-                                status: 'skipped',
-                                details: 'project-context.json is up to date',
-                            });
-                        }
-                    }
-                }
-                catch {
-                    actions.push({
-                        action: 'project_context_detection',
-                        status: 'preview',
-                        details: 'Would regenerate project-context.json (unreadable)',
-                    });
-                }
-            }
-        }
-        else {
-            const contextResult = await ensureProjectContext(projectRootForContext, {
-                staleDays: options.forceDetect ? 0 : 30,
-            });
-            actions.push({
-                action: 'project_context_detection',
-                status: contextResult.action === 'skipped' ? 'skipped' : 'applied',
-                details: contextResult.details ?? contextResult.action,
-            });
-        }
-    }
-    catch {
-        // Project context detection is best-effort
-    }
-    // ── Step 7: Refresh project-scope injection ────────────────────
-    // Strip legacy CLEO blocks and update CAAMP blocks.
-    if (!isDryRun) {
-        try {
-            const projectRootForInjection = getProjectRoot(options.cwd);
-            const injectionResult = await ensureInjection(projectRootForInjection);
-            actions.push({
-                action: 'injection_refresh',
-                status: injectionResult.action === 'skipped' ? 'skipped' : 'applied',
-                details: injectionResult.details ?? 'Project docs refreshed',
-            });
-        }
-        catch {
-            // Injection refresh is best-effort
-        }
-    }
-    else {
-        actions.push({
-            action: 'injection_refresh',
-            status: 'preview',
-            details: 'Would refresh project injection (strip legacy CLEO blocks, update CAAMP blocks)',
-        });
-    }
-    // ── Step 8: Structural maintenance ──────────────────────────────
-    if (!isDryRun) {
-        const projectRootForMaint = getProjectRoot(options.cwd);
-        // Create missing .cleo subdirs
-        try {
-            const structResult = await ensureCleoStructure(projectRootForMaint);
-            if (structResult.action !== 'skipped') {
-                actions.push({
-                    action: 'ensure_structure',
-                    status: 'applied',
-                    details: structResult.details ?? 'Created missing directories',
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Ensure .cleo/config.json exists and matches current template semantics
-        try {
-            const configResult = await ensureConfig(projectRootForMaint);
-            if (configResult.action !== 'skipped') {
-                actions.push({
-                    action: 'config_file',
-                    status: 'applied',
-                    details: configResult.details ?? 'Created or updated config.json',
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Install/update git hooks
-        try {
-            const hooksResult = await ensureGitHooks(projectRootForMaint);
-            if (hooksResult.action !== 'skipped') {
-                actions.push({
-                    action: 'git_hooks',
-                    status: 'applied',
-                    details: hooksResult.details ?? 'Installed git hooks',
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Create project-info.json if missing
-        try {
-            const infoResult = await ensureProjectInfo(projectRootForMaint);
-            if (infoResult.action !== 'skipped') {
-                actions.push({
-                    action: 'project_info',
-                    status: 'applied',
-                    details: infoResult.details ?? 'Created project-info.json',
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Install global schemas
-        try {
-            const schemasResult = ensureGlobalSchemas();
-            actions.push({
-                action: 'global_schemas',
-                status: 'applied',
-                details: `Installed ${schemasResult.installed} schemas (${schemasResult.updated} updated)`,
-            });
-        }
-        catch {
-            /* best-effort */
-        }
-        // Clean deprecated project schemas
-        try {
-            const cleanResult = await cleanProjectSchemas(projectRootForMaint);
-            if (cleanResult.cleaned) {
-                actions.push({
-                    action: 'clean_project_schemas',
-                    status: 'applied',
-                    details: 'Backed up and removed deprecated .cleo/schemas/',
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Initialize .cleo/.git checkpoint repo
-        try {
-            const gitRepoResult = await ensureCleoGitRepo(projectRootForMaint);
-            if (gitRepoResult.action !== 'skipped') {
-                actions.push({
-                    action: 'cleo_git_repo',
-                    status: 'applied',
-                    details: gitRepoResult.details ?? 'Created .cleo/.git checkpoint repository',
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Initialize SQLite database for fresh projects
-        try {
-            const dbResult = await ensureSqliteDb(projectRootForMaint);
-            if (dbResult.action !== 'skipped') {
-                actions.push({
-                    action: 'ensure_sqlite_db',
-                    status: 'applied',
-                    details: dbResult.details ?? 'SQLite database initialized',
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Initialize brain.db for BRAIN memory system
-        try {
-            const { ensureBrainDb } = await import('./scaffold.js');
-            const brainResult = await ensureBrainDb(projectRootForMaint);
-            if (brainResult.action !== 'skipped') {
-                actions.push({
-                    action: 'ensure_brain_db',
-                    status: 'applied',
-                    details: brainResult.details ?? 'brain.db initialized',
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Initialize/upgrade signaldock.db for local agent messaging (T224)
-        try {
-            const { ensureSignaldockDb } = await import('./store/signaldock-sqlite.js');
-            const sdResult = await ensureSignaldockDb(projectRootForMaint);
-            actions.push({
-                action: 'ensure_signaldock_db',
-                status: 'applied',
-                details: sdResult.action === 'created'
-                    ? 'signaldock.db created with full schema'
-                    : 'signaldock.db schema verified',
-            });
-        }
-        catch {
-            /* best-effort — signaldock.db will be created on first agent operation */
-        }
-        // Initialize conduit.db for project-tier agent messaging (T310)
-        try {
-            const { ensureConduitDb } = await import('./store/conduit-sqlite.js');
-            const cdResult = ensureConduitDb(projectRootForMaint);
-            if (cdResult.action === 'created') {
-                actions.push({
-                    action: 'ensure_conduit_db',
-                    status: 'applied',
-                    details: 'conduit.db created with full schema',
-                });
-            }
-        }
-        catch {
-            /* best-effort — conduit.db will be created on first agent operation */
-        }
-        // Regenerate memory-bridge.md
-        try {
-            const { writeMemoryBridge } = await import('./memory/memory-bridge.js');
-            const bridgeResult = await writeMemoryBridge(projectRootForMaint);
-            if (bridgeResult.written) {
-                actions.push({
-                    action: 'memory_bridge',
-                    status: 'applied',
-                    details: 'memory-bridge.md regenerated',
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Remove .cleo/ from root .gitignore if present
-        try {
-            const rootGitignoreResult = await removeCleoFromRootGitignore(projectRootForMaint);
-            if (rootGitignoreResult.removed) {
-                actions.push({
-                    action: 'root_gitignore_cleanup',
-                    status: 'applied',
-                    details: '.cleo/ removed from root .gitignore',
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Install cleo-subagent agent definition
-        try {
-            const agentCreated = [];
-            const agentWarnings = [];
-            await initAgentDefinition(agentCreated, agentWarnings);
-            if (agentCreated.length > 0) {
-                actions.push({
-                    action: 'agent_definition',
-                    status: 'applied',
-                    details: agentCreated.join(', '),
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Deploy starter CANT bundle (team + agents) to .cleo/cant/ if missing.
-        // Ensures existing projects get agent definitions on upgrade, not just init. (T555)
-        try {
-            const { deployStarterBundle } = await import('./init.js');
-            const cantCreated = [];
-            const cantWarnings = [];
-            await deployStarterBundle(cleoDir, cantCreated, cantWarnings);
-            if (cantCreated.length > 0) {
-                actions.push({
-                    action: 'cant_starter_bundle',
-                    status: 'applied',
-                    details: cantCreated.join(', '),
-                });
-            }
-            for (const w of cantWarnings) {
-                actions.push({
-                    action: 'cant_starter_bundle',
-                    status: 'skipped',
-                    details: w,
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Install core skills
-        try {
-            const skillsCreated = [];
-            const skillsWarnings = [];
-            await initCoreSkills(skillsCreated, skillsWarnings);
-            if (skillsCreated.length > 0) {
-                actions.push({
-                    action: 'core_skills',
-                    status: 'applied',
-                    details: skillsCreated.join(', '),
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Register with NEXUS
-        try {
-            const nexusCreated = [];
-            const nexusWarnings = [];
-            await initNexusRegistration(projectRootForMaint, nexusCreated, nexusWarnings);
-            if (nexusCreated.length > 0) {
-                actions.push({
-                    action: 'nexus_registration',
-                    status: 'applied',
-                    details: nexusCreated.join(', '),
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Run codebase mapping if requested (delegates to core mapCodebase)
-        if (options.mapCodebase) {
-            try {
-                const { mapCodebase } = await import('./codebase-map/index.js');
-                const mapResult = await mapCodebase(projectRootForMaint, { storeToBrain: true });
-                actions.push({
-                    action: 'codebase_map',
-                    status: 'applied',
-                    details: `Analyzed: ${mapResult.stack?.languages?.length ?? 0} languages, ${mapResult.concerns?.todos?.length ?? 0} TODOs found`,
-                });
-            }
-            catch (err) {
-                actions.push({
-                    action: 'codebase_map',
-                    status: 'error',
-                    details: `Codebase mapping failed: ${err instanceof Error ? err.message : String(err)}`,
-                });
-            }
-        }
-        // Update project name if requested (delegates to core updateProjectName)
-        if (options.projectName) {
-            try {
-                const { updateProjectName } = await import('./project-info.js');
-                await updateProjectName(projectRootForMaint, options.projectName);
-                actions.push({
-                    action: 'project_name_update',
-                    status: 'applied',
-                    details: `Project name set to "${options.projectName}"`,
-                });
-            }
-            catch {
-                /* best-effort */
-            }
-        }
-        // GitHub issue/PR templates — install missing ones, warn if absent
-        try {
-            const { existsSync: fsExistsSync } = await import('node:fs');
-            const { join: pathJoin } = await import('node:path');
-            const hasGit = fsExistsSync(pathJoin(projectRootForMaint, '.git'));
-            const hasGitHubTemplates = fsExistsSync(pathJoin(projectRootForMaint, '.github', 'ISSUE_TEMPLATE'));
-            if (hasGit && !hasGitHubTemplates) {
-                const ghCreated = [];
-                const ghSkipped = [];
-                await installGitHubTemplates(projectRootForMaint, ghCreated, ghSkipped);
-                if (ghCreated.length > 0) {
-                    actions.push({
-                        action: 'github_templates',
-                        status: 'applied',
-                        details: `Installed ${ghCreated.length} GitHub template(s): ${ghCreated.join(', ')}`,
-                    });
-                }
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-        // Adapter discovery, activation, and install (T5240)
-        // Ensures Claude Code settings.json hooks and other adapter configs stay current.
-        try {
-            const { AdapterManager } = await import('./adapters/index.js');
-            const mgr = AdapterManager.getInstance(projectRootForMaint);
-            const manifests = mgr.discover();
-            if (manifests.length > 0) {
-                const detected = mgr.detectActive();
-                for (const adapterId of detected) {
-                    try {
-                        const adapter = await mgr.activate(adapterId);
-                        const installResult = await adapter.install.install({
-                            projectDir: projectRootForMaint,
-                        });
-                        if (installResult.success) {
-                            actions.push({
-                                action: 'adapter_install',
-                                status: 'applied',
-                                details: `Adapter ${adapterId}: installed/updated`,
-                            });
-                        }
-                    }
-                    catch {
-                        /* best-effort — adapter may not support install */
-                    }
-                }
-            }
-        }
-        catch {
-            /* best-effort — adapters are optional */
-        }
-        // Ensure the global CleoOS Hub exists (idempotent)
-        try {
-            const { ensureCleoOsHub } = await import('./scaffold.js');
-            const hubResult = await ensureCleoOsHub();
-            if (hubResult.action === 'created') {
-                actions.push({
-                    action: 'cleoos_hub',
-                    status: 'applied',
-                    details: hubResult.details ?? 'CleoOS hub scaffolded',
-                });
-            }
-        }
-        catch {
-            /* best-effort */
-        }
-    }
-    else {
-        // Dry-run reporting for new steps
-        const { existsSync: fsExistsSync } = await import('node:fs');
-        const { join: pathJoin } = await import('node:path');
-        const hasGit = fsExistsSync(pathJoin(getProjectRoot(options.cwd), '.git'));
-        const hasGitHubTemplates = fsExistsSync(pathJoin(getProjectRoot(options.cwd), '.github', 'ISSUE_TEMPLATE'));
-        if (hasGit && !hasGitHubTemplates) {
-            actions.push({
-                action: 'github_templates',
-                status: 'preview',
-                details: 'Would install GitHub issue/PR templates to .github/ — run `cleo init` or `cleo upgrade --fix` to apply',
-                fix: 'cleo upgrade',
-            });
-        }
-        actions.push({
-            action: 'structural_maintenance',
-            status: 'preview',
-            details: 'Would create missing directories, ensure config, install hooks, schemas, project-info, agent definition, skills, and NEXUS registration',
-        });
-    }
-    const appliedActions = actions.filter((a) => a.status === 'applied');
-    const skippedActions = actions.filter((a) => a.status === 'skipped');
-    const errorActions = actions.filter((a) => a.status === 'error');
-    const hasErrors = errors.length > 0 || errorActions.length > 0;
-    const upToDate = !actions.some((a) => a.status === 'applied' || a.status === 'preview');
-    // Build summary of what was checked
-    const summaryWarnings = [];
-    for (const a of actions) {
-        if (a.status === 'skipped' && a.reason) {
-            summaryWarnings.push(`${a.action}: ${a.reason}`);
-        }
-    }
-    return {
-        success: !hasErrors,
-        upToDate,
-        dryRun: isDryRun,
-        actions,
-        applied: appliedActions.length,
-        errors,
-        summary: {
-            checked: actions.length,
-            applied: appliedActions.length,
-            skipped: skippedActions.length,
-            errors: errorActions.length,
-            warnings: summaryWarnings,
-        },
-        storageMigration: storageMigrationResult,
-    };
-}
-/**
- * Deep diagnostic inspection of schema and migration state.
- *
- * Unlike bare `cleo upgrade` which skips checks that "look OK",
- * --diagnose validates:
- * - tasks.db: all required columns present via PRAGMA table_info
- * - tasks.db: migration journal entries match local migration files
- * - brain.db: migration journal entries match local migration files
- * - brain.db: expected tables exist
- * - Stale/orphaned journal entries detected and reported
- *
- * Read-only: does not modify any data.
- *
- * @task T131
- */
-export async function diagnoseUpgrade(options = {}) {
-    const findings = [];
-    const cleoDir = getCleoDirAbsolute(options.cwd);
-    const dbPath = join(cleoDir, 'tasks.db');
-    const brainDbPath = join(cleoDir, 'brain.db');
-    // ── tasks.db column validation ──
-    if (existsSync(dbPath)) {
-        try {
-            const { getNativeDb, getDb } = await import('./store/sqlite.js');
-            const projectRoot = getProjectRoot(options.cwd);
-            await getDb(projectRoot);
-            const nativeDb = getNativeDb();
-            if (nativeDb) {
-                // Check required columns
-                const columns = nativeDb.prepare('PRAGMA table_info(tasks)').all();
-                const existingCols = new Set(columns.map((c) => c.name));
-                const requiredColumns = ['pipeline_stage'];
-                const missing = requiredColumns.filter((c) => !existingCols.has(c));
-                if (missing.length > 0) {
-                    findings.push({
-                        check: 'tasks.db.columns',
-                        status: 'error',
-                        details: `Missing required columns: ${missing.join(', ')}`,
-                        fix: 'Run: cleo upgrade',
-                    });
-                }
-                else {
-                    findings.push({
-                        check: 'tasks.db.columns',
-                        status: 'ok',
-                        details: `All ${requiredColumns.length} required column(s) present (${columns.length} total)`,
-                    });
-                }
-                // Check migration journal
-                const hasMigTable = nativeDb
-                    .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='__drizzle_migrations'")
-                    .get();
-                if (hasMigTable?.name) {
-                    const journalEntries = nativeDb
-                        .prepare('SELECT * FROM __drizzle_migrations')
-                        .all();
-                    const nullIdEntries = journalEntries.filter((e) => e.id === null || e.id === undefined);
-                    const staleEntries = journalEntries.filter((e) => e.created_at === null || e.created_at === undefined);
-                    if (nullIdEntries.length > 0) {
-                        findings.push({
-                            check: 'tasks.db.journal',
-                            status: 'warning',
-                            details: `${nullIdEntries.length} journal entry/entries with null IDs (orphaned from previous CLEO version)`,
-                            fix: 'Run: cleo upgrade (will reconcile automatically)',
-                        });
-                    }
-                    else if (staleEntries.length > 0) {
-                        findings.push({
-                            check: 'tasks.db.journal',
-                            status: 'warning',
-                            details: `${staleEntries.length} journal entry/entries with null timestamps`,
-                            fix: 'Run: cleo upgrade (will reconcile automatically)',
-                        });
-                    }
-                    else {
-                        findings.push({
-                            check: 'tasks.db.journal',
-                            status: 'ok',
-                            details: `${journalEntries.length} migration(s) in journal, all valid`,
-                        });
-                    }
-                }
-                else {
-                    findings.push({
-                        check: 'tasks.db.journal',
-                        status: 'warning',
-                        details: 'No migration journal table found — migrations may not have been tracked',
-                        fix: 'Run: cleo upgrade',
-                    });
-                }
-                // Integrity check
-                const integrity = nativeDb.prepare('PRAGMA integrity_check').get();
-                const ok = integrity?.integrity_check === 'ok';
-                findings.push({
-                    check: 'tasks.db.integrity',
-                    status: ok ? 'ok' : 'error',
-                    details: ok ? 'SQLite integrity check passed' : 'SQLite integrity check failed',
-                    ...(!ok ? { fix: 'Restore from backup: cleo admin backup --action restore' } : {}),
-                });
-            }
-            else {
-                findings.push({
-                    check: 'tasks.db.connection',
-                    status: 'error',
-                    details: 'Could not obtain native DB handle',
-                });
-            }
-        }
-        catch (err) {
-            findings.push({
-                check: 'tasks.db.connection',
-                status: 'error',
-                details: `Failed to connect: ${err instanceof Error ? err.message : String(err)}`,
-            });
-        }
-    }
-    else {
-        findings.push({
-            check: 'tasks.db',
-            status: 'error',
-            details: 'tasks.db not found',
-            fix: 'Run: cleo init',
-        });
-    }
-    // ── brain.db validation ──
-    if (existsSync(brainDbPath)) {
-        try {
-            const { getBrainNativeDb, getBrainDb } = await import('./store/brain-sqlite.js');
-            await getBrainDb(options.cwd);
-            const nativeDb = getBrainNativeDb();
-            if (nativeDb) {
-                // Check expected tables
-                const tables = nativeDb
-                    .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name NOT LIKE '__drizzle%' AND name NOT LIKE 'sqlite_%'")
-                    .all();
-                const tableNames = new Set(tables.map((t) => t.name));
-                const expectedTables = [
-                    'brain_observations',
-                    'brain_decisions',
-                    'brain_patterns',
-                    'brain_learnings',
-                ];
-                const missingTables = expectedTables.filter((t) => !tableNames.has(t));
-                if (missingTables.length > 0) {
-                    findings.push({
-                        check: 'brain.db.tables',
-                        status: 'error',
-                        details: `Missing tables: ${missingTables.join(', ')}`,
-                        fix: 'Run: cleo upgrade',
-                    });
-                }
-                else {
-                    findings.push({
-                        check: 'brain.db.tables',
-                        status: 'ok',
-                        details: `All ${expectedTables.length} expected tables present (${tables.length} total)`,
-                    });
-                }
-                // Check migration journal
-                const hasMigTable = nativeDb
-                    .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='__drizzle_migrations'")
-                    .get();
-                if (hasMigTable?.name) {
-                    const journalEntries = nativeDb
-                        .prepare('SELECT * FROM __drizzle_migrations')
-                        .all();
-                    const nullIdEntries = journalEntries.filter((e) => e.id === null || e.id === undefined);
-                    if (nullIdEntries.length > 0) {
-                        findings.push({
-                            check: 'brain.db.journal',
-                            status: 'warning',
-                            details: `${nullIdEntries.length} journal entry/entries with null IDs (orphaned from previous CLEO version)`,
-                            fix: 'Run: cleo upgrade (will reconcile automatically)',
-                        });
-                    }
-                    else {
-                        findings.push({
-                            check: 'brain.db.journal',
-                            status: 'ok',
-                            details: `${journalEntries.length} migration(s) in journal, all valid`,
-                        });
-                    }
-                }
-                else {
-                    findings.push({
-                        check: 'brain.db.journal',
-                        status: 'warning',
-                        details: 'No migration journal table found',
-                        fix: 'Run: cleo upgrade',
-                    });
-                }
-                // T528/T531/T549 column validation — ensure brain schema expansions applied
-                const brainColumnChecks = [
-                    {
-                        table: 'brain_page_nodes',
-                        columns: ['quality_score', 'content_hash', 'last_activity_at', 'updated_at'],
-                        task: 'T528',
-                    },
-                    {
-                        table: 'brain_decisions',
-                        columns: [
-                            'quality_score',
-                            'memory_tier',
-                            'memory_type',
-                            'verified',
-                            'valid_at',
-                            'invalid_at',
-                            'source_confidence',
-                            'citation_count',
-                        ],
-                        task: 'T531/T549',
-                    },
-                    {
-                        table: 'brain_observations',
-                        columns: ['quality_score', 'memory_tier', 'memory_type', 'verified'],
-                        task: 'T531/T549',
-                    },
-                ];
-                const allBrainColsMissing = [];
-                for (const { table, columns, task } of brainColumnChecks) {
-                    const hasTable = nativeDb
-                        .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name=?")
-                        .get(table);
-                    if (!hasTable?.name)
-                        continue;
-                    const cols = nativeDb.prepare(`PRAGMA table_info(${table})`).all();
-                    const colNames = new Set(cols.map((c) => c.name));
-                    const missing = columns.filter((c) => !colNames.has(c));
-                    if (missing.length > 0) {
-                        allBrainColsMissing.push(`${table}: ${missing.join(', ')} (${task})`);
-                    }
-                }
-                if (allBrainColsMissing.length > 0) {
-                    findings.push({
-                        check: 'brain.db.schema_columns',
-                        status: 'error',
-                        details: `Missing brain schema columns: ${allBrainColsMissing.join('; ')}`,
-                        fix: 'Run: cleo upgrade (will add missing columns automatically)',
-                    });
-                }
-                else {
-                    findings.push({
-                        check: 'brain.db.schema_columns',
-                        status: 'ok',
-                        details: 'All T528/T531/T549 brain schema columns present',
-                    });
-                }
-            }
-            else {
-                findings.push({
-                    check: 'brain.db.connection',
-                    status: 'error',
-                    details: 'Could not obtain native DB handle',
-                });
-            }
-        }
-        catch (err) {
-            findings.push({
-                check: 'brain.db.connection',
-                status: 'error',
-                details: `Failed to connect: ${err instanceof Error ? err.message : String(err)}`,
-            });
-        }
-    }
-    else {
-        findings.push({
-            check: 'brain.db',
-            status: 'warning',
-            details: 'brain.db not found (will be created on first use)',
-            fix: 'Run: cleo upgrade',
-        });
-    }
-    // ── signaldock.db validation ──
-    const signaldockDbPath = join(cleoDir, 'signaldock.db');
-    if (existsSync(signaldockDbPath)) {
-        findings.push({
-            check: 'signaldock.db',
-            status: 'ok',
-            details: 'signaldock.db exists',
-        });
-    }
-    else {
-        findings.push({
-            check: 'signaldock.db',
-            status: 'warning',
-            details: 'signaldock.db not found',
-            fix: 'Run: cleo upgrade',
-        });
-    }
-    // ── conduit.db validation ──
-    const conduitDbPath = join(cleoDir, 'conduit.db');
-    if (existsSync(conduitDbPath)) {
-        findings.push({
-            check: 'conduit.db',
-            status: 'ok',
-            details: 'conduit.db exists',
-        });
-    }
-    else {
-        findings.push({
-            check: 'conduit.db',
-            status: 'warning',
-            details: 'conduit.db not found',
-            fix: 'Run: cleo upgrade',
-        });
-    }
-    // ── memory-bridge.md validation ──
-    const memoryBridgePath = join(cleoDir, 'memory-bridge.md');
-    if (existsSync(memoryBridgePath)) {
-        try {
-            const content = readFileSync(memoryBridgePath, 'utf-8');
-            const hasAutoGenMarker = content.includes('Auto-generated');
-            const hasGarbage = content.includes('undefined') && content.length < 100;
-            if (hasGarbage) {
-                findings.push({
-                    check: 'memory-bridge.md',
-                    status: 'error',
-                    details: 'memory-bridge.md contains garbage content',
-                    fix: 'Run: cleo upgrade (will regenerate)',
-                });
-            }
-            else if (hasAutoGenMarker) {
-                findings.push({
-                    check: 'memory-bridge.md',
-                    status: 'ok',
-                    details: 'memory-bridge.md exists and has valid content',
-                });
-            }
-            else {
-                findings.push({
-                    check: 'memory-bridge.md',
-                    status: 'warning',
-                    details: 'memory-bridge.md exists but may be stale (no auto-generated marker)',
-                    fix: 'Run: cleo upgrade (will regenerate)',
-                });
-            }
-        }
-        catch {
-            findings.push({
-                check: 'memory-bridge.md',
-                status: 'warning',
-                details: 'memory-bridge.md exists but could not be read',
-            });
-        }
-    }
-    else {
-        findings.push({
-            check: 'memory-bridge.md',
-            status: 'warning',
-            details: 'memory-bridge.md not found',
-            fix: 'Run: cleo upgrade (will regenerate)',
-        });
-    }
-    const okCount = findings.filter((f) => f.status === 'ok').length;
-    const warnCount = findings.filter((f) => f.status === 'warning').length;
-    const errCount = findings.filter((f) => f.status === 'error').length;
-    return {
-        success: errCount === 0,
-        findings,
-        summary: { ok: okCount, warnings: warnCount, errors: errCount },
-    };
-}
-//# sourceMappingURL=upgrade.js.map