ultra-builder-pro-cli 0.25.0 → 0.26.0

package/mcp-server/lib/doctor.cjs

@@ -1,627 +0,0 @@
-'use strict';
-
-const crypto = require('node:crypto');
-const childProcess = require('node:child_process');
-const fs = require('node:fs');
-const path = require('node:path');
-
-const { REQUIRED_TABLES, tableNames } = require('./state-db.cjs');
-const ops = require('./state-ops.cjs');
-const runtime = require('./runtime-state.cjs');
-const projector = require('./projector.cjs');
-const recovery = require('../../orchestrator/recovery.cjs');
-const baselines = require('./baseline-workflow.cjs');
-const changes = require('./change-workflow.cjs');
-const archiveJournal = require('./archive-journal.cjs');
-const stageCheckpoints = require('./stage-checkpoints.cjs');
-const runtimePaths = require('./runtime-paths.cjs');
-const artifactRegistry = require('./artifact-registry.cjs');
-const planStore = require('./plan-store.cjs');
-const taskLedger = require('./task-ledger.cjs');
-const closeJournal = require('../../orchestrator/session-close-journal.cjs');
-
-const SPEC_CONSUMER = 'spec-staleness';
-const BACKUP_WORKER_FILENAME = 'doctor-backup-worker.cjs';
-const BACKUP_WORKER_TIMEOUT_MS = 120 * 1000;
-const BACKUP_WORKER_METHOD = 'sqlite-serialize-pinned-fd-v1';
-
-class DoctorError extends Error {
-  constructor(code, message, { cause, details } = {}) {
-    super(message);
-    this.name = 'DoctorError';
-    this.code = code;
-    if (cause) this.cause = cause;
-    if (details !== undefined) this.details = details;
-  }
-}
-
-function timestamp() {
-  return new Date().toISOString().replace(/[:.]/g, '-');
-}
-
-function inspectSessionCloses(db, {
-  rootDir = process.cwd(),
-  sessionsAvailable = true,
-} = {}) {
-  let intents;
-  try {
-    intents = closeJournal.list(rootDir);
-  } catch (error) {
-    return {
-      status: 'fail',
-      pending: 1,
-      items: [{
-        code: error.code || 'SESSION_CLOSE_JOURNAL_INVALID',
-        reason: 'journal_invalid',
-        message: error.message,
-      }],
-    };
-  }
-  const items = intents.map((intent) => {
-    const session = sessionsAvailable ? ops.readSession(db, intent.sid) : null;
-    let reason = 'recovery_required';
-    if (!sessionsAvailable) reason = 'session_state_unavailable';
-    else if (!session) reason = 'session_missing';
-    else if (session.status === intent.requested_status) reason = 'terminal_reconciliation_required';
-    else if (['completed', 'crashed'].includes(session.status)) {
-      reason = `terminal_status_conflict:${session.status}`;
-    } else if (recovery._internal.isPidAlive(session.pid)) {
-      reason = 'worker_still_alive';
-    }
-    return {
-      code: 'SESSION_CLOSE_PENDING',
-      sid: intent.sid,
-      task_id: intent.task_id,
-      requested_status: intent.requested_status,
-      phase: intent.phase,
-      reason,
-    };
-  });
-  return {
-    status: items.length === 0 ? 'pass' : 'fail',
-    pending: items.length,
-    items,
-  };
-}
-
-function inspectTeamTaskLedger(db, rootDir) {
-  try {
-    const health = taskLedger.inspectTaskLedger(db, { rootDir });
-    const taskCount = db.prepare('SELECT COUNT(*) AS count FROM tasks').get().count;
-    let status = 'warning';
-    if (health.status === 'current') status = 'pass';
-    return {
-      ...health,
-      condition: health.status,
-      status,
-      task_count: taskCount,
-    };
-  } catch (error) {
-    return {
-      status: 'fail',
-      condition: 'invalid',
-      code: error.code || 'TASK_LEDGER_INVALID',
-      message: error.message,
-    };
-  }
-}
-
-function inspectStageCheckpoints(db) {
-  const rows = db.prepare(
-    `SELECT id, stage, scope_type, scope_id, revision, status, payload_json,
-            evidence_json, diagnostics_json, context_envelope_id, digest,
-            supersedes_id
-     FROM stage_checkpoints ORDER BY stage, scope_type, scope_id, revision`,
-  ).all();
-  const counts = { draft: 0, accepted: 0, superseded: 0 };
-  const issues = [];
-  for (const row of rows) {
-    counts[row.status] = Number(counts[row.status] || 0) + 1;
-    let payload;
-    let evidence;
-    let diagnostics;
-    try {
-      payload = JSON.parse(row.payload_json);
-      evidence = JSON.parse(row.evidence_json);
-      diagnostics = JSON.parse(row.diagnostics_json);
-    } catch {
-      issues.push({ code: 'CHECKPOINT_JSON_INVALID', checkpoint_id: row.id });
-      continue;
-    }
-    const expected = stageCheckpoints.checkpointDigest({
-      stage: row.stage,
-      scope_type: row.scope_type,
-      scope_id: row.scope_id,
-      revision: row.revision,
-      payload,
-      evidence,
-      diagnostics,
-      context_envelope_id: row.context_envelope_id,
-      supersedes_id: row.supersedes_id,
-    });
-    if (expected !== row.digest) {
-      issues.push({ code: 'CHECKPOINT_DIGEST_MISMATCH', checkpoint_id: row.id });
-    }
-  }
-  return {
-    status: issues.length === 0 ? 'pass' : 'fail',
-    total: rows.length,
-    ...counts,
-    issues,
-  };
-}
-
-function inspectDecisionRecords(db) {
-  const rows = db.prepare(
-    `SELECT id, status, digest, artifact_path
-     FROM decision_records ORDER BY created_at, id`,
-  ).all();
-  return {
-    status: 'pass',
-    total: rows.length,
-    accepted: rows.filter((row) => row.status === 'accepted').length,
-    superseded: rows.filter((row) => row.status === 'superseded').length,
-  };
-}
-
-function inspectLegacyHistory(db) {
-  const count = (table) => db.prepare(`SELECT COUNT(*) AS count FROM ${table}`).get().count;
-  return {
-    status: 'informational',
-    workflow_runs: count('workflow_runs'),
-    workflow_steps: count('workflow_steps'),
-    decision_threads: count('decision_threads'),
-    decision_items: count('decision_items'),
-    authority: false,
-  };
-}
-
-function inspectSystem(db, { rootDir = process.cwd() } = {}) {
-  const tables = new Set(tableNames(db));
-  const missing = REQUIRED_TABLES.filter((name) => !tables.has(name));
-  const integrity = db.pragma('quick_check', { simple: true });
-  const incidents = missing.length === 0 ? runtime.listIncidents(db, { status: 'open' }) : [];
-  const pending = missing.length === 0 ? runtime.listProjectionJobs(db, { status: 'pending' }) : [];
-  const running = missing.length === 0 ? runtime.listProjectionJobs(db, { status: 'running' }) : [];
-  const failed = missing.length === 0 ? runtime.listProjectionJobs(db, { status: 'failed' }) : [];
-  const orphanSessions = missing.length === 0
-    ? db.prepare("SELECT COUNT(*) AS count FROM sessions WHERE status = 'orphan'").get().count
-    : 0;
-  const sessionCloses = inspectSessionCloses(db, {
-    rootDir,
-    sessionsAvailable: missing.length === 0,
-  });
-  const eventCursor = missing.length === 0
-    ? Number(db.prepare('SELECT COALESCE(MAX(id), 0) AS id FROM events').get().id)
-    : 0;
-  const projectedCursor = missing.length === 0
-    ? Number(db.prepare(
-        "SELECT COALESCE(MAX(event_cursor), 0) AS id FROM projection_jobs WHERE status = 'completed'",
-      ).get().id)
-    : 0;
-  const activeMissing = missing.length === 0
-    ? db.prepare(
-        `SELECT artifact_root FROM changes
-         WHERE status IN ('active', 'blocked', 'ready') AND artifact_root IS NOT NULL`,
-      ).all().filter((row) => row.artifact_root && !fs.existsSync(path.resolve(rootDir, row.artifact_root))).length
-    : 0;
-  const archiveIntents = missing.length === 0 ? archiveJournal.listArchiveIntents(rootDir) : [];
-  const corruptArchiveIntents = archiveIntents.filter((item) => item.error).length;
-  const baseline = missing.length === 0
-    ? baselines.inspectBaseline(db, { rootDir })
-    : { status: 'fail', blockers: ['BASELINE_STATE_UNAVAILABLE'], warnings: [], baseline: null };
-  const checkpointHealth = missing.length === 0
-    ? inspectStageCheckpoints(db)
-    : { status: 'fail', total: 0, issues: [{ code: 'STATE_DB_UNAVAILABLE' }] };
-  const decisionHealth = missing.length === 0
-    ? inspectDecisionRecords(db)
-    : { status: 'fail', total: 0, accepted: 0, superseded: 0 };
-  const legacyHistory = missing.length === 0
-    ? inspectLegacyHistory(db)
-    : {
-      status: 'informational',
-      workflow_runs: 0,
-      workflow_steps: 0,
-      decision_threads: 0,
-      decision_items: 0,
-      authority: false,
-    };
-  const artifactHealth = missing.length === 0
-    ? artifactRegistry.inspectArtifactHealth(db, { rootDir })
-    : { status: 'fail', registered: 0, issues: [], counts: {} };
-  const planPublications = missing.length === 0
-    ? planStore.inspectPlanPublications(db, { rootDir })
-    : { status: 'fail', pending: 0, transactions: [], issues: [] };
-  const taskLedgerHealth = missing.length === 0
-    ? inspectTeamTaskLedger(db, rootDir)
-    : { status: 'fail', condition: 'state_unavailable', code: 'STATE_DB_UNAVAILABLE' };
-  const baselineCheckStatus = baseline.status === 'pass'
-    ? 'pass'
-    : (baseline.baseline?.status === 'ready' ? 'fail' : 'warning');
-  const degraded = integrity !== 'ok' || missing.length > 0 || incidents.length > 0
-    || pending.length > 0 || running.length > 0 || failed.length > 0 || orphanSessions > 0 || activeMissing > 0
-    || sessionCloses.status === 'fail'
-    || archiveIntents.length > 0
-    || eventCursor > projectedCursor || checkpointHealth.status === 'fail'
-    || decisionHealth.status === 'fail'
-    || artifactHealth.status === 'fail'
-    || planPublications.status === 'fail'
-    || taskLedgerHealth.status === 'fail'
-    || baselineCheckStatus === 'fail';
-  return {
-    status: degraded ? 'degraded' : 'healthy',
-    checks: {
-      state_db: { status: integrity === 'ok' && missing.length === 0 ? 'pass' : 'fail', integrity, missing_tables: missing },
-      incidents: { status: incidents.length === 0 ? 'pass' : 'fail', open: incidents.length, items: incidents },
-      projections: {
-        status: pending.length === 0 && running.length === 0 && failed.length === 0 && eventCursor <= projectedCursor ? 'pass' : 'fail',
-        pending: pending.length, running: running.length, failed: failed.length,
-        event_cursor: eventCursor, projected_cursor: projectedCursor,
-      },
-      sessions: {
-        status: orphanSessions === 0 && sessionCloses.status === 'pass' ? 'pass' : 'fail',
-        orphan: orphanSessions,
-        close_pending: sessionCloses.pending,
-        close_intents: sessionCloses.items,
-      },
-      change_artifacts: { status: activeMissing === 0 ? 'pass' : 'fail', missing: activeMissing },
-      artifacts: artifactHealth,
-      task_ledger: taskLedgerHealth,
-      plan_publications: planPublications,
-      archive_recovery: {
-        status: archiveIntents.length === 0 ? 'pass' : 'fail',
-        pending: archiveIntents.length, corrupt: corruptArchiveIntents,
-      },
-      baseline: {
-        status: baselineCheckStatus,
-        readiness: baseline.status,
-        mode: baseline.baseline?.mode || null,
-        baseline_status: baseline.baseline?.status || null,
-        id: baseline.baseline?.id || null,
-        repository_revision: baseline.baseline?.repository_revision || null,
-        repository_branch: baseline.baseline?.repository_branch || null,
-        worktree_state: baseline.baseline?.worktree_state || 'unavailable',
-        gaps: baseline.baseline ? baselines.summarizeGaps(baseline.baseline.gaps) : null,
-        blockers: baseline.blockers,
-        warnings: baseline.warnings,
-      },
-      checkpoints: checkpointHealth,
-      decisions: decisionHealth,
-      legacy_history: legacyHistory,
-      external_providers: {
-        status: 'pass', ownership: 'external',
-        note: 'Ultra stores provider metadata references only and never owns memory or code-graph content.',
-      },
-    },
-  };
-}
-
-function statIdentity(stat) {
-  return { dev: String(stat.dev), ino: String(stat.ino) };
-}
-
-function sameIdentity(left, right) {
-  return String(left?.dev) === String(right?.dev)
-    && String(left?.ino) === String(right?.ino);
-}
-
-function backupWorkerPath() {
-  const runtimeRoot = process.env.UBP_RUNTIME_ROOT
-    ? path.resolve(process.env.UBP_RUNTIME_ROOT)
-    : null;
-  const candidate = runtimeRoot
-    ? path.join(runtimeRoot, 'runtime', BACKUP_WORKER_FILENAME)
-    : path.join(__dirname, BACKUP_WORKER_FILENAME);
-  const stat = fs.lstatSync(candidate, { throwIfNoEntry: false });
-  if (!stat || stat.isSymbolicLink() || !stat.isFile()) {
-    throw new DoctorError(
-      'BACKUP_FAILED',
-      `Doctor backup worker is missing or unsafe: ${candidate}`,
-    );
-  }
-  return candidate;
-}
-
-function canonicalStateDb(db) {
-  const main = db.pragma('database_list').find((row) => row.name === 'main');
-  const sourcePath = path.resolve(String(main?.file || ''));
-  const stat = fs.lstatSync(sourcePath, {
-    bigint: true,
-    throwIfNoEntry: false,
-  });
-  if (!main?.file || !stat || stat.isSymbolicLink() || !stat.isFile()) {
-    throw new DoctorError(
-      'BACKUP_FAILED',
-      `canonical state database is missing or unsafe: ${sourcePath}`,
-    );
-  }
-  return { sourcePath, sourceIdentity: statIdentity(stat) };
-}
-
-function decodeBackupWorker(result, expected) {
-  if (result.error) {
-    throw new DoctorError(
-      'BACKUP_FAILED',
-      `cannot start Doctor backup worker: ${result.error.message}`,
-      { cause: result.error },
-    );
-  }
-  let payload;
-  try {
-    payload = JSON.parse(String(result.stdout || '').trim());
-  } catch (cause) {
-    throw new DoctorError(
-      'BACKUP_FAILED',
-      `Doctor backup worker returned invalid output: ${String(result.stderr || '').trim()}`,
-      { cause },
-    );
-  }
-  if (!payload?.ok) {
-    throw new DoctorError(
-      'BACKUP_FAILED',
-      payload?.error?.message || 'Doctor backup worker failed',
-      { details: payload?.error },
-    );
-  }
-  const value = payload.result;
-  const valid = result.status === 0
-    && value && typeof value === 'object' && !Array.isArray(value)
-    && value.output_name === expected.outputName
-    && value.integrity === 'ok'
-    && value.method === BACKUP_WORKER_METHOD
-    && Number.isSafeInteger(value.size) && value.size > 0
-    && /^[0-9a-f]{64}$/.test(value.digest || '')
-    && sameIdentity(value.directory_identity, expected.directoryIdentity)
-    && sameIdentity(value.source_identity, expected.sourceIdentity)
-    && value.backup_identity && typeof value.backup_identity === 'object';
-  if (!valid) {
-    throw new DoctorError(
-      'BACKUP_FAILED',
-      'Doctor backup worker returned an invalid success payload',
-      { details: { status: result.status, payload } },
-    );
-  }
-  return value;
-}
-
-function verifyPublishedBackup(backupDir, backupPath, expected) {
-  const directory = fs.lstatSync(backupDir, {
-    bigint: true,
-    throwIfNoEntry: false,
-  });
-  if (!directory || directory.isSymbolicLink() || !directory.isDirectory()
-      || !sameIdentity(statIdentity(directory), expected.directoryIdentity)) {
-    throw new DoctorError(
-      'BACKUP_FAILED',
-      'Doctor backup directory changed before backup publication could be verified',
-    );
-  }
-  if (!Number.isInteger(fs.constants.O_NOFOLLOW) || fs.constants.O_NOFOLLOW === 0) {
-    throw new DoctorError(
-      'BACKUP_FAILED',
-      'Doctor cannot verify backups without no-follow file support on this platform',
-    );
-  }
-  let backupFd;
-  try {
-    backupFd = fs.openSync(
-      backupPath,
-      fs.constants.O_RDONLY | fs.constants.O_NOFOLLOW,
-    );
-  } catch (cause) {
-    throw new DoctorError(
-      'BACKUP_FAILED',
-      'Doctor backup publication is missing or unsafe',
-      { cause },
-    );
-  }
-  let backup;
-  let digest;
-  try {
-    backup = fs.fstatSync(backupFd, { bigint: true });
-    if (!backup.isFile()
-        || !sameIdentity(statIdentity(backup), expected.backupIdentity)) {
-      throw new DoctorError(
-        'BACKUP_FAILED',
-        'Doctor backup publication does not match the worker-pinned file',
-      );
-    }
-    digest = crypto.createHash('sha256').update(fs.readFileSync(backupFd)).digest('hex');
-  } finally {
-    fs.closeSync(backupFd);
-  }
-  if (digest !== expected.digest || Number(backup.size) !== expected.size) {
-    throw new DoctorError(
-      'BACKUP_FAILED',
-      'Doctor backup publication failed post-worker verification',
-    );
-  }
-}
-
-async function backupDatabase(db, rootDir, { beforeWorker = null } = {}) {
-  const backupDir = runtimePaths.pathsFor(rootDir).backupsDir;
-  const outputName = `state-${timestamp()}-${crypto.randomUUID()}.db`;
-  const backupPath = path.join(backupDir, outputName);
-  try {
-    runtimePaths.validateProjectLayout(rootDir, {
-      env: {},
-      validateRuntimeTree: true,
-    });
-    fs.mkdirSync(backupDir, { recursive: true, mode: 0o700 });
-    runtimePaths.assertManagedBackupDestination(rootDir, backupPath);
-    const backupDirectory = fs.lstatSync(backupDir, { bigint: true });
-    if (backupDirectory.isSymbolicLink() || !backupDirectory.isDirectory()) {
-      throw new DoctorError('BACKUP_FAILED', `backup root is unsafe: ${backupDir}`);
-    }
-    const directoryIdentity = statIdentity(backupDirectory);
-    const { sourcePath, sourceIdentity } = canonicalStateDb(db);
-    if (beforeWorker) {
-      beforeWorker({
-        backupDir,
-        backupPath,
-        directoryIdentity,
-        sourcePath,
-        sourceIdentity,
-      });
-    }
-    const result = childProcess.spawnSync(
-      process.execPath,
-      [backupWorkerPath()],
-      {
-        cwd: backupDir,
-        input: JSON.stringify({
-          directory_identity: directoryIdentity,
-          source_path: sourcePath,
-          source_identity: sourceIdentity,
-          output_name: outputName,
-        }),
-        encoding: 'utf8',
-        maxBuffer: 1024 * 1024,
-        timeout: BACKUP_WORKER_TIMEOUT_MS,
-        windowsHide: true,
-      },
-    );
-    const published = decodeBackupWorker(result, {
-      outputName,
-      directoryIdentity,
-      sourceIdentity,
-    });
-    verifyPublishedBackup(backupDir, backupPath, {
-      directoryIdentity,
-      backupIdentity: published.backup_identity,
-      digest: published.digest,
-      size: published.size,
-    });
-    return backupPath;
-  } catch (error) {
-    if (error instanceof DoctorError) throw error;
-    throw new DoctorError(
-      'BACKUP_FAILED',
-      `state.db backup failed: ${error.message}`,
-      { cause: error },
-    );
-  }
-}
-
-async function runDoctor(db, {
-  rootDir = process.cwd(), repair = false, project = projector.projectAll,
-  projectionStaleAfterMs = 5 * 60 * 1000,
-  _beforeBackupWorker = null,
-} = {}) {
-  if (!repair) return { ...inspectSystem(db, { rootDir }), repair_performed: false };
-  const backupPath = await backupDatabase(db, rootDir, {
-    beforeWorker: _beforeBackupWorker,
-  });
-  const recovered = recovery.recoverOnBoot(db, { repoRoot: rootDir });
-  if (recovered.close_pending.length > 0) {
-    const deferred = {
-      status: 'deferred',
-      code: 'SESSION_CLOSE_PENDING',
-      pending: recovered.close_pending,
-    };
-    return {
-      ...inspectSystem(db, { rootDir }),
-      repair_performed: true,
-      backup_path: backupPath,
-      repair: {
-        close_intents: recovered,
-        recovered,
-        plan_publications: deferred,
-        archives: deferred,
-        legacy_history: deferred,
-      },
-    };
-  }
-  const planPublications = planStore.recoverPlanPublications(db, { rootDir });
-  if (planPublications.pending > 0 || planPublications.issues.length > 0) {
-    const blocked = planPublications.issues.length > 0;
-    const planGate = {
-      ...planPublications,
-      status: blocked ? 'blocked' : 'deferred',
-      code: 'PLAN_RECOVERY_REQUIRED',
-    };
-    const deferred = {
-      status: 'deferred',
-      code: 'PLAN_RECOVERY_REQUIRED',
-      blocked_by: 'plan_publications',
-    };
-    return {
-      ...inspectSystem(db, { rootDir }),
-      status: 'degraded',
-      repair_performed: true,
-      backup_path: backupPath,
-      repair: {
-        close_intents: recovered,
-        recovered,
-        plan_publications: planGate,
-        archives: deferred,
-        legacy_history: deferred,
-        spec_events: deferred,
-        interrupted: deferred,
-        requeued: deferred,
-        ensured: deferred,
-        projections: deferred,
-      },
-    };
-  }
-  const archives = changes.recoverInterruptedArchives(db, { rootDir });
-  const unresolvedArchives = archiveJournal.listArchiveIntents(rootDir);
-  if (archives.failed > 0 || unresolvedArchives.length > 0) {
-    const archiveGate = {
-      ...archives,
-      pending: unresolvedArchives.length,
-      status: 'blocked',
-      code: 'ARCHIVE_RECOVERY_REQUIRED',
-    };
-    const deferred = {
-      status: 'deferred',
-      code: 'ARCHIVE_RECOVERY_REQUIRED',
-      blocked_by: 'archives',
-    };
-    return {
-      ...inspectSystem(db, { rootDir }),
-      status: 'degraded',
-      repair_performed: true,
-      backup_path: backupPath,
-      repair: {
-        close_intents: recovered,
-        recovered,
-        plan_publications: planPublications,
-        archives: archiveGate,
-        legacy_history: deferred,
-        spec_events: deferred,
-        interrupted: deferred,
-        requeued: deferred,
-        ensured: deferred,
-        projections: deferred,
-      },
-    };
-  }
-  const cursor = runtime.readConsumerCursor(db, SPEC_CONSUMER);
-  const consumed = ops.consumeSpecChangedEvents(db, { since_id: cursor, limit: 500 });
-  runtime.writeConsumerCursor(db, SPEC_CONSUMER, consumed.next_since_id);
-  const interrupted = runtime.requeueInterruptedProjections(db, {
-    staleBefore: new Date(Date.now() - Math.max(0, projectionStaleAfterMs)).toISOString(),
-  });
-  const requeued = runtime.requeueFailedProjections(db);
-  const ensured = runtime.ensureProjectionJob(db, { tool_name: 'system.doctor' });
-  const projections = runtime.processProjectionJobs(db, { rootDir, project, limit: 500 });
-  return {
-    ...inspectSystem(db, { rootDir }),
-    repair_performed: true,
-    backup_path: backupPath,
-    repair: {
-      close_intents: recovered,
-      plan_publications: planPublications,
-      archives, recovered, consumed,
-      interrupted, requeued, ensured, projections,
-    },
-  };
-}
-
-module.exports = {
-  DoctorError,
-  SPEC_CONSUMER,
-  inspectSystem,
-  runDoctor,
-};