feat(auth): add TOTP two-factor authentication with backup codes (#615)

* feat(auth): add TOTP two-factor authentication with backup codes

Adds RFC 6238 time-based one-time password support to every tier,
integrated with the existing password and SSO login paths.

Backend:
- New MfaService wrapping otplib with a plus or minus 1 step tolerance,
  base32 secret generation, and hashed single-use backup codes (bcrypt).
- user_mfa and mfa_used_tokens tables in DatabaseService. The second
  table is a DB-backed replay blacklist, purged on a 60s interval.
- authMiddleware now recognizes an mfa_pending scope. A token carrying
  that scope is rejected on every route except the MFA challenge and
  logout, so no API surface is reachable before the second factor
  clears.
- /api/auth/login issues only a short-lived mfa_pending cookie when the
  user has MFA enrolled. /api/auth/login/mfa consumes that cookie,
  verifies the code (or backup code), and swaps in a real session.
- /api/auth/mfa/* routes for status, enrol/start, enrol/confirm,
  disable, backup-code regenerate, and SSO-bypass opt-in.
- Admin recovery path: POST /api/users/:id/mfa/reset clears the target's
  MFA state, bumps token_version, and writes an audit log entry.
- CLI emergency fallback: backend/src/cli/resetMfa.ts is wired via
  `npm run reset-mfa <username>` and also exported for tests.
- SSO flows (LDAP and OIDC) gate on user_mfa.sso_enforce_mfa before
  issuing a session; default behaviour keeps the SSO path frictionless.
- Per-user lockout after 5 consecutive failed codes (15 min).

Frontend:
- AppStatus gains an mfa-challenge branch driven by /api/auth/status.
- New MfaChallenge screen, MfaEnrollDialog (QR plus manual secret plus
  backup codes), MfaDisableDialog, MfaBackupCodesDialog.
- Account section shows a Two-factor authentication card with enrol,
  regenerate, disable, and the SSO-enforce toggle (shown only when SSO
  providers are configured).
- Users section gains a Reset 2FA action for admins.

Docs:
- New user guide at features/two-factor-authentication.mdx.
- New admin guide at operations/two-factor-admin.mdx.
- SSO page cross-links to the 2FA doc.

* fix(mfa): drop unused TEST_PASSWORD import and stale eslint disable

* fix(mfa): simplify e2e openAccountSettings helper to match working pattern

* fix(mfa): make e2e suite self-contained and always clean up

Test #2 called loginAs() before the MFA challenge step, which waited for
the dashboard indicator that never appears once the previous test enrolled
the user. That timeout skipped the rest of the serial block, including
the disable step, leaving MFA enabled and breaking every later spec.

Two fixes:

- Tests #2 and #3 now navigate directly to the login page instead of
  piggybacking on loginAs, which only handles the password-only path.
- A new afterAll hook unconditionally disables MFA via the API using two
  unused backup codes, so the DB is reset even if a test fails midway.

* fix(e2e): use backup code for mfa recovery to avoid totp replay race

The final recovery step in the backup-code replay test previously
generated a fresh TOTP to sign back in. When the timing landed inside
the same 30-second window that test #2 consumed, the server's replay
blacklist correctly rejected it, producing a ~50% flake rate. Backup
codes are single-use and sidestep the replay window, so the recovery
becomes deterministic.

* fix(e2e): drive mfa disable test through the challenge screen

Test #4 called loginAs after test #3 left MFA enabled, but loginAs
waits for the dashboard indicator and does not handle the challenge
screen, so it timed out. Drive the login manually, satisfy the
challenge with a backup code, and use a backup code for the disable
step too to avoid any TOTP replay-window race against earlier tests
in the serial block.

backend/src/index.ts

@@ -31,6 +31,8 @@ import { NodeRegistry } from './services/NodeRegistry';
 import { LicenseService, type LicenseTier, type LicenseVariant, isLicenseTier, isLicenseVariant, normalizeTier, normalizeVariant, PROXY_TIER_HEADER, PROXY_VARIANT_HEADER } from './services/LicenseService';
 import { WebhookService } from './services/WebhookService';
 import { SSOService } from './services/SSOService';
+import { MfaService } from './services/MfaService';
+import { CryptoService } from './services/CryptoService';
 import { SchedulerService } from './services/SchedulerService';
 import { RegistryService } from './services/RegistryService';
 import { CacheService } from './services/CacheService';
@@ -95,6 +97,9 @@ const PORT = 3000;
 
 // Cookie settings
 const COOKIE_NAME = 'sencho_token';
+const MFA_PENDING_COOKIE_NAME = 'sencho_mfa_pending';
+const MFA_PENDING_SCOPE = 'mfa_pending';
+const MFA_PENDING_TTL_MS = 5 * 60 * 1000; // 5 minutes to complete the challenge
 
 // Helper to determine if request is secure (HTTPS or behind a proxy that terminates SSL)
 const isSecureRequest = (req: Request): boolean => {
@@ -405,6 +410,10 @@ declare global {
       proxyTier?: LicenseTier;
       /** License variant asserted by the main instance on proxied requests. Only set for trusted node_proxy tokens. */
       proxyVariant?: LicenseVariant;
+      /** User ID carried by a scoped `mfa_pending` token. Only set while the user is completing the MFA challenge. */
+      mfaPendingUserId?: number;
+      /** True when the pending MFA session originated from an SSO login (LDAP or OIDC) rather than a password login. */
+      mfaPendingSso?: boolean;
     }
   }
 }
@@ -436,7 +445,7 @@ const authMiddleware = async (req: Request, res: Response, next: NextFunction):
     const settings = DatabaseService.getInstance().getGlobalSettings();
     const jwtSecret = settings.auth_jwt_secret;
     if (!jwtSecret) throw new Error('No JWT secret');
-    const decoded = jwt.verify(token, jwtSecret) as { username?: string; role?: string; scope?: string; tv?: number };
+    const decoded = jwt.verify(token, jwtSecret) as { username?: string; role?: string; scope?: string; tv?: number; user_id?: number; sso?: boolean };
 
     if (isDebugEnabled()) console.log('[Auth:diag] Token type:', bearerToken ? 'bearer' : 'cookie', 'scope:', decoded.scope || 'user-session');
 
@@ -468,6 +477,23 @@ const authMiddleware = async (req: Request, res: Response, next: NextFunction):
       return;
     }
 
+    // Partial-auth session: a password/SSO credential has verified, but the
+    // TOTP second factor is still required. Such a token can only be used to
+    // complete the MFA challenge or to abort the flow by logging out. Every
+    // other route must reject it so no privileged action is reachable before
+    // the second factor clears.
+    if (decoded.scope === MFA_PENDING_SCOPE) {
+      const allowedPath = req.path === '/api/auth/login/mfa' || req.path === '/api/auth/logout';
+      if (!allowedPath) {
+        res.status(403).json({ error: 'Two-factor authentication required', code: 'MFA_PENDING' });
+        return;
+      }
+      req.mfaPendingUserId = typeof decoded.user_id === 'number' ? decoded.user_id : undefined;
+      req.mfaPendingSso = decoded.sso === true;
+      next();
+      return;
+    }
+
     // Node proxy tokens: Sencho-to-Sencho communication, not user sessions.
     // Handle before user resolution since proxy tokens have no username.
     if (decoded.scope === 'node_proxy') {
@@ -536,6 +562,36 @@ function issueSessionCookie(
   res.cookie(COOKIE_NAME, token, getCookieOptions(req));
 }
 
+/**
+ * Sign a short-lived `mfa_pending` JWT and set it as an httpOnly cookie. This
+ * represents the partial-auth session that exists between password (or SSO)
+ * success and TOTP verification. The scope is enforced in `authMiddleware`, so
+ * this cookie cannot be used to reach any route other than
+ * `/api/auth/login/mfa` or `/api/auth/logout`.
+ */
+function issueMfaPendingCookie(
+  res: Response,
+  req: Request,
+  user: { id: number; username: string },
+  jwtSecret: string,
+  opts: { sso?: boolean } = {},
+): void {
+  const token = jwt.sign(
+    { scope: MFA_PENDING_SCOPE, user_id: user.id, username: user.username, sso: opts.sso === true },
+    jwtSecret,
+    { expiresIn: Math.floor(MFA_PENDING_TTL_MS / 1000) },
+  );
+  res.cookie(MFA_PENDING_COOKIE_NAME, token, {
+    ...getCookieOptions(req),
+    maxAge: MFA_PENDING_TTL_MS,
+  });
+}
+
+/** Clear the partial-auth cookie. Called on successful MFA verification and on logout. */
+function clearMfaPendingCookie(res: Response, req: Request): void {
+  res.clearCookie(MFA_PENDING_COOKIE_NAME, getCookieOptions(req));
+}
+
 // Rate limiter for auth endpoints - prevents brute-force attacks.
 // Production: 5 attempts per 15-minute window per IP.
 // Development: 100 attempts (so E2E tests and local tooling are not blocked).
@@ -570,15 +626,30 @@ app.get('/api/meta', (_req: Request, res: Response): void => {
 
 // Auth Routes (no authentication required)
 
-// Check if setup is needed
+// Check if setup is needed, and whether the caller currently holds a valid
+// `mfa_pending` partial-auth cookie (so the frontend can route to the
+// challenge screen on a page reload mid-flow, for example after an OIDC
+// redirect).
 app.get('/api/auth/status', async (req: Request, res: Response): Promise<void> => {
   try {
     const settings = DatabaseService.getInstance().getGlobalSettings();
     const needsSetup = !settings.auth_username || !settings.auth_password_hash || !settings.auth_jwt_secret;
-    res.json({ needsSetup });
+
+    let mfaPending = false;
+    const mfaCookie = req.cookies?.[MFA_PENDING_COOKIE_NAME];
+    if (mfaCookie && settings.auth_jwt_secret) {
+      try {
+        const decoded = jwt.verify(mfaCookie, settings.auth_jwt_secret) as { scope?: string };
+        mfaPending = decoded.scope === MFA_PENDING_SCOPE;
+      } catch {
+        // Expired or invalid cookie; treat as no pending challenge.
+      }
+    }
+
+    res.json({ needsSetup, mfaPending });
   } catch (error) {
     console.error('Error checking setup status:', error);
-    res.json({ needsSetup: true });
+    res.json({ needsSetup: true, mfaPending: false });
   }
 });
 
@@ -654,6 +725,18 @@ app.post('/api/auth/login', authRateLimiter, async (req: Request, res: Response)
         const settings = db.getGlobalSettings();
         const jwtSecret = settings.auth_jwt_secret;
         if (!jwtSecret) throw new Error('JWT secret missing from DB');
+
+        // If MFA is enabled for this user, issue only the partial-auth cookie
+        // and signal the client to complete the TOTP challenge. No session
+        // cookie is set until the second factor is verified.
+        const mfa = db.getUserMfa(user.id);
+        if (mfa?.enabled) {
+          issueMfaPendingCookie(res, req, user, jwtSecret);
+          console.log('[Auth] Login password OK, MFA challenge pending:', user.username);
+          res.json({ success: true, mfaRequired: true });
+          return;
+        }
+
         issueSessionCookie(res, req, user, jwtSecret);
         console.log('[Auth] Login successful:', user.username);
         res.json({ success: true, message: 'Login successful' });
@@ -726,6 +809,9 @@ app.post('/api/auth/logout', (req: Request, res: Response): void => {
     secure: isSecureRequest(req),
     sameSite: 'strict',
   });
+  // Also clear any partial-auth cookie so a user aborting the MFA challenge
+  // is returned to a fully unauthenticated state.
+  clearMfaPendingCookie(res, req);
   res.json({ success: true, message: 'Logged out successfully' });
 });
 
@@ -806,6 +892,17 @@ app.post('/api/auth/sso/ldap', authRateLimiter, async (req: Request, res: Respon
 
     // Issue JWT (same as local login)
     const settings = DatabaseService.getInstance().getGlobalSettings();
+
+    // If MFA is enabled AND the user has opted into SSO enforcement, route
+    // through the TOTP challenge. Otherwise SSO bypasses MFA (default).
+    const mfa = DatabaseService.getInstance().getUserMfa(user.id);
+    if (mfa?.enabled && mfa.sso_enforce_mfa) {
+      issueMfaPendingCookie(res, req, user, settings.auth_jwt_secret, { sso: true });
+      console.log(`[SSO] LDAP login password OK, MFA challenge pending: ${user.username}`);
+      res.json({ success: true, mfaRequired: true });
+      return;
+    }
+
     issueSessionCookie(res, req, user, settings.auth_jwt_secret);
     console.log(`[SSO] LDAP login successful: ${user.username}`);
     res.json({ success: true, message: 'Login successful' });
@@ -918,6 +1015,18 @@ app.get('/api/auth/sso/oidc/:provider/callback', ssoRateLimiter, async (req: Req
 
     // Issue JWT + cookie (same as local login)
     const settings = DatabaseService.getInstance().getGlobalSettings();
+
+    // If MFA is enabled AND the user has opted into SSO enforcement, set only
+    // the partial-auth cookie. The frontend surfaces the challenge screen
+    // based on `/api/auth/status` after the redirect lands.
+    const mfa = DatabaseService.getInstance().getUserMfa(user.id);
+    if (mfa?.enabled && mfa.sso_enforce_mfa) {
+      issueMfaPendingCookie(res, req, user, settings.auth_jwt_secret, { sso: true });
+      console.log(`[SSO] OIDC login password OK, MFA challenge pending: ${user.username} via ${provider}`);
+      res.redirect('/');
+      return;
+    }
+
     issueSessionCookie(res, req, user, settings.auth_jwt_secret);
     console.log(`[SSO] OIDC login successful: ${user.username} via ${provider}`);
 
@@ -929,6 +1038,382 @@ app.get('/api/auth/sso/oidc/:provider/callback', ssoRateLimiter, async (req: Req
   }
 });
 
+// --- MFA (TOTP) Routes ---
+
+const MFA_MAX_FAILED = 5;
+const MFA_LOCKOUT_MS = 15 * 60 * 1000;
+const MFA_REPLAY_TTL_MS = 120 * 1000;
+const MFA_REPLAY_PURGE_INTERVAL_MS = 60 * 1000;
+
+/**
+ * Complete the second factor of login. Consumes the short-lived
+ * `sencho_mfa_pending` cookie and, on success, clears it and issues a full
+ * session cookie. Accepts either a 6-digit TOTP or one of the user's backup
+ * codes (single-use). Enforces per-user failure counter and lockout.
+ */
+app.post('/api/auth/login/mfa', authRateLimiter, async (req: Request, res: Response): Promise<void> => {
+  try {
+    const db = DatabaseService.getInstance();
+    const settings = db.getGlobalSettings();
+    const jwtSecret = settings.auth_jwt_secret;
+    if (!jwtSecret) {
+      res.status(500).json({ error: 'Server is not configured' });
+      return;
+    }
+
+    const pendingCookie = req.cookies?.[MFA_PENDING_COOKIE_NAME];
+    if (!pendingCookie) {
+      res.status(401).json({ error: 'No pending two-factor challenge. Please sign in again.' });
+      return;
+    }
+
+    let decoded: { scope?: string; user_id?: number; username?: string; sso?: boolean };
+    try {
+      decoded = jwt.verify(pendingCookie, jwtSecret) as typeof decoded;
+    } catch {
+      clearMfaPendingCookie(res, req);
+      res.status(401).json({ error: 'Two-factor challenge expired. Please sign in again.' });
+      return;
+    }
+
+    if (decoded.scope !== MFA_PENDING_SCOPE || typeof decoded.user_id !== 'number') {
+      clearMfaPendingCookie(res, req);
+      res.status(401).json({ error: 'Invalid two-factor challenge' });
+      return;
+    }
+
+    const user = db.getUserById(decoded.user_id);
+    const mfa = db.getUserMfa(decoded.user_id);
+    if (!user || !mfa?.enabled || !mfa.totp_secret_encrypted) {
+      clearMfaPendingCookie(res, req);
+      res.status(401).json({ error: 'Two-factor authentication is not configured' });
+      return;
+    }
+
+    // Lockout check
+    if (mfa.locked_until && mfa.locked_until > Date.now()) {
+      const retryAfter = Math.ceil((mfa.locked_until - Date.now()) / 1000);
+      res.setHeader('Retry-After', String(retryAfter));
+      res.status(423).json({ error: 'Too many failed attempts. Try again later.', retryAfter });
+      return;
+    }
+
+    const rawCode = typeof req.body?.code === 'string' ? req.body.code : '';
+    const isBackup = req.body?.isBackupCode === true;
+    if (!rawCode) {
+      res.status(400).json({ error: 'A verification code is required' });
+      return;
+    }
+
+    const cryptoSvc = CryptoService.getInstance();
+    const secret = cryptoSvc.decrypt(mfa.totp_secret_encrypted);
+    let verified = false;
+
+    if (isBackup) {
+      const hashes: string[] = mfa.backup_codes_json ? JSON.parse(mfa.backup_codes_json) : [];
+      const result = await MfaService.verifyBackupCode(hashes, rawCode);
+      if (result.matched) {
+        db.upsertUserMfa(decoded.user_id, { backup_codes_json: JSON.stringify(result.remainingHashes) });
+        verified = true;
+      }
+    } else {
+      const trimmed = rawCode.trim().replace(/\s+/g, '');
+      if (MfaService.verifyTotp(secret, trimmed)) {
+        const window = MfaService.currentWindow();
+        if (db.isMfaCodeUsed(decoded.user_id, trimmed, window)) {
+          db.recordMfaFailure(decoded.user_id);
+          res.status(401).json({ error: 'This code was already used. Please wait for the next one.', code: 'OTP_REPLAY' });
+          return;
+        }
+        db.markMfaCodeUsed(decoded.user_id, trimmed, window);
+        verified = true;
+      }
+    }
+
+    if (!verified) {
+      const failedCount = db.recordMfaFailure(decoded.user_id);
+      if (failedCount >= MFA_MAX_FAILED) {
+        db.lockMfa(decoded.user_id, Date.now() + MFA_LOCKOUT_MS);
+        res.setHeader('Retry-After', String(Math.ceil(MFA_LOCKOUT_MS / 1000)));
+        res.status(423).json({ error: 'Too many failed attempts. Try again later.', retryAfter: Math.ceil(MFA_LOCKOUT_MS / 1000) });
+        return;
+      }
+      res.status(401).json({ error: 'Invalid verification code' });
+      return;
+    }
+
+    db.clearMfaFailures(decoded.user_id);
+    clearMfaPendingCookie(res, req);
+    issueSessionCookie(res, req, user, jwtSecret);
+    console.log('[Auth] MFA challenge cleared:', user.username);
+    res.json({ success: true });
+  } catch (error: unknown) {
+    console.error('[Auth] MFA verification error:', (error as Error).message);
+    res.status(500).json({ error: 'Two-factor verification failed' });
+  }
+});
+
+/** Report the current user's MFA state. Used by the Account settings UI. */
+app.get('/api/auth/mfa/status', authMiddleware, (req: Request, res: Response): void => {
+  try {
+    if (!req.user) {
+      res.status(401).json({ error: 'Authentication required' });
+      return;
+    }
+    const db = DatabaseService.getInstance();
+    const mfa = db.getUserMfa(req.user.userId);
+    const hashes: string[] = mfa?.backup_codes_json ? JSON.parse(mfa.backup_codes_json) : [];
+    res.json({
+      enabled: mfa?.enabled === 1,
+      backupCodesRemaining: hashes.length,
+      sso_enforce_mfa: mfa?.sso_enforce_mfa === 1,
+    });
+  } catch (error: unknown) {
+    console.error('[MFA] status error:', (error as Error).message);
+    res.status(500).json({ error: 'Failed to load MFA status' });
+  }
+});
+
+/**
+ * Begin enrolment: generate a fresh TOTP secret, store it encrypted with
+ * `enabled=0`, and return the otpauth URI plus the raw base32 secret so the
+ * frontend can render a QR code and the manual-entry fallback.
+ */
+app.post('/api/auth/mfa/enroll/start', authMiddleware, (req: Request, res: Response): void => {
+  try {
+    if (!req.user) {
+      res.status(401).json({ error: 'Authentication required' });
+      return;
+    }
+    if (req.apiTokenScope) {
+      res.status(403).json({ error: 'API tokens cannot manage MFA.', code: 'SCOPE_DENIED' });
+      return;
+    }
+    const db = DatabaseService.getInstance();
+    const existing = db.getUserMfa(req.user.userId);
+    if (existing?.enabled) {
+      res.status(409).json({ error: 'Two-factor authentication is already enabled' });
+      return;
+    }
+
+    const secret = MfaService.generateSecret();
+    const cryptoSvc = CryptoService.getInstance();
+    db.upsertUserMfa(req.user.userId, {
+      enabled: false,
+      totp_secret_encrypted: cryptoSvc.encrypt(secret),
+      backup_codes_json: null,
+      failed_attempts: 0,
+      locked_until: null,
+    });
+
+    const otpauthUri = MfaService.buildOtpauthUri(secret, req.user.username);
+    res.json({ otpauthUri, secret });
+  } catch (error: unknown) {
+    console.error('[MFA] enroll start error:', (error as Error).message);
+    res.status(500).json({ error: 'Failed to start enrolment' });
+  }
+});
+
+/**
+ * Finalise enrolment: verify the user's first TOTP against the pending
+ * secret, flip `enabled=1`, generate + hash + return the backup codes ONCE,
+ * and bump `token_version` so any other sessions re-authenticate.
+ */
+app.post('/api/auth/mfa/enroll/confirm', authMiddleware, async (req: Request, res: Response): Promise<void> => {
+  try {
+    if (!req.user) {
+      res.status(401).json({ error: 'Authentication required' });
+      return;
+    }
+    if (req.apiTokenScope) {
+      res.status(403).json({ error: 'API tokens cannot manage MFA.', code: 'SCOPE_DENIED' });
+      return;
+    }
+    const code = typeof req.body?.code === 'string' ? req.body.code : '';
+    if (!code) {
+      res.status(400).json({ error: 'A verification code is required' });
+      return;
+    }
+
+    const db = DatabaseService.getInstance();
+    const mfa = db.getUserMfa(req.user.userId);
+    if (!mfa?.totp_secret_encrypted) {
+      res.status(400).json({ error: 'No enrolment in progress. Start enrolment first.' });
+      return;
+    }
+    if (mfa.enabled) {
+      res.status(409).json({ error: 'Two-factor authentication is already enabled' });
+      return;
+    }
+
+    const cryptoSvc = CryptoService.getInstance();
+    const secret = cryptoSvc.decrypt(mfa.totp_secret_encrypted);
+    if (!MfaService.verifyTotp(secret, code)) {
+      res.status(401).json({ error: 'Invalid verification code' });
+      return;
+    }
+
+    const backupCodes = MfaService.generateBackupCodes();
+    const hashes = await MfaService.hashBackupCodes(backupCodes);
+    db.upsertUserMfa(req.user.userId, {
+      enabled: true,
+      backup_codes_json: JSON.stringify(hashes),
+      failed_attempts: 0,
+      locked_until: null,
+    });
+    db.bumpTokenVersion(req.user.userId);
+
+    // The token_version bump invalidates the caller's current session cookie.
+    // Since the user has just proven possession of the TOTP secret, re-issue a
+    // session cookie that carries the new token_version so they stay signed in
+    // long enough to see and save the backup codes.
+    const refreshed = db.getUserById(req.user.userId);
+    const settings = db.getGlobalSettings();
+    if (refreshed && settings.auth_jwt_secret) {
+      issueSessionCookie(res, req, refreshed, settings.auth_jwt_secret);
+    }
+
+    res.json({ backupCodes: backupCodes.map((c) => MfaService.formatBackupCodeForDisplay(c)) });
+  } catch (error: unknown) {
+    console.error('[MFA] enroll confirm error:', (error as Error).message);
+    res.status(500).json({ error: 'Failed to confirm enrolment' });
+  }
+});
+
+/**
+ * Disable MFA for the current user. Requires a valid TOTP or backup code to
+ * prove possession, so a stolen session cookie alone cannot turn off the
+ * second factor. Bumps `token_version` on success.
+ */
+app.post('/api/auth/mfa/disable', authMiddleware, async (req: Request, res: Response): Promise<void> => {
+  try {
+    if (!req.user) {
+      res.status(401).json({ error: 'Authentication required' });
+      return;
+    }
+    if (req.apiTokenScope) {
+      res.status(403).json({ error: 'API tokens cannot manage MFA.', code: 'SCOPE_DENIED' });
+      return;
+    }
+    const code = typeof req.body?.code === 'string' ? req.body.code : '';
+    const isBackup = req.body?.isBackupCode === true;
+    if (!code) {
+      res.status(400).json({ error: 'A verification code is required to disable two-factor authentication' });
+      return;
+    }
+
+    const db = DatabaseService.getInstance();
+    const mfa = db.getUserMfa(req.user.userId);
+    if (!mfa?.enabled || !mfa.totp_secret_encrypted) {
+      res.status(400).json({ error: 'Two-factor authentication is not enabled' });
+      return;
+    }
+
+    let ok = false;
+    if (isBackup) {
+      const hashes: string[] = mfa.backup_codes_json ? JSON.parse(mfa.backup_codes_json) : [];
+      ok = (await MfaService.verifyBackupCode(hashes, code)).matched;
+    } else {
+      const cryptoSvc = CryptoService.getInstance();
+      ok = MfaService.verifyTotp(cryptoSvc.decrypt(mfa.totp_secret_encrypted), code);
+    }
+
+    if (!ok) {
+      res.status(401).json({ error: 'Invalid verification code' });
+      return;
+    }
+
+    db.deleteUserMfa(req.user.userId);
+    db.bumpTokenVersion(req.user.userId);
+
+    // Re-issue the session cookie so the user stays signed in after the bump.
+    // They just proved possession of a current factor, so granting them the
+    // new token_version is safe and avoids a surprising forced re-login.
+    const refreshed = db.getUserById(req.user.userId);
+    const settings = db.getGlobalSettings();
+    if (refreshed && settings.auth_jwt_secret) {
+      issueSessionCookie(res, req, refreshed, settings.auth_jwt_secret);
+    }
+
+    res.json({ success: true });
+  } catch (error: unknown) {
+    console.error('[MFA] disable error:', (error as Error).message);
+    res.status(500).json({ error: 'Failed to disable two-factor authentication' });
+  }
+});
+
+/**
+ * Regenerate backup codes. Requires a valid TOTP so a stolen session alone
+ * cannot print new codes. The old set is invalidated immediately; the new
+ * set is returned in cleartext ONCE.
+ */
+app.post('/api/auth/mfa/backup-codes/regenerate', authMiddleware, async (req: Request, res: Response): Promise<void> => {
+  try {
+    if (!req.user) {
+      res.status(401).json({ error: 'Authentication required' });
+      return;
+    }
+    if (req.apiTokenScope) {
+      res.status(403).json({ error: 'API tokens cannot manage MFA.', code: 'SCOPE_DENIED' });
+      return;
+    }
+    const code = typeof req.body?.code === 'string' ? req.body.code : '';
+    if (!code) {
+      res.status(400).json({ error: 'A verification code is required' });
+      return;
+    }
+
+    const db = DatabaseService.getInstance();
+    const mfa = db.getUserMfa(req.user.userId);
+    if (!mfa?.enabled || !mfa.totp_secret_encrypted) {
+      res.status(400).json({ error: 'Two-factor authentication is not enabled' });
+      return;
+    }
+
+    const cryptoSvc = CryptoService.getInstance();
+    if (!MfaService.verifyTotp(cryptoSvc.decrypt(mfa.totp_secret_encrypted), code)) {
+      res.status(401).json({ error: 'Invalid verification code' });
+      return;
+    }
+
+    const backupCodes = MfaService.generateBackupCodes();
+    const hashes = await MfaService.hashBackupCodes(backupCodes);
+    db.upsertUserMfa(req.user.userId, { backup_codes_json: JSON.stringify(hashes) });
+    res.json({ backupCodes: backupCodes.map((c) => MfaService.formatBackupCodeForDisplay(c)) });
+  } catch (error: unknown) {
+    console.error('[MFA] regenerate backup codes error:', (error as Error).message);
+    res.status(500).json({ error: 'Failed to regenerate backup codes' });
+  }
+});
+
+/** Toggle whether SSO logins must also complete the TOTP challenge. */
+app.put('/api/auth/mfa/sso-bypass', authMiddleware, (req: Request, res: Response): void => {
+  try {
+    if (!req.user) {
+      res.status(401).json({ error: 'Authentication required' });
+      return;
+    }
+    if (req.apiTokenScope) {
+      res.status(403).json({ error: 'API tokens cannot manage MFA.', code: 'SCOPE_DENIED' });
+      return;
+    }
+    const enforce = req.body?.enforce === true;
+    const db = DatabaseService.getInstance();
+    const mfa = db.getUserMfa(req.user.userId);
+    if (!mfa?.enabled) {
+      res.status(400).json({ error: 'Two-factor authentication is not enabled' });
+      return;
+    }
+    if ((mfa.sso_enforce_mfa === 1) !== enforce) {
+      db.upsertUserMfa(req.user.userId, { sso_enforce_mfa: enforce });
+    }
+    res.json({ success: true, sso_enforce_mfa: enforce });
+  } catch (error: unknown) {
+    console.error('[MFA] sso-bypass error:', (error as Error).message);
+    res.status(500).json({ error: 'Failed to update SSO enforcement' });
+  }
+});
+
 // Apply authentication middleware to all /api/* routes except /api/auth/*
 app.use('/api', (req: Request, res: Response, next: NextFunction): void => {
   if (req.path.startsWith('/auth/') || /^\/webhooks\/\d+\/trigger$/.test(req.path)) {
@@ -2393,8 +2878,14 @@ app.get('/api/users', authMiddleware, async (req: Request, res: Response): Promi
   }
   if (!requireAdmin(req, res)) return;
   try {
-    const users = DatabaseService.getInstance().getUsers();
-    res.json(users);
+    const db = DatabaseService.getInstance();
+    const users = db.getUsers();
+    const mfaUserIds = db.getUsersWithMfaEnabled();
+    const enriched = users.map((u) => ({
+      ...u,
+      mfaEnabled: mfaUserIds.has(u.id),
+    }));
+    res.json(enriched);
   } catch (error) {
     console.error('[Users] List error:', error);
     res.status(500).json({ error: 'Failed to fetch users' });
@@ -2574,6 +3065,54 @@ app.delete('/api/users/:id', authMiddleware, async (req: Request, res: Response)
   }
 });
 
+/**
+ * Admin reset: clear a target user's MFA enrolment and force re-auth. Used
+ * when a user has lost their authenticator AND exhausted their backup codes,
+ * and another admin is available. For total lockout (including sole admin),
+ * see the CLI `reset-mfa` command.
+ */
+app.post('/api/users/:id/mfa/reset', authMiddleware, (req: Request, res: Response): void => {
+  if (req.apiTokenScope) {
+    res.status(403).json({ error: 'API tokens cannot access user management.', code: 'SCOPE_DENIED' });
+    return;
+  }
+  if (!requireAdmin(req, res)) return;
+  try {
+    const id = parseInt(req.params.id as string, 10);
+    if (!Number.isFinite(id)) {
+      res.status(400).json({ error: 'Invalid user id' });
+      return;
+    }
+    const db = DatabaseService.getInstance();
+    const target = db.getUser(id);
+    if (!target) {
+      res.status(404).json({ error: 'User not found' });
+      return;
+    }
+    db.deleteUserMfa(id);
+    db.bumpTokenVersion(id);
+    try {
+      db.insertAuditLog({
+        timestamp: Date.now(),
+        username: req.user!.username,
+        method: 'POST',
+        path: req.originalUrl,
+        status_code: 200,
+        node_id: null,
+        ip_address: req.ip || 'unknown',
+        summary: `Admin reset two-factor authentication for ${target.username}`,
+      });
+    } catch (err) {
+      console.warn('[MFA] Admin reset audit log write failed:', (err as Error).message);
+    }
+    console.log('[MFA] Admin reset: target=', target.username, 'by=', req.user!.username);
+    res.json({ success: true });
+  } catch (error: unknown) {
+    console.error('[MFA] Admin reset error:', (error as Error).message);
+    res.status(500).json({ error: 'Failed to reset two-factor authentication' });
+  }
+});
+
 // --- Scoped Role Assignments (Admiral) ---
 
 app.get('/api/users/:id/roles', authMiddleware, (req: Request, res: Response): void => {
@@ -6798,6 +7337,8 @@ if (process.env.NODE_ENV === 'production') {
 }
 
 // Start server with migration
+let mfaReplayPurgeTimer: NodeJS.Timeout | null = null;
+
 async function startServer() {
   try {
     // Run migration before starting server
@@ -6833,6 +7374,18 @@ async function startServer() {
     console.warn('[GitSource] Temp dir sweep failed:', (err as Error).message);
   });
 
+  // Periodic purge of used-MFA-code rows so the replay blacklist stays
+  // bounded even without verification traffic. The table holds (user, code,
+  // window) tuples for the last ~2 minutes; older rows are safe to drop.
+  mfaReplayPurgeTimer = setInterval(() => {
+    try {
+      DatabaseService.getInstance().purgeOldMfaCodes(Date.now() - MFA_REPLAY_TTL_MS);
+    } catch (err) {
+      console.warn('[MFA] Replay purge failed:', (err as Error).message);
+    }
+  }, MFA_REPLAY_PURGE_INTERVAL_MS);
+  mfaReplayPurgeTimer.unref();
+
   server.listen(PORT, () => {
     console.log(`Server running on port ${PORT}`);
   });
@@ -6869,6 +7422,10 @@ const gracefulShutdown = (signal: string) => {
     try { SchedulerService.getInstance().stop(); } catch (e) {
       console.warn('[Shutdown] SchedulerService cleanup failed:', (e as Error).message);
     }
+    if (mfaReplayPurgeTimer) {
+      clearInterval(mfaReplayPurgeTimer);
+      mfaReplayPurgeTimer = null;
+    }
     try { DatabaseService.getInstance().getDb().close(); } catch (e) {
       console.warn('[Shutdown] Database close failed:', (e as Error).message);
     }