fix:Harden authentication and sensitive file handling

migrations/0001_init.sql

@@ -228,6 +228,16 @@ CREATE TABLE IF NOT EXISTS trusted_two_factor_device_tokens (
 CREATE INDEX IF NOT EXISTS idx_trusted_two_factor_device_tokens_user_device
   ON trusted_two_factor_device_tokens(user_id, device_identifier);
 
+CREATE TABLE IF NOT EXISTS totp_login_replays (
+  user_id TEXT NOT NULL,
+  time_counter INTEGER NOT NULL,
+  consumed_at INTEGER NOT NULL,
+  PRIMARY KEY (user_id, time_counter),
+  FOREIGN KEY (user_id) REFERENCES users(id) ON DELETE CASCADE
+);
+CREATE INDEX IF NOT EXISTS idx_totp_login_replays_consumed_at
+  ON totp_login_replays(consumed_at);
+
 CREATE TABLE IF NOT EXISTS webauthn_credentials (
   id TEXT PRIMARY KEY,
   user_id TEXT NOT NULL,

src/handlers/identity.ts

@@ -4,7 +4,7 @@ import { AuthService } from '../services/auth';
 import { RateLimitService, getClientIdentifier } from '../services/ratelimit';
 import { jsonResponse, errorResponse, identityErrorResponse } from '../utils/response';
 import { LIMITS } from '../config/limits';
-import { isTotpEnabled, verifyTotpToken } from '../utils/totp';
+import { findMatchingTotpCounter, isTotpEnabled } from '../utils/totp';
 import { createRefreshToken } from '../utils/jwt';
 import { readAuthRequestDeviceInfo } from '../utils/device';
 import { createRecoveryCode, recoveryCodeEquals } from '../utils/recovery-code';
@@ -409,8 +409,12 @@ export async function handleToken(request: Request, env: Env): Promise<Response>
           return twoFactorRequiredResponse('Two factor required.');
         }
       } else if (normalizedTwoFactorProvider === String(TWO_FACTOR_PROVIDER_AUTHENTICATOR)) {
-        const totpOk = await verifyTotpToken(effectiveTotpSecret, normalizedTwoFactorToken);
-        if (!totpOk) {
+        const matchedCounter = await findMatchingTotpCounter(effectiveTotpSecret, normalizedTwoFactorToken);
+        if (matchedCounter == null) {
+          return recordFailedTwoFactorAndBuildResponse(rateLimit, loginIdentifier);
+        }
+        const consumed = await storage.consumeTotpLoginCounter(user.id, matchedCounter);
+        if (!consumed) {
           return recordFailedTwoFactorAndBuildResponse(rateLimit, loginIdentifier);
         }
       } else if (

src/services/storage-schema.ts

@@ -127,6 +127,12 @@ const SCHEMA_STATEMENTS: readonly string[] = [
   'FOREIGN KEY (user_id) REFERENCES users(id) ON DELETE CASCADE)',
   'CREATE INDEX IF NOT EXISTS idx_trusted_two_factor_device_tokens_user_device ON trusted_two_factor_device_tokens(user_id, device_identifier)',
 
+  'CREATE TABLE IF NOT EXISTS totp_login_replays (' +
+  'user_id TEXT NOT NULL, time_counter INTEGER NOT NULL, consumed_at INTEGER NOT NULL, ' +
+  'PRIMARY KEY (user_id, time_counter), ' +
+  'FOREIGN KEY (user_id) REFERENCES users(id) ON DELETE CASCADE)',
+  'CREATE INDEX IF NOT EXISTS idx_totp_login_replays_consumed_at ON totp_login_replays(consumed_at)',
+
   'CREATE TABLE IF NOT EXISTS webauthn_credentials (' +
   'id TEXT PRIMARY KEY, user_id TEXT NOT NULL, name TEXT NOT NULL, public_key TEXT NOT NULL, credential_id TEXT NOT NULL, counter INTEGER NOT NULL DEFAULT 0, ' +
   'type TEXT, aa_guid TEXT, transports TEXT, encrypted_user_key TEXT, encrypted_public_key TEXT, encrypted_private_key TEXT, supports_prf INTEGER NOT NULL DEFAULT 0, ' +

src/services/storage-totp-replay-repo.ts

@@ -0,0 +1,35 @@
+type ShouldRunPeriodicCleanup = (lastRunAt: number, intervalMs: number) => boolean;
+
+export async function consumeTotpLoginCounter(
+  db: D1Database,
+  shouldRunPeriodicCleanup: ShouldRunPeriodicCleanup,
+  lastCleanupAt: number,
+  cleanupIntervalMs: number,
+  userId: string,
+  timeCounter: number,
+  consumedAtMs: number,
+  markerTtlMs: number
+): Promise<{ consumed: boolean; cleanedUpAt: number | null }> {
+  let cleanedUpAt: number | null = null;
+
+  if (shouldRunPeriodicCleanup(lastCleanupAt, cleanupIntervalMs)) {
+    await db
+      .prepare('DELETE FROM totp_login_replays WHERE consumed_at < ?')
+      .bind(consumedAtMs - markerTtlMs)
+      .run();
+    cleanedUpAt = consumedAtMs;
+  }
+
+  const result = await db
+    .prepare(
+      'INSERT INTO totp_login_replays(user_id, time_counter, consumed_at) VALUES(?, ?, ?) ' +
+        'ON CONFLICT(user_id, time_counter) DO NOTHING'
+    )
+    .bind(userId, timeCounter, consumedAtMs)
+    .run();
+
+  return {
+    consumed: (result.meta.changes ?? 0) > 0,
+    cleanedUpAt,
+  };
+}

src/services/storage.ts

@@ -123,6 +123,9 @@ import {
   ensureUsedAttachmentDownloadTokenTable as ensureStoredAttachmentTokenTable,
   consumeAttachmentDownloadToken as consumeStoredAttachmentDownloadToken,
 } from './storage-attachment-token-repo';
+import {
+  consumeTotpLoginCounter as consumeStoredTotpLoginCounter,
+} from './storage-totp-replay-repo';
 import {
   getRevisionDate as getStoredRevisionDate,
   updateRevisionDate as updateStoredRevisionDate,
@@ -150,8 +153,8 @@ const STORAGE_SCHEMA_VERSION_KEY = 'schema.version';
 // Bump this whenever src/services/storage-schema.ts or migrations/0001_init.sql
 // changes. Existing D1 installs only rerun ensureStorageSchema() when this value
 // differs from config.schema.version.
-const STORAGE_SCHEMA_VERSION = '2026-06-23-invite-used-by';
-const REQUIRED_SCHEMA_TABLES = ['webauthn_credentials', 'webauthn_challenges', 'auth_requests'] as const;
+const STORAGE_SCHEMA_VERSION = '2026-06-23-totp-login-replay';
+const REQUIRED_SCHEMA_TABLES = ['webauthn_credentials', 'webauthn_challenges', 'auth_requests', 'totp_login_replays'] as const;
 
 // D1-backed storage.
 // Contract:
@@ -164,10 +167,13 @@ export class StorageService {
   private static schemaVerified = false;
   private static lastRefreshTokenCleanupAt = 0;
   private static lastAttachmentTokenCleanupAt = 0;
+  private static lastTotpReplayCleanupAt = 0;
   private static readonly MAX_D1_SQL_VARIABLES = 100;
 
   private static readonly REFRESH_TOKEN_CLEANUP_INTERVAL_MS = LIMITS.cleanup.refreshTokenCleanupIntervalMs;
   private static readonly ATTACHMENT_TOKEN_CLEANUP_INTERVAL_MS = LIMITS.cleanup.attachmentTokenCleanupIntervalMs;
+  private static readonly TOTP_REPLAY_CLEANUP_INTERVAL_MS = 10 * 60 * 1000;
+  private static readonly TOTP_REPLAY_MARKER_TTL_MS = 5 * 60 * 1000;
   private static readonly PERIODIC_CLEANUP_PROBABILITY = LIMITS.cleanup.cleanupProbability;
 
   constructor(private db: D1Database) {}
@@ -833,6 +839,24 @@ export class StorageService {
     return findStoredTrustedTokenUserId(this.db, this.trustedTwoFactorTokenKey.bind(this), token, deviceIdentifier);
   }
 
+  async consumeTotpLoginCounter(userId: string, timeCounter: number, consumedAtMs: number = Date.now()): Promise<boolean> {
+    if (!Number.isSafeInteger(timeCounter) || timeCounter < 0) return false;
+    const result = await consumeStoredTotpLoginCounter(
+      this.db,
+      this.shouldRunPeriodicCleanup.bind(this),
+      StorageService.lastTotpReplayCleanupAt,
+      StorageService.TOTP_REPLAY_CLEANUP_INTERVAL_MS,
+      userId,
+      timeCounter,
+      consumedAtMs,
+      StorageService.TOTP_REPLAY_MARKER_TTL_MS
+    );
+    if (result.cleanedUpAt !== null) {
+      StorageService.lastTotpReplayCleanupAt = result.cleanedUpAt;
+    }
+    return result.consumed;
+  }
+
   // --- Revision dates ---
 
   async getRevisionDate(userId: string): Promise<string> {

src/utils/totp.ts

@@ -70,17 +70,22 @@ function normalizeToken(token: string): string {
   return token.replace(/\s+/g, '');
 }
 
-export async function verifyTotpToken(secretRaw: string, tokenRaw: string, nowMs: number = Date.now()): Promise<boolean> {
+export async function findMatchingTotpCounter(
+  secretRaw: string,
+  tokenRaw: string,
+  nowMs: number = Date.now()
+): Promise<number | null> {
   const token = normalizeToken(tokenRaw);
-  if (!/^\d{6}$/.test(token)) return false;
+  if (!/^\d{6}$/.test(token)) return null;
 
   const secret = base32Decode(secretRaw);
-  if (!secret) return false;
+  if (!secret) return null;
 
   const currentCounter = Math.floor(nowMs / 1000 / TOTP_STEP_SECONDS);
-  let matched = false;
+  let matchedCounter: number | null = null;
   for (let delta = -TOTP_WINDOW; delta <= TOTP_WINDOW; delta++) {
-    const expected = await hotp(secret, currentCounter + delta);
+    const candidateCounter = currentCounter + delta;
+    const expected = await hotp(secret, candidateCounter);
     // Constant-time comparison: always check all windows, never short-circuit.
     const a = new TextEncoder().encode(expected);
     const b = new TextEncoder().encode(token);
@@ -88,9 +93,13 @@ export async function verifyTotpToken(secretRaw: string, tokenRaw: string, nowMs
     for (let i = 0; i < a.length && i < b.length; i++) {
       diff |= a[i] ^ b[i];
     }
-    if (diff === 0) matched = true;
+    if (diff === 0 && matchedCounter == null) matchedCounter = candidateCounter;
   }
-  return matched;
+  return matchedCounter;
+}
+
+export async function verifyTotpToken(secretRaw: string, tokenRaw: string, nowMs: number = Date.now()): Promise<boolean> {
+  return (await findMatchingTotpCounter(secretRaw, tokenRaw, nowMs)) != null;
 }
 
 export function isTotpEnabled(secretRaw: string | undefined | null): boolean {