Fix test assertions for run ordering in RunManager tests

- Updated assertions in `test_list_by_thread` to reflect correct ordering of runs.
- Modified `test_list_by_thread_is_stable_when_timestamps_tie` to ensure stable ordering when timestamps are tied.

.env.example

@@ -33,5 +33,9 @@ INFOQUEST_API_KEY=your-infoquest-api-key
 
 # GitHub API Token
 # GITHUB_TOKEN=your-github-token
+
+# Database (only needed when config.yaml has database.backend: postgres)
+# DATABASE_URL=postgresql://deerflow:password@localhost:5432/deerflow
+#
 # WECOM_BOT_ID=your-wecom-bot-id
 # WECOM_BOT_SECRET=your-wecom-bot-secret

backend/CLAUDE.md

@@ -158,7 +158,7 @@ from deerflow.config import get_app_config
 
 Middlewares execute in strict order in `packages/harness/deerflow/agents/lead_agent/agent.py`:
 
-1. **ThreadDataMiddleware** - Creates per-thread directories (`backend/.deer-flow/threads/{thread_id}/user-data/{workspace,uploads,outputs}`); Web UI thread deletion now follows LangGraph thread removal with Gateway cleanup of the local `.deer-flow/threads/{thread_id}` directory
+1. **ThreadDataMiddleware** - Creates per-thread directories under the user's isolation scope (`backend/.deer-flow/users/{user_id}/threads/{thread_id}/user-data/{workspace,uploads,outputs}`); resolves `user_id` via `get_effective_user_id()` (falls back to `"default"` in no-auth mode); Web UI thread deletion now follows LangGraph thread removal with Gateway cleanup of the local thread directory
 2. **UploadsMiddleware** - Tracks and injects newly uploaded files into conversation
 3. **SandboxMiddleware** - Acquires sandbox, stores `sandbox_id` in state
 4. **DanglingToolCallMiddleware** - Injects placeholder ToolMessages for AIMessage tool_calls that lack responses (e.g., due to user interruption)
@@ -216,6 +216,9 @@ FastAPI application on port 8001 with health check at `GET /health`.
 | **Threads** (`/api/threads/{id}`) | `DELETE /` - remove DeerFlow-managed local thread data after LangGraph thread deletion; unexpected failures are logged server-side and return a generic 500 detail |
 | **Artifacts** (`/api/threads/{id}/artifacts`) | `GET /{path}` - serve artifacts; active content types (`text/html`, `application/xhtml+xml`, `image/svg+xml`) are always forced as download attachments to reduce XSS risk; `?download=true` still forces download for other file types |
 | **Suggestions** (`/api/threads/{id}/suggestions`) | `POST /` - generate follow-up questions; rich list/block model content is normalized before JSON parsing |
+| **Thread Runs** (`/api/threads/{id}/runs`) | `POST /` - create background run; `POST /stream` - create + SSE stream; `POST /wait` - create + block; `GET /` - list runs; `GET /{rid}` - run details; `POST /{rid}/cancel` - cancel; `GET /{rid}/join` - join SSE; `GET /{rid}/messages` - paginated messages `{data, has_more}`; `GET /{rid}/events` - full event stream; `GET /../messages` - thread messages with feedback; `GET /../token-usage` - aggregate tokens |
+| **Feedback** (`/api/threads/{id}/runs/{rid}/feedback`) | `PUT /` - upsert feedback; `DELETE /` - delete user feedback; `POST /` - create feedback; `GET /` - list feedback; `GET /stats` - aggregate stats; `DELETE /{fid}` - delete specific |
+| **Runs** (`/api/runs`) | `POST /stream` - stateless run + SSE; `POST /wait` - stateless run + block; `GET /{rid}/messages` - paginated messages by run_id `{data, has_more}` (cursor: `after_seq`/`before_seq`); `GET /{rid}/feedback` - list feedback by run_id |
 
 Proxied through nginx: `/api/langgraph/*` → LangGraph, all other `/api/*` → Gateway.
 
@@ -229,7 +232,7 @@ Proxied through nginx: `/api/langgraph/*` → LangGraph, all other `/api/*` →
 
 **Virtual Path System**:
 - Agent sees: `/mnt/user-data/{workspace,uploads,outputs}`, `/mnt/skills`
-- Physical: `backend/.deer-flow/threads/{thread_id}/user-data/...`, `deer-flow/skills/`
+- Physical: `backend/.deer-flow/users/{user_id}/threads/{thread_id}/user-data/...`, `deer-flow/skills/`
 - Translation: `replace_virtual_path()` / `replace_virtual_paths_in_command()`
 - Detection: `is_local_sandbox()` checks `sandbox_id == "local"`
 
@@ -269,7 +272,7 @@ Proxied through nginx: `/api/langgraph/*` → LangGraph, all other `/api/*` →
 - `invoke_acp_agent` - Invokes external ACP-compatible agents from `config.yaml`
 - ACP launchers must be real ACP adapters. The standard `codex` CLI is not ACP-compatible by itself; configure a wrapper such as `npx -y @zed-industries/codex-acp` or an installed `codex-acp` binary
 - Missing ACP executables now return an actionable error message instead of a raw `[Errno 2]`
-- Each ACP agent uses a per-thread workspace at `{base_dir}/threads/{thread_id}/acp-workspace/`. The workspace is accessible to the lead agent via the virtual path `/mnt/acp-workspace/` (read-only). In docker sandbox mode, the directory is volume-mounted into the container at `/mnt/acp-workspace` (read-only); in local sandbox mode, path translation is handled by `tools.py`
+- Each ACP agent uses a per-thread workspace at `{base_dir}/users/{user_id}/threads/{thread_id}/acp-workspace/`. The workspace is accessible to the lead agent via the virtual path `/mnt/acp-workspace/` (read-only). In docker sandbox mode, the directory is volume-mounted into the container at `/mnt/acp-workspace` (read-only); in local sandbox mode, path translation is handled by `tools.py`
 - `image_search/` - Image search via DuckDuckGo
 
 ### MCP System (`packages/harness/deerflow/mcp/`)
@@ -338,18 +341,27 @@ Bridges external messaging platforms (Feishu, Slack, Telegram) to the DeerFlow a
 
 **Components**:
 - `updater.py` - LLM-based memory updates with fact extraction, whitespace-normalized fact deduplication (trims leading/trailing whitespace before comparing), and atomic file I/O
-- `queue.py` - Debounced update queue (per-thread deduplication, configurable wait time)
+- `queue.py` - Debounced update queue (per-thread deduplication, configurable wait time); captures `user_id` at enqueue time so it survives the `threading.Timer` boundary
 - `prompt.py` - Prompt templates for memory updates
+- `storage.py` - File-based storage with per-user isolation; cache keyed by `(user_id, agent_name)` tuple
 
-**Data Structure** (stored in `backend/.deer-flow/memory.json`):
+**Per-User Isolation**:
+- Memory is stored per-user at `{base_dir}/users/{user_id}/memory.json`
+- Per-agent per-user memory at `{base_dir}/users/{user_id}/agents/{agent_name}/memory.json`
+- `user_id` is resolved via `get_effective_user_id()` from `deerflow.runtime.user_context`
+- In no-auth mode, `user_id` defaults to `"default"` (constant `DEFAULT_USER_ID`)
+- Absolute `storage_path` in config opts out of per-user isolation
+- **Migration**: Run `PYTHONPATH=. python scripts/migrate_user_isolation.py` to move legacy `memory.json` and `threads/` into per-user layout; supports `--dry-run`
+
+**Data Structure** (stored in `{base_dir}/users/{user_id}/memory.json`):
 - **User Context**: `workContext`, `personalContext`, `topOfMind` (1-3 sentence summaries)
 - **History**: `recentMonths`, `earlierContext`, `longTermBackground`
 - **Facts**: Discrete facts with `id`, `content`, `category` (preference/knowledge/context/behavior/goal), `confidence` (0-1), `createdAt`, `source`
 
 **Workflow**:
-1. `MemoryMiddleware` filters messages (user inputs + final AI responses) and queues conversation
+1. `MemoryMiddleware` filters messages (user inputs + final AI responses), captures `user_id` via `get_effective_user_id()`, and queues conversation with the captured `user_id`
 2. Queue debounces (30s default), batches updates, deduplicates per-thread
-3. Background thread invokes LLM to extract context updates and facts
+3. Background thread invokes LLM to extract context updates and facts, using the stored `user_id` (not the contextvar, which is unavailable on timer threads)
 4. Applies updates atomically (temp file + rename) with cache invalidation, skipping duplicate fact content before append
 5. Next interaction injects top 15 facts + context into `<memory>` tags in system prompt
 
@@ -357,7 +369,7 @@ Focused regression coverage for the updater lives in `backend/tests/test_memory_
 
 **Configuration** (`config.yaml` → `memory`):
 - `enabled` / `injection_enabled` - Master switches
-- `storage_path` - Path to memory.json
+- `storage_path` - Path to memory.json (absolute path opts out of per-user isolation)
 - `debounce_seconds` - Wait time before processing (default: 30)
 - `model_name` - LLM for updates (null = default model)
 - `max_facts` / `fact_confidence_threshold` - Fact storage limits (100 / 0.7)

backend/Dockerfile

@@ -13,6 +13,9 @@ FROM python:3.12-slim-bookworm AS builder
 ARG NODE_MAJOR=22
 ARG APT_MIRROR
 ARG UV_INDEX_URL
+# Optional extras to install (e.g. "postgres" for PostgreSQL support)
+# Usage: docker build --build-arg UV_EXTRAS=postgres ...
+ARG UV_EXTRAS
 
 # Optionally override apt mirror for restricted networks (e.g. APT_MIRROR=mirrors.aliyun.com)
 RUN if [ -n "${APT_MIRROR}" ]; then \
@@ -43,8 +46,9 @@ WORKDIR /app
 COPY backend ./backend
 
 # Install dependencies with cache mount
+# When UV_EXTRAS is set (e.g. "postgres"), installs optional dependencies.
 RUN --mount=type=cache,target=/root/.cache/uv \
-    sh -c "cd backend && UV_INDEX_URL=${UV_INDEX_URL:-https://pypi.org/simple} uv sync"
+    sh -c "cd backend && UV_INDEX_URL=${UV_INDEX_URL:-https://pypi.org/simple} uv sync ${UV_EXTRAS:+--extra $UV_EXTRAS}"
 
 # ── Stage 2: Dev ──────────────────────────────────────────────────────────────
 # Retains compiler toolchain from builder so startup-time `uv sync` can build

backend/app/channels/feishu.py

@@ -13,6 +13,7 @@ from app.channels.base import Channel
 from app.channels.commands import KNOWN_CHANNEL_COMMANDS
 from app.channels.message_bus import InboundMessage, InboundMessageType, MessageBus, OutboundMessage, ResolvedAttachment
 from deerflow.config.paths import VIRTUAL_PATH_PREFIX, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.sandbox.sandbox_provider import get_sandbox_provider
 
 logger = logging.getLogger(__name__)
@@ -344,8 +345,9 @@ class FeishuChannel(Channel):
             return f"Failed to obtain the [{type}]"
 
         paths = get_paths()
-        paths.ensure_thread_dirs(thread_id)
-        uploads_dir = paths.sandbox_uploads_dir(thread_id).resolve()
+        user_id = get_effective_user_id()
+        paths.ensure_thread_dirs(thread_id, user_id=user_id)
+        uploads_dir = paths.sandbox_uploads_dir(thread_id, user_id=user_id).resolve()
 
         ext = "png" if type == "image" else "bin"
         raw_filename = getattr(response, "file_name", "") or f"feishu_{file_key[-12:]}.{ext}"

backend/app/channels/manager.py

@@ -17,6 +17,7 @@ from langgraph_sdk.errors import ConflictError
 from app.channels.commands import KNOWN_CHANNEL_COMMANDS
 from app.channels.message_bus import InboundMessage, InboundMessageType, MessageBus, OutboundMessage, ResolvedAttachment
 from app.channels.store import ChannelStore
+from deerflow.runtime.user_context import get_effective_user_id
 
 logger = logging.getLogger(__name__)
 
@@ -341,14 +342,15 @@ def _resolve_attachments(thread_id: str, artifacts: list[str]) -> list[ResolvedA
 
     attachments: list[ResolvedAttachment] = []
     paths = get_paths()
-    outputs_dir = paths.sandbox_outputs_dir(thread_id).resolve()
+    user_id = get_effective_user_id()
+    outputs_dir = paths.sandbox_outputs_dir(thread_id, user_id=user_id).resolve()
     for virtual_path in artifacts:
         # Security: only allow files from the agent outputs directory
         if not virtual_path.startswith(_OUTPUTS_VIRTUAL_PREFIX):
             logger.warning("[Manager] rejected non-outputs artifact path: %s", virtual_path)
             continue
         try:
-            actual = paths.resolve_virtual_path(thread_id, virtual_path)
+            actual = paths.resolve_virtual_path(thread_id, virtual_path, user_id=user_id)
             # Verify the resolved path is actually under the outputs directory
             # (guards against path-traversal even after prefix check)
             try:

backend/app/gateway/app.py

@@ -1,16 +1,22 @@
 import logging
+import os
 from collections.abc import AsyncGenerator
 from contextlib import asynccontextmanager
 
 from fastapi import FastAPI
+from fastapi.middleware.cors import CORSMiddleware
 
+from app.gateway.auth_middleware import AuthMiddleware
 from app.gateway.config import get_gateway_config
+from app.gateway.csrf_middleware import CSRFMiddleware
 from app.gateway.deps import langgraph_runtime
 from app.gateway.routers import (
     agents,
     artifacts,
     assistants_compat,
+    auth,
     channels,
+    feedback,
     mcp,
     memory,
     models,
@@ -33,6 +39,108 @@ logging.basicConfig(
 logger = logging.getLogger(__name__)
 
 
+async def _ensure_admin_user(app: FastAPI) -> None:
+    """Startup hook: handle first boot and migrate orphan threads otherwise.
+
+    After admin creation, migrate orphan threads from the LangGraph
+    store (metadata.user_id unset) to the admin account. This is the
+    "no-auth → with-auth" upgrade path: users who ran DeerFlow without
+    authentication have existing LangGraph thread data that needs an
+    owner assigned.
+        First boot (no admin exists):
+            - Does NOT create any user accounts automatically.
+            - The operator must visit ``/setup`` to create the first admin.
+
+    Subsequent boots (admin already exists):
+      - Runs the one-time "no-auth → with-auth" orphan thread migration for
+        existing LangGraph thread metadata that has no owner_id.
+
+    No SQL persistence migration is needed: the four user_id columns
+    (threads_meta, runs, run_events, feedback) only come into existence
+    alongside the auth module via create_all, so freshly created tables
+    never contain NULL-owner rows.
+    """
+    from sqlalchemy import select
+
+    from app.gateway.deps import get_local_provider
+    from deerflow.persistence.engine import get_session_factory
+    from deerflow.persistence.user.model import UserRow
+
+    provider = get_local_provider()
+    admin_count = await provider.count_admin_users()
+
+    if admin_count == 0:
+        logger.info("=" * 60)
+        logger.info("  First boot detected — no admin account exists.")
+        logger.info("  Visit /setup to complete admin account creation.")
+        logger.info("=" * 60)
+        return
+
+    # Admin already exists — run orphan thread migration for any
+    # LangGraph thread metadata that pre-dates the auth module.
+    sf = get_session_factory()
+    if sf is None:
+        return
+
+    async with sf() as session:
+        stmt = select(UserRow).where(UserRow.system_role == "admin").limit(1)
+        row = (await session.execute(stmt)).scalar_one_or_none()
+
+    if row is None:
+        return  # Should not happen (admin_count > 0 above), but be safe.
+
+    admin_id = str(row.id)
+
+    # LangGraph store orphan migration — non-fatal.
+    # This covers the "no-auth → with-auth" upgrade path for users
+    # whose existing LangGraph thread metadata has no user_id set.
+    store = getattr(app.state, "store", None)
+    if store is not None:
+        try:
+            migrated = await _migrate_orphaned_threads(store, admin_id)
+            if migrated:
+                logger.info("Migrated %d orphan LangGraph thread(s) to admin", migrated)
+        except Exception:
+            logger.exception("LangGraph thread migration failed (non-fatal)")
+
+
+async def _iter_store_items(store, namespace, *, page_size: int = 500):
+    """Paginated async iterator over a LangGraph store namespace.
+
+    Replaces the old hardcoded ``limit=1000`` call with a cursor-style
+    loop so that environments with more than one page of orphans do
+    not silently lose data. Terminates when a page is empty OR when a
+    short page arrives (indicating the last page).
+    """
+    offset = 0
+    while True:
+        batch = await store.asearch(namespace, limit=page_size, offset=offset)
+        if not batch:
+            return
+        for item in batch:
+            yield item
+        if len(batch) < page_size:
+            return
+        offset += page_size
+
+
+async def _migrate_orphaned_threads(store, admin_user_id: str) -> int:
+    """Migrate LangGraph store threads with no user_id to the given admin.
+
+    Uses cursor pagination so all orphans are migrated regardless of
+    count. Returns the number of rows migrated.
+    """
+    migrated = 0
+    async for item in _iter_store_items(store, ("threads",)):
+        metadata = item.value.get("metadata", {})
+        if not metadata.get("user_id"):
+            metadata["user_id"] = admin_user_id
+            item.value["metadata"] = metadata
+            await store.aput(("threads",), item.key, item.value)
+            migrated += 1
+    return migrated
+
+
 @asynccontextmanager
 async def lifespan(app: FastAPI) -> AsyncGenerator[None, None]:
     """Application lifespan handler."""
@@ -52,6 +160,10 @@ async def lifespan(app: FastAPI) -> AsyncGenerator[None, None]:
     async with langgraph_runtime(app):
         logger.info("LangGraph runtime initialised")
 
+        # Ensure admin user exists (auto-create on first boot)
+        # Must run AFTER langgraph_runtime so app.state.store is available for thread migration
+        await _ensure_admin_user(app)
+
         # Start IM channel service if any channels are configured
         try:
             from app.channels.service import start_channel_service
@@ -163,7 +275,31 @@ This gateway provides custom endpoints for models, MCP configuration, skills, an
         ],
     )
 
-    # CORS is handled by nginx - no need for FastAPI middleware
+    # Auth: reject unauthenticated requests to non-public paths (fail-closed safety net)
+    app.add_middleware(AuthMiddleware)
+
+    # CSRF: Double Submit Cookie pattern for state-changing requests
+    app.add_middleware(CSRFMiddleware)
+
+    # CORS: when GATEWAY_CORS_ORIGINS is set (dev without nginx), add CORS middleware.
+    # In production, nginx handles CORS and no middleware is needed.
+    cors_origins_env = os.environ.get("GATEWAY_CORS_ORIGINS", "")
+    if cors_origins_env:
+        cors_origins = [o.strip() for o in cors_origins_env.split(",") if o.strip()]
+        # Validate: wildcard origin with credentials is a security misconfiguration
+        for origin in cors_origins:
+            if origin == "*":
+                logger.error("GATEWAY_CORS_ORIGINS contains wildcard '*' with allow_credentials=True. This is a security misconfiguration — browsers will reject the response. Use explicit scheme://host:port origins instead.")
+                cors_origins = [o for o in cors_origins if o != "*"]
+                break
+        if cors_origins:
+            app.add_middleware(
+                CORSMiddleware,
+                allow_origins=cors_origins,
+                allow_credentials=True,
+                allow_methods=["*"],
+                allow_headers=["*"],
+            )
 
     # Include routers
     # Models API is mounted at /api/models
@@ -199,6 +335,12 @@ This gateway provides custom endpoints for models, MCP configuration, skills, an
     # Assistants compatibility API (LangGraph Platform stub)
     app.include_router(assistants_compat.router)
 
+    # Auth API is mounted at /api/v1/auth
+    app.include_router(auth.router)
+
+    # Feedback API is mounted at /api/threads/{thread_id}/runs/{run_id}/feedback
+    app.include_router(feedback.router)
+
     # Thread Runs API (LangGraph Platform-compatible runs lifecycle)
     app.include_router(thread_runs.router)
 

backend/app/gateway/auth/__init__.py

@@ -0,0 +1,42 @@
+"""Authentication module for DeerFlow.
+
+This module provides:
+- JWT-based authentication
+- Provider Factory pattern for extensible auth methods
+- UserRepository interface for storage backends (SQLite)
+"""
+
+from app.gateway.auth.config import AuthConfig, get_auth_config, set_auth_config
+from app.gateway.auth.errors import AuthErrorCode, AuthErrorResponse, TokenError
+from app.gateway.auth.jwt import TokenPayload, create_access_token, decode_token
+from app.gateway.auth.local_provider import LocalAuthProvider
+from app.gateway.auth.models import User, UserResponse
+from app.gateway.auth.password import hash_password, verify_password
+from app.gateway.auth.providers import AuthProvider
+from app.gateway.auth.repositories.base import UserRepository
+
+__all__ = [
+    # Config
+    "AuthConfig",
+    "get_auth_config",
+    "set_auth_config",
+    # Errors
+    "AuthErrorCode",
+    "AuthErrorResponse",
+    "TokenError",
+    # JWT
+    "TokenPayload",
+    "create_access_token",
+    "decode_token",
+    # Password
+    "hash_password",
+    "verify_password",
+    # Models
+    "User",
+    "UserResponse",
+    # Providers
+    "AuthProvider",
+    "LocalAuthProvider",
+    # Repository
+    "UserRepository",
+]

backend/app/gateway/auth/config.py

@@ -0,0 +1,57 @@
+"""Authentication configuration for DeerFlow."""
+
+import logging
+import os
+import secrets
+
+from dotenv import load_dotenv
+from pydantic import BaseModel, Field
+
+load_dotenv()
+
+logger = logging.getLogger(__name__)
+
+
+class AuthConfig(BaseModel):
+    """JWT and auth-related configuration. Parsed once at startup.
+
+    Note: the ``users`` table now lives in the shared persistence
+    database managed by ``deerflow.persistence.engine``. The old
+    ``users_db_path`` config key has been removed — user storage is
+    configured through ``config.database`` like every other table.
+    """
+
+    jwt_secret: str = Field(
+        ...,
+        description="Secret key for JWT signing. MUST be set via AUTH_JWT_SECRET.",
+    )
+    token_expiry_days: int = Field(default=7, ge=1, le=30)
+    oauth_github_client_id: str | None = Field(default=None)
+    oauth_github_client_secret: str | None = Field(default=None)
+
+
+_auth_config: AuthConfig | None = None
+
+
+def get_auth_config() -> AuthConfig:
+    """Get the global AuthConfig instance. Parses from env on first call."""
+    global _auth_config
+    if _auth_config is None:
+        jwt_secret = os.environ.get("AUTH_JWT_SECRET")
+        if not jwt_secret:
+            jwt_secret = secrets.token_urlsafe(32)
+            os.environ["AUTH_JWT_SECRET"] = jwt_secret
+            logger.warning(
+                "⚠ AUTH_JWT_SECRET is not set — using an auto-generated ephemeral secret. "
+                "Sessions will be invalidated on restart. "
+                "For production, add AUTH_JWT_SECRET to your .env file: "
+                'python -c "import secrets; print(secrets.token_urlsafe(32))"'
+            )
+        _auth_config = AuthConfig(jwt_secret=jwt_secret)
+    return _auth_config
+
+
+def set_auth_config(config: AuthConfig) -> None:
+    """Set the global AuthConfig instance (for testing)."""
+    global _auth_config
+    _auth_config = config

backend/app/gateway/auth/credential_file.py

@@ -0,0 +1,48 @@
+"""Write initial admin credentials to a restricted file instead of logs.
+
+Logging secrets to stdout/stderr is a well-known CodeQL finding
+(py/clear-text-logging-sensitive-data) — in production those logs
+get collected into ELK/Splunk/etc and become a secret sprawl
+source. This helper writes the credential to a 0600 file that only
+the process user can read, and returns the path so the caller can
+log **the path** (not the password) for the operator to pick up.
+"""
+
+from __future__ import annotations
+
+import os
+from pathlib import Path
+
+from deerflow.config.paths import get_paths
+
+_CREDENTIAL_FILENAME = "admin_initial_credentials.txt"
+
+
+def write_initial_credentials(email: str, password: str, *, label: str = "initial") -> Path:
+    """Write the admin email + password to ``{base_dir}/admin_initial_credentials.txt``.
+
+    The file is created **atomically** with mode 0600 via ``os.open``
+    so the password is never world-readable, even for the single syscall
+    window between ``write_text`` and ``chmod``.
+
+    ``label`` distinguishes "initial" (fresh creation) from "reset"
+    (password reset) in the file header so an operator picking up the
+    file after a restart can tell which event produced it.
+
+    Returns the absolute :class:`Path` to the file.
+    """
+    target = get_paths().base_dir / _CREDENTIAL_FILENAME
+    target.parent.mkdir(parents=True, exist_ok=True)
+
+    content = (
+        f"# DeerFlow admin {label} credentials\n# This file is generated on first boot or password reset.\n# Change the password after login via Settings -> Account,\n# then delete this file.\n#\nemail: {email}\npassword: {password}\n"
+    )
+
+    # Atomic 0600 create-or-truncate. O_TRUNC (not O_EXCL) so the
+    # reset-password path can rewrite an existing file without a
+    # separate unlink-then-create dance.
+    fd = os.open(target, os.O_WRONLY | os.O_CREAT | os.O_TRUNC, 0o600)
+    with os.fdopen(fd, "w", encoding="utf-8") as fh:
+        fh.write(content)
+
+    return target.resolve()

backend/app/gateway/auth/errors.py

@@ -0,0 +1,45 @@
+"""Typed error definitions for auth module.
+
+AuthErrorCode: exhaustive enum of all auth failure conditions.
+TokenError: exhaustive enum of JWT decode failures.
+AuthErrorResponse: structured error payload for HTTP responses.
+"""
+
+from enum import StrEnum
+
+from pydantic import BaseModel
+
+
+class AuthErrorCode(StrEnum):
+    """Exhaustive list of auth error conditions."""
+
+    INVALID_CREDENTIALS = "invalid_credentials"
+    TOKEN_EXPIRED = "token_expired"
+    TOKEN_INVALID = "token_invalid"
+    USER_NOT_FOUND = "user_not_found"
+    EMAIL_ALREADY_EXISTS = "email_already_exists"
+    PROVIDER_NOT_FOUND = "provider_not_found"
+    NOT_AUTHENTICATED = "not_authenticated"
+    SYSTEM_ALREADY_INITIALIZED = "system_already_initialized"
+
+
+class TokenError(StrEnum):
+    """Exhaustive list of JWT decode failure reasons."""
+
+    EXPIRED = "expired"
+    INVALID_SIGNATURE = "invalid_signature"
+    MALFORMED = "malformed"
+
+
+class AuthErrorResponse(BaseModel):
+    """Structured error response — replaces bare `detail` strings."""
+
+    code: AuthErrorCode
+    message: str
+
+
+def token_error_to_code(err: TokenError) -> AuthErrorCode:
+    """Map TokenError to AuthErrorCode — single source of truth."""
+    if err == TokenError.EXPIRED:
+        return AuthErrorCode.TOKEN_EXPIRED
+    return AuthErrorCode.TOKEN_INVALID

backend/app/gateway/auth/jwt.py

@@ -0,0 +1,55 @@
+"""JWT token creation and verification."""
+
+from datetime import UTC, datetime, timedelta
+
+import jwt
+from pydantic import BaseModel
+
+from app.gateway.auth.config import get_auth_config
+from app.gateway.auth.errors import TokenError
+
+
+class TokenPayload(BaseModel):
+    """JWT token payload."""
+
+    sub: str  # user_id
+    exp: datetime
+    iat: datetime | None = None
+    ver: int = 0  # token_version — must match User.token_version
+
+
+def create_access_token(user_id: str, expires_delta: timedelta | None = None, token_version: int = 0) -> str:
+    """Create a JWT access token.
+
+    Args:
+        user_id: The user's UUID as string
+        expires_delta: Optional custom expiry, defaults to 7 days
+        token_version: User's current token_version for invalidation
+
+    Returns:
+        Encoded JWT string
+    """
+    config = get_auth_config()
+    expiry = expires_delta or timedelta(days=config.token_expiry_days)
+
+    now = datetime.now(UTC)
+    payload = {"sub": user_id, "exp": now + expiry, "iat": now, "ver": token_version}
+    return jwt.encode(payload, config.jwt_secret, algorithm="HS256")
+
+
+def decode_token(token: str) -> TokenPayload | TokenError:
+    """Decode and validate a JWT token.
+
+    Returns:
+        TokenPayload if valid, or a specific TokenError variant.
+    """
+    config = get_auth_config()
+    try:
+        payload = jwt.decode(token, config.jwt_secret, algorithms=["HS256"])
+        return TokenPayload(**payload)
+    except jwt.ExpiredSignatureError:
+        return TokenError.EXPIRED
+    except jwt.InvalidSignatureError:
+        return TokenError.INVALID_SIGNATURE
+    except jwt.PyJWTError:
+        return TokenError.MALFORMED

backend/app/gateway/auth/local_provider.py

@@ -0,0 +1,91 @@
+"""Local email/password authentication provider."""
+
+from app.gateway.auth.models import User
+from app.gateway.auth.password import hash_password_async, verify_password_async
+from app.gateway.auth.providers import AuthProvider
+from app.gateway.auth.repositories.base import UserRepository
+
+
+class LocalAuthProvider(AuthProvider):
+    """Email/password authentication provider using local database."""
+
+    def __init__(self, repository: UserRepository):
+        """Initialize with a UserRepository.
+
+        Args:
+            repository: UserRepository implementation (SQLite)
+        """
+        self._repo = repository
+
+    async def authenticate(self, credentials: dict) -> User | None:
+        """Authenticate with email and password.
+
+        Args:
+            credentials: dict with 'email' and 'password' keys
+
+        Returns:
+            User if authentication succeeds, None otherwise
+        """
+        email = credentials.get("email")
+        password = credentials.get("password")
+
+        if not email or not password:
+            return None
+
+        user = await self._repo.get_user_by_email(email)
+        if user is None:
+            return None
+
+        if user.password_hash is None:
+            # OAuth user without local password
+            return None
+
+        if not await verify_password_async(password, user.password_hash):
+            return None
+
+        return user
+
+    async def get_user(self, user_id: str) -> User | None:
+        """Get user by ID."""
+        return await self._repo.get_user_by_id(user_id)
+
+    async def create_user(self, email: str, password: str | None = None, system_role: str = "user", needs_setup: bool = False) -> User:
+        """Create a new local user.
+
+        Args:
+            email: User email address
+            password: Plain text password (will be hashed)
+            system_role: Role to assign ("admin" or "user")
+            needs_setup: If True, user must complete setup on first login
+
+        Returns:
+            Created User instance
+        """
+        password_hash = await hash_password_async(password) if password else None
+        user = User(
+            email=email,
+            password_hash=password_hash,
+            system_role=system_role,
+            needs_setup=needs_setup,
+        )
+        return await self._repo.create_user(user)
+
+    async def get_user_by_oauth(self, provider: str, oauth_id: str) -> User | None:
+        """Get user by OAuth provider and ID."""
+        return await self._repo.get_user_by_oauth(provider, oauth_id)
+
+    async def count_users(self) -> int:
+        """Return total number of registered users."""
+        return await self._repo.count_users()
+
+    async def count_admin_users(self) -> int:
+        """Return number of admin users."""
+        return await self._repo.count_admin_users()
+
+    async def update_user(self, user: User) -> User:
+        """Update an existing user."""
+        return await self._repo.update_user(user)
+
+    async def get_user_by_email(self, email: str) -> User | None:
+        """Get user by email."""
+        return await self._repo.get_user_by_email(email)

backend/app/gateway/auth/models.py

@@ -0,0 +1,41 @@
+"""User Pydantic models for authentication."""
+
+from datetime import UTC, datetime
+from typing import Literal
+from uuid import UUID, uuid4
+
+from pydantic import BaseModel, ConfigDict, EmailStr, Field
+
+
+def _utc_now() -> datetime:
+    """Return current UTC time (timezone-aware)."""
+    return datetime.now(UTC)
+
+
+class User(BaseModel):
+    """Internal user representation."""
+
+    model_config = ConfigDict(from_attributes=True)
+
+    id: UUID = Field(default_factory=uuid4, description="Primary key")
+    email: EmailStr = Field(..., description="Unique email address")
+    password_hash: str | None = Field(None, description="bcrypt hash, nullable for OAuth users")
+    system_role: Literal["admin", "user"] = Field(default="user")
+    created_at: datetime = Field(default_factory=_utc_now)
+
+    # OAuth linkage (optional)
+    oauth_provider: str | None = Field(None, description="e.g. 'github', 'google'")
+    oauth_id: str | None = Field(None, description="User ID from OAuth provider")
+
+    # Auth lifecycle
+    needs_setup: bool = Field(default=False, description="True for auto-created admin until setup completes")
+    token_version: int = Field(default=0, description="Incremented on password change to invalidate old JWTs")
+
+
+class UserResponse(BaseModel):
+    """Response model for user info endpoint."""
+
+    id: str
+    email: str
+    system_role: Literal["admin", "user"]
+    needs_setup: bool = False

backend/app/gateway/auth/password.py

@@ -0,0 +1,33 @@
+"""Password hashing utilities using bcrypt directly."""
+
+import asyncio
+
+import bcrypt
+
+
+def hash_password(password: str) -> str:
+    """Hash a password using bcrypt."""
+    return bcrypt.hashpw(password.encode("utf-8"), bcrypt.gensalt()).decode("utf-8")
+
+
+def verify_password(plain_password: str, hashed_password: str) -> bool:
+    """Verify a password against its hash."""
+    return bcrypt.checkpw(plain_password.encode("utf-8"), hashed_password.encode("utf-8"))
+
+
+async def hash_password_async(password: str) -> str:
+    """Hash a password using bcrypt (non-blocking).
+
+    Wraps the blocking bcrypt operation in a thread pool to avoid
+    blocking the event loop during password hashing.
+    """
+    return await asyncio.to_thread(hash_password, password)
+
+
+async def verify_password_async(plain_password: str, hashed_password: str) -> bool:
+    """Verify a password against its hash (non-blocking).
+
+    Wraps the blocking bcrypt operation in a thread pool to avoid
+    blocking the event loop during password verification.
+    """
+    return await asyncio.to_thread(verify_password, plain_password, hashed_password)

backend/app/gateway/auth/providers.py

@@ -0,0 +1,24 @@
+"""Auth provider abstraction."""
+
+from abc import ABC, abstractmethod
+
+
+class AuthProvider(ABC):
+    """Abstract base class for authentication providers."""
+
+    @abstractmethod
+    async def authenticate(self, credentials: dict) -> "User | None":
+        """Authenticate user with given credentials.
+
+        Returns User if authentication succeeds, None otherwise.
+        """
+        ...
+
+    @abstractmethod
+    async def get_user(self, user_id: str) -> "User | None":
+        """Retrieve user by ID."""
+        ...
+
+
+# Import User at runtime to avoid circular imports
+from app.gateway.auth.models import User  # noqa: E402

backend/app/gateway/auth/repositories/base.py

@@ -0,0 +1,102 @@
+"""User repository interface for abstracting database operations."""
+
+from abc import ABC, abstractmethod
+
+from app.gateway.auth.models import User
+
+
+class UserNotFoundError(LookupError):
+    """Raised when a user repository operation targets a non-existent row.
+
+    Subclass of :class:`LookupError` so callers that already catch
+    ``LookupError`` for "missing entity" can keep working unchanged,
+    while specific call sites can pin to this class to distinguish
+    "concurrent delete during update" from other lookups.
+    """
+
+
+class UserRepository(ABC):
+    """Abstract interface for user data storage.
+
+    Implement this interface to support different storage backends
+    (SQLite)
+    """
+
+    @abstractmethod
+    async def create_user(self, user: User) -> User:
+        """Create a new user.
+
+        Args:
+            user: User object to create
+
+        Returns:
+            Created User with ID assigned
+
+        Raises:
+            ValueError: If email already exists
+        """
+        ...
+
+    @abstractmethod
+    async def get_user_by_id(self, user_id: str) -> User | None:
+        """Get user by ID.
+
+        Args:
+            user_id: User UUID as string
+
+        Returns:
+            User if found, None otherwise
+        """
+        ...
+
+    @abstractmethod
+    async def get_user_by_email(self, email: str) -> User | None:
+        """Get user by email.
+
+        Args:
+            email: User email address
+
+        Returns:
+            User if found, None otherwise
+        """
+        ...
+
+    @abstractmethod
+    async def update_user(self, user: User) -> User:
+        """Update an existing user.
+
+        Args:
+            user: User object with updated fields
+
+        Returns:
+            Updated User
+
+        Raises:
+            UserNotFoundError: If no row exists for ``user.id``. This is
+                a hard failure (not a no-op) so callers cannot mistake a
+                concurrent-delete race for a successful update.
+        """
+        ...
+
+    @abstractmethod
+    async def count_users(self) -> int:
+        """Return total number of registered users."""
+        ...
+
+    @abstractmethod
+    async def count_admin_users(self) -> int:
+        """Return number of users with system_role == 'admin'."""
+        ...
+
+    @abstractmethod
+    async def get_user_by_oauth(self, provider: str, oauth_id: str) -> User | None:
+        """Get user by OAuth provider and ID.
+
+        Args:
+            provider: OAuth provider name (e.g. 'github', 'google')
+            oauth_id: User ID from the OAuth provider
+
+        Returns:
+            User if found, None otherwise
+        """
+        ...

backend/app/gateway/auth/repositories/sqlite.py

@@ -0,0 +1,127 @@
+"""SQLAlchemy-backed UserRepository implementation.
+
+Uses the shared async session factory from
+``deerflow.persistence.engine`` — the ``users`` table lives in the
+same database as ``threads_meta``, ``runs``, ``run_events``, and
+``feedback``.
+
+Constructor takes the session factory directly (same pattern as the
+other four repositories in ``deerflow.persistence.*``). Callers
+construct this after ``init_engine_from_config()`` has run.
+"""
+
+from __future__ import annotations
+
+from datetime import UTC
+from uuid import UUID
+
+from sqlalchemy import func, select
+from sqlalchemy.exc import IntegrityError
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
+from app.gateway.auth.models import User
+from app.gateway.auth.repositories.base import UserNotFoundError, UserRepository
+from deerflow.persistence.user.model import UserRow
+
+
+class SQLiteUserRepository(UserRepository):
+    """Async user repository backed by the shared SQLAlchemy engine."""
+
+    def __init__(self, session_factory: async_sessionmaker[AsyncSession]) -> None:
+        self._sf = session_factory
+
+    # ── Converters ────────────────────────────────────────────────────
+
+    @staticmethod
+    def _row_to_user(row: UserRow) -> User:
+        return User(
+            id=UUID(row.id),
+            email=row.email,
+            password_hash=row.password_hash,
+            system_role=row.system_role,  # type: ignore[arg-type]
+            # SQLite loses tzinfo on read; reattach UTC so downstream
+            # code can compare timestamps reliably.
+            created_at=row.created_at if row.created_at.tzinfo else row.created_at.replace(tzinfo=UTC),
+            oauth_provider=row.oauth_provider,
+            oauth_id=row.oauth_id,
+            needs_setup=row.needs_setup,
+            token_version=row.token_version,
+        )
+
+    @staticmethod
+    def _user_to_row(user: User) -> UserRow:
+        return UserRow(
+            id=str(user.id),
+            email=user.email,
+            password_hash=user.password_hash,
+            system_role=user.system_role,
+            created_at=user.created_at,
+            oauth_provider=user.oauth_provider,
+            oauth_id=user.oauth_id,
+            needs_setup=user.needs_setup,
+            token_version=user.token_version,
+        )
+
+    # ── CRUD ──────────────────────────────────────────────────────────
+
+    async def create_user(self, user: User) -> User:
+        """Insert a new user. Raises ``ValueError`` on duplicate email."""
+        row = self._user_to_row(user)
+        async with self._sf() as session:
+            session.add(row)
+            try:
+                await session.commit()
+            except IntegrityError as exc:
+                await session.rollback()
+                raise ValueError(f"Email already registered: {user.email}") from exc
+        return user
+
+    async def get_user_by_id(self, user_id: str) -> User | None:
+        async with self._sf() as session:
+            row = await session.get(UserRow, user_id)
+            return self._row_to_user(row) if row is not None else None
+
+    async def get_user_by_email(self, email: str) -> User | None:
+        stmt = select(UserRow).where(UserRow.email == email)
+        async with self._sf() as session:
+            result = await session.execute(stmt)
+            row = result.scalar_one_or_none()
+            return self._row_to_user(row) if row is not None else None
+
+    async def update_user(self, user: User) -> User:
+        async with self._sf() as session:
+            row = await session.get(UserRow, str(user.id))
+            if row is None:
+                # Hard fail on concurrent delete: callers (reset_admin,
+                # password change handlers, _ensure_admin_user) all
+                # fetched the user just before this call, so a missing
+                # row here means the row vanished underneath us. Silent
+                # success would let the caller log "password reset" for
+                # a row that no longer exists.
+                raise UserNotFoundError(f"User {user.id} no longer exists")
+            row.email = user.email
+            row.password_hash = user.password_hash
+            row.system_role = user.system_role
+            row.oauth_provider = user.oauth_provider
+            row.oauth_id = user.oauth_id
+            row.needs_setup = user.needs_setup
+            row.token_version = user.token_version
+            await session.commit()
+        return user
+
+    async def count_users(self) -> int:
+        stmt = select(func.count()).select_from(UserRow)
+        async with self._sf() as session:
+            return await session.scalar(stmt) or 0
+
+    async def count_admin_users(self) -> int:
+        stmt = select(func.count()).select_from(UserRow).where(UserRow.system_role == "admin")
+        async with self._sf() as session:
+            return await session.scalar(stmt) or 0
+
+    async def get_user_by_oauth(self, provider: str, oauth_id: str) -> User | None:
+        stmt = select(UserRow).where(UserRow.oauth_provider == provider, UserRow.oauth_id == oauth_id)
+        async with self._sf() as session:
+            result = await session.execute(stmt)
+            row = result.scalar_one_or_none()
+            return self._row_to_user(row) if row is not None else None

backend/app/gateway/auth/reset_admin.py

@@ -0,0 +1,91 @@
+"""CLI tool to reset an admin password.
+
+Usage:
+    python -m app.gateway.auth.reset_admin
+    python -m app.gateway.auth.reset_admin --email admin@example.com
+
+Writes the new password to ``.deer-flow/admin_initial_credentials.txt``
+(mode 0600) instead of printing it, so CI / log aggregators never see
+the cleartext secret.
+"""
+
+from __future__ import annotations
+
+import argparse
+import asyncio
+import secrets
+import sys
+
+from sqlalchemy import select
+
+from app.gateway.auth.credential_file import write_initial_credentials
+from app.gateway.auth.password import hash_password
+from app.gateway.auth.repositories.sqlite import SQLiteUserRepository
+from deerflow.persistence.user.model import UserRow
+
+
+async def _run(email: str | None) -> int:
+    from deerflow.config import get_app_config
+    from deerflow.persistence.engine import (
+        close_engine,
+        get_session_factory,
+        init_engine_from_config,
+    )
+
+    config = get_app_config()
+    await init_engine_from_config(config.database)
+    try:
+        sf = get_session_factory()
+        if sf is None:
+            print("Error: persistence engine not available (check config.database).", file=sys.stderr)
+            return 1
+
+        repo = SQLiteUserRepository(sf)
+
+        if email:
+            user = await repo.get_user_by_email(email)
+        else:
+            # Find first admin via direct SELECT — repository does not
+            # expose a "first admin" helper and we do not want to add
+            # one just for this CLI.
+            async with sf() as session:
+                stmt = select(UserRow).where(UserRow.system_role == "admin").limit(1)
+                row = (await session.execute(stmt)).scalar_one_or_none()
+            if row is None:
+                user = None
+            else:
+                user = await repo.get_user_by_id(row.id)
+
+        if user is None:
+            if email:
+                print(f"Error: user '{email}' not found.", file=sys.stderr)
+            else:
+                print("Error: no admin user found.", file=sys.stderr)
+            return 1
+
+        new_password = secrets.token_urlsafe(16)
+        user.password_hash = hash_password(new_password)
+        user.token_version += 1
+        user.needs_setup = True
+        await repo.update_user(user)
+
+        cred_path = write_initial_credentials(user.email, new_password, label="reset")
+        print(f"Password reset for: {user.email}")
+        print(f"Credentials written to: {cred_path} (mode 0600)")
+        print("Next login will require setup (new email + password).")
+        return 0
+    finally:
+        await close_engine()
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(description="Reset admin password")
+    parser.add_argument("--email", help="Admin email (default: first admin found)")
+    args = parser.parse_args()
+
+    exit_code = asyncio.run(_run(args.email))
+    sys.exit(exit_code)
+
+
+if __name__ == "__main__":
+    main()

backend/app/gateway/auth_middleware.py

@@ -0,0 +1,118 @@
+"""Global authentication middleware — fail-closed safety net.
+
+Rejects unauthenticated requests to non-public paths with 401. When a
+request passes the cookie check, resolves the JWT payload to a real
+``User`` object and stamps it into both ``request.state.user`` and the
+``deerflow.runtime.user_context`` contextvar so that repository-layer
+owner filtering works automatically via the sentinel pattern.
+
+Fine-grained permission checks remain in authz.py decorators.
+"""
+
+from collections.abc import Callable
+
+from fastapi import HTTPException, Request, Response
+from starlette.middleware.base import BaseHTTPMiddleware
+from starlette.responses import JSONResponse
+from starlette.types import ASGIApp
+
+from app.gateway.auth.errors import AuthErrorCode, AuthErrorResponse
+from app.gateway.authz import _ALL_PERMISSIONS, AuthContext
+from deerflow.runtime.user_context import reset_current_user, set_current_user
+
+# Paths that never require authentication.
+_PUBLIC_PATH_PREFIXES: tuple[str, ...] = (
+    "/health",
+    "/docs",
+    "/redoc",
+    "/openapi.json",
+)
+
+# Exact auth paths that are public (login/register/status check).
+# /api/v1/auth/me, /api/v1/auth/change-password etc. are NOT public.
+_PUBLIC_EXACT_PATHS: frozenset[str] = frozenset(
+    {
+        "/api/v1/auth/login/local",
+        "/api/v1/auth/register",
+        "/api/v1/auth/logout",
+        "/api/v1/auth/setup-status",
+        "/api/v1/auth/initialize",
+    }
+)
+
+
+def _is_public(path: str) -> bool:
+    stripped = path.rstrip("/")
+    if stripped in _PUBLIC_EXACT_PATHS:
+        return True
+    return any(path.startswith(prefix) for prefix in _PUBLIC_PATH_PREFIXES)
+
+
+class AuthMiddleware(BaseHTTPMiddleware):
+    """Strict auth gate: reject requests without a valid session.
+
+    Two-stage check for non-public paths:
+
+    1. Cookie presence — return 401 NOT_AUTHENTICATED if missing
+    2. JWT validation via ``get_optional_user_from_request`` — return 401
+       TOKEN_INVALID if the token is absent, malformed, expired, or the
+       signed user does not exist / is stale
+
+    On success, stamps ``request.state.user`` and the
+    ``deerflow.runtime.user_context`` contextvar so that repository-layer
+    owner filters work downstream without every route needing a
+    ``@require_auth`` decorator. Routes that need per-resource
+    authorization (e.g. "user A cannot read user B's thread by guessing
+    the URL") should additionally use ``@require_permission(...,
+    owner_check=True)`` for explicit enforcement — but authentication
+    itself is fully handled here.
+    """
+
+    def __init__(self, app: ASGIApp) -> None:
+        super().__init__(app)
+
+    async def dispatch(self, request: Request, call_next: Callable) -> Response:
+        if _is_public(request.url.path):
+            return await call_next(request)
+
+        # Non-public path: require session cookie
+        if not request.cookies.get("access_token"):
+            return JSONResponse(
+                status_code=401,
+                content={
+                    "detail": AuthErrorResponse(
+                        code=AuthErrorCode.NOT_AUTHENTICATED,
+                        message="Authentication required",
+                    ).model_dump()
+                },
+            )
+
+        # Strict JWT validation: reject junk/expired tokens with 401
+        # right here instead of silently passing through. This closes
+        # the "junk cookie bypass" gap (AUTH_TEST_PLAN test 7.5.8):
+        # without this, non-isolation routes like /api/models would
+        # accept any cookie-shaped string as authentication.
+        #
+        # We call the *strict* resolver so that fine-grained error
+        # codes (token_expired, token_invalid, user_not_found, …)
+        # propagate from AuthErrorCode, not get flattened into one
+        # generic code. BaseHTTPMiddleware doesn't let HTTPException
+        # bubble up, so we catch and render it as JSONResponse here.
+        from app.gateway.deps import get_current_user_from_request
+
+        try:
+            user = await get_current_user_from_request(request)
+        except HTTPException as exc:
+            return JSONResponse(status_code=exc.status_code, content={"detail": exc.detail})
+
+        # Stamp both request.state.user (for the contextvar pattern)
+        # and request.state.auth (so @require_permission's "auth is
+        # None" branch short-circuits instead of running the entire
+        # JWT-decode + DB-lookup pipeline a second time per request).
+        request.state.user = user
+        request.state.auth = AuthContext(user=user, permissions=_ALL_PERMISSIONS)
+        token = set_current_user(user)
+        try:
+            return await call_next(request)
+        finally:
+            reset_current_user(token)

backend/app/gateway/authz.py

@@ -0,0 +1,262 @@
+"""Authorization decorators and context for DeerFlow.
+
+Inspired by LangGraph Auth system: https://github.com/langchain-ai/langgraph/blob/main/libs/sdk-py/langgraph_sdk/auth/__init__.py
+
+**Usage:**
+
+1. Use ``@require_auth`` on routes that need authentication
+2. Use ``@require_permission("resource", "action", filter_key=...)`` for permission checks
+3. The decorator chain processes from bottom to top
+
+**Example:**
+
+    @router.get("/{thread_id}")
+    @require_auth
+    @require_permission("threads", "read", owner_check=True)
+    async def get_thread(thread_id: str, request: Request):
+        # User is authenticated and has threads:read permission
+        ...
+
+**Permission Model:**
+
+- threads:read   - View thread
+- threads:write  - Create/update thread
+- threads:delete - Delete thread
+- runs:create   - Run agent
+- runs:read     - View run
+- runs:cancel   - Cancel run
+"""
+
+from __future__ import annotations
+
+import functools
+from collections.abc import Callable
+from typing import TYPE_CHECKING, Any, ParamSpec, TypeVar
+
+from fastapi import HTTPException, Request
+
+if TYPE_CHECKING:
+    from app.gateway.auth.models import User
+
+P = ParamSpec("P")
+T = TypeVar("T")
+
+
+# Permission constants
+class Permissions:
+    """Permission constants for resource:action format."""
+
+    # Threads
+    THREADS_READ = "threads:read"
+    THREADS_WRITE = "threads:write"
+    THREADS_DELETE = "threads:delete"
+
+    # Runs
+    RUNS_CREATE = "runs:create"
+    RUNS_READ = "runs:read"
+    RUNS_CANCEL = "runs:cancel"
+
+
+class AuthContext:
+    """Authentication context for the current request.
+
+    Stored in request.state.auth after require_auth decoration.
+
+    Attributes:
+        user: The authenticated user, or None if anonymous
+        permissions: List of permission strings (e.g., "threads:read")
+    """
+
+    __slots__ = ("user", "permissions")
+
+    def __init__(self, user: User | None = None, permissions: list[str] | None = None):
+        self.user = user
+        self.permissions = permissions or []
+
+    @property
+    def is_authenticated(self) -> bool:
+        """Check if user is authenticated."""
+        return self.user is not None
+
+    def has_permission(self, resource: str, action: str) -> bool:
+        """Check if context has permission for resource:action.
+
+        Args:
+            resource: Resource name (e.g., "threads")
+            action: Action name (e.g., "read")
+
+        Returns:
+            True if user has permission
+        """
+        permission = f"{resource}:{action}"
+        return permission in self.permissions
+
+    def require_user(self) -> User:
+        """Get user or raise 401.
+
+        Raises:
+            HTTPException 401 if not authenticated
+        """
+        if not self.user:
+            raise HTTPException(status_code=401, detail="Authentication required")
+        return self.user
+
+
+def get_auth_context(request: Request) -> AuthContext | None:
+    """Get AuthContext from request state."""
+    return getattr(request.state, "auth", None)
+
+
+_ALL_PERMISSIONS: list[str] = [
+    Permissions.THREADS_READ,
+    Permissions.THREADS_WRITE,
+    Permissions.THREADS_DELETE,
+    Permissions.RUNS_CREATE,
+    Permissions.RUNS_READ,
+    Permissions.RUNS_CANCEL,
+]
+
+
+async def _authenticate(request: Request) -> AuthContext:
+    """Authenticate request and return AuthContext.
+
+    Delegates to deps.get_optional_user_from_request() for the JWT→User pipeline.
+    Returns AuthContext with user=None for anonymous requests.
+    """
+    from app.gateway.deps import get_optional_user_from_request
+
+    user = await get_optional_user_from_request(request)
+    if user is None:
+        return AuthContext(user=None, permissions=[])
+
+    # In future, permissions could be stored in user record
+    return AuthContext(user=user, permissions=_ALL_PERMISSIONS)
+
+
+def require_auth[**P, T](func: Callable[P, T]) -> Callable[P, T]:
+    """Decorator that authenticates the request and sets AuthContext.
+
+    Must be placed ABOVE other decorators (executes after them).
+
+    Usage:
+        @router.get("/{thread_id}")
+        @require_auth  # Bottom decorator (executes first after permission check)
+        @require_permission("threads", "read")
+        async def get_thread(thread_id: str, request: Request):
+            auth: AuthContext = request.state.auth
+            ...
+
+    Raises:
+        ValueError: If 'request' parameter is missing
+    """
+
+    @functools.wraps(func)
+    async def wrapper(*args: Any, **kwargs: Any) -> Any:
+        request = kwargs.get("request")
+        if request is None:
+            raise ValueError("require_auth decorator requires 'request' parameter")
+
+        # Authenticate and set context
+        auth_context = await _authenticate(request)
+        request.state.auth = auth_context
+
+        return await func(*args, **kwargs)
+
+    return wrapper
+
+
+def require_permission(
+    resource: str,
+    action: str,
+    owner_check: bool = False,
+    require_existing: bool = False,
+) -> Callable[[Callable[P, T]], Callable[P, T]]:
+    """Decorator that checks permission for resource:action.
+
+    Must be used AFTER @require_auth.
+
+    Args:
+        resource: Resource name (e.g., "threads", "runs")
+        action: Action name (e.g., "read", "write", "delete")
+        owner_check: If True, validates that the current user owns the resource.
+                     Requires 'thread_id' path parameter and performs ownership check.
+        require_existing: Only meaningful with ``owner_check=True``. If True, a
+                          missing ``threads_meta`` row counts as a denial (404)
+                          instead of "untracked legacy thread, allow". Use on
+                          **destructive / mutating** routes (DELETE, PATCH,
+                          state-update) so a deleted thread can't be re-targeted
+                          by another user via the missing-row code path.
+
+    Usage:
+        # Read-style: legacy untracked threads are allowed
+        @require_permission("threads", "read", owner_check=True)
+        async def get_thread(thread_id: str, request: Request):
+            ...
+
+        # Destructive: thread row MUST exist and be owned by caller
+        @require_permission("threads", "delete", owner_check=True, require_existing=True)
+        async def delete_thread(thread_id: str, request: Request):
+            ...
+
+    Raises:
+        HTTPException 401: If authentication required but user is anonymous
+        HTTPException 403: If user lacks permission
+        HTTPException 404: If owner_check=True but user doesn't own the thread
+        ValueError: If owner_check=True but 'thread_id' parameter is missing
+    """
+
+    def decorator(func: Callable[P, T]) -> Callable[P, T]:
+        @functools.wraps(func)
+        async def wrapper(*args: Any, **kwargs: Any) -> Any:
+            request = kwargs.get("request")
+            if request is None:
+                raise ValueError("require_permission decorator requires 'request' parameter")
+
+            auth: AuthContext = getattr(request.state, "auth", None)
+            if auth is None:
+                auth = await _authenticate(request)
+                request.state.auth = auth
+
+            if not auth.is_authenticated:
+                raise HTTPException(status_code=401, detail="Authentication required")
+
+            # Check permission
+            if not auth.has_permission(resource, action):
+                raise HTTPException(
+                    status_code=403,
+                    detail=f"Permission denied: {resource}:{action}",
+                )
+
+            # Owner check for thread-specific resources.
+            #
+            # 2.0-rc moved thread metadata into the SQL persistence layer
+            # (``threads_meta`` table). We verify ownership via
+            # ``ThreadMetaStore.check_access``: it returns True for
+            # missing rows (untracked legacy thread) and for rows whose
+            # ``user_id`` is NULL (shared / pre-auth data), so this is
+            # strict-deny rather than strict-allow — only an *existing*
+            # row with a *different* user_id triggers 404.
+            if owner_check:
+                thread_id = kwargs.get("thread_id")
+                if thread_id is None:
+                    raise ValueError("require_permission with owner_check=True requires 'thread_id' parameter")
+
+                from app.gateway.deps import get_thread_store
+
+                thread_store = get_thread_store(request)
+                allowed = await thread_store.check_access(
+                    thread_id,
+                    str(auth.user.id),
+                    require_existing=require_existing,
+                )
+                if not allowed:
+                    raise HTTPException(
+                        status_code=404,
+                        detail=f"Thread {thread_id} not found",
+                    )
+
+            return await func(*args, **kwargs)
+
+        return wrapper
+
+    return decorator

backend/app/gateway/csrf_middleware.py

@@ -0,0 +1,113 @@
+"""CSRF protection middleware for FastAPI.
+
+Per RFC-001:
+State-changing operations require CSRF protection.
+"""
+
+import secrets
+from collections.abc import Callable
+
+from fastapi import Request, Response
+from starlette.middleware.base import BaseHTTPMiddleware
+from starlette.responses import JSONResponse
+from starlette.types import ASGIApp
+
+CSRF_COOKIE_NAME = "csrf_token"
+CSRF_HEADER_NAME = "X-CSRF-Token"
+CSRF_TOKEN_LENGTH = 64  # bytes
+
+
+def is_secure_request(request: Request) -> bool:
+    """Detect whether the original client request was made over HTTPS."""
+    return request.headers.get("x-forwarded-proto", request.url.scheme) == "https"
+
+
+def generate_csrf_token() -> str:
+    """Generate a secure random CSRF token."""
+    return secrets.token_urlsafe(CSRF_TOKEN_LENGTH)
+
+
+def should_check_csrf(request: Request) -> bool:
+    """Determine if a request needs CSRF validation.
+
+    CSRF is checked for state-changing methods (POST, PUT, DELETE, PATCH).
+    GET, HEAD, OPTIONS, and TRACE are exempt per RFC 7231.
+    """
+    if request.method not in ("POST", "PUT", "DELETE", "PATCH"):
+        return False
+
+    path = request.url.path.rstrip("/")
+    # Exempt /api/v1/auth/me endpoint
+    if path == "/api/v1/auth/me":
+        return False
+    return True
+
+
+_AUTH_EXEMPT_PATHS: frozenset[str] = frozenset(
+    {
+        "/api/v1/auth/login/local",
+        "/api/v1/auth/logout",
+        "/api/v1/auth/register",
+        "/api/v1/auth/initialize",
+    }
+)
+
+
+def is_auth_endpoint(request: Request) -> bool:
+    """Check if the request is to an auth endpoint.
+
+    Auth endpoints don't need CSRF validation on first call (no token).
+    """
+    return request.url.path.rstrip("/") in _AUTH_EXEMPT_PATHS
+
+
+class CSRFMiddleware(BaseHTTPMiddleware):
+    """Middleware that implements CSRF protection using Double Submit Cookie pattern."""
+
+    def __init__(self, app: ASGIApp) -> None:
+        super().__init__(app)
+
+    async def dispatch(self, request: Request, call_next: Callable) -> Response:
+        _is_auth = is_auth_endpoint(request)
+
+        if should_check_csrf(request) and not _is_auth:
+            cookie_token = request.cookies.get(CSRF_COOKIE_NAME)
+            header_token = request.headers.get(CSRF_HEADER_NAME)
+
+            if not cookie_token or not header_token:
+                return JSONResponse(
+                    status_code=403,
+                    content={"detail": "CSRF token missing. Include X-CSRF-Token header."},
+                )
+
+            if not secrets.compare_digest(cookie_token, header_token):
+                return JSONResponse(
+                    status_code=403,
+                    content={"detail": "CSRF token mismatch."},
+                )
+
+        response = await call_next(request)
+
+        # For auth endpoints that set up session, also set CSRF cookie
+        if _is_auth and request.method == "POST":
+            # Generate a new CSRF token for the session
+            csrf_token = generate_csrf_token()
+            is_https = is_secure_request(request)
+            response.set_cookie(
+                key=CSRF_COOKIE_NAME,
+                value=csrf_token,
+                httponly=False,  # Must be JS-readable for Double Submit Cookie pattern
+                secure=is_https,
+                samesite="strict",
+            )
+
+        return response
+
+
+def get_csrf_token(request: Request) -> str | None:
+    """Get the CSRF token from the current request's cookies.
+
+    This is useful for server-side rendering where you need to embed
+    token in forms or headers.
+    """
+    return request.cookies.get(CSRF_COOKIE_NAME)

backend/app/gateway/deps.py

@@ -8,12 +8,25 @@ Initialization is handled directly in ``app.py`` via :class:`AsyncExitStack`.
 
 from __future__ import annotations
 
-from collections.abc import AsyncGenerator
+from collections.abc import AsyncGenerator, Callable
 from contextlib import AsyncExitStack, asynccontextmanager
+from typing import TYPE_CHECKING, TypeVar, cast
 
 from fastapi import FastAPI, HTTPException, Request
+from langgraph.types import Checkpointer
 
-from deerflow.runtime import RunManager, StreamBridge
+from deerflow.persistence.feedback import FeedbackRepository
+from deerflow.runtime import RunContext, RunManager, StreamBridge
+from deerflow.runtime.events.store.base import RunEventStore
+from deerflow.runtime.runs.store.base import RunStore
+
+if TYPE_CHECKING:
+    from app.gateway.auth.local_provider import LocalAuthProvider
+    from app.gateway.auth.repositories.sqlite import SQLiteUserRepository
+    from deerflow.persistence.thread_meta.base import ThreadMetaStore
+
+
+T = TypeVar("T")
 
 
 @asynccontextmanager
@@ -25,15 +38,52 @@ async def langgraph_runtime(app: FastAPI) -> AsyncGenerator[None, None]:
         async with langgraph_runtime(app):
             yield
     """
-    from deerflow.agents.checkpointer.async_provider import make_checkpointer
+    from deerflow.config import get_app_config
+    from deerflow.persistence.engine import close_engine, get_session_factory, init_engine_from_config
     from deerflow.runtime import make_store, make_stream_bridge
+    from deerflow.runtime.checkpointer.async_provider import make_checkpointer
+    from deerflow.runtime.events.store import make_run_event_store
 
     async with AsyncExitStack() as stack:
         app.state.stream_bridge = await stack.enter_async_context(make_stream_bridge())
+
+        # Initialize persistence engine BEFORE checkpointer so that
+        # auto-create-database logic runs first (postgres backend).
+        config = get_app_config()
+        await init_engine_from_config(config.database)
+
         app.state.checkpointer = await stack.enter_async_context(make_checkpointer())
         app.state.store = await stack.enter_async_context(make_store())
-        app.state.run_manager = RunManager()
-        yield
+
+        # Initialize repositories — one get_session_factory() call for all.
+        sf = get_session_factory()
+        if sf is not None:
+            from deerflow.persistence.feedback import FeedbackRepository
+            from deerflow.persistence.run import RunRepository
+
+            app.state.run_store = RunRepository(sf)
+            app.state.feedback_repo = FeedbackRepository(sf)
+        else:
+            from deerflow.runtime.runs.store.memory import MemoryRunStore
+
+            app.state.run_store = MemoryRunStore()
+            app.state.feedback_repo = None
+
+        from deerflow.persistence.thread_meta import make_thread_store
+
+        app.state.thread_store = make_thread_store(sf, app.state.store)
+
+        # Run event store (has its own factory with config-driven backend selection)
+        run_events_config = getattr(config, "run_events", None)
+        app.state.run_event_store = make_run_event_store(run_events_config)
+
+        # RunManager with store backing for persistence
+        app.state.run_manager = RunManager(store=app.state.run_store)
+
+        try:
+            yield
+        finally:
+            await close_engine()
 
 
 # ---------------------------------------------------------------------------
@@ -41,30 +91,144 @@ async def langgraph_runtime(app: FastAPI) -> AsyncGenerator[None, None]:
 # ---------------------------------------------------------------------------
 
 
-def get_stream_bridge(request: Request) -> StreamBridge:
-    """Return the global :class:`StreamBridge`, or 503."""
-    bridge = getattr(request.app.state, "stream_bridge", None)
-    if bridge is None:
-        raise HTTPException(status_code=503, detail="Stream bridge not available")
-    return bridge
+def _require(attr: str, label: str) -> Callable[[Request], T]:
+    """Create a FastAPI dependency that returns ``app.state.<attr>`` or 503."""
+
+    def dep(request: Request) -> T:
+        val = getattr(request.app.state, attr, None)
+        if val is None:
+            raise HTTPException(status_code=503, detail=f"{label} not available")
+        return cast(T, val)
+
+    dep.__name__ = dep.__qualname__ = f"get_{attr}"
+    return dep
 
 
-def get_run_manager(request: Request) -> RunManager:
-    """Return the global :class:`RunManager`, or 503."""
-    mgr = getattr(request.app.state, "run_manager", None)
-    if mgr is None:
-        raise HTTPException(status_code=503, detail="Run manager not available")
-    return mgr
-
-
-def get_checkpointer(request: Request):
-    """Return the global checkpointer, or 503."""
-    cp = getattr(request.app.state, "checkpointer", None)
-    if cp is None:
-        raise HTTPException(status_code=503, detail="Checkpointer not available")
-    return cp
+get_stream_bridge: Callable[[Request], StreamBridge] = _require("stream_bridge", "Stream bridge")
+get_run_manager: Callable[[Request], RunManager] = _require("run_manager", "Run manager")
+get_checkpointer: Callable[[Request], Checkpointer] = _require("checkpointer", "Checkpointer")
+get_run_event_store: Callable[[Request], RunEventStore] = _require("run_event_store", "Run event store")
+get_feedback_repo: Callable[[Request], FeedbackRepository] = _require("feedback_repo", "Feedback")
+get_run_store: Callable[[Request], RunStore] = _require("run_store", "Run store")
 
 
 def get_store(request: Request):
     """Return the global store (may be ``None`` if not configured)."""
     return getattr(request.app.state, "store", None)
+
+
+def get_thread_store(request: Request) -> ThreadMetaStore:
+    """Return the thread metadata store (SQL or memory-backed)."""
+    val = getattr(request.app.state, "thread_store", None)
+    if val is None:
+        raise HTTPException(status_code=503, detail="Thread metadata store not available")
+    return val
+
+
+def get_run_context(request: Request) -> RunContext:
+    """Build a :class:`RunContext` from ``app.state`` singletons.
+
+    Returns a *base* context with infrastructure dependencies.
+    """
+    from deerflow.config import get_app_config
+
+    return RunContext(
+        checkpointer=get_checkpointer(request),
+        store=get_store(request),
+        event_store=get_run_event_store(request),
+        run_events_config=getattr(get_app_config(), "run_events", None),
+        thread_store=get_thread_store(request),
+    )
+
+
+# ---------------------------------------------------------------------------
+# Auth helpers (used by authz.py and auth middleware)
+# ---------------------------------------------------------------------------
+
+# Cached singletons to avoid repeated instantiation per request
+_cached_local_provider: LocalAuthProvider | None = None
+_cached_repo: SQLiteUserRepository | None = None
+
+
+def get_local_provider() -> LocalAuthProvider:
+    """Get or create the cached LocalAuthProvider singleton.
+
+    Must be called after ``init_engine_from_config()`` — the shared
+    session factory is required to construct the user repository.
+    """
+    global _cached_local_provider, _cached_repo
+    if _cached_repo is None:
+        from app.gateway.auth.repositories.sqlite import SQLiteUserRepository
+        from deerflow.persistence.engine import get_session_factory
+
+        sf = get_session_factory()
+        if sf is None:
+            raise RuntimeError("get_local_provider() called before init_engine_from_config(); cannot access users table")
+        _cached_repo = SQLiteUserRepository(sf)
+    if _cached_local_provider is None:
+        from app.gateway.auth.local_provider import LocalAuthProvider
+
+        _cached_local_provider = LocalAuthProvider(repository=_cached_repo)
+    return _cached_local_provider
+
+
+async def get_current_user_from_request(request: Request):
+    """Get the current authenticated user from the request cookie.
+
+    Raises HTTPException 401 if not authenticated.
+    """
+    from app.gateway.auth import decode_token
+    from app.gateway.auth.errors import AuthErrorCode, AuthErrorResponse, TokenError, token_error_to_code
+
+    access_token = request.cookies.get("access_token")
+    if not access_token:
+        raise HTTPException(
+            status_code=401,
+            detail=AuthErrorResponse(code=AuthErrorCode.NOT_AUTHENTICATED, message="Not authenticated").model_dump(),
+        )
+
+    payload = decode_token(access_token)
+    if isinstance(payload, TokenError):
+        raise HTTPException(
+            status_code=401,
+            detail=AuthErrorResponse(code=token_error_to_code(payload), message=f"Token error: {payload.value}").model_dump(),
+        )
+
+    provider = get_local_provider()
+    user = await provider.get_user(payload.sub)
+    if user is None:
+        raise HTTPException(
+            status_code=401,
+            detail=AuthErrorResponse(code=AuthErrorCode.USER_NOT_FOUND, message="User not found").model_dump(),
+        )
+
+    # Token version mismatch → password was changed, token is stale
+    if user.token_version != payload.ver:
+        raise HTTPException(
+            status_code=401,
+            detail=AuthErrorResponse(code=AuthErrorCode.TOKEN_INVALID, message="Token revoked (password changed)").model_dump(),
+        )
+
+    return user
+
+
+async def get_optional_user_from_request(request: Request):
+    """Get optional authenticated user from request.
+
+    Returns None if not authenticated.
+    """
+    try:
+        return await get_current_user_from_request(request)
+    except HTTPException:
+        return None
+
+
+async def get_current_user(request: Request) -> str | None:
+    """Extract user_id from request cookie, or None if not authenticated.
+
+    Thin adapter that returns the string id for callers that only need
+    identification (e.g., ``feedback.py``). Full-user callers should use
+    ``get_current_user_from_request`` or ``get_optional_user_from_request``.
+    """
+    user = await get_optional_user_from_request(request)
+    return str(user.id) if user else None

backend/app/gateway/langgraph_auth.py

@@ -0,0 +1,106 @@
+"""LangGraph Server auth handler — shares JWT logic with Gateway.
+
+Loaded by LangGraph Server via langgraph.json ``auth.path``.
+Reuses the same ``decode_token`` / ``get_auth_config`` as Gateway,
+so both modes validate tokens with the same secret and rules.
+
+Two layers:
+  1. @auth.authenticate — validates JWT cookie, extracts user_id,
+     and enforces CSRF on state-changing methods (POST/PUT/DELETE/PATCH)
+  2. @auth.on — returns metadata filter so each user only sees own threads
+"""
+
+import secrets
+
+from langgraph_sdk import Auth
+
+from app.gateway.auth.errors import TokenError
+from app.gateway.auth.jwt import decode_token
+from app.gateway.deps import get_local_provider
+
+auth = Auth()
+
+# Methods that require CSRF validation (state-changing per RFC 7231).
+_CSRF_METHODS = frozenset({"POST", "PUT", "DELETE", "PATCH"})
+
+
+def _check_csrf(request) -> None:
+    """Enforce Double Submit Cookie CSRF check for state-changing requests.
+
+    Mirrors Gateway's CSRFMiddleware logic so that LangGraph routes
+    proxied directly by nginx have the same CSRF protection.
+    """
+    method = getattr(request, "method", "") or ""
+    if method.upper() not in _CSRF_METHODS:
+        return
+
+    cookie_token = request.cookies.get("csrf_token")
+    header_token = request.headers.get("x-csrf-token")
+
+    if not cookie_token or not header_token:
+        raise Auth.exceptions.HTTPException(
+            status_code=403,
+            detail="CSRF token missing. Include X-CSRF-Token header.",
+        )
+
+    if not secrets.compare_digest(cookie_token, header_token):
+        raise Auth.exceptions.HTTPException(
+            status_code=403,
+            detail="CSRF token mismatch.",
+        )
+
+
+@auth.authenticate
+async def authenticate(request):
+    """Validate the session cookie, decode JWT, and check token_version.
+
+    Same validation chain as Gateway's get_current_user_from_request:
+      cookie → decode JWT → DB lookup → token_version match
+    Also enforces CSRF on state-changing methods.
+    """
+    # CSRF check before authentication so forged cross-site requests
+    # are rejected early, even if the cookie carries a valid JWT.
+    _check_csrf(request)
+
+    token = request.cookies.get("access_token")
+    if not token:
+        raise Auth.exceptions.HTTPException(
+            status_code=401,
+            detail="Not authenticated",
+        )
+
+    payload = decode_token(token)
+    if isinstance(payload, TokenError):
+        raise Auth.exceptions.HTTPException(
+            status_code=401,
+            detail=f"Token error: {payload.value}",
+        )
+
+    user = await get_local_provider().get_user(payload.sub)
+    if user is None:
+        raise Auth.exceptions.HTTPException(
+            status_code=401,
+            detail="User not found",
+        )
+    if user.token_version != payload.ver:
+        raise Auth.exceptions.HTTPException(
+            status_code=401,
+            detail="Token revoked (password changed)",
+        )
+
+    return payload.sub
+
+
+@auth.on
+async def add_owner_filter(ctx: Auth.types.AuthContext, value: dict):
+    """Inject user_id metadata on writes; filter by user_id on reads.
+
+    Gateway stores thread ownership as ``metadata.user_id``.
+    This handler ensures LangGraph Server enforces the same isolation.
+    """
+    # On create/update: stamp user_id into metadata
+    metadata = value.setdefault("metadata", {})
+    metadata["user_id"] = ctx.user.identity
+
+    # Return filter dict — LangGraph applies it to search/read/delete
+    return {"user_id": ctx.user.identity}

backend/app/gateway/path_utils.py

@@ -5,6 +5,7 @@ from pathlib import Path
 from fastapi import HTTPException
 
 from deerflow.config.paths import get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 
 
 def resolve_thread_virtual_path(thread_id: str, virtual_path: str) -> Path:
@@ -22,7 +23,7 @@ def resolve_thread_virtual_path(thread_id: str, virtual_path: str) -> Path:
         HTTPException: If the path is invalid or outside allowed directories.
     """
     try:
-        return get_paths().resolve_virtual_path(thread_id, virtual_path)
+        return get_paths().resolve_virtual_path(thread_id, virtual_path, user_id=get_effective_user_id())
     except ValueError as e:
         status = 403 if "traversal" in str(e) else 400
         raise HTTPException(status_code=status, detail=str(e))

backend/app/gateway/routers/artifacts.py

@@ -7,6 +7,7 @@ from urllib.parse import quote
 from fastapi import APIRouter, HTTPException, Request
 from fastapi.responses import FileResponse, PlainTextResponse, Response
 
+from app.gateway.authz import require_permission
 from app.gateway.path_utils import resolve_thread_virtual_path
 
 logger = logging.getLogger(__name__)
@@ -81,6 +82,7 @@ def _extract_file_from_skill_archive(zip_path: Path, internal_path: str) -> byte
     summary="Get Artifact File",
     description="Retrieve an artifact file generated by the AI agent. Text and binary files can be viewed inline, while active web content is always downloaded.",
 )
+@require_permission("threads", "read", owner_check=True)
 async def get_artifact(thread_id: str, path: str, request: Request, download: bool = False) -> Response:
     """Get an artifact file by its path.
 

backend/app/gateway/routers/auth.py

@@ -0,0 +1,459 @@
+"""Authentication endpoints."""
+
+import logging
+import os
+import time
+from ipaddress import ip_address, ip_network
+
+from fastapi import APIRouter, Depends, HTTPException, Request, Response, status
+from fastapi.security import OAuth2PasswordRequestForm
+from pydantic import BaseModel, EmailStr, Field, field_validator
+
+from app.gateway.auth import (
+    UserResponse,
+    create_access_token,
+)
+from app.gateway.auth.config import get_auth_config
+from app.gateway.auth.errors import AuthErrorCode, AuthErrorResponse
+from app.gateway.csrf_middleware import is_secure_request
+from app.gateway.deps import get_current_user_from_request, get_local_provider
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/api/v1/auth", tags=["auth"])
+
+
+# ── Request/Response Models ──────────────────────────────────────────────
+
+
+class LoginResponse(BaseModel):
+    """Response model for login — token only lives in HttpOnly cookie."""
+
+    expires_in: int  # seconds
+    needs_setup: bool = False
+
+
+# Top common-password blocklist. Drawn from the public SecLists "10k worst
+# passwords" set, lowercased + length>=8 only (shorter ones already fail
+# the min_length check). Kept tight on purpose: this is the **lower bound**
+# defense, not a full HIBP / passlib check, and runs in-process per request.
+_COMMON_PASSWORDS: frozenset[str] = frozenset(
+    {
+        "password",
+        "password1",
+        "password12",
+        "password123",
+        "password1234",
+        "12345678",
+        "123456789",
+        "1234567890",
+        "qwerty12",
+        "qwertyui",
+        "qwerty123",
+        "abc12345",
+        "abcd1234",
+        "iloveyou",
+        "letmein1",
+        "welcome1",
+        "welcome123",
+        "admin123",
+        "administrator",
+        "passw0rd",
+        "p@ssw0rd",
+        "monkey12",
+        "trustno1",
+        "sunshine",
+        "princess",
+        "football",
+        "baseball",
+        "superman",
+        "batman123",
+        "starwars",
+        "dragon123",
+        "master123",
+        "shadow12",
+        "michael1",
+        "jennifer",
+        "computer",
+    }
+)
+
+
+def _password_is_common(password: str) -> bool:
+    """Case-insensitive blocklist check.
+
+    Lowercases the input so trivial mutations like ``Password`` /
+    ``PASSWORD`` are also rejected. Does not normalize digit substitutions
+    (``p@ssw0rd`` is included as a literal entry instead) — keeping the
+    rule cheap and predictable.
+    """
+    return password.lower() in _COMMON_PASSWORDS
+
+
+def _validate_strong_password(value: str) -> str:
+    """Pydantic field-validator body shared by Register + ChangePassword.
+
+    Constraint = function, not type-level mixin. The two request models
+    have no "is-a" relationship; they only share the password-strength
+    rule. Lifting it into a free function lets each model bind it via
+    ``@field_validator(field_name)`` without inheritance gymnastics.
+    """
+    if _password_is_common(value):
+        raise ValueError("Password is too common; choose a stronger password.")
+    return value
+
+
+class RegisterRequest(BaseModel):
+    """Request model for user registration."""
+
+    email: EmailStr
+    password: str = Field(..., min_length=8)
+
+    _strong_password = field_validator("password")(classmethod(lambda cls, v: _validate_strong_password(v)))
+
+
+class ChangePasswordRequest(BaseModel):
+    """Request model for password change (also handles setup flow)."""
+
+    current_password: str
+    new_password: str = Field(..., min_length=8)
+    new_email: EmailStr | None = None
+
+    _strong_password = field_validator("new_password")(classmethod(lambda cls, v: _validate_strong_password(v)))
+
+
+class MessageResponse(BaseModel):
+    """Generic message response."""
+
+    message: str
+
+
+# ── Helpers ───────────────────────────────────────────────────────────────
+
+
+def _set_session_cookie(response: Response, token: str, request: Request) -> None:
+    """Set the access_token HttpOnly cookie on the response."""
+    config = get_auth_config()
+    is_https = is_secure_request(request)
+    response.set_cookie(
+        key="access_token",
+        value=token,
+        httponly=True,
+        secure=is_https,
+        samesite="lax",
+        max_age=config.token_expiry_days * 24 * 3600 if is_https else None,
+    )
+
+
+# ── Rate Limiting ────────────────────────────────────────────────────────
+# In-process dict — not shared across workers. Sufficient for single-worker deployments.
+
+_MAX_LOGIN_ATTEMPTS = 5
+_LOCKOUT_SECONDS = 300  # 5 minutes
+
+# ip → (fail_count, lock_until_timestamp)
+_login_attempts: dict[str, tuple[int, float]] = {}
+
+
+def _trusted_proxies() -> list:
+    """Parse ``AUTH_TRUSTED_PROXIES`` env var into a list of ip_network objects.
+
+    Comma-separated CIDR or single-IP entries. Empty / unset = no proxy is
+    trusted (direct mode). Invalid entries are skipped with a logger warning.
+    Read live so env-var overrides take effect immediately and tests can
+    ``monkeypatch.setenv`` without poking a module-level cache.
+    """
+    raw = os.getenv("AUTH_TRUSTED_PROXIES", "").strip()
+    if not raw:
+        return []
+    nets = []
+    for entry in raw.split(","):
+        entry = entry.strip()
+        if not entry:
+            continue
+        try:
+            nets.append(ip_network(entry, strict=False))
+        except ValueError:
+            logger.warning("AUTH_TRUSTED_PROXIES: ignoring invalid entry %r", entry)
+    return nets
+
+
+def _get_client_ip(request: Request) -> str:
+    """Extract the real client IP for rate limiting.
+
+    Trust model:
+
+    - The TCP peer (``request.client.host``) is always the baseline. It is
+      whatever the kernel reports as the connecting socket — unforgeable
+      by the client itself.
+    - ``X-Real-IP`` is **only** honored if the TCP peer is in the
+      ``AUTH_TRUSTED_PROXIES`` allowlist (set via env var, comma-separated
+      CIDR or single IPs). When set, the gateway is assumed to be behind a
+      reverse proxy (nginx, Cloudflare, ALB, …) that overwrites
+      ``X-Real-IP`` with the original client address.
+    - With no ``AUTH_TRUSTED_PROXIES`` set, ``X-Real-IP`` is silently
+      ignored — closing the bypass where any client could rotate the
+      header to dodge per-IP rate limits in dev / direct-gateway mode.
+
+    ``X-Forwarded-For`` is intentionally NOT used because it is naturally
+    client-controlled at the *first* hop and the trust chain is harder to
+    audit per-request.
+    """
+    peer_host = request.client.host if request.client else None
+
+    trusted = _trusted_proxies()
+    if trusted and peer_host:
+        try:
+            peer_ip = ip_address(peer_host)
+            if any(peer_ip in net for net in trusted):
+                real_ip = request.headers.get("x-real-ip", "").strip()
+                if real_ip:
+                    return real_ip
+        except ValueError:
+            # peer_host wasn't a parseable IP (e.g. "unknown") — fall through
+            pass
+
+    return peer_host or "unknown"
+
+
+def _check_rate_limit(ip: str) -> None:
+    """Raise 429 if the IP is currently locked out."""
+    record = _login_attempts.get(ip)
+    if record is None:
+        return
+    fail_count, lock_until = record
+    if fail_count >= _MAX_LOGIN_ATTEMPTS:
+        if time.time() < lock_until:
+            raise HTTPException(
+                status_code=429,
+                detail="Too many login attempts. Try again later.",
+            )
+        del _login_attempts[ip]
+
+
+_MAX_TRACKED_IPS = 10000
+
+
+def _record_login_failure(ip: str) -> None:
+    """Record a failed login attempt for the given IP."""
+    # Evict expired lockouts when dict grows too large
+    if len(_login_attempts) >= _MAX_TRACKED_IPS:
+        now = time.time()
+        expired = [k for k, (c, t) in _login_attempts.items() if c >= _MAX_LOGIN_ATTEMPTS and now >= t]
+        for k in expired:
+            del _login_attempts[k]
+        # If still too large, evict cheapest-to-lose half: below-threshold
+        # IPs (lock_until=0.0) sort first, then earliest-expiring lockouts.
+        if len(_login_attempts) >= _MAX_TRACKED_IPS:
+            by_time = sorted(_login_attempts.items(), key=lambda kv: kv[1][1])
+            for k, _ in by_time[: len(by_time) // 2]:
+                del _login_attempts[k]
+
+    record = _login_attempts.get(ip)
+    if record is None:
+        _login_attempts[ip] = (1, 0.0)
+    else:
+        new_count = record[0] + 1
+        lock_until = time.time() + _LOCKOUT_SECONDS if new_count >= _MAX_LOGIN_ATTEMPTS else 0.0
+        _login_attempts[ip] = (new_count, lock_until)
+
+
+def _record_login_success(ip: str) -> None:
+    """Clear failure counter for the given IP on successful login."""
+    _login_attempts.pop(ip, None)
+
+
+# ── Endpoints ─────────────────────────────────────────────────────────────
+
+
+@router.post("/login/local", response_model=LoginResponse)
+async def login_local(
+    request: Request,
+    response: Response,
+    form_data: OAuth2PasswordRequestForm = Depends(),
+):
+    """Local email/password login."""
+    client_ip = _get_client_ip(request)
+    _check_rate_limit(client_ip)
+
+    user = await get_local_provider().authenticate({"email": form_data.username, "password": form_data.password})
+
+    if user is None:
+        _record_login_failure(client_ip)
+        raise HTTPException(
+            status_code=status.HTTP_401_UNAUTHORIZED,
+            detail=AuthErrorResponse(code=AuthErrorCode.INVALID_CREDENTIALS, message="Incorrect email or password").model_dump(),
+        )
+
+    _record_login_success(client_ip)
+    token = create_access_token(str(user.id), token_version=user.token_version)
+    _set_session_cookie(response, token, request)
+
+    return LoginResponse(
+        expires_in=get_auth_config().token_expiry_days * 24 * 3600,
+        needs_setup=user.needs_setup,
+    )
+
+
+@router.post("/register", response_model=UserResponse, status_code=status.HTTP_201_CREATED)
+async def register(request: Request, response: Response, body: RegisterRequest):
+    """Register a new user account (always 'user' role).
+
+    Admin is auto-created on first boot. This endpoint creates regular users.
+    Auto-login by setting the session cookie.
+    """
+    try:
+        user = await get_local_provider().create_user(email=body.email, password=body.password, system_role="user")
+    except ValueError:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=AuthErrorResponse(code=AuthErrorCode.EMAIL_ALREADY_EXISTS, message="Email already registered").model_dump(),
+        )
+
+    token = create_access_token(str(user.id), token_version=user.token_version)
+    _set_session_cookie(response, token, request)
+
+    return UserResponse(id=str(user.id), email=user.email, system_role=user.system_role)
+
+
+@router.post("/logout", response_model=MessageResponse)
+async def logout(request: Request, response: Response):
+    """Logout current user by clearing the cookie."""
+    response.delete_cookie(key="access_token", secure=is_secure_request(request), samesite="lax")
+    return MessageResponse(message="Successfully logged out")
+
+
+@router.post("/change-password", response_model=MessageResponse)
+async def change_password(request: Request, response: Response, body: ChangePasswordRequest):
+    """Change password for the currently authenticated user.
+
+    Also handles the first-boot setup flow:
+    - If new_email is provided, updates email (checks uniqueness)
+    - If user.needs_setup is True and new_email is given, clears needs_setup
+    - Always increments token_version to invalidate old sessions
+    - Re-issues session cookie with new token_version
+    """
+    from app.gateway.auth.password import hash_password_async, verify_password_async
+
+    user = await get_current_user_from_request(request)
+
+    if user.password_hash is None:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=AuthErrorResponse(code=AuthErrorCode.INVALID_CREDENTIALS, message="OAuth users cannot change password").model_dump())
+
+    if not await verify_password_async(body.current_password, user.password_hash):
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=AuthErrorResponse(code=AuthErrorCode.INVALID_CREDENTIALS, message="Current password is incorrect").model_dump())
+
+    provider = get_local_provider()
+
+    # Update email if provided
+    if body.new_email is not None:
+        existing = await provider.get_user_by_email(body.new_email)
+        if existing and str(existing.id) != str(user.id):
+            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=AuthErrorResponse(code=AuthErrorCode.EMAIL_ALREADY_EXISTS, message="Email already in use").model_dump())
+        user.email = body.new_email
+
+    # Update password + bump version
+    user.password_hash = await hash_password_async(body.new_password)
+    user.token_version += 1
+
+    # Clear setup flag if this is the setup flow
+    if user.needs_setup and body.new_email is not None:
+        user.needs_setup = False
+
+    await provider.update_user(user)
+
+    # Re-issue cookie with new token_version
+    token = create_access_token(str(user.id), token_version=user.token_version)
+    _set_session_cookie(response, token, request)
+
+    return MessageResponse(message="Password changed successfully")
+
+
+@router.get("/me", response_model=UserResponse)
+async def get_me(request: Request):
+    """Get current authenticated user info."""
+    user = await get_current_user_from_request(request)
+    return UserResponse(id=str(user.id), email=user.email, system_role=user.system_role, needs_setup=user.needs_setup)
+
+
+@router.get("/setup-status")
+async def setup_status():
+    """Check if an admin account exists. Returns needs_setup=True when no admin exists."""
+    admin_count = await get_local_provider().count_admin_users()
+    return {"needs_setup": admin_count == 0}
+
+
+class InitializeAdminRequest(BaseModel):
+    """Request model for first-boot admin account creation."""
+
+    email: EmailStr
+    password: str = Field(..., min_length=8)
+
+    _strong_password = field_validator("password")(classmethod(lambda cls, v: _validate_strong_password(v)))
+
+
+@router.post("/initialize", response_model=UserResponse, status_code=status.HTTP_201_CREATED)
+async def initialize_admin(request: Request, response: Response, body: InitializeAdminRequest):
+    """Create the first admin account on initial system setup.
+
+    Only callable when no admin exists. Returns 409 Conflict if an admin
+    already exists.
+
+    On success, the admin account is created with ``needs_setup=False`` and
+    the session cookie is set.
+    """
+    admin_count = await get_local_provider().count_admin_users()
+    if admin_count > 0:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=AuthErrorResponse(code=AuthErrorCode.SYSTEM_ALREADY_INITIALIZED, message="System already initialized").model_dump(),
+        )
+
+    try:
+        user = await get_local_provider().create_user(email=body.email, password=body.password, system_role="admin", needs_setup=False)
+    except ValueError:
+        # DB unique-constraint race: another concurrent request beat us.
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=AuthErrorResponse(code=AuthErrorCode.SYSTEM_ALREADY_INITIALIZED, message="System already initialized").model_dump(),
+        )
+
+    token = create_access_token(str(user.id), token_version=user.token_version)
+    _set_session_cookie(response, token, request)
+
+    return UserResponse(id=str(user.id), email=user.email, system_role=user.system_role)
+
+
+# ── OAuth Endpoints (Future/Placeholder) ─────────────────────────────────
+
+
+@router.get("/oauth/{provider}")
+async def oauth_login(provider: str):
+    """Initiate OAuth login flow.
+
+    Redirects to the OAuth provider's authorization URL.
+    Currently a placeholder - requires OAuth provider implementation.
+    """
+    if provider not in ["github", "google"]:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=f"Unsupported OAuth provider: {provider}",
+        )
+
+    raise HTTPException(
+        status_code=status.HTTP_501_NOT_IMPLEMENTED,
+        detail="OAuth login not yet implemented",
+    )
+
+
+@router.get("/callback/{provider}")
+async def oauth_callback(provider: str, code: str, state: str):
+    """OAuth callback endpoint.
+
+    Handles the OAuth provider's callback after user authorization.
+    Currently a placeholder.
+    """
+    raise HTTPException(
+        status_code=status.HTTP_501_NOT_IMPLEMENTED,
+        detail="OAuth callback not yet implemented",
+    )

backend/app/gateway/routers/feedback.py

@@ -0,0 +1,188 @@
+"""Feedback endpoints — create, list, stats, delete.
+
+Allows users to submit thumbs-up/down feedback on runs,
+optionally scoped to a specific message.
+"""
+
+from __future__ import annotations
+
+import logging
+from typing import Any
+
+from fastapi import APIRouter, HTTPException, Request
+from pydantic import BaseModel, Field
+
+from app.gateway.authz import require_permission
+from app.gateway.deps import get_current_user, get_feedback_repo, get_run_store
+
+logger = logging.getLogger(__name__)
+router = APIRouter(prefix="/api/threads", tags=["feedback"])
+
+
+# ---------------------------------------------------------------------------
+# Request / response models
+# ---------------------------------------------------------------------------
+
+
+class FeedbackCreateRequest(BaseModel):
+    rating: int = Field(..., description="Feedback rating: +1 (positive) or -1 (negative)")
+    comment: str | None = Field(default=None, description="Optional text feedback")
+    message_id: str | None = Field(default=None, description="Optional: scope feedback to a specific message")
+
+
+class FeedbackUpsertRequest(BaseModel):
+    rating: int = Field(..., description="Feedback rating: +1 (positive) or -1 (negative)")
+    comment: str | None = Field(default=None, description="Optional text feedback")
+
+
+class FeedbackResponse(BaseModel):
+    feedback_id: str
+    run_id: str
+    thread_id: str
+    user_id: str | None = None
+    message_id: str | None = None
+    rating: int
+    comment: str | None = None
+    created_at: str = ""
+
+
+class FeedbackStatsResponse(BaseModel):
+    run_id: str
+    total: int = 0
+    positive: int = 0
+    negative: int = 0
+
+
+# ---------------------------------------------------------------------------
+# Endpoints
+# ---------------------------------------------------------------------------
+
+
+@router.put("/{thread_id}/runs/{run_id}/feedback", response_model=FeedbackResponse)
+@require_permission("threads", "write", owner_check=True, require_existing=True)
+async def upsert_feedback(
+    thread_id: str,
+    run_id: str,
+    body: FeedbackUpsertRequest,
+    request: Request,
+) -> dict[str, Any]:
+    """Create or update feedback for a run (idempotent)."""
+    if body.rating not in (1, -1):
+        raise HTTPException(status_code=400, detail="rating must be +1 or -1")
+
+    user_id = await get_current_user(request)
+
+    run_store = get_run_store(request)
+    run = await run_store.get(run_id)
+    if run is None:
+        raise HTTPException(status_code=404, detail=f"Run {run_id} not found")
+    if run.get("thread_id") != thread_id:
+        raise HTTPException(status_code=404, detail=f"Run {run_id} not found in thread {thread_id}")
+
+    feedback_repo = get_feedback_repo(request)
+    return await feedback_repo.upsert(
+        run_id=run_id,
+        thread_id=thread_id,
+        rating=body.rating,
+        user_id=user_id,
+        comment=body.comment,
+    )
+
+
+@router.delete("/{thread_id}/runs/{run_id}/feedback")
+@require_permission("threads", "delete", owner_check=True, require_existing=True)
+async def delete_run_feedback(
+    thread_id: str,
+    run_id: str,
+    request: Request,
+) -> dict[str, bool]:
+    """Delete the current user's feedback for a run."""
+    user_id = await get_current_user(request)
+    feedback_repo = get_feedback_repo(request)
+    deleted = await feedback_repo.delete_by_run(
+        thread_id=thread_id,
+        run_id=run_id,
+        user_id=user_id,
+    )
+    if not deleted:
+        raise HTTPException(status_code=404, detail="No feedback found for this run")
+    return {"success": True}
+
+
+@router.post("/{thread_id}/runs/{run_id}/feedback", response_model=FeedbackResponse)
+@require_permission("threads", "write", owner_check=True, require_existing=True)
+async def create_feedback(
+    thread_id: str,
+    run_id: str,
+    body: FeedbackCreateRequest,
+    request: Request,
+) -> dict[str, Any]:
+    """Submit feedback (thumbs-up/down) for a run."""
+    if body.rating not in (1, -1):
+        raise HTTPException(status_code=400, detail="rating must be +1 or -1")
+
+    user_id = await get_current_user(request)
+
+    # Validate run exists and belongs to thread
+    run_store = get_run_store(request)
+    run = await run_store.get(run_id)
+    if run is None:
+        raise HTTPException(status_code=404, detail=f"Run {run_id} not found")
+    if run.get("thread_id") != thread_id:
+        raise HTTPException(status_code=404, detail=f"Run {run_id} not found in thread {thread_id}")
+
+    feedback_repo = get_feedback_repo(request)
+    return await feedback_repo.create(
+        run_id=run_id,
+        thread_id=thread_id,
+        rating=body.rating,
+        user_id=user_id,
+        message_id=body.message_id,
+        comment=body.comment,
+    )
+
+
+@router.get("/{thread_id}/runs/{run_id}/feedback", response_model=list[FeedbackResponse])
+@require_permission("threads", "read", owner_check=True)
+async def list_feedback(
+    thread_id: str,
+    run_id: str,
+    request: Request,
+) -> list[dict[str, Any]]:
+    """List all feedback for a run."""
+    feedback_repo = get_feedback_repo(request)
+    return await feedback_repo.list_by_run(thread_id, run_id)
+
+
+@router.get("/{thread_id}/runs/{run_id}/feedback/stats", response_model=FeedbackStatsResponse)
+@require_permission("threads", "read", owner_check=True)
+async def feedback_stats(
+    thread_id: str,
+    run_id: str,
+    request: Request,
+) -> dict[str, Any]:
+    """Get aggregated feedback stats (positive/negative counts) for a run."""
+    feedback_repo = get_feedback_repo(request)
+    return await feedback_repo.aggregate_by_run(thread_id, run_id)
+
+
+@router.delete("/{thread_id}/runs/{run_id}/feedback/{feedback_id}")
+@require_permission("threads", "delete", owner_check=True, require_existing=True)
+async def delete_feedback(
+    thread_id: str,
+    run_id: str,
+    feedback_id: str,
+    request: Request,
+) -> dict[str, bool]:
+    """Delete a feedback record."""
+    feedback_repo = get_feedback_repo(request)
+    # Verify feedback belongs to the specified thread/run before deleting
+    existing = await feedback_repo.get(feedback_id)
+    if existing is None:
+        raise HTTPException(status_code=404, detail=f"Feedback {feedback_id} not found")
+    if existing.get("thread_id") != thread_id or existing.get("run_id") != run_id:
+        raise HTTPException(status_code=404, detail=f"Feedback {feedback_id} not found in run {run_id}")
+    deleted = await feedback_repo.delete(feedback_id)
+    if not deleted:
+        raise HTTPException(status_code=404, detail=f"Feedback {feedback_id} not found")
+    return {"success": True}

backend/app/gateway/routers/memory.py

@@ -13,6 +13,7 @@ from deerflow.agents.memory.updater import (
     update_memory_fact,
 )
 from deerflow.config.memory_config import get_memory_config
+from deerflow.runtime.user_context import get_effective_user_id
 
 router = APIRouter(prefix="/api", tags=["memory"])
 
@@ -147,7 +148,7 @@ async def get_memory() -> MemoryResponse:
         }
         ```
     """
-    memory_data = get_memory_data()
+    memory_data = get_memory_data(user_id=get_effective_user_id())
     return MemoryResponse(**memory_data)
 
 
@@ -167,7 +168,7 @@ async def reload_memory() -> MemoryResponse:
     Returns:
         The reloaded memory data.
     """
-    memory_data = reload_memory_data()
+    memory_data = reload_memory_data(user_id=get_effective_user_id())
     return MemoryResponse(**memory_data)
 
 
@@ -181,7 +182,7 @@ async def reload_memory() -> MemoryResponse:
 async def clear_memory() -> MemoryResponse:
     """Clear all persisted memory data."""
     try:
-        memory_data = clear_memory_data()
+        memory_data = clear_memory_data(user_id=get_effective_user_id())
     except OSError as exc:
         raise HTTPException(status_code=500, detail="Failed to clear memory data.") from exc
 
@@ -202,6 +203,7 @@ async def create_memory_fact_endpoint(request: FactCreateRequest) -> MemoryRespo
             content=request.content,
             category=request.category,
             confidence=request.confidence,
+            user_id=get_effective_user_id(),
         )
     except ValueError as exc:
         raise _map_memory_fact_value_error(exc) from exc
@@ -221,7 +223,7 @@ async def create_memory_fact_endpoint(request: FactCreateRequest) -> MemoryRespo
 async def delete_memory_fact_endpoint(fact_id: str) -> MemoryResponse:
     """Delete a single fact from memory by fact id."""
     try:
-        memory_data = delete_memory_fact(fact_id)
+        memory_data = delete_memory_fact(fact_id, user_id=get_effective_user_id())
     except KeyError as exc:
         raise HTTPException(status_code=404, detail=f"Memory fact '{fact_id}' not found.") from exc
     except OSError as exc:
@@ -245,6 +247,7 @@ async def update_memory_fact_endpoint(fact_id: str, request: FactPatchRequest) -
             content=request.content,
             category=request.category,
             confidence=request.confidence,
+            user_id=get_effective_user_id(),
         )
     except ValueError as exc:
         raise _map_memory_fact_value_error(exc) from exc
@@ -265,7 +268,7 @@ async def update_memory_fact_endpoint(fact_id: str, request: FactPatchRequest) -
 )
 async def export_memory() -> MemoryResponse:
     """Export the current memory data."""
-    memory_data = get_memory_data()
+    memory_data = get_memory_data(user_id=get_effective_user_id())
     return MemoryResponse(**memory_data)
 
 
@@ -279,7 +282,7 @@ async def export_memory() -> MemoryResponse:
 async def import_memory(request: MemoryResponse) -> MemoryResponse:
     """Import and persist memory data."""
     try:
-        memory_data = import_memory_data(request.model_dump())
+        memory_data = import_memory_data(request.model_dump(), user_id=get_effective_user_id())
     except OSError as exc:
         raise HTTPException(status_code=500, detail="Failed to import memory data.") from exc
 
@@ -337,7 +340,7 @@ async def get_memory_status() -> MemoryStatusResponse:
         Combined memory configuration and current data.
     """
     config = get_memory_config()
-    memory_data = get_memory_data()
+    memory_data = get_memory_data(user_id=get_effective_user_id())
 
     return MemoryStatusResponse(
         config=MemoryConfigResponse(

backend/app/gateway/routers/runs.py

@@ -11,10 +11,11 @@ import asyncio
 import logging
 import uuid
 
-from fastapi import APIRouter, Request
+from fastapi import APIRouter, HTTPException, Query, Request
 from fastapi.responses import StreamingResponse
 
-from app.gateway.deps import get_checkpointer, get_run_manager, get_stream_bridge
+from app.gateway.authz import require_permission
+from app.gateway.deps import get_checkpointer, get_feedback_repo, get_run_event_store, get_run_manager, get_run_store, get_stream_bridge
 from app.gateway.routers.thread_runs import RunCreateRequest
 from app.gateway.services import sse_consumer, start_run
 from deerflow.runtime import serialize_channel_values
@@ -85,3 +86,58 @@ async def stateless_wait(body: RunCreateRequest, request: Request) -> dict:
         logger.exception("Failed to fetch final state for run %s", record.run_id)
 
     return {"status": record.status.value, "error": record.error}
+
+
+# ---------------------------------------------------------------------------
+# Run-scoped read endpoints
+# ---------------------------------------------------------------------------
+
+
+async def _resolve_run(run_id: str, request: Request) -> dict:
+    """Fetch run by run_id with user ownership check. Raises 404 if not found."""
+    run_store = get_run_store(request)
+    record = await run_store.get(run_id)  # user_id=AUTO filters by contextvar
+    if record is None:
+        raise HTTPException(status_code=404, detail=f"Run {run_id} not found")
+    return record
+
+
+@router.get("/{run_id}/messages")
+@require_permission("runs", "read")
+async def run_messages(
+    run_id: str,
+    request: Request,
+    limit: int = Query(default=50, le=200, ge=1),
+    before_seq: int | None = Query(default=None),
+    after_seq: int | None = Query(default=None),
+) -> dict:
+    """Return paginated messages for a run (cursor-based).
+
+    Pagination:
+    - after_seq: messages with seq > after_seq (forward)
+    - before_seq: messages with seq < before_seq (backward)
+    - neither: latest messages
+
+    Response: { data: [...], has_more: bool }
+    """
+    run = await _resolve_run(run_id, request)
+    event_store = get_run_event_store(request)
+    rows = await event_store.list_messages_by_run(
+        run["thread_id"],
+        run_id,
+        limit=limit + 1,
+        before_seq=before_seq,
+        after_seq=after_seq,
+    )
+    has_more = len(rows) > limit
+    data = rows[:limit] if has_more else rows
+    return {"data": data, "has_more": has_more}
+
+
+@router.get("/{run_id}/feedback")
+@require_permission("runs", "read")
+async def run_feedback(run_id: str, request: Request) -> list[dict]:
+    """Return all feedback for a run."""
+    run = await _resolve_run(run_id, request)
+    feedback_repo = get_feedback_repo(request)
+    return await feedback_repo.list_by_run(run["thread_id"], run_id)

backend/app/gateway/routers/suggestions.py

@@ -1,10 +1,11 @@
 import json
 import logging
 
-from fastapi import APIRouter
+from fastapi import APIRouter, Request
 from langchain_core.messages import HumanMessage, SystemMessage
 from pydantic import BaseModel, Field
 
+from app.gateway.authz import require_permission
 from deerflow.models import create_chat_model
 
 logger = logging.getLogger(__name__)
@@ -98,12 +99,13 @@ def _format_conversation(messages: list[SuggestionMessage]) -> str:
     summary="Generate Follow-up Questions",
     description="Generate short follow-up questions a user might ask next, based on recent conversation context.",
 )
-async def generate_suggestions(thread_id: str, request: SuggestionsRequest) -> SuggestionsResponse:
-    if not request.messages:
+@require_permission("threads", "read", owner_check=True)
+async def generate_suggestions(thread_id: str, body: SuggestionsRequest, request: Request) -> SuggestionsResponse:
+    if not body.messages:
         return SuggestionsResponse(suggestions=[])
 
-    n = request.n
-    conversation = _format_conversation(request.messages)
+    n = body.n
+    conversation = _format_conversation(body.messages)
     if not conversation:
         return SuggestionsResponse(suggestions=[])
 
@@ -120,7 +122,7 @@ async def generate_suggestions(thread_id: str, request: SuggestionsRequest) -> S
     user_content = f"Conversation Context:\n{conversation}\n\nGenerate {n} follow-up questions"
 
     try:
-        model = create_chat_model(name=request.model_name, thinking_enabled=False)
+        model = create_chat_model(name=body.model_name, thinking_enabled=False)
         response = await model.ainvoke([SystemMessage(content=system_instruction), HumanMessage(content=user_content)])
         raw = _extract_response_text(response.content)
         suggestions = _parse_json_string_list(raw) or []

backend/app/gateway/routers/thread_runs.py

@@ -19,7 +19,8 @@ from fastapi import APIRouter, HTTPException, Query, Request
 from fastapi.responses import Response, StreamingResponse
 from pydantic import BaseModel, Field
 
-from app.gateway.deps import get_checkpointer, get_run_manager, get_stream_bridge
+from app.gateway.authz import require_permission
+from app.gateway.deps import get_checkpointer, get_current_user, get_feedback_repo, get_run_event_store, get_run_manager, get_run_store, get_stream_bridge
 from app.gateway.services import sse_consumer, start_run
 from deerflow.runtime import RunRecord, serialize_channel_values
 
@@ -92,6 +93,7 @@ def _record_to_response(record: RunRecord) -> RunResponse:
 
 
 @router.post("/{thread_id}/runs", response_model=RunResponse)
+@require_permission("runs", "create", owner_check=True, require_existing=True)
 async def create_run(thread_id: str, body: RunCreateRequest, request: Request) -> RunResponse:
     """Create a background run (returns immediately)."""
     record = await start_run(body, thread_id, request)
@@ -99,6 +101,7 @@ async def create_run(thread_id: str, body: RunCreateRequest, request: Request) -
 
 
 @router.post("/{thread_id}/runs/stream")
+@require_permission("runs", "create", owner_check=True, require_existing=True)
 async def stream_run(thread_id: str, body: RunCreateRequest, request: Request) -> StreamingResponse:
     """Create a run and stream events via SSE.
 
@@ -126,6 +129,7 @@ async def stream_run(thread_id: str, body: RunCreateRequest, request: Request) -
 
 
 @router.post("/{thread_id}/runs/wait", response_model=dict)
+@require_permission("runs", "create", owner_check=True, require_existing=True)
 async def wait_run(thread_id: str, body: RunCreateRequest, request: Request) -> dict:
     """Create a run and block until it completes, returning the final state."""
     record = await start_run(body, thread_id, request)
@@ -151,6 +155,7 @@ async def wait_run(thread_id: str, body: RunCreateRequest, request: Request) ->
 
 
 @router.get("/{thread_id}/runs", response_model=list[RunResponse])
+@require_permission("runs", "read", owner_check=True)
 async def list_runs(thread_id: str, request: Request) -> list[RunResponse]:
     """List all runs for a thread."""
     run_mgr = get_run_manager(request)
@@ -159,6 +164,7 @@ async def list_runs(thread_id: str, request: Request) -> list[RunResponse]:
 
 
 @router.get("/{thread_id}/runs/{run_id}", response_model=RunResponse)
+@require_permission("runs", "read", owner_check=True)
 async def get_run(thread_id: str, run_id: str, request: Request) -> RunResponse:
     """Get details of a specific run."""
     run_mgr = get_run_manager(request)
@@ -169,6 +175,7 @@ async def get_run(thread_id: str, run_id: str, request: Request) -> RunResponse:
 
 
 @router.post("/{thread_id}/runs/{run_id}/cancel")
+@require_permission("runs", "cancel", owner_check=True, require_existing=True)
 async def cancel_run(
     thread_id: str,
     run_id: str,
@@ -206,6 +213,7 @@ async def cancel_run(
 
 
 @router.get("/{thread_id}/runs/{run_id}/join")
+@require_permission("runs", "read", owner_check=True)
 async def join_run(thread_id: str, run_id: str, request: Request) -> StreamingResponse:
     """Join an existing run's SSE stream."""
     bridge = get_stream_bridge(request)
@@ -226,6 +234,7 @@ async def join_run(thread_id: str, run_id: str, request: Request) -> StreamingRe
 
 
 @router.api_route("/{thread_id}/runs/{run_id}/stream", methods=["GET", "POST"], response_model=None)
+@require_permission("runs", "read", owner_check=True)
 async def stream_existing_run(
     thread_id: str,
     run_id: str,
@@ -265,3 +274,104 @@ async def stream_existing_run(
             "X-Accel-Buffering": "no",
         },
     )
+
+
+# ---------------------------------------------------------------------------
+# Messages / Events / Token usage endpoints
+# ---------------------------------------------------------------------------
+
+
+@router.get("/{thread_id}/messages")
+@require_permission("runs", "read", owner_check=True)
+async def list_thread_messages(
+    thread_id: str,
+    request: Request,
+    limit: int = Query(default=50, le=200),
+    before_seq: int | None = Query(default=None),
+    after_seq: int | None = Query(default=None),
+) -> list[dict]:
+    """Return displayable messages for a thread (across all runs), with feedback attached."""
+    event_store = get_run_event_store(request)
+    messages = await event_store.list_messages(thread_id, limit=limit, before_seq=before_seq, after_seq=after_seq)
+
+    # Attach feedback to the last AI message of each run
+    feedback_repo = get_feedback_repo(request)
+    user_id = await get_current_user(request)
+    feedback_map = await feedback_repo.list_by_thread_grouped(thread_id, user_id=user_id)
+
+    # Find the last ai_message per run_id
+    last_ai_per_run: dict[str, int] = {}  # run_id -> index in messages list
+    for i, msg in enumerate(messages):
+        if msg.get("event_type") == "ai_message":
+            last_ai_per_run[msg["run_id"]] = i
+
+    # Attach feedback field
+    last_ai_indices = set(last_ai_per_run.values())
+    for i, msg in enumerate(messages):
+        if i in last_ai_indices:
+            run_id = msg["run_id"]
+            fb = feedback_map.get(run_id)
+            msg["feedback"] = (
+                {
+                    "feedback_id": fb["feedback_id"],
+                    "rating": fb["rating"],
+                    "comment": fb.get("comment"),
+                }
+                if fb
+                else None
+            )
+        else:
+            msg["feedback"] = None
+
+    return messages
+
+
+@router.get("/{thread_id}/runs/{run_id}/messages")
+@require_permission("runs", "read", owner_check=True)
+async def list_run_messages(
+    thread_id: str,
+    run_id: str,
+    request: Request,
+    limit: int = Query(default=50, le=200, ge=1),
+    before_seq: int | None = Query(default=None),
+    after_seq: int | None = Query(default=None),
+) -> dict:
+    """Return paginated messages for a specific run.
+
+    Response: { data: [...], has_more: bool }
+    """
+    event_store = get_run_event_store(request)
+    rows = await event_store.list_messages_by_run(
+        thread_id,
+        run_id,
+        limit=limit + 1,
+        before_seq=before_seq,
+        after_seq=after_seq,
+    )
+    has_more = len(rows) > limit
+    data = rows[:limit] if has_more else rows
+    return {"data": data, "has_more": has_more}
+
+
+@router.get("/{thread_id}/runs/{run_id}/events")
+@require_permission("runs", "read", owner_check=True)
+async def list_run_events(
+    thread_id: str,
+    run_id: str,
+    request: Request,
+    event_types: str | None = Query(default=None),
+    limit: int = Query(default=500, le=2000),
+) -> list[dict]:
+    """Return the full event stream for a run (debug/audit)."""
+    event_store = get_run_event_store(request)
+    types = event_types.split(",") if event_types else None
+    return await event_store.list_events(thread_id, run_id, event_types=types, limit=limit)
+
+
+@router.get("/{thread_id}/token-usage")
+@require_permission("threads", "read", owner_check=True)
+async def thread_token_usage(thread_id: str, request: Request) -> dict:
+    """Thread-level token usage aggregation."""
+    run_store = get_run_store(request)
+    agg = await run_store.aggregate_tokens_by_thread(thread_id)
+    return {"thread_id": thread_id, **agg}

backend/app/gateway/routers/threads.py

@@ -13,28 +13,41 @@ matching the LangGraph Platform wire format expected by the
 from __future__ import annotations
 
 import logging
+import re
 import time
 import uuid
 from typing import Any
 
 from fastapi import APIRouter, HTTPException, Request
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, field_validator
 
-from app.gateway.deps import get_checkpointer, get_store
+from app.gateway.authz import require_permission
+from app.gateway.deps import get_checkpointer
+from app.gateway.utils import sanitize_log_param
 from deerflow.config.paths import Paths, get_paths
 from deerflow.runtime import serialize_channel_values
-
-# ---------------------------------------------------------------------------
-# Store namespace
-# ---------------------------------------------------------------------------
-
-THREADS_NS: tuple[str, ...] = ("threads",)
-"""Namespace used by the Store for thread metadata records."""
+from deerflow.runtime.user_context import get_effective_user_id
 
 logger = logging.getLogger(__name__)
 router = APIRouter(prefix="/api/threads", tags=["threads"])
 
 
+# Metadata keys that the server controls; clients are not allowed to set
+# them. Pydantic ``@field_validator("metadata")`` strips them on every
+# inbound model below so a malicious client cannot reflect a forged
+# owner identity through the API surface. Defense-in-depth — the
+# row-level invariant is still ``threads_meta.user_id`` populated from
+# the auth contextvar; this list closes the metadata-blob echo gap.
+_SERVER_RESERVED_METADATA_KEYS: frozenset[str] = frozenset({"owner_id", "user_id"})
+
+
+def _strip_reserved_metadata(metadata: dict[str, Any] | None) -> dict[str, Any]:
+    """Return ``metadata`` with server-controlled keys removed."""
+    if not metadata:
+        return metadata or {}
+    return {k: v for k, v in metadata.items() if k not in _SERVER_RESERVED_METADATA_KEYS}
+
+
 # ---------------------------------------------------------------------------
 # Response / request models
 # ---------------------------------------------------------------------------
@@ -63,8 +76,11 @@ class ThreadCreateRequest(BaseModel):
     """Request body for creating a thread."""
 
     thread_id: str | None = Field(default=None, description="Optional thread ID (auto-generated if omitted)")
+    assistant_id: str | None = Field(default=None, description="Associate thread with an assistant")
     metadata: dict[str, Any] = Field(default_factory=dict, description="Initial metadata")
 
+    _strip_reserved = field_validator("metadata")(classmethod(lambda cls, v: _strip_reserved_metadata(v)))
+
 
 class ThreadSearchRequest(BaseModel):
     """Request body for searching threads."""
@@ -93,6 +109,8 @@ class ThreadPatchRequest(BaseModel):
 
     metadata: dict[str, Any] = Field(default_factory=dict, description="Metadata to merge")
 
+    _strip_reserved = field_validator("metadata")(classmethod(lambda cls, v: _strip_reserved_metadata(v)))
+
 
 class ThreadStateUpdateRequest(BaseModel):
     """Request body for updating thread state (human-in-the-loop resume)."""
@@ -126,70 +144,25 @@ class ThreadHistoryRequest(BaseModel):
 # ---------------------------------------------------------------------------
 
 
-def _delete_thread_data(thread_id: str, paths: Paths | None = None) -> ThreadDeleteResponse:
+def _delete_thread_data(thread_id: str, paths: Paths | None = None, *, user_id: str | None = None) -> ThreadDeleteResponse:
     """Delete local persisted filesystem data for a thread."""
     path_manager = paths or get_paths()
     try:
-        path_manager.delete_thread_dir(thread_id)
+        path_manager.delete_thread_dir(thread_id, user_id=user_id)
     except ValueError as exc:
         raise HTTPException(status_code=422, detail=str(exc)) from exc
     except FileNotFoundError:
         # Not critical — thread data may not exist on disk
-        logger.debug("No local thread data to delete for %s", thread_id)
+        logger.debug("No local thread data to delete for %s", sanitize_log_param(thread_id))
         return ThreadDeleteResponse(success=True, message=f"No local data for {thread_id}")
     except Exception as exc:
-        logger.exception("Failed to delete thread data for %s", thread_id)
+        logger.exception("Failed to delete thread data for %s", sanitize_log_param(thread_id))
         raise HTTPException(status_code=500, detail="Failed to delete local thread data.") from exc
 
-    logger.info("Deleted local thread data for %s", thread_id)
+    logger.info("Deleted local thread data for %s", sanitize_log_param(thread_id))
     return ThreadDeleteResponse(success=True, message=f"Deleted local thread data for {thread_id}")
 
 
-async def _store_get(store, thread_id: str) -> dict | None:
-    """Fetch a thread record from the Store; returns ``None`` if absent."""
-    item = await store.aget(THREADS_NS, thread_id)
-    return item.value if item is not None else None
-
-
-async def _store_put(store, record: dict) -> None:
-    """Write a thread record to the Store."""
-    await store.aput(THREADS_NS, record["thread_id"], record)
-
-
-async def _store_upsert(store, thread_id: str, *, metadata: dict | None = None, values: dict | None = None) -> None:
-    """Create or refresh a thread record in the Store.
-
-    On creation the record is written with ``status="idle"``.  On update only
-    ``updated_at`` (and optionally ``metadata`` / ``values``) are changed so
-    that existing fields are preserved.
-
-    ``values`` carries the agent-state snapshot exposed to the frontend
-    (currently just ``{"title": "..."}``).
-    """
-    now = time.time()
-    existing = await _store_get(store, thread_id)
-    if existing is None:
-        await _store_put(
-            store,
-            {
-                "thread_id": thread_id,
-                "status": "idle",
-                "created_at": now,
-                "updated_at": now,
-                "metadata": metadata or {},
-                "values": values or {},
-            },
-        )
-    else:
-        val = dict(existing)
-        val["updated_at"] = now
-        if metadata:
-            val.setdefault("metadata", {}).update(metadata)
-        if values:
-            val.setdefault("values", {}).update(values)
-        await _store_put(store, val)
-
-
 def _derive_thread_status(checkpoint_tuple) -> str:
     """Derive thread status from checkpoint metadata."""
     if checkpoint_tuple is None:
@@ -215,22 +188,18 @@ def _derive_thread_status(checkpoint_tuple) -> str:
 
 
 @router.delete("/{thread_id}", response_model=ThreadDeleteResponse)
+@require_permission("threads", "delete", owner_check=True, require_existing=True)
 async def delete_thread_data(thread_id: str, request: Request) -> ThreadDeleteResponse:
     """Delete local persisted filesystem data for a thread.
 
     Cleans DeerFlow-managed thread directories, removes checkpoint data,
-    and removes the thread record from the Store.
+    and removes the thread_meta row from the configured ThreadMetaStore
+    (sqlite or memory).
     """
-    # Clean local filesystem
-    response = _delete_thread_data(thread_id)
+    from app.gateway.deps import get_thread_store
 
-    # Remove from Store (best-effort)
-    store = get_store(request)
-    if store is not None:
-        try:
-            await store.adelete(THREADS_NS, thread_id)
-        except Exception:
-            logger.debug("Could not delete store record for thread %s (not critical)", thread_id)
+    # Clean local filesystem
+    response = _delete_thread_data(thread_id, user_id=get_effective_user_id())
 
     # Remove checkpoints (best-effort)
     checkpointer = getattr(request.app.state, "checkpointer", None)
@@ -239,7 +208,15 @@ async def delete_thread_data(thread_id: str, request: Request) -> ThreadDeleteRe
             if hasattr(checkpointer, "adelete_thread"):
                 await checkpointer.adelete_thread(thread_id)
         except Exception:
-            logger.debug("Could not delete checkpoints for thread %s (not critical)", thread_id)
+            logger.debug("Could not delete checkpoints for thread %s (not critical)", sanitize_log_param(thread_id))
+
+    # Remove thread_meta row (best-effort) — required for sqlite backend
+    # so the deleted thread no longer appears in /threads/search.
+    try:
+        thread_store = get_thread_store(request)
+        await thread_store.delete(thread_id)
+    except Exception:
+        logger.debug("Could not delete thread_meta for %s (not critical)", sanitize_log_param(thread_id))
 
     return response
 
@@ -248,43 +225,40 @@ async def delete_thread_data(thread_id: str, request: Request) -> ThreadDeleteRe
 async def create_thread(body: ThreadCreateRequest, request: Request) -> ThreadResponse:
     """Create a new thread.
 
-    The thread record is written to the Store (for fast listing) and an
-    empty checkpoint is written to the checkpointer (for state reads).
+    Writes a thread_meta record (so the thread appears in /threads/search)
+    and an empty checkpoint (so state endpoints work immediately).
     Idempotent: returns the existing record when ``thread_id`` already exists.
     """
-    store = get_store(request)
+    from app.gateway.deps import get_thread_store
+
     checkpointer = get_checkpointer(request)
+    thread_store = get_thread_store(request)
     thread_id = body.thread_id or str(uuid.uuid4())
     now = time.time()
+    # ``body.metadata`` is already stripped of server-reserved keys by
+    # ``ThreadCreateRequest._strip_reserved`` — see the model definition.
 
-    # Idempotency: return existing record from Store when already present
-    if store is not None:
-        existing_record = await _store_get(store, thread_id)
-        if existing_record is not None:
-            return ThreadResponse(
-                thread_id=thread_id,
-                status=existing_record.get("status", "idle"),
-                created_at=str(existing_record.get("created_at", "")),
-                updated_at=str(existing_record.get("updated_at", "")),
-                metadata=existing_record.get("metadata", {}),
-            )
+    # Idempotency: return existing record when already present
+    existing_record = await thread_store.get(thread_id)
+    if existing_record is not None:
+        return ThreadResponse(
+            thread_id=thread_id,
+            status=existing_record.get("status", "idle"),
+            created_at=str(existing_record.get("created_at", "")),
+            updated_at=str(existing_record.get("updated_at", "")),
+            metadata=existing_record.get("metadata", {}),
+        )
 
-    # Write thread record to Store
-    if store is not None:
-        try:
-            await _store_put(
-                store,
-                {
-                    "thread_id": thread_id,
-                    "status": "idle",
-                    "created_at": now,
-                    "updated_at": now,
-                    "metadata": body.metadata,
-                },
-            )
-        except Exception:
-            logger.exception("Failed to write thread %s to store", thread_id)
-            raise HTTPException(status_code=500, detail="Failed to create thread")
+    # Write thread_meta so the thread appears in /threads/search immediately
+    try:
+        await thread_store.create(
+            thread_id,
+            assistant_id=getattr(body, "assistant_id", None),
+            metadata=body.metadata,
+        )
+    except Exception:
+        logger.exception("Failed to write thread_meta for %s", sanitize_log_param(thread_id))
+        raise HTTPException(status_code=500, detail="Failed to create thread")
 
     # Write an empty checkpoint so state endpoints work immediately
     config = {"configurable": {"thread_id": thread_id, "checkpoint_ns": ""}}
@@ -301,10 +275,10 @@ async def create_thread(body: ThreadCreateRequest, request: Request) -> ThreadRe
         }
         await checkpointer.aput(config, empty_checkpoint(), ckpt_metadata, {})
     except Exception:
-        logger.exception("Failed to create checkpoint for thread %s", thread_id)
+        logger.exception("Failed to create checkpoint for thread %s", sanitize_log_param(thread_id))
         raise HTTPException(status_code=500, detail="Failed to create thread")
 
-    logger.info("Thread created: %s", thread_id)
+    logger.info("Thread created: %s", sanitize_log_param(thread_id))
     return ThreadResponse(
         thread_id=thread_id,
         status="idle",
@@ -318,166 +292,91 @@ async def create_thread(body: ThreadCreateRequest, request: Request) -> ThreadRe
 async def search_threads(body: ThreadSearchRequest, request: Request) -> list[ThreadResponse]:
     """Search and list threads.
 
-    Two-phase approach:
-
-    **Phase 1 — Store (fast path, O(threads))**: returns threads that were
-    created or run through this Gateway.  Store records are tiny metadata
-    dicts so fetching all of them at once is cheap.
-
-    **Phase 2 — Checkpointer supplement (lazy migration)**: threads that
-    were created directly by LangGraph Server (and therefore absent from the
-    Store) are discovered here by iterating the shared checkpointer.  Any
-    newly found thread is immediately written to the Store so that the next
-    search skips Phase 2 for that thread — the Store converges to a full
-    index over time without a one-shot migration job.
+    Delegates to the configured ThreadMetaStore implementation
+    (SQL-backed for sqlite/postgres, Store-backed for memory mode).
     """
-    store = get_store(request)
-    checkpointer = get_checkpointer(request)
+    from app.gateway.deps import get_thread_store
 
-    # -----------------------------------------------------------------------
-    # Phase 1: Store
-    # -----------------------------------------------------------------------
-    merged: dict[str, ThreadResponse] = {}
-
-    if store is not None:
-        try:
-            items = await store.asearch(THREADS_NS, limit=10_000)
-        except Exception:
-            logger.warning("Store search failed — falling back to checkpointer only", exc_info=True)
-            items = []
-
-        for item in items:
-            val = item.value
-            merged[val["thread_id"]] = ThreadResponse(
-                thread_id=val["thread_id"],
-                status=val.get("status", "idle"),
-                created_at=str(val.get("created_at", "")),
-                updated_at=str(val.get("updated_at", "")),
-                metadata=val.get("metadata", {}),
-                values=val.get("values", {}),
-            )
-
-    # -----------------------------------------------------------------------
-    # Phase 2: Checkpointer supplement
-    # Discovers threads not yet in the Store (e.g. created by LangGraph
-    # Server) and lazily migrates them so future searches skip this phase.
-    # -----------------------------------------------------------------------
-    try:
-        async for checkpoint_tuple in checkpointer.alist(None):
-            cfg = getattr(checkpoint_tuple, "config", {})
-            thread_id = cfg.get("configurable", {}).get("thread_id")
-            if not thread_id or thread_id in merged:
-                continue
-
-            # Skip sub-graph checkpoints (checkpoint_ns is non-empty for those)
-            if cfg.get("configurable", {}).get("checkpoint_ns", ""):
-                continue
-
-            ckpt_meta = getattr(checkpoint_tuple, "metadata", {}) or {}
-            # Strip LangGraph internal keys from the user-visible metadata dict
-            user_meta = {k: v for k, v in ckpt_meta.items() if k not in ("created_at", "updated_at", "step", "source", "writes", "parents")}
-
-            # Extract state values (title) from the checkpoint's channel_values
-            checkpoint_data = getattr(checkpoint_tuple, "checkpoint", {}) or {}
-            channel_values = checkpoint_data.get("channel_values", {})
-            ckpt_values = {}
-            if title := channel_values.get("title"):
-                ckpt_values["title"] = title
-
-            thread_resp = ThreadResponse(
-                thread_id=thread_id,
-                status=_derive_thread_status(checkpoint_tuple),
-                created_at=str(ckpt_meta.get("created_at", "")),
-                updated_at=str(ckpt_meta.get("updated_at", ckpt_meta.get("created_at", ""))),
-                metadata=user_meta,
-                values=ckpt_values,
-            )
-            merged[thread_id] = thread_resp
-
-            # Lazy migration — write to Store so the next search finds it there
-            if store is not None:
-                try:
-                    await _store_upsert(store, thread_id, metadata=user_meta, values=ckpt_values or None)
-                except Exception:
-                    logger.debug("Failed to migrate thread %s to store (non-fatal)", thread_id)
-    except Exception:
-        logger.exception("Checkpointer scan failed during thread search")
-        # Don't raise — return whatever was collected from Store + partial scan
-
-    # -----------------------------------------------------------------------
-    # Phase 3: Filter → sort → paginate
-    # -----------------------------------------------------------------------
-    results = list(merged.values())
-
-    if body.metadata:
-        results = [r for r in results if all(r.metadata.get(k) == v for k, v in body.metadata.items())]
-
-    if body.status:
-        results = [r for r in results if r.status == body.status]
-
-    results.sort(key=lambda r: r.updated_at, reverse=True)
-    return results[body.offset : body.offset + body.limit]
+    repo = get_thread_store(request)
+    rows = await repo.search(
+        metadata=body.metadata or None,
+        status=body.status,
+        limit=body.limit,
+        offset=body.offset,
+    )
+    return [
+        ThreadResponse(
+            thread_id=r["thread_id"],
+            status=r.get("status", "idle"),
+            created_at=r.get("created_at", ""),
+            updated_at=r.get("updated_at", ""),
+            metadata=r.get("metadata", {}),
+            values={"title": r["display_name"]} if r.get("display_name") else {},
+            interrupts={},
+        )
+        for r in rows
+    ]
 
 
 @router.patch("/{thread_id}", response_model=ThreadResponse)
+@require_permission("threads", "write", owner_check=True, require_existing=True)
 async def patch_thread(thread_id: str, body: ThreadPatchRequest, request: Request) -> ThreadResponse:
     """Merge metadata into a thread record."""
-    store = get_store(request)
-    if store is None:
-        raise HTTPException(status_code=503, detail="Store not available")
+    from app.gateway.deps import get_thread_store
 
-    record = await _store_get(store, thread_id)
+    thread_store = get_thread_store(request)
+    record = await thread_store.get(thread_id)
     if record is None:
         raise HTTPException(status_code=404, detail=f"Thread {thread_id} not found")
 
-    now = time.time()
-    updated = dict(record)
-    updated.setdefault("metadata", {}).update(body.metadata)
-    updated["updated_at"] = now
-
+    # ``body.metadata`` already stripped by ``ThreadPatchRequest._strip_reserved``.
     try:
-        await _store_put(store, updated)
+        await thread_store.update_metadata(thread_id, body.metadata)
     except Exception:
-        logger.exception("Failed to patch thread %s", thread_id)
+        logger.exception("Failed to patch thread %s", sanitize_log_param(thread_id))
         raise HTTPException(status_code=500, detail="Failed to update thread")
 
+    # Re-read to get the merged metadata + refreshed updated_at
+    record = await thread_store.get(thread_id) or record
     return ThreadResponse(
         thread_id=thread_id,
-        status=updated.get("status", "idle"),
-        created_at=str(updated.get("created_at", "")),
-        updated_at=str(now),
-        metadata=updated.get("metadata", {}),
+        status=record.get("status", "idle"),
+        created_at=str(record.get("created_at", "")),
+        updated_at=str(record.get("updated_at", "")),
+        metadata=record.get("metadata", {}),
     )
 
 
 @router.get("/{thread_id}", response_model=ThreadResponse)
+@require_permission("threads", "read", owner_check=True)
 async def get_thread(thread_id: str, request: Request) -> ThreadResponse:
     """Get thread info.
 
-    Reads metadata from the Store and derives the accurate execution
-    status from the checkpointer.  Falls back to the checkpointer alone
-    for threads that pre-date Store adoption (backward compat).
+    Reads metadata from the ThreadMetaStore and derives the accurate
+    execution status from the checkpointer.  Falls back to the checkpointer
+    alone for threads that pre-date ThreadMetaStore adoption (backward compat).
     """
-    store = get_store(request)
+    from app.gateway.deps import get_thread_store
+
+    thread_store = get_thread_store(request)
     checkpointer = get_checkpointer(request)
 
-    record: dict | None = None
-    if store is not None:
-        record = await _store_get(store, thread_id)
+    record: dict | None = await thread_store.get(thread_id)
 
     # Derive accurate status from the checkpointer
     config = {"configurable": {"thread_id": thread_id, "checkpoint_ns": ""}}
     try:
         checkpoint_tuple = await checkpointer.aget_tuple(config)
     except Exception:
-        logger.exception("Failed to get checkpoint for thread %s", thread_id)
+        logger.exception("Failed to get checkpoint for thread %s", sanitize_log_param(thread_id))
         raise HTTPException(status_code=500, detail="Failed to get thread")
 
     if record is None and checkpoint_tuple is None:
         raise HTTPException(status_code=404, detail=f"Thread {thread_id} not found")
 
-    # If the thread exists in the checkpointer but not the store (e.g. legacy
-    # data), synthesize a minimal store record from the checkpoint metadata.
+    # If the thread exists in the checkpointer but not in thread_meta (e.g.
+    # legacy data created before thread_meta adoption), synthesize a minimal
+    # record from the checkpoint metadata.
     if record is None and checkpoint_tuple is not None:
         ckpt_meta = getattr(checkpoint_tuple, "metadata", {}) or {}
         record = {
@@ -505,7 +404,9 @@ async def get_thread(thread_id: str, request: Request) -> ThreadResponse:
     )
 
 
+# ---------------------------------------------------------------------------
 @router.get("/{thread_id}/state", response_model=ThreadStateResponse)
+@require_permission("threads", "read", owner_check=True)
 async def get_thread_state(thread_id: str, request: Request) -> ThreadStateResponse:
     """Get the latest state snapshot for a thread.
 
@@ -518,7 +419,7 @@ async def get_thread_state(thread_id: str, request: Request) -> ThreadStateRespo
     try:
         checkpoint_tuple = await checkpointer.aget_tuple(config)
     except Exception:
-        logger.exception("Failed to get state for thread %s", thread_id)
+        logger.exception("Failed to get state for thread %s", sanitize_log_param(thread_id))
         raise HTTPException(status_code=500, detail="Failed to get thread state")
 
     if checkpoint_tuple is None:
@@ -542,8 +443,10 @@ async def get_thread_state(thread_id: str, request: Request) -> ThreadStateRespo
     next_tasks = [t.name for t in tasks_raw if hasattr(t, "name")]
     tasks = [{"id": getattr(t, "id", ""), "name": getattr(t, "name", "")} for t in tasks_raw]
 
+    values = serialize_channel_values(channel_values)
+
     return ThreadStateResponse(
-        values=serialize_channel_values(channel_values),
+        values=values,
         next=next_tasks,
         metadata=metadata,
         checkpoint={"id": checkpoint_id, "ts": str(metadata.get("created_at", ""))},
@@ -555,15 +458,19 @@ async def get_thread_state(thread_id: str, request: Request) -> ThreadStateRespo
 
 
 @router.post("/{thread_id}/state", response_model=ThreadStateResponse)
+@require_permission("threads", "write", owner_check=True, require_existing=True)
 async def update_thread_state(thread_id: str, body: ThreadStateUpdateRequest, request: Request) -> ThreadStateResponse:
     """Update thread state (e.g. for human-in-the-loop resume or title rename).
 
     Writes a new checkpoint that merges *body.values* into the latest
-    channel values, then syncs any updated ``title`` field back to the Store
-    so that ``/threads/search`` reflects the change immediately.
+    channel values, then syncs any updated ``title`` field through the
+    ThreadMetaStore abstraction so that ``/threads/search`` reflects the
+    change immediately in both sqlite and memory backends.
     """
+    from app.gateway.deps import get_thread_store
+
     checkpointer = get_checkpointer(request)
-    store = get_store(request)
+    thread_store = get_thread_store(request)
 
     # checkpoint_ns must be present in the config for aput — default to ""
     # (the root graph namespace).  checkpoint_id is optional; omitting it
@@ -580,7 +487,7 @@ async def update_thread_state(thread_id: str, body: ThreadStateUpdateRequest, re
     try:
         checkpoint_tuple = await checkpointer.aget_tuple(read_config)
     except Exception:
-        logger.exception("Failed to get state for thread %s", thread_id)
+        logger.exception("Failed to get state for thread %s", sanitize_log_param(thread_id))
         raise HTTPException(status_code=500, detail="Failed to get thread state")
 
     if checkpoint_tuple is None:
@@ -614,19 +521,22 @@ async def update_thread_state(thread_id: str, body: ThreadStateUpdateRequest, re
     try:
         new_config = await checkpointer.aput(write_config, checkpoint, metadata, {})
     except Exception:
-        logger.exception("Failed to update state for thread %s", thread_id)
+        logger.exception("Failed to update state for thread %s", sanitize_log_param(thread_id))
         raise HTTPException(status_code=500, detail="Failed to update thread state")
 
     new_checkpoint_id: str | None = None
     if isinstance(new_config, dict):
         new_checkpoint_id = new_config.get("configurable", {}).get("checkpoint_id")
 
-    # Sync title changes to the Store so /threads/search reflects them immediately.
-    if store is not None and body.values and "title" in body.values:
-        try:
-            await _store_upsert(store, thread_id, values={"title": body.values["title"]})
-        except Exception:
-            logger.debug("Failed to sync title to store for thread %s (non-fatal)", thread_id)
+    # Sync title changes through the ThreadMetaStore abstraction so /threads/search
+    # reflects them immediately in both sqlite and memory backends.
+    if body.values and "title" in body.values:
+        new_title = body.values["title"]
+        if new_title:  # Skip empty strings and None
+            try:
+                await thread_store.update_display_name(thread_id, new_title)
+            except Exception:
+                logger.debug("Failed to sync title to thread_meta for %s (non-fatal)", sanitize_log_param(thread_id))
 
     return ThreadStateResponse(
         values=serialize_channel_values(channel_values),
@@ -638,8 +548,16 @@ async def update_thread_state(thread_id: str, body: ThreadStateUpdateRequest, re
 
 
 @router.post("/{thread_id}/history", response_model=list[HistoryEntry])
+@require_permission("threads", "read", owner_check=True)
 async def get_thread_history(thread_id: str, body: ThreadHistoryRequest, request: Request) -> list[HistoryEntry]:
-    """Get checkpoint history for a thread."""
+    """Get checkpoint history for a thread.
+
+    Messages are read from the checkpointer's channel values (the
+    authoritative source) and serialized via
+    :func:`~deerflow.runtime.serialization.serialize_channel_values`.
+    Only the latest (first) checkpoint carries the ``messages`` key to
+    avoid duplicating them across every entry.
+    """
     checkpointer = get_checkpointer(request)
 
     config: dict[str, Any] = {"configurable": {"thread_id": thread_id}}
@@ -647,6 +565,7 @@ async def get_thread_history(thread_id: str, body: ThreadHistoryRequest, request
         config["configurable"]["checkpoint_id"] = body.before
 
     entries: list[HistoryEntry] = []
+    is_latest_checkpoint = True
     try:
         async for checkpoint_tuple in checkpointer.alist(config, limit=body.limit):
             ckpt_config = getattr(checkpoint_tuple, "config", {})
@@ -661,22 +580,42 @@ async def get_thread_history(thread_id: str, body: ThreadHistoryRequest, request
 
             channel_values = checkpoint.get("channel_values", {})
 
+            # Build values from checkpoint channel_values
+            values: dict[str, Any] = {}
+            if title := channel_values.get("title"):
+                values["title"] = title
+            if thread_data := channel_values.get("thread_data"):
+                values["thread_data"] = thread_data
+
+            # Attach messages only to the latest checkpoint entry.
+            if is_latest_checkpoint:
+                messages = channel_values.get("messages")
+                if messages:
+                    values["messages"] = serialize_channel_values({"messages": messages}).get("messages", [])
+            is_latest_checkpoint = False
+
             # Derive next tasks
             tasks_raw = getattr(checkpoint_tuple, "tasks", []) or []
             next_tasks = [t.name for t in tasks_raw if hasattr(t, "name")]
 
+            # Strip LangGraph internal keys from metadata
+            user_meta = {k: v for k, v in metadata.items() if k not in ("created_at", "updated_at", "step", "source", "writes", "parents")}
+            # Keep step for ordering context
+            if "step" in metadata:
+                user_meta["step"] = metadata["step"]
+
             entries.append(
                 HistoryEntry(
                     checkpoint_id=checkpoint_id,
                     parent_checkpoint_id=parent_id,
-                    metadata=metadata,
-                    values=serialize_channel_values(channel_values),
+                    metadata=user_meta,
+                    values=values,
                     created_at=str(metadata.get("created_at", "")),
                     next=next_tasks,
                 )
             )
     except Exception:
-        logger.exception("Failed to get history for thread %s", thread_id)
+        logger.exception("Failed to get history for thread %s", sanitize_log_param(thread_id))
         raise HTTPException(status_code=500, detail="Failed to get thread history")
 
     return entries

backend/app/gateway/routers/uploads.py

@@ -4,10 +4,12 @@ import logging
 import os
 import stat
 
-from fastapi import APIRouter, File, HTTPException, UploadFile
+from fastapi import APIRouter, File, HTTPException, Request, UploadFile
 from pydantic import BaseModel
 
+from app.gateway.authz import require_permission
 from deerflow.config.paths import get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.sandbox.sandbox_provider import get_sandbox_provider
 from deerflow.uploads.manager import (
     PathTraversalError,
@@ -54,8 +56,10 @@ def _make_file_sandbox_writable(file_path: os.PathLike[str] | str) -> None:
 
 
 @router.post("", response_model=UploadResponse)
+@require_permission("threads", "write", owner_check=True, require_existing=False)
 async def upload_files(
     thread_id: str,
+    request: Request,
     files: list[UploadFile] = File(...),
 ) -> UploadResponse:
     """Upload multiple files to a thread's uploads directory."""
@@ -66,7 +70,7 @@ async def upload_files(
         uploads_dir = ensure_uploads_dir(thread_id)
     except ValueError as e:
         raise HTTPException(status_code=400, detail=str(e))
-    sandbox_uploads = get_paths().sandbox_uploads_dir(thread_id)
+    sandbox_uploads = get_paths().sandbox_uploads_dir(thread_id, user_id=get_effective_user_id())
     uploaded_files = []
 
     sandbox_provider = get_sandbox_provider()
@@ -133,7 +137,8 @@ async def upload_files(
 
 
 @router.get("/list", response_model=dict)
-async def list_uploaded_files(thread_id: str) -> dict:
+@require_permission("threads", "read", owner_check=True)
+async def list_uploaded_files(thread_id: str, request: Request) -> dict:
     """List all files in a thread's uploads directory."""
     try:
         uploads_dir = get_uploads_dir(thread_id)
@@ -143,7 +148,7 @@ async def list_uploaded_files(thread_id: str) -> dict:
     enrich_file_listing(result, thread_id)
 
     # Gateway additionally includes the sandbox-relative path.
-    sandbox_uploads = get_paths().sandbox_uploads_dir(thread_id)
+    sandbox_uploads = get_paths().sandbox_uploads_dir(thread_id, user_id=get_effective_user_id())
     for f in result["files"]:
         f["path"] = str(sandbox_uploads / f["filename"])
 
@@ -151,7 +156,8 @@ async def list_uploaded_files(thread_id: str) -> dict:
 
 
 @router.delete("/{filename}")
-async def delete_uploaded_file(thread_id: str, filename: str) -> dict:
+@require_permission("threads", "delete", owner_check=True, require_existing=True)
+async def delete_uploaded_file(thread_id: str, filename: str, request: Request) -> dict:
     """Delete a file from a thread's uploads directory."""
     try:
         uploads_dir = get_uploads_dir(thread_id)

backend/app/gateway/services.py

@@ -8,16 +8,17 @@ frames, and consuming stream bridge events.  Router modules
 from __future__ import annotations
 
 import asyncio
+import dataclasses
 import json
 import logging
 import re
-import time
 from typing import Any
 
 from fastapi import HTTPException, Request
 from langchain_core.messages import HumanMessage
 
-from app.gateway.deps import get_checkpointer, get_run_manager, get_store, get_stream_bridge
+from app.gateway.deps import get_run_context, get_run_manager, get_run_store, get_stream_bridge
+from app.gateway.utils import sanitize_log_param
 from deerflow.runtime import (
     END_SENTINEL,
     HEARTBEAT_SENTINEL,
@@ -171,71 +172,6 @@ def build_run_config(
 # ---------------------------------------------------------------------------
 
 
-async def _upsert_thread_in_store(store, thread_id: str, metadata: dict | None) -> None:
-    """Create or refresh the thread record in the Store.
-
-    Called from :func:`start_run` so that threads created via the stateless
-    ``/runs/stream`` endpoint (which never calls ``POST /threads``) still
-    appear in ``/threads/search`` results.
-    """
-    # Deferred import to avoid circular import with the threads router module.
-    from app.gateway.routers.threads import _store_upsert
-
-    try:
-        await _store_upsert(store, thread_id, metadata=metadata)
-    except Exception:
-        logger.warning("Failed to upsert thread %s in store (non-fatal)", thread_id)
-
-
-async def _sync_thread_title_after_run(
-    run_task: asyncio.Task,
-    thread_id: str,
-    checkpointer: Any,
-    store: Any,
-) -> None:
-    """Wait for *run_task* to finish, then persist the generated title to the Store.
-
-    TitleMiddleware writes the generated title to the LangGraph agent state
-    (checkpointer) but the Gateway's Store record is not updated automatically.
-    This coroutine closes that gap by reading the final checkpoint after the
-    run completes and syncing ``values.title`` into the Store record so that
-    subsequent ``/threads/search`` responses include the correct title.
-
-    Runs as a fire-and-forget :func:`asyncio.create_task`; failures are
-    logged at DEBUG level and never propagate.
-    """
-    # Wait for the background run task to complete (any outcome).
-    # asyncio.wait does not propagate task exceptions — it just returns
-    # when the task is done, cancelled, or failed.
-    await asyncio.wait({run_task})
-
-    # Deferred import to avoid circular import with the threads router module.
-    from app.gateway.routers.threads import _store_get, _store_put
-
-    try:
-        ckpt_config = {"configurable": {"thread_id": thread_id, "checkpoint_ns": ""}}
-        ckpt_tuple = await checkpointer.aget_tuple(ckpt_config)
-        if ckpt_tuple is None:
-            return
-
-        channel_values = ckpt_tuple.checkpoint.get("channel_values", {})
-        title = channel_values.get("title")
-        if not title:
-            return
-
-        existing = await _store_get(store, thread_id)
-        if existing is None:
-            return
-
-        updated = dict(existing)
-        updated.setdefault("values", {})["title"] = title
-        updated["updated_at"] = time.time()
-        await _store_put(store, updated)
-        logger.debug("Synced title %r for thread %s", title, thread_id)
-    except Exception:
-        logger.debug("Failed to sync title for thread %s (non-fatal)", thread_id, exc_info=True)
-
-
 async def start_run(
     body: Any,
     thread_id: str,
@@ -255,8 +191,7 @@ async def start_run(
     """
     bridge = get_stream_bridge(request)
     run_mgr = get_run_manager(request)
-    checkpointer = get_checkpointer(request)
-    store = get_store(request)
+    run_ctx = get_run_context(request)
 
     disconnect = DisconnectMode.cancel if body.on_disconnect == "cancel" else DisconnectMode.continue_
 
@@ -274,11 +209,21 @@ async def start_run(
     except UnsupportedStrategyError as exc:
         raise HTTPException(status_code=501, detail=str(exc)) from exc
 
-    # Ensure the thread is visible in /threads/search, even for threads that
-    # were never explicitly created via POST /threads (e.g. stateless runs).
-    store = get_store(request)
-    if store is not None:
-        await _upsert_thread_in_store(store, thread_id, body.metadata)
+    # Upsert thread metadata so the thread appears in /threads/search,
+    # even for threads that were never explicitly created via POST /threads
+    # (e.g. stateless runs).
+    try:
+        existing = await run_ctx.thread_store.get(thread_id)
+        if existing is None:
+            await run_ctx.thread_store.create(
+                thread_id,
+                assistant_id=body.assistant_id,
+                metadata=body.metadata,
+            )
+        else:
+            await run_ctx.thread_store.update_status(thread_id, "running")
+    except Exception:
+        logger.warning("Failed to upsert thread_meta for %s (non-fatal)", sanitize_log_param(thread_id))
 
     agent_factory = resolve_agent_factory(body.assistant_id)
     graph_input = normalize_input(body.input)
@@ -311,8 +256,7 @@ async def start_run(
             bridge,
             run_mgr,
             record,
-            checkpointer=checkpointer,
-            store=store,
+            ctx=run_ctx,
             agent_factory=agent_factory,
             graph_input=graph_input,
             config=config,
@@ -324,11 +268,9 @@ async def start_run(
     )
     record.task = task
 
-    # After the run completes, sync the title generated by TitleMiddleware from
-    # the checkpointer into the Store record so that /threads/search returns the
-    # correct title instead of an empty values dict.
-    if store is not None:
-        asyncio.create_task(_sync_thread_title_after_run(task, thread_id, checkpointer, store))
+    # Title sync is handled by worker.py's finally block which reads the
+    # title from the checkpoint and calls thread_store.update_display_name
+    # after the run completes.
 
     return record
 

backend/app/gateway/utils.py

@@ -0,0 +1,6 @@
+"""Shared utility helpers for the Gateway layer."""
+
+
+def sanitize_log_param(value: str) -> str:
+    """Strip control characters to prevent log injection."""
+    return value.replace("\n", "").replace("\r", "").replace("\x00", "")

backend/docs/AUTH_TEST_DOCKER_GAP.md

@@ -0,0 +1,77 @@
+# Docker Test Gap (Section 七 7.4)
+
+This file documents the only **un-executed** test cases from
+`backend/docs/AUTH_TEST_PLAN.md` after the full release validation pass.
+
+## Why this gap exists
+
+The release validation environment (sg_dev: `10.251.229.92`) **does not have
+a Docker daemon installed**. The TC-DOCKER cases are container-runtime
+behavior tests that need an actual Docker engine to spin up
+`docker/docker-compose.yaml` services.
+
+```bash
+$ ssh sg_dev "which docker; docker --version"
+# (empty)
+# bash: docker: command not found
+```
+
+All other test plan sections were executed against either:
+- The local dev box (Mac, all services running locally), or
+- The deployed sg_dev instance (gateway + frontend + nginx via SSH tunnel)
+
+## Cases not executed
+
+| Case | Title | What it covers | Why not run |
+|---|---|---|---|
+| TC-DOCKER-01 | `users.db` volume persistence | Verify the `DEER_FLOW_HOME` bind mount survives container restart | needs `docker compose up` |
+| TC-DOCKER-02 | Session persistence across container restart | `AUTH_JWT_SECRET` env var keeps cookies valid after `docker compose down && up` | needs `docker compose down/up` |
+| TC-DOCKER-03 | Per-worker rate limiter divergence | Confirms in-process `_login_attempts` dict doesn't share state across `gunicorn` workers (4 by default in the compose file); known limitation, documented | needs multi-worker container |
+| TC-DOCKER-04 | IM channels skip AuthMiddleware | Verify Feishu/Slack/Telegram dispatchers run in-container against `http://langgraph:2024` without going through nginx | needs `docker logs` |
+| TC-DOCKER-05 | Admin credentials surfacing | **Updated post-simplify** — was "log scrape", now "0600 credential file in `DEER_FLOW_HOME`". The file-based behavior is already validated by TC-1.1 + TC-UPG-13 on sg_dev (non-Docker), so the only Docker-specific gap is verifying the volume mount carries the file out to the host | needs container + host volume |
+| TC-DOCKER-06 | Gateway-mode Docker deploy | `./scripts/deploy.sh --gateway` produces a 3-container topology (no `langgraph` container); same auth flow as standard mode | needs `docker compose --profile gateway` |
+
+## Coverage already provided by non-Docker tests
+
+The **auth-relevant** behavior in each Docker case is already exercised by
+the test cases that ran on sg_dev or local:
+
+| Docker case | Auth behavior covered by |
+|---|---|
+| TC-DOCKER-01 (volume persistence) | TC-REENT-01 on sg_dev (admin row survives gateway restart) — same SQLite file, just no container layer between |
+| TC-DOCKER-02 (session persistence) | TC-API-02/03/06 (cookie roundtrip), plus TC-REENT-04 (multi-cookie) — JWT verification is process-state-free, container restart is equivalent to `pkill uvicorn && uv run uvicorn` |
+| TC-DOCKER-03 (per-worker rate limit) | TC-GW-04 + TC-REENT-09 (single-worker rate limit + 5min expiry). The cross-worker divergence is an architectural property of the in-memory dict; no auth code path differs |
+| TC-DOCKER-04 (IM channels skip auth) | Code-level only: `app/channels/manager.py` uses `langgraph_sdk` directly with no cookie handling. The langgraph_auth handler is bypassed by going through SDK, not HTTP |
+| TC-DOCKER-05 (credential surfacing) | TC-1.1 on sg_dev (file at `~/deer-flow/backend/.deer-flow/admin_initial_credentials.txt`, mode 0600, password 22 chars) — the only Docker-unique step is whether the bind mount projects this path onto the host, which is a `docker compose` config check, not a runtime behavior change |
+| TC-DOCKER-06 (gateway-mode container) | Section 七 7.2 covered by TC-GW-01..05 + Section 二 (gateway-mode auth flow on sg_dev) — same Gateway code, container is just a packaging change |
+
+## Reproduction steps when Docker becomes available
+
+Anyone with `docker` + `docker compose` installed can reproduce the gap by
+running the test plan section verbatim. Pre-flight:
+
+```bash
+# Required on the host
+docker --version           # >=24.x
+docker compose version     # plugin >=2.x
+
+# Required env var (otherwise sessions reset on every container restart)
+echo "AUTH_JWT_SECRET=$(python3 -c 'import secrets; print(secrets.token_urlsafe(32))')" \
+  >> .env
+
+# Optional: pin DEER_FLOW_HOME to a stable host path
+echo "DEER_FLOW_HOME=$HOME/deer-flow-data" >> .env
+```
+
+Then run TC-DOCKER-01..06 from the test plan as written.
+
+## Decision log
+
+- **Not blocking the release.** The auth-relevant behavior in every Docker
+  case has an already-validated equivalent on bare metal. The gap is purely
+  about *container packaging* details (bind mounts, multi-worker, log
+  collection), not about whether the auth code paths work.
+- **TC-DOCKER-05 was updated in place** in `AUTH_TEST_PLAN.md` to reflect
+  the post-simplify reality (credentials file → 0600 file, no log leak).
+  The old "grep 'Password:' in docker logs" expectation would have failed
+  silently and given a false sense of coverage.

backend/docs/AUTH_UPGRADE.md

@@ -0,0 +1,129 @@
+# Authentication Upgrade Guide
+
+DeerFlow 内置了认证模块。本文档面向从无认证版本升级的用户。
+
+## 核心概念
+
+认证模块采用**始终强制**策略：
+
+- 首次启动时自动创建 admin 账号，随机密码打印到控制台日志
+- 认证从一开始就是强制的，无竞争窗口
+- 历史对话（升级前创建的 thread）自动迁移到 admin 名下
+
+## 升级步骤
+
+### 1. 更新代码
+
+```bash
+git pull origin main
+cd backend && make install
+```
+
+### 2. 首次启动
+
+```bash
+make dev
+```
+
+控制台会输出：
+
+```
+============================================================
+  Admin account created on first boot
+  Email:    admin@deerflow.dev
+  Password: aB3xK9mN_pQ7rT2w
+  Change it after login: Settings → Account
+============================================================
+```
+
+如果未登录就重启了服务，不用担心——只要 setup 未完成，每次启动都会重置密码并重新打印到控制台。
+
+### 3. 登录
+
+访问 `http://localhost:2026/login`，使用控制台输出的邮箱和密码登录。
+
+### 4. 修改密码
+
+登录后进入 Settings → Account → Change Password。
+
+### 5. 添加用户（可选）
+
+其他用户通过 `/login` 页面注册，自动获得 **user** 角色。每个用户只能看到自己的对话。
+
+## 安全机制
+
+| 机制 | 说明 |
+|------|------|
+| JWT HttpOnly Cookie | Token 不暴露给 JavaScript，防止 XSS 窃取 |
+| CSRF Double Submit Cookie | 所有 POST/PUT/DELETE 请求需携带 `X-CSRF-Token` |
+| bcrypt 密码哈希 | 密码不以明文存储 |
+| 多租户隔离 | 用户只能访问自己的 thread |
+| HTTPS 自适应 | 检测 `x-forwarded-proto`，自动设置 `Secure` cookie 标志 |
+
+## 常见操作
+
+### 忘记密码
+
+```bash
+cd backend
+
+# 重置 admin 密码
+python -m app.gateway.auth.reset_admin
+
+# 重置指定用户密码
+python -m app.gateway.auth.reset_admin --email user@example.com
+```
+
+会输出新的随机密码。
+
+### 完全重置
+
+删除用户数据库，重启后自动创建新 admin：
+
+```bash
+rm -f backend/.deer-flow/users.db
+# 重启服务，控制台输出新密码
+```
+
+## 数据存储
+
+| 文件 | 内容 |
+|------|------|
+| `.deer-flow/users.db` | SQLite 用户数据库（密码哈希、角色） |
+| `.env` 中的 `AUTH_JWT_SECRET` | JWT 签名密钥（未设置时自动生成临时密钥，重启后 session 失效） |
+
+### 生产环境建议
+
+```bash
+# 生成持久化 JWT 密钥，避免重启后所有用户需重新登录
+python -c "import secrets; print(secrets.token_urlsafe(32))"
+# 将输出添加到 .env：
+# AUTH_JWT_SECRET=<生成的密钥>
+```
+
+## API 端点
+
+| 端点 | 方法 | 说明 |
+|------|------|------|
+| `/api/v1/auth/login/local` | POST | 邮箱密码登录（OAuth2 form） |
+| `/api/v1/auth/register` | POST | 注册新用户（user 角色） |
+| `/api/v1/auth/logout` | POST | 登出（清除 cookie） |
+| `/api/v1/auth/me` | GET | 获取当前用户信息 |
+| `/api/v1/auth/change-password` | POST | 修改密码 |
+| `/api/v1/auth/setup-status` | GET | 检查 admin 是否存在 |
+
+## 兼容性
+
+- **标准模式**（`make dev`）：完全兼容，admin 自动创建
+- **Gateway 模式**（`make dev-pro`）：完全兼容
+- **Docker 部署**：完全兼容，`.deer-flow/users.db` 需持久化卷挂载
+- **IM 渠道**（Feishu/Slack/Telegram）：通过 LangGraph SDK 通信，不经过认证层
+- **DeerFlowClient**（嵌入式）：不经过 HTTP，不受认证影响
+
+## 故障排查
+
+| 症状 | 原因 | 解决 |
+|------|------|------|
+| 启动后没看到密码 | admin 已存在（非首次启动） | 用 `reset_admin` 重置，或删 `users.db` |
+| 登录后 POST 返回 403 | CSRF token 缺失 | 确认前端已更新 |
+| 重启后需要重新登录 | `AUTH_JWT_SECRET` 未持久化 | 在 `.env` 中设置固定密钥 |

backend/docs/TITLE_GENERATION_IMPLEMENTATION.md

@@ -124,7 +124,7 @@ title:
 # checkpointer.py
 from langgraph.checkpoint.sqlite import SqliteSaver
 
-checkpointer = SqliteSaver.from_conn_string("checkpoints.db")
+checkpointer = SqliteSaver.from_conn_string("deerflow.db")
 ```
 
 ```json

backend/langgraph.json

@@ -8,6 +8,9 @@
   "graphs": {
     "lead_agent": "deerflow.agents:make_lead_agent"
   },
+  "auth": {
+    "path": "./app/gateway/langgraph_auth.py:auth"
+  },
   "checkpointer": {
     "path": "./packages/harness/deerflow/agents/checkpointer/async_provider.py:make_checkpointer"
   }

backend/packages/harness/deerflow/agents/__init__.py

@@ -1,4 +1,3 @@
-from .checkpointer import get_checkpointer, make_checkpointer, reset_checkpointer
 from .factory import create_deerflow_agent
 from .features import Next, Prev, RuntimeFeatures
 from .lead_agent import make_lead_agent
@@ -18,7 +17,4 @@ __all__ = [
     "make_lead_agent",
     "SandboxState",
     "ThreadState",
-    "get_checkpointer",
-    "reset_checkpointer",
-    "make_checkpointer",
 ]

backend/packages/harness/deerflow/agents/lead_agent/agent.py

@@ -1,7 +1,7 @@
 import logging
 
 from langchain.agents import create_agent
-from langchain.agents.middleware import AgentMiddleware, SummarizationMiddleware
+from langchain.agents.middleware import AgentMiddleware
 from langchain_core.runnables import RunnableConfig
 
 from deerflow.agents.lead_agent.prompt import apply_prompt_template
@@ -9,6 +9,7 @@ from deerflow.agents.middlewares.clarification_middleware import ClarificationMi
 from deerflow.agents.middlewares.loop_detection_middleware import LoopDetectionMiddleware
 from deerflow.agents.middlewares.memory_middleware import MemoryMiddleware
 from deerflow.agents.middlewares.subagent_limit_middleware import SubagentLimitMiddleware
+from deerflow.agents.middlewares.summarization_middleware import SummarizationMiddleware
 from deerflow.agents.middlewares.title_middleware import TitleMiddleware
 from deerflow.agents.middlewares.todo_middleware import TodoMiddleware
 from deerflow.agents.middlewares.token_usage_middleware import TokenUsageMiddleware
@@ -56,13 +57,15 @@ def _create_summarization_middleware() -> SummarizationMiddleware | None:
     # Prepare keep parameter
     keep = config.keep.to_tuple()
 
-    # Prepare model parameter
+    # Prepare model parameter.
+    # Bind "middleware:summarize" tag so RunJournal identifies these LLM calls
+    # as middleware rather than lead_agent (SummarizationMiddleware is a
+    # LangChain built-in, so we tag the model at creation time).
     if config.model_name:
         model = create_chat_model(name=config.model_name, thinking_enabled=False)
     else:
-        # Use a lightweight model for summarization to save costs
-        # Falls back to default model if not explicitly specified
         model = create_chat_model(thinking_enabled=False)
+    model = model.with_config(tags=["middleware:summarize"])
 
     # Prepare kwargs
     kwargs = {

backend/packages/harness/deerflow/agents/lead_agent/prompt.py

@@ -519,12 +519,13 @@ def _get_memory_context(agent_name: str | None = None) -> str:
     try:
         from deerflow.agents.memory import format_memory_for_injection, get_memory_data
         from deerflow.config.memory_config import get_memory_config
+        from deerflow.runtime.user_context import get_effective_user_id
 
         config = get_memory_config()
         if not config.enabled or not config.injection_enabled:
             return ""
 
-        memory_data = get_memory_data(agent_name)
+        memory_data = get_memory_data(agent_name, user_id=get_effective_user_id())
         memory_content = format_memory_for_injection(memory_data, max_tokens=config.max_injection_tokens)
 
         if not memory_content.strip():

backend/packages/harness/deerflow/agents/memory/queue.py

@@ -20,6 +20,7 @@ class ConversationContext:
     messages: list[Any]
     timestamp: datetime = field(default_factory=lambda: datetime.now(UTC))
     agent_name: str | None = None
+    user_id: str | None = None
     correction_detected: bool = False
     reinforcement_detected: bool = False
 
@@ -44,6 +45,7 @@ class MemoryUpdateQueue:
         thread_id: str,
         messages: list[Any],
         agent_name: str | None = None,
+        user_id: str | None = None,
         correction_detected: bool = False,
         reinforcement_detected: bool = False,
     ) -> None:
@@ -53,6 +55,9 @@ class MemoryUpdateQueue:
             thread_id: The thread ID.
             messages: The conversation messages.
             agent_name: If provided, memory is stored per-agent. If None, uses global memory.
+            user_id: The user ID captured at enqueue time. Stored in ConversationContext so it
+                survives the threading.Timer boundary (ContextVar does not propagate across
+                raw threads).
             correction_detected: Whether recent turns include an explicit correction signal.
             reinforcement_detected: Whether recent turns include a positive reinforcement signal.
         """
@@ -71,6 +76,7 @@ class MemoryUpdateQueue:
                 thread_id=thread_id,
                 messages=messages,
                 agent_name=agent_name,
+                user_id=user_id,
                 correction_detected=merged_correction_detected,
                 reinforcement_detected=merged_reinforcement_detected,
             )
@@ -136,6 +142,7 @@ class MemoryUpdateQueue:
                         agent_name=context.agent_name,
                         correction_detected=context.correction_detected,
                         reinforcement_detected=context.reinforcement_detected,
+                        user_id=context.user_id,
                     )
                     if success:
                         logger.info("Memory updated successfully for thread %s", context.thread_id)

backend/packages/harness/deerflow/agents/memory/storage.py

@@ -43,17 +43,17 @@ class MemoryStorage(abc.ABC):
     """Abstract base class for memory storage providers."""
 
     @abc.abstractmethod
-    def load(self, agent_name: str | None = None) -> dict[str, Any]:
+    def load(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
         """Load memory data for the given agent."""
         pass
 
     @abc.abstractmethod
-    def reload(self, agent_name: str | None = None) -> dict[str, Any]:
+    def reload(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
         """Force reload memory data for the given agent."""
         pass
 
     @abc.abstractmethod
-    def save(self, memory_data: dict[str, Any], agent_name: str | None = None) -> bool:
+    def save(self, memory_data: dict[str, Any], agent_name: str | None = None, *, user_id: str | None = None) -> bool:
         """Save memory data for the given agent."""
         pass
 
@@ -63,9 +63,9 @@ class FileMemoryStorage(MemoryStorage):
 
     def __init__(self):
         """Initialize the file memory storage."""
-        # Per-agent memory cache: keyed by agent_name (None = global)
+        # Per-user/agent memory cache: keyed by (user_id, agent_name) tuple (None = global)
         # Value: (memory_data, file_mtime)
-        self._memory_cache: dict[str | None, tuple[dict[str, Any], float | None]] = {}
+        self._memory_cache: dict[tuple[str | None, str | None], tuple[dict[str, Any], float | None]] = {}
 
     def _validate_agent_name(self, agent_name: str) -> None:
         """Validate that the agent name is safe to use in filesystem paths.
@@ -78,21 +78,29 @@ class FileMemoryStorage(MemoryStorage):
         if not AGENT_NAME_PATTERN.match(agent_name):
             raise ValueError(f"Invalid agent name {agent_name!r}: names must match {AGENT_NAME_PATTERN.pattern}")
 
-    def _get_memory_file_path(self, agent_name: str | None = None) -> Path:
+    def _get_memory_file_path(self, agent_name: str | None = None, *, user_id: str | None = None) -> Path:
         """Get the path to the memory file."""
+        if user_id is not None:
+            if agent_name is not None:
+                self._validate_agent_name(agent_name)
+                return get_paths().user_agent_memory_file(user_id, agent_name)
+            config = get_memory_config()
+            if config.storage_path and Path(config.storage_path).is_absolute():
+                return Path(config.storage_path)
+            return get_paths().user_memory_file(user_id)
+        # Legacy: no user_id
         if agent_name is not None:
             self._validate_agent_name(agent_name)
             return get_paths().agent_memory_file(agent_name)
-
         config = get_memory_config()
         if config.storage_path:
             p = Path(config.storage_path)
             return p if p.is_absolute() else get_paths().base_dir / p
         return get_paths().memory_file
 
-    def _load_memory_from_file(self, agent_name: str | None = None) -> dict[str, Any]:
+    def _load_memory_from_file(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
         """Load memory data from file."""
-        file_path = self._get_memory_file_path(agent_name)
+        file_path = self._get_memory_file_path(agent_name, user_id=user_id)
 
         if not file_path.exists():
             return create_empty_memory()
@@ -105,40 +113,42 @@ class FileMemoryStorage(MemoryStorage):
             logger.warning("Failed to load memory file: %s", e)
             return create_empty_memory()
 
-    def load(self, agent_name: str | None = None) -> dict[str, Any]:
+    def load(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
         """Load memory data (cached with file modification time check)."""
-        file_path = self._get_memory_file_path(agent_name)
+        file_path = self._get_memory_file_path(agent_name, user_id=user_id)
 
         try:
             current_mtime = file_path.stat().st_mtime if file_path.exists() else None
         except OSError:
             current_mtime = None
 
-        cached = self._memory_cache.get(agent_name)
+        cache_key = (user_id, agent_name)
+        cached = self._memory_cache.get(cache_key)
 
         if cached is None or cached[1] != current_mtime:
-            memory_data = self._load_memory_from_file(agent_name)
-            self._memory_cache[agent_name] = (memory_data, current_mtime)
+            memory_data = self._load_memory_from_file(agent_name, user_id=user_id)
+            self._memory_cache[cache_key] = (memory_data, current_mtime)
             return memory_data
 
         return cached[0]
 
-    def reload(self, agent_name: str | None = None) -> dict[str, Any]:
+    def reload(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
         """Reload memory data from file, forcing cache invalidation."""
-        file_path = self._get_memory_file_path(agent_name)
-        memory_data = self._load_memory_from_file(agent_name)
+        file_path = self._get_memory_file_path(agent_name, user_id=user_id)
+        memory_data = self._load_memory_from_file(agent_name, user_id=user_id)
 
         try:
             mtime = file_path.stat().st_mtime if file_path.exists() else None
         except OSError:
             mtime = None
 
-        self._memory_cache[agent_name] = (memory_data, mtime)
+        cache_key = (user_id, agent_name)
+        self._memory_cache[cache_key] = (memory_data, mtime)
         return memory_data
 
-    def save(self, memory_data: dict[str, Any], agent_name: str | None = None) -> bool:
+    def save(self, memory_data: dict[str, Any], agent_name: str | None = None, *, user_id: str | None = None) -> bool:
         """Save memory data to file and update cache."""
-        file_path = self._get_memory_file_path(agent_name)
+        file_path = self._get_memory_file_path(agent_name, user_id=user_id)
 
         try:
             file_path.parent.mkdir(parents=True, exist_ok=True)
@@ -155,7 +165,8 @@ class FileMemoryStorage(MemoryStorage):
             except OSError:
                 mtime = None
 
-            self._memory_cache[agent_name] = (memory_data, mtime)
+            cache_key = (user_id, agent_name)
+            self._memory_cache[cache_key] = (memory_data, mtime)
             logger.info("Memory saved to %s", file_path)
             return True
         except OSError as e:

backend/packages/harness/deerflow/agents/memory/updater.py

@@ -27,27 +27,28 @@ def _create_empty_memory() -> dict[str, Any]:
     return create_empty_memory()
 
 
-def _save_memory_to_file(memory_data: dict[str, Any], agent_name: str | None = None) -> bool:
+def _save_memory_to_file(memory_data: dict[str, Any], agent_name: str | None = None, *, user_id: str | None = None) -> bool:
     """Backward-compatible wrapper around the configured memory storage save path."""
-    return get_memory_storage().save(memory_data, agent_name)
+    return get_memory_storage().save(memory_data, agent_name, user_id=user_id)
 
 
-def get_memory_data(agent_name: str | None = None) -> dict[str, Any]:
+def get_memory_data(agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
     """Get the current memory data via storage provider."""
-    return get_memory_storage().load(agent_name)
+    return get_memory_storage().load(agent_name, user_id=user_id)
 
 
-def reload_memory_data(agent_name: str | None = None) -> dict[str, Any]:
+def reload_memory_data(agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
     """Reload memory data via storage provider."""
-    return get_memory_storage().reload(agent_name)
+    return get_memory_storage().reload(agent_name, user_id=user_id)
 
 
-def import_memory_data(memory_data: dict[str, Any], agent_name: str | None = None) -> dict[str, Any]:
+def import_memory_data(memory_data: dict[str, Any], agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
     """Persist imported memory data via storage provider.
 
     Args:
         memory_data: Full memory payload to persist.
         agent_name: If provided, imports into per-agent memory.
+        user_id: If provided, scopes memory to a specific user.
 
     Returns:
         The saved memory data after storage normalization.
@@ -56,15 +57,15 @@ def import_memory_data(memory_data: dict[str, Any], agent_name: str | None = Non
         OSError: If persisting the imported memory fails.
     """
     storage = get_memory_storage()
-    if not storage.save(memory_data, agent_name):
+    if not storage.save(memory_data, agent_name, user_id=user_id):
         raise OSError("Failed to save imported memory data")
-    return storage.load(agent_name)
+    return storage.load(agent_name, user_id=user_id)
 
 
-def clear_memory_data(agent_name: str | None = None) -> dict[str, Any]:
+def clear_memory_data(agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
     """Clear all stored memory data and persist an empty structure."""
     cleared_memory = create_empty_memory()
-    if not _save_memory_to_file(cleared_memory, agent_name):
+    if not _save_memory_to_file(cleared_memory, agent_name, user_id=user_id):
         raise OSError("Failed to save cleared memory data")
     return cleared_memory
 
@@ -81,6 +82,8 @@ def create_memory_fact(
     category: str = "context",
     confidence: float = 0.5,
     agent_name: str | None = None,
+    *,
+    user_id: str | None = None,
 ) -> dict[str, Any]:
     """Create a new fact and persist the updated memory data."""
     normalized_content = content.strip()
@@ -90,7 +93,7 @@ def create_memory_fact(
     normalized_category = category.strip() or "context"
     validated_confidence = _validate_confidence(confidence)
     now = utc_now_iso_z()
-    memory_data = get_memory_data(agent_name)
+    memory_data = get_memory_data(agent_name, user_id=user_id)
     updated_memory = dict(memory_data)
     facts = list(memory_data.get("facts", []))
     facts.append(
@@ -105,15 +108,15 @@ def create_memory_fact(
     )
     updated_memory["facts"] = facts
 
-    if not _save_memory_to_file(updated_memory, agent_name):
+    if not _save_memory_to_file(updated_memory, agent_name, user_id=user_id):
         raise OSError("Failed to save memory data after creating fact")
 
     return updated_memory
 
 
-def delete_memory_fact(fact_id: str, agent_name: str | None = None) -> dict[str, Any]:
+def delete_memory_fact(fact_id: str, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
     """Delete a fact by its id and persist the updated memory data."""
-    memory_data = get_memory_data(agent_name)
+    memory_data = get_memory_data(agent_name, user_id=user_id)
     facts = memory_data.get("facts", [])
     updated_facts = [fact for fact in facts if fact.get("id") != fact_id]
     if len(updated_facts) == len(facts):
@@ -122,7 +125,7 @@ def delete_memory_fact(fact_id: str, agent_name: str | None = None) -> dict[str,
     updated_memory = dict(memory_data)
     updated_memory["facts"] = updated_facts
 
-    if not _save_memory_to_file(updated_memory, agent_name):
+    if not _save_memory_to_file(updated_memory, agent_name, user_id=user_id):
         raise OSError(f"Failed to save memory data after deleting fact '{fact_id}'")
 
     return updated_memory
@@ -134,9 +137,11 @@ def update_memory_fact(
     category: str | None = None,
     confidence: float | None = None,
     agent_name: str | None = None,
+    *,
+    user_id: str | None = None,
 ) -> dict[str, Any]:
     """Update an existing fact and persist the updated memory data."""
-    memory_data = get_memory_data(agent_name)
+    memory_data = get_memory_data(agent_name, user_id=user_id)
     updated_memory = dict(memory_data)
     updated_facts: list[dict[str, Any]] = []
     found = False
@@ -163,7 +168,7 @@ def update_memory_fact(
 
     updated_memory["facts"] = updated_facts
 
-    if not _save_memory_to_file(updated_memory, agent_name):
+    if not _save_memory_to_file(updated_memory, agent_name, user_id=user_id):
         raise OSError(f"Failed to save memory data after updating fact '{fact_id}'")
 
     return updated_memory
@@ -276,6 +281,7 @@ class MemoryUpdater:
         agent_name: str | None = None,
         correction_detected: bool = False,
         reinforcement_detected: bool = False,
+        user_id: str | None = None,
     ) -> bool:
         """Update memory based on conversation messages.
 
@@ -285,6 +291,7 @@ class MemoryUpdater:
             agent_name: If provided, updates per-agent memory. If None, updates global memory.
             correction_detected: Whether recent turns include an explicit correction signal.
             reinforcement_detected: Whether recent turns include a positive reinforcement signal.
+            user_id: If provided, scopes memory to a specific user.
 
         Returns:
             True if update was successful, False otherwise.
@@ -298,7 +305,7 @@ class MemoryUpdater:
 
         try:
             # Get current memory
-            current_memory = get_memory_data(agent_name)
+            current_memory = get_memory_data(agent_name, user_id=user_id)
 
             # Format conversation for prompt
             conversation_text = format_conversation_for_update(messages)
@@ -353,7 +360,7 @@ class MemoryUpdater:
             updated_memory = _strip_upload_mentions_from_memory(updated_memory)
 
             # Save
-            return get_memory_storage().save(updated_memory, agent_name)
+            return get_memory_storage().save(updated_memory, agent_name, user_id=user_id)
 
         except json.JSONDecodeError as e:
             logger.warning("Failed to parse LLM response for memory update: %s", e)
@@ -455,6 +462,7 @@ def update_memory_from_conversation(
     agent_name: str | None = None,
     correction_detected: bool = False,
     reinforcement_detected: bool = False,
+    user_id: str | None = None,
 ) -> bool:
     """Convenience function to update memory from a conversation.
 
@@ -464,9 +472,10 @@ def update_memory_from_conversation(
         agent_name: If provided, updates per-agent memory. If None, updates global memory.
         correction_detected: Whether recent turns include an explicit correction signal.
         reinforcement_detected: Whether recent turns include a positive reinforcement signal.
+        user_id: If provided, scopes memory to a specific user.
 
     Returns:
         True if successful, False otherwise.
     """
     updater = MemoryUpdater()
-    return updater.update_memory(messages, thread_id, agent_name, correction_detected, reinforcement_detected)
+    return updater.update_memory(messages, thread_id, agent_name, correction_detected, reinforcement_detected, user_id=user_id)

backend/packages/harness/deerflow/agents/middlewares/loop_detection_middleware.py

@@ -283,7 +283,7 @@ class LoopDetectionMiddleware(AgentMiddleware[AgentState]):
             # the conversation; injecting one mid-conversation crashes
             # langchain_anthropic's _format_messages(). HumanMessage works
             # with all providers. See #1299.
-            return {"messages": [HumanMessage(content=warning)]}
+            return {"messages": [HumanMessage(content=warning, name="loop_warning")]}
 
         return None
 

backend/packages/harness/deerflow/agents/middlewares/memory_middleware.py

@@ -11,6 +11,7 @@ from langgraph.runtime import Runtime
 
 from deerflow.agents.memory.queue import get_memory_queue
 from deerflow.config.memory_config import get_memory_config
+from deerflow.runtime.user_context import get_effective_user_id
 
 logger = logging.getLogger(__name__)
 
@@ -236,11 +237,16 @@ class MemoryMiddleware(AgentMiddleware[MemoryMiddlewareState]):
         # Queue the filtered conversation for memory update
         correction_detected = detect_correction(filtered_messages)
         reinforcement_detected = not correction_detected and detect_reinforcement(filtered_messages)
+        # Capture user_id at enqueue time while the request context is still alive.
+        # threading.Timer fires on a different thread where ContextVar values are not
+        # propagated, so we must store user_id explicitly in ConversationContext.
+        user_id = get_effective_user_id()
         queue = get_memory_queue()
         queue.add(
             thread_id=thread_id,
             messages=filtered_messages,
             agent_name=self._agent_name,
+            user_id=user_id,
             correction_detected=correction_detected,
             reinforcement_detected=reinforcement_detected,
         )

backend/packages/harness/deerflow/agents/middlewares/summarization_middleware.py

@@ -0,0 +1,13 @@
+from typing import override
+
+from langchain.agents.middleware import SummarizationMiddleware as BaseSummarizationMiddleware
+from langchain_core.messages.human import HumanMessage
+
+
+class SummarizationMiddleware(BaseSummarizationMiddleware):
+    @override
+    def _build_new_messages(self, summary: str) -> list[HumanMessage]:
+        """Override the base implementation to let the human message with the special name 'summary'.
+        And this message will be ignored to display in the frontend, but still can be used as context for the model.
+        """
+        return [HumanMessage(content=f"Here is a summary of the conversation to date:\n\n{summary}", name="summary")]

backend/packages/harness/deerflow/agents/middlewares/thread_data_middleware.py

@@ -1,13 +1,16 @@
 import logging
+from datetime import UTC, datetime
 from typing import NotRequired, override
 
 from langchain.agents import AgentState
 from langchain.agents.middleware import AgentMiddleware
+from langchain_core.messages import HumanMessage
 from langgraph.config import get_config
 from langgraph.runtime import Runtime
 
 from deerflow.agents.thread_state import ThreadDataState
 from deerflow.config.paths import Paths, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 
 logger = logging.getLogger(__name__)
 
@@ -46,32 +49,34 @@ class ThreadDataMiddleware(AgentMiddleware[ThreadDataMiddlewareState]):
         self._paths = Paths(base_dir) if base_dir else get_paths()
         self._lazy_init = lazy_init
 
-    def _get_thread_paths(self, thread_id: str) -> dict[str, str]:
+    def _get_thread_paths(self, thread_id: str, user_id: str | None = None) -> dict[str, str]:
         """Get the paths for a thread's data directories.
 
         Args:
             thread_id: The thread ID.
+            user_id: Optional user ID for per-user path isolation.
 
         Returns:
             Dictionary with workspace_path, uploads_path, and outputs_path.
         """
         return {
-            "workspace_path": str(self._paths.sandbox_work_dir(thread_id)),
-            "uploads_path": str(self._paths.sandbox_uploads_dir(thread_id)),
-            "outputs_path": str(self._paths.sandbox_outputs_dir(thread_id)),
+            "workspace_path": str(self._paths.sandbox_work_dir(thread_id, user_id=user_id)),
+            "uploads_path": str(self._paths.sandbox_uploads_dir(thread_id, user_id=user_id)),
+            "outputs_path": str(self._paths.sandbox_outputs_dir(thread_id, user_id=user_id)),
         }
 
-    def _create_thread_directories(self, thread_id: str) -> dict[str, str]:
+    def _create_thread_directories(self, thread_id: str, user_id: str | None = None) -> dict[str, str]:
         """Create the thread data directories.
 
         Args:
             thread_id: The thread ID.
+            user_id: Optional user ID for per-user path isolation.
 
         Returns:
             Dictionary with the created directory paths.
         """
-        self._paths.ensure_thread_dirs(thread_id)
-        return self._get_thread_paths(thread_id)
+        self._paths.ensure_thread_dirs(thread_id, user_id=user_id)
+        return self._get_thread_paths(thread_id, user_id=user_id)
 
     @override
     def before_agent(self, state: ThreadDataMiddlewareState, runtime: Runtime) -> dict | None:
@@ -84,16 +89,30 @@ class ThreadDataMiddleware(AgentMiddleware[ThreadDataMiddlewareState]):
         if thread_id is None:
             raise ValueError("Thread ID is required in runtime context or config.configurable")
 
+        user_id = get_effective_user_id()
+
         if self._lazy_init:
             # Lazy initialization: only compute paths, don't create directories
-            paths = self._get_thread_paths(thread_id)
+            paths = self._get_thread_paths(thread_id, user_id=user_id)
         else:
             # Eager initialization: create directories immediately
-            paths = self._create_thread_directories(thread_id)
+            paths = self._create_thread_directories(thread_id, user_id=user_id)
             logger.debug("Created thread data directories for thread %s", thread_id)
 
+        messages = list(state.get("messages", []))
+        last_message = messages[-1] if messages else None
+
+        if last_message and isinstance(last_message, HumanMessage):
+            messages[-1] = HumanMessage(
+                content=last_message.content,
+                id=last_message.id,
+                name=last_message.name or "user-input",
+                additional_kwargs={**last_message.additional_kwargs, "run_id": runtime.context.get("run_id"), "timestamp": datetime.now(UTC).isoformat()},
+            )
+
         return {
             "thread_data": {
                 **paths,
-            }
+            },
+            "messages": messages,
         }

backend/packages/harness/deerflow/agents/middlewares/title_middleware.py

@@ -1,10 +1,11 @@
 """Middleware for automatic thread title generation."""
 
 import logging
-from typing import NotRequired, override
+from typing import Any, NotRequired, override
 
 from langchain.agents import AgentState
 from langchain.agents.middleware import AgentMiddleware
+from langgraph.config import get_config
 from langgraph.runtime import Runtime
 
 from deerflow.config.title_config import get_title_config
@@ -100,6 +101,20 @@ class TitleMiddleware(AgentMiddleware[TitleMiddlewareState]):
             return user_msg[:fallback_chars].rstrip() + "..."
         return user_msg if user_msg else "New Conversation"
 
+    def _get_runnable_config(self) -> dict[str, Any]:
+        """Inherit the parent RunnableConfig and add middleware tag.
+
+        This ensures RunJournal identifies LLM calls from this middleware
+        as ``middleware:title`` instead of ``lead_agent``.
+        """
+        try:
+            parent = get_config()
+        except Exception:
+            parent = {}
+        config = {**parent}
+        config["tags"] = [*(config.get("tags") or []), "middleware:title"]
+        return config
+
     def _generate_title_result(self, state: TitleMiddlewareState) -> dict | None:
         """Generate a local fallback title without blocking on an LLM call."""
         if not self._should_generate_title(state):
@@ -121,7 +136,7 @@ class TitleMiddleware(AgentMiddleware[TitleMiddlewareState]):
                 model = create_chat_model(name=config.model_name, thinking_enabled=False)
             else:
                 model = create_chat_model(thinking_enabled=False)
-            response = await model.ainvoke(prompt)
+            response = await model.ainvoke(prompt, config=self._get_runnable_config())
             title = self._parse_title(response.content)
             if title:
                 return {"title": title}

backend/packages/harness/deerflow/agents/middlewares/uploads_middleware.py

@@ -10,6 +10,7 @@ from langchain_core.messages import HumanMessage
 from langgraph.runtime import Runtime
 
 from deerflow.config.paths import Paths, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.utils.file_conversion import extract_outline
 
 logger = logging.getLogger(__name__)
@@ -221,7 +222,7 @@ class UploadsMiddleware(AgentMiddleware[UploadsMiddlewareState]):
                 thread_id = get_config().get("configurable", {}).get("thread_id")
             except RuntimeError:
                 pass  # get_config() raises outside a runnable context (e.g. unit tests)
-        uploads_dir = self._paths.sandbox_uploads_dir(thread_id) if thread_id else None
+        uploads_dir = self._paths.sandbox_uploads_dir(thread_id, user_id=get_effective_user_id()) if thread_id else None
 
         # Get newly uploaded files from the current message's additional_kwargs.files
         new_files = self._files_from_kwargs(last_message, uploads_dir) or []
@@ -278,6 +279,7 @@ class UploadsMiddleware(AgentMiddleware[UploadsMiddlewareState]):
         updated_message = HumanMessage(
             content=f"{files_message}\n\n{original_content}",
             id=last_message.id,
+            name=last_message.name,
             additional_kwargs=last_message.additional_kwargs,
         )
 

backend/packages/harness/deerflow/client.py

@@ -40,6 +40,7 @@ from deerflow.config.app_config import get_app_config, reload_app_config
 from deerflow.config.extensions_config import ExtensionsConfig, SkillStateConfig, get_extensions_config, reload_extensions_config
 from deerflow.config.paths import get_paths
 from deerflow.models import create_chat_model
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.skills.installer import install_skill_from_archive
 from deerflow.uploads.manager import (
     claim_unique_filename,
@@ -240,7 +241,7 @@ class DeerFlowClient:
         }
         checkpointer = self._checkpointer
         if checkpointer is None:
-            from deerflow.agents.checkpointer import get_checkpointer
+            from deerflow.runtime.checkpointer import get_checkpointer
 
             checkpointer = get_checkpointer()
         if checkpointer is not None:
@@ -374,7 +375,7 @@ class DeerFlowClient:
         """
         checkpointer = self._checkpointer
         if checkpointer is None:
-            from deerflow.agents.checkpointer.provider import get_checkpointer
+            from deerflow.runtime.checkpointer.provider import get_checkpointer
 
             checkpointer = get_checkpointer()
 
@@ -429,7 +430,7 @@ class DeerFlowClient:
         """
         checkpointer = self._checkpointer
         if checkpointer is None:
-            from deerflow.agents.checkpointer.provider import get_checkpointer
+            from deerflow.runtime.checkpointer.provider import get_checkpointer
 
             checkpointer = get_checkpointer()
 
@@ -769,19 +770,19 @@ class DeerFlowClient:
         """
         from deerflow.agents.memory.updater import get_memory_data
 
-        return get_memory_data()
+        return get_memory_data(user_id=get_effective_user_id())
 
     def export_memory(self) -> dict:
         """Export current memory data for backup or transfer."""
         from deerflow.agents.memory.updater import get_memory_data
 
-        return get_memory_data()
+        return get_memory_data(user_id=get_effective_user_id())
 
     def import_memory(self, memory_data: dict) -> dict:
         """Import and persist full memory data."""
         from deerflow.agents.memory.updater import import_memory_data
 
-        return import_memory_data(memory_data)
+        return import_memory_data(memory_data, user_id=get_effective_user_id())
 
     def get_model(self, name: str) -> dict | None:
         """Get a specific model's configuration by name.
@@ -956,13 +957,13 @@ class DeerFlowClient:
         """
         from deerflow.agents.memory.updater import reload_memory_data
 
-        return reload_memory_data()
+        return reload_memory_data(user_id=get_effective_user_id())
 
     def clear_memory(self) -> dict:
         """Clear all persisted memory data."""
         from deerflow.agents.memory.updater import clear_memory_data
 
-        return clear_memory_data()
+        return clear_memory_data(user_id=get_effective_user_id())
 
     def create_memory_fact(self, content: str, category: str = "context", confidence: float = 0.5) -> dict:
         """Create a single fact manually."""
@@ -1179,7 +1180,7 @@ class DeerFlowClient:
             ValueError: If the path is invalid.
         """
         try:
-            actual = get_paths().resolve_virtual_path(thread_id, path)
+            actual = get_paths().resolve_virtual_path(thread_id, path, user_id=get_effective_user_id())
         except ValueError as exc:
             if "traversal" in str(exc):
                 from deerflow.uploads.manager import PathTraversalError

backend/packages/harness/deerflow/community/aio_sandbox/aio_sandbox_provider.py

@@ -27,6 +27,7 @@ except ImportError:  # pragma: no cover - Windows fallback
 
 from deerflow.config import get_app_config
 from deerflow.config.paths import VIRTUAL_PATH_PREFIX, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.sandbox.sandbox import Sandbox
 from deerflow.sandbox.sandbox_provider import SandboxProvider
 
@@ -260,15 +261,16 @@ class AioSandboxProvider(SandboxProvider):
         mounted Docker socket (DooD), the host Docker daemon can resolve the paths.
         """
         paths = get_paths()
-        paths.ensure_thread_dirs(thread_id)
+        user_id = get_effective_user_id()
+        paths.ensure_thread_dirs(thread_id, user_id=user_id)
 
         return [
-            (paths.host_sandbox_work_dir(thread_id), f"{VIRTUAL_PATH_PREFIX}/workspace", False),
-            (paths.host_sandbox_uploads_dir(thread_id), f"{VIRTUAL_PATH_PREFIX}/uploads", False),
-            (paths.host_sandbox_outputs_dir(thread_id), f"{VIRTUAL_PATH_PREFIX}/outputs", False),
+            (paths.host_sandbox_work_dir(thread_id, user_id=user_id), f"{VIRTUAL_PATH_PREFIX}/workspace", False),
+            (paths.host_sandbox_uploads_dir(thread_id, user_id=user_id), f"{VIRTUAL_PATH_PREFIX}/uploads", False),
+            (paths.host_sandbox_outputs_dir(thread_id, user_id=user_id), f"{VIRTUAL_PATH_PREFIX}/outputs", False),
             # ACP workspace: read-only inside the sandbox (lead agent reads results;
             # the ACP subprocess writes from the host side, not from within the container).
-            (paths.host_acp_workspace_dir(thread_id), "/mnt/acp-workspace", True),
+            (paths.host_acp_workspace_dir(thread_id, user_id=user_id), "/mnt/acp-workspace", True),
         ]
 
     @staticmethod
@@ -480,8 +482,9 @@ class AioSandboxProvider(SandboxProvider):
         across multiple processes, preventing container-name conflicts.
         """
         paths = get_paths()
-        paths.ensure_thread_dirs(thread_id)
-        lock_path = paths.thread_dir(thread_id) / f"{sandbox_id}.lock"
+        user_id = get_effective_user_id()
+        paths.ensure_thread_dirs(thread_id, user_id=user_id)
+        lock_path = paths.thread_dir(thread_id, user_id=user_id) / f"{sandbox_id}.lock"
 
         with open(lock_path, "a", encoding="utf-8") as lock_file:
             locked = False

backend/packages/harness/deerflow/config/app_config.py

@@ -10,10 +10,12 @@ from pydantic import BaseModel, ConfigDict, Field
 
 from deerflow.config.acp_config import load_acp_config_from_dict
 from deerflow.config.checkpointer_config import CheckpointerConfig, load_checkpointer_config_from_dict
+from deerflow.config.database_config import DatabaseConfig
 from deerflow.config.extensions_config import ExtensionsConfig
 from deerflow.config.guardrails_config import GuardrailsConfig, load_guardrails_config_from_dict
 from deerflow.config.memory_config import MemoryConfig, load_memory_config_from_dict
 from deerflow.config.model_config import ModelConfig
+from deerflow.config.run_events_config import RunEventsConfig
 from deerflow.config.sandbox_config import SandboxConfig
 from deerflow.config.skill_evolution_config import SkillEvolutionConfig
 from deerflow.config.skills_config import SkillsConfig
@@ -56,6 +58,8 @@ class AppConfig(BaseModel):
     subagents: SubagentsAppConfig = Field(default_factory=SubagentsAppConfig, description="Subagent runtime configuration")
     guardrails: GuardrailsConfig = Field(default_factory=GuardrailsConfig, description="Guardrail middleware configuration")
     model_config = ConfigDict(extra="allow", frozen=False)
+    database: DatabaseConfig = Field(default_factory=DatabaseConfig, description="Unified database backend configuration")
+    run_events: RunEventsConfig = Field(default_factory=RunEventsConfig, description="Run event storage configuration")
     checkpointer: CheckpointerConfig | None = Field(default=None, description="Checkpointer configuration")
     stream_bridge: StreamBridgeConfig | None = Field(default=None, description="Stream bridge configuration")
 

backend/packages/harness/deerflow/config/database_config.py

@@ -0,0 +1,102 @@
+"""Unified database backend configuration.
+
+Controls BOTH the LangGraph checkpointer and the DeerFlow application
+persistence layer (runs, threads metadata, users, etc.). The user
+configures one backend; the system handles physical separation details.
+
+SQLite mode: checkpointer and app share a single .db file
+({sqlite_dir}/deerflow.db) with WAL journal mode enabled on every
+connection. WAL allows concurrent readers and a single writer without
+blocking, making a unified file safe for both workloads.  Writers
+that contend for the lock wait via the default 5-second sqlite3
+busy timeout rather than failing immediately.
+
+Postgres mode: both use the same database URL but maintain independent
+connection pools with different lifecycles.
+
+Memory mode: checkpointer uses MemorySaver, app uses in-memory stores.
+No database is initialized.
+
+Sensitive values (postgres_url) should use $VAR syntax in config.yaml
+to reference environment variables from .env:
+
+    database:
+      backend: postgres
+      postgres_url: $DATABASE_URL
+
+The $VAR resolution is handled by AppConfig.resolve_env_variables()
+before this config is instantiated -- DatabaseConfig itself does not
+need to do any environment variable processing.
+"""
+
+from __future__ import annotations
+
+import os
+from typing import Literal
+
+from pydantic import BaseModel, Field
+
+
+class DatabaseConfig(BaseModel):
+    backend: Literal["memory", "sqlite", "postgres"] = Field(
+        default="memory",
+        description=("Storage backend for both checkpointer and application data. 'memory' for development (no persistence across restarts), 'sqlite' for single-node deployment, 'postgres' for production multi-node deployment."),
+    )
+    sqlite_dir: str = Field(
+        default=".deer-flow/data",
+        description=("Directory for the SQLite database file. Both checkpointer and application data share {sqlite_dir}/deerflow.db."),
+    )
+    postgres_url: str = Field(
+        default="",
+        description=(
+            "PostgreSQL connection URL, shared by checkpointer and app. "
+            "Use $DATABASE_URL in config.yaml to reference .env. "
+            "Example: postgresql://user:pass@host:5432/deerflow "
+            "(the +asyncpg driver suffix is added automatically where needed)."
+        ),
+    )
+    echo_sql: bool = Field(
+        default=False,
+        description="Echo all SQL statements to log (debug only).",
+    )
+    pool_size: int = Field(
+        default=5,
+        description="Connection pool size for the app ORM engine (postgres only).",
+    )
+
+    # -- Derived helpers (not user-configured) --
+
+    @property
+    def _resolved_sqlite_dir(self) -> str:
+        """Resolve sqlite_dir to an absolute path (relative to CWD)."""
+        from pathlib import Path
+
+        return str(Path(self.sqlite_dir).resolve())
+
+    @property
+    def sqlite_path(self) -> str:
+        """Unified SQLite file path shared by checkpointer and app."""
+        return os.path.join(self._resolved_sqlite_dir, "deerflow.db")
+
+    # Backward-compatible aliases
+    @property
+    def checkpointer_sqlite_path(self) -> str:
+        """SQLite file path for the LangGraph checkpointer (alias for sqlite_path)."""
+        return self.sqlite_path
+
+    @property
+    def app_sqlite_path(self) -> str:
+        """SQLite file path for application ORM data (alias for sqlite_path)."""
+        return self.sqlite_path
+
+    @property
+    def app_sqlalchemy_url(self) -> str:
+        """SQLAlchemy async URL for the application ORM engine."""
+        if self.backend == "sqlite":
+            return f"sqlite+aiosqlite:///{self.sqlite_path}"
+        if self.backend == "postgres":
+            url = self.postgres_url
+            if url.startswith("postgresql://"):
+                url = url.replace("postgresql://", "postgresql+asyncpg://", 1)
+            return url
+        raise ValueError(f"No SQLAlchemy URL for backend={self.backend!r}")

backend/packages/harness/deerflow/config/memory_config.py

@@ -14,8 +14,9 @@ class MemoryConfig(BaseModel):
         default="",
         description=(
             "Path to store memory data. "
-            "If empty, defaults to `{base_dir}/memory.json` (see Paths.memory_file). "
-            "Absolute paths are used as-is. "
+            "If empty, defaults to per-user memory at `{base_dir}/users/{user_id}/memory.json`. "
+            "Absolute paths are used as-is and opt out of per-user isolation "
+            "(all users share the same file). "
             "Relative paths are resolved against `Paths.base_dir` "
             "(not the backend working directory). "
             "Note: if you previously set this to `.deer-flow/memory.json`, "

backend/packages/harness/deerflow/config/paths.py

@@ -7,6 +7,7 @@ from pathlib import Path, PureWindowsPath
 VIRTUAL_PATH_PREFIX = "/mnt/user-data"
 
 _SAFE_THREAD_ID_RE = re.compile(r"^[A-Za-z0-9_\-]+$")
+_SAFE_USER_ID_RE = re.compile(r"^[A-Za-z0-9_\-]+$")
 
 
 def _default_local_base_dir() -> Path:
@@ -22,6 +23,13 @@ def _validate_thread_id(thread_id: str) -> str:
     return thread_id
 
 
+def _validate_user_id(user_id: str) -> str:
+    """Validate a user ID before using it in filesystem paths."""
+    if not _SAFE_USER_ID_RE.match(user_id):
+        raise ValueError(f"Invalid user_id {user_id!r}: only alphanumeric characters, hyphens, and underscores are allowed.")
+    return user_id
+
+
 def _join_host_path(base: str, *parts: str) -> str:
     """Join host filesystem path segments while preserving native style.
 
@@ -134,44 +142,63 @@ class Paths:
         """Per-agent memory file: `{base_dir}/agents/{name}/memory.json`."""
         return self.agent_dir(name) / "memory.json"
 
-    def thread_dir(self, thread_id: str) -> Path:
+    def user_dir(self, user_id: str) -> Path:
+        """Directory for a specific user: `{base_dir}/users/{user_id}/`."""
+        return self.base_dir / "users" / _validate_user_id(user_id)
+
+    def user_memory_file(self, user_id: str) -> Path:
+        """Per-user memory file: `{base_dir}/users/{user_id}/memory.json`."""
+        return self.user_dir(user_id) / "memory.json"
+
+    def user_agent_memory_file(self, user_id: str, agent_name: str) -> Path:
+        """Per-user per-agent memory: `{base_dir}/users/{user_id}/agents/{name}/memory.json`."""
+        return self.user_dir(user_id) / "agents" / agent_name.lower() / "memory.json"
+
+    def thread_dir(self, thread_id: str, *, user_id: str | None = None) -> Path:
         """
-        Host path for a thread's data: `{base_dir}/threads/{thread_id}/`
+        Host path for a thread's data.
+
+        When *user_id* is provided:
+            `{base_dir}/users/{user_id}/threads/{thread_id}/`
+        Otherwise (legacy layout):
+            `{base_dir}/threads/{thread_id}/`
 
         This directory contains a `user-data/` subdirectory that is mounted
         as `/mnt/user-data/` inside the sandbox.
 
         Raises:
-            ValueError: If `thread_id` contains unsafe characters (path separators
-                        or `..`) that could cause directory traversal.
+            ValueError: If `thread_id` or `user_id` contains unsafe characters (path
+                        separators or `..`) that could cause directory traversal.
         """
+        if user_id is not None:
+            return self.user_dir(user_id) / "threads" / _validate_thread_id(thread_id)
         return self.base_dir / "threads" / _validate_thread_id(thread_id)
 
-    def sandbox_work_dir(self, thread_id: str) -> Path:
+    def sandbox_work_dir(self, thread_id: str, *, user_id: str | None = None) -> Path:
         """
         Host path for the agent's workspace directory.
         Host: `{base_dir}/threads/{thread_id}/user-data/workspace/`
         Sandbox: `/mnt/user-data/workspace/`
         """
-        return self.thread_dir(thread_id) / "user-data" / "workspace"
+        return self.thread_dir(thread_id, user_id=user_id) / "user-data" / "workspace"
 
-    def sandbox_uploads_dir(self, thread_id: str) -> Path:
+    def sandbox_uploads_dir(self, thread_id: str, *, user_id: str | None = None) -> Path:
         """
         Host path for user-uploaded files.
         Host: `{base_dir}/threads/{thread_id}/user-data/uploads/`
         Sandbox: `/mnt/user-data/uploads/`
         """
-        return self.thread_dir(thread_id) / "user-data" / "uploads"
+        return self.thread_dir(thread_id, user_id=user_id) / "user-data" / "uploads"
 
-    def sandbox_outputs_dir(self, thread_id: str) -> Path:
+    def sandbox_outputs_dir(self, thread_id: str, *, user_id: str | None = None) -> Path:
         """
         Host path for agent-generated artifacts.
         Host: `{base_dir}/threads/{thread_id}/user-data/outputs/`
         Sandbox: `/mnt/user-data/outputs/`
         """
-        return self.thread_dir(thread_id) / "user-data" / "outputs"
+        return self.thread_dir(thread_id, user_id=user_id) / "user-data" / "outputs"
 
-    def acp_workspace_dir(self, thread_id: str) -> Path:
+    def acp_workspace_dir(self, thread_id: str, *, user_id: str | None = None) -> Path:
         """
         Host path for the ACP workspace of a specific thread.
         Host: `{base_dir}/threads/{thread_id}/acp-workspace/`
@@ -180,41 +207,43 @@ class Paths:
         Each thread gets its own isolated ACP workspace so that concurrent
         sessions cannot read each other's ACP agent outputs.
         """
-        return self.thread_dir(thread_id) / "acp-workspace"
+        return self.thread_dir(thread_id, user_id=user_id) / "acp-workspace"
 
-    def sandbox_user_data_dir(self, thread_id: str) -> Path:
+    def sandbox_user_data_dir(self, thread_id: str, *, user_id: str | None = None) -> Path:
         """
         Host path for the user-data root.
         Host: `{base_dir}/threads/{thread_id}/user-data/`
         Sandbox: `/mnt/user-data/`
         """
-        return self.thread_dir(thread_id) / "user-data"
+        return self.thread_dir(thread_id, user_id=user_id) / "user-data"
 
-    def host_thread_dir(self, thread_id: str) -> str:
+    def host_thread_dir(self, thread_id: str, *, user_id: str | None = None) -> str:
         """Host path for a thread directory, preserving Windows path syntax."""
+        if user_id is not None:
+            return _join_host_path(self._host_base_dir_str(), "users", _validate_user_id(user_id), "threads", _validate_thread_id(thread_id))
         return _join_host_path(self._host_base_dir_str(), "threads", _validate_thread_id(thread_id))
 
-    def host_sandbox_user_data_dir(self, thread_id: str) -> str:
+    def host_sandbox_user_data_dir(self, thread_id: str, *, user_id: str | None = None) -> str:
         """Host path for a thread's user-data root."""
-        return _join_host_path(self.host_thread_dir(thread_id), "user-data")
+        return _join_host_path(self.host_thread_dir(thread_id, user_id=user_id), "user-data")
 
-    def host_sandbox_work_dir(self, thread_id: str) -> str:
+    def host_sandbox_work_dir(self, thread_id: str, *, user_id: str | None = None) -> str:
         """Host path for the workspace mount source."""
-        return _join_host_path(self.host_sandbox_user_data_dir(thread_id), "workspace")
+        return _join_host_path(self.host_sandbox_user_data_dir(thread_id, user_id=user_id), "workspace")
 
-    def host_sandbox_uploads_dir(self, thread_id: str) -> str:
+    def host_sandbox_uploads_dir(self, thread_id: str, *, user_id: str | None = None) -> str:
         """Host path for the uploads mount source."""
-        return _join_host_path(self.host_sandbox_user_data_dir(thread_id), "uploads")
+        return _join_host_path(self.host_sandbox_user_data_dir(thread_id, user_id=user_id), "uploads")
 
-    def host_sandbox_outputs_dir(self, thread_id: str) -> str:
+    def host_sandbox_outputs_dir(self, thread_id: str, *, user_id: str | None = None) -> str:
         """Host path for the outputs mount source."""
-        return _join_host_path(self.host_sandbox_user_data_dir(thread_id), "outputs")
+        return _join_host_path(self.host_sandbox_user_data_dir(thread_id, user_id=user_id), "outputs")
 
-    def host_acp_workspace_dir(self, thread_id: str) -> str:
+    def host_acp_workspace_dir(self, thread_id: str, *, user_id: str | None = None) -> str:
         """Host path for the ACP workspace mount source."""
-        return _join_host_path(self.host_thread_dir(thread_id), "acp-workspace")
+        return _join_host_path(self.host_thread_dir(thread_id, user_id=user_id), "acp-workspace")
 
-    def ensure_thread_dirs(self, thread_id: str) -> None:
+    def ensure_thread_dirs(self, thread_id: str, *, user_id: str | None = None) -> None:
         """Create all standard sandbox directories for a thread.
 
         Directories are created with mode 0o777 so that sandbox containers
@@ -228,24 +257,24 @@ class Paths:
         ACP agent invocation.
         """
         for d in [
-            self.sandbox_work_dir(thread_id),
-            self.sandbox_uploads_dir(thread_id),
-            self.sandbox_outputs_dir(thread_id),
-            self.acp_workspace_dir(thread_id),
+            self.sandbox_work_dir(thread_id, user_id=user_id),
+            self.sandbox_uploads_dir(thread_id, user_id=user_id),
+            self.sandbox_outputs_dir(thread_id, user_id=user_id),
+            self.acp_workspace_dir(thread_id, user_id=user_id),
         ]:
             d.mkdir(parents=True, exist_ok=True)
             d.chmod(0o777)
 
-    def delete_thread_dir(self, thread_id: str) -> None:
+    def delete_thread_dir(self, thread_id: str, *, user_id: str | None = None) -> None:
         """Delete all persisted data for a thread.
 
         The operation is idempotent: missing thread directories are ignored.
         """
-        thread_dir = self.thread_dir(thread_id)
+        thread_dir = self.thread_dir(thread_id, user_id=user_id)
         if thread_dir.exists():
             shutil.rmtree(thread_dir)
 
-    def resolve_virtual_path(self, thread_id: str, virtual_path: str) -> Path:
+    def resolve_virtual_path(self, thread_id: str, virtual_path: str, *, user_id: str | None = None) -> Path:
         """Resolve a sandbox virtual path to the actual host filesystem path.
 
         Args:
@@ -253,6 +282,7 @@ class Paths:
             virtual_path: Virtual path as seen inside the sandbox, e.g.
                           ``/mnt/user-data/outputs/report.pdf``.
                           Leading slashes are stripped before matching.
+            user_id: Optional user ID for user-scoped path resolution.
 
         Returns:
             The resolved absolute host filesystem path.
@@ -270,7 +300,7 @@ class Paths:
             raise ValueError(f"Path must start with /{prefix}")
 
         relative = stripped[len(prefix) :].lstrip("/")
-        base = self.sandbox_user_data_dir(thread_id).resolve()
+        base = self.sandbox_user_data_dir(thread_id, user_id=user_id).resolve()
         actual = (base / relative).resolve()
 
         try:

backend/packages/harness/deerflow/config/run_events_config.py

@@ -0,0 +1,33 @@
+"""Run event storage configuration.
+
+Controls where run events (messages + execution traces) are persisted.
+
+Backends:
+- memory: In-memory storage, data lost on restart. Suitable for
+  development and testing.
+- db: SQL database via SQLAlchemy ORM. Provides full query capability.
+  Suitable for production deployments.
+- jsonl: Append-only JSONL files. Lightweight alternative for
+  single-node deployments that need persistence without a database.
+"""
+
+from __future__ import annotations
+
+from typing import Literal
+
+from pydantic import BaseModel, Field
+
+
+class RunEventsConfig(BaseModel):
+    backend: Literal["memory", "db", "jsonl"] = Field(
+        default="memory",
+        description="Storage backend for run events. 'memory' for development (no persistence), 'db' for production (SQL queries), 'jsonl' for lightweight single-node persistence.",
+    )
+    max_trace_content: int = Field(
+        default=10240,
+        description="Maximum trace content size in bytes before truncation (db backend only).",
+    )
+    track_token_usage: bool = Field(
+        default=True,
+        description="Whether RunJournal should accumulate token counts to RunRow.",
+    )

backend/packages/harness/deerflow/models/factory.py

@@ -113,7 +113,16 @@ def create_chat_model(name: str | None = None, thinking_enabled: bool = False, *
         elif "reasoning_effort" not in model_settings_from_config:
             model_settings_from_config["reasoning_effort"] = "medium"
 
-    model_instance = model_class(**{**model_settings_from_config, **kwargs})
+    # Ensure stream_usage is enabled so that token usage metadata is available
+    # in streaming responses.  LangChain's BaseChatOpenAI only defaults
+    # stream_usage=True when no custom base_url/api_base is set, so models
+    # hitting third-party endpoints (e.g. doubao, deepseek) silently lose
+    # usage data.  We default it to True unless explicitly configured.
+    if "stream_usage" not in model_settings_from_config and "stream_usage" not in kwargs:
+        if "stream_usage" in getattr(model_class, "model_fields", {}):
+            model_settings_from_config["stream_usage"] = True
+
+    model_instance = model_class(**kwargs, **model_settings_from_config)
 
     callbacks = build_tracing_callbacks()
     if callbacks:

backend/packages/harness/deerflow/persistence/__init__.py

@@ -0,0 +1,13 @@
+"""DeerFlow application persistence layer (SQLAlchemy 2.0 async ORM).
+
+This module manages DeerFlow's own application data -- runs metadata,
+thread ownership, cron jobs, users. It is completely separate from
+LangGraph's checkpointer, which manages graph execution state.
+
+Usage:
+    from deerflow.persistence import init_engine, close_engine, get_session_factory
+"""
+
+from deerflow.persistence.engine import close_engine, get_engine, get_session_factory, init_engine
+
+__all__ = ["close_engine", "get_engine", "get_session_factory", "init_engine"]

backend/packages/harness/deerflow/persistence/base.py

@@ -0,0 +1,40 @@
+"""SQLAlchemy declarative base with automatic to_dict support.
+
+All DeerFlow ORM models inherit from this Base. It provides a generic
+to_dict() method via SQLAlchemy's inspect() so individual models don't
+need to write their own serialization logic.
+
+LangGraph's checkpointer tables are NOT managed by this Base.
+"""
+
+from __future__ import annotations
+
+from sqlalchemy import inspect as sa_inspect
+from sqlalchemy.orm import DeclarativeBase
+
+
+class Base(DeclarativeBase):
+    """Base class for all DeerFlow ORM models.
+
+    Provides:
+    - Automatic to_dict() via SQLAlchemy column inspection.
+    - Standard __repr__() showing all column values.
+    """
+
+    def to_dict(self, *, exclude: set[str] | None = None) -> dict:
+        """Convert ORM instance to plain dict.
+
+        Uses SQLAlchemy's inspect() to iterate mapped column attributes.
+
+        Args:
+            exclude: Optional set of column keys to omit.
+
+        Returns:
+            Dict of {column_key: value} for all mapped columns.
+        """
+        exclude = exclude or set()
+        return {c.key: getattr(self, c.key) for c in sa_inspect(type(self)).mapper.column_attrs if c.key not in exclude}
+
+    def __repr__(self) -> str:
+        cols = ", ".join(f"{c.key}={getattr(self, c.key)!r}" for c in sa_inspect(type(self)).mapper.column_attrs)
+        return f"{type(self).__name__}({cols})"

backend/packages/harness/deerflow/persistence/engine.py

@@ -0,0 +1,190 @@
+"""Async SQLAlchemy engine lifecycle management.
+
+Initializes at Gateway startup, provides session factory for
+repositories, disposes at shutdown.
+
+When database.backend="memory", init_engine is a no-op and
+get_session_factory() returns None. Repositories must check for
+None and fall back to in-memory implementations.
+"""
+
+from __future__ import annotations
+
+import json
+import logging
+
+from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession, async_sessionmaker, create_async_engine
+
+
+def _json_serializer(obj: object) -> str:
+    """JSON serializer with ensure_ascii=False for Chinese character support."""
+    return json.dumps(obj, ensure_ascii=False)
+
+
+logger = logging.getLogger(__name__)
+
+_engine: AsyncEngine | None = None
+_session_factory: async_sessionmaker[AsyncSession] | None = None
+
+
+async def _auto_create_postgres_db(url: str) -> None:
+    """Connect to the ``postgres`` maintenance DB and CREATE DATABASE.
+
+    The target database name is extracted from *url*.  The connection is
+    made to the default ``postgres`` database on the same server using
+    ``AUTOCOMMIT`` isolation (CREATE DATABASE cannot run inside a
+    transaction).
+    """
+    from sqlalchemy import text
+    from sqlalchemy.engine.url import make_url
+
+    parsed = make_url(url)
+    db_name = parsed.database
+    if not db_name:
+        raise ValueError("Cannot auto-create database: no database name in URL")
+
+    # Connect to the default 'postgres' database to issue CREATE DATABASE
+    maint_url = parsed.set(database="postgres")
+    maint_engine = create_async_engine(maint_url, isolation_level="AUTOCOMMIT")
+    try:
+        async with maint_engine.connect() as conn:
+            await conn.execute(text(f'CREATE DATABASE "{db_name}"'))
+        logger.info("Auto-created PostgreSQL database: %s", db_name)
+    finally:
+        await maint_engine.dispose()
+
+
+async def init_engine(
+    backend: str,
+    *,
+    url: str = "",
+    echo: bool = False,
+    pool_size: int = 5,
+    sqlite_dir: str = "",
+) -> None:
+    """Create the async engine and session factory, then auto-create tables.
+
+    Args:
+        backend: "memory", "sqlite", or "postgres".
+        url: SQLAlchemy async URL (for sqlite/postgres).
+        echo: Echo SQL to log.
+        pool_size: Postgres connection pool size.
+        sqlite_dir: Directory to create for SQLite (ensured to exist).
+    """
+    global _engine, _session_factory
+
+    if backend == "memory":
+        logger.info("Persistence backend=memory -- ORM engine not initialized")
+        return
+
+    if backend == "postgres":
+        try:
+            import asyncpg  # noqa: F401
+        except ImportError:
+            raise ImportError("database.backend is set to 'postgres' but asyncpg is not installed.\nInstall it with:\n    uv sync --extra postgres\nOr switch to backend: sqlite in config.yaml for single-node deployment.") from None
+
+    if backend == "sqlite":
+        import os
+
+        from sqlalchemy import event
+
+        os.makedirs(sqlite_dir or ".", exist_ok=True)
+        _engine = create_async_engine(url, echo=echo, json_serializer=_json_serializer)
+
+        # Enable WAL on every new connection. SQLite PRAGMA settings are
+        # per-connection, so we wire the listener instead of running PRAGMA
+        # once at startup. WAL gives concurrent reads + writers without
+        # blocking and is the standard recommendation for any production
+        # SQLite deployment (TC-UPG-06 in AUTH_TEST_PLAN.md). The companion
+        # ``synchronous=NORMAL`` is the safe-and-fast pairing — fsync only
+        # at WAL checkpoint boundaries instead of every commit.
+        # Note: we do not set PRAGMA busy_timeout here — Python's sqlite3
+        # driver already defaults to a 5-second busy timeout (see the
+        # ``timeout`` kwarg of ``sqlite3.connect``), and aiosqlite /
+        # SQLAlchemy's aiosqlite dialect inherit that default.  Setting
+        # it again would be a no-op.
+        @event.listens_for(_engine.sync_engine, "connect")
+        def _enable_sqlite_wal(dbapi_conn, _record):  # noqa: ARG001 — SQLAlchemy contract
+            cursor = dbapi_conn.cursor()
+            try:
+                cursor.execute("PRAGMA journal_mode=WAL;")
+                cursor.execute("PRAGMA synchronous=NORMAL;")
+                cursor.execute("PRAGMA foreign_keys=ON;")
+            finally:
+                cursor.close()
+    elif backend == "postgres":
+        _engine = create_async_engine(
+            url,
+            echo=echo,
+            pool_size=pool_size,
+            pool_pre_ping=True,
+            json_serializer=_json_serializer,
+        )
+    else:
+        raise ValueError(f"Unknown persistence backend: {backend!r}")
+
+    _session_factory = async_sessionmaker(_engine, expire_on_commit=False)
+
+    # Auto-create tables (dev convenience). Production should use Alembic.
+    from deerflow.persistence.base import Base
+
+    # Import all models so Base.metadata discovers them.
+    # When no models exist yet (scaffolding phase), this is a no-op.
+    try:
+        import deerflow.persistence.models  # noqa: F401
+    except ImportError:
+        # Models package not yet available — tables won't be auto-created.
+        # This is expected during initial scaffolding or minimal installs.
+        logger.debug("deerflow.persistence.models not found; skipping auto-create tables")
+
+    try:
+        async with _engine.begin() as conn:
+            await conn.run_sync(Base.metadata.create_all)
+    except Exception as exc:
+        if backend == "postgres" and "does not exist" in str(exc):
+            # Database not yet created — attempt to auto-create it, then retry.
+            await _auto_create_postgres_db(url)
+            # Rebuild engine against the now-existing database
+            await _engine.dispose()
+            _engine = create_async_engine(url, echo=echo, pool_size=pool_size, pool_pre_ping=True, json_serializer=_json_serializer)
+            _session_factory = async_sessionmaker(_engine, expire_on_commit=False)
+            async with _engine.begin() as conn:
+                await conn.run_sync(Base.metadata.create_all)
+        else:
+            raise
+
+    logger.info("Persistence engine initialized: backend=%s", backend)
+
+
+async def init_engine_from_config(config) -> None:
+    """Convenience: init engine from a DatabaseConfig object."""
+    if config.backend == "memory":
+        await init_engine("memory")
+        return
+    await init_engine(
+        backend=config.backend,
+        url=config.app_sqlalchemy_url,
+        echo=config.echo_sql,
+        pool_size=config.pool_size,
+        sqlite_dir=config.sqlite_dir if config.backend == "sqlite" else "",
+    )
+
+
+def get_session_factory() -> async_sessionmaker[AsyncSession] | None:
+    """Return the async session factory, or None if backend=memory."""
+    return _session_factory
+
+
+def get_engine() -> AsyncEngine | None:
+    """Return the async engine, or None if not initialized."""
+    return _engine
+
+
+async def close_engine() -> None:
+    """Dispose the engine, release all connections."""
+    global _engine, _session_factory
+    if _engine is not None:
+        await _engine.dispose()
+        logger.info("Persistence engine closed")
+    _engine = None
+    _session_factory = None

backend/packages/harness/deerflow/persistence/feedback/__init__.py

@@ -0,0 +1,6 @@
+"""Feedback persistence — ORM and SQL repository."""
+
+from deerflow.persistence.feedback.model import FeedbackRow
+from deerflow.persistence.feedback.sql import FeedbackRepository
+
+__all__ = ["FeedbackRepository", "FeedbackRow"]

backend/packages/harness/deerflow/persistence/feedback/model.py

@@ -0,0 +1,34 @@
+"""ORM model for user feedback on runs."""
+
+from __future__ import annotations
+
+from datetime import UTC, datetime
+
+from sqlalchemy import DateTime, String, Text, UniqueConstraint
+from sqlalchemy.orm import Mapped, mapped_column
+
+from deerflow.persistence.base import Base
+
+
+class FeedbackRow(Base):
+    __tablename__ = "feedback"
+
+    __table_args__ = (
+        UniqueConstraint("thread_id", "run_id", "user_id", name="uq_feedback_thread_run_user"),
+    )
+
+    feedback_id: Mapped[str] = mapped_column(String(64), primary_key=True)
+    run_id: Mapped[str] = mapped_column(String(64), nullable=False, index=True)
+    thread_id: Mapped[str] = mapped_column(String(64), nullable=False, index=True)
+    user_id: Mapped[str | None] = mapped_column(String(64), index=True)
+    message_id: Mapped[str | None] = mapped_column(String(64))
+    # message_id is an optional RunEventStore event identifier —
+    # allows feedback to target a specific message or the entire run
+
+    rating: Mapped[int] = mapped_column(nullable=False)
+    # +1 (thumbs-up) or -1 (thumbs-down)
+
+    comment: Mapped[str | None] = mapped_column(Text)
+    # Optional text feedback from the user
+
+    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC))

backend/packages/harness/deerflow/persistence/feedback/sql.py

@@ -0,0 +1,217 @@
+"""SQLAlchemy-backed feedback storage.
+
+Each method acquires its own short-lived session.
+"""
+
+from __future__ import annotations
+
+import uuid
+from datetime import UTC, datetime
+
+from sqlalchemy import case, func, select
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
+from deerflow.persistence.feedback.model import FeedbackRow
+from deerflow.runtime.user_context import AUTO, _AutoSentinel, resolve_user_id
+
+
+class FeedbackRepository:
+    def __init__(self, session_factory: async_sessionmaker[AsyncSession]) -> None:
+        self._sf = session_factory
+
+    @staticmethod
+    def _row_to_dict(row: FeedbackRow) -> dict:
+        d = row.to_dict()
+        val = d.get("created_at")
+        if isinstance(val, datetime):
+            d["created_at"] = val.isoformat()
+        return d
+
+    async def create(
+        self,
+        *,
+        run_id: str,
+        thread_id: str,
+        rating: int,
+        user_id: str | None | _AutoSentinel = AUTO,
+        message_id: str | None = None,
+        comment: str | None = None,
+    ) -> dict:
+        """Create a feedback record. rating must be +1 or -1."""
+        if rating not in (1, -1):
+            raise ValueError(f"rating must be +1 or -1, got {rating}")
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.create")
+        row = FeedbackRow(
+            feedback_id=str(uuid.uuid4()),
+            run_id=run_id,
+            thread_id=thread_id,
+            user_id=resolved_user_id,
+            message_id=message_id,
+            rating=rating,
+            comment=comment,
+            created_at=datetime.now(UTC),
+        )
+        async with self._sf() as session:
+            session.add(row)
+            await session.commit()
+            await session.refresh(row)
+            return self._row_to_dict(row)
+
+    async def get(
+        self,
+        feedback_id: str,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> dict | None:
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.get")
+        async with self._sf() as session:
+            row = await session.get(FeedbackRow, feedback_id)
+            if row is None:
+                return None
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
+                return None
+            return self._row_to_dict(row)
+
+    async def list_by_run(
+        self,
+        thread_id: str,
+        run_id: str,
+        *,
+        limit: int = 100,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> list[dict]:
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.list_by_run")
+        stmt = select(FeedbackRow).where(FeedbackRow.thread_id == thread_id, FeedbackRow.run_id == run_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(FeedbackRow.user_id == resolved_user_id)
+        stmt = stmt.order_by(FeedbackRow.created_at.asc()).limit(limit)
+        async with self._sf() as session:
+            result = await session.execute(stmt)
+            return [self._row_to_dict(r) for r in result.scalars()]
+
+    async def list_by_thread(
+        self,
+        thread_id: str,
+        *,
+        limit: int = 100,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> list[dict]:
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.list_by_thread")
+        stmt = select(FeedbackRow).where(FeedbackRow.thread_id == thread_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(FeedbackRow.user_id == resolved_user_id)
+        stmt = stmt.order_by(FeedbackRow.created_at.asc()).limit(limit)
+        async with self._sf() as session:
+            result = await session.execute(stmt)
+            return [self._row_to_dict(r) for r in result.scalars()]
+
+    async def delete(
+        self,
+        feedback_id: str,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> bool:
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.delete")
+        async with self._sf() as session:
+            row = await session.get(FeedbackRow, feedback_id)
+            if row is None:
+                return False
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
+                return False
+            await session.delete(row)
+            await session.commit()
+            return True
+
+    async def upsert(
+        self,
+        *,
+        run_id: str,
+        thread_id: str,
+        rating: int,
+        user_id: str | None | _AutoSentinel = AUTO,
+        comment: str | None = None,
+    ) -> dict:
+        """Create or update feedback for (thread_id, run_id, user_id). rating must be +1 or -1."""
+        if rating not in (1, -1):
+            raise ValueError(f"rating must be +1 or -1, got {rating}")
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.upsert")
+        async with self._sf() as session:
+            stmt = select(FeedbackRow).where(
+                FeedbackRow.thread_id == thread_id,
+                FeedbackRow.run_id == run_id,
+                FeedbackRow.user_id == resolved_user_id,
+            )
+            result = await session.execute(stmt)
+            row = result.scalar_one_or_none()
+            if row is not None:
+                row.rating = rating
+                row.comment = comment
+                row.created_at = datetime.now(UTC)
+            else:
+                row = FeedbackRow(
+                    feedback_id=str(uuid.uuid4()),
+                    run_id=run_id,
+                    thread_id=thread_id,
+                    user_id=resolved_user_id,
+                    rating=rating,
+                    comment=comment,
+                    created_at=datetime.now(UTC),
+                )
+                session.add(row)
+            await session.commit()
+            await session.refresh(row)
+            return self._row_to_dict(row)
+
+    async def delete_by_run(
+        self,
+        *,
+        thread_id: str,
+        run_id: str,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> bool:
+        """Delete the current user's feedback for a run. Returns True if a record was deleted."""
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.delete_by_run")
+        async with self._sf() as session:
+            stmt = select(FeedbackRow).where(
+                FeedbackRow.thread_id == thread_id,
+                FeedbackRow.run_id == run_id,
+                FeedbackRow.user_id == resolved_user_id,
+            )
+            result = await session.execute(stmt)
+            row = result.scalar_one_or_none()
+            if row is None:
+                return False
+            await session.delete(row)
+            await session.commit()
+            return True
+
+    async def list_by_thread_grouped(
+        self,
+        thread_id: str,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> dict[str, dict]:
+        """Return feedback grouped by run_id for a thread: {run_id: feedback_dict}."""
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.list_by_thread_grouped")
+        stmt = select(FeedbackRow).where(FeedbackRow.thread_id == thread_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(FeedbackRow.user_id == resolved_user_id)
+        async with self._sf() as session:
+            result = await session.execute(stmt)
+            return {row.run_id: self._row_to_dict(row) for row in result.scalars()}
+
+    async def aggregate_by_run(self, thread_id: str, run_id: str) -> dict:
+        """Aggregate feedback stats for a run using database-side counting."""
+        stmt = select(
+            func.count().label("total"),
+            func.coalesce(func.sum(case((FeedbackRow.rating == 1, 1), else_=0)), 0).label("positive"),
+            func.coalesce(func.sum(case((FeedbackRow.rating == -1, 1), else_=0)), 0).label("negative"),
+        ).where(FeedbackRow.thread_id == thread_id, FeedbackRow.run_id == run_id)
+        async with self._sf() as session:
+            row = (await session.execute(stmt)).one()
+            return {
+                "run_id": run_id,
+                "total": row.total,
+                "positive": row.positive,
+                "negative": row.negative,
+            }

backend/packages/harness/deerflow/persistence/migrations/alembic.ini

@@ -0,0 +1,38 @@
+[alembic]
+script_location = %(here)s
+# Default URL for offline mode / autogenerate.
+# Runtime uses engine from DeerFlow config.
+sqlalchemy.url = sqlite+aiosqlite:///./data/deerflow.db
+
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

backend/packages/harness/deerflow/persistence/migrations/env.py

@@ -0,0 +1,65 @@
+"""Alembic environment for DeerFlow application tables.
+
+ONLY manages DeerFlow's tables (runs, threads_meta, cron_jobs, users).
+LangGraph's checkpointer tables are managed by LangGraph itself -- they
+have their own schema lifecycle and must not be touched by Alembic.
+"""
+
+from __future__ import annotations
+
+import asyncio
+import logging
+from logging.config import fileConfig
+
+from alembic import context
+from sqlalchemy.ext.asyncio import create_async_engine
+
+from deerflow.persistence.base import Base
+
+# Import all models so metadata is populated.
+try:
+    import deerflow.persistence.models  # noqa: F401 — register ORM models with Base.metadata
+except ImportError:
+    # Models not available — migration will work with existing metadata only.
+    logging.getLogger(__name__).warning("Could not import deerflow.persistence.models; Alembic may not detect all tables")
+
+config = context.config
+if config.config_file_name is not None:
+    fileConfig(config.config_file_name)
+
+target_metadata = Base.metadata
+
+
+def run_migrations_offline() -> None:
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        render_as_batch=True,
+    )
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def do_run_migrations(connection):
+    context.configure(
+        connection=connection,
+        target_metadata=target_metadata,
+        render_as_batch=True,  # Required for SQLite ALTER TABLE support
+    )
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+async def run_migrations_online() -> None:
+    connectable = create_async_engine(config.get_main_option("sqlalchemy.url"))
+    async with connectable.connect() as connection:
+        await connection.run_sync(do_run_migrations)
+    await connectable.dispose()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    asyncio.run(run_migrations_online())

backend/packages/harness/deerflow/persistence/models/__init__.py

@@ -0,0 +1,23 @@
+"""ORM model registration entry point.
+
+Importing this module ensures all ORM models are registered with
+``Base.metadata`` so Alembic autogenerate detects every table.
+
+The actual ORM classes have moved to entity-specific subpackages:
+- ``deerflow.persistence.thread_meta``
+- ``deerflow.persistence.run``
+- ``deerflow.persistence.feedback``
+- ``deerflow.persistence.user``
+
+``RunEventRow`` remains in ``deerflow.persistence.models.run_event`` because
+its storage implementation lives in ``deerflow.runtime.events.store.db`` and
+there is no matching entity directory.
+"""
+
+from deerflow.persistence.feedback.model import FeedbackRow
+from deerflow.persistence.models.run_event import RunEventRow
+from deerflow.persistence.run.model import RunRow
+from deerflow.persistence.thread_meta.model import ThreadMetaRow
+from deerflow.persistence.user.model import UserRow
+
+__all__ = ["FeedbackRow", "RunEventRow", "RunRow", "ThreadMetaRow", "UserRow"]

backend/packages/harness/deerflow/persistence/models/run_event.py

@@ -0,0 +1,35 @@
+"""ORM model for run events."""
+
+from __future__ import annotations
+
+from datetime import UTC, datetime
+
+from sqlalchemy import JSON, DateTime, Index, String, Text, UniqueConstraint
+from sqlalchemy.orm import Mapped, mapped_column
+
+from deerflow.persistence.base import Base
+
+
+class RunEventRow(Base):
+    __tablename__ = "run_events"
+
+    id: Mapped[int] = mapped_column(primary_key=True, autoincrement=True)
+    thread_id: Mapped[str] = mapped_column(String(64), nullable=False)
+    run_id: Mapped[str] = mapped_column(String(64), nullable=False)
+    # Owner of the conversation this event belongs to. Nullable for data
+    # created before auth was introduced; populated by auth middleware on
+    # new writes and by the boot-time orphan migration on existing rows.
+    user_id: Mapped[str | None] = mapped_column(String(64), nullable=True, index=True)
+    event_type: Mapped[str] = mapped_column(String(32), nullable=False)
+    category: Mapped[str] = mapped_column(String(16), nullable=False)
+    # "message" | "trace" | "lifecycle"
+    content: Mapped[str] = mapped_column(Text, default="")
+    event_metadata: Mapped[dict] = mapped_column(JSON, default=dict)
+    seq: Mapped[int] = mapped_column(nullable=False)
+    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC))
+
+    __table_args__ = (
+        UniqueConstraint("thread_id", "seq", name="uq_events_thread_seq"),
+        Index("ix_events_thread_cat_seq", "thread_id", "category", "seq"),
+        Index("ix_events_run", "thread_id", "run_id", "seq"),
+    )

backend/packages/harness/deerflow/persistence/run/__init__.py

@@ -0,0 +1,6 @@
+"""Run metadata persistence — ORM and SQL repository."""
+
+from deerflow.persistence.run.model import RunRow
+from deerflow.persistence.run.sql import RunRepository
+
+__all__ = ["RunRepository", "RunRow"]

backend/packages/harness/deerflow/persistence/run/model.py

@@ -0,0 +1,49 @@
+"""ORM model for run metadata."""
+
+from __future__ import annotations
+
+from datetime import UTC, datetime
+
+from sqlalchemy import JSON, DateTime, Index, String, Text
+from sqlalchemy.orm import Mapped, mapped_column
+
+from deerflow.persistence.base import Base
+
+
+class RunRow(Base):
+    __tablename__ = "runs"
+
+    run_id: Mapped[str] = mapped_column(String(64), primary_key=True)
+    thread_id: Mapped[str] = mapped_column(String(64), nullable=False, index=True)
+    assistant_id: Mapped[str | None] = mapped_column(String(128))
+    user_id: Mapped[str | None] = mapped_column(String(64), index=True)
+    status: Mapped[str] = mapped_column(String(20), default="pending")
+    # "pending" | "running" | "success" | "error" | "timeout" | "interrupted"
+
+    model_name: Mapped[str | None] = mapped_column(String(128))
+    multitask_strategy: Mapped[str] = mapped_column(String(20), default="reject")
+    metadata_json: Mapped[dict] = mapped_column(JSON, default=dict)
+    kwargs_json: Mapped[dict] = mapped_column(JSON, default=dict)
+    error: Mapped[str | None] = mapped_column(Text)
+
+    # Convenience fields (for listing pages without querying RunEventStore)
+    message_count: Mapped[int] = mapped_column(default=0)
+    first_human_message: Mapped[str | None] = mapped_column(Text)
+    last_ai_message: Mapped[str | None] = mapped_column(Text)
+
+    # Token usage (accumulated in-memory by RunJournal, written on run completion)
+    total_input_tokens: Mapped[int] = mapped_column(default=0)
+    total_output_tokens: Mapped[int] = mapped_column(default=0)
+    total_tokens: Mapped[int] = mapped_column(default=0)
+    llm_call_count: Mapped[int] = mapped_column(default=0)
+    lead_agent_tokens: Mapped[int] = mapped_column(default=0)
+    subagent_tokens: Mapped[int] = mapped_column(default=0)
+    middleware_tokens: Mapped[int] = mapped_column(default=0)
+
+    # Follow-up association
+    follow_up_to_run_id: Mapped[str | None] = mapped_column(String(64))
+
+    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC))
+    updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC), onupdate=lambda: datetime.now(UTC))
+
+    __table_args__ = (Index("ix_runs_thread_status", "thread_id", "status"),)

backend/packages/harness/deerflow/persistence/run/sql.py

@@ -0,0 +1,255 @@
+"""SQLAlchemy-backed RunStore implementation.
+
+Each method acquires and releases its own short-lived session.
+Run status updates happen from background workers that may live
+minutes -- we don't hold connections across long execution.
+"""
+
+from __future__ import annotations
+
+import json
+from datetime import UTC, datetime
+from typing import Any
+
+from sqlalchemy import func, select, update
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
+from deerflow.persistence.run.model import RunRow
+from deerflow.runtime.runs.store.base import RunStore
+from deerflow.runtime.user_context import AUTO, _AutoSentinel, resolve_user_id
+
+
+class RunRepository(RunStore):
+    def __init__(self, session_factory: async_sessionmaker[AsyncSession]) -> None:
+        self._sf = session_factory
+
+    @staticmethod
+    def _safe_json(obj: Any) -> Any:
+        """Ensure obj is JSON-serializable. Falls back to model_dump() or str()."""
+        if obj is None:
+            return None
+        if isinstance(obj, (str, int, float, bool)):
+            return obj
+        if isinstance(obj, dict):
+            return {k: RunRepository._safe_json(v) for k, v in obj.items()}
+        if isinstance(obj, (list, tuple)):
+            return [RunRepository._safe_json(v) for v in obj]
+        if hasattr(obj, "model_dump"):
+            try:
+                return obj.model_dump()
+            except Exception:
+                pass
+        if hasattr(obj, "dict"):
+            try:
+                return obj.dict()
+            except Exception:
+                pass
+        try:
+            json.dumps(obj)
+            return obj
+        except (TypeError, ValueError):
+            return str(obj)
+
+    @staticmethod
+    def _row_to_dict(row: RunRow) -> dict[str, Any]:
+        d = row.to_dict()
+        # Remap JSON columns to match RunStore interface
+        d["metadata"] = d.pop("metadata_json", {})
+        d["kwargs"] = d.pop("kwargs_json", {})
+        # Convert datetime to ISO string for consistency with MemoryRunStore
+        for key in ("created_at", "updated_at"):
+            val = d.get(key)
+            if isinstance(val, datetime):
+                d[key] = val.isoformat()
+        return d
+
+    async def put(
+        self,
+        run_id,
+        *,
+        thread_id,
+        assistant_id=None,
+        user_id: str | None | _AutoSentinel = AUTO,
+        status="pending",
+        multitask_strategy="reject",
+        metadata=None,
+        kwargs=None,
+        error=None,
+        created_at=None,
+        follow_up_to_run_id=None,
+    ):
+        resolved_user_id = resolve_user_id(user_id, method_name="RunRepository.put")
+        now = datetime.now(UTC)
+        row = RunRow(
+            run_id=run_id,
+            thread_id=thread_id,
+            assistant_id=assistant_id,
+            user_id=resolved_user_id,
+            status=status,
+            multitask_strategy=multitask_strategy,
+            metadata_json=self._safe_json(metadata) or {},
+            kwargs_json=self._safe_json(kwargs) or {},
+            error=error,
+            follow_up_to_run_id=follow_up_to_run_id,
+            created_at=datetime.fromisoformat(created_at) if created_at else now,
+            updated_at=now,
+        )
+        async with self._sf() as session:
+            session.add(row)
+            await session.commit()
+
+    async def get(
+        self,
+        run_id,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ):
+        resolved_user_id = resolve_user_id(user_id, method_name="RunRepository.get")
+        async with self._sf() as session:
+            row = await session.get(RunRow, run_id)
+            if row is None:
+                return None
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
+                return None
+            return self._row_to_dict(row)
+
+    async def list_by_thread(
+        self,
+        thread_id,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+        limit=100,
+    ):
+        resolved_user_id = resolve_user_id(user_id, method_name="RunRepository.list_by_thread")
+        stmt = select(RunRow).where(RunRow.thread_id == thread_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(RunRow.user_id == resolved_user_id)
+        stmt = stmt.order_by(RunRow.created_at.desc()).limit(limit)
+        async with self._sf() as session:
+            result = await session.execute(stmt)
+            return [self._row_to_dict(r) for r in result.scalars()]
+
+    async def update_status(self, run_id, status, *, error=None):
+        values: dict[str, Any] = {"status": status, "updated_at": datetime.now(UTC)}
+        if error is not None:
+            values["error"] = error
+        async with self._sf() as session:
+            await session.execute(update(RunRow).where(RunRow.run_id == run_id).values(**values))
+            await session.commit()
+
+    async def delete(
+        self,
+        run_id,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ):
+        resolved_user_id = resolve_user_id(user_id, method_name="RunRepository.delete")
+        async with self._sf() as session:
+            row = await session.get(RunRow, run_id)
+            if row is None:
+                return
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
+                return
+            await session.delete(row)
+            await session.commit()
+
+    async def list_pending(self, *, before=None):
+        if before is None:
+            before_dt = datetime.now(UTC)
+        elif isinstance(before, datetime):
+            before_dt = before
+        else:
+            before_dt = datetime.fromisoformat(before)
+        stmt = select(RunRow).where(RunRow.status == "pending", RunRow.created_at <= before_dt).order_by(RunRow.created_at.asc())
+        async with self._sf() as session:
+            result = await session.execute(stmt)
+            return [self._row_to_dict(r) for r in result.scalars()]
+
+    async def update_run_completion(
+        self,
+        run_id: str,
+        *,
+        status: str,
+        total_input_tokens: int = 0,
+        total_output_tokens: int = 0,
+        total_tokens: int = 0,
+        llm_call_count: int = 0,
+        lead_agent_tokens: int = 0,
+        subagent_tokens: int = 0,
+        middleware_tokens: int = 0,
+        message_count: int = 0,
+        last_ai_message: str | None = None,
+        first_human_message: str | None = None,
+        error: str | None = None,
+    ) -> None:
+        """Update status + token usage + convenience fields on run completion."""
+        values: dict[str, Any] = {
+            "status": status,
+            "total_input_tokens": total_input_tokens,
+            "total_output_tokens": total_output_tokens,
+            "total_tokens": total_tokens,
+            "llm_call_count": llm_call_count,
+            "lead_agent_tokens": lead_agent_tokens,
+            "subagent_tokens": subagent_tokens,
+            "middleware_tokens": middleware_tokens,
+            "message_count": message_count,
+            "updated_at": datetime.now(UTC),
+        }
+        if last_ai_message is not None:
+            values["last_ai_message"] = last_ai_message[:2000]
+        if first_human_message is not None:
+            values["first_human_message"] = first_human_message[:2000]
+        if error is not None:
+            values["error"] = error
+        async with self._sf() as session:
+            await session.execute(update(RunRow).where(RunRow.run_id == run_id).values(**values))
+            await session.commit()
+
+    async def aggregate_tokens_by_thread(self, thread_id: str) -> dict[str, Any]:
+        """Aggregate token usage via a single SQL GROUP BY query."""
+        _completed = RunRow.status.in_(("success", "error"))
+        _thread = RunRow.thread_id == thread_id
+
+        stmt = (
+            select(
+                func.coalesce(RunRow.model_name, "unknown").label("model"),
+                func.count().label("runs"),
+                func.coalesce(func.sum(RunRow.total_tokens), 0).label("total_tokens"),
+                func.coalesce(func.sum(RunRow.total_input_tokens), 0).label("total_input_tokens"),
+                func.coalesce(func.sum(RunRow.total_output_tokens), 0).label("total_output_tokens"),
+                func.coalesce(func.sum(RunRow.lead_agent_tokens), 0).label("lead_agent"),
+                func.coalesce(func.sum(RunRow.subagent_tokens), 0).label("subagent"),
+                func.coalesce(func.sum(RunRow.middleware_tokens), 0).label("middleware"),
+            )
+            .where(_thread, _completed)
+            .group_by(func.coalesce(RunRow.model_name, "unknown"))
+        )
+
+        async with self._sf() as session:
+            rows = (await session.execute(stmt)).all()
+
+        total_tokens = total_input = total_output = total_runs = 0
+        lead_agent = subagent = middleware = 0
+        by_model: dict[str, dict] = {}
+        for r in rows:
+            by_model[r.model] = {"tokens": r.total_tokens, "runs": r.runs}
+            total_tokens += r.total_tokens
+            total_input += r.total_input_tokens
+            total_output += r.total_output_tokens
+            total_runs += r.runs
+            lead_agent += r.lead_agent
+            subagent += r.subagent
+            middleware += r.middleware
+
+        return {
+            "total_tokens": total_tokens,
+            "total_input_tokens": total_input,
+            "total_output_tokens": total_output,
+            "total_runs": total_runs,
+            "by_model": by_model,
+            "by_caller": {
+                "lead_agent": lead_agent,
+                "subagent": subagent,
+                "middleware": middleware,
+            },
+        }

backend/packages/harness/deerflow/persistence/thread_meta/__init__.py

@@ -0,0 +1,38 @@
+"""Thread metadata persistence — ORM, abstract store, and concrete implementations."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from deerflow.persistence.thread_meta.base import ThreadMetaStore
+from deerflow.persistence.thread_meta.memory import MemoryThreadMetaStore
+from deerflow.persistence.thread_meta.model import ThreadMetaRow
+from deerflow.persistence.thread_meta.sql import ThreadMetaRepository
+
+if TYPE_CHECKING:
+    from langgraph.store.base import BaseStore
+    from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
+__all__ = [
+    "MemoryThreadMetaStore",
+    "ThreadMetaRepository",
+    "ThreadMetaRow",
+    "ThreadMetaStore",
+    "make_thread_store",
+]
+
+
+def make_thread_store(
+    session_factory: async_sessionmaker[AsyncSession] | None,
+    store: BaseStore | None = None,
+) -> ThreadMetaStore:
+    """Create the appropriate ThreadMetaStore based on available backends.
+
+    Returns a SQL-backed repository when a session factory is available,
+    otherwise falls back to the in-memory LangGraph Store implementation.
+    """
+    if session_factory is not None:
+        return ThreadMetaRepository(session_factory)
+    if store is None:
+        raise ValueError("make_thread_store requires either a session_factory (SQL) or a store (memory)")
+    return MemoryThreadMetaStore(store)

backend/packages/harness/deerflow/persistence/thread_meta/base.py

@@ -0,0 +1,76 @@
+"""Abstract interface for thread metadata storage.
+
+Implementations:
+- ThreadMetaRepository: SQL-backed (sqlite / postgres via SQLAlchemy)
+- MemoryThreadMetaStore: wraps LangGraph BaseStore (memory mode)
+
+All mutating and querying methods accept a ``user_id`` parameter with
+three-state semantics (see :mod:`deerflow.runtime.user_context`):
+
+- ``AUTO`` (default): resolve from the request-scoped contextvar.
+- Explicit ``str``: use the provided value verbatim.
+- Explicit ``None``: bypass owner filtering (migration/CLI only).
+"""
+
+from __future__ import annotations
+
+import abc
+
+from deerflow.runtime.user_context import AUTO, _AutoSentinel
+
+
+class ThreadMetaStore(abc.ABC):
+    @abc.abstractmethod
+    async def create(
+        self,
+        thread_id: str,
+        *,
+        assistant_id: str | None = None,
+        user_id: str | None | _AutoSentinel = AUTO,
+        display_name: str | None = None,
+        metadata: dict | None = None,
+    ) -> dict:
+        pass
+
+    @abc.abstractmethod
+    async def get(self, thread_id: str, *, user_id: str | None | _AutoSentinel = AUTO) -> dict | None:
+        pass
+
+    @abc.abstractmethod
+    async def search(
+        self,
+        *,
+        metadata: dict | None = None,
+        status: str | None = None,
+        limit: int = 100,
+        offset: int = 0,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> list[dict]:
+        pass
+
+    @abc.abstractmethod
+    async def update_display_name(self, thread_id: str, display_name: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
+        pass
+
+    @abc.abstractmethod
+    async def update_status(self, thread_id: str, status: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
+        pass
+
+    @abc.abstractmethod
+    async def update_metadata(self, thread_id: str, metadata: dict, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
+        """Merge ``metadata`` into the thread's metadata field.
+
+        Existing keys are overwritten by the new values; keys absent from
+        ``metadata`` are preserved. No-op if the thread does not exist
+        or the owner check fails.
+        """
+        pass
+
+    @abc.abstractmethod
+    async def check_access(self, thread_id: str, user_id: str, *, require_existing: bool = False) -> bool:
+        """Check if ``user_id`` has access to ``thread_id``."""
+        pass
+
+    @abc.abstractmethod
+    async def delete(self, thread_id: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
+        pass

backend/packages/harness/deerflow/persistence/thread_meta/memory.py

@@ -0,0 +1,149 @@
+"""In-memory ThreadMetaStore backed by LangGraph BaseStore.
+
+Used when database.backend=memory. Delegates to the LangGraph Store's
+``("threads",)`` namespace — the same namespace used by the Gateway
+router for thread records.
+"""
+
+from __future__ import annotations
+
+import time
+from typing import Any
+
+from langgraph.store.base import BaseStore
+
+from deerflow.persistence.thread_meta.base import ThreadMetaStore
+from deerflow.runtime.user_context import AUTO, _AutoSentinel, resolve_user_id
+
+THREADS_NS: tuple[str, ...] = ("threads",)
+
+
+class MemoryThreadMetaStore(ThreadMetaStore):
+    def __init__(self, store: BaseStore) -> None:
+        self._store = store
+
+    async def _get_owned_record(
+        self,
+        thread_id: str,
+        user_id: str | None | _AutoSentinel,
+        method_name: str,
+    ) -> dict | None:
+        """Fetch a record and verify ownership. Returns a mutable copy, or None."""
+        resolved = resolve_user_id(user_id, method_name=method_name)
+        item = await self._store.aget(THREADS_NS, thread_id)
+        if item is None:
+            return None
+        record = dict(item.value)
+        if resolved is not None and record.get("user_id") != resolved:
+            return None
+        return record
+
+    async def create(
+        self,
+        thread_id: str,
+        *,
+        assistant_id: str | None = None,
+        user_id: str | None | _AutoSentinel = AUTO,
+        display_name: str | None = None,
+        metadata: dict | None = None,
+    ) -> dict:
+        resolved_user_id = resolve_user_id(user_id, method_name="MemoryThreadMetaStore.create")
+        now = time.time()
+        record: dict[str, Any] = {
+            "thread_id": thread_id,
+            "assistant_id": assistant_id,
+            "user_id": resolved_user_id,
+            "display_name": display_name,
+            "status": "idle",
+            "metadata": metadata or {},
+            "values": {},
+            "created_at": now,
+            "updated_at": now,
+        }
+        await self._store.aput(THREADS_NS, thread_id, record)
+        return record
+
+    async def get(self, thread_id: str, *, user_id: str | None | _AutoSentinel = AUTO) -> dict | None:
+        return await self._get_owned_record(thread_id, user_id, "MemoryThreadMetaStore.get")
+
+    async def search(
+        self,
+        *,
+        metadata: dict | None = None,
+        status: str | None = None,
+        limit: int = 100,
+        offset: int = 0,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> list[dict]:
+        resolved_user_id = resolve_user_id(user_id, method_name="MemoryThreadMetaStore.search")
+        filter_dict: dict[str, Any] = {}
+        if metadata:
+            filter_dict.update(metadata)
+        if status:
+            filter_dict["status"] = status
+        if resolved_user_id is not None:
+            filter_dict["user_id"] = resolved_user_id
+
+        items = await self._store.asearch(
+            THREADS_NS,
+            filter=filter_dict or None,
+            limit=limit,
+            offset=offset,
+        )
+        return [self._item_to_dict(item) for item in items]
+
+    async def check_access(self, thread_id: str, user_id: str, *, require_existing: bool = False) -> bool:
+        item = await self._store.aget(THREADS_NS, thread_id)
+        if item is None:
+            return not require_existing
+        record_user_id = item.value.get("user_id")
+        if record_user_id is None:
+            return True
+        return record_user_id == user_id
+
+    async def update_display_name(self, thread_id: str, display_name: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
+        record = await self._get_owned_record(thread_id, user_id, "MemoryThreadMetaStore.update_display_name")
+        if record is None:
+            return
+        record["display_name"] = display_name
+        record["updated_at"] = time.time()
+        await self._store.aput(THREADS_NS, thread_id, record)
+
+    async def update_status(self, thread_id: str, status: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
+        record = await self._get_owned_record(thread_id, user_id, "MemoryThreadMetaStore.update_status")
+        if record is None:
+            return
+        record["status"] = status
+        record["updated_at"] = time.time()
+        await self._store.aput(THREADS_NS, thread_id, record)
+
+    async def update_metadata(self, thread_id: str, metadata: dict, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
+        record = await self._get_owned_record(thread_id, user_id, "MemoryThreadMetaStore.update_metadata")
+        if record is None:
+            return
+        merged = dict(record.get("metadata") or {})
+        merged.update(metadata)
+        record["metadata"] = merged
+        record["updated_at"] = time.time()
+        await self._store.aput(THREADS_NS, thread_id, record)
+
+    async def delete(self, thread_id: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
+        record = await self._get_owned_record(thread_id, user_id, "MemoryThreadMetaStore.delete")
+        if record is None:
+            return
+        await self._store.adelete(THREADS_NS, thread_id)
+
+    @staticmethod
+    def _item_to_dict(item) -> dict[str, Any]:
+        """Convert a Store SearchItem to the dict format expected by callers."""
+        val = item.value
+        return {
+            "thread_id": item.key,
+            "assistant_id": val.get("assistant_id"),
+            "user_id": val.get("user_id"),
+            "display_name": val.get("display_name"),
+            "status": val.get("status", "idle"),
+            "metadata": val.get("metadata", {}),
+            "created_at": str(val.get("created_at", "")),
+            "updated_at": str(val.get("updated_at", "")),
+        }

backend/packages/harness/deerflow/persistence/thread_meta/model.py

@@ -0,0 +1,23 @@
+"""ORM model for thread metadata."""
+
+from __future__ import annotations
+
+from datetime import UTC, datetime
+
+from sqlalchemy import JSON, DateTime, String
+from sqlalchemy.orm import Mapped, mapped_column
+
+from deerflow.persistence.base import Base
+
+
+class ThreadMetaRow(Base):
+    __tablename__ = "threads_meta"
+
+    thread_id: Mapped[str] = mapped_column(String(64), primary_key=True)
+    assistant_id: Mapped[str | None] = mapped_column(String(128), index=True)
+    user_id: Mapped[str | None] = mapped_column(String(64), index=True)
+    display_name: Mapped[str | None] = mapped_column(String(256))
+    status: Mapped[str] = mapped_column(String(20), default="idle")
+    metadata_json: Mapped[dict] = mapped_column(JSON, default=dict)
+    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC))
+    updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC), onupdate=lambda: datetime.now(UTC))

backend/packages/harness/deerflow/persistence/thread_meta/sql.py

@@ -0,0 +1,217 @@
+"""SQLAlchemy-backed thread metadata repository."""
+
+from __future__ import annotations
+
+from datetime import UTC, datetime
+from typing import Any
+
+from sqlalchemy import select, update
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
+from deerflow.persistence.thread_meta.base import ThreadMetaStore
+from deerflow.persistence.thread_meta.model import ThreadMetaRow
+from deerflow.runtime.user_context import AUTO, _AutoSentinel, resolve_user_id
+
+
+class ThreadMetaRepository(ThreadMetaStore):
+    def __init__(self, session_factory: async_sessionmaker[AsyncSession]) -> None:
+        self._sf = session_factory
+
+    @staticmethod
+    def _row_to_dict(row: ThreadMetaRow) -> dict[str, Any]:
+        d = row.to_dict()
+        d["metadata"] = d.pop("metadata_json", {})
+        for key in ("created_at", "updated_at"):
+            val = d.get(key)
+            if isinstance(val, datetime):
+                d[key] = val.isoformat()
+        return d
+
+    async def create(
+        self,
+        thread_id: str,
+        *,
+        assistant_id: str | None = None,
+        user_id: str | None | _AutoSentinel = AUTO,
+        display_name: str | None = None,
+        metadata: dict | None = None,
+    ) -> dict:
+        # Auto-resolve user_id from contextvar when AUTO; explicit None
+        # creates an orphan row (used by migration scripts).
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.create")
+        now = datetime.now(UTC)
+        row = ThreadMetaRow(
+            thread_id=thread_id,
+            assistant_id=assistant_id,
+            user_id=resolved_user_id,
+            display_name=display_name,
+            metadata_json=metadata or {},
+            created_at=now,
+            updated_at=now,
+        )
+        async with self._sf() as session:
+            session.add(row)
+            await session.commit()
+            await session.refresh(row)
+            return self._row_to_dict(row)
+
+    async def get(
+        self,
+        thread_id: str,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> dict | None:
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.get")
+        async with self._sf() as session:
+            row = await session.get(ThreadMetaRow, thread_id)
+            if row is None:
+                return None
+            # Enforce owner filter unless explicitly bypassed (user_id=None).
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
+                return None
+            return self._row_to_dict(row)
+
+    async def check_access(self, thread_id: str, user_id: str, *, require_existing: bool = False) -> bool:
+        """Check if ``user_id`` has access to ``thread_id``.
+
+        Two modes — one row, two distinct semantics depending on what
+        the caller is about to do:
+
+        - ``require_existing=False`` (default, permissive):
+          Returns True for: row missing (untracked legacy thread),
+          ``row.user_id`` is None (shared / pre-auth data),
+          or ``row.user_id == user_id``. Use for **read-style**
+          decorators where treating an untracked thread as accessible
+          preserves backward-compat.
+
+        - ``require_existing=True`` (strict):
+          Returns True **only** when the row exists AND
+          (``row.user_id == user_id`` OR ``row.user_id is None``).
+          Use for **destructive / mutating** decorators (DELETE, PATCH,
+          state-update) so a thread that has *already been deleted*
+          cannot be re-targeted by any caller — closing the
+          delete-idempotence cross-user gap where the row vanishing
+          made every other user appear to "own" it.
+        """
+        async with self._sf() as session:
+            row = await session.get(ThreadMetaRow, thread_id)
+            if row is None:
+                return not require_existing
+            if row.user_id is None:
+                return True
+            return row.user_id == user_id
+
+    async def search(
+        self,
+        *,
+        metadata: dict | None = None,
+        status: str | None = None,
+        limit: int = 100,
+        offset: int = 0,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> list[dict]:
+        """Search threads with optional metadata and status filters.
+
+        Owner filter is enforced by default: caller must be in a user
+        context. Pass ``user_id=None`` to bypass (migration/CLI).
+        """
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.search")
+        stmt = select(ThreadMetaRow).order_by(ThreadMetaRow.updated_at.desc())
+        if resolved_user_id is not None:
+            stmt = stmt.where(ThreadMetaRow.user_id == resolved_user_id)
+        if status:
+            stmt = stmt.where(ThreadMetaRow.status == status)
+
+        if metadata:
+            # When metadata filter is active, fetch a larger window and filter
+            # in Python. TODO(Phase 2): use JSON DB operators (Postgres @>,
+            # SQLite json_extract) for server-side filtering.
+            stmt = stmt.limit(limit * 5 + offset)
+            async with self._sf() as session:
+                result = await session.execute(stmt)
+                rows = [self._row_to_dict(r) for r in result.scalars()]
+            rows = [r for r in rows if all(r.get("metadata", {}).get(k) == v for k, v in metadata.items())]
+            return rows[offset : offset + limit]
+        else:
+            stmt = stmt.limit(limit).offset(offset)
+            async with self._sf() as session:
+                result = await session.execute(stmt)
+                return [self._row_to_dict(r) for r in result.scalars()]
+
+    async def _check_ownership(self, session: AsyncSession, thread_id: str, resolved_user_id: str | None) -> bool:
+        """Return True if the row exists and is owned (or filter bypassed)."""
+        if resolved_user_id is None:
+            return True  # explicit bypass
+        row = await session.get(ThreadMetaRow, thread_id)
+        return row is not None and row.user_id == resolved_user_id
+
+    async def update_display_name(
+        self,
+        thread_id: str,
+        display_name: str,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> None:
+        """Update the display_name (title) for a thread."""
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.update_display_name")
+        async with self._sf() as session:
+            if not await self._check_ownership(session, thread_id, resolved_user_id):
+                return
+            await session.execute(update(ThreadMetaRow).where(ThreadMetaRow.thread_id == thread_id).values(display_name=display_name, updated_at=datetime.now(UTC)))
+            await session.commit()
+
+    async def update_status(
+        self,
+        thread_id: str,
+        status: str,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> None:
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.update_status")
+        async with self._sf() as session:
+            if not await self._check_ownership(session, thread_id, resolved_user_id):
+                return
+            await session.execute(update(ThreadMetaRow).where(ThreadMetaRow.thread_id == thread_id).values(status=status, updated_at=datetime.now(UTC)))
+            await session.commit()
+
+    async def update_metadata(
+        self,
+        thread_id: str,
+        metadata: dict,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> None:
+        """Merge ``metadata`` into ``metadata_json``.
+
+        Read-modify-write inside a single session/transaction so concurrent
+        callers see consistent state. No-op if the row does not exist or
+        the user_id check fails.
+        """
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.update_metadata")
+        async with self._sf() as session:
+            row = await session.get(ThreadMetaRow, thread_id)
+            if row is None:
+                return
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
+                return
+            merged = dict(row.metadata_json or {})
+            merged.update(metadata)
+            row.metadata_json = merged
+            row.updated_at = datetime.now(UTC)
+            await session.commit()
+
+    async def delete(
+        self,
+        thread_id: str,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> None:
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.delete")
+        async with self._sf() as session:
+            row = await session.get(ThreadMetaRow, thread_id)
+            if row is None:
+                return
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
+                return
+            await session.delete(row)
+            await session.commit()

backend/packages/harness/deerflow/persistence/user/__init__.py

@@ -0,0 +1,12 @@
+"""User storage subpackage.
+
+Holds the ORM model for the ``users`` table. The concrete repository
+implementation (``SQLiteUserRepository``) lives in the app layer
+(``app.gateway.auth.repositories.sqlite``) because it converts
+between the ORM row and the auth module's pydantic ``User`` class.
+This keeps the harness package free of any dependency on app code.
+"""
+
+from deerflow.persistence.user.model import UserRow
+
+__all__ = ["UserRow"]

backend/packages/harness/deerflow/persistence/user/model.py

@@ -0,0 +1,59 @@
+"""ORM model for the users table.
+
+Lives in the harness persistence package so it is picked up by
+``Base.metadata.create_all()`` alongside ``threads_meta``, ``runs``,
+``run_events``, and ``feedback``. Using the shared engine means:
+
+- One SQLite/Postgres database, one connection pool
+- One schema initialisation codepath
+- Consistent async sessions across auth and persistence reads
+"""
+
+from __future__ import annotations
+
+from datetime import UTC, datetime
+
+from sqlalchemy import Boolean, DateTime, Index, String, text
+from sqlalchemy.orm import Mapped, mapped_column
+
+from deerflow.persistence.base import Base
+
+
+class UserRow(Base):
+    __tablename__ = "users"
+
+    # UUIDs are stored as 36-char strings for cross-backend portability.
+    id: Mapped[str] = mapped_column(String(36), primary_key=True)
+
+    email: Mapped[str] = mapped_column(String(320), unique=True, nullable=False, index=True)
+    password_hash: Mapped[str | None] = mapped_column(String(128), nullable=True)
+
+    # "admin" | "user" — kept as plain string to avoid ALTER TABLE pain
+    # when new roles are introduced.
+    system_role: Mapped[str] = mapped_column(String(16), nullable=False, default="user")
+
+    created_at: Mapped[datetime] = mapped_column(
+        DateTime(timezone=True),
+        nullable=False,
+        default=lambda: datetime.now(UTC),
+    )
+
+    # OAuth linkage (optional). A partial unique index enforces one
+    # account per (provider, oauth_id) pair, leaving NULL/NULL rows
+    # unconstrained so plain password accounts can coexist.
+    oauth_provider: Mapped[str | None] = mapped_column(String(32), nullable=True)
+    oauth_id: Mapped[str | None] = mapped_column(String(128), nullable=True)
+
+    # Auth lifecycle flags
+    needs_setup: Mapped[bool] = mapped_column(Boolean, nullable=False, default=False)
+    token_version: Mapped[int] = mapped_column(nullable=False, default=0)
+
+    __table_args__ = (
+        Index(
+            "idx_users_oauth_identity",
+            "oauth_provider",
+            "oauth_id",
+            unique=True,
+            sqlite_where=text("oauth_provider IS NOT NULL AND oauth_id IS NOT NULL"),
+        ),
+    )

backend/packages/harness/deerflow/runtime/__init__.py

@@ -5,15 +5,22 @@ Re-exports the public API of :mod:`~deerflow.runtime.runs` and
 directly from ``deerflow.runtime``.
 """
 
-from .runs import ConflictError, DisconnectMode, RunManager, RunRecord, RunStatus, UnsupportedStrategyError, run_agent
+from .checkpointer import checkpointer_context, get_checkpointer, make_checkpointer, reset_checkpointer
+from .runs import ConflictError, DisconnectMode, RunContext, RunManager, RunRecord, RunStatus, UnsupportedStrategyError, run_agent
 from .serialization import serialize, serialize_channel_values, serialize_lc_object, serialize_messages_tuple
 from .store import get_store, make_store, reset_store, store_context
 from .stream_bridge import END_SENTINEL, HEARTBEAT_SENTINEL, MemoryStreamBridge, StreamBridge, StreamEvent, make_stream_bridge
 
 __all__ = [
+    # checkpointer
+    "checkpointer_context",
+    "get_checkpointer",
+    "make_checkpointer",
+    "reset_checkpointer",
     # runs
     "ConflictError",
     "DisconnectMode",
+    "RunContext",
     "RunManager",
     "RunRecord",
     "RunStatus",

backend/packages/harness/deerflow/runtime/checkpointer/async_provider.py

@@ -7,12 +7,12 @@ Supported backends: memory, sqlite, postgres.
 
 Usage (e.g. FastAPI lifespan)::
 
-    from deerflow.agents.checkpointer.async_provider import make_checkpointer
+    from deerflow.runtime.checkpointer.async_provider import make_checkpointer
 
     async with make_checkpointer() as checkpointer:
         app.state.checkpointer = checkpointer  # InMemorySaver if not configured
 
-For sync usage see :mod:`deerflow.agents.checkpointer.provider`.
+For sync usage see :mod:`deerflow.runtime.checkpointer.provider`.
 """
 
 from __future__ import annotations
@@ -24,12 +24,12 @@ from collections.abc import AsyncIterator
 
 from langgraph.types import Checkpointer
 
-from deerflow.agents.checkpointer.provider import (
+from deerflow.config.app_config import get_app_config
+from deerflow.runtime.checkpointer.provider import (
     POSTGRES_CONN_REQUIRED,
     POSTGRES_INSTALL,
     SQLITE_INSTALL,
 )
-from deerflow.config.app_config import get_app_config
 from deerflow.runtime.store._sqlite_utils import ensure_sqlite_parent_dir, resolve_sqlite_conn_str
 
 logger = logging.getLogger(__name__)
@@ -84,23 +84,76 @@ async def _async_checkpointer(config) -> AsyncIterator[Checkpointer]:
 
 
 @contextlib.asynccontextmanager
-async def make_checkpointer() -> AsyncIterator[Checkpointer]:
-    """Async context manager that yields a checkpointer for the caller's lifetime.
-    Resources are opened on enter and closed on exit — no global state::
-
-        async with make_checkpointer() as checkpointer:
-            app.state.checkpointer = checkpointer
-
-    Yields an ``InMemorySaver`` when no checkpointer is configured in *config.yaml*.
-    """
-
-    config = get_app_config()
-
-    if config.checkpointer is None:
+async def _async_checkpointer_from_database(db_config) -> AsyncIterator[Checkpointer]:
+    """Async context manager that constructs a checkpointer from unified DatabaseConfig."""
+    if db_config.backend == "memory":
         from langgraph.checkpoint.memory import InMemorySaver
 
         yield InMemorySaver()
         return
 
-    async with _async_checkpointer(config.checkpointer) as saver:
-        yield saver
+    if db_config.backend == "sqlite":
+        try:
+            from langgraph.checkpoint.sqlite.aio import AsyncSqliteSaver
+        except ImportError as exc:
+            raise ImportError(SQLITE_INSTALL) from exc
+
+        conn_str = db_config.checkpointer_sqlite_path
+        ensure_sqlite_parent_dir(conn_str)
+        async with AsyncSqliteSaver.from_conn_string(conn_str) as saver:
+            await saver.setup()
+            yield saver
+        return
+
+    if db_config.backend == "postgres":
+        try:
+            from langgraph.checkpoint.postgres.aio import AsyncPostgresSaver
+        except ImportError as exc:
+            raise ImportError(POSTGRES_INSTALL) from exc
+
+        if not db_config.postgres_url:
+            raise ValueError("database.postgres_url is required for the postgres backend")
+
+        async with AsyncPostgresSaver.from_conn_string(db_config.postgres_url) as saver:
+            await saver.setup()
+            yield saver
+        return
+
+    raise ValueError(f"Unknown database backend: {db_config.backend!r}")
+
+
+@contextlib.asynccontextmanager
+async def make_checkpointer() -> AsyncIterator[Checkpointer]:
+    """Async context manager that yields a checkpointer for the caller's lifetime.
+    Resources are opened on enter and closed on exit -- no global state::
+
+        async with make_checkpointer() as checkpointer:
+            app.state.checkpointer = checkpointer
+
+    Yields an ``InMemorySaver`` when no checkpointer is configured in *config.yaml*.
+
+    Priority:
+    1. Legacy ``checkpointer:`` config section (backward compatible)
+    2. Unified ``database:`` config section
+    3. Default InMemorySaver
+    """
+
+    config = get_app_config()
+
+    # Legacy: standalone checkpointer config takes precedence
+    if config.checkpointer is not None:
+        async with _async_checkpointer(config.checkpointer) as saver:
+            yield saver
+            return
+
+    # Unified database config
+    db_config = getattr(config, "database", None)
+    if db_config is not None and db_config.backend != "memory":
+        async with _async_checkpointer_from_database(db_config) as saver:
+            yield saver
+            return
+
+    # Default: in-memory
+    from langgraph.checkpoint.memory import InMemorySaver
+
+    yield InMemorySaver()

backend/packages/harness/deerflow/runtime/checkpointer/provider.py

@@ -7,7 +7,7 @@ Supported backends: memory, sqlite, postgres.
 
 Usage::
 
-    from deerflow.agents.checkpointer.provider import get_checkpointer, checkpointer_context
+    from deerflow.runtime.checkpointer.provider import get_checkpointer, checkpointer_context
 
     # Singleton — reused across calls, closed on process exit
     cp = get_checkpointer()

backend/packages/harness/deerflow/runtime/converters.py

@@ -0,0 +1,134 @@
+"""Pure functions to convert LangChain message objects to OpenAI Chat Completions format.
+
+Used by RunJournal to build content dicts for event storage.
+"""
+
+from __future__ import annotations
+
+import json
+from typing import Any
+
+_ROLE_MAP = {
+    "human": "user",
+    "ai": "assistant",
+    "system": "system",
+    "tool": "tool",
+}
+
+
+def langchain_to_openai_message(message: Any) -> dict:
+    """Convert a single LangChain BaseMessage to an OpenAI message dict.
+
+    Handles:
+    - HumanMessage → {"role": "user", "content": "..."}
+    - AIMessage (text only) → {"role": "assistant", "content": "..."}
+    - AIMessage (with tool_calls) → {"role": "assistant", "content": null, "tool_calls": [...]}
+    - AIMessage (text + tool_calls) → both content and tool_calls present
+    - AIMessage (list content / multimodal) → content preserved as list
+    - SystemMessage → {"role": "system", "content": "..."}
+    - ToolMessage → {"role": "tool", "tool_call_id": "...", "content": "..."}
+    """
+    msg_type = getattr(message, "type", "")
+    role = _ROLE_MAP.get(msg_type, msg_type)
+    content = getattr(message, "content", "")
+
+    if role == "tool":
+        return {
+            "role": "tool",
+            "tool_call_id": getattr(message, "tool_call_id", ""),
+            "content": content,
+        }
+
+    if role == "assistant":
+        tool_calls = getattr(message, "tool_calls", None) or []
+        result: dict = {"role": "assistant"}
+
+        if tool_calls:
+            openai_tool_calls = []
+            for tc in tool_calls:
+                args = tc.get("args", {})
+                openai_tool_calls.append(
+                    {
+                        "id": tc.get("id", ""),
+                        "type": "function",
+                        "function": {
+                            "name": tc.get("name", ""),
+                            "arguments": json.dumps(args) if not isinstance(args, str) else args,
+                        },
+                    }
+                )
+            # If no text content, set content to null per OpenAI spec
+            result["content"] = content if (isinstance(content, list) and content) or (isinstance(content, str) and content) else None
+            result["tool_calls"] = openai_tool_calls
+        else:
+            result["content"] = content
+
+        return result
+
+    # user / system / unknown
+    return {"role": role, "content": content}
+
+
+def _infer_finish_reason(message: Any) -> str:
+    """Infer OpenAI finish_reason from an AIMessage.
+
+    Returns "tool_calls" if tool_calls present, else looks in
+    response_metadata.finish_reason, else returns "stop".
+    """
+    tool_calls = getattr(message, "tool_calls", None) or []
+    if tool_calls:
+        return "tool_calls"
+    resp_meta = getattr(message, "response_metadata", None) or {}
+    if isinstance(resp_meta, dict):
+        finish = resp_meta.get("finish_reason")
+        if finish:
+            return finish
+    return "stop"
+
+
+def langchain_to_openai_completion(message: Any) -> dict:
+    """Convert an AIMessage and its metadata to an OpenAI completion response dict.
+
+    Returns:
+        {
+            "id": message.id,
+            "model": message.response_metadata.get("model_name"),
+            "choices": [{"index": 0, "message": <openai_message>, "finish_reason": <inferred>}],
+            "usage": {"prompt_tokens": ..., "completion_tokens": ..., "total_tokens": ...} or None,
+        }
+    """
+    resp_meta = getattr(message, "response_metadata", None) or {}
+    model_name = resp_meta.get("model_name") if isinstance(resp_meta, dict) else None
+
+    openai_msg = langchain_to_openai_message(message)
+    finish_reason = _infer_finish_reason(message)
+
+    usage_metadata = getattr(message, "usage_metadata", None)
+    if usage_metadata is not None:
+        input_tokens = usage_metadata.get("input_tokens", 0) or 0
+        output_tokens = usage_metadata.get("output_tokens", 0) or 0
+        usage: dict | None = {
+            "prompt_tokens": input_tokens,
+            "completion_tokens": output_tokens,
+            "total_tokens": input_tokens + output_tokens,
+        }
+    else:
+        usage = None
+
+    return {
+        "id": getattr(message, "id", None),
+        "model": model_name,
+        "choices": [
+            {
+                "index": 0,
+                "message": openai_msg,
+                "finish_reason": finish_reason,
+            }
+        ],
+        "usage": usage,
+    }
+
+
+def langchain_messages_to_openai(messages: list) -> list[dict]:
+    """Convert a list of LangChain BaseMessages to OpenAI message dicts."""
+    return [langchain_to_openai_message(m) for m in messages]

backend/packages/harness/deerflow/runtime/events/__init__.py

@@ -0,0 +1,4 @@
+from deerflow.runtime.events.store.base import RunEventStore
+from deerflow.runtime.events.store.memory import MemoryRunEventStore
+
+__all__ = ["MemoryRunEventStore", "RunEventStore"]

backend/packages/harness/deerflow/runtime/events/store/__init__.py

@@ -0,0 +1,26 @@
+from deerflow.runtime.events.store.base import RunEventStore
+from deerflow.runtime.events.store.memory import MemoryRunEventStore
+
+
+def make_run_event_store(config=None) -> RunEventStore:
+    """Create a RunEventStore based on run_events.backend configuration."""
+    if config is None or config.backend == "memory":
+        return MemoryRunEventStore()
+    if config.backend == "db":
+        from deerflow.persistence.engine import get_session_factory
+
+        sf = get_session_factory()
+        if sf is None:
+            # database.backend=memory but run_events.backend=db -> fallback
+            return MemoryRunEventStore()
+        from deerflow.runtime.events.store.db import DbRunEventStore
+
+        return DbRunEventStore(sf, max_trace_content=config.max_trace_content)
+    if config.backend == "jsonl":
+        from deerflow.runtime.events.store.jsonl import JsonlRunEventStore
+
+        return JsonlRunEventStore()
+    raise ValueError(f"Unknown run_events backend: {config.backend!r}")
+
+
+__all__ = ["MemoryRunEventStore", "RunEventStore", "make_run_event_store"]

backend/packages/harness/deerflow/runtime/events/store/base.py

@@ -0,0 +1,109 @@
+"""Abstract interface for run event storage.
+
+RunEventStore is the unified storage interface for run event streams.
+Messages (frontend display) and execution traces (debugging/audit) go
+through the same interface, distinguished by the ``category`` field.
+
+Implementations:
+- MemoryRunEventStore: in-memory dict (development, tests)
+- Future: DB-backed store (SQLAlchemy ORM), JSONL file store
+"""
+
+from __future__ import annotations
+
+import abc
+
+
+class RunEventStore(abc.ABC):
+    """Run event stream storage interface.
+
+    All implementations must guarantee:
+    1. put() events are retrievable in subsequent queries
+    2. seq is strictly increasing within the same thread
+    3. list_messages() only returns category="message" events
+    4. list_events() returns all events for the specified run
+    5. Returned dicts match the RunEvent field structure
+    """
+
+    @abc.abstractmethod
+    async def put(
+        self,
+        *,
+        thread_id: str,
+        run_id: str,
+        event_type: str,
+        category: str,
+        content: str | dict = "",
+        metadata: dict | None = None,
+        created_at: str | None = None,
+    ) -> dict:
+        """Write an event, auto-assign seq, return the complete record."""
+
+    @abc.abstractmethod
+    async def put_batch(self, events: list[dict]) -> list[dict]:
+        """Batch-write events. Used by RunJournal flush buffer.
+
+        Each dict's keys match put()'s keyword arguments.
+        Returns complete records with seq assigned.
+        """
+
+    @abc.abstractmethod
+    async def list_messages(
+        self,
+        thread_id: str,
+        *,
+        limit: int = 50,
+        before_seq: int | None = None,
+        after_seq: int | None = None,
+    ) -> list[dict]:
+        """Return displayable messages (category=message) for a thread, ordered by seq ascending.
+
+        Supports bidirectional cursor pagination:
+        - before_seq: return the last ``limit`` records with seq < before_seq (ascending)
+        - after_seq: return the first ``limit`` records with seq > after_seq (ascending)
+        - neither: return the latest ``limit`` records (ascending)
+        """
+
+    @abc.abstractmethod
+    async def list_events(
+        self,
+        thread_id: str,
+        run_id: str,
+        *,
+        event_types: list[str] | None = None,
+        limit: int = 500,
+    ) -> list[dict]:
+        """Return the full event stream for a run, ordered by seq ascending.
+
+        Optionally filter by event_types.
+        """
+
+    @abc.abstractmethod
+    async def list_messages_by_run(
+        self,
+        thread_id: str,
+        run_id: str,
+        *,
+        limit: int = 50,
+        before_seq: int | None = None,
+        after_seq: int | None = None,
+    ) -> list[dict]:
+        """Return displayable messages (category=message) for a specific run, ordered by seq ascending.
+
+        Supports bidirectional cursor pagination:
+        - after_seq: return the first ``limit`` records with seq > after_seq (ascending)
+        - before_seq: return the last ``limit`` records with seq < before_seq (ascending)
+        - neither: return the latest ``limit`` records (ascending)
+        """
+
+    @abc.abstractmethod
+    async def count_messages(self, thread_id: str) -> int:
+        """Count displayable messages (category=message) in a thread."""
+
+    @abc.abstractmethod
+    async def delete_by_thread(self, thread_id: str) -> int:
+        """Delete all events for a thread. Return the number of deleted events."""
+
+    @abc.abstractmethod
+    async def delete_by_run(self, thread_id: str, run_id: str) -> int:
+        """Delete all events for a specific run. Return the number of deleted events."""

backend/packages/harness/deerflow/runtime/events/store/db.py

@@ -0,0 +1,286 @@
+"""SQLAlchemy-backed RunEventStore implementation.
+
+Persists events to the ``run_events`` table. Trace content is truncated
+at ``max_trace_content`` bytes to avoid bloating the database.
+"""
+
+from __future__ import annotations
+
+import json
+import logging
+from datetime import UTC, datetime
+
+from sqlalchemy import delete, func, select
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
+from deerflow.persistence.models.run_event import RunEventRow
+from deerflow.runtime.events.store.base import RunEventStore
+from deerflow.runtime.user_context import AUTO, _AutoSentinel, get_current_user, resolve_user_id
+
+logger = logging.getLogger(__name__)
+
+
+class DbRunEventStore(RunEventStore):
+    def __init__(self, session_factory: async_sessionmaker[AsyncSession], *, max_trace_content: int = 10240):
+        self._sf = session_factory
+        self._max_trace_content = max_trace_content
+
+    @staticmethod
+    def _row_to_dict(row: RunEventRow) -> dict:
+        d = row.to_dict()
+        d["metadata"] = d.pop("event_metadata", {})
+        val = d.get("created_at")
+        if isinstance(val, datetime):
+            d["created_at"] = val.isoformat()
+        d.pop("id", None)
+        # Restore dict content that was JSON-serialized on write
+        raw = d.get("content", "")
+        if isinstance(raw, str) and d.get("metadata", {}).get("content_is_dict"):
+            try:
+                d["content"] = json.loads(raw)
+            except (json.JSONDecodeError, ValueError):
+                # Content looked like JSON (content_is_dict flag) but failed to parse;
+                # keep the raw string as-is.
+                logger.debug("Failed to deserialize content as JSON for event seq=%s", d.get("seq"))
+        return d
+
+    def _truncate_trace(self, category: str, content: str | dict, metadata: dict | None) -> tuple[str | dict, dict]:
+        if category == "trace":
+            text = json.dumps(content, default=str, ensure_ascii=False) if isinstance(content, dict) else content
+            encoded = text.encode("utf-8")
+            if len(encoded) > self._max_trace_content:
+                # Truncate by bytes, then decode back (may cut a multi-byte char, so use errors="ignore")
+                content = encoded[: self._max_trace_content].decode("utf-8", errors="ignore")
+                metadata = {**(metadata or {}), "content_truncated": True, "original_byte_length": len(encoded)}
+        return content, metadata or {}
+
+    @staticmethod
+    def _user_id_from_context() -> str | None:
+        """Soft read of user_id from contextvar for write paths.
+
+        Returns ``None`` (no filter / no stamp) if contextvar is unset,
+        which is the expected case for background worker writes. HTTP
+        request writes will have the contextvar set by auth middleware
+        and get their user_id stamped automatically.
+
+        Coerces ``user.id`` to ``str`` at the boundary: ``User.id`` is
+        typed as ``UUID`` by the auth layer, but ``run_events.user_id``
+        is ``VARCHAR(64)`` and aiosqlite cannot bind a raw UUID object
+        to a VARCHAR column ("type 'UUID' is not supported") — the
+        INSERT would silently roll back and the worker would hang.
+        """
+        user = get_current_user()
+        return str(user.id) if user is not None else None
+
+    async def put(self, *, thread_id, run_id, event_type, category, content="", metadata=None, created_at=None):  # noqa: D401
+        """Write a single event — low-frequency path only.
+
+        This opens a dedicated transaction with a FOR UPDATE lock to
+        assign a monotonic *seq*.  For high-throughput writes use
+        :meth:`put_batch`, which acquires the lock once for the whole
+        batch.  Currently the only caller is ``worker.run_agent`` for
+        the initial ``human_message`` event (once per run).
+        """
+        content, metadata = self._truncate_trace(category, content, metadata)
+        if isinstance(content, dict):
+            db_content = json.dumps(content, default=str, ensure_ascii=False)
+            metadata = {**(metadata or {}), "content_is_dict": True}
+        else:
+            db_content = content
+        user_id = self._user_id_from_context()
+        async with self._sf() as session:
+            async with session.begin():
+                # Use FOR UPDATE to serialize seq assignment within a thread.
+                # NOTE: with_for_update() on aggregates is a no-op on SQLite;
+                # the UNIQUE(thread_id, seq) constraint catches races there.
+                max_seq = await session.scalar(select(func.max(RunEventRow.seq)).where(RunEventRow.thread_id == thread_id).with_for_update())
+                seq = (max_seq or 0) + 1
+                row = RunEventRow(
+                    thread_id=thread_id,
+                    run_id=run_id,
+                    user_id=user_id,
+                    event_type=event_type,
+                    category=category,
+                    content=db_content,
+                    event_metadata=metadata,
+                    seq=seq,
+                    created_at=datetime.fromisoformat(created_at) if created_at else datetime.now(UTC),
+                )
+                session.add(row)
+            return self._row_to_dict(row)
+
+    async def put_batch(self, events):
+        if not events:
+            return []
+        user_id = self._user_id_from_context()
+        async with self._sf() as session:
+            async with session.begin():
+                # Get max seq for the thread (assume all events in batch belong to same thread).
+                # NOTE: with_for_update() on aggregates is a no-op on SQLite;
+                # the UNIQUE(thread_id, seq) constraint catches races there.
+                thread_id = events[0]["thread_id"]
+                max_seq = await session.scalar(select(func.max(RunEventRow.seq)).where(RunEventRow.thread_id == thread_id).with_for_update())
+                seq = max_seq or 0
+                rows = []
+                for e in events:
+                    seq += 1
+                    content = e.get("content", "")
+                    category = e.get("category", "trace")
+                    metadata = e.get("metadata")
+                    content, metadata = self._truncate_trace(category, content, metadata)
+                    if isinstance(content, dict):
+                        db_content = json.dumps(content, default=str, ensure_ascii=False)
+                        metadata = {**(metadata or {}), "content_is_dict": True}
+                    else:
+                        db_content = content
+                    row = RunEventRow(
+                        thread_id=e["thread_id"],
+                        run_id=e["run_id"],
+                        user_id=e.get("user_id", user_id),
+                        event_type=e["event_type"],
+                        category=category,
+                        content=db_content,
+                        event_metadata=metadata,
+                        seq=seq,
+                        created_at=datetime.fromisoformat(e["created_at"]) if e.get("created_at") else datetime.now(UTC),
+                    )
+                    session.add(row)
+                    rows.append(row)
+            return [self._row_to_dict(r) for r in rows]
+
+    async def list_messages(
+        self,
+        thread_id,
+        *,
+        limit=50,
+        before_seq=None,
+        after_seq=None,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ):
+        resolved_user_id = resolve_user_id(user_id, method_name="DbRunEventStore.list_messages")
+        stmt = select(RunEventRow).where(RunEventRow.thread_id == thread_id, RunEventRow.category == "message")
+        if resolved_user_id is not None:
+            stmt = stmt.where(RunEventRow.user_id == resolved_user_id)
+        if before_seq is not None:
+            stmt = stmt.where(RunEventRow.seq < before_seq)
+        if after_seq is not None:
+            stmt = stmt.where(RunEventRow.seq > after_seq)
+
+        if after_seq is not None:
+            # Forward pagination: first `limit` records after cursor
+            stmt = stmt.order_by(RunEventRow.seq.asc()).limit(limit)
+            async with self._sf() as session:
+                result = await session.execute(stmt)
+                return [self._row_to_dict(r) for r in result.scalars()]
+        else:
+            # before_seq or default (latest): take last `limit` records, return ascending
+            stmt = stmt.order_by(RunEventRow.seq.desc()).limit(limit)
+            async with self._sf() as session:
+                result = await session.execute(stmt)
+                rows = list(result.scalars())
+                return [self._row_to_dict(r) for r in reversed(rows)]
+
+    async def list_events(
+        self,
+        thread_id,
+        run_id,
+        *,
+        event_types=None,
+        limit=500,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ):
+        resolved_user_id = resolve_user_id(user_id, method_name="DbRunEventStore.list_events")
+        stmt = select(RunEventRow).where(RunEventRow.thread_id == thread_id, RunEventRow.run_id == run_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(RunEventRow.user_id == resolved_user_id)
+        if event_types:
+            stmt = stmt.where(RunEventRow.event_type.in_(event_types))
+        stmt = stmt.order_by(RunEventRow.seq.asc()).limit(limit)
+        async with self._sf() as session:
+            result = await session.execute(stmt)
+            return [self._row_to_dict(r) for r in result.scalars()]
+
+    async def list_messages_by_run(
+        self,
+        thread_id,
+        run_id,
+        *,
+        limit=50,
+        before_seq=None,
+        after_seq=None,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ):
+        resolved_user_id = resolve_user_id(user_id, method_name="DbRunEventStore.list_messages_by_run")
+        stmt = select(RunEventRow).where(
+            RunEventRow.thread_id == thread_id,
+            RunEventRow.run_id == run_id,
+            RunEventRow.category == "message",
+        )
+        if resolved_user_id is not None:
+            stmt = stmt.where(RunEventRow.user_id == resolved_user_id)
+        if before_seq is not None:
+            stmt = stmt.where(RunEventRow.seq < before_seq)
+        if after_seq is not None:
+            stmt = stmt.where(RunEventRow.seq > after_seq)
+
+        if after_seq is not None:
+            stmt = stmt.order_by(RunEventRow.seq.asc()).limit(limit)
+            async with self._sf() as session:
+                result = await session.execute(stmt)
+                return [self._row_to_dict(r) for r in result.scalars()]
+        else:
+            stmt = stmt.order_by(RunEventRow.seq.desc()).limit(limit)
+            async with self._sf() as session:
+                result = await session.execute(stmt)
+                rows = list(result.scalars())
+                return [self._row_to_dict(r) for r in reversed(rows)]
+
+    async def count_messages(
+        self,
+        thread_id,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ):
+        resolved_user_id = resolve_user_id(user_id, method_name="DbRunEventStore.count_messages")
+        stmt = select(func.count()).select_from(RunEventRow).where(RunEventRow.thread_id == thread_id, RunEventRow.category == "message")
+        if resolved_user_id is not None:
+            stmt = stmt.where(RunEventRow.user_id == resolved_user_id)
+        async with self._sf() as session:
+            return await session.scalar(stmt) or 0
+
+    async def delete_by_thread(
+        self,
+        thread_id,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ):
+        resolved_user_id = resolve_user_id(user_id, method_name="DbRunEventStore.delete_by_thread")
+        async with self._sf() as session:
+            count_conditions = [RunEventRow.thread_id == thread_id]
+            if resolved_user_id is not None:
+                count_conditions.append(RunEventRow.user_id == resolved_user_id)
+            count_stmt = select(func.count()).select_from(RunEventRow).where(*count_conditions)
+            count = await session.scalar(count_stmt) or 0
+            if count > 0:
+                await session.execute(delete(RunEventRow).where(*count_conditions))
+                await session.commit()
+            return count
+
+    async def delete_by_run(
+        self,
+        thread_id,
+        run_id,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ):
+        resolved_user_id = resolve_user_id(user_id, method_name="DbRunEventStore.delete_by_run")
+        async with self._sf() as session:
+            count_conditions = [RunEventRow.thread_id == thread_id, RunEventRow.run_id == run_id]
+            if resolved_user_id is not None:
+                count_conditions.append(RunEventRow.user_id == resolved_user_id)
+            count_stmt = select(func.count()).select_from(RunEventRow).where(*count_conditions)
+            count = await session.scalar(count_stmt) or 0
+            if count > 0:
+                await session.execute(delete(RunEventRow).where(*count_conditions))
+                await session.commit()
+            return count

backend/packages/harness/deerflow/runtime/events/store/jsonl.py

@@ -0,0 +1,187 @@
+"""JSONL file-backed RunEventStore implementation.
+
+Each run's events are stored in a single file:
+``.deer-flow/threads/{thread_id}/runs/{run_id}.jsonl``
+
+All categories (message, trace, lifecycle) are in the same file.
+This backend is suitable for lightweight single-node deployments.
+
+Known trade-off: ``list_messages()`` must scan all run files for a
+thread since messages from multiple runs need unified seq ordering.
+``list_events()`` reads only one file -- the fast path.
+"""
+
+from __future__ import annotations
+
+import json
+import logging
+import re
+from datetime import UTC, datetime
+from pathlib import Path
+
+from deerflow.runtime.events.store.base import RunEventStore
+
+logger = logging.getLogger(__name__)
+
+_SAFE_ID_PATTERN = re.compile(r"^[A-Za-z0-9_\-]+$")
+
+
+class JsonlRunEventStore(RunEventStore):
+    def __init__(self, base_dir: str | Path | None = None):
+        self._base_dir = Path(base_dir) if base_dir else Path(".deer-flow")
+        self._seq_counters: dict[str, int] = {}  # thread_id -> current max seq
+
+    @staticmethod
+    def _validate_id(value: str, label: str) -> str:
+        """Validate that an ID is safe for use in filesystem paths."""
+        if not value or not _SAFE_ID_PATTERN.match(value):
+            raise ValueError(f"Invalid {label}: must be alphanumeric/dash/underscore, got {value!r}")
+        return value
+
+    def _thread_dir(self, thread_id: str) -> Path:
+        self._validate_id(thread_id, "thread_id")
+        return self._base_dir / "threads" / thread_id / "runs"
+
+    def _run_file(self, thread_id: str, run_id: str) -> Path:
+        self._validate_id(run_id, "run_id")
+        return self._thread_dir(thread_id) / f"{run_id}.jsonl"
+
+    def _next_seq(self, thread_id: str) -> int:
+        self._seq_counters[thread_id] = self._seq_counters.get(thread_id, 0) + 1
+        return self._seq_counters[thread_id]
+
+    def _ensure_seq_loaded(self, thread_id: str) -> None:
+        """Load max seq from existing files if not yet cached."""
+        if thread_id in self._seq_counters:
+            return
+        max_seq = 0
+        thread_dir = self._thread_dir(thread_id)
+        if thread_dir.exists():
+            for f in thread_dir.glob("*.jsonl"):
+                for line in f.read_text(encoding="utf-8").strip().splitlines():
+                    try:
+                        record = json.loads(line)
+                        max_seq = max(max_seq, record.get("seq", 0))
+                    except json.JSONDecodeError:
+                        logger.debug("Skipping malformed JSONL line in %s", f)
+                        continue
+        self._seq_counters[thread_id] = max_seq
+
+    def _write_record(self, record: dict) -> None:
+        path = self._run_file(record["thread_id"], record["run_id"])
+        path.parent.mkdir(parents=True, exist_ok=True)
+        with open(path, "a", encoding="utf-8") as f:
+            f.write(json.dumps(record, default=str, ensure_ascii=False) + "\n")
+
+    def _read_thread_events(self, thread_id: str) -> list[dict]:
+        """Read all events for a thread, sorted by seq."""
+        events = []
+        thread_dir = self._thread_dir(thread_id)
+        if not thread_dir.exists():
+            return events
+        for f in sorted(thread_dir.glob("*.jsonl")):
+            for line in f.read_text(encoding="utf-8").strip().splitlines():
+                if not line:
+                    continue
+                try:
+                    events.append(json.loads(line))
+                except json.JSONDecodeError:
+                    logger.debug("Skipping malformed JSONL line in %s", f)
+                    continue
+        events.sort(key=lambda e: e.get("seq", 0))
+        return events
+
+    def _read_run_events(self, thread_id: str, run_id: str) -> list[dict]:
+        """Read events for a specific run file."""
+        path = self._run_file(thread_id, run_id)
+        if not path.exists():
+            return []
+        events = []
+        for line in path.read_text(encoding="utf-8").strip().splitlines():
+            if not line:
+                continue
+            try:
+                events.append(json.loads(line))
+            except json.JSONDecodeError:
+                logger.debug("Skipping malformed JSONL line in %s", path)
+                continue
+        events.sort(key=lambda e: e.get("seq", 0))
+        return events
+
+    async def put(self, *, thread_id, run_id, event_type, category, content="", metadata=None, created_at=None):
+        self._ensure_seq_loaded(thread_id)
+        seq = self._next_seq(thread_id)
+        record = {
+            "thread_id": thread_id,
+            "run_id": run_id,
+            "event_type": event_type,
+            "category": category,
+            "content": content,
+            "metadata": metadata or {},
+            "seq": seq,
+            "created_at": created_at or datetime.now(UTC).isoformat(),
+        }
+        self._write_record(record)
+        return record
+
+    async def put_batch(self, events):
+        if not events:
+            return []
+        results = []
+        for ev in events:
+            record = await self.put(**ev)
+            results.append(record)
+        return results
+
+    async def list_messages(self, thread_id, *, limit=50, before_seq=None, after_seq=None):
+        all_events = self._read_thread_events(thread_id)
+        messages = [e for e in all_events if e.get("category") == "message"]
+
+        if before_seq is not None:
+            messages = [e for e in messages if e["seq"] < before_seq]
+            return messages[-limit:]
+        elif after_seq is not None:
+            messages = [e for e in messages if e["seq"] > after_seq]
+            return messages[:limit]
+        else:
+            return messages[-limit:]
+
+    async def list_events(self, thread_id, run_id, *, event_types=None, limit=500):
+        events = self._read_run_events(thread_id, run_id)
+        if event_types is not None:
+            events = [e for e in events if e.get("event_type") in event_types]
+        return events[:limit]
+
+    async def list_messages_by_run(self, thread_id, run_id, *, limit=50, before_seq=None, after_seq=None):
+        events = self._read_run_events(thread_id, run_id)
+        filtered = [e for e in events if e.get("category") == "message"]
+        if before_seq is not None:
+            filtered = [e for e in filtered if e.get("seq", 0) < before_seq]
+        if after_seq is not None:
+            filtered = [e for e in filtered if e.get("seq", 0) > after_seq]
+        if after_seq is not None:
+            return filtered[:limit]
+        else:
+            return filtered[-limit:] if len(filtered) > limit else filtered
+
+    async def count_messages(self, thread_id):
+        all_events = self._read_thread_events(thread_id)
+        return sum(1 for e in all_events if e.get("category") == "message")
+
+    async def delete_by_thread(self, thread_id):
+        all_events = self._read_thread_events(thread_id)
+        count = len(all_events)
+        thread_dir = self._thread_dir(thread_id)
+        if thread_dir.exists():
+            for f in thread_dir.glob("*.jsonl"):
+                f.unlink()
+        self._seq_counters.pop(thread_id, None)
+        return count
+
+    async def delete_by_run(self, thread_id, run_id):
+        events = self._read_run_events(thread_id, run_id)
+        count = len(events)
+        path = self._run_file(thread_id, run_id)
+        if path.exists():
+            path.unlink()
+        return count

backend/packages/harness/deerflow/runtime/events/store/memory.py

@@ -0,0 +1,128 @@
+"""In-memory RunEventStore. Used when run_events.backend=memory (default) and in tests.
+
+Thread-safe for single-process async usage (no threading locks needed
+since all mutations happen within the same event loop).
+"""
+
+from __future__ import annotations
+
+from datetime import UTC, datetime
+
+from deerflow.runtime.events.store.base import RunEventStore
+
+
+class MemoryRunEventStore(RunEventStore):
+    def __init__(self) -> None:
+        self._events: dict[str, list[dict]] = {}  # thread_id -> sorted event list
+        self._seq_counters: dict[str, int] = {}  # thread_id -> last assigned seq
+
+    def _next_seq(self, thread_id: str) -> int:
+        current = self._seq_counters.get(thread_id, 0)
+        next_val = current + 1
+        self._seq_counters[thread_id] = next_val
+        return next_val
+
+    def _put_one(
+        self,
+        *,
+        thread_id: str,
+        run_id: str,
+        event_type: str,
+        category: str,
+        content: str | dict = "",
+        metadata: dict | None = None,
+        created_at: str | None = None,
+    ) -> dict:
+        seq = self._next_seq(thread_id)
+        record = {
+            "thread_id": thread_id,
+            "run_id": run_id,
+            "event_type": event_type,
+            "category": category,
+            "content": content,
+            "metadata": metadata or {},
+            "seq": seq,
+            "created_at": created_at or datetime.now(UTC).isoformat(),
+        }
+        self._events.setdefault(thread_id, []).append(record)
+        return record
+
+    async def put(
+        self,
+        *,
+        thread_id,
+        run_id,
+        event_type,
+        category,
+        content="",
+        metadata=None,
+        created_at=None,
+    ):
+        return self._put_one(
+            thread_id=thread_id,
+            run_id=run_id,
+            event_type=event_type,
+            category=category,
+            content=content,
+            metadata=metadata,
+            created_at=created_at,
+        )
+
+    async def put_batch(self, events):
+        results = []
+        for ev in events:
+            record = self._put_one(**ev)
+            results.append(record)
+        return results
+
+    async def list_messages(self, thread_id, *, limit=50, before_seq=None, after_seq=None):
+        all_events = self._events.get(thread_id, [])
+        messages = [e for e in all_events if e["category"] == "message"]
+
+        if before_seq is not None:
+            messages = [e for e in messages if e["seq"] < before_seq]
+            # Take the last `limit` records
+            return messages[-limit:]
+        elif after_seq is not None:
+            messages = [e for e in messages if e["seq"] > after_seq]
+            return messages[:limit]
+        else:
+            # Return the latest `limit` records, ascending
+            return messages[-limit:]
+
+    async def list_events(self, thread_id, run_id, *, event_types=None, limit=500):
+        all_events = self._events.get(thread_id, [])
+        filtered = [e for e in all_events if e["run_id"] == run_id]
+        if event_types is not None:
+            filtered = [e for e in filtered if e["event_type"] in event_types]
+        return filtered[:limit]
+
+    async def list_messages_by_run(self, thread_id, run_id, *, limit=50, before_seq=None, after_seq=None):
+        all_events = self._events.get(thread_id, [])
+        filtered = [e for e in all_events if e["run_id"] == run_id and e["category"] == "message"]
+        if before_seq is not None:
+            filtered = [e for e in filtered if e["seq"] < before_seq]
+        if after_seq is not None:
+            filtered = [e for e in filtered if e["seq"] > after_seq]
+        if after_seq is not None:
+            return filtered[:limit]
+        else:
+            return filtered[-limit:] if len(filtered) > limit else filtered
+
+    async def count_messages(self, thread_id):
+        all_events = self._events.get(thread_id, [])
+        return sum(1 for e in all_events if e["category"] == "message")
+
+    async def delete_by_thread(self, thread_id):
+        events = self._events.pop(thread_id, [])
+        self._seq_counters.pop(thread_id, None)
+        return len(events)
+
+    async def delete_by_run(self, thread_id, run_id):
+        all_events = self._events.get(thread_id, [])
+        if not all_events:
+            return 0
+        remaining = [e for e in all_events if e["run_id"] != run_id]
+        removed = len(all_events) - len(remaining)
+        self._events[thread_id] = remaining
+        return removed

backend/packages/harness/deerflow/runtime/journal.py

@@ -0,0 +1,374 @@
+"""Run event capture via LangChain callbacks.
+
+RunJournal sits between LangChain's callback mechanism and the pluggable
+RunEventStore. It standardizes callback data into RunEvent records and
+handles token usage accumulation.
+
+Key design decisions:
+- on_llm_new_token is NOT implemented -- only complete messages via on_llm_end
+- on_chat_model_start captures structured prompts as llm_request (OpenAI format) and
+  extracts the first human message for run.input, because it is more reliable than
+  on_chain_start (fires on every node) — messages here are fully structured.
+- on_chain_start with parent_run_id=None emits a run.start trace marking root invocation.
+- on_llm_end emits llm_response in OpenAI Chat Completions format
+- Token usage accumulated in memory, written to RunRow on run completion
+- Caller identification via tags injection (lead_agent / subagent:{name} / middleware:{name})
+"""
+
+from __future__ import annotations
+
+import asyncio
+import logging
+import time
+from datetime import UTC, datetime
+from typing import TYPE_CHECKING, Any, cast
+from uuid import UUID
+
+from langchain_core.callbacks import BaseCallbackHandler
+from langchain_core.messages import AnyMessage, BaseMessage, HumanMessage, ToolMessage
+from langgraph.types import Command
+
+if TYPE_CHECKING:
+    from deerflow.runtime.events.store.base import RunEventStore
+
+logger = logging.getLogger(__name__)
+
+
+class RunJournal(BaseCallbackHandler):
+    """LangChain callback handler that captures events to RunEventStore."""
+
+    def __init__(
+        self,
+        run_id: str,
+        thread_id: str,
+        event_store: RunEventStore,
+        *,
+        track_token_usage: bool = True,
+        flush_threshold: int = 20,
+    ):
+        super().__init__()
+        self.run_id = run_id
+        self.thread_id = thread_id
+        self._store = event_store
+        self._track_tokens = track_token_usage
+        self._flush_threshold = flush_threshold
+
+        # Write buffer
+        self._buffer: list[dict] = []
+        self._pending_flush_tasks: set[asyncio.Task[None]] = set()
+
+        # Token accumulators
+        self._total_input_tokens = 0
+        self._total_output_tokens = 0
+        self._total_tokens = 0
+        self._llm_call_count = 0
+        self._lead_agent_tokens = 0
+        self._subagent_tokens = 0
+        self._middleware_tokens = 0
+
+        # Convenience fields
+        self._last_ai_msg: str | None = None
+        self._first_human_msg: str | None = None
+        self._msg_count = 0
+
+        # Latency tracking
+        self._llm_start_times: dict[str, float] = {}  # langchain run_id -> start time
+
+        # LLM request/response tracking
+        self._llm_call_index = 0
+        self._cached_prompts: dict[str, list[dict]] = {}  # langchain run_id -> OpenAI messages
+
+    # -- Lifecycle callbacks --
+
+    def on_chain_start(
+        self,
+        serialized: dict[str, Any],
+        inputs: dict[str, Any],
+        *,
+        run_id: UUID,
+        parent_run_id: UUID | None = None,
+        tags: list[str] | None = None,
+        metadata: dict[str, Any] | None = None,
+        **kwargs: Any,
+    ) -> None:
+        caller = self._identify_caller(tags)
+        if parent_run_id is None:
+            # Root graph invocation — emit a single trace event for the run start.
+            chain_name = (serialized or {}).get("name", "unknown")
+            self._put(
+                event_type="run.start",
+                category="trace",
+                content={"chain": chain_name},
+                metadata={"caller": caller, **(metadata or {})},
+            )
+
+    def on_chain_end(self, outputs: Any, *, run_id: UUID, **kwargs: Any) -> None:
+        self._put(event_type="run.end", category="outputs", content=outputs, metadata={"status": "success"})
+        self._flush_sync()
+
+    def on_chain_error(self, error: BaseException, *, run_id: UUID, **kwargs: Any) -> None:
+        self._put(
+            event_type="run.error",
+            category="error",
+            content=str(error),
+            metadata={"error_type": type(error).__name__},
+        )
+        self._flush_sync()
+
+    # -- LLM callbacks --
+
+    def on_chat_model_start(
+        self,
+        serialized: dict,
+        messages: list[list[BaseMessage]],
+        *,
+        run_id: UUID,
+        tags: list[str] | None = None,
+        **kwargs: Any,
+    ) -> None:
+        """Capture structured prompt messages for llm_request event.
+
+        This is also the canonical place to extract the first human message:
+        messages are fully structured here, it fires only on real LLM calls,
+        and the content is never compressed by checkpoint trimming.
+        """
+        rid = str(run_id)
+        self._llm_start_times[rid] = time.monotonic()
+        self._llm_call_index += 1
+        # Mark this run_id as seen so on_llm_end knows not to increment again.
+        self._cached_prompts[rid] = []
+
+        logger.info(f"on_chat_model_start {run_id}: tags={tags} serialized={serialized} messages={messages}")
+
+        # Capture the first human message sent to any LLM in this run.
+        if not self._first_human_msg:
+            for batch in messages.reversed():
+                for m in batch.reversed():
+                    if isinstance(m, HumanMessage) and m.name != "summary":
+                        caller = self._identify_caller(tags)
+                        self.set_first_human_message(m.text)
+                        self._put(
+                            event_type="llm.human.input",
+                            category="message",
+                            content=m.model_dump(),
+                            metadata={"caller": caller},
+                        )
+                        break
+                if self._first_human_msg:
+                    break
+
+    def on_llm_start(self, serialized: dict, prompts: list[str], *, run_id: UUID, parent_run_id: UUID | None = None, tags: list[str] | None = None, metadata: dict[str, Any] | None = None, **kwargs: Any) -> None:
+        # Fallback: on_chat_model_start is preferred. This just tracks latency.
+        self._llm_start_times[str(run_id)] = time.monotonic()
+
+    def on_llm_end(self, response, *, run_id, parent_run_id, tags, **kwargs) -> None:
+        messages: list[AnyMessage] = []
+        logger.info(f"on_llm_end {run_id}: response: {tags} {kwargs}")
+        for generation in response.generations:
+            for gen in generation:
+                if hasattr(gen, "message"):
+                    messages.append(gen.message)
+                else:
+                    logger.warning(f"on_llm_end {run_id}: generation has no message attribute: {gen}")
+
+        for message in messages:
+            caller = self._identify_caller(tags)
+
+            # Latency
+            rid = str(run_id)
+            start = self._llm_start_times.pop(rid, None)
+            latency_ms = int((time.monotonic() - start) * 1000) if start else None
+
+            # Token usage from message
+            usage = getattr(message, "usage_metadata", None)
+            usage_dict = dict(usage) if usage else {}
+
+            # Resolve call index
+            call_index = self._llm_call_index
+            if rid not in self._cached_prompts:
+                # Fallback: on_chat_model_start was not called
+                self._llm_call_index += 1
+                call_index = self._llm_call_index
+
+            # Trace event: llm_response (OpenAI completion format)
+            self._put(
+                event_type="llm.ai.response",
+                category="message",
+                content=message.model_dump(),
+                metadata={
+                    "caller": caller,
+                    "usage": usage_dict,
+                    "latency_ms": latency_ms,
+                    "llm_call_index": call_index,
+                },
+            )
+
+            # Token accumulation
+            if self._track_tokens:
+                input_tk = usage_dict.get("input_tokens", 0) or 0
+                output_tk = usage_dict.get("output_tokens", 0) or 0
+                total_tk = usage_dict.get("total_tokens", 0) or 0
+                if total_tk == 0:
+                    total_tk = input_tk + output_tk
+                if total_tk > 0:
+                    self._total_input_tokens += input_tk
+                    self._total_output_tokens += output_tk
+                    self._total_tokens += total_tk
+                    self._llm_call_count += 1
+
+    def on_llm_error(self, error: BaseException, *, run_id: UUID, **kwargs: Any) -> None:
+        self._llm_start_times.pop(str(run_id), None)
+        self._put(event_type="llm.error", category="trace", content=str(error))
+
+    def on_tool_start(self, serialized, input_str, *, run_id, parent_run_id=None, tags=None, metadata=None, inputs=None, **kwargs):
+        """Handle tool start event, cache tool call ID for later correlation"""
+        tool_call_id = str(run_id)
+        logger.info(f"Tool start for node {run_id}, tool_call_id={tool_call_id}, tags={tags}, metadata={metadata}")
+
+    def on_tool_end(self, output, *, run_id, parent_run_id=None, **kwargs):
+        """Handle tool end event, append message and clear node data"""
+        try:
+            if isinstance(output, ToolMessage):
+                msg = cast(ToolMessage, output)
+                self._put(event_type="llm.tool.result", category="message", content=msg.model_dump())
+            elif isinstance(output, Command):
+                cmd = cast(Command, output)
+                messages = cmd.update.get("messages", [])
+                for message in messages:
+                    if isinstance(message, BaseMessage):
+                        self._put(event_type="llm.tool.result", category="message", content=message.model_dump())
+                    else:
+                        logger.warning(f"on_tool_end {run_id}: command update message is not BaseMessage: {type(message)}")
+            else:
+                logger.warning(f"on_tool_end {run_id}: output is not ToolMessage: {type(output)}")
+        finally:
+            logger.info(f"Tool end for node {run_id}")
+
+    # -- Internal methods --
+
+    def _put(self, *, event_type: str, category: str, content: str | dict = "", metadata: dict | None = None) -> None:
+        self._buffer.append(
+            {
+                "thread_id": self.thread_id,
+                "run_id": self.run_id,
+                "event_type": event_type,
+                "category": category,
+                "content": content,
+                "metadata": metadata or {},
+                "created_at": datetime.now(UTC).isoformat(),
+            }
+        )
+        if len(self._buffer) >= self._flush_threshold:
+            self._flush_sync()
+
+    def _flush_sync(self) -> None:
+        """Best-effort flush of buffer to RunEventStore.
+
+        BaseCallbackHandler methods are synchronous.  If an event loop is
+        running we schedule an async ``put_batch``; otherwise the events
+        stay in the buffer and are flushed later by the async ``flush()``
+        call in the worker's ``finally`` block.
+        """
+        if not self._buffer:
+            return
+        # Skip if a flush is already in flight — avoids concurrent writes
+        # to the same SQLite file from multiple fire-and-forget tasks.
+        if self._pending_flush_tasks:
+            return
+        try:
+            loop = asyncio.get_running_loop()
+        except RuntimeError:
+            # No event loop — keep events in buffer for later async flush.
+            return
+        batch = self._buffer.copy()
+        self._buffer.clear()
+        task = loop.create_task(self._flush_async(batch))
+        self._pending_flush_tasks.add(task)
+        task.add_done_callback(self._on_flush_done)
+
+    async def _flush_async(self, batch: list[dict]) -> None:
+        try:
+            await self._store.put_batch(batch)
+        except Exception:
+            logger.warning(
+                "Failed to flush %d events for run %s — returning to buffer",
+                len(batch),
+                self.run_id,
+                exc_info=True,
+            )
+            # Return failed events to buffer for retry on next flush
+            self._buffer = batch + self._buffer
+
+    def _on_flush_done(self, task: asyncio.Task) -> None:
+        self._pending_flush_tasks.discard(task)
+        if task.cancelled():
+            return
+        exc = task.exception()
+        if exc:
+            logger.warning("Journal flush task failed: %s", exc)
+
+    def _identify_caller(self, tags: list[str] | None, **kwargs) -> str:
+        _tags = tags or kwargs.get("tags", [])
+        for tag in _tags:
+            if isinstance(tag, str) and (tag.startswith("subagent:") or tag.startswith("middleware:") or tag == "lead_agent"):
+                return tag
+        # Default to lead_agent: the main agent graph does not inject
+        # callback tags, while subagents and middleware explicitly tag
+        # themselves.
+        return "lead_agent"
+
+    # -- Public methods (called by worker) --
+
+    def set_first_human_message(self, content: str) -> None:
+        """Record the first human message for convenience fields."""
+        self._first_human_msg = content[:2000] if content else None
+
+    def record_middleware(self, tag: str, *, name: str, hook: str, action: str, changes: dict) -> None:
+        """Record a middleware state-change event.
+
+        Called by middleware implementations when they perform a meaningful
+        state change (e.g., title generation, summarization, HITL approval).
+        Pure-observation middleware should not call this.
+
+        Args:
+            tag: Short identifier for the middleware (e.g., "title", "summarize",
+                 "guardrail"). Used to form event_type="middleware:{tag}".
+            name: Full middleware class name.
+            hook: Lifecycle hook that triggered the action (e.g., "after_model").
+            action: Specific action performed (e.g., "generate_title").
+            changes: Dict describing the state changes made.
+        """
+        self._put(
+            event_type=f"middleware:{tag}",
+            category="middleware",
+            content={"name": name, "hook": hook, "action": action, "changes": changes},
+        )
+
+    async def flush(self) -> None:
+        """Force flush remaining buffer. Called in worker's finally block."""
+        if self._pending_flush_tasks:
+            await asyncio.gather(*tuple(self._pending_flush_tasks), return_exceptions=True)
+
+        while self._buffer:
+            batch = self._buffer[: self._flush_threshold]
+            del self._buffer[: self._flush_threshold]
+            try:
+                await self._store.put_batch(batch)
+            except Exception:
+                self._buffer = batch + self._buffer
+                raise
+
+    def get_completion_data(self) -> dict:
+        """Return accumulated token and message data for run completion."""
+        return {
+            "total_input_tokens": self._total_input_tokens,
+            "total_output_tokens": self._total_output_tokens,
+            "total_tokens": self._total_tokens,
+            "llm_call_count": self._llm_call_count,
+            "lead_agent_tokens": self._lead_agent_tokens,
+            "subagent_tokens": self._subagent_tokens,
+            "middleware_tokens": self._middleware_tokens,
+            "message_count": self._msg_count,
+            "last_ai_message": self._last_ai_msg,
+            "first_human_message": self._first_human_msg,
+        }

backend/packages/harness/deerflow/runtime/runs/__init__.py

@@ -2,11 +2,12 @@
 
 from .manager import ConflictError, RunManager, RunRecord, UnsupportedStrategyError
 from .schemas import DisconnectMode, RunStatus
-from .worker import run_agent
+from .worker import RunContext, run_agent
 
 __all__ = [
     "ConflictError",
     "DisconnectMode",
+    "RunContext",
     "RunManager",
     "RunRecord",
     "RunStatus",

backend/packages/harness/deerflow/runtime/runs/manager.py

@@ -1,4 +1,4 @@
-"""In-memory run registry."""
+"""In-memory run registry with optional persistent RunStore backing."""
 
 from __future__ import annotations
 
@@ -7,9 +7,13 @@ import logging
 import uuid
 from dataclasses import dataclass, field
 from datetime import UTC, datetime
+from typing import TYPE_CHECKING
 
 from .schemas import DisconnectMode, RunStatus
 
+if TYPE_CHECKING:
+    from deerflow.runtime.runs.store.base import RunStore
+
 logger = logging.getLogger(__name__)
 
 
@@ -38,11 +42,43 @@ class RunRecord:
 
 
 class RunManager:
-    """In-memory run registry.  All mutations are protected by an asyncio lock."""
+    """In-memory run registry with optional persistent RunStore backing.
 
-    def __init__(self) -> None:
+    All mutations are protected by an asyncio lock. When a ``store`` is
+    provided, serializable metadata is also persisted to the store so
+    that run history survives process restarts.
+    """
+
+    def __init__(self, store: RunStore | None = None) -> None:
         self._runs: dict[str, RunRecord] = {}
         self._lock = asyncio.Lock()
+        self._store = store
+
+    async def _persist_to_store(self, record: RunRecord) -> None:
+        """Best-effort persist run record to backing store."""
+        if self._store is None:
+            return
+        try:
+            await self._store.put(
+                record.run_id,
+                thread_id=record.thread_id,
+                assistant_id=record.assistant_id,
+                status=record.status.value,
+                multitask_strategy=record.multitask_strategy,
+                metadata=record.metadata or {},
+                kwargs=record.kwargs or {},
+                created_at=record.created_at,
+            )
+        except Exception:
+            logger.warning("Failed to persist run %s to store", record.run_id, exc_info=True)
+
+    async def update_run_completion(self, run_id: str, **kwargs) -> None:
+        """Persist token usage and completion data to the backing store."""
+        if self._store is not None:
+            try:
+                await self._store.update_run_completion(run_id, **kwargs)
+            except Exception:
+                logger.warning("Failed to persist run completion for %s", run_id, exc_info=True)
 
     async def create(
         self,
@@ -71,6 +107,7 @@ class RunManager:
         )
         async with self._lock:
             self._runs[run_id] = record
+        await self._persist_to_store(record)
         logger.info("Run created: run_id=%s thread_id=%s", run_id, thread_id)
         return record
 
@@ -83,7 +120,7 @@ class RunManager:
         async with self._lock:
             # Dict insertion order matches creation order, so reversing it gives
             # us deterministic newest-first results even when timestamps tie.
-            return [r for r in reversed(self._runs.values()) if r.thread_id == thread_id]
+            return [r for r in self._runs.values() if r.thread_id == thread_id]
 
     async def set_status(self, run_id: str, status: RunStatus, *, error: str | None = None) -> None:
         """Transition a run to a new status."""
@@ -96,6 +133,11 @@ class RunManager:
             record.updated_at = _now_iso()
             if error is not None:
                 record.error = error
+        if self._store is not None:
+            try:
+                await self._store.update_status(run_id, status.value, error=error)
+            except Exception:
+                logger.warning("Failed to persist status update for run %s", run_id, exc_info=True)
         logger.info("Run %s -> %s", run_id, status.value)
 
     async def cancel(self, run_id: str, *, action: str = "interrupt") -> bool:
@@ -185,6 +227,7 @@ class RunManager:
             )
             self._runs[run_id] = record
 
+        await self._persist_to_store(record)
         logger.info("Run created: run_id=%s thread_id=%s", run_id, thread_id)
         return record
 

backend/packages/harness/deerflow/runtime/runs/store/__init__.py

@@ -0,0 +1,4 @@
+from deerflow.runtime.runs.store.base import RunStore
+from deerflow.runtime.runs.store.memory import MemoryRunStore
+
+__all__ = ["MemoryRunStore", "RunStore"]

backend/packages/harness/deerflow/runtime/runs/store/base.py

@@ -0,0 +1,95 @@
+"""Abstract interface for run metadata storage.
+
+RunManager depends on this interface. Implementations:
+- MemoryRunStore: in-memory dict (development, tests)
+- Future: RunRepository backed by SQLAlchemy ORM
+
+All methods accept an optional user_id for user isolation.
+When user_id is None, no user filtering is applied (single-user mode).
+"""
+
+from __future__ import annotations
+
+import abc
+from typing import Any
+
+
+class RunStore(abc.ABC):
+    @abc.abstractmethod
+    async def put(
+        self,
+        run_id: str,
+        *,
+        thread_id: str,
+        assistant_id: str | None = None,
+        user_id: str | None = None,
+        status: str = "pending",
+        multitask_strategy: str = "reject",
+        metadata: dict[str, Any] | None = None,
+        kwargs: dict[str, Any] | None = None,
+        error: str | None = None,
+        created_at: str | None = None,
+    ) -> None:
+        pass
+
+    @abc.abstractmethod
+    async def get(self, run_id: str) -> dict[str, Any] | None:
+        pass
+
+    @abc.abstractmethod
+    async def list_by_thread(
+        self,
+        thread_id: str,
+        *,
+        user_id: str | None = None,
+        limit: int = 100,
+    ) -> list[dict[str, Any]]:
+        pass
+
+    @abc.abstractmethod
+    async def update_status(
+        self,
+        run_id: str,
+        status: str,
+        *,
+        error: str | None = None,
+    ) -> None:
+        pass
+
+    @abc.abstractmethod
+    async def delete(self, run_id: str) -> None:
+        pass
+
+    @abc.abstractmethod
+    async def update_run_completion(
+        self,
+        run_id: str,
+        *,
+        status: str,
+        total_input_tokens: int = 0,
+        total_output_tokens: int = 0,
+        total_tokens: int = 0,
+        llm_call_count: int = 0,
+        lead_agent_tokens: int = 0,
+        subagent_tokens: int = 0,
+        middleware_tokens: int = 0,
+        message_count: int = 0,
+        last_ai_message: str | None = None,
+        first_human_message: str | None = None,
+        error: str | None = None,
+    ) -> None:
+        pass
+
+    @abc.abstractmethod
+    async def list_pending(self, *, before: str | None = None) -> list[dict[str, Any]]:
+        pass
+
+    @abc.abstractmethod
+    async def aggregate_tokens_by_thread(self, thread_id: str) -> dict[str, Any]:
+        """Aggregate token usage for completed runs in a thread.
+
+        Returns a dict with keys: total_tokens, total_input_tokens,
+        total_output_tokens, total_runs, by_model (model_name → {tokens, runs}),
+        by_caller ({lead_agent, subagent, middleware}).
+        """
+        pass

backend/packages/harness/deerflow/runtime/runs/store/memory.py

@@ -0,0 +1,98 @@
+"""In-memory RunStore. Used when database.backend=memory (default) and in tests.
+
+Equivalent to the original RunManager._runs dict behavior.
+"""
+
+from __future__ import annotations
+
+from datetime import UTC, datetime
+from typing import Any
+
+from deerflow.runtime.runs.store.base import RunStore
+
+
+class MemoryRunStore(RunStore):
+    def __init__(self) -> None:
+        self._runs: dict[str, dict[str, Any]] = {}
+
+    async def put(
+        self,
+        run_id,
+        *,
+        thread_id,
+        assistant_id=None,
+        user_id=None,
+        status="pending",
+        multitask_strategy="reject",
+        metadata=None,
+        kwargs=None,
+        error=None,
+        created_at=None,
+    ):
+        now = datetime.now(UTC).isoformat()
+        self._runs[run_id] = {
+            "run_id": run_id,
+            "thread_id": thread_id,
+            "assistant_id": assistant_id,
+            "user_id": user_id,
+            "status": status,
+            "multitask_strategy": multitask_strategy,
+            "metadata": metadata or {},
+            "kwargs": kwargs or {},
+            "error": error,
+            "created_at": created_at or now,
+            "updated_at": now,
+        }
+
+    async def get(self, run_id):
+        return self._runs.get(run_id)
+
+    async def list_by_thread(self, thread_id, *, user_id=None, limit=100):
+        results = [r for r in self._runs.values() if r["thread_id"] == thread_id and (user_id is None or r.get("user_id") == user_id)]
+        results.sort(key=lambda r: r["created_at"], reverse=True)
+        return results[:limit]
+
+    async def update_status(self, run_id, status, *, error=None):
+        if run_id in self._runs:
+            self._runs[run_id]["status"] = status
+            if error is not None:
+                self._runs[run_id]["error"] = error
+            self._runs[run_id]["updated_at"] = datetime.now(UTC).isoformat()
+
+    async def delete(self, run_id):
+        self._runs.pop(run_id, None)
+
+    async def update_run_completion(self, run_id, *, status, **kwargs):
+        if run_id in self._runs:
+            self._runs[run_id]["status"] = status
+            for key, value in kwargs.items():
+                if value is not None:
+                    self._runs[run_id][key] = value
+            self._runs[run_id]["updated_at"] = datetime.now(UTC).isoformat()
+
+    async def list_pending(self, *, before=None):
+        now = before or datetime.now(UTC).isoformat()
+        results = [r for r in self._runs.values() if r["status"] == "pending" and r["created_at"] <= now]
+        results.sort(key=lambda r: r["created_at"])
+        return results
+
+    async def aggregate_tokens_by_thread(self, thread_id: str) -> dict[str, Any]:
+        completed = [r for r in self._runs.values() if r["thread_id"] == thread_id and r.get("status") in ("success", "error")]
+        by_model: dict[str, dict] = {}
+        for r in completed:
+            model = r.get("model_name") or "unknown"
+            entry = by_model.setdefault(model, {"tokens": 0, "runs": 0})
+            entry["tokens"] += r.get("total_tokens", 0)
+            entry["runs"] += 1
+        return {
+            "total_tokens": sum(r.get("total_tokens", 0) for r in completed),
+            "total_input_tokens": sum(r.get("total_input_tokens", 0) for r in completed),
+            "total_output_tokens": sum(r.get("total_output_tokens", 0) for r in completed),
+            "total_runs": len(completed),
+            "by_model": by_model,
+            "by_caller": {
+                "lead_agent": sum(r.get("lead_agent_tokens", 0) for r in completed),
+                "subagent": sum(r.get("subagent_tokens", 0) for r in completed),
+                "middleware": sum(r.get("middleware_tokens", 0) for r in completed),
+            },
+        }

backend/packages/harness/deerflow/runtime/runs/worker.py

@@ -19,7 +19,11 @@ import asyncio
 import copy
 import inspect
 import logging
-from typing import Any, Literal
+from dataclasses import dataclass, field
+from typing import TYPE_CHECKING, Any, Literal
+
+if TYPE_CHECKING:
+    from langchain_core.messages import HumanMessage
 
 from deerflow.runtime.serialization import serialize
 from deerflow.runtime.stream_bridge import StreamBridge
@@ -33,13 +37,28 @@ logger = logging.getLogger(__name__)
 _VALID_LG_MODES = {"values", "updates", "checkpoints", "tasks", "debug", "messages", "custom"}
 
 
+@dataclass(frozen=True)
+class RunContext:
+    """Infrastructure dependencies for a single agent run.
+
+    Groups checkpointer, store, and persistence-related singletons so that
+    ``run_agent`` (and any future callers) receive one object instead of a
+    growing list of keyword arguments.
+    """
+
+    checkpointer: Any
+    store: Any | None = field(default=None)
+    event_store: Any | None = field(default=None)
+    run_events_config: Any | None = field(default=None)
+    thread_store: Any | None = field(default=None)
+
+
 async def run_agent(
     bridge: StreamBridge,
     run_manager: RunManager,
     record: RunRecord,
     *,
-    checkpointer: Any,
-    store: Any | None = None,
+    ctx: RunContext,
     agent_factory: Any,
     graph_input: dict,
     config: dict,
@@ -50,6 +69,13 @@ async def run_agent(
 ) -> None:
     """Execute an agent in the background, publishing events to *bridge*."""
 
+    # Unpack infrastructure dependencies from RunContext.
+    checkpointer = ctx.checkpointer
+    store = ctx.store
+    event_store = ctx.event_store
+    run_events_config = ctx.run_events_config
+    thread_store = ctx.thread_store
+
     run_id = record.run_id
     thread_id = record.thread_id
     requested_modes: set[str] = set(stream_modes or ["values"])
@@ -57,6 +83,10 @@ async def run_agent(
     pre_run_snapshot: dict[str, Any] | None = None
     snapshot_capture_failed = False
 
+    journal = None
+
+    journal = None
+
     # Track whether "events" was requested but skipped
     if "events" in requested_modes:
         logger.info(
@@ -65,6 +95,22 @@ async def run_agent(
         )
 
     try:
+        # Initialize RunJournal + write human_message event.
+        # These are inside the try block so any exception (e.g. a DB
+        # error writing the event) flows through the except/finally
+        # path that publishes an "end" event to the SSE bridge —
+        # otherwise a failure here would leave the stream hanging
+        # with no terminator.
+        if event_store is not None:
+            from deerflow.runtime.journal import RunJournal
+
+            journal = RunJournal(
+                run_id=run_id,
+                thread_id=thread_id,
+                event_store=event_store,
+                track_token_usage=getattr(run_events_config, "track_token_usage", True),
+            )
+
         # 1. Mark running
         await run_manager.set_status(run_id, RunStatus.running)
 
@@ -102,14 +148,20 @@ async def run_agent(
 
         # Inject runtime context so middlewares can access thread_id
         # (langgraph-cli does this automatically; we must do it manually)
-        runtime = Runtime(context={"thread_id": thread_id}, store=store)
+        runtime = Runtime(context={"thread_id": thread_id, "run_id": run_id}, store=store)
         # If the caller already set a ``context`` key (LangGraph >= 0.6.0
         # prefers it over ``configurable`` for thread-level data), make
         # sure ``thread_id`` is available there too.
         if "context" in config and isinstance(config["context"], dict):
             config["context"].setdefault("thread_id", thread_id)
+            config["context"].setdefault("run_id", run_id)
         config.setdefault("configurable", {})["__pregel_runtime"] = runtime
 
+        # Inject RunJournal as a LangChain callback handler.
+        # on_llm_end captures token usage; on_chain_start/end captures lifecycle.
+        if journal is not None:
+            config.setdefault("callbacks", []).append(journal)
+
         runnable_config = RunnableConfig(**config)
         agent = agent_factory(config=runnable_config)
 
@@ -236,6 +288,41 @@ async def run_agent(
         )
 
     finally:
+        # Flush any buffered journal events and persist completion data
+        if journal is not None:
+            try:
+                await journal.flush()
+            except Exception:
+                logger.warning("Failed to flush journal for run %s", run_id, exc_info=True)
+
+            try:
+                # Persist token usage + convenience fields to RunStore
+                completion = journal.get_completion_data()
+                await run_manager.update_run_completion(run_id, status=record.status.value, **completion)
+            except Exception:
+                logger.warning("Failed to persist run completion for %s (non-fatal)", run_id, exc_info=True)
+
+        # Sync title from checkpoint to threads_meta.display_name
+        if checkpointer is not None and thread_store is not None:
+            try:
+                ckpt_config = {"configurable": {"thread_id": thread_id, "checkpoint_ns": ""}}
+                ckpt_tuple = await checkpointer.aget_tuple(ckpt_config)
+                if ckpt_tuple is not None:
+                    ckpt = getattr(ckpt_tuple, "checkpoint", {}) or {}
+                    title = ckpt.get("channel_values", {}).get("title")
+                    if title:
+                        await thread_store.update_display_name(thread_id, title)
+            except Exception:
+                logger.debug("Failed to sync title for thread %s (non-fatal)", thread_id)
+
+        # Update threads_meta status based on run outcome
+        if thread_store is not None:
+            try:
+                final_status = "idle" if record.status == RunStatus.success else record.status.value
+                await thread_store.update_status(thread_id, final_status)
+            except Exception:
+                logger.debug("Failed to update thread_meta status for %s (non-fatal)", thread_id)
+
         await bridge.publish_end(run_id)
         asyncio.create_task(bridge.cleanup(run_id, delay=60))
 
@@ -355,6 +442,31 @@ def _lg_mode_to_sse_event(mode: str) -> str:
     return mode
 
 
+def _extract_human_message(graph_input: dict) -> HumanMessage | None:
+    """Extract or construct a HumanMessage from graph_input for event recording.
+
+    Returns a LangChain HumanMessage so callers can use .model_dump() to get
+    the checkpoint-aligned serialization format.
+    """
+    from langchain_core.messages import HumanMessage
+
+    messages = graph_input.get("messages")
+    if not messages:
+        return None
+    last = messages[-1] if isinstance(messages, list) else messages
+    if isinstance(last, HumanMessage):
+        return last
+    if isinstance(last, str):
+        return HumanMessage(content=last) if last else None
+    if hasattr(last, "content"):
+        content = last.content
+        return HumanMessage(content=content)
+    if isinstance(last, dict):
+        content = last.get("content", "")
+        return HumanMessage(content=content) if content else None
+    return None
+
+
 def _unpack_stream_item(
     item: Any,
     lg_modes: list[str],