fix(task): tolerate invalid default config in usage cache

* fix(memory): isolate queued memory updates by agent

* fix(memory): include user in queue identity

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* Fix the lint error

---------

Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

backend/docs/Storage_Design.md

@@ -0,0 +1,401 @@
+# Storage Package Design
+
+## Background
+
+DeerFlow currently has several persistence responsibilities spread across app, gateway, runtime, and legacy persistence modules. This makes the persistence boundary difficult to reason about and creates several migration risks:
+
+- Routers and runtime services can accidentally depend on concrete persistence implementations instead of stable contracts.
+- User/auth, run metadata, thread metadata, feedback, run events, and checkpointer setup are initialized through different paths.
+- Some persistence behavior is duplicated between memory, SQLite, and PostgreSQL-oriented code paths.
+- Incremental migration is hard because app-level code and storage-level code are coupled.
+- Adding or validating another SQL backend requires touching app/runtime code instead of a storage-owned package.
+
+The storage package is introduced to make application data persistence a package-level capability with explicit contracts, a clear boundary, and SQL backend compatibility.
+
+## Goals
+
+- Provide a standalone `packages/storage` package for durable application data.
+- Support SQLite, PostgreSQL, and MySQL through a shared persistence construction flow.
+- Keep LangGraph checkpointer initialization compatible with the same database backend.
+- Expose repository contracts as the only package-level data access boundary.
+- Let the app layer depend on app-owned adapters under `app.infra.storage`, not on storage DB implementation classes.
+- Allow the app/gateway migration to happen in small steps without forcing a large rewrite.
+
+## Non-Goals
+
+- This design does not remove legacy persistence in the first PR.
+- This design does not move routers directly onto storage package models.
+- This design does not make app routers own SQLAlchemy sessions.
+- Cron persistence is intentionally out of scope for the storage package foundation.
+- Memory backend is not part of the durable storage package. Memory compatibility, if still needed by app runtime, belongs outside `packages/storage`.
+
+## Storage Design Principles
+
+### Package-Owned Durable Storage
+
+`packages/storage` owns durable application data persistence. It defines:
+
+- configuration shape for storage-backed persistence
+- SQLAlchemy models
+- repository contracts and DTOs
+- SQL repository implementations
+- persistence factory functions
+- compatibility helpers for config-driven initialization
+
+The package should be usable without importing `app.gateway`, routers, auth providers, or runtime-specific gateway objects.
+
+### SQL Backend Compatibility
+
+The package supports three SQL backends:
+
+- SQLite for local/single-node deployments
+- PostgreSQL for production multi-node deployments
+- MySQL for deployments that standardize on MySQL
+
+Backend-specific differences are handled inside the storage package:
+
+- SQLAlchemy async engine URL construction
+- LangGraph checkpointer connection-string compatibility
+- JSON metadata filtering across SQLite/PostgreSQL/MySQL
+- SQL dialect behavior around locking, aggregation, and JSON type semantics
+
+### Unified Persistence Bundle
+
+Storage initialization returns an `AppPersistence` bundle:
+
+```python
+@dataclass(slots=True)
+class AppPersistence:
+    checkpointer: Checkpointer
+    engine: AsyncEngine
+    session_factory: async_sessionmaker[AsyncSession]
+    setup: Callable[[], Awaitable[None]]
+    aclose: Callable[[], Awaitable[None]]
+```
+
+The app runtime can initialize persistence once, call `setup()`, and then inject:
+
+- `checkpointer`
+- `session_factory`
+- repository adapters
+
+This keeps checkpointer and application data aligned to the same backend without requiring routers to understand database configuration.
+
+## Package Layout
+
+```text
+backend/packages/storage/
+  store/
+    config/
+      storage_config.py
+      app_config.py
+    persistence/
+      factory.py
+      types.py
+      base_model.py
+      json_compat.py
+      drivers/
+        sqlite.py
+        postgres.py
+        mysql.py
+    repositories/
+      contracts/
+        user.py
+        run.py
+        thread_meta.py
+        feedback.py
+        run_event.py
+      models/
+        user.py
+        run.py
+        thread_meta.py
+        feedback.py
+        run_event.py
+      db/
+        user.py
+        run.py
+        thread_meta.py
+        feedback.py
+        run_event.py
+      factory.py
+```
+
+## Persistence Construction
+
+The primary storage entrypoint is:
+
+```python
+from store.persistence import create_persistence_from_storage_config
+
+persistence = await create_persistence_from_storage_config(storage_config)
+await persistence.setup()
+```
+
+For app-level compatibility with existing database config shape:
+
+```python
+from store.persistence import create_persistence_from_database_config
+
+persistence = await create_persistence_from_database_config(config.database)
+await persistence.setup()
+```
+
+Expected app startup flow:
+
+```python
+persistence = await create_persistence_from_database_config(config.database)
+await persistence.setup()
+
+app.state.persistence = persistence
+app.state.checkpointer = persistence.checkpointer
+app.state.session_factory = persistence.session_factory
+```
+
+Expected app shutdown flow:
+
+```python
+await app.state.persistence.aclose()
+```
+
+## Repository Contract Design
+
+Repository contracts are the storage package's public data access boundary. They live under `store.repositories.contracts` and are re-exported from `store.repositories`.
+
+The key contract groups are:
+
+- `UserRepositoryProtocol`
+- `RunRepositoryProtocol`
+- `ThreadMetaRepositoryProtocol`
+- `FeedbackRepositoryProtocol`
+- `RunEventRepositoryProtocol`
+
+Each contract owns:
+
+- input DTOs, such as `UserCreate`, `RunCreate`, `ThreadMetaCreate`
+- output DTOs, such as `User`, `Run`, `ThreadMeta`
+- repository protocol methods
+- domain-specific exceptions when needed, such as `InvalidMetadataFilterError`
+
+Repository construction is session-based:
+
+```python
+from store.repositories import build_run_repository
+
+async with persistence.session_factory() as session:
+    repo = build_run_repository(session)
+    run = await repo.get_run(run_id)
+```
+
+This keeps transaction ownership explicit. The storage package does not hide commits or session lifecycle inside global singletons.
+
+## App/Infra Calling Contract
+
+The app layer should not call `store.repositories.db.*` directly. The intended app boundary is `app.infra.storage`.
+
+`app.infra.storage` is responsible for:
+
+- receiving `session_factory` from FastAPI runtime initialization
+- owning session lifecycle for app-facing repository methods
+- translating storage DTOs to app/gateway DTOs only when needed
+- preserving the existing app-facing names during migration
+- depending on storage repository protocols, not concrete DB classes
+
+Expected adapter pattern:
+
+```python
+class StorageRunRepository(RunRepositoryProtocol):
+    def __init__(self, session_factory):
+        self._session_factory = session_factory
+
+    async def get_run(self, run_id: str):
+        async with self._session_factory() as session:
+            repo = build_run_repository(session)
+            return await repo.get_run(run_id)
+```
+
+For gateway compatibility, app state can keep existing names while the implementation changes:
+
+```python
+app.state.run_store = StorageRunStore(run_repository)
+app.state.feedback_repo = StorageFeedbackStore(feedback_repository)
+app.state.thread_store = StorageThreadMetaStore(thread_meta_repository)
+app.state.run_event_store = StorageRunEventStore(run_event_repository)
+app.state.checkpointer = persistence.checkpointer
+app.state.session_factory = persistence.session_factory
+```
+
+The app-facing objects may expose legacy method names during migration, but their internal data access should go through storage contracts.
+
+## Boundary Rules
+
+### Allowed Calls
+
+Storage package callers may use:
+
+```python
+from store.persistence import create_persistence_from_database_config
+from store.persistence import create_persistence_from_storage_config
+from store.repositories import build_run_repository
+from store.repositories import build_user_repository
+from store.repositories import build_thread_meta_repository
+from store.repositories import build_feedback_repository
+from store.repositories import build_run_event_repository
+from store.repositories import RunRepositoryProtocol
+from store.repositories import UserRepositoryProtocol
+```
+
+App layer callers should use:
+
+```python
+from app.infra.storage import StorageRunRepository
+from app.infra.storage import StorageUserDataRepository
+from app.infra.storage import StorageThreadMetaRepository
+from app.infra.storage import StorageFeedbackRepository
+from app.infra.storage import StorageRunEventRepository
+```
+
+### Prohibited Calls
+
+App/gateway/router/auth code must not import:
+
+```python
+from store.repositories.db import DbRunRepository
+from store.repositories.models import Run
+from store.persistence.base_model import MappedBase
+```
+
+Routers must not:
+
+- create SQLAlchemy engines
+- create SQLAlchemy sessions directly
+- call storage DB repository classes directly
+- commit/rollback storage transactions directly unless explicitly scoped by an infra adapter
+- depend on storage SQLAlchemy model classes
+
+Storage package code must not import:
+
+```python
+import app.gateway
+import app.infra
+import deerflow.runtime
+```
+
+The dependency direction is:
+
+```text
+app/gateway -> app.infra.storage -> packages/storage contracts/factories -> packages/storage db implementations
+```
+
+The reverse direction is forbidden.
+
+## Checkpointer Compatibility
+
+The storage persistence bundle initializes the LangGraph checkpointer alongside application data persistence.
+
+Backend-specific notes:
+
+- SQLite uses `langgraph-checkpoint-sqlite`.
+- PostgreSQL uses `langgraph-checkpoint-postgres` and requires a string `postgresql://...` connection URL.
+- MySQL uses `langgraph-checkpoint-mysql` and requires a string MySQL connection URL.
+
+SQLAlchemy may use async driver URLs such as `postgresql+asyncpg://...` or `mysql+aiomysql://...`, but LangGraph checkpointer constructors expect plain string connection URLs. This conversion belongs inside the storage driver implementation.
+
+## JSON Metadata Filtering
+
+Thread metadata search supports dialect-aware JSON filtering through `store.persistence.json_compat`.
+
+The matcher supports:
+
+- `None`
+- `bool`
+- `int`
+- `float`
+- `str`
+
+It rejects:
+
+- unsafe keys
+- nested JSON path expressions
+- dict/list values
+- integers outside signed 64-bit range
+
+This prevents SQL/JSON path injection, avoids compiled-cache type drift, and preserves type semantics such as `True != 1` and explicit JSON `null` not matching a missing key.
+
+## Step-by-Step Implementation Plan
+
+### Step 1: Introduce Storage Package Foundation
+
+- Add `backend/packages/storage`.
+- Add storage config models.
+- Add `AppPersistence`.
+- Add SQLite/PostgreSQL/MySQL persistence drivers.
+- Add repository contracts, models, DB implementations, and factory helpers.
+- Add package dependency wiring.
+- Exclude cron persistence.
+
+### Step 2: Harden Storage Backend Compatibility
+
+- Validate SQLite setup and repository behavior.
+- Validate PostgreSQL and MySQL with local E2E tests.
+- Fix checkpointer connection-string compatibility.
+- Fix PostgreSQL locking and aggregation differences.
+- Add dialect-aware JSON metadata filtering.
+
+### Step 3: Add App Infra Adapters
+
+- Add `backend/app/infra/storage`.
+- Implement app-facing repositories that own session lifecycle.
+- Keep storage contracts as the only data access boundary.
+- Add legacy compatibility adapters for existing app/gateway method shapes.
+- Keep app/gateway imports out of `packages/storage`.
+
+### Step 4: Switch FastAPI Runtime Injection
+
+- Initialize storage persistence in FastAPI startup/lifespan.
+- Attach `persistence`, `checkpointer`, and `session_factory` to `app.state`.
+- Preserve existing external state names:
+  - `run_store`
+  - `feedback_repo`
+  - `thread_store`
+  - `run_event_store`
+  - `checkpointer`
+  - `session_factory`
+- Start with user/auth provider construction, then migrate run/thread/feedback/run_event.
+
+### Step 5: Router and Auth Compatibility
+
+- Ensure routers consume app-facing adapters, not storage DB classes.
+- Ensure auth providers depend on user repository contracts.
+- Keep router response shapes unchanged.
+- Add focused auth/admin/router regression tests.
+
+### Step 6: Cleanup Legacy Persistence
+
+- Compare old persistence usage after app/gateway migration.
+- Remove unused old repository implementations only after all call sites move.
+- Keep compatibility shims only where needed for a transition window.
+- Delete memory backend paths from storage-owned durable persistence.
+
+## Testing Strategy
+
+Unit tests should cover:
+
+- config parsing
+- persistence setup
+- table creation
+- repository CRUD/query behavior
+- typed JSON metadata filtering
+- dialect SQL compilation
+- cron exclusion
+
+E2E tests should cover:
+
+- SQLite persistence setup
+- PostgreSQL temporary database setup
+- MySQL temporary database setup
+- repository contract behavior across all supported SQL backends
+- JSON/Unicode round trip
+- rollback behavior
+- persistence close/cleanup
+
+E2E tests may remain local-only if CI does not provide PostgreSQL/MySQL services.

backend/docs/Storage_Design_ZH.md

@@ -0,0 +1,401 @@
+# Storage Package 设计文档
+
+## 背景
+
+DeerFlow 当前有多类持久化职责分散在 app、gateway、runtime 和旧 persistence 模块中。这会带来几个问题：
+
+- routers 和 runtime services 容易依赖具体 persistence 实现，而不是稳定契约。
+- user/auth、run metadata、thread metadata、feedback、run events、checkpointer setup 的初始化路径不统一。
+- memory、SQLite、PostgreSQL 相关路径中存在部分重复逻辑。
+- app 层代码和 storage 层代码耦合，导致增量迁移困难。
+- 增加或验证新的 SQL backend 时，需要改动 app/runtime，而不是只改 storage package。
+
+引入 storage package 的目标，是把应用数据持久化抽象成 package 级能力，并提供明确契约、清晰边界和 SQL backend 兼容性。
+
+## 目标
+
+- 新增独立的 `packages/storage`，负责 durable application data。
+- 通过统一 persistence 构造流程支持 SQLite、PostgreSQL、MySQL。
+- 保持 LangGraph checkpointer 与同一个数据库 backend 兼容。
+- 将 repository contracts 作为 package 对外唯一数据访问边界。
+- app 层通过 `app.infra.storage` 适配 storage，而不是直接依赖 storage DB 实现类。
+- 支持 app/gateway 后续小步迁移，避免一次性大重构。
+
+## 非目标
+
+- 第一阶段不删除旧 persistence。
+- 不让 routers 直接依赖 storage package models。
+- 不让 app routers 管理 SQLAlchemy sessions。
+- cron persistence 不属于 storage package 基础迁移范围。
+- memory backend 不属于 durable storage package。若 app runtime 仍需要 memory 兼容，应放在 `packages/storage` 之外。
+
+## Storage 设计理念
+
+### Package 自己负责 Durable Storage
+
+`packages/storage` 负责应用数据的 durable persistence，包括：
+
+- storage 持久化配置
+- SQLAlchemy models
+- repository contracts 和 DTOs
+- SQL repository 实现
+- persistence factory functions
+- 面向现有 config 的兼容初始化入口
+
+该 package 不应该 import `app.gateway`、routers、auth providers 或 runtime 中的 gateway 对象。
+
+### SQL Backend 兼容
+
+该 package 支持三种 SQL backend：
+
+- SQLite：本地或单节点部署
+- PostgreSQL：生产多节点部署
+- MySQL：使用 MySQL 作为标准数据库的部署
+
+backend 差异在 storage package 内部处理：
+
+- SQLAlchemy async engine URL 构造
+- LangGraph checkpointer 连接串兼容
+- SQLite/PostgreSQL/MySQL 的 JSON metadata filter
+- 不同 SQL 方言在 locking、aggregation、JSON 类型语义上的差异
+
+### 统一 Persistence Bundle
+
+Storage 初始化返回 `AppPersistence` bundle：
+
+```python
+@dataclass(slots=True)
+class AppPersistence:
+    checkpointer: Checkpointer
+    engine: AsyncEngine
+    session_factory: async_sessionmaker[AsyncSession]
+    setup: Callable[[], Awaitable[None]]
+    aclose: Callable[[], Awaitable[None]]
+```
+
+app runtime 只需要初始化一次 persistence，调用 `setup()`，然后注入：
+
+- `checkpointer`
+- `session_factory`
+- repository adapters
+
+这样 checkpointer 和应用数据可以对齐到同一个 backend，同时 routers 不需要理解数据库配置。
+
+## Package 结构
+
+```text
+backend/packages/storage/
+  store/
+    config/
+      storage_config.py
+      app_config.py
+    persistence/
+      factory.py
+      types.py
+      base_model.py
+      json_compat.py
+      drivers/
+        sqlite.py
+        postgres.py
+        mysql.py
+    repositories/
+      contracts/
+        user.py
+        run.py
+        thread_meta.py
+        feedback.py
+        run_event.py
+      models/
+        user.py
+        run.py
+        thread_meta.py
+        feedback.py
+        run_event.py
+      db/
+        user.py
+        run.py
+        thread_meta.py
+        feedback.py
+        run_event.py
+      factory.py
+```
+
+## Persistence 构造
+
+storage 的主要入口：
+
+```python
+from store.persistence import create_persistence_from_storage_config
+
+persistence = await create_persistence_from_storage_config(storage_config)
+await persistence.setup()
+```
+
+为了兼容现有 app database config，也提供：
+
+```python
+from store.persistence import create_persistence_from_database_config
+
+persistence = await create_persistence_from_database_config(config.database)
+await persistence.setup()
+```
+
+预期 app startup 流程：
+
+```python
+persistence = await create_persistence_from_database_config(config.database)
+await persistence.setup()
+
+app.state.persistence = persistence
+app.state.checkpointer = persistence.checkpointer
+app.state.session_factory = persistence.session_factory
+```
+
+预期 app shutdown 流程：
+
+```python
+await app.state.persistence.aclose()
+```
+
+## Repository 契约设计
+
+Repository contracts 是 storage package 对外公开的数据访问边界。它们位于 `store.repositories.contracts`，并通过 `store.repositories` re-export。
+
+主要契约包括：
+
+- `UserRepositoryProtocol`
+- `RunRepositoryProtocol`
+- `ThreadMetaRepositoryProtocol`
+- `FeedbackRepositoryProtocol`
+- `RunEventRepositoryProtocol`
+
+每组契约包含：
+
+- 输入 DTO，例如 `UserCreate`、`RunCreate`、`ThreadMetaCreate`
+- 输出 DTO，例如 `User`、`Run`、`ThreadMeta`
+- repository protocol methods
+- 必要的领域异常，例如 `InvalidMetadataFilterError`
+
+Repository 通过 session 构造：
+
+```python
+from store.repositories import build_run_repository
+
+async with persistence.session_factory() as session:
+    repo = build_run_repository(session)
+    run = await repo.get_run(run_id)
+```
+
+这样可以让 transaction ownership 保持明确。storage package 不通过全局 singleton 隐式隐藏 commit 或 session 生命周期。
+
+## App/Infra 调用契约
+
+app 层不应该直接调用 `store.repositories.db.*`。预期的 app 边界是 `app.infra.storage`。
+
+`app.infra.storage` 负责：
+
+- 从 FastAPI runtime 初始化中接收 `session_factory`
+- 为 app-facing repository methods 管理 session 生命周期
+- 在必要时将 storage DTOs 转成 app/gateway DTOs
+- 迁移期间保留现有 app-facing 名称
+- 依赖 storage repository protocols，而不是具体 DB classes
+
+预期 adapter 模式：
+
+```python
+class StorageRunRepository(RunRepositoryProtocol):
+    def __init__(self, session_factory):
+        self._session_factory = session_factory
+
+    async def get_run(self, run_id: str):
+        async with self._session_factory() as session:
+            repo = build_run_repository(session)
+            return await repo.get_run(run_id)
+```
+
+为了兼容 gateway，app state 可以暂时保持现有名字，只替换内部实现：
+
+```python
+app.state.run_store = StorageRunStore(run_repository)
+app.state.feedback_repo = StorageFeedbackStore(feedback_repository)
+app.state.thread_store = StorageThreadMetaStore(thread_meta_repository)
+app.state.run_event_store = StorageRunEventStore(run_event_repository)
+app.state.checkpointer = persistence.checkpointer
+app.state.session_factory = persistence.session_factory
+```
+
+app-facing objects 可以在迁移期间保留旧方法名，但内部数据访问必须经过 storage contracts。
+
+## 边界规则
+
+### 允许调用的范围
+
+storage package 调用方可以使用：
+
+```python
+from store.persistence import create_persistence_from_database_config
+from store.persistence import create_persistence_from_storage_config
+from store.repositories import build_run_repository
+from store.repositories import build_user_repository
+from store.repositories import build_thread_meta_repository
+from store.repositories import build_feedback_repository
+from store.repositories import build_run_event_repository
+from store.repositories import RunRepositoryProtocol
+from store.repositories import UserRepositoryProtocol
+```
+
+app 层应该使用：
+
+```python
+from app.infra.storage import StorageRunRepository
+from app.infra.storage import StorageUserDataRepository
+from app.infra.storage import StorageThreadMetaRepository
+from app.infra.storage import StorageFeedbackRepository
+from app.infra.storage import StorageRunEventRepository
+```
+
+### 禁止调用的范围
+
+app/gateway/router/auth 代码不应该 import：
+
+```python
+from store.repositories.db import DbRunRepository
+from store.repositories.models import Run
+from store.persistence.base_model import MappedBase
+```
+
+routers 禁止：
+
+- 创建 SQLAlchemy engines
+- 直接创建 SQLAlchemy sessions
+- 直接调用 storage DB repository classes
+- 直接 commit/rollback storage transactions，除非这是 infra adapter 明确管理的范围
+- 依赖 storage SQLAlchemy model classes
+
+storage package 禁止 import：
+
+```python
+import app.gateway
+import app.infra
+import deerflow.runtime
+```
+
+依赖方向必须是：
+
+```text
+app/gateway -> app.infra.storage -> packages/storage contracts/factories -> packages/storage db implementations
+```
+
+禁止反向依赖。
+
+## Checkpointer 兼容
+
+storage persistence bundle 会同时初始化 LangGraph checkpointer 和应用数据持久化。
+
+backend 说明：
+
+- SQLite 使用 `langgraph-checkpoint-sqlite`。
+- PostgreSQL 使用 `langgraph-checkpoint-postgres`，需要字符串形式的 `postgresql://...` 连接串。
+- MySQL 使用 `langgraph-checkpoint-mysql`，需要字符串形式的 MySQL 连接串。
+
+SQLAlchemy 可以使用 `postgresql+asyncpg://...` 或 `mysql+aiomysql://...` 这类 async driver URL，但 LangGraph checkpointer 构造函数需要普通字符串连接串。这个转换应该封装在 storage driver implementation 内部。
+
+## JSON Metadata Filtering
+
+Thread metadata search 通过 `store.persistence.json_compat` 支持跨方言 JSON filtering。
+
+支持的 filter value 类型：
+
+- `None`
+- `bool`
+- `int`
+- `float`
+- `str`
+
+拒绝：
+
+- unsafe keys
+- nested JSON path expressions
+- dict/list values
+- 超出 signed 64-bit 范围的整数
+
+这样可以避免 SQL/JSON path injection，避免 compiled-cache 类型漂移，并保留类型语义，例如 `True != 1`，显式 JSON `null` 不等于 missing key。
+
+## 分步实现方案
+
+### 第 1 步：新增 Storage Package 基础
+
+- 新增 `backend/packages/storage`。
+- 增加 storage config models。
+- 增加 `AppPersistence`。
+- 增加 SQLite/PostgreSQL/MySQL persistence drivers。
+- 增加 repository contracts、models、DB implementations 和 factory helpers。
+- 接入 package dependency。
+- 排除 cron persistence。
+
+### 第 2 步：补齐 Storage Backend 兼容性
+
+- 验证 SQLite setup 和 repository 行为。
+- 使用本地 E2E 验证 PostgreSQL 和 MySQL。
+- 修复 checkpointer 连接串兼容。
+- 修复 PostgreSQL locking 和 aggregation 差异。
+- 增加跨方言 JSON metadata filtering。
+
+### 第 3 步：新增 App Infra Adapters
+
+- 新增 `backend/app/infra/storage`。
+- 实现 app-facing repositories，由它们管理 session 生命周期。
+- 保持 storage contracts 作为唯一数据访问边界。
+- 为现有 app/gateway method shape 增加兼容 adapters。
+- 避免 `packages/storage` import app/gateway。
+
+### 第 4 步：切换 FastAPI Runtime 注入
+
+- 在 FastAPI startup/lifespan 中初始化 storage persistence。
+- 将 `persistence`、`checkpointer`、`session_factory` 注入 `app.state`。
+- 暂时保留现有对外 state 名称：
+  - `run_store`
+  - `feedback_repo`
+  - `thread_store`
+  - `run_event_store`
+  - `checkpointer`
+  - `session_factory`
+- 先切 user/auth provider 构造，再逐步迁移 run/thread/feedback/run_event。
+
+### 第 5 步：Router 和 Auth 兼容
+
+- 确保 routers 消费 app-facing adapters，而不是 storage DB classes。
+- 确保 auth providers 依赖 user repository contracts。
+- 保持 router response shapes 不变。
+- 增加 auth/admin/router regression tests。
+
+### 第 6 步：清理旧 Persistence
+
+- app/gateway 迁移完成后，再比较旧 persistence usage。
+- 所有 call sites 迁移完成后，再删除未使用的旧 repository implementations。
+- 只在必要时保留短期 compatibility shims。
+- 从 storage-owned durable persistence 中移除 memory backend 路径。
+
+## 测试策略
+
+单测应覆盖：
+
+- config parsing
+- persistence setup
+- table creation
+- repository CRUD/query behavior
+- typed JSON metadata filtering
+- dialect SQL compilation
+- cron exclusion
+
+E2E 应覆盖：
+
+- SQLite persistence setup
+- PostgreSQL temporary database setup
+- MySQL temporary database setup
+- 所有支持 SQL backend 下的 repository contract 行为
+- JSON/Unicode round trip
+- rollback behavior
+- persistence close/cleanup
+
+如果 CI 暂时没有 PostgreSQL/MySQL services，E2E 可以先作为 local-only 验证保留。

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

@@ -40,6 +40,15 @@ class MemoryUpdateQueue:
         self._timer: threading.Timer | None = None
         self._processing = False
 
+    @staticmethod
+    def _queue_key(
+        thread_id: str,
+        user_id: str | None,
+        agent_name: str | None,
+    ) -> tuple[str, str | None, str | None]:
+        """Return the debounce identity for a memory update target."""
+        return (thread_id, user_id, agent_name)
+
     def add(
         self,
         thread_id: str,
@@ -115,8 +124,9 @@ class MemoryUpdateQueue:
         correction_detected: bool,
         reinforcement_detected: bool,
     ) -> None:
+        queue_key = self._queue_key(thread_id, user_id, agent_name)
         existing_context = next(
-            (context for context in self._queue if context.thread_id == thread_id),
+            (context for context in self._queue if self._queue_key(context.thread_id, context.user_id, context.agent_name) == queue_key),
             None,
         )
         merged_correction_detected = correction_detected or (existing_context.correction_detected if existing_context is not None else False)
@@ -130,7 +140,7 @@ class MemoryUpdateQueue:
             reinforcement_detected=merged_reinforcement_detected,
         )
 
-        self._queue = [c for c in self._queue if c.thread_id != thread_id]
+        self._queue = [context for context in self._queue if self._queue_key(context.thread_id, context.user_id, context.agent_name) != queue_key]
         self._queue.append(context)
 
     def _reset_timer(self) -> None:

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

@@ -6,6 +6,7 @@ from deerflow.agents.memory.message_processing import detect_correction, detect_
 from deerflow.agents.memory.queue import get_memory_queue
 from deerflow.agents.middlewares.summarization_middleware import SummarizationEvent
 from deerflow.config.memory_config import get_memory_config
+from deerflow.runtime.user_context import resolve_runtime_user_id
 
 
 def memory_flush_hook(event: SummarizationEvent) -> None:
@@ -21,11 +22,13 @@ def memory_flush_hook(event: SummarizationEvent) -> None:
 
     correction_detected = detect_correction(filtered_messages)
     reinforcement_detected = not correction_detected and detect_reinforcement(filtered_messages)
+    user_id = resolve_runtime_user_id(event.runtime)
     queue = get_memory_queue()
     queue.add_nowait(
         thread_id=event.thread_id,
         messages=filtered_messages,
         agent_name=event.agent_name,
+        user_id=user_id,
         correction_detected=correction_detected,
         reinforcement_detected=reinforcement_detected,
     )

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

@@ -11,7 +11,7 @@ import logging
 from datetime import UTC, datetime
 from typing import Any
 
-from sqlalchemy import delete, func, select
+from sqlalchemy import delete, func, select, text
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
 from deerflow.persistence.models.run_event import RunEventRow
@@ -86,6 +86,28 @@ class DbRunEventStore(RunEventStore):
         user = get_current_user()
         return str(user.id) if user is not None else None
 
+    @staticmethod
+    async def _max_seq_for_thread(session: AsyncSession, thread_id: str) -> int | None:
+        """Return the current max seq while serializing writers per thread.
+
+        PostgreSQL rejects ``SELECT max(...) FOR UPDATE`` because aggregate
+        results are not lockable rows. As a release-safe workaround, take a
+        transaction-level advisory lock keyed by thread_id before reading the
+        aggregate. Other dialects keep the existing row-locking statement.
+        """
+        stmt = select(func.max(RunEventRow.seq)).where(RunEventRow.thread_id == thread_id)
+        bind = session.get_bind()
+        dialect_name = bind.dialect.name if bind is not None else ""
+
+        if dialect_name == "postgresql":
+            await session.execute(
+                text("SELECT pg_advisory_xact_lock(hashtext(CAST(:thread_id AS text))::bigint)"),
+                {"thread_id": thread_id},
+            )
+            return await session.scalar(stmt)
+
+        return await session.scalar(stmt.with_for_update())
+
     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.
 
@@ -100,10 +122,7 @@ class DbRunEventStore(RunEventStore):
         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())
+                max_seq = await self._max_seq_for_thread(session, thread_id)
                 seq = (max_seq or 0) + 1
                 row = RunEventRow(
                     thread_id=thread_id,
@@ -126,10 +145,8 @@ class DbRunEventStore(RunEventStore):
         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())
+                max_seq = await self._max_seq_for_thread(session, thread_id)
                 seq = max_seq or 0
                 rows = []
                 for e in events:

backend/packages/harness/deerflow/tools/builtins/task_tool.py

@@ -35,7 +35,7 @@ def _token_usage_cache_enabled(app_config: "AppConfig | None") -> bool:
     if app_config is None:
         try:
             app_config = get_app_config()
-        except FileNotFoundError:
+        except (FileNotFoundError, ValueError):
             return False
     return bool(getattr(getattr(app_config, "token_usage", None), "enabled", False))
 

backend/packages/storage/pyproject.toml

@@ -0,0 +1,35 @@
+[project]
+name = "deerflow-storage"
+version = "0.1.0"
+description = "DeerFlow storage framework"
+requires-python = ">=3.12"
+dependencies = [
+    "dotenv>=0.9.9",
+    "pydantic>=2.12.5",
+    "pyyaml>=6.0.3",
+    "sqlalchemy[asyncio]>=2.0,<3.0",
+    "alembic>=1.13",
+    "langgraph>=1.1.9",
+]
+[project.optional-dependencies]
+postgres = [
+    "asyncpg>=0.29",
+    "langgraph-checkpoint-postgres>=3.0.5",
+    "psycopg[binary]>=3.3.3",
+    "psycopg-pool>=3.3.0",
+]
+mysql = [
+    "aiomysql>=0.2",
+    "langgraph-checkpoint-mysql>=3.0.0",
+]
+sqlite = [
+    "aiosqlite>=0.22.1",
+    "langgraph-checkpoint-sqlite>=3.0.3"
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["store"]

backend/packages/storage/store/common/__init__.py

@@ -0,0 +1,5 @@
+from .enums import DataBaseType
+
+__all__ = [
+    "DataBaseType",
+]

backend/packages/storage/store/common/enums.py

@@ -0,0 +1,41 @@
+from enum import Enum
+from enum import IntEnum as SourceIntEnum
+from enum import StrEnum as SourceStrEnum
+from typing import Any, TypeVar
+
+T = TypeVar("T", bound=Enum)
+
+
+class _EnumBase:
+    """Base enum class with common utility methods."""
+
+    @classmethod
+    def get_member_keys(cls) -> list[str]:
+        """Return a list of enum member names."""
+        return list(cls.__members__.keys())
+
+    @classmethod
+    def get_member_values(cls) -> list:
+        """Return a list of enum member values."""
+        return [item.value for item in cls.__members__.values()]
+
+    @classmethod
+    def get_member_dict(cls) -> dict[str, Any]:
+        """Return a dict mapping member names to values."""
+        return {name: item.value for name, item in cls.__members__.items()}
+
+
+class IntEnum(_EnumBase, SourceIntEnum):
+    """Integer enum base class."""
+
+
+class StrEnum(_EnumBase, SourceStrEnum):
+    """String enum base class."""
+
+
+class DataBaseType(StrEnum):
+    """Database type."""
+
+    sqlite = "sqlite"
+    mysql = "mysql"
+    postgresql = "postgresql"

backend/packages/storage/store/config/app_config.py

@@ -0,0 +1,286 @@
+import logging
+import os
+from contextvars import ContextVar
+from pathlib import Path
+from typing import Any, Self
+
+import yaml
+from dotenv import load_dotenv
+from pydantic import BaseModel, ConfigDict, Field
+
+from store.config.storage_config import StorageConfig
+
+load_dotenv()
+
+logger = logging.getLogger(__name__)
+
+
+def _default_config_candidates() -> tuple[Path, ...]:
+    """Return deterministic config.yaml locations without relying on cwd."""
+    backend_dir = Path(__file__).resolve().parents[4]
+    repo_root = backend_dir.parent
+    cwd = Path.cwd().resolve()
+    candidates = (
+        cwd / "config.yaml",
+        backend_dir / "config.yaml",
+        repo_root / "config.yaml",
+    )
+    return tuple(dict.fromkeys(candidates))
+
+
+def _storage_from_database_config(config_data: dict[str, Any]) -> None:
+    """Keep the existing public `database:` config compatible with storage."""
+    if "storage" in config_data:
+        return
+
+    database = config_data.get("database")
+    if not isinstance(database, dict):
+        return
+
+    backend = database.get("backend")
+    if backend == "memory":
+        raise ValueError("database.backend='memory' is not supported by storage; handle memory mode before loading storage config")
+
+    storage: dict[str, Any] = {
+        "driver": "postgres" if backend == "postgres" else backend,
+        "sqlite_dir": database.get("sqlite_dir", ".deer-flow/data"),
+        "echo_sql": database.get("echo_sql", False),
+        "pool_size": database.get("pool_size", 5),
+    }
+
+    postgres_url = database.get("postgres_url")
+    if backend == "postgres" and isinstance(postgres_url, str) and postgres_url:
+        from sqlalchemy.engine.url import make_url
+
+        parsed = make_url(postgres_url)
+        storage["database_url"] = postgres_url
+        storage.update(
+            {
+                "username": parsed.username or "",
+                "password": parsed.password or "",
+                "host": parsed.host or "localhost",
+                "port": parsed.port or 5432,
+                "db_name": parsed.database or "deerflow",
+            }
+        )
+
+    config_data["storage"] = storage
+
+
+class AppConfig(BaseModel):
+    """DeerFlow application configuration."""
+
+    timezone: str = Field(default="UTC", description="Timezone for scheduling and timestamps (e.g. 'UTC', 'America/New_York')")
+    log_level: str = Field(default="info", description="Logging level for deerflow modules (debug/info/warning/error)")
+    storage: StorageConfig = Field(default=StorageConfig())
+    model_config = ConfigDict(extra="allow", frozen=False)
+
+    @classmethod
+    def resolve_config_path(cls, config_path: str | None = None) -> Path:
+        """Resolve the config file path.
+
+        Priority:
+        1. If provided `config_path` argument, use it.
+        2. If provided `DEER_FLOW_CONFIG_PATH` environment variable, use it.
+        3. Otherwise, search deterministic backend/repository-root defaults from `_default_config_candidates()`.
+        """
+        if config_path:
+            path = Path(config_path)
+            if not Path.exists(path):
+                raise FileNotFoundError(f"Config file specified by param `config_path` not found at {path}")
+            return path
+        elif os.getenv("DEER_FLOW_CONFIG_PATH"):
+            path = Path(os.getenv("DEER_FLOW_CONFIG_PATH"))
+            if not Path.exists(path):
+                raise FileNotFoundError(f"Config file specified by environment variable `DEER_FLOW_CONFIG_PATH` not found at {path}")
+            return path
+        else:
+            for path in _default_config_candidates():
+                if path.exists():
+                    return path
+            raise FileNotFoundError("`config.yaml` file not found at the default backend or repository root locations")
+
+    @classmethod
+    def from_file(cls, config_path: str | None = None) -> Self:
+        """Load and validate config from YAML. See `resolve_config_path` for path resolution."""
+        resolved_path = cls.resolve_config_path(config_path)
+        with open(resolved_path, encoding="utf-8") as f:
+            config_data = yaml.safe_load(f) or {}
+
+        cls._check_config_version(config_data, resolved_path)
+
+        config_data = cls.resolve_env_variables(config_data)
+        _storage_from_database_config(config_data)
+
+        if os.getenv("TIMEZONE"):
+            config_data["timezone"] = os.getenv("TIMEZONE")
+
+        result = cls.model_validate(config_data)
+        return result
+
+    @classmethod
+    def _check_config_version(cls, config_data: dict, config_path: Path) -> None:
+        """Check if the user's config.yaml is outdated compared to config.example.yaml.
+
+        Emits a warning if the user's config_version is lower than the example's.
+        Missing config_version is treated as version 0 (pre-versioning).
+        """
+        try:
+            user_version = int(config_data.get("config_version", 0))
+        except (TypeError, ValueError):
+            user_version = 0
+
+        # Find config.example.yaml by searching config.yaml's directory and its parents
+        example_path = None
+        search_dir = config_path.parent
+        for _ in range(5):  # search up to 5 levels
+            candidate = search_dir / "config.example.yaml"
+            if candidate.exists():
+                example_path = candidate
+                break
+            parent = search_dir.parent
+            if parent == search_dir:
+                break
+            search_dir = parent
+        if example_path is None:
+            return
+
+        try:
+            with open(example_path, encoding="utf-8") as f:
+                example_data = yaml.safe_load(f)
+            raw = example_data.get("config_version", 0) if example_data else 0
+            try:
+                example_version = int(raw)
+            except (TypeError, ValueError):
+                example_version = 0
+        except Exception:
+            return
+
+        if user_version < example_version:
+            logger.warning(
+                "Your config.yaml (version %d) is outdated — the latest version is %d. Run `make config-upgrade` to merge new fields into your config.",
+                user_version,
+                example_version,
+            )
+
+    @classmethod
+    def resolve_env_variables(cls, config: Any) -> Any:
+        """Recursively replace $VAR strings with their environment variable values (e.g. $OPENAI_API_KEY)."""
+        if isinstance(config, str):
+            if config.startswith("$"):
+                env_value = os.getenv(config[1:])
+                if env_value is None:
+                    raise ValueError(f"Environment variable {config[1:]} not found for config value {config}")
+                return env_value
+            return config
+        elif isinstance(config, dict):
+            return {k: cls.resolve_env_variables(v) for k, v in config.items()}
+        elif isinstance(config, list):
+            return [cls.resolve_env_variables(item) for item in config]
+        return config
+
+
+_app_config: AppConfig | None = None
+_app_config_path: Path | None = None
+_app_config_mtime: float | None = None
+_app_config_is_custom = False
+_current_app_config: ContextVar[AppConfig | None] = ContextVar("deerflow_current_app_config", default=None)
+_current_app_config_stack: ContextVar[tuple[AppConfig | None, ...]] = ContextVar("deerflow_current_app_config_stack", default=())
+
+
+def _get_config_mtime(config_path: Path) -> float | None:
+    """Get the modification time of a config file if it exists."""
+    try:
+        return config_path.stat().st_mtime
+    except OSError:
+        return None
+
+
+def _load_and_cache_app_config(config_path: str | None = None) -> AppConfig:
+    """Load config from disk and refresh cache metadata."""
+    global _app_config, _app_config_path, _app_config_mtime, _app_config_is_custom
+
+    resolved_path = AppConfig.resolve_config_path(config_path)
+    _app_config = AppConfig.from_file(str(resolved_path))
+    _app_config_path = resolved_path
+    _app_config_mtime = _get_config_mtime(resolved_path)
+    _app_config_is_custom = False
+    return _app_config
+
+
+def get_app_config() -> AppConfig:
+    """Get the DeerFlow config instance.
+
+    Returns a cached singleton instance and automatically reloads it when the
+    underlying config file path or modification time changes. Use
+    `reload_app_config()` to force a reload, or `reset_app_config()` to clear
+    the cache.
+    """
+    global _app_config, _app_config_path, _app_config_mtime
+
+    runtime_override = _current_app_config.get()
+    if runtime_override is not None:
+        return runtime_override
+
+    if _app_config is not None and _app_config_is_custom:
+        return _app_config
+
+    resolved_path = AppConfig.resolve_config_path()
+    current_mtime = _get_config_mtime(resolved_path)
+
+    should_reload = _app_config is None or _app_config_path != resolved_path or _app_config_mtime != current_mtime
+    if should_reload:
+        if _app_config_path == resolved_path and _app_config_mtime is not None and current_mtime is not None and _app_config_mtime != current_mtime:
+            logger.info(
+                "Config file has been modified (mtime: %s -> %s), reloading AppConfig",
+                _app_config_mtime,
+                current_mtime,
+            )
+        _load_and_cache_app_config(str(resolved_path))
+    return _app_config
+
+
+def reload_app_config(config_path: str | None = None) -> AppConfig:
+    """Force reload from file and update the cache."""
+    return _load_and_cache_app_config(config_path)
+
+
+def reset_app_config() -> None:
+    """Clear the cache so the next `get_app_config()` reloads from file."""
+    global _app_config, _app_config_path, _app_config_mtime, _app_config_is_custom
+    _app_config = None
+    _app_config_path = None
+    _app_config_mtime = None
+    _app_config_is_custom = False
+
+
+def set_app_config(config: AppConfig) -> None:
+    """Inject a config instance directly, bypassing file loading (for testing)."""
+    global _app_config, _app_config_path, _app_config_mtime, _app_config_is_custom
+    _app_config = config
+    _app_config_path = None
+    _app_config_mtime = None
+    _app_config_is_custom = True
+
+
+def peek_current_app_config() -> AppConfig | None:
+    """Return the runtime-scoped AppConfig override, if one is active."""
+    return _current_app_config.get()
+
+
+def push_current_app_config(config: AppConfig) -> None:
+    """Push a runtime-scoped AppConfig override for the current execution context."""
+    stack = _current_app_config_stack.get()
+    _current_app_config_stack.set(stack + (_current_app_config.get(),))
+    _current_app_config.set(config)
+
+
+def pop_current_app_config() -> None:
+    """Pop the latest runtime-scoped AppConfig override for the current execution context."""
+    stack = _current_app_config_stack.get()
+    if not stack:
+        _current_app_config.set(None)
+        return
+    previous = stack[-1]
+    _current_app_config_stack.set(stack[:-1])
+    _current_app_config.set(previous)

backend/packages/storage/store/config/storage_config.py

@@ -0,0 +1,69 @@
+"""Unified storage backend configuration for checkpointer and application data.
+
+SQLite: checkpointer → {sqlite_dir}/checkpoints.db, app → {sqlite_dir}/deerflow.db
+        (separate files to avoid write-lock contention)
+Postgres: shared URL, independent connection pools per layer.
+
+Sensitive values use $VAR syntax resolved by AppConfig.resolve_env_variables()
+before this config is instantiated.
+"""
+
+from __future__ import annotations
+
+import os
+from typing import Literal
+
+from pydantic import BaseModel, Field
+
+
+def _strip_legacy_state_prefix(path: str) -> str:
+    """Keep old .deer-flow/* config values compatible with Paths.base_dir."""
+    prefix = ".deer-flow/"
+    if path == ".deer-flow":
+        return "."
+    if path.startswith(prefix):
+        return path[len(prefix) :]
+    return path
+
+
+class StorageConfig(BaseModel):
+    driver: Literal["mysql", "sqlite", "postgres", "postgresql"] = Field(
+        default="sqlite",
+        description="Storage driver for both checkpointer and application data. 'sqlite' for single-node deployment (default),'postgres' for production multi-node deployment, 'mysql' for MySQL databases.",
+    )
+    sqlite_dir: str = Field(
+        default=".deer-flow/data",
+        description="Directory for SQLite .db files (sqlite driver only).",
+    )
+    username: str = Field(default="", description="db username ")
+    password: str = Field(default="", description="db password. Use $VAR syntax in config.yaml to read from .env.")
+    host: str = Field(default="localhost", description="db host.")
+    port: int = Field(default=5432, description="db port.")
+    db_name: str = Field(default="deerflow", description="db database name.")
+    database_url: str = Field(default="", description="Complete SQLAlchemy database URL. Takes precedence for non-SQLite drivers.")
+    sqlite_db_path: str = Field(default=".deer-flow/data", description="Directory for SQLite .db files (sqlite driver only).")
+    echo_sql: bool = Field(default=False, description="Log all SQL statements (debug only).")
+    pool_size: int = Field(default=5, description="Connection pool size per layer.")
+
+    # -- Derived helpers (not user-configured) --
+
+    @property
+    def _resolved_sqlite_dir(self) -> str:
+        """Resolve sqlite_dir to an absolute path under DeerFlow's base dir."""
+        from pathlib import Path
+
+        path = Path(self.sqlite_dir)
+        if path.is_absolute():
+            return str(path.resolve())
+
+        try:
+            from deerflow.config.paths import resolve_path
+
+            return str(resolve_path(_strip_legacy_state_prefix(self.sqlite_dir)))
+        except ImportError:
+            return str(path.resolve())
+
+    @property
+    def sqlite_storage_path(self) -> str:
+        """SQLite file path for storage-owned app data and checkpointer."""
+        return os.path.join(self._resolved_sqlite_dir, "deerflow.db")

backend/packages/storage/store/persistence/__init__.py

@@ -0,0 +1,32 @@
+from store.persistence.base_model import (
+    Base,
+    DataClassBase,
+    DateTimeMixin,
+    MappedBase,
+    TimeZone,
+    UniversalText,
+    id_key,
+)
+
+from .factory import (
+    create_persistence,
+    create_persistence_from_database_config,
+    create_persistence_from_storage_config,
+    storage_config_from_database_config,
+)
+from .types import AppPersistence
+
+__all__ = [
+    "Base",
+    "DataClassBase",
+    "DateTimeMixin",
+    "MappedBase",
+    "TimeZone",
+    "UniversalText",
+    "id_key",
+    "create_persistence",
+    "create_persistence_from_database_config",
+    "create_persistence_from_storage_config",
+    "storage_config_from_database_config",
+    "AppPersistence",
+]

backend/packages/storage/store/persistence/base_model.py

@@ -0,0 +1,111 @@
+from datetime import datetime
+from typing import Annotated
+
+from sqlalchemy import BigInteger, DateTime, Integer, Text, TypeDecorator
+from sqlalchemy.dialects.mysql import LONGTEXT
+from sqlalchemy.ext.asyncio import AsyncAttrs
+from sqlalchemy.orm import DeclarativeBase, Mapped, MappedAsDataclass, declared_attr, mapped_column
+
+from store.utils import get_timezone
+
+
+def current_time() -> datetime:
+    return get_timezone().now()
+
+
+id_key = Annotated[
+    int,
+    mapped_column(
+        BigInteger().with_variant(Integer, "sqlite"),
+        primary_key=True,
+        unique=True,
+        index=True,
+        autoincrement=True,
+        sort_order=-999,
+        comment="Primary key ID",
+    ),
+]
+
+
+class UniversalText(TypeDecorator[str]):
+    """Cross-dialect long text type (LONGTEXT on MySQL, Text on PostgreSQL)."""
+
+    impl = Text
+    cache_ok = True
+
+    def load_dialect_impl(self, dialect):  # noqa: ANN001
+        if dialect.name == "mysql":
+            return dialect.type_descriptor(LONGTEXT())
+        return dialect.type_descriptor(Text())
+
+    def process_bind_param(self, value: str | None, dialect) -> str | None:  # noqa: ANN001
+        return value
+
+    def process_result_value(self, value: str | None, dialect) -> str | None:  # noqa: ANN001
+        return value
+
+
+class TimeZone(TypeDecorator[datetime]):
+    """Timezone-aware datetime type compatible with PostgreSQL and MySQL."""
+
+    impl = DateTime(timezone=True)
+    cache_ok = True
+
+    @property
+    def python_type(self) -> type[datetime]:
+        return datetime
+
+    def process_bind_param(self, value: datetime | None, dialect) -> datetime | None:  # noqa: ANN001
+        timezone = get_timezone()
+        if value is not None and value.utcoffset() != timezone.now().utcoffset():
+            value = timezone.from_datetime(value)
+        return value
+
+    def process_result_value(self, value: datetime | None, dialect) -> datetime | None:  # noqa: ANN001
+        timezone = get_timezone()
+        if value is not None and value.tzinfo is None:
+            value = value.replace(tzinfo=timezone.tz_info)
+        return value
+
+
+class DateTimeMixin(MappedAsDataclass):
+    """Mixin that adds created_time / updated_time columns."""
+
+    created_time: Mapped[datetime] = mapped_column(
+        TimeZone,
+        init=False,
+        default_factory=current_time,
+        sort_order=999,
+        comment="Created at",
+    )
+    updated_time: Mapped[datetime | None] = mapped_column(
+        TimeZone,
+        init=False,
+        onupdate=current_time,
+        sort_order=999,
+        comment="Updated at",
+    )
+
+
+class MappedBase(AsyncAttrs, DeclarativeBase):
+    """Async-capable declarative base for all ORM models."""
+
+    @declared_attr.directive
+    def __tablename__(self) -> str:
+        return self.__name__.lower()
+
+    @declared_attr.directive
+    def __table_args__(self) -> dict:
+        return {"comment": self.__doc__ or ""}
+
+
+class DataClassBase(MappedAsDataclass, MappedBase):
+    """Declarative base with native dataclass integration."""
+
+    __abstract__ = True
+
+
+class Base(DataClassBase, DateTimeMixin):
+    """Declarative dataclass base with created_time / updated_time columns."""
+
+    __abstract__ = True

backend/packages/storage/store/persistence/drivers/__init__.py

@@ -0,0 +1,9 @@
+from .mysql import build_mysql_persistence
+from .postgres import build_postgres_persistence
+from .sqlite import build_sqlite_persistence
+
+__all__ = [
+    "build_postgres_persistence",
+    "build_mysql_persistence",
+    "build_sqlite_persistence",
+]

backend/packages/storage/store/persistence/drivers/mysql.py

@@ -0,0 +1,76 @@
+from __future__ import annotations
+
+import json
+
+from sqlalchemy import URL
+from sqlalchemy.engine import make_url
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
+
+from store.persistence import MappedBase
+from store.persistence.shared import close_in_order
+from store.persistence.types import AppPersistence
+
+
+def _validate_mysql_driver(db_url: URL) -> str:
+    url = make_url(db_url)
+    driver = url.get_driver_name()
+
+    if driver not in {"aiomysql", "asyncmy"}:
+        raise ValueError(f"MySQL persistence requires async SQLAlchemy driver (aiomysql/asyncmy), got: {driver!r}")
+    return driver
+
+
+def _checkpoint_conn_string(db_url: URL) -> str:
+    return db_url.render_as_string(hide_password=False)
+
+
+async def build_mysql_persistence(db_url: URL, *, echo: bool = False, pool_size: int = 5) -> AppPersistence:
+    _validate_mysql_driver(db_url)
+
+    from langgraph.checkpoint.mysql.aio import AIOMySQLSaver
+
+    import store.repositories.models  # noqa: F401
+
+    engine = create_async_engine(
+        db_url,
+        echo=echo,
+        future=True,
+        pool_pre_ping=True,
+        pool_size=pool_size,
+        json_serializer=lambda obj: json.dumps(obj, ensure_ascii=False),
+    )
+
+    session_factory = async_sessionmaker(
+        bind=engine,
+        class_=AsyncSession,
+        expire_on_commit=False,
+        autoflush=False,
+    )
+
+    saver_cm = AIOMySQLSaver.from_conn_string(_checkpoint_conn_string(db_url))
+    checkpointer = await saver_cm.__aenter__()
+
+    async def setup() -> None:
+        # 1. LangGraph checkpoint tables / migrations
+        await checkpointer.setup()
+
+        # 2. ORM business tables
+        async with engine.begin() as conn:
+            await conn.run_sync(MappedBase.metadata.create_all)
+
+    async def _close_saver() -> None:
+        await saver_cm.__aexit__(None, None, None)
+
+    async def aclose() -> None:
+        await close_in_order(
+            engine.dispose,
+            _close_saver,
+        )
+
+    return AppPersistence(
+        checkpointer=checkpointer,
+        engine=engine,
+        session_factory=session_factory,
+        setup=setup,
+        aclose=aclose,
+    )

backend/packages/storage/store/persistence/drivers/postgres.py

@@ -0,0 +1,64 @@
+from __future__ import annotations
+
+import json
+
+from sqlalchemy import URL
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
+
+from store.persistence import MappedBase
+from store.persistence.shared import close_in_order
+from store.persistence.types import AppPersistence
+
+
+def _checkpoint_conn_string(db_url: URL) -> str:
+    return db_url.set(drivername="postgresql").render_as_string(hide_password=False)
+
+
+async def build_postgres_persistence(db_url: URL, *, echo: bool = False, pool_size: int = 5) -> AppPersistence:
+    from langgraph.checkpoint.postgres.aio import AsyncPostgresSaver
+
+    import store.repositories.models  # noqa: F401
+
+    engine = create_async_engine(
+        db_url,
+        echo=echo,
+        future=True,
+        pool_pre_ping=True,
+        pool_size=pool_size,
+        json_serializer=lambda obj: json.dumps(obj, ensure_ascii=False),
+    )
+
+    session_factory = async_sessionmaker(
+        bind=engine,
+        class_=AsyncSession,
+        expire_on_commit=False,
+        autoflush=False,
+    )
+
+    saver_cm = AsyncPostgresSaver.from_conn_string(_checkpoint_conn_string(db_url))
+    checkpointer = await saver_cm.__aenter__()
+
+    async def setup() -> None:
+        # 1. LangGraph checkpoint tables / migrations
+        await checkpointer.setup()
+
+        # 2. ORM business tables
+        async with engine.begin() as conn:
+            await conn.run_sync(MappedBase.metadata.create_all)
+
+    async def _close_saver() -> None:
+        await saver_cm.__aexit__(None, None, None)
+
+    async def aclose() -> None:
+        await close_in_order(
+            engine.dispose,
+            _close_saver,
+        )
+
+    return AppPersistence(
+        checkpointer=checkpointer,
+        engine=engine,
+        session_factory=session_factory,
+        setup=setup,
+        aclose=aclose,
+    )

backend/packages/storage/store/persistence/drivers/sqlite.py

@@ -0,0 +1,68 @@
+from __future__ import annotations
+
+import json
+
+from sqlalchemy import URL, event
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
+
+from store.persistence import MappedBase
+from store.persistence.shared import close_in_order
+from store.persistence.types import AppPersistence
+
+
+async def build_sqlite_persistence(db_url: URL, *, echo: bool = False) -> AppPersistence:
+    from langgraph.checkpoint.sqlite.aio import AsyncSqliteSaver
+
+    import store.repositories.models  # noqa: F401
+
+    engine = create_async_engine(
+        db_url,
+        echo=echo,
+        future=True,
+        json_serializer=lambda obj: json.dumps(obj, ensure_ascii=False),
+    )
+
+    @event.listens_for(engine.sync_engine, "connect")
+    def _enable_sqlite_pragmas(dbapi_conn, _record):  # noqa: ANN001
+        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()
+
+    session_factory = async_sessionmaker(
+        bind=engine,
+        class_=AsyncSession,
+        expire_on_commit=False,
+        autoflush=False,
+    )
+
+    saver_cm = AsyncSqliteSaver.from_conn_string(db_url.database)
+    checkpointer = await saver_cm.__aenter__()
+
+    async def setup() -> None:
+        # 1. LangGraph checkpoint tables
+        await checkpointer.setup()
+
+        # 2. ORM business tables
+        async with engine.begin() as conn:
+            await conn.run_sync(MappedBase.metadata.create_all)
+
+    async def _close_saver() -> None:
+        await saver_cm.__aexit__(None, None, None)
+
+    async def aclose() -> None:
+        await close_in_order(
+            engine.dispose,
+            _close_saver,
+        )
+
+    return AppPersistence(
+        checkpointer=checkpointer,
+        engine=engine,
+        session_factory=session_factory,
+        setup=setup,
+        aclose=aclose,
+    )

backend/packages/storage/store/persistence/factory.py

@@ -0,0 +1,123 @@
+from typing import Any
+
+from sqlalchemy import URL
+from sqlalchemy.engine.url import make_url
+
+from store.common import DataBaseType
+from store.config.app_config import get_app_config
+from store.config.storage_config import StorageConfig
+from store.persistence.types import AppPersistence
+
+
+def storage_config_from_database_config(database_config: Any) -> StorageConfig:
+    """Convert the existing public DatabaseConfig shape to StorageConfig.
+
+    Storage only owns durable database-backed persistence. The app bridge
+    should handle memory mode before calling into this package.
+    """
+    backend = getattr(database_config, "backend", None)
+    if backend == "sqlite":
+        return StorageConfig(
+            driver="sqlite",
+            sqlite_dir=getattr(database_config, "sqlite_dir", ".deer-flow/data"),
+            echo_sql=getattr(database_config, "echo_sql", False),
+            pool_size=getattr(database_config, "pool_size", 5),
+        )
+
+    if backend == "postgres":
+        postgres_url = getattr(database_config, "postgres_url", "")
+        if not postgres_url:
+            raise ValueError("database.postgres_url is required when database.backend is 'postgres'")
+        parsed = make_url(postgres_url)
+        return StorageConfig(
+            driver="postgres",
+            database_url=postgres_url,
+            username=parsed.username or "",
+            password=parsed.password or "",
+            host=parsed.host or "localhost",
+            port=parsed.port or 5432,
+            db_name=parsed.database or "deerflow",
+            echo_sql=getattr(database_config, "echo_sql", False),
+            pool_size=getattr(database_config, "pool_size", 5),
+        )
+
+    raise ValueError(f"Unsupported database backend for storage persistence: {backend!r}")
+
+
+def _create_database_url(storage_config: StorageConfig) -> URL:
+    """Build an async SQLAlchemy URL from StorageConfig (sqlite/mysql/postgres)."""
+
+    if storage_config.driver == DataBaseType.sqlite:
+        driver = "sqlite+aiosqlite"
+    elif storage_config.driver == DataBaseType.mysql:
+        driver = "mysql+aiomysql"
+    elif storage_config.driver in (DataBaseType.postgresql, "postgres"):
+        driver = "postgresql+asyncpg"
+    else:
+        raise ValueError(f"Unsupported database driver: {storage_config.driver}")
+
+    if storage_config.driver == DataBaseType.sqlite:
+        import os
+
+        db_path = storage_config.sqlite_storage_path
+        os.makedirs(os.path.dirname(db_path), exist_ok=True)
+
+        url = URL.create(
+            drivername=driver,
+            database=db_path,
+        )
+    elif storage_config.database_url:
+        url = make_url(storage_config.database_url)
+        if storage_config.driver in (DataBaseType.postgresql, "postgres") and url.drivername == "postgresql":
+            url = url.set(drivername="postgresql+asyncpg")
+        elif storage_config.driver == DataBaseType.mysql and url.drivername == "mysql":
+            url = url.set(drivername="mysql+aiomysql")
+    else:
+        url = URL.create(
+            drivername=driver,
+            username=storage_config.username,
+            password=storage_config.password,
+            host=storage_config.host,
+            port=storage_config.port,
+            database=storage_config.db_name or "deerflow",
+        )
+
+    return url
+
+
+async def create_persistence_from_storage_config(storage_config: StorageConfig) -> AppPersistence:
+    from .drivers.mysql import build_mysql_persistence
+    from .drivers.postgres import build_postgres_persistence
+    from .drivers.sqlite import build_sqlite_persistence
+
+    driver = storage_config.driver
+    db_url = _create_database_url(storage_config)
+
+    if driver in ("postgres", "postgresql"):
+        return await build_postgres_persistence(
+            db_url,
+            echo=storage_config.echo_sql,
+            pool_size=storage_config.pool_size,
+        )
+
+    if driver == "mysql":
+        return await build_mysql_persistence(
+            db_url,
+            echo=storage_config.echo_sql,
+            pool_size=storage_config.pool_size,
+        )
+
+    if driver == "sqlite":
+        return await build_sqlite_persistence(db_url, echo=storage_config.echo_sql)
+
+    raise ValueError(f"Unsupported database driver: {driver}")
+
+
+async def create_persistence_from_database_config(database_config: Any) -> AppPersistence:
+    storage_config = storage_config_from_database_config(database_config)
+    return await create_persistence_from_storage_config(storage_config)
+
+
+async def create_persistence() -> AppPersistence:
+    app_config = get_app_config()
+    return await create_persistence_from_storage_config(app_config.storage)

backend/packages/storage/store/persistence/json_compat.py

@@ -0,0 +1,189 @@
+"""Dialect-aware JSON value matching for storage SQLAlchemy repositories."""
+
+from __future__ import annotations
+
+import re
+from dataclasses import dataclass
+from typing import Any
+
+from sqlalchemy import BigInteger, Float, String, bindparam
+from sqlalchemy.ext.compiler import compiles
+from sqlalchemy.sql.compiler import SQLCompiler
+from sqlalchemy.sql.expression import ColumnElement
+from sqlalchemy.sql.visitors import InternalTraversal
+from sqlalchemy.types import Boolean, TypeEngine
+
+_KEY_CHARSET_RE = re.compile(r"^[A-Za-z0-9_\-]+$")
+ALLOWED_FILTER_VALUE_TYPES: tuple[type, ...] = (type(None), bool, int, float, str)
+
+_INT64_MIN = -(2**63)
+_INT64_MAX = 2**63 - 1
+
+
+def validate_metadata_filter_key(key: object) -> bool:
+    """Return True when *key* is safe for JSON metadata filter SQL paths."""
+    return isinstance(key, str) and bool(_KEY_CHARSET_RE.match(key))
+
+
+def validate_metadata_filter_value(value: object) -> bool:
+    """Return True when *value* can be compiled into a portable JSON predicate."""
+    if not isinstance(value, ALLOWED_FILTER_VALUE_TYPES):
+        return False
+    if isinstance(value, int) and not isinstance(value, bool):
+        return _INT64_MIN <= value <= _INT64_MAX
+    return True
+
+
+class JsonMatch(ColumnElement[bool]):
+    """Dialect-portable ``column[key] == value`` for JSON columns."""
+
+    inherit_cache = True
+    type = Boolean()
+    _is_implicitly_boolean = True
+
+    _traverse_internals = [
+        ("column", InternalTraversal.dp_clauseelement),
+        ("key", InternalTraversal.dp_string),
+        ("value", InternalTraversal.dp_plain_obj),
+        ("value_type", InternalTraversal.dp_string),
+    ]
+
+    def __init__(self, column: ColumnElement[Any], key: str, value: object) -> None:
+        if not validate_metadata_filter_key(key):
+            raise ValueError(f"JsonMatch key must match {_KEY_CHARSET_RE.pattern!r}; got: {key!r}")
+        if not validate_metadata_filter_value(value):
+            if isinstance(value, int) and not isinstance(value, bool):
+                raise TypeError(f"JsonMatch int value out of signed 64-bit range [-2**63, 2**63-1]: {value!r}")
+            raise TypeError(f"JsonMatch value must be None, bool, int, float, or str; got: {type(value).__name__!r}")
+        self.column = column
+        self.key = key
+        self.value = value
+        self.value_type = type(value).__qualname__
+        super().__init__()
+
+
+@dataclass(frozen=True)
+class _Dialect:
+    null_type: str
+    num_types: tuple[str, ...]
+    num_cast: str
+    int_types: tuple[str, ...]
+    int_cast: str
+    int_guard: str | None
+    string_type: str
+    bool_type: str | None
+    true_value: str
+    false_value: str
+
+
+_SQLITE = _Dialect(
+    null_type="null",
+    num_types=("integer", "real"),
+    num_cast="REAL",
+    int_types=("integer",),
+    int_cast="INTEGER",
+    int_guard=None,
+    string_type="text",
+    bool_type=None,
+    true_value="true",
+    false_value="false",
+)
+
+_POSTGRES = _Dialect(
+    null_type="null",
+    num_types=("number",),
+    num_cast="DOUBLE PRECISION",
+    int_types=("number",),
+    int_cast="BIGINT",
+    int_guard="'^-?[0-9]+$'",
+    string_type="string",
+    bool_type="boolean",
+    true_value="true",
+    false_value="false",
+)
+
+_MYSQL = _Dialect(
+    null_type="NULL",
+    num_types=("INTEGER", "DOUBLE", "DECIMAL"),
+    num_cast="DOUBLE",
+    int_types=("INTEGER",),
+    int_cast="SIGNED",
+    int_guard=None,
+    string_type="STRING",
+    bool_type="BOOLEAN",
+    true_value="true",
+    false_value="false",
+)
+
+
+def _bind(compiler: SQLCompiler, value: object, sa_type: TypeEngine[Any], **kw: Any) -> str:
+    param = bindparam(None, value, type_=sa_type)
+    return compiler.process(param, **kw)
+
+
+def _type_check(typeof: str, types: tuple[str, ...]) -> str:
+    if len(types) == 1:
+        return f"{typeof} = '{types[0]}'"
+    quoted = ", ".join(f"'{type_name}'" for type_name in types)
+    return f"{typeof} IN ({quoted})"
+
+
+def _build_clause(compiler: SQLCompiler, typeof: str, extract: str, value: object, dialect: _Dialect, **kw: Any) -> str:
+    if value is None:
+        return f"{typeof} = '{dialect.null_type}'"
+    if isinstance(value, bool):
+        bool_str = dialect.true_value if value else dialect.false_value
+        if dialect.bool_type is None:
+            return f"{typeof} = '{bool_str}'"
+        return f"({typeof} = '{dialect.bool_type}' AND {extract} = '{bool_str}')"
+    if isinstance(value, int):
+        bp = _bind(compiler, value, BigInteger(), **kw)
+        if dialect.int_guard:
+            return f"(CASE WHEN {_type_check(typeof, dialect.int_types)} AND {extract} ~ {dialect.int_guard} THEN CAST({extract} AS {dialect.int_cast}) END = {bp})"
+        return f"({_type_check(typeof, dialect.int_types)} AND CAST({extract} AS {dialect.int_cast}) = {bp})"
+    if isinstance(value, float):
+        bp = _bind(compiler, value, Float(), **kw)
+        return f"({_type_check(typeof, dialect.num_types)} AND CAST({extract} AS {dialect.num_cast}) = {bp})"
+    bp = _bind(compiler, str(value), String(), **kw)
+    return f"({typeof} = '{dialect.string_type}' AND {extract} = {bp})"
+
+
+@compiles(JsonMatch, "sqlite")
+def _compile_sqlite(element: JsonMatch, compiler: SQLCompiler, **kw: Any) -> str:
+    if not validate_metadata_filter_key(element.key):
+        raise ValueError(f"Key escaped validation: {element.key!r}")
+    col = compiler.process(element.column, **kw)
+    path = f'$."{element.key}"'
+    typeof = f"json_type({col}, '{path}')"
+    extract = f"json_extract({col}, '{path}')"
+    return _build_clause(compiler, typeof, extract, element.value, _SQLITE, **kw)
+
+
+@compiles(JsonMatch, "postgresql")
+def _compile_postgres(element: JsonMatch, compiler: SQLCompiler, **kw: Any) -> str:
+    if not validate_metadata_filter_key(element.key):
+        raise ValueError(f"Key escaped validation: {element.key!r}")
+    col = compiler.process(element.column, **kw)
+    typeof = f"json_typeof({col} -> '{element.key}')"
+    extract = f"({col} ->> '{element.key}')"
+    return _build_clause(compiler, typeof, extract, element.value, _POSTGRES, **kw)
+
+
+@compiles(JsonMatch, "mysql")
+def _compile_mysql(element: JsonMatch, compiler: SQLCompiler, **kw: Any) -> str:
+    if not validate_metadata_filter_key(element.key):
+        raise ValueError(f"Key escaped validation: {element.key!r}")
+    col = compiler.process(element.column, **kw)
+    path = f'$."{element.key}"'
+    typeof = f"JSON_TYPE(JSON_EXTRACT({col}, '{path}'))"
+    extract = f"JSON_UNQUOTE(JSON_EXTRACT({col}, '{path}'))"
+    return _build_clause(compiler, typeof, extract, element.value, _MYSQL, **kw)
+
+
+@compiles(JsonMatch)
+def _compile_default(element: JsonMatch, compiler: SQLCompiler, **kw: Any) -> str:
+    raise NotImplementedError(f"JsonMatch supports sqlite, postgresql, and mysql; got dialect: {compiler.dialect.name}")
+
+
+def json_match(column: ColumnElement[Any], key: str, value: object) -> JsonMatch:
+    return JsonMatch(column, key, value)

backend/packages/storage/store/persistence/shared/__init__.py

@@ -0,0 +1,3 @@
+from .close import close_in_order
+
+__all__ = ["close_in_order"]

backend/packages/storage/store/persistence/shared/close.py

@@ -0,0 +1,28 @@
+from __future__ import annotations
+
+from collections.abc import Awaitable, Callable
+
+AsyncCloser = Callable[[], Awaitable[None]]
+
+
+async def close_in_order(*closers: AsyncCloser) -> None:
+    """
+    Run async closers in order and raise the first error, if any.
+
+    Notes
+    -----
+    - Used to keep driver-specific close logic readable.
+    - We intentionally do not stop at first failure, so later resources
+      still get a chance to close.
+    """
+    first_error: Exception | None = None
+
+    for closer in closers:
+        try:
+            await closer()
+        except Exception as exc:
+            if first_error is None:
+                first_error = exc
+
+    if first_error is not None:
+        raise first_error

backend/packages/storage/store/persistence/types.py

@@ -0,0 +1,23 @@
+from __future__ import annotations
+
+from collections.abc import Awaitable, Callable
+from dataclasses import dataclass
+
+from langgraph.types import Checkpointer
+from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession, async_sessionmaker
+
+AsyncSetup = Callable[[], Awaitable[None]]
+AsyncClose = Callable[[], Awaitable[None]]
+
+
+@dataclass(slots=True)
+class AppPersistence:
+    """
+    Unified runtime persistence bundle.
+    """
+
+    checkpointer: Checkpointer
+    engine: AsyncEngine
+    session_factory: async_sessionmaker[AsyncSession]
+    setup: AsyncSetup
+    aclose: AsyncClose

backend/packages/storage/store/repositories/__init__.py

@@ -0,0 +1,53 @@
+from store.repositories.contracts import (
+    Feedback,
+    FeedbackAggregate,
+    FeedbackCreate,
+    FeedbackRepositoryProtocol,
+    InvalidMetadataFilterError,
+    Run,
+    RunCreate,
+    RunEvent,
+    RunEventCreate,
+    RunEventRepositoryProtocol,
+    RunRepositoryProtocol,
+    ThreadMeta,
+    ThreadMetaCreate,
+    ThreadMetaRepositoryProtocol,
+    User,
+    UserCreate,
+    UserNotFoundError,
+    UserRepositoryProtocol,
+)
+from store.repositories.factory import (
+    build_feedback_repository,
+    build_run_event_repository,
+    build_run_repository,
+    build_thread_meta_repository,
+    build_user_repository,
+)
+
+__all__ = [
+    "Feedback",
+    "FeedbackAggregate",
+    "FeedbackCreate",
+    "FeedbackRepositoryProtocol",
+    "InvalidMetadataFilterError",
+    "Run",
+    "RunCreate",
+    "RunEvent",
+    "RunEventCreate",
+    "RunEventRepositoryProtocol",
+    "RunRepositoryProtocol",
+    "ThreadMeta",
+    "ThreadMetaCreate",
+    "ThreadMetaRepositoryProtocol",
+    "User",
+    "UserCreate",
+    "UserNotFoundError",
+    "UserRepositoryProtocol",
+    "build_run_repository",
+    "build_run_event_repository",
+    "build_thread_meta_repository",
+    "build_feedback_repository",
+    "build_user_repository",
+]

backend/packages/storage/store/repositories/contracts/__init__.py

@@ -0,0 +1,49 @@
+from store.repositories.contracts.feedback import (
+    Feedback,
+    FeedbackAggregate,
+    FeedbackCreate,
+    FeedbackRepositoryProtocol,
+)
+from store.repositories.contracts.run import (
+    Run,
+    RunCreate,
+    RunRepositoryProtocol,
+)
+from store.repositories.contracts.run_event import (
+    RunEvent,
+    RunEventCreate,
+    RunEventRepositoryProtocol,
+)
+from store.repositories.contracts.thread_meta import (
+    InvalidMetadataFilterError,
+    ThreadMeta,
+    ThreadMetaCreate,
+    ThreadMetaRepositoryProtocol,
+)
+from store.repositories.contracts.user import (
+    User,
+    UserCreate,
+    UserNotFoundError,
+    UserRepositoryProtocol,
+)
+
+__all__ = [
+    "Feedback",
+    "FeedbackAggregate",
+    "FeedbackCreate",
+    "FeedbackRepositoryProtocol",
+    "Run",
+    "RunCreate",
+    "RunEvent",
+    "RunEventCreate",
+    "RunEventRepositoryProtocol",
+    "RunRepositoryProtocol",
+    "InvalidMetadataFilterError",
+    "ThreadMeta",
+    "ThreadMetaCreate",
+    "ThreadMetaRepositoryProtocol",
+    "User",
+    "UserCreate",
+    "UserNotFoundError",
+    "UserRepositoryProtocol",
+]

backend/packages/storage/store/repositories/contracts/feedback.py

@@ -0,0 +1,77 @@
+from __future__ import annotations
+
+from datetime import datetime
+from typing import Protocol, TypedDict
+
+from pydantic import BaseModel, ConfigDict
+
+
+class FeedbackCreate(BaseModel):
+    model_config = ConfigDict(extra="forbid")
+
+    feedback_id: str
+    run_id: str
+    thread_id: str
+    rating: int
+    user_id: str | None = None
+    message_id: str | None = None
+    comment: str | None = None
+
+
+class Feedback(BaseModel):
+    model_config = ConfigDict(frozen=True)
+
+    feedback_id: str
+    run_id: str
+    thread_id: str
+    rating: int
+    user_id: str | None
+    message_id: str | None
+    comment: str | None
+    created_time: datetime
+
+
+class FeedbackAggregate(TypedDict):
+    run_id: str
+    total: int
+    positive: int
+    negative: int
+
+
+class FeedbackRepositoryProtocol(Protocol):
+    async def create_feedback(self, data: FeedbackCreate) -> Feedback:
+        pass
+
+    async def upsert_feedback(self, data: FeedbackCreate) -> Feedback:
+        pass
+
+    async def get_feedback(self, feedback_id: str) -> Feedback | None:
+        pass
+
+    async def list_feedback_by_run(
+        self,
+        run_id: str,
+        *,
+        thread_id: str | None = None,
+        user_id: str | None = None,
+        limit: int | None = None,
+    ) -> list[Feedback]:
+        pass
+
+    async def list_feedback_by_thread(
+        self,
+        thread_id: str,
+        *,
+        user_id: str | None = None,
+        limit: int | None = None,
+    ) -> list[Feedback]:
+        pass
+
+    async def delete_feedback(self, feedback_id: str) -> bool:
+        pass
+
+    async def delete_feedback_by_run(self, thread_id: str, run_id: str, *, user_id: str | None = None) -> bool:
+        pass
+
+    async def aggregate_feedback_by_run(self, thread_id: str, run_id: str) -> FeedbackAggregate:
+        pass

backend/packages/storage/store/repositories/contracts/run.py

@@ -0,0 +1,100 @@
+from __future__ import annotations
+
+from datetime import datetime
+from typing import Any, Protocol
+
+from pydantic import BaseModel, ConfigDict, Field
+
+
+class RunCreate(BaseModel):
+    model_config = ConfigDict(extra="forbid")
+
+    run_id: str
+    thread_id: str
+    assistant_id: str | None = None
+    user_id: str | None = None
+    status: str = "pending"
+    model_name: str | None = None
+    multitask_strategy: str = "reject"
+    error: str | None = None
+    follow_up_to_run_id: str | None = None
+    metadata: dict[str, Any] = Field(default_factory=dict)
+    kwargs: dict[str, Any] = Field(default_factory=dict)
+    created_time: datetime | None = None
+
+
+class Run(BaseModel):
+    model_config = ConfigDict(frozen=True)
+
+    run_id: str
+    thread_id: str
+    assistant_id: str | None
+    user_id: str | None
+    status: str
+    model_name: str | None
+    multitask_strategy: str
+    error: str | None
+    follow_up_to_run_id: str | None
+    metadata: dict[str, Any]
+    kwargs: dict[str, Any]
+    total_input_tokens: int
+    total_output_tokens: int
+    total_tokens: int
+    llm_call_count: int
+    lead_agent_tokens: int
+    subagent_tokens: int
+    middleware_tokens: int
+    message_count: int
+    first_human_message: str | None
+    last_ai_message: str | None
+    created_time: datetime
+    updated_time: datetime | None
+
+
+class RunRepositoryProtocol(Protocol):
+    async def create_run(self, data: RunCreate) -> Run:
+        pass
+
+    async def get_run(self, run_id: str) -> Run | None:
+        pass
+
+    async def list_runs_by_thread(
+        self,
+        thread_id: str,
+        *,
+        user_id: str | None = None,
+        limit: int = 50,
+        offset: int = 0,
+    ) -> list[Run]:
+        pass
+
+    async def update_run_status(self, run_id: str, status: str, *, error: str | None = None) -> None:
+        pass
+
+    async def delete_run(self, run_id: str) -> None:
+        pass
+
+    async def list_pending(self, *, before: datetime | str | None = None) -> list[Run]:
+        pass
+
+    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,
+        first_human_message: str | None = None,
+        last_ai_message: str | None = None,
+        error: str | None = None,
+    ) -> None:
+        pass
+
+    async def aggregate_tokens_by_thread(self, thread_id: str) -> dict[str, Any]:
+        pass

backend/packages/storage/store/repositories/contracts/run_event.py

@@ -0,0 +1,83 @@
+from __future__ import annotations
+
+from datetime import datetime
+from typing import Any, Protocol
+
+from pydantic import BaseModel, ConfigDict, Field
+
+
+class RunEventCreate(BaseModel):
+    model_config = ConfigDict(extra="forbid")
+
+    thread_id: str
+    run_id: str
+    user_id: str | None = None
+    event_type: str
+    category: str
+    content: Any = ""
+    metadata: dict[str, Any] = Field(default_factory=dict)
+    created_at: datetime | None = None
+
+
+class RunEvent(BaseModel):
+    model_config = ConfigDict(frozen=True)
+
+    thread_id: str
+    run_id: str
+    user_id: str | None
+    event_type: str
+    category: str
+    content: Any
+    metadata: dict[str, Any]
+    seq: int
+    created_at: datetime
+
+
+class RunEventRepositoryProtocol(Protocol):
+    # Sequence values are time-ordered integer cursors. The application layer
+    # owns the single-writer invariant for a thread while a run is active.
+    async def append_batch(self, events: list[RunEventCreate]) -> list[RunEvent]:
+        pass
+
+    async def list_messages(
+        self,
+        thread_id: str,
+        *,
+        limit: int = 50,
+        before_seq: int | None = None,
+        after_seq: int | None = None,
+        user_id: str | None = None,
+    ) -> list[RunEvent]:
+        pass
+
+    async def list_events(
+        self,
+        thread_id: str,
+        run_id: str,
+        *,
+        event_types: list[str] | None = None,
+        limit: int = 500,
+        user_id: str | None = None,
+    ) -> list[RunEvent]:
+        pass
+
+    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,
+        user_id: str | None = None,
+    ) -> list[RunEvent]:
+        pass
+
+    async def count_messages(self, thread_id: str, *, user_id: str | None = None) -> int:
+        pass
+
+    async def delete_by_thread(self, thread_id: str, *, user_id: str | None = None) -> int:
+        pass
+
+    async def delete_by_run(self, thread_id: str, run_id: str, *, user_id: str | None = None) -> int:
+        pass

backend/packages/storage/store/repositories/contracts/thread_meta.py

@@ -0,0 +1,67 @@
+from __future__ import annotations
+
+from datetime import datetime
+from typing import Any, Protocol
+
+from pydantic import BaseModel, ConfigDict, Field
+
+
+class InvalidMetadataFilterError(ValueError):
+    """Raised when all client-supplied metadata filters are rejected."""
+
+
+class ThreadMetaCreate(BaseModel):
+    model_config = ConfigDict(extra="forbid")
+
+    thread_id: str
+    assistant_id: str | None = None
+    user_id: str | None = None
+    display_name: str | None = None
+    status: str = "idle"
+    metadata: dict[str, Any] = Field(default_factory=dict)
+
+
+class ThreadMeta(BaseModel):
+    model_config = ConfigDict(frozen=True)
+
+    thread_id: str
+    assistant_id: str | None
+    user_id: str | None
+    display_name: str | None
+    status: str
+    metadata: dict[str, Any]
+    created_time: datetime
+    updated_time: datetime | None
+
+
+class ThreadMetaRepositoryProtocol(Protocol):
+    async def create_thread_meta(self, data: ThreadMetaCreate) -> ThreadMeta:
+        pass
+
+    async def get_thread_meta(self, thread_id: str) -> ThreadMeta | None:
+        pass
+
+    async def update_thread_meta(
+        self,
+        thread_id: str,
+        *,
+        display_name: str | None = None,
+        status: str | None = None,
+        metadata: dict[str, Any] | None = None,
+    ) -> None:
+        pass
+
+    async def delete_thread(self, thread_id: str) -> None:
+        pass
+
+    async def search_threads(
+        self,
+        *,
+        metadata: dict[str, Any] | None = None,
+        status: str | None = None,
+        user_id: str | None = None,
+        assistant_id: str | None = None,
+        limit: int = 100,
+        offset: int = 0,
+    ) -> list[ThreadMeta]:
+        pass

backend/packages/storage/store/repositories/contracts/user.py

@@ -0,0 +1,64 @@
+from __future__ import annotations
+
+from datetime import datetime
+from typing import Literal, Protocol
+
+from pydantic import BaseModel, ConfigDict
+
+
+class UserNotFoundError(LookupError):
+    """Raised when an update targets a user row that no longer exists."""
+
+
+class UserCreate(BaseModel):
+    model_config = ConfigDict(extra="forbid")
+
+    id: str
+    email: str
+    password_hash: str | None = None
+    system_role: Literal["admin", "user"] = "user"
+    created_at: datetime | None = None
+    oauth_provider: str | None = None
+    oauth_id: str | None = None
+    needs_setup: bool = False
+    token_version: int = 0
+
+
+class User(BaseModel):
+    model_config = ConfigDict(frozen=True)
+
+    id: str
+    email: str
+    password_hash: str | None
+    system_role: Literal["admin", "user"]
+    created_at: datetime
+    oauth_provider: str | None
+    oauth_id: str | None
+    needs_setup: bool
+    token_version: int
+
+
+class UserRepositoryProtocol(Protocol):
+    async def create_user(self, data: UserCreate) -> User:
+        pass
+
+    async def get_user_by_id(self, user_id: str) -> User | None:
+        pass
+
+    async def get_user_by_email(self, email: str) -> User | None:
+        pass
+
+    async def get_user_by_oauth(self, provider: str, oauth_id: str) -> User | None:
+        pass
+
+    async def get_first_admin(self) -> User | None:
+        pass
+
+    async def update_user(self, data: User) -> User:
+        pass
+
+    async def count_users(self) -> int:
+        pass
+
+    async def count_admin_users(self) -> int:
+        pass

backend/packages/storage/store/repositories/db/__init__.py

@@ -0,0 +1,13 @@
+from store.repositories.db.feedback import DbFeedbackRepository
+from store.repositories.db.run import DbRunRepository
+from store.repositories.db.run_event import DbRunEventRepository
+from store.repositories.db.thread_meta import DbThreadMetaRepository
+from store.repositories.db.user import DbUserRepository
+
+__all__ = [
+    "DbFeedbackRepository",
+    "DbRunRepository",
+    "DbRunEventRepository",
+    "DbThreadMetaRepository",
+    "DbUserRepository",
+]

backend/packages/storage/store/repositories/db/feedback.py

@@ -0,0 +1,142 @@
+from __future__ import annotations
+
+from datetime import UTC, datetime
+
+from sqlalchemy import case, delete, func, select
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from store.repositories.contracts.feedback import Feedback, FeedbackAggregate, FeedbackCreate, FeedbackRepositoryProtocol
+from store.repositories.models.feedback import Feedback as FeedbackModel
+
+
+def _to_feedback(m: FeedbackModel) -> Feedback:
+    return Feedback(
+        feedback_id=m.feedback_id,
+        run_id=m.run_id,
+        thread_id=m.thread_id,
+        rating=m.rating,
+        user_id=m.user_id,
+        message_id=m.message_id,
+        comment=m.comment,
+        created_time=m.created_time,
+    )
+
+
+class DbFeedbackRepository(FeedbackRepositoryProtocol):
+    def __init__(self, session: AsyncSession) -> None:
+        self._session = session
+
+    async def create_feedback(self, data: FeedbackCreate) -> Feedback:
+        if data.rating not in (1, -1):
+            raise ValueError(f"rating must be +1 or -1, got {data.rating}")
+        model = FeedbackModel(
+            feedback_id=data.feedback_id,
+            run_id=data.run_id,
+            thread_id=data.thread_id,
+            rating=data.rating,
+            user_id=data.user_id,
+            message_id=data.message_id,
+            comment=data.comment,
+        )
+        self._session.add(model)
+        await self._session.flush()
+        await self._session.refresh(model)
+        return _to_feedback(model)
+
+    async def upsert_feedback(self, data: FeedbackCreate) -> Feedback:
+        if data.rating not in (1, -1):
+            raise ValueError(f"rating must be +1 or -1, got {data.rating}")
+
+        result = await self._session.execute(
+            select(FeedbackModel).where(
+                FeedbackModel.thread_id == data.thread_id,
+                FeedbackModel.run_id == data.run_id,
+                FeedbackModel.user_id == data.user_id,
+            )
+        )
+        model = result.scalar_one_or_none()
+        if model is None:
+            return await self.create_feedback(data)
+
+        model.rating = data.rating
+        model.message_id = data.message_id
+        model.comment = data.comment
+        model.created_time = datetime.now(UTC)
+        await self._session.flush()
+        await self._session.refresh(model)
+        return _to_feedback(model)
+
+    async def get_feedback(self, feedback_id: str) -> Feedback | None:
+        result = await self._session.execute(select(FeedbackModel).where(FeedbackModel.feedback_id == feedback_id))
+        model = result.scalar_one_or_none()
+        return _to_feedback(model) if model else None
+
+    async def list_feedback_by_run(
+        self,
+        run_id: str,
+        *,
+        thread_id: str | None = None,
+        user_id: str | None = None,
+        limit: int | None = None,
+    ) -> list[Feedback]:
+        stmt = select(FeedbackModel).where(FeedbackModel.run_id == run_id)
+        if thread_id is not None:
+            stmt = stmt.where(FeedbackModel.thread_id == thread_id)
+        if user_id is not None:
+            stmt = stmt.where(FeedbackModel.user_id == user_id)
+        stmt = stmt.order_by(FeedbackModel.created_time.desc())
+        if limit is not None:
+            stmt = stmt.limit(limit)
+        result = await self._session.execute(stmt)
+        return [_to_feedback(m) for m in result.scalars().all()]
+
+    async def list_feedback_by_thread(
+        self,
+        thread_id: str,
+        *,
+        user_id: str | None = None,
+        limit: int | None = None,
+    ) -> list[Feedback]:
+        stmt = select(FeedbackModel).where(FeedbackModel.thread_id == thread_id)
+        if user_id is not None:
+            stmt = stmt.where(FeedbackModel.user_id == user_id)
+        stmt = stmt.order_by(FeedbackModel.created_time.desc())
+        if limit is not None:
+            stmt = stmt.limit(limit)
+        result = await self._session.execute(stmt)
+        return [_to_feedback(m) for m in result.scalars().all()]
+
+    async def delete_feedback(self, feedback_id: str) -> bool:
+        existing = await self.get_feedback(feedback_id)
+        if existing is None:
+            return False
+        await self._session.execute(delete(FeedbackModel).where(FeedbackModel.feedback_id == feedback_id))
+        return True
+
+    async def delete_feedback_by_run(self, thread_id: str, run_id: str, *, user_id: str | None = None) -> bool:
+        stmt = select(FeedbackModel).where(
+            FeedbackModel.thread_id == thread_id,
+            FeedbackModel.run_id == run_id,
+        )
+        if user_id is not None:
+            stmt = stmt.where(FeedbackModel.user_id == user_id)
+        result = await self._session.execute(stmt)
+        model = result.scalar_one_or_none()
+        if model is None:
+            return False
+        await self._session.delete(model)
+        return True
+
+    async def aggregate_feedback_by_run(self, thread_id: str, run_id: str) -> FeedbackAggregate:
+        stmt = select(
+            func.count().label("total"),
+            func.coalesce(func.sum(case((FeedbackModel.rating == 1, 1), else_=0)), 0).label("positive"),
+            func.coalesce(func.sum(case((FeedbackModel.rating == -1, 1), else_=0)), 0).label("negative"),
+        ).where(FeedbackModel.thread_id == thread_id, FeedbackModel.run_id == run_id)
+        row = (await self._session.execute(stmt)).one()
+        return {
+            "run_id": run_id,
+            "total": int(row.total),
+            "positive": int(row.positive),
+            "negative": int(row.negative),
+        }

backend/packages/storage/store/repositories/db/run.py

@@ -0,0 +1,185 @@
+from __future__ import annotations
+
+from datetime import datetime
+from typing import Any
+
+from sqlalchemy import delete, func, select, update
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from store.repositories.contracts.run import Run, RunCreate, RunRepositoryProtocol
+from store.repositories.models.run import Run as RunModel
+
+
+def _to_run(m: RunModel) -> Run:
+    return Run(
+        run_id=m.run_id,
+        thread_id=m.thread_id,
+        assistant_id=m.assistant_id,
+        user_id=m.user_id,
+        status=m.status,
+        model_name=m.model_name,
+        multitask_strategy=m.multitask_strategy,
+        error=m.error,
+        follow_up_to_run_id=m.follow_up_to_run_id,
+        metadata=dict(m.meta or {}),
+        kwargs=dict(m.kwargs or {}),
+        total_input_tokens=m.total_input_tokens,
+        total_output_tokens=m.total_output_tokens,
+        total_tokens=m.total_tokens,
+        llm_call_count=m.llm_call_count,
+        lead_agent_tokens=m.lead_agent_tokens,
+        subagent_tokens=m.subagent_tokens,
+        middleware_tokens=m.middleware_tokens,
+        message_count=m.message_count,
+        first_human_message=m.first_human_message,
+        last_ai_message=m.last_ai_message,
+        created_time=m.created_time,
+        updated_time=m.updated_time,
+    )
+
+
+class DbRunRepository(RunRepositoryProtocol):
+    def __init__(self, session: AsyncSession) -> None:
+        self._session = session
+
+    async def create_run(self, data: RunCreate) -> Run:
+        model = RunModel(
+            run_id=data.run_id,
+            thread_id=data.thread_id,
+            assistant_id=data.assistant_id,
+            user_id=data.user_id,
+            status=data.status,
+            model_name=data.model_name,
+            multitask_strategy=data.multitask_strategy,
+            error=data.error,
+            follow_up_to_run_id=data.follow_up_to_run_id,
+            meta=dict(data.metadata),
+            kwargs=dict(data.kwargs),
+        )
+        if data.created_time is not None:
+            model.created_time = data.created_time
+        self._session.add(model)
+        await self._session.flush()
+        await self._session.refresh(model)
+        return _to_run(model)
+
+    async def get_run(self, run_id: str) -> Run | None:
+        result = await self._session.execute(select(RunModel).where(RunModel.run_id == run_id))
+        model = result.scalar_one_or_none()
+        return _to_run(model) if model else None
+
+    async def list_runs_by_thread(
+        self,
+        thread_id: str,
+        *,
+        user_id: str | None = None,
+        limit: int = 50,
+        offset: int = 0,
+    ) -> list[Run]:
+        stmt = select(RunModel).where(RunModel.thread_id == thread_id)
+        if user_id is not None:
+            stmt = stmt.where(RunModel.user_id == user_id)
+        stmt = stmt.order_by(RunModel.created_time.desc()).limit(limit).offset(offset)
+        result = await self._session.execute(stmt)
+        return [_to_run(m) for m in result.scalars().all()]
+
+    async def update_run_status(self, run_id: str, status: str, *, error: str | None = None) -> None:
+        values: dict = {"status": status}
+        if error is not None:
+            values["error"] = error
+        await self._session.execute(update(RunModel).where(RunModel.run_id == run_id).values(**values))
+
+    async def delete_run(self, run_id: str) -> None:
+        await self._session.execute(delete(RunModel).where(RunModel.run_id == run_id))
+
+    async def list_pending(self, *, before: datetime | str | None = None) -> list[Run]:
+        if before is None:
+            before_dt = datetime.now().astimezone()
+        elif isinstance(before, datetime):
+            before_dt = before
+        else:
+            before_dt = datetime.fromisoformat(before)
+
+        result = await self._session.execute(select(RunModel).where(RunModel.status == "pending", RunModel.created_time <= before_dt).order_by(RunModel.created_time.asc()))
+        return [_to_run(m) for m in result.scalars().all()]
+
+    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,
+        first_human_message: str | None = None,
+        last_ai_message: str | None = None,
+        error: str | None = None,
+    ) -> None:
+        values = {
+            "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,
+        }
+        if first_human_message is not None:
+            values["first_human_message"] = first_human_message[:2000]
+        if last_ai_message is not None:
+            values["last_ai_message"] = last_ai_message[:2000]
+        if error is not None:
+            values["error"] = error
+        await self._session.execute(update(RunModel).where(RunModel.run_id == run_id).values(**values))
+
+    async def aggregate_tokens_by_thread(self, thread_id: str) -> dict[str, Any]:
+        completed = RunModel.status.in_(("success", "error"))
+        model_expr = func.coalesce(RunModel.model_name, "unknown")
+        stmt = (
+            select(
+                model_expr.label("model"),
+                func.count().label("runs"),
+                func.coalesce(func.sum(RunModel.total_tokens), 0).label("total_tokens"),
+                func.coalesce(func.sum(RunModel.total_input_tokens), 0).label("total_input_tokens"),
+                func.coalesce(func.sum(RunModel.total_output_tokens), 0).label("total_output_tokens"),
+                func.coalesce(func.sum(RunModel.lead_agent_tokens), 0).label("lead_agent"),
+                func.coalesce(func.sum(RunModel.subagent_tokens), 0).label("subagent"),
+                func.coalesce(func.sum(RunModel.middleware_tokens), 0).label("middleware"),
+            )
+            .where(RunModel.thread_id == thread_id, completed)
+            .group_by(model_expr)
+        )
+
+        rows = (await self._session.execute(stmt)).all()
+        total_tokens = total_input = total_output = total_runs = 0
+        lead_agent = subagent = middleware = 0
+        by_model: dict[str, dict] = {}
+        for row in rows:
+            by_model[row.model] = {"tokens": row.total_tokens, "runs": row.runs}
+            total_tokens += row.total_tokens
+            total_input += row.total_input_tokens
+            total_output += row.total_output_tokens
+            total_runs += row.runs
+            lead_agent += row.lead_agent
+            subagent += row.subagent
+            middleware += row.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/storage/store/repositories/db/run_event.py

@@ -0,0 +1,207 @@
+from __future__ import annotations
+
+import json
+import secrets
+import threading
+import time
+from typing import Any
+
+from sqlalchemy import delete, func, select
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from store.repositories.contracts.run_event import RunEvent, RunEventCreate, RunEventRepositoryProtocol
+from store.repositories.models.run_event import RunEvent as RunEventModel
+
+_SEQ_COUNTER_BITS = 12
+_SEQ_PROCESS_BITS = 9
+_SEQ_PROCESS_SALT = secrets.randbits(_SEQ_PROCESS_BITS)
+_SEQ_COUNTER_LIMIT = 1 << _SEQ_COUNTER_BITS
+_SEQ_TIMESTAMP_SHIFT = _SEQ_COUNTER_BITS + _SEQ_PROCESS_BITS
+
+
+class _SequenceAllocator:
+    def __init__(self) -> None:
+        self._last_millis = 0
+        self._lock = threading.Lock()
+
+    def allocate_base(self, batch_size: int) -> int:
+        if batch_size >= _SEQ_COUNTER_LIMIT:
+            raise ValueError(f"Run event batch is too large: {batch_size} >= {_SEQ_COUNTER_LIMIT}")
+
+        now_ms = time.time_ns() // 1_000_000
+        with self._lock:
+            seq_ms = max(now_ms, self._last_millis + 1)
+            self._last_millis = seq_ms
+        return (seq_ms << _SEQ_TIMESTAMP_SHIFT) | (_SEQ_PROCESS_SALT << _SEQ_COUNTER_BITS)
+
+
+_sequence_allocator = _SequenceAllocator()
+
+
+def _serialize_content(content: Any, metadata: dict[str, Any]) -> tuple[str, dict[str, Any]]:
+    if not isinstance(content, str):
+        next_metadata = {**metadata, "content_is_json": True}
+        if isinstance(content, dict):
+            next_metadata["content_is_dict"] = True
+        return json.dumps(content, default=str, ensure_ascii=False), next_metadata
+    return content, metadata
+
+
+def _deserialize_content(content: str, metadata: dict[str, Any]) -> Any:
+    if not (metadata.get("content_is_json") or metadata.get("content_is_dict")):
+        return content
+    try:
+        return json.loads(content)
+    except json.JSONDecodeError:
+        return content
+
+
+def _to_run_event(model: RunEventModel) -> RunEvent:
+    raw_metadata = dict(model.meta or {})
+    metadata = {key: value for key, value in raw_metadata.items() if key != "content_is_dict"}
+    return RunEvent(
+        thread_id=model.thread_id,
+        run_id=model.run_id,
+        user_id=model.user_id,
+        event_type=model.event_type,
+        category=model.category,
+        content=_deserialize_content(model.content, raw_metadata),
+        metadata=metadata,
+        seq=model.seq,
+        created_at=model.created_at,
+    )
+
+
+class DbRunEventRepository(RunEventRepositoryProtocol):
+    def __init__(self, session: AsyncSession) -> None:
+        self._session = session
+
+    async def append_batch(self, events: list[RunEventCreate]) -> list[RunEvent]:
+        if not events:
+            return []
+
+        seq_base = _sequence_allocator.allocate_base(len(events))
+
+        rows: list[RunEventModel] = []
+
+        for index, event in enumerate(events, start=1):
+            content, metadata = _serialize_content(event.content, dict(event.metadata))
+            row = RunEventModel(
+                thread_id=event.thread_id,
+                run_id=event.run_id,
+                user_id=event.user_id,
+                seq=seq_base + index,
+                event_type=event.event_type,
+                category=event.category,
+                content=content,
+                meta=metadata,
+            )
+            if event.created_at is not None:
+                row.created_at = event.created_at
+            self._session.add(row)
+            rows.append(row)
+
+        await self._session.flush()
+        return [_to_run_event(row) for row in rows]
+
+    async def list_messages(
+        self,
+        thread_id: str,
+        *,
+        limit: int = 50,
+        before_seq: int | None = None,
+        after_seq: int | None = None,
+        user_id: str | None = None,
+    ) -> list[RunEvent]:
+        stmt = select(RunEventModel).where(
+            RunEventModel.thread_id == thread_id,
+            RunEventModel.category == "message",
+        )
+        if user_id is not None:
+            stmt = stmt.where(RunEventModel.user_id == user_id)
+        if before_seq is not None:
+            stmt = stmt.where(RunEventModel.seq < before_seq).order_by(RunEventModel.seq.desc()).limit(limit)
+            result = await self._session.execute(stmt)
+            return list(reversed([_to_run_event(row) for row in result.scalars().all()]))
+        if after_seq is not None:
+            stmt = stmt.where(RunEventModel.seq > after_seq).order_by(RunEventModel.seq.asc()).limit(limit)
+            result = await self._session.execute(stmt)
+            return [_to_run_event(row) for row in result.scalars().all()]
+
+        stmt = stmt.order_by(RunEventModel.seq.desc()).limit(limit)
+        result = await self._session.execute(stmt)
+        return list(reversed([_to_run_event(row) for row in result.scalars().all()]))
+
+    async def list_events(
+        self,
+        thread_id: str,
+        run_id: str,
+        *,
+        event_types: list[str] | None = None,
+        limit: int = 500,
+        user_id: str | None = None,
+    ) -> list[RunEvent]:
+        stmt = select(RunEventModel).where(
+            RunEventModel.thread_id == thread_id,
+            RunEventModel.run_id == run_id,
+        )
+        if user_id is not None:
+            stmt = stmt.where(RunEventModel.user_id == user_id)
+        if event_types is not None:
+            stmt = stmt.where(RunEventModel.event_type.in_(event_types))
+        stmt = stmt.order_by(RunEventModel.seq.asc()).limit(limit)
+        result = await self._session.execute(stmt)
+        return [_to_run_event(row) for row in result.scalars().all()]
+
+    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,
+        user_id: str | None = None,
+    ) -> list[RunEvent]:
+        stmt = select(RunEventModel).where(
+            RunEventModel.thread_id == thread_id,
+            RunEventModel.run_id == run_id,
+            RunEventModel.category == "message",
+        )
+        if user_id is not None:
+            stmt = stmt.where(RunEventModel.user_id == user_id)
+        if before_seq is not None:
+            stmt = stmt.where(RunEventModel.seq < before_seq).order_by(RunEventModel.seq.desc()).limit(limit)
+            result = await self._session.execute(stmt)
+            return list(reversed([_to_run_event(row) for row in result.scalars().all()]))
+        if after_seq is not None:
+            stmt = stmt.where(RunEventModel.seq > after_seq).order_by(RunEventModel.seq.asc()).limit(limit)
+            result = await self._session.execute(stmt)
+            return [_to_run_event(row) for row in result.scalars().all()]
+
+        stmt = stmt.order_by(RunEventModel.seq.desc()).limit(limit)
+        result = await self._session.execute(stmt)
+        return list(reversed([_to_run_event(row) for row in result.scalars().all()]))
+
+    async def count_messages(self, thread_id: str, *, user_id: str | None = None) -> int:
+        stmt = select(func.count()).select_from(RunEventModel).where(RunEventModel.thread_id == thread_id, RunEventModel.category == "message")
+        if user_id is not None:
+            stmt = stmt.where(RunEventModel.user_id == user_id)
+        count = await self._session.scalar(stmt)
+        return int(count or 0)
+
+    async def delete_by_thread(self, thread_id: str, *, user_id: str | None = None) -> int:
+        conditions = [RunEventModel.thread_id == thread_id]
+        if user_id is not None:
+            conditions.append(RunEventModel.user_id == user_id)
+        count = await self._session.scalar(select(func.count()).select_from(RunEventModel).where(*conditions))
+        await self._session.execute(delete(RunEventModel).where(*conditions))
+        return int(count or 0)
+
+    async def delete_by_run(self, thread_id: str, run_id: str, *, user_id: str | None = None) -> int:
+        conditions = [RunEventModel.thread_id == thread_id, RunEventModel.run_id == run_id]
+        if user_id is not None:
+            conditions.append(RunEventModel.user_id == user_id)
+        count = await self._session.scalar(select(func.count()).select_from(RunEventModel).where(*conditions))
+        await self._session.execute(delete(RunEventModel).where(*conditions))
+        return int(count or 0)

backend/packages/storage/store/repositories/db/thread_meta.py

@@ -0,0 +1,113 @@
+from __future__ import annotations
+
+import logging
+from typing import Any
+
+from sqlalchemy import delete, select, update
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from store.persistence.json_compat import json_match
+from store.repositories.contracts.thread_meta import (
+    InvalidMetadataFilterError,
+    ThreadMeta,
+    ThreadMetaCreate,
+    ThreadMetaRepositoryProtocol,
+)
+from store.repositories.models.thread_meta import ThreadMeta as ThreadMetaModel
+
+logger = logging.getLogger(__name__)
+
+
+def _to_thread_meta(m: ThreadMetaModel) -> ThreadMeta:
+    return ThreadMeta(
+        thread_id=m.thread_id,
+        assistant_id=m.assistant_id,
+        user_id=m.user_id,
+        display_name=m.display_name,
+        status=m.status,
+        metadata=dict(m.meta or {}),
+        created_time=m.created_time,
+        updated_time=m.updated_time,
+    )
+
+
+class DbThreadMetaRepository(ThreadMetaRepositoryProtocol):
+    def __init__(self, session: AsyncSession) -> None:
+        self._session = session
+
+    async def create_thread_meta(self, data: ThreadMetaCreate) -> ThreadMeta:
+        model = ThreadMetaModel(
+            thread_id=data.thread_id,
+            assistant_id=data.assistant_id,
+            user_id=data.user_id,
+            display_name=data.display_name,
+            status=data.status,
+            meta=dict(data.metadata),
+        )
+        self._session.add(model)
+        await self._session.flush()
+        await self._session.refresh(model)
+        return _to_thread_meta(model)
+
+    async def get_thread_meta(self, thread_id: str) -> ThreadMeta | None:
+        result = await self._session.execute(select(ThreadMetaModel).where(ThreadMetaModel.thread_id == thread_id))
+        model = result.scalar_one_or_none()
+        return _to_thread_meta(model) if model else None
+
+    async def update_thread_meta(
+        self,
+        thread_id: str,
+        *,
+        display_name: str | None = None,
+        status: str | None = None,
+        metadata: dict[str, Any] | None = None,
+    ) -> None:
+        values: dict = {}
+        if display_name is not None:
+            values["display_name"] = display_name
+        if status is not None:
+            values["status"] = status
+        if metadata is not None:
+            values["meta"] = dict(metadata)
+        if not values:
+            return
+        await self._session.execute(update(ThreadMetaModel).where(ThreadMetaModel.thread_id == thread_id).values(**values))
+
+    async def delete_thread(self, thread_id: str) -> None:
+        await self._session.execute(delete(ThreadMetaModel).where(ThreadMetaModel.thread_id == thread_id))
+
+    async def search_threads(
+        self,
+        *,
+        metadata: dict[str, Any] | None = None,
+        status: str | None = None,
+        user_id: str | None = None,
+        assistant_id: str | None = None,
+        limit: int = 100,
+        offset: int = 0,
+    ) -> list[ThreadMeta]:
+        stmt = select(ThreadMetaModel)
+
+        if status is not None:
+            stmt = stmt.where(ThreadMetaModel.status == status)
+        if user_id is not None:
+            stmt = stmt.where(ThreadMetaModel.user_id == user_id)
+        if assistant_id is not None:
+            stmt = stmt.where(ThreadMetaModel.assistant_id == assistant_id)
+        if metadata:
+            applied = 0
+            for key, value in metadata.items():
+                try:
+                    stmt = stmt.where(json_match(ThreadMetaModel.meta, key, value))
+                    applied += 1
+                except (ValueError, TypeError) as exc:
+                    logger.warning("Skipping metadata filter key %s: %s", ascii(key), exc)
+            if applied == 0:
+                rejected_keys = ", ".join(sorted(str(key) for key in metadata))
+                raise InvalidMetadataFilterError(f"All metadata filter keys were rejected as unsafe: {rejected_keys}")
+
+        stmt = stmt.order_by(ThreadMetaModel.created_time.desc(), ThreadMetaModel.thread_id.desc())
+        stmt = stmt.limit(limit).offset(offset)
+
+        result = await self._session.execute(stmt)
+        return [_to_thread_meta(m) for m in result.scalars().all()]

backend/packages/storage/store/repositories/db/user.py

@@ -0,0 +1,98 @@
+from __future__ import annotations
+
+from sqlalchemy import func, select
+from sqlalchemy.exc import IntegrityError
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from store.repositories.contracts.user import User, UserCreate, UserNotFoundError, UserRepositoryProtocol
+from store.repositories.models.user import User as UserModel
+
+
+def _to_user(model: UserModel) -> User:
+    return User(
+        id=model.id,
+        email=model.email,
+        password_hash=model.password_hash,
+        system_role=model.system_role,  # type: ignore[arg-type]
+        created_at=model.created_at,
+        oauth_provider=model.oauth_provider,
+        oauth_id=model.oauth_id,
+        needs_setup=model.needs_setup,
+        token_version=model.token_version,
+    )
+
+
+class DbUserRepository(UserRepositoryProtocol):
+    def __init__(self, session: AsyncSession) -> None:
+        self._session = session
+
+    async def create_user(self, data: UserCreate) -> User:
+        model = UserModel(
+            id=data.id,
+            email=data.email,
+            system_role=data.system_role,
+            password_hash=data.password_hash,
+            oauth_provider=data.oauth_provider,
+            oauth_id=data.oauth_id,
+            needs_setup=data.needs_setup,
+            token_version=data.token_version,
+        )
+        if data.created_at is not None:
+            model.created_at = data.created_at
+        self._session.add(model)
+        try:
+            await self._session.flush()
+        except IntegrityError as exc:
+            await self._session.rollback()
+            raise ValueError(f"Email already registered: {data.email}") from exc
+        await self._session.refresh(model)
+        return _to_user(model)
+
+    async def get_user_by_id(self, user_id: str) -> User | None:
+        model = await self._session.get(UserModel, user_id)
+        return _to_user(model) if model is not None else None
+
+    async def get_user_by_email(self, email: str) -> User | None:
+        result = await self._session.execute(select(UserModel).where(UserModel.email == email))
+        model = result.scalar_one_or_none()
+        return _to_user(model) if model is not None else None
+
+    async def get_user_by_oauth(self, provider: str, oauth_id: str) -> User | None:
+        result = await self._session.execute(
+            select(UserModel).where(
+                UserModel.oauth_provider == provider,
+                UserModel.oauth_id == oauth_id,
+            )
+        )
+        model = result.scalar_one_or_none()
+        return _to_user(model) if model is not None else None
+
+    async def get_first_admin(self) -> User | None:
+        result = await self._session.execute(select(UserModel).where(UserModel.system_role == "admin").limit(1))
+        model = result.scalar_one_or_none()
+        return _to_user(model) if model is not None else None
+
+    async def update_user(self, data: User) -> User:
+        model = await self._session.get(UserModel, data.id)
+        if model is None:
+            raise UserNotFoundError(f"User {data.id} no longer exists")
+
+        model.email = data.email
+        model.password_hash = data.password_hash
+        model.system_role = data.system_role
+        model.oauth_provider = data.oauth_provider
+        model.oauth_id = data.oauth_id
+        model.needs_setup = data.needs_setup
+        model.token_version = data.token_version
+
+        await self._session.flush()
+        await self._session.refresh(model)
+        return _to_user(model)
+
+    async def count_users(self) -> int:
+        count = await self._session.scalar(select(func.count()).select_from(UserModel))
+        return int(count or 0)
+
+    async def count_admin_users(self) -> int:
+        count = await self._session.scalar(select(func.count()).select_from(UserModel).where(UserModel.system_role == "admin"))
+        return int(count or 0)

backend/packages/storage/store/repositories/factory.py

@@ -0,0 +1,36 @@
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from store.repositories import (
+    FeedbackRepositoryProtocol,
+    RunEventRepositoryProtocol,
+    RunRepositoryProtocol,
+    ThreadMetaRepositoryProtocol,
+    UserRepositoryProtocol,
+)
+from store.repositories.db import (
+    DbFeedbackRepository,
+    DbRunEventRepository,
+    DbRunRepository,
+    DbThreadMetaRepository,
+    DbUserRepository,
+)
+
+
+def build_thread_meta_repository(session: AsyncSession) -> ThreadMetaRepositoryProtocol:
+    return DbThreadMetaRepository(session)
+
+
+def build_run_repository(session: AsyncSession) -> RunRepositoryProtocol:
+    return DbRunRepository(session)
+
+
+def build_feedback_repository(session: AsyncSession) -> FeedbackRepositoryProtocol:
+    return DbFeedbackRepository(session)
+
+
+def build_run_event_repository(session: AsyncSession) -> RunEventRepositoryProtocol:
+    return DbRunEventRepository(session)
+
+
+def build_user_repository(session: AsyncSession) -> UserRepositoryProtocol:
+    return DbUserRepository(session)

backend/packages/storage/store/repositories/models/__init__.py

@@ -0,0 +1,7 @@
+from store.repositories.models.feedback import Feedback
+from store.repositories.models.run import Run
+from store.repositories.models.run_event import RunEvent
+from store.repositories.models.thread_meta import ThreadMeta
+from store.repositories.models.user import User
+
+__all__ = ["Feedback", "Run", "RunEvent", "ThreadMeta", "User"]

backend/packages/storage/store/repositories/models/feedback.py

@@ -0,0 +1,36 @@
+from __future__ import annotations
+
+from datetime import datetime
+
+from sqlalchemy import Integer, String, UniqueConstraint
+from sqlalchemy.orm import Mapped, mapped_column
+
+from store.persistence.base_model import DataClassBase, TimeZone, UniversalText, current_time
+
+
+class Feedback(DataClassBase):
+    """Feedback table (create-only, no updated_time)."""
+
+    __tablename__ = "feedback"
+    __table_args__ = (
+        UniqueConstraint("thread_id", "run_id", "user_id", name="uq_feedback_thread_run_user"),
+        {"comment": "Feedback table."},
+    )
+
+    feedback_id: Mapped[str] = mapped_column(String(64), primary_key=True)
+    run_id: Mapped[str] = mapped_column(String(64), index=True)
+    thread_id: Mapped[str] = mapped_column(String(64), index=True)
+    rating: Mapped[int] = mapped_column(Integer)
+
+    user_id: Mapped[str | None] = mapped_column(String(64), default=None, index=True)
+    message_id: Mapped[str | None] = mapped_column(String(64), default=None)
+    comment: Mapped[str | None] = mapped_column(UniversalText, default=None)
+
+    created_time: Mapped[datetime] = mapped_column(
+        "created_at",
+        TimeZone,
+        init=False,
+        default_factory=current_time,
+        sort_order=999,
+        comment="Created at",
+    )

backend/packages/storage/store/repositories/models/run.py

@@ -0,0 +1,63 @@
+from __future__ import annotations
+
+from datetime import datetime
+from typing import Any
+
+from sqlalchemy import JSON, Index, Integer, String
+from sqlalchemy.orm import Mapped, mapped_column
+
+from store.persistence.base_model import DataClassBase, TimeZone, UniversalText, current_time
+
+
+class Run(DataClassBase):
+    """Run metadata table."""
+
+    __tablename__ = "runs"
+    __table_args__ = (
+        Index("ix_runs_thread_status", "thread_id", "status"),
+        {"comment": "Run metadata table."},
+    )
+
+    run_id: Mapped[str] = mapped_column(String(64), primary_key=True)
+    thread_id: Mapped[str] = mapped_column(String(64), index=True)
+
+    assistant_id: Mapped[str | None] = mapped_column(String(128), default=None)
+    user_id: Mapped[str | None] = mapped_column(String(64), default=None, index=True)
+    status: Mapped[str] = mapped_column(String(20), default="pending", index=True)
+    model_name: Mapped[str | None] = mapped_column(String(128), default=None)
+    multitask_strategy: Mapped[str] = mapped_column(String(20), default="reject")
+    error: Mapped[str | None] = mapped_column(UniversalText, default=None)
+    follow_up_to_run_id: Mapped[str | None] = mapped_column(String(64), default=None)
+
+    meta: Mapped[dict[str, Any]] = mapped_column("metadata_json", JSON, default_factory=dict)
+    kwargs: Mapped[dict[str, Any]] = mapped_column("kwargs_json", JSON, default_factory=dict)
+
+    total_input_tokens: Mapped[int] = mapped_column(Integer, default=0)
+    total_output_tokens: Mapped[int] = mapped_column(Integer, default=0)
+    total_tokens: Mapped[int] = mapped_column(Integer, default=0)
+    llm_call_count: Mapped[int] = mapped_column(Integer, default=0)
+    lead_agent_tokens: Mapped[int] = mapped_column(Integer, default=0)
+    subagent_tokens: Mapped[int] = mapped_column(Integer, default=0)
+    middleware_tokens: Mapped[int] = mapped_column(Integer, default=0)
+
+    message_count: Mapped[int] = mapped_column(Integer, default=0)
+    first_human_message: Mapped[str | None] = mapped_column(UniversalText, default=None)
+    last_ai_message: Mapped[str | None] = mapped_column(UniversalText, default=None)
+
+    created_time: Mapped[datetime] = mapped_column(
+        "created_at",
+        TimeZone,
+        init=False,
+        default_factory=current_time,
+        sort_order=999,
+        comment="Created at",
+    )
+    updated_time: Mapped[datetime | None] = mapped_column(
+        "updated_at",
+        TimeZone,
+        init=False,
+        default=None,
+        onupdate=current_time,
+        sort_order=999,
+        comment="Updated at",
+    )

backend/packages/storage/store/repositories/models/run_event.py

@@ -0,0 +1,46 @@
+from __future__ import annotations
+
+from datetime import datetime
+from typing import Any
+
+from sqlalchemy import JSON, BigInteger, Index, String, UniqueConstraint
+from sqlalchemy.orm import Mapped, mapped_column
+
+from store.persistence.base_model import (
+    DataClassBase,
+    TimeZone,
+    UniversalText,
+    current_time,
+    id_key,
+)
+
+
+class RunEvent(DataClassBase):
+    """Run event table."""
+
+    __tablename__ = "run_events"
+    __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"),
+        {"comment": "Run event table."},
+    )
+
+    id: Mapped[id_key] = mapped_column(init=False)
+
+    thread_id: Mapped[str] = mapped_column(String(64), index=True)
+    run_id: Mapped[str] = mapped_column(String(64), index=True)
+    event_type: Mapped[str] = mapped_column(String(32), index=True)
+    category: Mapped[str] = mapped_column(String(16), index=True)
+
+    user_id: Mapped[str | None] = mapped_column(String(64), default=None, index=True)
+    seq: Mapped[int] = mapped_column(BigInteger, default=0, index=True)
+    content: Mapped[str] = mapped_column(UniversalText, default="")
+    meta: Mapped[dict[str, Any]] = mapped_column("event_metadata", JSON, default_factory=dict)
+    created_at: Mapped[datetime] = mapped_column(
+        TimeZone,
+        init=False,
+        default_factory=current_time,
+        sort_order=999,
+        comment="Event timestamp",
+    )

backend/packages/storage/store/repositories/models/thread_meta.py

@@ -0,0 +1,43 @@
+from __future__ import annotations
+
+from datetime import datetime
+from typing import Any
+
+from sqlalchemy import JSON, String
+from sqlalchemy.orm import Mapped, mapped_column
+
+from store.persistence.base_model import DataClassBase, TimeZone, current_time
+
+
+class ThreadMeta(DataClassBase):
+    """Thread metadata table."""
+
+    __tablename__ = "threads_meta"
+    __table_args__ = {"comment": "Thread metadata table."}
+
+    thread_id: Mapped[str] = mapped_column(String(64), primary_key=True)
+
+    assistant_id: Mapped[str | None] = mapped_column(String(128), default=None, index=True)
+    user_id: Mapped[str | None] = mapped_column(String(64), default=None, index=True)
+    display_name: Mapped[str | None] = mapped_column(String(256), default=None)
+    status: Mapped[str] = mapped_column(String(20), default="idle", index=True)
+
+    meta: Mapped[dict[str, Any]] = mapped_column("metadata_json", JSON, default_factory=dict)
+
+    created_time: Mapped[datetime] = mapped_column(
+        "created_at",
+        TimeZone,
+        init=False,
+        default_factory=current_time,
+        sort_order=999,
+        comment="Created at",
+    )
+    updated_time: Mapped[datetime | None] = mapped_column(
+        "updated_at",
+        TimeZone,
+        init=False,
+        default=None,
+        onupdate=current_time,
+        sort_order=999,
+        comment="Updated at",
+    )

backend/packages/storage/store/repositories/models/user.py

@@ -0,0 +1,42 @@
+from __future__ import annotations
+
+from datetime import datetime
+
+from sqlalchemy import Boolean, Index, String, text
+from sqlalchemy.orm import Mapped, mapped_column
+
+from store.persistence.base_model import DataClassBase, TimeZone, current_time
+
+
+class User(DataClassBase):
+    """User account table."""
+
+    __tablename__ = "users"
+    __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"),
+        ),
+        {"comment": "User account table."},
+    )
+
+    id: Mapped[str] = mapped_column(String(36), primary_key=True)
+    email: Mapped[str] = mapped_column(String(320), unique=True, nullable=False, index=True)
+    system_role: Mapped[str] = mapped_column(String(16), default="user")
+
+    password_hash: Mapped[str | None] = mapped_column(String(128), default=None)
+    oauth_provider: Mapped[str | None] = mapped_column(String(32), default=None)
+    oauth_id: Mapped[str | None] = mapped_column(String(128), default=None)
+    needs_setup: Mapped[bool] = mapped_column(Boolean, default=False)
+    token_version: Mapped[int] = mapped_column(default=0)
+
+    created_at: Mapped[datetime] = mapped_column(
+        TimeZone,
+        init=False,
+        default_factory=current_time,
+        sort_order=999,
+        comment="Created at",
+    )

backend/packages/storage/store/utils/__init__.py

@@ -0,0 +1,3 @@
+from .timezone import get_timezone
+
+__all__ = ["get_timezone"]

backend/packages/storage/store/utils/timezone.py

@@ -0,0 +1,51 @@
+import zoneinfo
+from datetime import UTC, datetime
+
+from store.config.app_config import get_app_config
+
+# IANA identifiers that map to UTC — see https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
+_UTC_IDENTIFIERS = frozenset({"Etc/UCT", "Etc/Universal", "Etc/UTC", "Etc/Zulu", "UCT", "Universal", "UTC", "Zulu"})
+
+
+class TimeZone:
+    def __init__(self) -> None:
+        app_config = get_app_config()
+        if app_config.timezone in _UTC_IDENTIFIERS:
+            self.tz_info = UTC
+        else:
+            self.tz_info = zoneinfo.ZoneInfo(app_config.timezone)
+
+    def now(self) -> datetime:
+        """Return the current time in the configured timezone."""
+        return datetime.now(self.tz_info)
+
+    def from_datetime(self, t: datetime) -> datetime:
+        """Convert a datetime to the configured timezone."""
+        return t.astimezone(self.tz_info)
+
+    def from_str(self, t_str: str, format_str: str = "%Y-%m-%d %H:%M:%S") -> datetime:
+        """Parse a time string and attach the configured timezone."""
+        return datetime.strptime(t_str, format_str).replace(tzinfo=self.tz_info)
+
+    @staticmethod
+    def to_str(t: datetime, format_str: str = "%Y-%m-%d %H:%M:%S") -> str:
+        """Format a datetime to string."""
+        return t.strftime(format_str)
+
+    @staticmethod
+    def to_utc(t: datetime | int) -> datetime:
+        """Convert a datetime or Unix timestamp to UTC."""
+        if isinstance(t, datetime):
+            return t.astimezone(UTC)
+        return datetime.fromtimestamp(t, tz=UTC)
+
+
+_timezone = None
+
+
+def get_timezone() -> TimeZone:
+    """Return the global TimeZone singleton (lazy-initialized)."""
+    global _timezone
+    if _timezone is None:
+        _timezone = TimeZone()
+    return _timezone

backend/pyproject.toml

@@ -6,6 +6,7 @@ readme = "README.md"
 requires-python = ">=3.12"
 dependencies = [
     "deerflow-harness",
+    "deerflow-storage",
     "fastapi>=0.115.0",
     "httpx>=0.28.0",
     "python-multipart>=0.0.27",
@@ -24,7 +25,8 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-postgres = ["deerflow-harness[postgres]"]
+postgres = ["deerflow-harness[postgres]", "deerflow-storage[postgres]"]
+mysql = ["deerflow-storage[mysql]"]
 
 [dependency-groups]
 dev = [
@@ -43,7 +45,8 @@ markers = [
 index-url = "https://pypi.org/simple"
 
 [tool.uv.workspace]
-members = ["packages/harness"]
+members = ["packages/harness", "packages/storage"]
 
 [tool.uv.sources]
 deerflow-harness = { workspace = true }
+deerflow-storage = { workspace = true }

backend/tests/test_checkpointer.py

@@ -94,12 +94,15 @@ class TestHarnessPackaging:
             "psycopg-pool>=3.3.0",
         ]
 
-    def test_workspace_pyproject_forwards_postgres_extra_to_harness(self):
+    def test_workspace_pyproject_forwards_postgres_extra_to_storage_packages(self):
         pyproject_path = Path(__file__).resolve().parents[1] / "pyproject.toml"
         data = tomllib.loads(pyproject_path.read_text())
 
         optional_dependencies = data["project"]["optional-dependencies"]
-        assert optional_dependencies["postgres"] == ["deerflow-harness[postgres]"]
+        assert optional_dependencies["postgres"] == [
+            "deerflow-harness[postgres]",
+            "deerflow-storage[postgres]",
+        ]
 
     def test_postgres_missing_dependency_messages_recommend_package_extra(self):
         assert "deerflow-harness[postgres]" in POSTGRES_INSTALL

backend/tests/test_memory_queue.py

@@ -1,6 +1,6 @@
 import threading
 import time
-from unittest.mock import MagicMock, patch
+from unittest.mock import MagicMock, call, patch
 
 from deerflow.agents.memory.queue import ConversationContext, MemoryUpdateQueue
 from deerflow.config.memory_config import MemoryConfig
@@ -164,3 +164,85 @@ def test_flush_nowait_is_non_blocking() -> None:
     assert elapsed < 0.1
     assert finished.is_set() is False
     assert finished.wait(1.0) is True
+
+
+def test_queue_keeps_updates_for_different_agents_in_same_thread() -> None:
+    queue = MemoryUpdateQueue()
+
+    with (
+        patch("deerflow.agents.memory.queue.get_memory_config", return_value=_memory_config(enabled=True)),
+        patch.object(queue, "_reset_timer"),
+    ):
+        queue.add(thread_id="thread-1", messages=["agent-a"], agent_name="agent-a")
+        queue.add(thread_id="thread-1", messages=["agent-b"], agent_name="agent-b")
+
+    assert queue.pending_count == 2
+    assert [context.agent_name for context in queue._queue] == ["agent-a", "agent-b"]
+
+
+def test_queue_still_coalesces_updates_for_same_agent_in_same_thread() -> None:
+    queue = MemoryUpdateQueue()
+
+    with (
+        patch("deerflow.agents.memory.queue.get_memory_config", return_value=_memory_config(enabled=True)),
+        patch.object(queue, "_reset_timer"),
+    ):
+        queue.add(
+            thread_id="thread-1",
+            messages=["first"],
+            agent_name="agent-a",
+            correction_detected=True,
+        )
+        queue.add(
+            thread_id="thread-1",
+            messages=["second"],
+            agent_name="agent-a",
+            correction_detected=False,
+        )
+
+    assert queue.pending_count == 1
+    assert queue._queue[0].agent_name == "agent-a"
+    assert queue._queue[0].messages == ["second"]
+    assert queue._queue[0].correction_detected is True
+
+
+def test_process_queue_updates_different_agents_in_same_thread_separately() -> None:
+    queue = MemoryUpdateQueue()
+
+    with (
+        patch("deerflow.agents.memory.queue.get_memory_config", return_value=_memory_config(enabled=True)),
+        patch.object(queue, "_reset_timer"),
+    ):
+        queue.add(thread_id="thread-1", messages=["agent-a"], agent_name="agent-a")
+        queue.add(thread_id="thread-1", messages=["agent-b"], agent_name="agent-b")
+
+    mock_updater = MagicMock()
+    mock_updater.update_memory.return_value = True
+
+    with (
+        patch("deerflow.agents.memory.updater.MemoryUpdater", return_value=mock_updater),
+        patch("deerflow.agents.memory.queue.time.sleep"),
+    ):
+        queue.flush()
+
+    assert mock_updater.update_memory.call_count == 2
+    mock_updater.update_memory.assert_has_calls(
+        [
+            call(
+                messages=["agent-a"],
+                thread_id="thread-1",
+                agent_name="agent-a",
+                correction_detected=False,
+                reinforcement_detected=False,
+                user_id=None,
+            ),
+            call(
+                messages=["agent-b"],
+                thread_id="thread-1",
+                agent_name="agent-b",
+                correction_detected=False,
+                reinforcement_detected=False,
+                user_id=None,
+            ),
+        ]
+    )

backend/tests/test_memory_queue_user_isolation.py

@@ -38,3 +38,42 @@ def test_queue_process_passes_user_id_to_updater():
     mock_updater.update_memory.assert_called_once()
     call_kwargs = mock_updater.update_memory.call_args.kwargs
     assert call_kwargs["user_id"] == "alice"
+
+
+def test_queue_keeps_updates_for_different_users_in_same_thread_and_agent():
+    q = MemoryUpdateQueue()
+
+    with patch("deerflow.agents.memory.queue.get_memory_config", return_value=MemoryConfig(enabled=True)), patch.object(q, "_reset_timer"):
+        q.add(thread_id="main", messages=["alice update"], agent_name="researcher", user_id="alice")
+        q.add(thread_id="main", messages=["bob update"], agent_name="researcher", user_id="bob")
+
+    assert q.pending_count == 2
+    assert [context.user_id for context in q._queue] == ["alice", "bob"]
+    assert [context.messages for context in q._queue] == [["alice update"], ["bob update"]]
+
+
+def test_queue_still_coalesces_updates_for_same_user_thread_and_agent():
+    q = MemoryUpdateQueue()
+
+    with patch("deerflow.agents.memory.queue.get_memory_config", return_value=MemoryConfig(enabled=True)), patch.object(q, "_reset_timer"):
+        q.add(thread_id="main", messages=["first"], agent_name="researcher", user_id="alice")
+        q.add(thread_id="main", messages=["second"], agent_name="researcher", user_id="alice")
+
+    assert q.pending_count == 1
+    assert q._queue[0].messages == ["second"]
+    assert q._queue[0].user_id == "alice"
+    assert q._queue[0].agent_name == "researcher"
+
+
+def test_add_nowait_keeps_different_users_separate():
+    q = MemoryUpdateQueue()
+
+    with (
+        patch("deerflow.agents.memory.queue.get_memory_config", return_value=MemoryConfig(enabled=True)),
+        patch.object(q, "_schedule_timer"),
+    ):
+        q.add_nowait(thread_id="main", messages=["alice update"], agent_name="researcher", user_id="alice")
+        q.add_nowait(thread_id="main", messages=["bob update"], agent_name="researcher", user_id="bob")
+
+    assert q.pending_count == 2
+    assert [context.user_id for context in q._queue] == ["alice", "bob"]

backend/tests/test_run_event_store.py

@@ -268,6 +268,39 @@ class TestEdgeCases:
 class TestDbRunEventStore:
     """Tests for DbRunEventStore with temp SQLite."""
 
+    @pytest.mark.anyio
+    async def test_postgres_max_seq_uses_advisory_lock_without_for_update(self):
+        from sqlalchemy.dialects import postgresql
+
+        from deerflow.runtime.events.store.db import DbRunEventStore
+
+        class FakeSession:
+            def __init__(self):
+                self.dialect = postgresql.dialect()
+                self.execute_calls = []
+                self.scalar_stmt = None
+
+            def get_bind(self):
+                return self
+
+            async def execute(self, stmt, params=None):
+                self.execute_calls.append((stmt, params))
+
+            async def scalar(self, stmt):
+                self.scalar_stmt = stmt
+                return 41
+
+        session = FakeSession()
+
+        max_seq = await DbRunEventStore._max_seq_for_thread(session, "thread-1")
+
+        assert max_seq == 41
+        assert session.execute_calls
+        assert session.execute_calls[0][1] == {"thread_id": "thread-1"}
+        assert "pg_advisory_xact_lock" in str(session.execute_calls[0][0])
+        compiled = str(session.scalar_stmt.compile(dialect=postgresql.dialect()))
+        assert "FOR UPDATE" not in compiled
+
     @pytest.mark.anyio
     async def test_basic_crud(self, tmp_path):
         from deerflow.persistence.engine import close_engine, get_session_factory, init_engine

backend/tests/test_storage_json_compat.py

@@ -0,0 +1,81 @@
+from __future__ import annotations
+
+import os
+from pathlib import Path
+
+import pytest
+from sqlalchemy import Column, MetaData, String, Table
+from sqlalchemy.dialects import mysql, postgresql
+from sqlalchemy.types import JSON
+
+os.environ.setdefault("DEER_FLOW_CONFIG_PATH", str(Path(__file__).resolve().parents[2] / "config.example.yaml"))
+
+from store.persistence.json_compat import json_match
+
+
+def _table():
+    metadata = MetaData()
+    return Table("t", metadata, Column("data", JSON), Column("id", String))
+
+
+def test_storage_json_match_compiles_sqlite() -> None:
+    from sqlalchemy import create_engine
+
+    table = _table()
+    dialect = create_engine("sqlite://").dialect
+
+    assert str(json_match(table.c.data, "k", None).compile(dialect=dialect, compile_kwargs={"literal_binds": True})) == ("json_type(t.data, '$.\"k\"') = 'null'")
+    assert str(json_match(table.c.data, "k", True).compile(dialect=dialect, compile_kwargs={"literal_binds": True})) == ("json_type(t.data, '$.\"k\"') = 'true'")
+
+    int_sql = str(json_match(table.c.data, "k", 42).compile(dialect=dialect, compile_kwargs={"literal_binds": True}))
+    assert "= 'integer'" in int_sql
+    assert "CAST" in int_sql
+
+    float_sql = str(json_match(table.c.data, "k", 3.14).compile(dialect=dialect, compile_kwargs={"literal_binds": True}))
+    assert "IN ('integer', 'real')" in float_sql
+    assert "REAL" in float_sql
+
+
+def test_storage_json_match_compiles_postgres() -> None:
+    table = _table()
+    dialect = postgresql.dialect()
+
+    assert str(json_match(table.c.data, "k", None).compile(dialect=dialect, compile_kwargs={"literal_binds": True})) == ("json_typeof(t.data -> 'k') = 'null'")
+    assert str(json_match(table.c.data, "k", False).compile(dialect=dialect, compile_kwargs={"literal_binds": True})) == ("(json_typeof(t.data -> 'k') = 'boolean' AND (t.data ->> 'k') = 'false')")
+
+    int_sql = str(json_match(table.c.data, "k", 42).compile(dialect=dialect, compile_kwargs={"literal_binds": True}))
+    assert "CASE WHEN" in int_sql
+    assert "BIGINT" in int_sql
+    assert "'^-?[0-9]+$'" in int_sql
+
+
+def test_storage_json_match_compiles_mysql() -> None:
+    table = _table()
+    dialect = mysql.dialect()
+
+    null_sql = str(json_match(table.c.data, "k", None).compile(dialect=dialect, compile_kwargs={"literal_binds": True}))
+    assert null_sql == "JSON_TYPE(JSON_EXTRACT(t.data, '$.\"k\"')) = 'NULL'"
+
+    bool_sql = str(json_match(table.c.data, "k", True).compile(dialect=dialect, compile_kwargs={"literal_binds": True}))
+    assert "JSON_TYPE(JSON_EXTRACT" in bool_sql
+    assert "= 'BOOLEAN'" in bool_sql
+    assert "= 'true'" in bool_sql
+
+    int_sql = str(json_match(table.c.data, "k", 42).compile(dialect=dialect, compile_kwargs={"literal_binds": True}))
+    assert "= 'INTEGER'" in int_sql
+    assert "SIGNED" in int_sql
+
+
+def test_storage_json_match_rejects_unsafe_keys_and_values() -> None:
+    table = _table()
+
+    for bad_key in ["a.b", "bad;key", "with space", "", 42, None]:
+        with pytest.raises(ValueError, match="JsonMatch key must match"):
+            json_match(table.c.data, bad_key, "x")  # type: ignore[arg-type]
+
+    for bad_value in [[], {}, object()]:
+        with pytest.raises(TypeError, match="JsonMatch value must be"):
+            json_match(table.c.data, "k", bad_value)
+
+    with pytest.raises(TypeError, match="out of signed 64-bit range"):
+        json_match(table.c.data, "k", 2**63)

backend/tests/test_storage_persistence_config.py

@@ -0,0 +1,122 @@
+from __future__ import annotations
+
+import os
+import subprocess
+import sys
+from pathlib import Path
+from types import SimpleNamespace
+
+import pytest
+
+os.environ.setdefault("DEER_FLOW_CONFIG_PATH", str(Path(__file__).resolve().parents[2] / "config.example.yaml"))
+
+from store.config.storage_config import StorageConfig
+from store.persistence.factory import _create_database_url, storage_config_from_database_config
+
+
+def test_database_sqlite_config_maps_to_storage_config(tmp_path):
+    database = SimpleNamespace(
+        backend="sqlite",
+        sqlite_dir=str(tmp_path),
+        echo_sql=True,
+        pool_size=9,
+    )
+
+    storage = storage_config_from_database_config(database)
+
+    assert storage == StorageConfig(
+        driver="sqlite",
+        sqlite_dir=str(tmp_path),
+        echo_sql=True,
+        pool_size=9,
+    )
+    assert storage.sqlite_storage_path == str(tmp_path / "deerflow.db")
+
+
+def test_database_memory_config_is_not_a_storage_backend():
+    database = SimpleNamespace(backend="memory")
+
+    with pytest.raises(ValueError, match="Unsupported database backend"):
+        storage_config_from_database_config(database)
+
+
+def test_database_postgres_config_preserves_url_and_pool_options():
+    database = SimpleNamespace(
+        backend="postgres",
+        postgres_url="postgresql://user:pass@db.example:5544/deerflow",
+        echo_sql=True,
+        pool_size=11,
+    )
+
+    storage = storage_config_from_database_config(database)
+    url = _create_database_url(storage)
+
+    assert storage.driver == "postgres"
+    assert storage.database_url == "postgresql://user:pass@db.example:5544/deerflow"
+    assert storage.username == "user"
+    assert storage.password == "pass"
+    assert storage.host == "db.example"
+    assert storage.port == 5544
+    assert storage.db_name == "deerflow"
+    assert storage.echo_sql is True
+    assert storage.pool_size == 11
+    assert url.drivername == "postgresql+asyncpg"
+    assert url.database == "deerflow"
+
+
+def test_mysql_database_url_is_normalized_to_async_driver():
+    storage = StorageConfig(
+        driver="mysql",
+        database_url="mysql://user:pass@db.example:3306/deerflow",
+    )
+
+    url = _create_database_url(storage)
+
+    assert url.drivername == "mysql+aiomysql"
+    assert url.database == "deerflow"
+
+
+def test_mysql_async_database_url_is_preserved():
+    storage = StorageConfig(
+        driver="mysql",
+        database_url="mysql+asyncmy://user:pass@db.example:3306/deerflow",
+    )
+
+    url = _create_database_url(storage)
+
+    assert url.drivername == "mysql+asyncmy"
+    assert url.database == "deerflow"
+
+
+def test_database_postgres_requires_url():
+    database = SimpleNamespace(backend="postgres", postgres_url="")
+
+    with pytest.raises(ValueError, match="database.postgres_url is required"):
+        storage_config_from_database_config(database)
+
+
+def test_unsupported_database_backend_rejected():
+    database = SimpleNamespace(backend="oracle")
+
+    with pytest.raises(ValueError, match="Unsupported database backend"):
+        storage_config_from_database_config(database)
+
+
+def test_storage_models_import_without_config_file(tmp_path):
+    env = os.environ.copy()
+    env["DEER_FLOW_CONFIG_PATH"] = str(tmp_path / "missing-config.yaml")
+
+    result = subprocess.run(
+        [
+            sys.executable,
+            "-c",
+            "from store.persistence.base_model import UniversalText, id_key; from store.repositories.models import RunEvent; print(UniversalText.__name__, RunEvent.__tablename__, id_key)",
+        ],
+        check=False,
+        capture_output=True,
+        env=env,
+        text=True,
+    )
+
+    assert result.returncode == 0, result.stderr
+    assert "UniversalText run_events" in result.stdout

backend/tests/test_storage_persistence_sqlite.py

@@ -0,0 +1,58 @@
+from __future__ import annotations
+
+import asyncio
+import os
+from pathlib import Path
+from types import SimpleNamespace
+from uuid import uuid4
+
+os.environ.setdefault("DEER_FLOW_CONFIG_PATH", str(Path(__file__).resolve().parents[2] / "config.example.yaml"))
+
+from sqlalchemy import inspect
+from store.persistence import create_persistence_from_database_config
+from store.repositories import UserCreate, build_user_repository
+
+
+def test_sqlite_persistence_from_database_config_creates_storage_tables(tmp_path):
+    async def run() -> None:
+        persistence = await create_persistence_from_database_config(
+            SimpleNamespace(
+                backend="sqlite",
+                sqlite_dir=str(tmp_path),
+                echo_sql=False,
+                pool_size=5,
+            )
+        )
+        assert persistence is not None
+        try:
+            await persistence.setup()
+
+            async with persistence.engine.connect() as conn:
+                tables = await conn.run_sync(lambda sync_conn: set(inspect(sync_conn).get_table_names()))
+
+            assert {
+                "users",
+                "runs",
+                "run_events",
+                "threads_meta",
+                "feedback",
+            }.issubset(tables)
+
+            async with persistence.session_factory() as session:
+                repo = build_user_repository(session)
+                user = await repo.create_user(
+                    UserCreate(
+                        id=str(uuid4()),
+                        email="storage-user@example.com",
+                        password_hash="hash",
+                    )
+                )
+                await session.commit()
+
+            async with persistence.session_factory() as session:
+                repo = build_user_repository(session)
+                assert await repo.get_user_by_id(user.id) == user
+        finally:
+            await persistence.aclose()
+
+    asyncio.run(run())

backend/tests/test_storage_repositories.py

@@ -0,0 +1,395 @@
+from __future__ import annotations
+
+import os
+from datetime import UTC, datetime, timedelta
+from pathlib import Path
+from types import SimpleNamespace
+
+import pytest
+
+os.environ.setdefault("DEER_FLOW_CONFIG_PATH", str(Path(__file__).resolve().parents[2] / "config.example.yaml"))
+
+from store.persistence import create_persistence_from_database_config
+from store.repositories import (
+    FeedbackCreate,
+    InvalidMetadataFilterError,
+    RunCreate,
+    RunEventCreate,
+    ThreadMetaCreate,
+    build_feedback_repository,
+    build_run_event_repository,
+    build_run_repository,
+    build_thread_meta_repository,
+)
+
+
+async def _make_persistence(tmp_path):
+    persistence = await create_persistence_from_database_config(
+        SimpleNamespace(
+            backend="sqlite",
+            sqlite_dir=str(tmp_path),
+            echo_sql=False,
+            pool_size=5,
+        )
+    )
+    await persistence.setup()
+    return persistence
+
+
+@pytest.mark.anyio
+async def test_storage_run_repository_filters_and_aggregates(tmp_path):
+    persistence = await _make_persistence(tmp_path)
+    old = datetime.now(UTC) - timedelta(hours=1)
+    newer = datetime.now(UTC)
+    try:
+        async with persistence.session_factory() as session:
+            repo = build_run_repository(session)
+            await repo.create_run(
+                RunCreate(
+                    run_id="run-old",
+                    thread_id="thread-1",
+                    user_id="alice",
+                    status="pending",
+                    model_name="model-a",
+                    metadata={"kind": "draft"},
+                    kwargs={"temperature": 0.2},
+                    created_time=old,
+                )
+            )
+            await repo.create_run(
+                RunCreate(
+                    run_id="run-new",
+                    thread_id="thread-1",
+                    user_id="bob",
+                    status="running",
+                    model_name="model-b",
+                    error="queued",
+                    created_time=newer,
+                )
+            )
+            await repo.create_run(RunCreate(run_id="run-other", thread_id="thread-2", status="running"))
+            await repo.update_run_completion(
+                "run-old",
+                status="success",
+                total_input_tokens=7,
+                total_output_tokens=3,
+                total_tokens=10,
+                llm_call_count=1,
+                lead_agent_tokens=8,
+                subagent_tokens=2,
+                first_human_message="hello",
+                last_ai_message="world",
+            )
+            await repo.update_run_completion(
+                "run-new",
+                status="error",
+                total_tokens=5,
+                middleware_tokens=5,
+                error="failed",
+            )
+            await session.commit()
+
+        async with persistence.session_factory() as session:
+            repo = build_run_repository(session)
+            fetched = await repo.get_run("run-old")
+            assert fetched is not None
+            assert fetched.metadata == {"kind": "draft"}
+            assert fetched.kwargs == {"temperature": 0.2}
+            assert fetched.first_human_message == "hello"
+            assert fetched.last_ai_message == "world"
+
+            all_thread_runs = await repo.list_runs_by_thread("thread-1")
+            assert [run.run_id for run in all_thread_runs] == ["run-new", "run-old"]
+            alice_runs = await repo.list_runs_by_thread("thread-1", user_id="alice")
+            assert [run.run_id for run in alice_runs] == ["run-old"]
+
+            pending = await repo.list_pending(before=datetime.now(UTC).isoformat())
+            assert [run.run_id for run in pending] == []
+
+            agg = await repo.aggregate_tokens_by_thread("thread-1")
+            assert agg["total_tokens"] == 15
+            assert agg["total_input_tokens"] == 7
+            assert agg["total_output_tokens"] == 3
+            assert agg["total_runs"] == 2
+            assert agg["by_model"] == {
+                "model-a": {"tokens": 10, "runs": 1},
+                "model-b": {"tokens": 5, "runs": 1},
+            }
+            assert agg["by_caller"] == {"lead_agent": 8, "subagent": 2, "middleware": 5}
+    finally:
+        await persistence.aclose()
+
+
+@pytest.mark.anyio
+async def test_storage_thread_meta_repository_search_update_delete(tmp_path):
+    persistence = await _make_persistence(tmp_path)
+    try:
+        async with persistence.session_factory() as session:
+            repo = build_thread_meta_repository(session)
+            await repo.create_thread_meta(
+                ThreadMetaCreate(
+                    thread_id="thread-1",
+                    assistant_id="agent-a",
+                    user_id="alice",
+                    display_name="Initial",
+                    status="idle",
+                    metadata={"topic": "finance", "region": "cn"},
+                )
+            )
+            await repo.create_thread_meta(
+                ThreadMetaCreate(
+                    thread_id="thread-2",
+                    assistant_id="agent-b",
+                    user_id="bob",
+                    status="running",
+                    metadata={"topic": "legal"},
+                )
+            )
+            await repo.update_thread_meta(
+                "thread-1",
+                display_name="Updated",
+                status="running",
+                metadata={"topic": "finance", "region": "us"},
+            )
+            await session.commit()
+
+        async with persistence.session_factory() as session:
+            repo = build_thread_meta_repository(session)
+            fetched = await repo.get_thread_meta("thread-1")
+            assert fetched is not None
+            assert fetched.display_name == "Updated"
+            assert fetched.status == "running"
+            assert fetched.metadata == {"topic": "finance", "region": "us"}
+
+            by_metadata = await repo.search_threads(metadata={"topic": "finance"}, user_id="alice")
+            assert [thread.thread_id for thread in by_metadata] == ["thread-1"]
+            by_assistant = await repo.search_threads(assistant_id="agent-b")
+            assert [thread.thread_id for thread in by_assistant] == ["thread-2"]
+
+            await repo.delete_thread("thread-1")
+            await session.commit()
+
+        async with persistence.session_factory() as session:
+            repo = build_thread_meta_repository(session)
+            assert await repo.get_thread_meta("thread-1") is None
+    finally:
+        await persistence.aclose()
+
+
+@pytest.mark.anyio
+async def test_storage_thread_meta_metadata_filters_are_type_safe(tmp_path):
+    persistence = await _make_persistence(tmp_path)
+    try:
+        async with persistence.session_factory() as session:
+            repo = build_thread_meta_repository(session)
+            await repo.create_thread_meta(ThreadMetaCreate(thread_id="bool-true", metadata={"value": True}))
+            await repo.create_thread_meta(ThreadMetaCreate(thread_id="bool-false", metadata={"value": False}))
+            await repo.create_thread_meta(ThreadMetaCreate(thread_id="int-one", metadata={"value": 1}))
+            await repo.create_thread_meta(ThreadMetaCreate(thread_id="null-value", metadata={"value": None}))
+            await repo.create_thread_meta(ThreadMetaCreate(thread_id="missing-value", metadata={"other": "x"}))
+            await session.commit()
+
+        async with persistence.session_factory() as session:
+            repo = build_thread_meta_repository(session)
+            assert [row.thread_id for row in await repo.search_threads(metadata={"value": True})] == ["bool-true"]
+            assert [row.thread_id for row in await repo.search_threads(metadata={"value": False})] == ["bool-false"]
+            assert [row.thread_id for row in await repo.search_threads(metadata={"value": 1})] == ["int-one"]
+            assert [row.thread_id for row in await repo.search_threads(metadata={"value": None})] == ["null-value"]
+    finally:
+        await persistence.aclose()
+
+
+@pytest.mark.anyio
+async def test_storage_thread_meta_metadata_filters_paginate_after_sql_match(tmp_path):
+    persistence = await _make_persistence(tmp_path)
+    try:
+        async with persistence.session_factory() as session:
+            repo = build_thread_meta_repository(session)
+            for index in range(30):
+                metadata = {"target": "yes"} if index % 3 == 0 else {"target": "no"}
+                await repo.create_thread_meta(ThreadMetaCreate(thread_id=f"thread-{index:02d}", metadata=metadata))
+            await session.commit()
+
+        async with persistence.session_factory() as session:
+            repo = build_thread_meta_repository(session)
+            first_page = await repo.search_threads(metadata={"target": "yes"}, limit=3, offset=0)
+            second_page = await repo.search_threads(metadata={"target": "yes"}, limit=3, offset=3)
+            last_page = await repo.search_threads(metadata={"target": "yes"}, limit=3, offset=9)
+
+        assert len(first_page) == 3
+        assert len(second_page) == 3
+        assert len(last_page) == 1
+        assert {row.thread_id for row in first_page}.isdisjoint({row.thread_id for row in second_page})
+    finally:
+        await persistence.aclose()
+
+
+@pytest.mark.anyio
+async def test_storage_thread_meta_metadata_filter_rejects_invalid_entries(tmp_path):
+    persistence = await _make_persistence(tmp_path)
+    try:
+        async with persistence.session_factory() as session:
+            repo = build_thread_meta_repository(session)
+            await repo.create_thread_meta(ThreadMetaCreate(thread_id="thread-1", metadata={"env": "prod"}))
+            await repo.create_thread_meta(ThreadMetaCreate(thread_id="thread-2", metadata={"env": "staging"}))
+            await session.commit()
+
+        async with persistence.session_factory() as session:
+            repo = build_thread_meta_repository(session)
+            partial = await repo.search_threads(metadata={"env": "prod", "bad;key": "ignored"})
+            assert [row.thread_id for row in partial] == ["thread-1"]
+
+            with pytest.raises(InvalidMetadataFilterError, match="rejected"):
+                await repo.search_threads(metadata={"bad;key": "x"})
+            with pytest.raises(InvalidMetadataFilterError, match="rejected"):
+                await repo.search_threads(metadata={"env": ["prod", "staging"]})
+    finally:
+        await persistence.aclose()
+
+
+@pytest.mark.anyio
+async def test_storage_feedback_repository_lists_and_deletes(tmp_path):
+    persistence = await _make_persistence(tmp_path)
+    try:
+        async with persistence.session_factory() as session:
+            repo = build_feedback_repository(session)
+            first = await repo.create_feedback(
+                FeedbackCreate(
+                    feedback_id="fb-1",
+                    run_id="run-1",
+                    thread_id="thread-1",
+                    rating=1,
+                    user_id="alice",
+                    message_id="msg-1",
+                    comment="good",
+                )
+            )
+            second = await repo.create_feedback(
+                FeedbackCreate(
+                    feedback_id="fb-2",
+                    run_id="run-1",
+                    thread_id="thread-1",
+                    rating=-1,
+                    user_id="bob",
+                )
+            )
+            await session.commit()
+
+        async with persistence.session_factory() as session:
+            repo = build_feedback_repository(session)
+            assert await repo.get_feedback(first.feedback_id) == first
+            assert [item.feedback_id for item in await repo.list_feedback_by_run("run-1")] == [
+                second.feedback_id,
+                first.feedback_id,
+            ]
+            assert {item.feedback_id for item in await repo.list_feedback_by_thread("thread-1")} == {
+                "fb-1",
+                "fb-2",
+            }
+            assert await repo.delete_feedback("fb-1") is True
+            assert await repo.delete_feedback("missing") is False
+            with pytest.raises(ValueError, match="rating must be"):
+                await repo.create_feedback(
+                    FeedbackCreate(
+                        feedback_id="fb-bad",
+                        run_id="run-1",
+                        thread_id="thread-1",
+                        rating=0,
+                    )
+                )
+            await session.commit()
+
+        async with persistence.session_factory() as session:
+            repo = build_feedback_repository(session)
+            assert await repo.get_feedback("fb-1") is None
+    finally:
+        await persistence.aclose()
+
+
+@pytest.mark.anyio
+async def test_storage_run_event_repository_sequences_paginates_and_deletes(tmp_path):
+    persistence = await _make_persistence(tmp_path)
+    try:
+        async with persistence.session_factory() as session:
+            repo = build_run_event_repository(session)
+            rows = await repo.append_batch(
+                [
+                    RunEventCreate(
+                        thread_id="thread-1",
+                        run_id="run-1",
+                        user_id="alice",
+                        event_type="message",
+                        category="message",
+                        content={"role": "user", "content": "hello"},
+                        metadata={"source": "input"},
+                    ),
+                    RunEventCreate(
+                        thread_id="thread-1",
+                        run_id="run-1",
+                        event_type="tool",
+                        category="debug",
+                        content="tool-call",
+                    ),
+                    RunEventCreate(
+                        thread_id="thread-1",
+                        run_id="run-2",
+                        event_type="message",
+                        category="message",
+                        content="second",
+                    ),
+                    RunEventCreate(
+                        thread_id="thread-2",
+                        run_id="run-3",
+                        event_type="message",
+                        category="message",
+                        content="other-thread",
+                    ),
+                ]
+            )
+            await session.commit()
+
+        assert [row.thread_id for row in rows] == ["thread-1", "thread-1", "thread-1", "thread-2"]
+        assert [row.seq for row in rows] == sorted(row.seq for row in rows)
+        assert rows[1].seq == rows[0].seq + 1
+        assert rows[2].seq == rows[1].seq + 1
+        assert rows[0].content == {"role": "user", "content": "hello"}
+        assert rows[0].metadata == {"source": "input", "content_is_json": True}
+
+        async with persistence.session_factory() as session:
+            repo = build_run_event_repository(session)
+            messages = await repo.list_messages("thread-1", limit=2)
+            assert [event.seq for event in messages] == [rows[0].seq, rows[2].seq]
+            assert await repo.count_messages("thread-1") == 2
+
+            after = await repo.list_messages_by_run("thread-1", "run-1", after_seq=0, limit=5)
+            assert [event.seq for event in after] == [rows[0].seq]
+            before = await repo.list_messages("thread-1", before_seq=rows[2].seq, limit=5)
+            assert [event.seq for event in before] == [rows[0].seq]
+
+            events = await repo.list_events("thread-1", "run-1", event_types=["tool"])
+            assert [event.content for event in events] == ["tool-call"]
+
+            assert await repo.delete_by_run("thread-1", "run-1") == 2
+            assert await repo.delete_by_thread("thread-2") == 1
+            await session.commit()
+
+        async with persistence.session_factory() as session:
+            repo = build_run_event_repository(session)
+            remaining = await repo.list_events("thread-1", "run-2")
+            assert [event.seq for event in remaining] == [rows[2].seq]
+            assert await repo.count_messages("thread-2") == 0
+
+            later = await repo.append_batch(
+                [
+                    RunEventCreate(
+                        thread_id="thread-1",
+                        run_id="run-4",
+                        event_type="message",
+                        category="message",
+                        content="after-delete",
+                    )
+                ]
+            )
+            assert later[0].seq > rows[2].seq
+    finally:
+        await persistence.aclose()

backend/tests/test_storage_user_repository.py

@@ -0,0 +1,177 @@
+from __future__ import annotations
+
+import asyncio
+import os
+from collections.abc import AsyncGenerator
+from contextlib import asynccontextmanager
+from pathlib import Path
+from uuid import uuid4
+
+import pytest
+
+os.environ.setdefault("DEER_FLOW_CONFIG_PATH", str(Path(__file__).resolve().parents[2] / "config.example.yaml"))
+
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
+from store.repositories import UserCreate, UserNotFoundError, build_user_repository
+from store.repositories.models import User as UserModel
+
+
+@asynccontextmanager
+async def _session_factory(tmp_path) -> AsyncGenerator[async_sessionmaker[AsyncSession]]:
+    db_path = tmp_path / "storage-users.db"
+    engine = create_async_engine(f"sqlite+aiosqlite:///{db_path}")
+    async with engine.begin() as conn:
+        await conn.run_sync(UserModel.metadata.create_all)
+
+    try:
+        yield async_sessionmaker(engine, expire_on_commit=False)
+    finally:
+        await engine.dispose()
+
+
+async def _create_user(
+    session_factory: async_sessionmaker[AsyncSession],
+    *,
+    email: str = "user@example.com",
+    system_role: str = "user",
+    oauth_provider: str | None = None,
+    oauth_id: str | None = None,
+):
+    async with session_factory() as session:
+        repo = build_user_repository(session)
+        user = await repo.create_user(
+            UserCreate(
+                id=str(uuid4()),
+                email=email,
+                password_hash="hash",
+                system_role=system_role,  # type: ignore[arg-type]
+                oauth_provider=oauth_provider,
+                oauth_id=oauth_id,
+            )
+        )
+        await session.commit()
+        return user
+
+
+def test_create_and_get_user_by_id_and_email(tmp_path):
+    async def run() -> None:
+        async with _session_factory(tmp_path) as session_factory:
+            created = await _create_user(session_factory)
+
+            async with session_factory() as session:
+                repo = build_user_repository(session)
+
+                by_id = await repo.get_user_by_id(created.id)
+                by_email = await repo.get_user_by_email(created.email)
+
+            assert by_id == created
+            assert by_email == created
+            assert created.system_role == "user"
+            assert created.needs_setup is False
+            assert created.token_version == 0
+
+    asyncio.run(run())
+
+
+def test_duplicate_email_raises_value_error(tmp_path):
+    async def run() -> None:
+        async with _session_factory(tmp_path) as session_factory:
+            await _create_user(session_factory, email="dupe@example.com")
+
+            async with session_factory() as session:
+                repo = build_user_repository(session)
+                with pytest.raises(ValueError, match="Email already registered"):
+                    await repo.create_user(
+                        UserCreate(
+                            id=str(uuid4()),
+                            email="dupe@example.com",
+                            password_hash="hash",
+                        )
+                    )
+
+    asyncio.run(run())
+
+
+def test_oauth_lookup_and_plain_users_without_oauth(tmp_path):
+    async def run() -> None:
+        async with _session_factory(tmp_path) as session_factory:
+            await _create_user(session_factory, email="local-1@example.com")
+            await _create_user(session_factory, email="local-2@example.com")
+            oauth_user = await _create_user(
+                session_factory,
+                email="oauth@example.com",
+                oauth_provider="github",
+                oauth_id="gh-123",
+            )
+
+            async with session_factory() as session:
+                repo = build_user_repository(session)
+
+                assert await repo.count_users() == 3
+                assert await repo.get_user_by_oauth("github", "gh-123") == oauth_user
+                assert await repo.get_user_by_oauth("github", "missing") is None
+
+    asyncio.run(run())
+
+
+def test_count_admins_and_get_first_admin(tmp_path):
+    async def run() -> None:
+        async with _session_factory(tmp_path) as session_factory:
+            await _create_user(session_factory, email="user@example.com")
+            admin = await _create_user(
+                session_factory,
+                email="admin@example.com",
+                system_role="admin",
+            )
+
+            async with session_factory() as session:
+                repo = build_user_repository(session)
+
+                assert await repo.count_users() == 2
+                assert await repo.count_admin_users() == 1
+                assert await repo.get_first_admin() == admin
+
+    asyncio.run(run())
+
+
+def test_update_user_round_trips_token_version_and_setup_state(tmp_path):
+    async def run() -> None:
+        async with _session_factory(tmp_path) as session_factory:
+            created = await _create_user(session_factory)
+            updated = created.model_copy(
+                update={
+                    "email": "renamed@example.com",
+                    "token_version": 4,
+                    "needs_setup": True,
+                }
+            )
+
+            async with session_factory() as session:
+                repo = build_user_repository(session)
+                saved = await repo.update_user(updated)
+                await session.commit()
+
+            async with session_factory() as session:
+                repo = build_user_repository(session)
+                fetched = await repo.get_user_by_id(created.id)
+
+            assert saved.email == "renamed@example.com"
+            assert fetched == updated
+
+    asyncio.run(run())
+
+
+def test_update_missing_user_raises(tmp_path):
+    async def run() -> None:
+        async with _session_factory(tmp_path) as session_factory:
+            missing = UserCreate(id=str(uuid4()), email="missing@example.com")
+
+            async with session_factory() as session:
+                repo = build_user_repository(session)
+                created_shape = await repo.create_user(missing)
+                await session.rollback()
+
+                with pytest.raises(UserNotFoundError):
+                    await repo.update_user(created_shape)
+
+    asyncio.run(run())

backend/tests/test_summarization_middleware.py

@@ -30,12 +30,18 @@ def _dynamic_context_reminder(msg_id: str = "reminder-1") -> HumanMessage:
     )
 
 
-def _runtime(thread_id: str | None = "thread-1", agent_name: str | None = None) -> SimpleNamespace:
+def _runtime(
+    thread_id: str | None = "thread-1",
+    agent_name: str | None = None,
+    user_id: str | None = None,
+) -> SimpleNamespace:
     context = {}
     if thread_id is not None:
         context["thread_id"] = thread_id
     if agent_name is not None:
         context["agent_name"] = agent_name
+    if user_id is not None:
+        context["user_id"] = user_id
     return SimpleNamespace(context=context)
 
 
@@ -634,3 +640,22 @@ def test_memory_flush_hook_preserves_agent_scoped_memory(monkeypatch: pytest.Mon
 
     queue.add_nowait.assert_called_once()
     assert queue.add_nowait.call_args.kwargs["agent_name"] == "research-agent"
+
+
+def test_memory_flush_hook_passes_runtime_user_id(monkeypatch: pytest.MonkeyPatch) -> None:
+    queue = MagicMock()
+    monkeypatch.setattr("deerflow.agents.memory.summarization_hook.get_memory_config", lambda: MemoryConfig(enabled=True))
+    monkeypatch.setattr("deerflow.agents.memory.summarization_hook.get_memory_queue", lambda: queue)
+
+    memory_flush_hook(
+        SummarizationEvent(
+            messages_to_summarize=tuple(_messages()[:2]),
+            preserved_messages=(),
+            thread_id="main",
+            agent_name="researcher",
+            runtime=_runtime(thread_id="main", agent_name="researcher", user_id="alice"),
+        )
+    )
+
+    queue.add_nowait.assert_called_once()
+    assert queue.add_nowait.call_args.kwargs["user_id"] == "alice"

backend/tests/test_task_tool_core_logic.py

@@ -1214,11 +1214,12 @@ def test_terminal_event_usage_none_when_no_records(monkeypatch):
     assert completed[0]["usage"] is None
 
 
-def test_subagent_usage_cache_is_skipped_when_config_file_is_missing(monkeypatch):
+@pytest.mark.parametrize("error", [FileNotFoundError("missing config"), ValueError("invalid config")])
+def test_subagent_usage_cache_is_skipped_when_default_config_cannot_load(monkeypatch, error):
     monkeypatch.setattr(
         task_tool_module,
         "get_app_config",
-        MagicMock(side_effect=FileNotFoundError("missing config")),
+        MagicMock(side_effect=error),
     )
 
     assert task_tool_module._token_usage_cache_enabled(None) is False

backend/uv.lock

@@ -14,6 +14,7 @@ resolution-markers = [
 members = [
     "deer-flow",
     "deerflow-harness",
+    "deerflow-storage",
 ]
 
 [[package]]
@@ -136,6 +137,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/62/29/2f8418269e46454a26171bfdd6a055d74febf32234e474930f2f60a17145/aiohttp-3.13.5-cp314-cp314t-win_amd64.whl", hash = "sha256:18a2f6c1182c51baa1d28d68fea51513cb2a76612f038853c0ad3c145423d3d9", size = 505441, upload-time = "2026-03-31T22:00:12.791Z" },
 ]
 
+[[package]]
+name = "aiomysql"
+version = "0.3.2"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "pymysql" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/29/e0/302aeffe8d90853556f47f3106b89c16cc2ec2a4d269bdfd82e3f4ae12cc/aiomysql-0.3.2.tar.gz", hash = "sha256:72d15ef5cfc34c03468eb41e1b90adb9fd9347b0b589114bd23ead569a02ac1a", size = 108311, upload-time = "2025-10-22T00:15:21.278Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/4c/af/aae0153c3e28712adaf462328f6c7a3c196a1c1c27b491de4377dd3e6b52/aiomysql-0.3.2-py3-none-any.whl", hash = "sha256:c82c5ba04137d7afd5c693a258bea8ead2aad77101668044143a991e04632eb2", size = 71834, upload-time = "2025-10-22T00:15:15.905Z" },
+]
+
 [[package]]
 name = "aiosignal"
 version = "1.4.0"
@@ -746,6 +759,7 @@ source = { virtual = "." }
 dependencies = [
     { name = "bcrypt" },
     { name = "deerflow-harness" },
+    { name = "deerflow-storage" },
     { name = "dingtalk-stream" },
     { name = "email-validator" },
     { name = "fastapi" },
@@ -763,8 +777,12 @@ dependencies = [
 ]
 
 [package.optional-dependencies]
+mysql = [
+    { name = "deerflow-storage", extra = ["mysql"] },
+]
 postgres = [
     { name = "deerflow-harness", extra = ["postgres"] },
+    { name = "deerflow-storage", extra = ["postgres"] },
 ]
 
 [package.dev-dependencies]
@@ -780,6 +798,9 @@ requires-dist = [
     { name = "bcrypt", specifier = ">=4.0.0" },
     { name = "deerflow-harness", editable = "packages/harness" },
     { name = "deerflow-harness", extras = ["postgres"], marker = "extra == 'postgres'", editable = "packages/harness" },
+    { name = "deerflow-storage", editable = "packages/storage" },
+    { name = "deerflow-storage", extras = ["mysql"], marker = "extra == 'mysql'", editable = "packages/storage" },
+    { name = "deerflow-storage", extras = ["postgres"], marker = "extra == 'postgres'", editable = "packages/storage" },
     { name = "dingtalk-stream", specifier = ">=0.24.3" },
     { name = "email-validator", specifier = ">=2.0.0" },
     { name = "fastapi", specifier = ">=0.115.0" },
@@ -795,7 +816,7 @@ requires-dist = [
     { name = "uvicorn", extras = ["standard"], specifier = ">=0.34.0" },
     { name = "wecom-aibot-python-sdk", specifier = ">=0.1.6" },
 ]
-provides-extras = ["postgres"]
+provides-extras = ["postgres", "mysql"]
 
 [package.metadata.requires-dev]
 dev = [
@@ -901,6 +922,54 @@ requires-dist = [
 ]
 provides-extras = ["ollama", "postgres", "pymupdf"]
 
+[[package]]
+name = "deerflow-storage"
+version = "0.1.0"
+source = { editable = "packages/storage" }
+dependencies = [
+    { name = "alembic" },
+    { name = "dotenv" },
+    { name = "langgraph" },
+    { name = "pydantic" },
+    { name = "pyyaml" },
+    { name = "sqlalchemy", extra = ["asyncio"] },
+]
+
+[package.optional-dependencies]
+mysql = [
+    { name = "aiomysql" },
+    { name = "langgraph-checkpoint-mysql" },
+]
+postgres = [
+    { name = "asyncpg" },
+    { name = "langgraph-checkpoint-postgres" },
+    { name = "psycopg", extra = ["binary"] },
+    { name = "psycopg-pool" },
+]
+sqlite = [
+    { name = "aiosqlite" },
+    { name = "langgraph-checkpoint-sqlite" },
+]
+
+[package.metadata]
+requires-dist = [
+    { name = "aiomysql", marker = "extra == 'mysql'", specifier = ">=0.2" },
+    { name = "aiosqlite", marker = "extra == 'sqlite'", specifier = ">=0.22.1" },
+    { name = "alembic", specifier = ">=1.13" },
+    { name = "asyncpg", marker = "extra == 'postgres'", specifier = ">=0.29" },
+    { name = "dotenv", specifier = ">=0.9.9" },
+    { name = "langgraph", specifier = ">=1.1.9" },
+    { name = "langgraph-checkpoint-mysql", marker = "extra == 'mysql'", specifier = ">=3.0.0" },
+    { name = "langgraph-checkpoint-postgres", marker = "extra == 'postgres'", specifier = ">=3.0.5" },
+    { name = "langgraph-checkpoint-sqlite", marker = "extra == 'sqlite'", specifier = ">=3.0.3" },
+    { name = "psycopg", extras = ["binary"], marker = "extra == 'postgres'", specifier = ">=3.3.3" },
+    { name = "psycopg-pool", marker = "extra == 'postgres'", specifier = ">=3.3.0" },
+    { name = "pydantic", specifier = ">=2.12.5" },
+    { name = "pyyaml", specifier = ">=6.0.3" },
+    { name = "sqlalchemy", extras = ["asyncio"], specifier = ">=2.0,<3.0" },
+]
+provides-extras = ["postgres", "mysql", "sqlite"]
+
 [[package]]
 name = "defusedxml"
 version = "0.7.1"
@@ -1914,6 +1983,20 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/b9/5a/6dba29dd89b0a46ae21c707da0f9d17e94f27d3e481ed15bc99d6bd20aa6/langgraph_checkpoint-4.0.2-py3-none-any.whl", hash = "sha256:59b0f29216128a629c58dd07c98aa004f82f51805d5573126ffb419b753ff253", size = 51000, upload-time = "2026-04-15T21:02:59.096Z" },
 ]
 
+[[package]]
+name = "langgraph-checkpoint-mysql"
+version = "3.0.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "langgraph-checkpoint" },
+    { name = "orjson" },
+    { name = "typing-extensions" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/e0/4e/0a6c78e5d3f2ca1525903c2363e721873594b6b77dd83537a6369193c474/langgraph_checkpoint_mysql-3.0.0.tar.gz", hash = "sha256:006aaa089f4c2fbd7b2c113b800ccd3dbb95f92203e656451677256b4b4f880f", size = 213142, upload-time = "2026-01-23T11:11:15.74Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/08/68/343103a7fae05523f9cecabbec2babdb737e66b4bf6ea48ae00c685ed11c/langgraph_checkpoint_mysql-3.0.0-py3-none-any.whl", hash = "sha256:7560ccd16e7596a047e15a307cec12dbd88fdcaab45a75759e5c6adef22a27d1", size = 38009, upload-time = "2026-01-23T11:11:14.697Z" },
+]
+
 [[package]]
 name = "langgraph-checkpoint-postgres"
 version = "3.0.5"
@@ -3442,6 +3525,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/e6/38/84bf29f4dd72e6c450546df6ca8f53021f764fd945ba67dcc235d39bc20e/pymupdf4llm-1.27.2.3-py3-none-any.whl", hash = "sha256:bd724b79fa3f06a5b28d7a65f7acfa8de56e04bdb603ac2d6dff315e0d151aaa", size = 77348, upload-time = "2026-04-24T14:11:04.305Z" },
 ]
 
+[[package]]
+name = "pymysql"
+version = "1.1.3"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/7f/ec/8d45c920e90445f0b75c590b32851853ed319763b0d8dff8d283052da8cf/pymysql-1.1.3.tar.gz", hash = "sha256:e70ebf2047a4edf6138cf79c68ad418ef620af65900aa585c5e8bfc95044d43a", size = 48207, upload-time = "2026-05-01T09:09:54.532Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/8e/dc/9085f3d6f497e9b25fb40d6e8ecef3ddbb5cf977a949b933624a299f5c16/pymysql-1.1.3-py3-none-any.whl", hash = "sha256:8164ba62c552f6105f3b11753352d0f16b90d1703ba67d81923d5a8a5d1c5289", size = 45356, upload-time = "2026-05-01T09:09:53.316Z" },
+]
+
 [[package]]
 name = "pypdfium2"
 version = "5.7.1"