test(custom_agent + task_tool): set app.state.config + drop obsolete skills monkeypatches

test(tool_deduplication): pass app_config explicitly instead of patching removed singleton
refactor(config): eliminate global mutable state — explicit parameter passing on top of main
2026-04-27 18:09:43 +08:00 · 2026-04-27 16:51:28 +08:00 · 2026-04-26 21:45:02 +08:00 · 2026-04-26 10:09:55 +08:00 · 2026-04-26 09:40:17 +08:00 · 2026-04-25 19:40:52 +08:00
468 changed files with 40205 additions and 5215 deletions
@@ -24,6 +24,7 @@ INFOQUEST_API_KEY=your-infoquest-api-key
 # SLACK_BOT_TOKEN=your-slack-bot-token
 # SLACK_APP_TOKEN=your-slack-app-token
 # TELEGRAM_BOT_TOKEN=your-telegram-bot-token
+# DISCORD_BOT_TOKEN=your-discord-bot-token

 # Enable LangSmith to monitor and debug your LLM calls, agent runs, and tool executions.
 # LANGSMITH_TRACING=true
@@ -33,5 +34,9 @@ INFOQUEST_API_KEY=your-infoquest-api-key

 # GitHub API Token
 # GITHUB_TOKEN=your-github-token
+
+# Database (only needed when config.yaml has database.backend: postgres)
+# DATABASE_URL=postgresql://deerflow:password@localhost:5432/deerflow
+#
 # WECOM_BOT_ID=your-wecom-bot-id
 # WECOM_BOT_SECRET=your-wecom-bot-secret
@@ -0,0 +1,63 @@
+name: E2E Tests
+
+on:
+  push:
+    branches: [ 'main' ]
+    paths:
+      - 'frontend/**'
+      - '.github/workflows/e2e-tests.yml'
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+    paths:
+      - 'frontend/**'
+      - '.github/workflows/e2e-tests.yml'
+
+concurrency:
+  group: e2e-tests-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  e2e-tests:
+    if: ${{ github.event_name != 'pull_request' || github.event.pull_request.draft == false }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '22'
+
+      - name: Enable Corepack
+        run: corepack enable
+
+      - name: Use pinned pnpm version
+        run: corepack prepare pnpm@10.26.2 --activate
+
+      - name: Install frontend dependencies
+        working-directory: frontend
+        run: pnpm install --frozen-lockfile
+
+      - name: Install Playwright Chromium
+        working-directory: frontend
+        run: npx playwright install chromium --with-deps
+
+      - name: Run E2E tests
+        working-directory: frontend
+        run: pnpm exec playwright test
+        env:
+          SKIP_ENV_VALIDATION: '1'
+
+      - name: Upload Playwright report
+        uses: actions/upload-artifact@v4
+        if: ${{ !cancelled() }}
+        with:
+          name: playwright-report
+          path: frontend/playwright-report/
+          retention-days: 7
@@ -0,0 +1,43 @@
+name: Frontend Unit Tests
+
+on:
+  push:
+    branches: [ 'main' ]
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+
+concurrency:
+  group: frontend-unit-tests-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  frontend-unit-tests:
+    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '22'
+
+      - name: Enable Corepack
+        run: corepack enable
+
+      - name: Use pinned pnpm version
+        run: corepack prepare pnpm@10.26.2 --activate
+
+      - name: Install frontend dependencies
+        working-directory: frontend
+        run: pnpm install --frozen-lockfile
+
+      - name: Run unit tests of frontend
+        working-directory: frontend
+        run: make test
@@ -40,6 +40,7 @@ coverage/
 skills/custom/*
 logs/
 log/
+debug.log

 # Local git hooks (keep only on this machine, do not push)
 .githooks/
@@ -55,5 +56,7 @@ web/
 backend/Dockerfile.langgraph
 config.yaml.bak
 .playwright-mcp
+/frontend/test-results/
+/frontend/playwright-report/
 .gstack/
 .worktrees
@@ -0,0 +1,33 @@
+repos:
+  # Backend: ruff lint + format via uv (uses the same ruff version as backend deps)
+  - repo: local
+    hooks:
+      - id: ruff
+        name: ruff lint
+        entry: bash -c 'cd backend && uv run ruff check --fix "${@/#backend\//}"' --
+        language: system
+        types_or: [python]
+        files: ^backend/
+      - id: ruff-format
+        name: ruff format
+        entry: bash -c 'cd backend && uv run ruff format "${@/#backend\//}"' --
+        language: system
+        types_or: [python]
+        files: ^backend/
+
+  # Frontend: eslint + prettier (must run from frontend/ for node_modules resolution)
+  - repo: local
+    hooks:
+      - id: frontend-eslint
+        name: eslint (frontend)
+        entry: bash -c 'cd frontend && npx eslint --fix "${@/#frontend\//}"' --
+        language: system
+        types_or: [javascript, tsx, ts]
+        files: ^frontend/
+
+      - id: frontend-prettier
+        name: prettier (frontend)
+        entry: bash -c 'cd frontend && npx prettier --write "${@/#frontend\//}"' --
+        language: system
+        files: ^frontend/
+        types_or: [javascript, tsx, ts, json, css]
@@ -166,7 +166,7 @@ Required tools:

 1. **Configure the application** (same as Docker setup above)

-2. **Install dependencies**:
+2. **Install dependencies** (this also sets up pre-commit hooks):
   ```bash
   make install
   ```
@@ -298,19 +298,24 @@ Nginx (port 2026) ← Unified entry point
 ```bash
 # Backend tests
 cd backend
-uv run pytest
+make test

-# Frontend checks
+# Frontend unit tests
 cd frontend
-pnpm check
+make test
+
+# Frontend E2E tests (requires Chromium; builds and auto-starts the Next.js production server)
+cd frontend
+make test-e2e
 ```

 ### PR Regression Checks

-Every pull request runs the backend regression workflow at [.github/workflows/backend-unit-tests.yml](.github/workflows/backend-unit-tests.yml), including:
+Every pull request triggers the following CI workflows:

- `tests/test_provisioner_kubeconfig.py`
- `tests/test_docker_sandbox_mode_detection.py`
+- **Backend unit tests** — [.github/workflows/backend-unit-tests.yml](.github/workflows/backend-unit-tests.yml)
+- **Frontend unit tests** — [.github/workflows/frontend-unit-tests.yml](.github/workflows/frontend-unit-tests.yml)
+- **Frontend E2E tests** — [.github/workflows/e2e-tests.yml](.github/workflows/e2e-tests.yml) (triggered only when `frontend/` files change)

 ## Code Style

@@ -23,7 +23,7 @@ help:
 	@echo "  make config          - Generate local config files (aborts if config already exists)"
 	@echo "  make config-upgrade  - Merge new fields from config.example.yaml into config.yaml"
 	@echo "  make check           - Check if all required tools are installed"
-	@echo "  make install         - Install all dependencies (frontend + backend)"
+	@echo "  make install         - Install all dependencies (frontend + backend + pre-commit hooks)"
 	@echo "  make setup-sandbox   - Pre-pull sandbox container image (recommended)"
 	@echo "  make dev             - Start all services in development mode (with hot-reloading)"
 	@echo "  make dev-pro         - Start in dev + Gateway mode (experimental, no LangGraph server)"
@@ -73,6 +73,8 @@ install:
 	@cd backend && uv sync
 	@echo "Installing frontend dependencies..."
 	@cd frontend && pnpm install
+	@echo "Installing pre-commit hooks..."
+	@$(BACKEND_UV_RUN) --with pre-commit pre-commit install
 	@echo "✓ All dependencies installed"
 	@echo ""
 	@echo "=========================================="
@@ -99,7 +101,7 @@ setup-sandbox:
 	echo ""; \
 	if command -v container >/dev/null 2>&1 && [ "$$(uname)" = "Darwin" ]; then \
 		echo "Detected Apple Container on macOS, pulling image..."; \
-		container pull "$$IMAGE" || echo "⚠ Apple Container pull failed, will try Docker"; \
+		container image pull "$$IMAGE" || echo "⚠ Apple Container pull failed, will try Docker"; \
 	fi; \
 	if command -v docker >/dev/null 2>&1; then \
 		echo "Pulling image using Docker..."; \
@@ -264,7 +264,7 @@ On Windows, run the local development flow from Git Bash. Native `cmd.exe` and P

 2. **Install dependencies**:
   ```bash
-   make install  # Install backend + frontend dependencies
+   make install  # Install backend + frontend dependencies + pre-commit hooks
   ```

 3. **(Optional) Pre-pull sandbox image**:
@@ -658,6 +658,8 @@ This is the difference between a chatbot with tool access and an agent with an a

 **Summarization**: Within a session, DeerFlow manages context aggressively — summarizing completed sub-tasks, offloading intermediate results to the filesystem, compressing what's no longer immediately relevant. This lets it stay sharp across long, multi-step tasks without blowing the context window.

+**Strict Tool-Call Recovery**: When a provider or middleware interrupts a tool-call loop, DeerFlow now strips provider-level raw tool-call metadata on forced-stop assistant messages and injects placeholder tool results for dangling calls before the next model invocation. This keeps OpenAI-compatible reasoning models that strictly validate `tool_call_id` sequences from failing with malformed history errors.
+
 ### Long-Term Memory

 Most agents forget everything the moment a conversation ends. DeerFlow remembers.
@@ -130,7 +130,7 @@ from app.gateway.app import app
 from app.channels.service import start_channel_service

 # App → Harness (allowed)
-from deerflow.config import get_app_config
+from deerflow.config.app_config import AppConfig

 # Harness → App (FORBIDDEN — enforced by test_harness_boundary.py)
 # from app.gateway.routers.uploads import ...  # ← will fail CI
@@ -156,20 +156,26 @@ from deerflow.config import get_app_config

 ### Middleware Chain

-Middlewares execute in strict order in `packages/harness/deerflow/agents/lead_agent/agent.py`:
+Lead-agent middlewares are assembled in strict append order across `packages/harness/deerflow/agents/middlewares/tool_error_handling_middleware.py` (`build_lead_runtime_middlewares`) and `packages/harness/deerflow/agents/lead_agent/agent.py` (`_build_middlewares`):

-1. **ThreadDataMiddleware** - Creates per-thread directories (`backend/.deer-flow/threads/{thread_id}/user-data/{workspace,uploads,outputs}`); Web UI thread deletion now follows LangGraph thread removal with Gateway cleanup of the local `.deer-flow/threads/{thread_id}` directory
+1. **ThreadDataMiddleware** - Creates per-thread directories under the user's isolation scope (`backend/.deer-flow/users/{user_id}/threads/{thread_id}/user-data/{workspace,uploads,outputs}`); resolves `user_id` via `get_effective_user_id()` (falls back to `"default"` in no-auth mode); Web UI thread deletion now follows LangGraph thread removal with Gateway cleanup of the local thread directory
 2. **UploadsMiddleware** - Tracks and injects newly uploaded files into conversation
 3. **SandboxMiddleware** - Acquires sandbox, stores `sandbox_id` in state
-4. **DanglingToolCallMiddleware** - Injects placeholder ToolMessages for AIMessage tool_calls that lack responses (e.g., due to user interruption)
-5. **GuardrailMiddleware** - Pre-tool-call authorization via pluggable `GuardrailProvider` protocol (optional, if `guardrails.enabled` in config). Evaluates each tool call and returns error ToolMessage on deny. Three provider options: built-in `AllowlistProvider` (zero deps), OAP policy providers (e.g. `aport-agent-guardrails`), or custom providers. See [docs/GUARDRAILS.md](docs/GUARDRAILS.md) for setup, usage, and how to implement a provider.
-6. **SummarizationMiddleware** - Context reduction when approaching token limits (optional, if enabled)
-7. **TodoListMiddleware** - Task tracking with `write_todos` tool (optional, if plan_mode)
-8. **TitleMiddleware** - Auto-generates thread title after first complete exchange and normalizes structured message content before prompting the title model
-9. **MemoryMiddleware** - Queues conversations for async memory update (filters to user + final AI responses)
-10. **ViewImageMiddleware** - Injects base64 image data before LLM call (conditional on vision support)
-11. **SubagentLimitMiddleware** - Truncates excess `task` tool calls from model response to enforce `MAX_CONCURRENT_SUBAGENTS` limit (optional, if subagent_enabled)
-12. **ClarificationMiddleware** - Intercepts `ask_clarification` tool calls, interrupts via `Command(goto=END)` (must be last)
+4. **DanglingToolCallMiddleware** - Injects placeholder ToolMessages for AIMessage tool_calls that lack responses (e.g., due to user interruption), including raw provider tool-call payloads preserved only in `additional_kwargs["tool_calls"]`
+5. **LLMErrorHandlingMiddleware** - Normalizes provider/model invocation failures into recoverable assistant-facing errors before later middleware/tool stages run
+6. **GuardrailMiddleware** - Pre-tool-call authorization via pluggable `GuardrailProvider` protocol (optional, if `guardrails.enabled` in config). Evaluates each tool call and returns error ToolMessage on deny. Three provider options: built-in `AllowlistProvider` (zero deps), OAP policy providers (e.g. `aport-agent-guardrails`), or custom providers. See [docs/GUARDRAILS.md](docs/GUARDRAILS.md) for setup, usage, and how to implement a provider.
+7. **SandboxAuditMiddleware** - Audits sandboxed shell/file operations for security logging before tool execution continues
+8. **ToolErrorHandlingMiddleware** - Converts tool exceptions into error `ToolMessage`s so the run can continue instead of aborting
+9. **SummarizationMiddleware** - Context reduction when approaching token limits (optional, if enabled)
+10. **TodoListMiddleware** - Task tracking with `write_todos` tool (optional, if plan_mode)
+11. **TokenUsageMiddleware** - Records token usage metrics when token tracking is enabled (optional)
+12. **TitleMiddleware** - Auto-generates thread title after first complete exchange and normalizes structured message content before prompting the title model
+13. **MemoryMiddleware** - Queues conversations for async memory update (filters to user + final AI responses)
+14. **ViewImageMiddleware** - Injects base64 image data before LLM call (conditional on vision support)
+15. **DeferredToolFilterMiddleware** - Hides deferred tool schemas from the bound model until tool search is enabled (optional)
+16. **SubagentLimitMiddleware** - Truncates excess `task` tool calls from model response to enforce `MAX_CONCURRENT_SUBAGENTS` limit (optional, if `subagent_enabled`)
+17. **LoopDetectionMiddleware** - Detects repeated tool-call loops; hard-stop responses clear both structured `tool_calls` and raw provider tool-call metadata before forcing a final text answer
+18. **ClarificationMiddleware** - Intercepts `ask_clarification` tool calls, interrupts via `Command(goto=END)` (must be last)

 ### Configuration System

@@ -179,7 +185,16 @@ Setup: Copy `config.example.yaml` to `config.yaml` in the **project root** direc

 **Config Versioning**: `config.example.yaml` has a `config_version` field. On startup, `AppConfig.from_file()` compares user version vs example version and emits a warning if outdated. Missing `config_version` = version 0. Run `make config-upgrade` to auto-merge missing fields. When changing the config schema, bump `config_version` in `config.example.yaml`.

-**Config Caching**: `get_app_config()` caches the parsed config, but automatically reloads it when the resolved config path changes or the file's mtime increases. This keeps Gateway and LangGraph reads aligned with `config.yaml` edits without requiring a manual process restart.
+**Config Lifecycle**: All config models are `frozen=True` (immutable after construction). `AppConfig.from_file()` is a pure function — no side effects, no process-global state. The resolved `AppConfig` is passed as an explicit parameter down every consumer lane:
+
+- **Gateway**: `app.state.config` populated in lifespan; routers receive it via `Depends(get_config)` from `app/gateway/deps.py`.
+- **Client**: `DeerFlowClient._app_config` captured in the constructor; every method reads `self._app_config`.
+- **Agent run**: wrapped in `DeerFlowContext(app_config=…)` and injected via LangGraph `Runtime[DeerFlowContext].context`. Middleware and tools read `runtime.context.app_config` directly or via `resolve_context(runtime)`.
+- **LangGraph Server bootstrap**: `make_lead_agent` (registered in `langgraph.json`) calls `AppConfig.from_file()` itself — the only place in production that loads from disk at agent-build time.
+
+To update config at runtime (Gateway API mutations for MCP/Skills), write the new file and call `AppConfig.from_file()` to build a fresh snapshot, then swap `app.state.config`. No mtime detection, no auto-reload, no ambient ContextVar lookup (`AppConfig.current()` has been removed).
+
+**DeerFlowContext**: Per-invocation typed context for the agent execution path, injected via LangGraph `Runtime[DeerFlowContext]`. Holds `app_config: AppConfig`, `thread_id: str`, `agent_name: str | None`. Gateway runtime and `DeerFlowClient` construct full `DeerFlowContext` at invoke time; the LangGraph Server boundary builds one inside `make_lead_agent`. Middleware and tools access context through `resolve_context(runtime)` which returns the typed `DeerFlowContext` — legacy dict/None shapes are rejected. Mutable runtime state (`sandbox_id`) flows through `ThreadState.sandbox`, not context.

 Configuration priority:
 1. Explicit `config_path` argument
@@ -216,6 +231,9 @@ FastAPI application on port 8001 with health check at `GET /health`.
 | **Threads** (`/api/threads/{id}`) | `DELETE /` - remove DeerFlow-managed local thread data after LangGraph thread deletion; unexpected failures are logged server-side and return a generic 500 detail |
 | **Artifacts** (`/api/threads/{id}/artifacts`) | `GET /{path}` - serve artifacts; active content types (`text/html`, `application/xhtml+xml`, `image/svg+xml`) are always forced as download attachments to reduce XSS risk; `?download=true` still forces download for other file types |
 | **Suggestions** (`/api/threads/{id}/suggestions`) | `POST /` - generate follow-up questions; rich list/block model content is normalized before JSON parsing |
+| **Thread Runs** (`/api/threads/{id}/runs`) | `POST /` - create background run; `POST /stream` - create + SSE stream; `POST /wait` - create + block; `GET /` - list runs; `GET /{rid}` - run details; `POST /{rid}/cancel` - cancel; `GET /{rid}/join` - join SSE; `GET /{rid}/messages` - paginated messages `{data, has_more}`; `GET /{rid}/events` - full event stream; `GET /../messages` - thread messages with feedback; `GET /../token-usage` - aggregate tokens |
+| **Feedback** (`/api/threads/{id}/runs/{rid}/feedback`) | `PUT /` - upsert feedback; `DELETE /` - delete user feedback; `POST /` - create feedback; `GET /` - list feedback; `GET /stats` - aggregate stats; `DELETE /{fid}` - delete specific |
+| **Runs** (`/api/runs`) | `POST /stream` - stateless run + SSE; `POST /wait` - stateless run + block; `GET /{rid}/messages` - paginated messages by run_id `{data, has_more}` (cursor: `after_seq`/`before_seq`); `GET /{rid}/feedback` - list feedback by run_id |

 Proxied through nginx: `/api/langgraph/*` → LangGraph, all other `/api/*` → Gateway.

@@ -229,7 +247,7 @@ Proxied through nginx: `/api/langgraph/*` → LangGraph, all other `/api/*` →

 **Virtual Path System**:
 - Agent sees: `/mnt/user-data/{workspace,uploads,outputs}`, `/mnt/skills`
- Physical: `backend/.deer-flow/threads/{thread_id}/user-data/...`, `deer-flow/skills/`
+- Physical: `backend/.deer-flow/users/{user_id}/threads/{thread_id}/user-data/...`, `deer-flow/skills/`
 - Translation: `replace_virtual_path()` / `replace_virtual_paths_in_command()`
 - Detection: `is_local_sandbox()` checks `sandbox_id == "local"`

@@ -269,7 +287,7 @@ Proxied through nginx: `/api/langgraph/*` → LangGraph, all other `/api/*` →
 - `invoke_acp_agent` - Invokes external ACP-compatible agents from `config.yaml`
 - ACP launchers must be real ACP adapters. The standard `codex` CLI is not ACP-compatible by itself; configure a wrapper such as `npx -y @zed-industries/codex-acp` or an installed `codex-acp` binary
 - Missing ACP executables now return an actionable error message instead of a raw `[Errno 2]`
- Each ACP agent uses a per-thread workspace at `{base_dir}/threads/{thread_id}/acp-workspace/`. The workspace is accessible to the lead agent via the virtual path `/mnt/acp-workspace/` (read-only). In docker sandbox mode, the directory is volume-mounted into the container at `/mnt/acp-workspace` (read-only); in local sandbox mode, path translation is handled by `tools.py`
+- Each ACP agent uses a per-thread workspace at `{base_dir}/users/{user_id}/threads/{thread_id}/acp-workspace/`. The workspace is accessible to the lead agent via the virtual path `/mnt/acp-workspace/` (read-only). In docker sandbox mode, the directory is volume-mounted into the container at `/mnt/acp-workspace` (read-only); in local sandbox mode, path translation is handled by `tools.py`
 - `image_search/` - Image search via DuckDuckGo

 ### MCP System (`packages/harness/deerflow/mcp/`)
@@ -338,18 +356,27 @@ Bridges external messaging platforms (Feishu, Slack, Telegram) to the DeerFlow a

 **Components**:
 - `updater.py` - LLM-based memory updates with fact extraction, whitespace-normalized fact deduplication (trims leading/trailing whitespace before comparing), and atomic file I/O
- `queue.py` - Debounced update queue (per-thread deduplication, configurable wait time)
+- `queue.py` - Debounced update queue (per-thread deduplication, configurable wait time); captures `user_id` at enqueue time so it survives the `threading.Timer` boundary
 - `prompt.py` - Prompt templates for memory updates
+- `storage.py` - File-based storage with per-user isolation; cache keyed by `(user_id, agent_name)` tuple

-**Data Structure** (stored in `backend/.deer-flow/memory.json`):
+**Per-User Isolation**:
+- Memory is stored per-user at `{base_dir}/users/{user_id}/memory.json`
+- Per-agent per-user memory at `{base_dir}/users/{user_id}/agents/{agent_name}/memory.json`
+- `user_id` is resolved via `get_effective_user_id()` from `deerflow.runtime.user_context`
+- In no-auth mode, `user_id` defaults to `"default"` (constant `DEFAULT_USER_ID`)
+- Absolute `storage_path` in config opts out of per-user isolation
+- **Migration**: Run `PYTHONPATH=. python scripts/migrate_user_isolation.py` to move legacy `memory.json` and `threads/` into per-user layout; supports `--dry-run`
+
+**Data Structure** (stored in `{base_dir}/users/{user_id}/memory.json`):
 - **User Context**: `workContext`, `personalContext`, `topOfMind` (1-3 sentence summaries)
 - **History**: `recentMonths`, `earlierContext`, `longTermBackground`
 - **Facts**: Discrete facts with `id`, `content`, `category` (preference/knowledge/context/behavior/goal), `confidence` (0-1), `createdAt`, `source`

 **Workflow**:
-1. `MemoryMiddleware` filters messages (user inputs + final AI responses) and queues conversation
+1. `MemoryMiddleware` filters messages (user inputs + final AI responses), captures `user_id` via `get_effective_user_id()`, and queues conversation with the captured `user_id`
 2. Queue debounces (30s default), batches updates, deduplicates per-thread
-3. Background thread invokes LLM to extract context updates and facts
+3. Background thread invokes LLM to extract context updates and facts, using the stored `user_id` (not the contextvar, which is unavailable on timer threads)
 4. Applies updates atomically (temp file + rename) with cache invalidation, skipping duplicate fact content before append
 5. Next interaction injects top 15 facts + context into `<memory>` tags in system prompt

@@ -357,7 +384,7 @@ Focused regression coverage for the updater lives in `backend/tests/test_memory_

 **Configuration** (`config.yaml` → `memory`):
 - `enabled` / `injection_enabled` - Master switches
- `storage_path` - Path to memory.json
+- `storage_path` - Path to memory.json (absolute path opts out of per-user isolation)
 - `debounce_seconds` - Wait time before processing (default: 30)
 - `model_name` - LLM for updates (null = default model)
 - `max_facts` / `fact_confidence_threshold` - Fact storage limits (100 / 0.7)
@@ -13,6 +13,9 @@ FROM python:3.12-slim-bookworm AS builder
 ARG NODE_MAJOR=22
 ARG APT_MIRROR
 ARG UV_INDEX_URL
+# Optional extras to install (e.g. "postgres" for PostgreSQL support)
+# Usage: docker build --build-arg UV_EXTRAS=postgres ...
+ARG UV_EXTRAS

 # Optionally override apt mirror for restricted networks (e.g. APT_MIRROR=mirrors.aliyun.com)
 RUN if [ -n "${APT_MIRROR}" ]; then \
@@ -43,8 +46,9 @@ WORKDIR /app
 COPY backend ./backend

 # Install dependencies with cache mount
+# When UV_EXTRAS is set (e.g. "postgres"), installs optional dependencies.
 RUN --mount=type=cache,target=/root/.cache/uv \
-    sh -c "cd backend && UV_INDEX_URL=${UV_INDEX_URL:-https://pypi.org/simple} uv sync"
+    sh -c "cd backend && UV_INDEX_URL=${UV_INDEX_URL:-https://pypi.org/simple} uv sync ${UV_EXTRAS:+--extra $UV_EXTRAS}"

 # ── Stage 2: Dev ──────────────────────────────────────────────────────────────
 # Retains compiler toolchain from builder so startup-time `uv sync` can build
@@ -0,0 +1,273 @@
+"""Discord channel integration using discord.py."""
+
+from __future__ import annotations
+
+import asyncio
+import logging
+import threading
+from typing import Any
+
+from app.channels.base import Channel
+from app.channels.message_bus import InboundMessageType, MessageBus, OutboundMessage, ResolvedAttachment
+
+logger = logging.getLogger(__name__)
+
+_DISCORD_MAX_MESSAGE_LEN = 2000
+
+
+class DiscordChannel(Channel):
+    """Discord bot channel.
+
+    Configuration keys (in ``config.yaml`` under ``channels.discord``):
+        - ``bot_token``: Discord Bot token.
+        - ``allowed_guilds``: (optional) List of allowed Discord guild IDs. Empty = allow all.
+    """
+
+    def __init__(self, bus: MessageBus, config: dict[str, Any]) -> None:
+        super().__init__(name="discord", bus=bus, config=config)
+        self._bot_token = str(config.get("bot_token", "")).strip()
+        self._allowed_guilds: set[int] = set()
+        for guild_id in config.get("allowed_guilds", []):
+            try:
+                self._allowed_guilds.add(int(guild_id))
+            except (TypeError, ValueError):
+                continue
+
+        self._client = None
+        self._thread: threading.Thread | None = None
+        self._discord_loop: asyncio.AbstractEventLoop | None = None
+        self._main_loop: asyncio.AbstractEventLoop | None = None
+        self._discord_module = None
+
+    async def start(self) -> None:
+        if self._running:
+            return
+
+        try:
+            import discord
+        except ImportError:
+            logger.error("discord.py is not installed. Install it with: uv add discord.py")
+            return
+
+        if not self._bot_token:
+            logger.error("Discord channel requires bot_token")
+            return
+
+        intents = discord.Intents.default()
+        intents.messages = True
+        intents.guilds = True
+        intents.message_content = True
+
+        client = discord.Client(
+            intents=intents,
+            allowed_mentions=discord.AllowedMentions.none(),
+        )
+        self._client = client
+        self._discord_module = discord
+        self._main_loop = asyncio.get_event_loop()
+
+        @client.event
+        async def on_message(message) -> None:
+            await self._on_message(message)
+
+        self._running = True
+        self.bus.subscribe_outbound(self._on_outbound)
+
+        self._thread = threading.Thread(target=self._run_client, daemon=True)
+        self._thread.start()
+        logger.info("Discord channel started")
+
+    async def stop(self) -> None:
+        self._running = False
+        self.bus.unsubscribe_outbound(self._on_outbound)
+
+        if self._client and self._discord_loop and self._discord_loop.is_running():
+            close_future = asyncio.run_coroutine_threadsafe(self._client.close(), self._discord_loop)
+            try:
+                await asyncio.wait_for(asyncio.wrap_future(close_future), timeout=10)
+            except TimeoutError:
+                logger.warning("[Discord] client close timed out after 10s")
+            except Exception:
+                logger.exception("[Discord] error while closing client")
+
+        if self._thread:
+            self._thread.join(timeout=10)
+            self._thread = None
+
+        self._client = None
+        self._discord_loop = None
+        self._discord_module = None
+        logger.info("Discord channel stopped")
+
+    async def send(self, msg: OutboundMessage) -> None:
+        target = await self._resolve_target(msg)
+        if target is None:
+            logger.error("[Discord] target not found for chat_id=%s thread_ts=%s", msg.chat_id, msg.thread_ts)
+            return
+
+        text = msg.text or ""
+        for chunk in self._split_text(text):
+            send_future = asyncio.run_coroutine_threadsafe(target.send(chunk), self._discord_loop)
+            await asyncio.wrap_future(send_future)
+
+    async def send_file(self, msg: OutboundMessage, attachment: ResolvedAttachment) -> bool:
+        target = await self._resolve_target(msg)
+        if target is None:
+            logger.error("[Discord] target not found for file upload chat_id=%s thread_ts=%s", msg.chat_id, msg.thread_ts)
+            return False
+
+        if self._discord_module is None:
+            return False
+
+        try:
+            fp = open(str(attachment.actual_path), "rb")  # noqa: SIM115
+            file = self._discord_module.File(fp, filename=attachment.filename)
+            send_future = asyncio.run_coroutine_threadsafe(target.send(file=file), self._discord_loop)
+            await asyncio.wrap_future(send_future)
+            logger.info("[Discord] file uploaded: %s", attachment.filename)
+            return True
+        except Exception:
+            logger.exception("[Discord] failed to upload file: %s", attachment.filename)
+            return False
+
+    async def _on_message(self, message) -> None:
+        if not self._running or not self._client:
+            return
+
+        if message.author.bot:
+            return
+
+        if self._client.user and message.author.id == self._client.user.id:
+            return
+
+        guild = message.guild
+        if self._allowed_guilds:
+            if guild is None or guild.id not in self._allowed_guilds:
+                return
+
+        text = (message.content or "").strip()
+        if not text:
+            return
+
+        if self._discord_module is None:
+            return
+
+        if isinstance(message.channel, self._discord_module.Thread):
+            chat_id = str(message.channel.parent_id or message.channel.id)
+            thread_id = str(message.channel.id)
+        else:
+            thread = await self._create_thread(message)
+            if thread is None:
+                return
+            chat_id = str(message.channel.id)
+            thread_id = str(thread.id)
+
+        msg_type = InboundMessageType.COMMAND if text.startswith("/") else InboundMessageType.CHAT
+        inbound = self._make_inbound(
+            chat_id=chat_id,
+            user_id=str(message.author.id),
+            text=text,
+            msg_type=msg_type,
+            thread_ts=thread_id,
+            metadata={
+                "guild_id": str(guild.id) if guild else None,
+                "channel_id": str(message.channel.id),
+                "message_id": str(message.id),
+            },
+        )
+        inbound.topic_id = thread_id
+
+        if self._main_loop and self._main_loop.is_running():
+            future = asyncio.run_coroutine_threadsafe(self.bus.publish_inbound(inbound), self._main_loop)
+            future.add_done_callback(lambda f: logger.exception("[Discord] publish_inbound failed", exc_info=f.exception()) if f.exception() else None)
+
+    def _run_client(self) -> None:
+        self._discord_loop = asyncio.new_event_loop()
+        asyncio.set_event_loop(self._discord_loop)
+        try:
+            self._discord_loop.run_until_complete(self._client.start(self._bot_token))
+        except Exception:
+            if self._running:
+                logger.exception("Discord client error")
+        finally:
+            try:
+                if self._client and not self._client.is_closed():
+                    self._discord_loop.run_until_complete(self._client.close())
+            except Exception:
+                logger.exception("Error during Discord shutdown")
+
+    async def _create_thread(self, message):
+        try:
+            thread_name = f"deerflow-{message.author.display_name}-{message.id}"[:100]
+            return await message.create_thread(name=thread_name)
+        except Exception:
+            logger.exception("[Discord] failed to create thread for message=%s (threads may be disabled or missing permissions)", message.id)
+            try:
+                await message.channel.send("Could not create a thread for your message. Please check that threads are enabled in this channel.")
+            except Exception:
+                pass
+            return None
+
+    async def _resolve_target(self, msg: OutboundMessage):
+        if not self._client or not self._discord_loop:
+            return None
+
+        target_ids: list[str] = []
+        if msg.thread_ts:
+            target_ids.append(msg.thread_ts)
+        if msg.chat_id and msg.chat_id not in target_ids:
+            target_ids.append(msg.chat_id)
+
+        for raw_id in target_ids:
+            target = await self._get_channel_or_thread(raw_id)
+            if target is not None:
+                return target
+        return None
+
+    async def _get_channel_or_thread(self, raw_id: str):
+        if not self._client or not self._discord_loop:
+            return None
+
+        try:
+            target_id = int(raw_id)
+        except (TypeError, ValueError):
+            return None
+
+        get_future = asyncio.run_coroutine_threadsafe(self._fetch_channel(target_id), self._discord_loop)
+        try:
+            return await asyncio.wrap_future(get_future)
+        except Exception:
+            logger.exception("[Discord] failed to resolve target id=%s", raw_id)
+            return None
+
+    async def _fetch_channel(self, target_id: int):
+        if not self._client:
+            return None
+
+        channel = self._client.get_channel(target_id)
+        if channel is not None:
+            return channel
+
+        try:
+            return await self._client.fetch_channel(target_id)
+        except Exception:
+            return None
+
+    @staticmethod
+    def _split_text(text: str) -> list[str]:
+        if not text:
+            return [""]
+
+        chunks: list[str] = []
+        remaining = text
+        while len(remaining) > _DISCORD_MAX_MESSAGE_LEN:
+            split_at = remaining.rfind("\n", 0, _DISCORD_MAX_MESSAGE_LEN)
+            if split_at <= 0:
+                split_at = _DISCORD_MAX_MESSAGE_LEN
+            chunks.append(remaining[:split_at])
+            remaining = remaining[split_at:].lstrip("\n")
+
+        if remaining:
+            chunks.append(remaining)
+
+        return chunks
@@ -13,6 +13,7 @@ from app.channels.base import Channel
 from app.channels.commands import KNOWN_CHANNEL_COMMANDS
 from app.channels.message_bus import InboundMessage, InboundMessageType, MessageBus, OutboundMessage, ResolvedAttachment
 from deerflow.config.paths import VIRTUAL_PATH_PREFIX, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.sandbox.sandbox_provider import get_sandbox_provider

 logger = logging.getLogger(__name__)
@@ -344,8 +345,9 @@ class FeishuChannel(Channel):
            return f"Failed to obtain the [{type}]"

        paths = get_paths()
-        paths.ensure_thread_dirs(thread_id)
-        uploads_dir = paths.sandbox_uploads_dir(thread_id).resolve()
+        user_id = get_effective_user_id()
+        paths.ensure_thread_dirs(thread_id, user_id=user_id)
+        uploads_dir = paths.sandbox_uploads_dir(thread_id, user_id=user_id).resolve()

        ext = "png" if type == "image" else "bin"
        raw_filename = getattr(response, "file_name", "") or f"feishu_{file_key[-12:]}.{ext}"
@@ -373,7 +375,9 @@ class FeishuChannel(Channel):
        virtual_path = f"{VIRTUAL_PATH_PREFIX}/uploads/{resolved_target.name}"

        try:
-            sandbox_provider = get_sandbox_provider()
+            from deerflow.config.app_config import AppConfig
+
+            sandbox_provider = get_sandbox_provider(AppConfig.from_file())
            sandbox_id = sandbox_provider.acquire(thread_id)
            if sandbox_id != "local":
                sandbox = sandbox_provider.get(sandbox_id)
@@ -17,6 +17,7 @@ from langgraph_sdk.errors import ConflictError
 from app.channels.commands import KNOWN_CHANNEL_COMMANDS
 from app.channels.message_bus import InboundMessage, InboundMessageType, MessageBus, OutboundMessage, ResolvedAttachment
 from app.channels.store import ChannelStore
+from deerflow.runtime.user_context import get_effective_user_id

 logger = logging.getLogger(__name__)

@@ -35,6 +36,7 @@ STREAM_UPDATE_MIN_INTERVAL_SECONDS = 0.35
 THREAD_BUSY_MESSAGE = "This conversation is already processing another request. Please wait for it to finish and try again."

 CHANNEL_CAPABILITIES = {
+    "discord": {"supports_streaming": False},
    "feishu": {"supports_streaming": True},
    "slack": {"supports_streaming": False},
    "telegram": {"supports_streaming": False},
@@ -341,14 +343,15 @@ def _resolve_attachments(thread_id: str, artifacts: list[str]) -> list[ResolvedA

    attachments: list[ResolvedAttachment] = []
    paths = get_paths()
-    outputs_dir = paths.sandbox_outputs_dir(thread_id).resolve()
+    user_id = get_effective_user_id()
+    outputs_dir = paths.sandbox_outputs_dir(thread_id, user_id=user_id).resolve()
    for virtual_path in artifacts:
        # Security: only allow files from the agent outputs directory
        if not virtual_path.startswith(_OUTPUTS_VIRTUAL_PREFIX):
            logger.warning("[Manager] rejected non-outputs artifact path: %s", virtual_path)
            continue
        try:
-            actual = paths.resolve_virtual_path(thread_id, virtual_path)
+            actual = paths.resolve_virtual_path(thread_id, virtual_path, user_id=user_id)
            # Verify the resolved path is actually under the outputs directory
            # (guards against path-traversal even after prefix check)
            try:
@@ -4,17 +4,21 @@ from __future__ import annotations

 import logging
 import os
-from typing import Any
+from typing import TYPE_CHECKING, Any

 from app.channels.base import Channel
 from app.channels.manager import DEFAULT_GATEWAY_URL, DEFAULT_LANGGRAPH_URL, ChannelManager
 from app.channels.message_bus import MessageBus
 from app.channels.store import ChannelStore

+if TYPE_CHECKING:
+    from deerflow.config.app_config import AppConfig
+
 logger = logging.getLogger(__name__)

 # Channel name → import path for lazy loading
 _CHANNEL_REGISTRY: dict[str, str] = {
+    "discord": "app.channels.discord:DiscordChannel",
    "feishu": "app.channels.feishu:FeishuChannel",
    "slack": "app.channels.slack:SlackChannel",
    "telegram": "app.channels.telegram:TelegramChannel",
@@ -22,6 +26,16 @@ _CHANNEL_REGISTRY: dict[str, str] = {
    "wecom": "app.channels.wecom:WeComChannel",
 }

+# Keys that indicate a user has configured credentials for a channel.
+_CHANNEL_CREDENTIAL_KEYS: dict[str, list[str]] = {
+    "discord": ["bot_token"],
+    "feishu": ["app_id", "app_secret"],
+    "slack": ["bot_token", "app_token"],
+    "telegram": ["bot_token"],
+    "wecom": ["bot_id", "bot_secret"],
+    "wechat": ["bot_token"],
+}
+
 _CHANNELS_LANGGRAPH_URL_ENV = "DEER_FLOW_CHANNELS_LANGGRAPH_URL"
 _CHANNELS_GATEWAY_URL_ENV = "DEER_FLOW_CHANNELS_GATEWAY_URL"

@@ -64,14 +78,11 @@ class ChannelService:
        self._running = False

    @classmethod
-    def from_app_config(cls) -> ChannelService:
-        """Create a ChannelService from the application config."""
-        from deerflow.config.app_config import get_app_config
-
-        config = get_app_config()
+    def from_app_config(cls, app_config: AppConfig) -> ChannelService:
+        """Create a ChannelService from an explicit application config."""
        channels_config = {}
        # extra fields are allowed by AppConfig (extra="allow")
-        extra = config.model_extra or {}
+        extra = app_config.model_extra or {}
        if "channels" in extra:
            channels_config = extra["channels"]
        return cls(channels_config=channels_config)
@@ -87,7 +98,16 @@ class ChannelService:
            if not isinstance(channel_config, dict):
                continue
            if not channel_config.get("enabled", False):
-                logger.info("Channel %s is disabled, skipping", name)
+                cred_keys = _CHANNEL_CREDENTIAL_KEYS.get(name, [])
+                has_creds = any(not isinstance(channel_config.get(k), bool) and channel_config.get(k) is not None and str(channel_config[k]).strip() for k in cred_keys)
+                if has_creds:
+                    logger.warning(
+                        "Channel '%s' has credentials configured but is disabled. Set enabled: true under channels.%s in config.yaml to activate it.",
+                        name,
+                        name,
+                    )
+                else:
+                    logger.info("Channel %s is disabled, skipping", name)
                continue

            await self._start_channel(name, channel_config)
@@ -181,12 +201,12 @@ def get_channel_service() -> ChannelService | None:
    return _channel_service


-async def start_channel_service() -> ChannelService:
+async def start_channel_service(app_config: AppConfig) -> ChannelService:
    """Create and start the global ChannelService from app config."""
    global _channel_service
    if _channel_service is not None:
        return _channel_service
-    _channel_service = ChannelService.from_app_config()
+    _channel_service = ChannelService.from_app_config(app_config)
    await _channel_service.start()
    return _channel_service

@@ -16,13 +16,31 @@ logger = logging.getLogger(__name__)
 _slack_md_converter = SlackMarkdownConverter()


+def _normalize_allowed_users(allowed_users: Any) -> set[str]:
+    if allowed_users is None:
+        return set()
+    if isinstance(allowed_users, str):
+        values = [allowed_users]
+    elif isinstance(allowed_users, list | tuple | set):
+        values = allowed_users
+    else:
+        logger.warning(
+            "Slack allowed_users should be a list of Slack user IDs or a single Slack user ID string; treating %s as one string value",
+            type(allowed_users).__name__,
+        )
+        values = [allowed_users]
+    return {str(user_id) for user_id in values if str(user_id)}
+
+
 class SlackChannel(Channel):
    """Slack IM channel using Socket Mode (WebSocket, no public IP).

    Configuration keys (in ``config.yaml`` under ``channels.slack``):
        - ``bot_token``: Slack Bot User OAuth Token (xoxb-...).
        - ``app_token``: Slack App-Level Token (xapp-...) for Socket Mode.
-        - ``allowed_users``: (optional) List of allowed Slack user IDs. Empty = allow all.
+        - ``allowed_users``: (optional) List of allowed Slack user IDs, or a
+          single Slack user ID string as shorthand. Empty = allow all. Other
+          scalar values are treated as a single string with a warning.
    """

    def __init__(self, bus: MessageBus, config: dict[str, Any]) -> None:
@@ -30,7 +48,7 @@ class SlackChannel(Channel):
        self._socket_client = None
        self._web_client = None
        self._loop: asyncio.AbstractEventLoop | None = None
-        self._allowed_users: set[str] = {str(user_id) for user_id in config.get("allowed_users", [])}
+        self._allowed_users = _normalize_allowed_users(config.get("allowed_users", []))

    async def start(self) -> None:
        if self._running:
@@ -1,16 +1,23 @@
+import asyncio
 import logging
+import os
 from collections.abc import AsyncGenerator
 from contextlib import asynccontextmanager

 from fastapi import FastAPI
+from fastapi.middleware.cors import CORSMiddleware

+from app.gateway.auth_middleware import AuthMiddleware
 from app.gateway.config import get_gateway_config
+from app.gateway.csrf_middleware import CSRFMiddleware
 from app.gateway.deps import langgraph_runtime
 from app.gateway.routers import (
    agents,
    artifacts,
    assistants_compat,
+    auth,
    channels,
+    feedback,
    mcp,
    memory,
    models,
@@ -21,7 +28,7 @@ from app.gateway.routers import (
    threads,
    uploads,
 )
-from deerflow.config.app_config import get_app_config
+from deerflow.config.app_config import AppConfig

 # Configure logging
 logging.basicConfig(
@@ -32,14 +39,123 @@ logging.basicConfig(

 logger = logging.getLogger(__name__)

+# Upper bound (seconds) each lifespan shutdown hook is allowed to run.
+# Bounds worker exit time so uvicorn's reload supervisor does not keep
+# firing signals into a worker that is stuck waiting for shutdown cleanup.
+_SHUTDOWN_HOOK_TIMEOUT_SECONDS = 5.0
+
+
+async def _ensure_admin_user(app: FastAPI) -> None:
+    """Startup hook: handle first boot and migrate orphan threads otherwise.
+
+    After admin creation, migrate orphan threads from the LangGraph
+    store (metadata.user_id unset) to the admin account. This is the
+    "no-auth → with-auth" upgrade path: users who ran DeerFlow without
+    authentication have existing LangGraph thread data that needs an
+    owner assigned.
+        First boot (no admin exists):
+            - Does NOT create any user accounts automatically.
+            - The operator must visit ``/setup`` to create the first admin.
+
+    Subsequent boots (admin already exists):
+      - Runs the one-time "no-auth → with-auth" orphan thread migration for
+        existing LangGraph thread metadata that has no owner_id.
+
+    No SQL persistence migration is needed: the four user_id columns
+    (threads_meta, runs, run_events, feedback) only come into existence
+    alongside the auth module via create_all, so freshly created tables
+    never contain NULL-owner rows.
+    """
+    from sqlalchemy import select
+
+    from app.gateway.deps import get_local_provider
+    from deerflow.persistence.engine import get_session_factory
+    from deerflow.persistence.user.model import UserRow
+
+    provider = get_local_provider()
+    admin_count = await provider.count_admin_users()
+
+    if admin_count == 0:
+        logger.info("=" * 60)
+        logger.info("  First boot detected — no admin account exists.")
+        logger.info("  Visit /setup to complete admin account creation.")
+        logger.info("=" * 60)
+        return
+
+    # Admin already exists — run orphan thread migration for any
+    # LangGraph thread metadata that pre-dates the auth module.
+    sf = get_session_factory()
+    if sf is None:
+        return
+
+    async with sf() as session:
+        stmt = select(UserRow).where(UserRow.system_role == "admin").limit(1)
+        row = (await session.execute(stmt)).scalar_one_or_none()
+
+    if row is None:
+        return  # Should not happen (admin_count > 0 above), but be safe.
+
+    admin_id = str(row.id)
+
+    # LangGraph store orphan migration — non-fatal.
+    # This covers the "no-auth → with-auth" upgrade path for users
+    # whose existing LangGraph thread metadata has no user_id set.
+    store = getattr(app.state, "store", None)
+    if store is not None:
+        try:
+            migrated = await _migrate_orphaned_threads(store, admin_id)
+            if migrated:
+                logger.info("Migrated %d orphan LangGraph thread(s) to admin", migrated)
+        except Exception:
+            logger.exception("LangGraph thread migration failed (non-fatal)")
+
+
+async def _iter_store_items(store, namespace, *, page_size: int = 500):
+    """Paginated async iterator over a LangGraph store namespace.
+
+    Replaces the old hardcoded ``limit=1000`` call with a cursor-style
+    loop so that environments with more than one page of orphans do
+    not silently lose data. Terminates when a page is empty OR when a
+    short page arrives (indicating the last page).
+    """
+    offset = 0
+    while True:
+        batch = await store.asearch(namespace, limit=page_size, offset=offset)
+        if not batch:
+            return
+        for item in batch:
+            yield item
+        if len(batch) < page_size:
+            return
+        offset += page_size
+
+
+async def _migrate_orphaned_threads(store, admin_user_id: str) -> int:
+    """Migrate LangGraph store threads with no user_id to the given admin.
+
+    Uses cursor pagination so all orphans are migrated regardless of
+    count. Returns the number of rows migrated.
+    """
+    migrated = 0
+    async for item in _iter_store_items(store, ("threads",)):
+        metadata = item.value.get("metadata", {})
+        if not metadata.get("user_id"):
+            metadata["user_id"] = admin_user_id
+            item.value["metadata"] = metadata
+            await store.aput(("threads",), item.key, item.value)
+            migrated += 1
+    return migrated
+

@asynccontextmanager
 async def lifespan(app: FastAPI) -> AsyncGenerator[None, None]:
    """Application lifespan handler."""

-    # Load config and check necessary environment variables at startup
    try:
-        get_app_config()
+        # ``app.state.config`` is the sole source of truth for
+        # ``Depends(get_config)``. Consumers that want AppConfig must receive
+        # it as an explicit parameter; there is no ambient singleton.
+        app.state.config = AppConfig.from_file()
        logger.info("Configuration loaded successfully")
    except Exception as e:
        error_msg = f"Failed to load configuration during gateway startup: {e}"
@@ -52,22 +168,34 @@ async def lifespan(app: FastAPI) -> AsyncGenerator[None, None]:
    async with langgraph_runtime(app):
        logger.info("LangGraph runtime initialised")

+        # Ensure admin user exists (auto-create on first boot)
+        # Must run AFTER langgraph_runtime so app.state.store is available for thread migration
+        await _ensure_admin_user(app)
+
        # Start IM channel service if any channels are configured
        try:
            from app.channels.service import start_channel_service

-            channel_service = await start_channel_service()
+            channel_service = await start_channel_service(app.state.config)
            logger.info("Channel service started: %s", channel_service.get_status())
        except Exception:
            logger.exception("No IM channels configured or channel service failed to start")

        yield

-        # Stop channel service on shutdown
+        # Stop channel service on shutdown (bounded to prevent worker hang)
        try:
            from app.channels.service import stop_channel_service

-            await stop_channel_service()
+            await asyncio.wait_for(
+                stop_channel_service(),
+                timeout=_SHUTDOWN_HOOK_TIMEOUT_SECONDS,
+            )
+        except TimeoutError:
+            logger.warning(
+                "Channel service shutdown exceeded %.1fs; proceeding with worker exit.",
+                _SHUTDOWN_HOOK_TIMEOUT_SECONDS,
+            )
        except Exception:
            logger.exception("Failed to stop channel service")

@@ -163,7 +291,31 @@ This gateway provides custom endpoints for models, MCP configuration, skills, an
        ],
    )

-    # CORS is handled by nginx - no need for FastAPI middleware
+    # Auth: reject unauthenticated requests to non-public paths (fail-closed safety net)
+    app.add_middleware(AuthMiddleware)
+
+    # CSRF: Double Submit Cookie pattern for state-changing requests
+    app.add_middleware(CSRFMiddleware)
+
+    # CORS: when GATEWAY_CORS_ORIGINS is set (dev without nginx), add CORS middleware.
+    # In production, nginx handles CORS and no middleware is needed.
+    cors_origins_env = os.environ.get("GATEWAY_CORS_ORIGINS", "")
+    if cors_origins_env:
+        cors_origins = [o.strip() for o in cors_origins_env.split(",") if o.strip()]
+        # Validate: wildcard origin with credentials is a security misconfiguration
+        for origin in cors_origins:
+            if origin == "*":
+                logger.error("GATEWAY_CORS_ORIGINS contains wildcard '*' with allow_credentials=True. This is a security misconfiguration — browsers will reject the response. Use explicit scheme://host:port origins instead.")
+                cors_origins = [o for o in cors_origins if o != "*"]
+                break
+        if cors_origins:
+            app.add_middleware(
+                CORSMiddleware,
+                allow_origins=cors_origins,
+                allow_credentials=True,
+                allow_methods=["*"],
+                allow_headers=["*"],
+            )

    # Include routers
    # Models API is mounted at /api/models
@@ -199,6 +351,12 @@ This gateway provides custom endpoints for models, MCP configuration, skills, an
    # Assistants compatibility API (LangGraph Platform stub)
    app.include_router(assistants_compat.router)

+    # Auth API is mounted at /api/v1/auth
+    app.include_router(auth.router)
+
+    # Feedback API is mounted at /api/threads/{thread_id}/runs/{run_id}/feedback
+    app.include_router(feedback.router)
+
    # Thread Runs API (LangGraph Platform-compatible runs lifecycle)
    app.include_router(thread_runs.router)

@@ -0,0 +1,42 @@
+"""Authentication module for DeerFlow.
+
+This module provides:
+- JWT-based authentication
+- Provider Factory pattern for extensible auth methods
+- UserRepository interface for storage backends (SQLite)
+"""
+
+from app.gateway.auth.config import AuthConfig, get_auth_config, set_auth_config
+from app.gateway.auth.errors import AuthErrorCode, AuthErrorResponse, TokenError
+from app.gateway.auth.jwt import TokenPayload, create_access_token, decode_token
+from app.gateway.auth.local_provider import LocalAuthProvider
+from app.gateway.auth.models import User, UserResponse
+from app.gateway.auth.password import hash_password, verify_password
+from app.gateway.auth.providers import AuthProvider
+from app.gateway.auth.repositories.base import UserRepository
+
+__all__ = [
+    # Config
+    "AuthConfig",
+    "get_auth_config",
+    "set_auth_config",
+    # Errors
+    "AuthErrorCode",
+    "AuthErrorResponse",
+    "TokenError",
+    # JWT
+    "TokenPayload",
+    "create_access_token",
+    "decode_token",
+    # Password
+    "hash_password",
+    "verify_password",
+    # Models
+    "User",
+    "UserResponse",
+    # Providers
+    "AuthProvider",
+    "LocalAuthProvider",
+    # Repository
+    "UserRepository",
+]
@@ -0,0 +1,57 @@
+"""Authentication configuration for DeerFlow."""
+
+import logging
+import os
+import secrets
+
+from dotenv import load_dotenv
+from pydantic import BaseModel, Field
+
+load_dotenv()
+
+logger = logging.getLogger(__name__)
+
+
+class AuthConfig(BaseModel):
+    """JWT and auth-related configuration. Parsed once at startup.
+
+    Note: the ``users`` table now lives in the shared persistence
+    database managed by ``deerflow.persistence.engine``. The old
+    ``users_db_path`` config key has been removed — user storage is
+    configured through ``config.database`` like every other table.
+    """
+
+    jwt_secret: str = Field(
+        ...,
+        description="Secret key for JWT signing. MUST be set via AUTH_JWT_SECRET.",
+    )
+    token_expiry_days: int = Field(default=7, ge=1, le=30)
+    oauth_github_client_id: str | None = Field(default=None)
+    oauth_github_client_secret: str | None = Field(default=None)
+
+
+_auth_config: AuthConfig | None = None
+
+
+def get_auth_config() -> AuthConfig:
+    """Get the global AuthConfig instance. Parses from env on first call."""
+    global _auth_config
+    if _auth_config is None:
+        jwt_secret = os.environ.get("AUTH_JWT_SECRET")
+        if not jwt_secret:
+            jwt_secret = secrets.token_urlsafe(32)
+            os.environ["AUTH_JWT_SECRET"] = jwt_secret
+            logger.warning(
+                "⚠ AUTH_JWT_SECRET is not set — using an auto-generated ephemeral secret. "
+                "Sessions will be invalidated on restart. "
+                "For production, add AUTH_JWT_SECRET to your .env file: "
+                'python -c "import secrets; print(secrets.token_urlsafe(32))"'
+            )
+        _auth_config = AuthConfig(jwt_secret=jwt_secret)
+    return _auth_config
+
+
+def set_auth_config(config: AuthConfig) -> None:
+    """Set the global AuthConfig instance (for testing)."""
+    global _auth_config
+    _auth_config = config
@@ -0,0 +1,48 @@
+"""Write initial admin credentials to a restricted file instead of logs.
+
+Logging secrets to stdout/stderr is a well-known CodeQL finding
+(py/clear-text-logging-sensitive-data) — in production those logs
+get collected into ELK/Splunk/etc and become a secret sprawl
+source. This helper writes the credential to a 0600 file that only
+the process user can read, and returns the path so the caller can
+log **the path** (not the password) for the operator to pick up.
+"""
+
+from __future__ import annotations
+
+import os
+from pathlib import Path
+
+from deerflow.config.paths import get_paths
+
+_CREDENTIAL_FILENAME = "admin_initial_credentials.txt"
+
+
+def write_initial_credentials(email: str, password: str, *, label: str = "initial") -> Path:
+    """Write the admin email + password to ``{base_dir}/admin_initial_credentials.txt``.
+
+    The file is created **atomically** with mode 0600 via ``os.open``
+    so the password is never world-readable, even for the single syscall
+    window between ``write_text`` and ``chmod``.
+
+    ``label`` distinguishes "initial" (fresh creation) from "reset"
+    (password reset) in the file header so an operator picking up the
+    file after a restart can tell which event produced it.
+
+    Returns the absolute :class:`Path` to the file.
+    """
+    target = get_paths().base_dir / _CREDENTIAL_FILENAME
+    target.parent.mkdir(parents=True, exist_ok=True)
+
+    content = (
+        f"# DeerFlow admin {label} credentials\n# This file is generated on first boot or password reset.\n# Change the password after login via Settings -> Account,\n# then delete this file.\n#\nemail: {email}\npassword: {password}\n"
+    )
+
+    # Atomic 0600 create-or-truncate. O_TRUNC (not O_EXCL) so the
+    # reset-password path can rewrite an existing file without a
+    # separate unlink-then-create dance.
+    fd = os.open(target, os.O_WRONLY | os.O_CREAT | os.O_TRUNC, 0o600)
+    with os.fdopen(fd, "w", encoding="utf-8") as fh:
+        fh.write(content)
+
+    return target.resolve()
@@ -0,0 +1,45 @@
+"""Typed error definitions for auth module.
+
+AuthErrorCode: exhaustive enum of all auth failure conditions.
+TokenError: exhaustive enum of JWT decode failures.
+AuthErrorResponse: structured error payload for HTTP responses.
+"""
+
+from enum import StrEnum
+
+from pydantic import BaseModel
+
+
+class AuthErrorCode(StrEnum):
+    """Exhaustive list of auth error conditions."""
+
+    INVALID_CREDENTIALS = "invalid_credentials"
+    TOKEN_EXPIRED = "token_expired"
+    TOKEN_INVALID = "token_invalid"
+    USER_NOT_FOUND = "user_not_found"
+    EMAIL_ALREADY_EXISTS = "email_already_exists"
+    PROVIDER_NOT_FOUND = "provider_not_found"
+    NOT_AUTHENTICATED = "not_authenticated"
+    SYSTEM_ALREADY_INITIALIZED = "system_already_initialized"
+
+
+class TokenError(StrEnum):
+    """Exhaustive list of JWT decode failure reasons."""
+
+    EXPIRED = "expired"
+    INVALID_SIGNATURE = "invalid_signature"
+    MALFORMED = "malformed"
+
+
+class AuthErrorResponse(BaseModel):
+    """Structured error response — replaces bare `detail` strings."""
+
+    code: AuthErrorCode
+    message: str
+
+
+def token_error_to_code(err: TokenError) -> AuthErrorCode:
+    """Map TokenError to AuthErrorCode — single source of truth."""
+    if err == TokenError.EXPIRED:
+        return AuthErrorCode.TOKEN_EXPIRED
+    return AuthErrorCode.TOKEN_INVALID
@@ -0,0 +1,55 @@
+"""JWT token creation and verification."""
+
+from datetime import UTC, datetime, timedelta
+
+import jwt
+from pydantic import BaseModel
+
+from app.gateway.auth.config import get_auth_config
+from app.gateway.auth.errors import TokenError
+
+
+class TokenPayload(BaseModel):
+    """JWT token payload."""
+
+    sub: str  # user_id
+    exp: datetime
+    iat: datetime | None = None
+    ver: int = 0  # token_version — must match User.token_version
+
+
+def create_access_token(user_id: str, expires_delta: timedelta | None = None, token_version: int = 0) -> str:
+    """Create a JWT access token.
+
+    Args:
+        user_id: The user's UUID as string
+        expires_delta: Optional custom expiry, defaults to 7 days
+        token_version: User's current token_version for invalidation
+
+    Returns:
+        Encoded JWT string
+    """
+    config = get_auth_config()
+    expiry = expires_delta or timedelta(days=config.token_expiry_days)
+
+    now = datetime.now(UTC)
+    payload = {"sub": user_id, "exp": now + expiry, "iat": now, "ver": token_version}
+    return jwt.encode(payload, config.jwt_secret, algorithm="HS256")
+
+
+def decode_token(token: str) -> TokenPayload | TokenError:
+    """Decode and validate a JWT token.
+
+    Returns:
+        TokenPayload if valid, or a specific TokenError variant.
+    """
+    config = get_auth_config()
+    try:
+        payload = jwt.decode(token, config.jwt_secret, algorithms=["HS256"])
+        return TokenPayload(**payload)
+    except jwt.ExpiredSignatureError:
+        return TokenError.EXPIRED
+    except jwt.InvalidSignatureError:
+        return TokenError.INVALID_SIGNATURE
+    except jwt.PyJWTError:
+        return TokenError.MALFORMED
@@ -0,0 +1,91 @@
+"""Local email/password authentication provider."""
+
+from app.gateway.auth.models import User
+from app.gateway.auth.password import hash_password_async, verify_password_async
+from app.gateway.auth.providers import AuthProvider
+from app.gateway.auth.repositories.base import UserRepository
+
+
+class LocalAuthProvider(AuthProvider):
+    """Email/password authentication provider using local database."""
+
+    def __init__(self, repository: UserRepository):
+        """Initialize with a UserRepository.
+
+        Args:
+            repository: UserRepository implementation (SQLite)
+        """
+        self._repo = repository
+
+    async def authenticate(self, credentials: dict) -> User | None:
+        """Authenticate with email and password.
+
+        Args:
+            credentials: dict with 'email' and 'password' keys
+
+        Returns:
+            User if authentication succeeds, None otherwise
+        """
+        email = credentials.get("email")
+        password = credentials.get("password")
+
+        if not email or not password:
+            return None
+
+        user = await self._repo.get_user_by_email(email)
+        if user is None:
+            return None
+
+        if user.password_hash is None:
+            # OAuth user without local password
+            return None
+
+        if not await verify_password_async(password, user.password_hash):
+            return None
+
+        return user
+
+    async def get_user(self, user_id: str) -> User | None:
+        """Get user by ID."""
+        return await self._repo.get_user_by_id(user_id)
+
+    async def create_user(self, email: str, password: str | None = None, system_role: str = "user", needs_setup: bool = False) -> User:
+        """Create a new local user.
+
+        Args:
+            email: User email address
+            password: Plain text password (will be hashed)
+            system_role: Role to assign ("admin" or "user")
+            needs_setup: If True, user must complete setup on first login
+
+        Returns:
+            Created User instance
+        """
+        password_hash = await hash_password_async(password) if password else None
+        user = User(
+            email=email,
+            password_hash=password_hash,
+            system_role=system_role,
+            needs_setup=needs_setup,
+        )
+        return await self._repo.create_user(user)
+
+    async def get_user_by_oauth(self, provider: str, oauth_id: str) -> User | None:
+        """Get user by OAuth provider and ID."""
+        return await self._repo.get_user_by_oauth(provider, oauth_id)
+
+    async def count_users(self) -> int:
+        """Return total number of registered users."""
+        return await self._repo.count_users()
+
+    async def count_admin_users(self) -> int:
+        """Return number of admin users."""
+        return await self._repo.count_admin_users()
+
+    async def update_user(self, user: User) -> User:
+        """Update an existing user."""
+        return await self._repo.update_user(user)
+
+    async def get_user_by_email(self, email: str) -> User | None:
+        """Get user by email."""
+        return await self._repo.get_user_by_email(email)
@@ -0,0 +1,41 @@
+"""User Pydantic models for authentication."""
+
+from datetime import UTC, datetime
+from typing import Literal
+from uuid import UUID, uuid4
+
+from pydantic import BaseModel, ConfigDict, EmailStr, Field
+
+
+def _utc_now() -> datetime:
+    """Return current UTC time (timezone-aware)."""
+    return datetime.now(UTC)
+
+
+class User(BaseModel):
+    """Internal user representation."""
+
+    model_config = ConfigDict(from_attributes=True)
+
+    id: UUID = Field(default_factory=uuid4, description="Primary key")
+    email: EmailStr = Field(..., description="Unique email address")
+    password_hash: str | None = Field(None, description="bcrypt hash, nullable for OAuth users")
+    system_role: Literal["admin", "user"] = Field(default="user")
+    created_at: datetime = Field(default_factory=_utc_now)
+
+    # OAuth linkage (optional)
+    oauth_provider: str | None = Field(None, description="e.g. 'github', 'google'")
+    oauth_id: str | None = Field(None, description="User ID from OAuth provider")
+
+    # Auth lifecycle
+    needs_setup: bool = Field(default=False, description="True for auto-created admin until setup completes")
+    token_version: int = Field(default=0, description="Incremented on password change to invalidate old JWTs")
+
+
+class UserResponse(BaseModel):
+    """Response model for user info endpoint."""
+
+    id: str
+    email: str
+    system_role: Literal["admin", "user"]
+    needs_setup: bool = False
@@ -0,0 +1,33 @@
+"""Password hashing utilities using bcrypt directly."""
+
+import asyncio
+
+import bcrypt
+
+
+def hash_password(password: str) -> str:
+    """Hash a password using bcrypt."""
+    return bcrypt.hashpw(password.encode("utf-8"), bcrypt.gensalt()).decode("utf-8")
+
+
+def verify_password(plain_password: str, hashed_password: str) -> bool:
+    """Verify a password against its hash."""
+    return bcrypt.checkpw(plain_password.encode("utf-8"), hashed_password.encode("utf-8"))
+
+
+async def hash_password_async(password: str) -> str:
+    """Hash a password using bcrypt (non-blocking).
+
+    Wraps the blocking bcrypt operation in a thread pool to avoid
+    blocking the event loop during password hashing.
+    """
+    return await asyncio.to_thread(hash_password, password)
+
+
+async def verify_password_async(plain_password: str, hashed_password: str) -> bool:
+    """Verify a password against its hash (non-blocking).
+
+    Wraps the blocking bcrypt operation in a thread pool to avoid
+    blocking the event loop during password verification.
+    """
+    return await asyncio.to_thread(verify_password, plain_password, hashed_password)
@@ -0,0 +1,24 @@
+"""Auth provider abstraction."""
+
+from abc import ABC, abstractmethod
+
+
+class AuthProvider(ABC):
+    """Abstract base class for authentication providers."""
+
+    @abstractmethod
+    async def authenticate(self, credentials: dict) -> "User | None":
+        """Authenticate user with given credentials.
+
+        Returns User if authentication succeeds, None otherwise.
+        """
+        ...
+
+    @abstractmethod
+    async def get_user(self, user_id: str) -> "User | None":
+        """Retrieve user by ID."""
+        ...
+
+
+# Import User at runtime to avoid circular imports
+from app.gateway.auth.models import User  # noqa: E402
@@ -0,0 +1,102 @@
+"""User repository interface for abstracting database operations."""
+
+from abc import ABC, abstractmethod
+
+from app.gateway.auth.models import User
+
+
+class UserNotFoundError(LookupError):
+    """Raised when a user repository operation targets a non-existent row.
+
+    Subclass of :class:`LookupError` so callers that already catch
+    ``LookupError`` for "missing entity" can keep working unchanged,
+    while specific call sites can pin to this class to distinguish
+    "concurrent delete during update" from other lookups.
+    """
+
+
+class UserRepository(ABC):
+    """Abstract interface for user data storage.
+
+    Implement this interface to support different storage backends
+    (SQLite)
+    """
+
+    @abstractmethod
+    async def create_user(self, user: User) -> User:
+        """Create a new user.
+
+        Args:
+            user: User object to create
+
+        Returns:
+            Created User with ID assigned
+
+        Raises:
+            ValueError: If email already exists
+        """
+        ...
+
+    @abstractmethod
+    async def get_user_by_id(self, user_id: str) -> User | None:
+        """Get user by ID.
+
+        Args:
+            user_id: User UUID as string
+
+        Returns:
+            User if found, None otherwise
+        """
+        ...
+
+    @abstractmethod
+    async def get_user_by_email(self, email: str) -> User | None:
+        """Get user by email.
+
+        Args:
+            email: User email address
+
+        Returns:
+            User if found, None otherwise
+        """
+        ...
+
+    @abstractmethod
+    async def update_user(self, user: User) -> User:
+        """Update an existing user.
+
+        Args:
+            user: User object with updated fields
+
+        Returns:
+            Updated User
+
+        Raises:
+            UserNotFoundError: If no row exists for ``user.id``. This is
+                a hard failure (not a no-op) so callers cannot mistake a
+                concurrent-delete race for a successful update.
+        """
+        ...
+
+    @abstractmethod
+    async def count_users(self) -> int:
+        """Return total number of registered users."""
+        ...
+
+    @abstractmethod
+    async def count_admin_users(self) -> int:
+        """Return number of users with system_role == 'admin'."""
+        ...
+
+    @abstractmethod
+    async def get_user_by_oauth(self, provider: str, oauth_id: str) -> User | None:
+        """Get user by OAuth provider and ID.
+
+        Args:
+            provider: OAuth provider name (e.g. 'github', 'google')
+            oauth_id: User ID from the OAuth provider
+
+        Returns:
+            User if found, None otherwise
+        """
+        ...
@@ -0,0 +1,127 @@
+"""SQLAlchemy-backed UserRepository implementation.
+
+Uses the shared async session factory from
+``deerflow.persistence.engine`` — the ``users`` table lives in the
+same database as ``threads_meta``, ``runs``, ``run_events``, and
+``feedback``.
+
+Constructor takes the session factory directly (same pattern as the
+other four repositories in ``deerflow.persistence.*``). Callers
+construct this after ``init_engine_from_config()`` has run.
+"""
+
+from __future__ import annotations
+
+from datetime import UTC
+from uuid import UUID
+
+from sqlalchemy import func, select
+from sqlalchemy.exc import IntegrityError
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
+from app.gateway.auth.models import User
+from app.gateway.auth.repositories.base import UserNotFoundError, UserRepository
+from deerflow.persistence.user.model import UserRow
+
+
+class SQLiteUserRepository(UserRepository):
+    """Async user repository backed by the shared SQLAlchemy engine."""
+
+    def __init__(self, session_factory: async_sessionmaker[AsyncSession]) -> None:
+        self._sf = session_factory
+
+    # ── Converters ────────────────────────────────────────────────────
+
+    @staticmethod
+    def _row_to_user(row: UserRow) -> User:
+        return User(
+            id=UUID(row.id),
+            email=row.email,
+            password_hash=row.password_hash,
+            system_role=row.system_role,  # type: ignore[arg-type]
+            # SQLite loses tzinfo on read; reattach UTC so downstream
+            # code can compare timestamps reliably.
+            created_at=row.created_at if row.created_at.tzinfo else row.created_at.replace(tzinfo=UTC),
+            oauth_provider=row.oauth_provider,
+            oauth_id=row.oauth_id,
+            needs_setup=row.needs_setup,
+            token_version=row.token_version,
+        )
+
+    @staticmethod
+    def _user_to_row(user: User) -> UserRow:
+        return UserRow(
+            id=str(user.id),
+            email=user.email,
+            password_hash=user.password_hash,
+            system_role=user.system_role,
+            created_at=user.created_at,
+            oauth_provider=user.oauth_provider,
+            oauth_id=user.oauth_id,
+            needs_setup=user.needs_setup,
+            token_version=user.token_version,
+        )
+
+    # ── CRUD ──────────────────────────────────────────────────────────
+
+    async def create_user(self, user: User) -> User:
+        """Insert a new user. Raises ``ValueError`` on duplicate email."""
+        row = self._user_to_row(user)
+        async with self._sf() as session:
+            session.add(row)
+            try:
+                await session.commit()
+            except IntegrityError as exc:
+                await session.rollback()
+                raise ValueError(f"Email already registered: {user.email}") from exc
+        return user
+
+    async def get_user_by_id(self, user_id: str) -> User | None:
+        async with self._sf() as session:
+            row = await session.get(UserRow, user_id)
+            return self._row_to_user(row) if row is not None else None
+
+    async def get_user_by_email(self, email: str) -> User | None:
+        stmt = select(UserRow).where(UserRow.email == email)
+        async with self._sf() as session:
+            result = await session.execute(stmt)
+            row = result.scalar_one_or_none()
+            return self._row_to_user(row) if row is not None else None
+
+    async def update_user(self, user: User) -> User:
+        async with self._sf() as session:
+            row = await session.get(UserRow, str(user.id))
+            if row is None:
+                # Hard fail on concurrent delete: callers (reset_admin,
+                # password change handlers, _ensure_admin_user) all
+                # fetched the user just before this call, so a missing
+                # row here means the row vanished underneath us. Silent
+                # success would let the caller log "password reset" for
+                # a row that no longer exists.
+                raise UserNotFoundError(f"User {user.id} no longer exists")
+            row.email = user.email
+            row.password_hash = user.password_hash
+            row.system_role = user.system_role
+            row.oauth_provider = user.oauth_provider
+            row.oauth_id = user.oauth_id
+            row.needs_setup = user.needs_setup
+            row.token_version = user.token_version
+            await session.commit()
+        return user
+
+    async def count_users(self) -> int:
+        stmt = select(func.count()).select_from(UserRow)
+        async with self._sf() as session:
+            return await session.scalar(stmt) or 0
+
+    async def count_admin_users(self) -> int:
+        stmt = select(func.count()).select_from(UserRow).where(UserRow.system_role == "admin")
+        async with self._sf() as session:
+            return await session.scalar(stmt) or 0
+
+    async def get_user_by_oauth(self, provider: str, oauth_id: str) -> User | None:
+        stmt = select(UserRow).where(UserRow.oauth_provider == provider, UserRow.oauth_id == oauth_id)
+        async with self._sf() as session:
+            result = await session.execute(stmt)
+            row = result.scalar_one_or_none()
+            return self._row_to_user(row) if row is not None else None
@@ -0,0 +1,92 @@
+"""CLI tool to reset an admin password.
+
+Usage:
+    python -m app.gateway.auth.reset_admin
+    python -m app.gateway.auth.reset_admin --email admin@example.com
+
+Writes the new password to ``.deer-flow/admin_initial_credentials.txt``
+(mode 0600) instead of printing it, so CI / log aggregators never see
+the cleartext secret.
+"""
+
+from __future__ import annotations
+
+import argparse
+import asyncio
+import secrets
+import sys
+
+from sqlalchemy import select
+
+from app.gateway.auth.credential_file import write_initial_credentials
+from app.gateway.auth.password import hash_password
+from app.gateway.auth.repositories.sqlite import SQLiteUserRepository
+from deerflow.persistence.user.model import UserRow
+
+
+async def _run(email: str | None) -> int:
+    from deerflow.config import AppConfig
+    from deerflow.persistence.engine import (
+        close_engine,
+        get_session_factory,
+        init_engine_from_config,
+    )
+
+    # CLI entry: load config explicitly at the top, pass down through the closure.
+    config = AppConfig.from_file()
+    await init_engine_from_config(config.database)
+    try:
+        sf = get_session_factory()
+        if sf is None:
+            print("Error: persistence engine not available (check config.database).", file=sys.stderr)
+            return 1
+
+        repo = SQLiteUserRepository(sf)
+
+        if email:
+            user = await repo.get_user_by_email(email)
+        else:
+            # Find first admin via direct SELECT — repository does not
+            # expose a "first admin" helper and we do not want to add
+            # one just for this CLI.
+            async with sf() as session:
+                stmt = select(UserRow).where(UserRow.system_role == "admin").limit(1)
+                row = (await session.execute(stmt)).scalar_one_or_none()
+            if row is None:
+                user = None
+            else:
+                user = await repo.get_user_by_id(row.id)
+
+        if user is None:
+            if email:
+                print(f"Error: user '{email}' not found.", file=sys.stderr)
+            else:
+                print("Error: no admin user found.", file=sys.stderr)
+            return 1
+
+        new_password = secrets.token_urlsafe(16)
+        user.password_hash = hash_password(new_password)
+        user.token_version += 1
+        user.needs_setup = True
+        await repo.update_user(user)
+
+        cred_path = write_initial_credentials(user.email, new_password, label="reset")
+        print(f"Password reset for: {user.email}")
+        print(f"Credentials written to: {cred_path} (mode 0600)")
+        print("Next login will require setup (new email + password).")
+        return 0
+    finally:
+        await close_engine()
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(description="Reset admin password")
+    parser.add_argument("--email", help="Admin email (default: first admin found)")
+    args = parser.parse_args()
+
+    exit_code = asyncio.run(_run(args.email))
+    sys.exit(exit_code)
+
+
+if __name__ == "__main__":
+    main()
@@ -0,0 +1,118 @@
+"""Global authentication middleware — fail-closed safety net.
+
+Rejects unauthenticated requests to non-public paths with 401. When a
+request passes the cookie check, resolves the JWT payload to a real
+``User`` object and stamps it into both ``request.state.user`` and the
+``deerflow.runtime.user_context`` contextvar so that repository-layer
+owner filtering works automatically via the sentinel pattern.
+
+Fine-grained permission checks remain in authz.py decorators.
+"""
+
+from collections.abc import Callable
+
+from fastapi import HTTPException, Request, Response
+from starlette.middleware.base import BaseHTTPMiddleware
+from starlette.responses import JSONResponse
+from starlette.types import ASGIApp
+
+from app.gateway.auth.errors import AuthErrorCode, AuthErrorResponse
+from app.gateway.authz import _ALL_PERMISSIONS, AuthContext
+from deerflow.runtime.user_context import reset_current_user, set_current_user
+
+# Paths that never require authentication.
+_PUBLIC_PATH_PREFIXES: tuple[str, ...] = (
+    "/health",
+    "/docs",
+    "/redoc",
+    "/openapi.json",
+)
+
+# Exact auth paths that are public (login/register/status check).
+# /api/v1/auth/me, /api/v1/auth/change-password etc. are NOT public.
+_PUBLIC_EXACT_PATHS: frozenset[str] = frozenset(
+    {
+        "/api/v1/auth/login/local",
+        "/api/v1/auth/register",
+        "/api/v1/auth/logout",
+        "/api/v1/auth/setup-status",
+        "/api/v1/auth/initialize",
+    }
+)
+
+
+def _is_public(path: str) -> bool:
+    stripped = path.rstrip("/")
+    if stripped in _PUBLIC_EXACT_PATHS:
+        return True
+    return any(path.startswith(prefix) for prefix in _PUBLIC_PATH_PREFIXES)
+
+
+class AuthMiddleware(BaseHTTPMiddleware):
+    """Strict auth gate: reject requests without a valid session.
+
+    Two-stage check for non-public paths:
+
+    1. Cookie presence — return 401 NOT_AUTHENTICATED if missing
+    2. JWT validation via ``get_optional_user_from_request`` — return 401
+       TOKEN_INVALID if the token is absent, malformed, expired, or the
+       signed user does not exist / is stale
+
+    On success, stamps ``request.state.user`` and the
+    ``deerflow.runtime.user_context`` contextvar so that repository-layer
+    owner filters work downstream without every route needing a
+    ``@require_auth`` decorator. Routes that need per-resource
+    authorization (e.g. "user A cannot read user B's thread by guessing
+    the URL") should additionally use ``@require_permission(...,
+    owner_check=True)`` for explicit enforcement — but authentication
+    itself is fully handled here.
+    """
+
+    def __init__(self, app: ASGIApp) -> None:
+        super().__init__(app)
+
+    async def dispatch(self, request: Request, call_next: Callable) -> Response:
+        if _is_public(request.url.path):
+            return await call_next(request)
+
+        # Non-public path: require session cookie
+        if not request.cookies.get("access_token"):
+            return JSONResponse(
+                status_code=401,
+                content={
+                    "detail": AuthErrorResponse(
+                        code=AuthErrorCode.NOT_AUTHENTICATED,
+                        message="Authentication required",
+                    ).model_dump()
+                },
+            )
+
+        # Strict JWT validation: reject junk/expired tokens with 401
+        # right here instead of silently passing through. This closes
+        # the "junk cookie bypass" gap (AUTH_TEST_PLAN test 7.5.8):
+        # without this, non-isolation routes like /api/models would
+        # accept any cookie-shaped string as authentication.
+        #
+        # We call the *strict* resolver so that fine-grained error
+        # codes (token_expired, token_invalid, user_not_found, …)
+        # propagate from AuthErrorCode, not get flattened into one
+        # generic code. BaseHTTPMiddleware doesn't let HTTPException
+        # bubble up, so we catch and render it as JSONResponse here.
+        from app.gateway.deps import get_current_user_from_request
+
+        try:
+            user = await get_current_user_from_request(request)
+        except HTTPException as exc:
+            return JSONResponse(status_code=exc.status_code, content={"detail": exc.detail})
+
+        # Stamp both request.state.user (for the contextvar pattern)
+        # and request.state.auth (so @require_permission's "auth is
+        # None" branch short-circuits instead of running the entire
+        # JWT-decode + DB-lookup pipeline a second time per request).
+        request.state.user = user
+        request.state.auth = AuthContext(user=user, permissions=_ALL_PERMISSIONS)
+        token = set_current_user(user)
+        try:
+            return await call_next(request)
+        finally:
+            reset_current_user(token)
@@ -0,0 +1,262 @@
+"""Authorization decorators and context for DeerFlow.
+
+Inspired by LangGraph Auth system: https://github.com/langchain-ai/langgraph/blob/main/libs/sdk-py/langgraph_sdk/auth/__init__.py
+
+**Usage:**
+
+1. Use ``@require_auth`` on routes that need authentication
+2. Use ``@require_permission("resource", "action", filter_key=...)`` for permission checks
+3. The decorator chain processes from bottom to top
+
+**Example:**
+
+    @router.get("/{thread_id}")
+    @require_auth
+    @require_permission("threads", "read", owner_check=True)
+    async def get_thread(thread_id: str, request: Request):
+        # User is authenticated and has threads:read permission
+        ...
+
+**Permission Model:**
+
+- threads:read   - View thread
+- threads:write  - Create/update thread
+- threads:delete - Delete thread
+- runs:create   - Run agent
+- runs:read     - View run
+- runs:cancel   - Cancel run
+"""
+
+from __future__ import annotations
+
+import functools
+from collections.abc import Callable
+from typing import TYPE_CHECKING, Any, ParamSpec, TypeVar
+
+from fastapi import HTTPException, Request
+
+if TYPE_CHECKING:
+    from app.gateway.auth.models import User
+
+P = ParamSpec("P")
+T = TypeVar("T")
+
+
+# Permission constants
+class Permissions:
+    """Permission constants for resource:action format."""
+
+    # Threads
+    THREADS_READ = "threads:read"
+    THREADS_WRITE = "threads:write"
+    THREADS_DELETE = "threads:delete"
+
+    # Runs
+    RUNS_CREATE = "runs:create"
+    RUNS_READ = "runs:read"
+    RUNS_CANCEL = "runs:cancel"
+
+
+class AuthContext:
+    """Authentication context for the current request.
+
+    Stored in request.state.auth after require_auth decoration.
+
+    Attributes:
+        user: The authenticated user, or None if anonymous
+        permissions: List of permission strings (e.g., "threads:read")
+    """
+
+    __slots__ = ("user", "permissions")
+
+    def __init__(self, user: User | None = None, permissions: list[str] | None = None):
+        self.user = user
+        self.permissions = permissions or []
+
+    @property
+    def is_authenticated(self) -> bool:
+        """Check if user is authenticated."""
+        return self.user is not None
+
+    def has_permission(self, resource: str, action: str) -> bool:
+        """Check if context has permission for resource:action.
+
+        Args:
+            resource: Resource name (e.g., "threads")
+            action: Action name (e.g., "read")
+
+        Returns:
+            True if user has permission
+        """
+        permission = f"{resource}:{action}"
+        return permission in self.permissions
+
+    def require_user(self) -> User:
+        """Get user or raise 401.
+
+        Raises:
+            HTTPException 401 if not authenticated
+        """
+        if not self.user:
+            raise HTTPException(status_code=401, detail="Authentication required")
+        return self.user
+
+
+def get_auth_context(request: Request) -> AuthContext | None:
+    """Get AuthContext from request state."""
+    return getattr(request.state, "auth", None)
+
+
+_ALL_PERMISSIONS: list[str] = [
+    Permissions.THREADS_READ,
+    Permissions.THREADS_WRITE,
+    Permissions.THREADS_DELETE,
+    Permissions.RUNS_CREATE,
+    Permissions.RUNS_READ,
+    Permissions.RUNS_CANCEL,
+]
+
+
+async def _authenticate(request: Request) -> AuthContext:
+    """Authenticate request and return AuthContext.
+
+    Delegates to deps.get_optional_user_from_request() for the JWT→User pipeline.
+    Returns AuthContext with user=None for anonymous requests.
+    """
+    from app.gateway.deps import get_optional_user_from_request
+
+    user = await get_optional_user_from_request(request)
+    if user is None:
+        return AuthContext(user=None, permissions=[])
+
+    # In future, permissions could be stored in user record
+    return AuthContext(user=user, permissions=_ALL_PERMISSIONS)
+
+
+def require_auth[**P, T](func: Callable[P, T]) -> Callable[P, T]:
+    """Decorator that authenticates the request and sets AuthContext.
+
+    Must be placed ABOVE other decorators (executes after them).
+
+    Usage:
+        @router.get("/{thread_id}")
+        @require_auth  # Bottom decorator (executes first after permission check)
+        @require_permission("threads", "read")
+        async def get_thread(thread_id: str, request: Request):
+            auth: AuthContext = request.state.auth
+            ...
+
+    Raises:
+        ValueError: If 'request' parameter is missing
+    """
+
+    @functools.wraps(func)
+    async def wrapper(*args: Any, **kwargs: Any) -> Any:
+        request = kwargs.get("request")
+        if request is None:
+            raise ValueError("require_auth decorator requires 'request' parameter")
+
+        # Authenticate and set context
+        auth_context = await _authenticate(request)
+        request.state.auth = auth_context
+
+        return await func(*args, **kwargs)
+
+    return wrapper
+
+
+def require_permission(
+    resource: str,
+    action: str,
+    owner_check: bool = False,
+    require_existing: bool = False,
+) -> Callable[[Callable[P, T]], Callable[P, T]]:
+    """Decorator that checks permission for resource:action.
+
+    Must be used AFTER @require_auth.
+
+    Args:
+        resource: Resource name (e.g., "threads", "runs")
+        action: Action name (e.g., "read", "write", "delete")
+        owner_check: If True, validates that the current user owns the resource.
+                     Requires 'thread_id' path parameter and performs ownership check.
+        require_existing: Only meaningful with ``owner_check=True``. If True, a
+                          missing ``threads_meta`` row counts as a denial (404)
+                          instead of "untracked legacy thread, allow". Use on
+                          **destructive / mutating** routes (DELETE, PATCH,
+                          state-update) so a deleted thread can't be re-targeted
+                          by another user via the missing-row code path.
+
+    Usage:
+        # Read-style: legacy untracked threads are allowed
+        @require_permission("threads", "read", owner_check=True)
+        async def get_thread(thread_id: str, request: Request):
+            ...
+
+        # Destructive: thread row MUST exist and be owned by caller
+        @require_permission("threads", "delete", owner_check=True, require_existing=True)
+        async def delete_thread(thread_id: str, request: Request):
+            ...
+
+    Raises:
+        HTTPException 401: If authentication required but user is anonymous
+        HTTPException 403: If user lacks permission
+        HTTPException 404: If owner_check=True but user doesn't own the thread
+        ValueError: If owner_check=True but 'thread_id' parameter is missing
+    """
+
+    def decorator(func: Callable[P, T]) -> Callable[P, T]:
+        @functools.wraps(func)
+        async def wrapper(*args: Any, **kwargs: Any) -> Any:
+            request = kwargs.get("request")
+            if request is None:
+                raise ValueError("require_permission decorator requires 'request' parameter")
+
+            auth: AuthContext = getattr(request.state, "auth", None)
+            if auth is None:
+                auth = await _authenticate(request)
+                request.state.auth = auth
+
+            if not auth.is_authenticated:
+                raise HTTPException(status_code=401, detail="Authentication required")
+
+            # Check permission
+            if not auth.has_permission(resource, action):
+                raise HTTPException(
+                    status_code=403,
+                    detail=f"Permission denied: {resource}:{action}",
+                )
+
+            # Owner check for thread-specific resources.
+            #
+            # 2.0-rc moved thread metadata into the SQL persistence layer
+            # (``threads_meta`` table). We verify ownership via
+            # ``ThreadMetaStore.check_access``: it returns True for
+            # missing rows (untracked legacy thread) and for rows whose
+            # ``user_id`` is NULL (shared / pre-auth data), so this is
+            # strict-deny rather than strict-allow — only an *existing*
+            # row with a *different* user_id triggers 404.
+            if owner_check:
+                thread_id = kwargs.get("thread_id")
+                if thread_id is None:
+                    raise ValueError("require_permission with owner_check=True requires 'thread_id' parameter")
+
+                from app.gateway.deps import get_thread_store
+
+                thread_store = get_thread_store(request)
+                allowed = await thread_store.check_access(
+                    thread_id,
+                    str(auth.user.id),
+                    require_existing=require_existing,
+                )
+                if not allowed:
+                    raise HTTPException(
+                        status_code=404,
+                        detail=f"Thread {thread_id} not found",
+                    )
+
+            return await func(*args, **kwargs)
+
+        return wrapper
+
+    return decorator
@@ -0,0 +1,113 @@
+"""CSRF protection middleware for FastAPI.
+
+Per RFC-001:
+State-changing operations require CSRF protection.
+"""
+
+import secrets
+from collections.abc import Callable
+
+from fastapi import Request, Response
+from starlette.middleware.base import BaseHTTPMiddleware
+from starlette.responses import JSONResponse
+from starlette.types import ASGIApp
+
+CSRF_COOKIE_NAME = "csrf_token"
+CSRF_HEADER_NAME = "X-CSRF-Token"
+CSRF_TOKEN_LENGTH = 64  # bytes
+
+
+def is_secure_request(request: Request) -> bool:
+    """Detect whether the original client request was made over HTTPS."""
+    return request.headers.get("x-forwarded-proto", request.url.scheme) == "https"
+
+
+def generate_csrf_token() -> str:
+    """Generate a secure random CSRF token."""
+    return secrets.token_urlsafe(CSRF_TOKEN_LENGTH)
+
+
+def should_check_csrf(request: Request) -> bool:
+    """Determine if a request needs CSRF validation.
+
+    CSRF is checked for state-changing methods (POST, PUT, DELETE, PATCH).
+    GET, HEAD, OPTIONS, and TRACE are exempt per RFC 7231.
+    """
+    if request.method not in ("POST", "PUT", "DELETE", "PATCH"):
+        return False
+
+    path = request.url.path.rstrip("/")
+    # Exempt /api/v1/auth/me endpoint
+    if path == "/api/v1/auth/me":
+        return False
+    return True
+
+
+_AUTH_EXEMPT_PATHS: frozenset[str] = frozenset(
+    {
+        "/api/v1/auth/login/local",
+        "/api/v1/auth/logout",
+        "/api/v1/auth/register",
+        "/api/v1/auth/initialize",
+    }
+)
+
+
+def is_auth_endpoint(request: Request) -> bool:
+    """Check if the request is to an auth endpoint.
+
+    Auth endpoints don't need CSRF validation on first call (no token).
+    """
+    return request.url.path.rstrip("/") in _AUTH_EXEMPT_PATHS
+
+
+class CSRFMiddleware(BaseHTTPMiddleware):
+    """Middleware that implements CSRF protection using Double Submit Cookie pattern."""
+
+    def __init__(self, app: ASGIApp) -> None:
+        super().__init__(app)
+
+    async def dispatch(self, request: Request, call_next: Callable) -> Response:
+        _is_auth = is_auth_endpoint(request)
+
+        if should_check_csrf(request) and not _is_auth:
+            cookie_token = request.cookies.get(CSRF_COOKIE_NAME)
+            header_token = request.headers.get(CSRF_HEADER_NAME)
+
+            if not cookie_token or not header_token:
+                return JSONResponse(
+                    status_code=403,
+                    content={"detail": "CSRF token missing. Include X-CSRF-Token header."},
+                )
+
+            if not secrets.compare_digest(cookie_token, header_token):
+                return JSONResponse(
+                    status_code=403,
+                    content={"detail": "CSRF token mismatch."},
+                )
+
+        response = await call_next(request)
+
+        # For auth endpoints that set up session, also set CSRF cookie
+        if _is_auth and request.method == "POST":
+            # Generate a new CSRF token for the session
+            csrf_token = generate_csrf_token()
+            is_https = is_secure_request(request)
+            response.set_cookie(
+                key=CSRF_COOKIE_NAME,
+                value=csrf_token,
+                httponly=False,  # Must be JS-readable for Double Submit Cookie pattern
+                secure=is_https,
+                samesite="strict",
+            )
+
+        return response
+
+
+def get_csrf_token(request: Request) -> str | None:
+    """Get the CSRF token from the current request's cookies.
+
+    This is useful for server-side rendering where you need to embed
+    token in forms or headers.
+    """
+    return request.cookies.get(CSRF_COOKIE_NAME)
@@ -10,10 +10,30 @@ from __future__ import annotations

 from collections.abc import AsyncGenerator
 from contextlib import AsyncExitStack, asynccontextmanager
+from typing import TYPE_CHECKING

 from fastapi import FastAPI, HTTPException, Request

-from deerflow.runtime import RunManager, StreamBridge
+from deerflow.config.app_config import AppConfig
+from deerflow.runtime import RunContext, RunManager
+
+if TYPE_CHECKING:
+    from app.gateway.auth.local_provider import LocalAuthProvider
+    from app.gateway.auth.repositories.sqlite import SQLiteUserRepository
+    from deerflow.persistence.thread_meta.base import ThreadMetaStore
+
+
+def get_config(request: Request) -> AppConfig:
+    """FastAPI dependency returning the app-scoped ``AppConfig``.
+
+    Reads from ``request.app.state.config`` which is set at startup
+    (``app.py`` lifespan) and swapped on config reload (``routers/mcp.py``,
+    ``routers/skills.py``).
+    """
+    cfg = getattr(request.app.state, "config", None)
+    if cfg is None:
+        raise HTTPException(status_code=503, detail="Configuration not available")
+    return cfg


@asynccontextmanager
@@ -25,15 +45,54 @@ async def langgraph_runtime(app: FastAPI) -> AsyncGenerator[None, None]:
        async with langgraph_runtime(app):
            yield
    """
-    from deerflow.agents.checkpointer.async_provider import make_checkpointer
+    from deerflow.persistence.engine import close_engine, get_session_factory, init_engine_from_config
    from deerflow.runtime import make_store, make_stream_bridge
+    from deerflow.runtime.checkpointer.async_provider import make_checkpointer
+    from deerflow.runtime.events.store import make_run_event_store

    async with AsyncExitStack() as stack:
-        app.state.stream_bridge = await stack.enter_async_context(make_stream_bridge())
-        app.state.checkpointer = await stack.enter_async_context(make_checkpointer())
-        app.state.store = await stack.enter_async_context(make_store())
-        app.state.run_manager = RunManager()
-        yield
+        # app.state.config is populated earlier in lifespan(); thread it
+        # explicitly into every provider below.
+        config = app.state.config
+
+        app.state.stream_bridge = await stack.enter_async_context(make_stream_bridge(config))
+
+        # Initialize persistence engine BEFORE checkpointer so that
+        # auto-create-database logic runs first (postgres backend).
+        await init_engine_from_config(config.database)
+
+        app.state.checkpointer = await stack.enter_async_context(make_checkpointer(config))
+        app.state.store = await stack.enter_async_context(make_store(config))
+
+        # Initialize repositories — one get_session_factory() call for all.
+        sf = get_session_factory()
+        if sf is not None:
+            from deerflow.persistence.feedback import FeedbackRepository
+            from deerflow.persistence.run import RunRepository
+
+            app.state.run_store = RunRepository(sf)
+            app.state.feedback_repo = FeedbackRepository(sf)
+        else:
+            from deerflow.runtime.runs.store.memory import MemoryRunStore
+
+            app.state.run_store = MemoryRunStore()
+            app.state.feedback_repo = None
+
+        from deerflow.persistence.thread_meta import make_thread_store
+
+        app.state.thread_store = make_thread_store(sf, app.state.store)
+
+        # Run event store (has its own factory with config-driven backend selection)
+        run_events_config = getattr(config, "run_events", None)
+        app.state.run_event_store = make_run_event_store(run_events_config)
+
+        # RunManager with store backing for persistence
+        app.state.run_manager = RunManager(store=app.state.run_store)
+
+        try:
+            yield
+        finally:
+            await close_engine()


 # ---------------------------------------------------------------------------
@@ -41,30 +100,148 @@ async def langgraph_runtime(app: FastAPI) -> AsyncGenerator[None, None]:
 # ---------------------------------------------------------------------------


-def get_stream_bridge(request: Request) -> StreamBridge:
-    """Return the global :class:`StreamBridge`, or 503."""
-    bridge = getattr(request.app.state, "stream_bridge", None)
-    if bridge is None:
-        raise HTTPException(status_code=503, detail="Stream bridge not available")
-    return bridge
+def _require(attr: str, label: str):
+    """Create a FastAPI dependency that returns ``app.state.<attr>`` or 503."""
+
+    def dep(request: Request):
+        val = getattr(request.app.state, attr, None)
+        if val is None:
+            raise HTTPException(status_code=503, detail=f"{label} not available")
+        return val
+
+    dep.__name__ = dep.__qualname__ = f"get_{attr}"
+    return dep


-def get_run_manager(request: Request) -> RunManager:
-    """Return the global :class:`RunManager`, or 503."""
-    mgr = getattr(request.app.state, "run_manager", None)
-    if mgr is None:
-        raise HTTPException(status_code=503, detail="Run manager not available")
-    return mgr
-
-
-def get_checkpointer(request: Request):
-    """Return the global checkpointer, or 503."""
-    cp = getattr(request.app.state, "checkpointer", None)
-    if cp is None:
-        raise HTTPException(status_code=503, detail="Checkpointer not available")
-    return cp
+get_stream_bridge = _require("stream_bridge", "Stream bridge")
+get_run_manager = _require("run_manager", "Run manager")
+get_checkpointer = _require("checkpointer", "Checkpointer")
+get_run_event_store = _require("run_event_store", "Run event store")
+get_feedback_repo = _require("feedback_repo", "Feedback")
+get_run_store = _require("run_store", "Run store")


 def get_store(request: Request):
    """Return the global store (may be ``None`` if not configured)."""
    return getattr(request.app.state, "store", None)
+
+
+def get_thread_store(request: Request) -> ThreadMetaStore:
+    """Return the thread metadata store (SQL or memory-backed)."""
+    val = getattr(request.app.state, "thread_store", None)
+    if val is None:
+        raise HTTPException(status_code=503, detail="Thread metadata store not available")
+    return val
+
+
+def get_run_context(request: Request) -> RunContext:
+    """Build a :class:`RunContext` from ``app.state`` singletons.
+
+    Returns a *base* context with infrastructure dependencies.  Callers that
+    need per-run fields (e.g. ``follow_up_to_run_id``) should use
+    ``dataclasses.replace(ctx, follow_up_to_run_id=...)`` before passing it
+    to :func:`run_agent`.
+    """
+    config = get_config(request)
+    return RunContext(
+        checkpointer=get_checkpointer(request),
+        store=get_store(request),
+        event_store=get_run_event_store(request),
+        run_events_config=getattr(config, "run_events", None),
+        thread_store=get_thread_store(request),
+        app_config=config,
+    )
+
+
+
+# ---------------------------------------------------------------------------
+# Auth helpers (used by authz.py and auth middleware)
+# ---------------------------------------------------------------------------
+
+# Cached singletons to avoid repeated instantiation per request
+_cached_local_provider: LocalAuthProvider | None = None
+_cached_repo: SQLiteUserRepository | None = None
+
+
+def get_local_provider() -> LocalAuthProvider:
+    """Get or create the cached LocalAuthProvider singleton.
+
+    Must be called after ``init_engine_from_config()`` — the shared
+    session factory is required to construct the user repository.
+    """
+    global _cached_local_provider, _cached_repo
+    if _cached_repo is None:
+        from app.gateway.auth.repositories.sqlite import SQLiteUserRepository
+        from deerflow.persistence.engine import get_session_factory
+
+        sf = get_session_factory()
+        if sf is None:
+            raise RuntimeError("get_local_provider() called before init_engine_from_config(); cannot access users table")
+        _cached_repo = SQLiteUserRepository(sf)
+    if _cached_local_provider is None:
+        from app.gateway.auth.local_provider import LocalAuthProvider
+
+        _cached_local_provider = LocalAuthProvider(repository=_cached_repo)
+    return _cached_local_provider
+
+
+async def get_current_user_from_request(request: Request):
+    """Get the current authenticated user from the request cookie.
+
+    Raises HTTPException 401 if not authenticated.
+    """
+    from app.gateway.auth import decode_token
+    from app.gateway.auth.errors import AuthErrorCode, AuthErrorResponse, TokenError, token_error_to_code
+
+    access_token = request.cookies.get("access_token")
+    if not access_token:
+        raise HTTPException(
+            status_code=401,
+            detail=AuthErrorResponse(code=AuthErrorCode.NOT_AUTHENTICATED, message="Not authenticated").model_dump(),
+        )
+
+    payload = decode_token(access_token)
+    if isinstance(payload, TokenError):
+        raise HTTPException(
+            status_code=401,
+            detail=AuthErrorResponse(code=token_error_to_code(payload), message=f"Token error: {payload.value}").model_dump(),
+        )
+
+    provider = get_local_provider()
+    user = await provider.get_user(payload.sub)
+    if user is None:
+        raise HTTPException(
+            status_code=401,
+            detail=AuthErrorResponse(code=AuthErrorCode.USER_NOT_FOUND, message="User not found").model_dump(),
+        )
+
+    # Token version mismatch → password was changed, token is stale
+    if user.token_version != payload.ver:
+        raise HTTPException(
+            status_code=401,
+            detail=AuthErrorResponse(code=AuthErrorCode.TOKEN_INVALID, message="Token revoked (password changed)").model_dump(),
+        )
+
+    return user
+
+
+async def get_optional_user_from_request(request: Request):
+    """Get optional authenticated user from request.
+
+    Returns None if not authenticated.
+    """
+    try:
+        return await get_current_user_from_request(request)
+    except HTTPException:
+        return None
+
+
+async def get_current_user(request: Request) -> str | None:
+    """Extract user_id from request cookie, or None if not authenticated.
+
+    Thin adapter that returns the string id for callers that only need
+    identification (e.g., ``feedback.py``). Full-user callers should use
+    ``get_current_user_from_request`` or ``get_optional_user_from_request``.
+    """
+    user = await get_optional_user_from_request(request)
+    return str(user.id) if user else None
@@ -0,0 +1,106 @@
+"""LangGraph Server auth handler — shares JWT logic with Gateway.
+
+Loaded by LangGraph Server via langgraph.json ``auth.path``.
+Reuses the same ``decode_token`` / ``get_auth_config`` as Gateway,
+so both modes validate tokens with the same secret and rules.
+
+Two layers:
+  1. @auth.authenticate — validates JWT cookie, extracts user_id,
+     and enforces CSRF on state-changing methods (POST/PUT/DELETE/PATCH)
+  2. @auth.on — returns metadata filter so each user only sees own threads
+"""
+
+import secrets
+
+from langgraph_sdk import Auth
+
+from app.gateway.auth.errors import TokenError
+from app.gateway.auth.jwt import decode_token
+from app.gateway.deps import get_local_provider
+
+auth = Auth()
+
+# Methods that require CSRF validation (state-changing per RFC 7231).
+_CSRF_METHODS = frozenset({"POST", "PUT", "DELETE", "PATCH"})
+
+
+def _check_csrf(request) -> None:
+    """Enforce Double Submit Cookie CSRF check for state-changing requests.
+
+    Mirrors Gateway's CSRFMiddleware logic so that LangGraph routes
+    proxied directly by nginx have the same CSRF protection.
+    """
+    method = getattr(request, "method", "") or ""
+    if method.upper() not in _CSRF_METHODS:
+        return
+
+    cookie_token = request.cookies.get("csrf_token")
+    header_token = request.headers.get("x-csrf-token")
+
+    if not cookie_token or not header_token:
+        raise Auth.exceptions.HTTPException(
+            status_code=403,
+            detail="CSRF token missing. Include X-CSRF-Token header.",
+        )
+
+    if not secrets.compare_digest(cookie_token, header_token):
+        raise Auth.exceptions.HTTPException(
+            status_code=403,
+            detail="CSRF token mismatch.",
+        )
+
+
+@auth.authenticate
+async def authenticate(request):
+    """Validate the session cookie, decode JWT, and check token_version.
+
+    Same validation chain as Gateway's get_current_user_from_request:
+      cookie → decode JWT → DB lookup → token_version match
+    Also enforces CSRF on state-changing methods.
+    """
+    # CSRF check before authentication so forged cross-site requests
+    # are rejected early, even if the cookie carries a valid JWT.
+    _check_csrf(request)
+
+    token = request.cookies.get("access_token")
+    if not token:
+        raise Auth.exceptions.HTTPException(
+            status_code=401,
+            detail="Not authenticated",
+        )
+
+    payload = decode_token(token)
+    if isinstance(payload, TokenError):
+        raise Auth.exceptions.HTTPException(
+            status_code=401,
+            detail=f"Token error: {payload.value}",
+        )
+
+    user = await get_local_provider().get_user(payload.sub)
+    if user is None:
+        raise Auth.exceptions.HTTPException(
+            status_code=401,
+            detail="User not found",
+        )
+    if user.token_version != payload.ver:
+        raise Auth.exceptions.HTTPException(
+            status_code=401,
+            detail="Token revoked (password changed)",
+        )
+
+    return payload.sub
+
+
+@auth.on
+async def add_owner_filter(ctx: Auth.types.AuthContext, value: dict):
+    """Inject user_id metadata on writes; filter by user_id on reads.
+
+    Gateway stores thread ownership as ``metadata.user_id``.
+    This handler ensures LangGraph Server enforces the same isolation.
+    """
+    # On create/update: stamp user_id into metadata
+    metadata = value.setdefault("metadata", {})
+    metadata["user_id"] = ctx.user.identity
+
+    # Return filter dict — LangGraph applies it to search/read/delete
+    return {"user_id": ctx.user.identity}
@@ -5,6 +5,7 @@ from pathlib import Path
 from fastapi import HTTPException

 from deerflow.config.paths import get_paths
+from deerflow.runtime.user_context import get_effective_user_id


 def resolve_thread_virtual_path(thread_id: str, virtual_path: str) -> Path:
@@ -22,7 +23,7 @@ def resolve_thread_virtual_path(thread_id: str, virtual_path: str) -> Path:
        HTTPException: If the path is invalid or outside allowed directories.
    """
    try:
-        return get_paths().resolve_virtual_path(thread_id, virtual_path)
+        return get_paths().resolve_virtual_path(thread_id, virtual_path, user_id=get_effective_user_id())
    except ValueError as e:
        status = 403 if "traversal" in str(e) else 400
        raise HTTPException(status_code=status, detail=str(e))
@@ -5,10 +5,12 @@ import re
 import shutil

 import yaml
-from fastapi import APIRouter, HTTPException
+from fastapi import APIRouter, Depends, HTTPException
 from pydantic import BaseModel, Field

+from app.gateway.deps import get_config
 from deerflow.config.agents_config import AgentConfig, list_custom_agents, load_agent_config, load_agent_soul
+from deerflow.config.app_config import AppConfig
 from deerflow.config.paths import get_paths

 logger = logging.getLogger(__name__)
@@ -24,6 +26,7 @@ class AgentResponse(BaseModel):
    description: str = Field(default="", description="Agent description")
    model: str | None = Field(default=None, description="Optional model override")
    tool_groups: list[str] | None = Field(default=None, description="Optional tool group whitelist")
+    skills: list[str] | None = Field(default=None, description="Optional skill whitelist (None=all, []=none)")
    soul: str | None = Field(default=None, description="SOUL.md content")


@@ -40,6 +43,7 @@ class AgentCreateRequest(BaseModel):
    description: str = Field(default="", description="Agent description")
    model: str | None = Field(default=None, description="Optional model override")
    tool_groups: list[str] | None = Field(default=None, description="Optional tool group whitelist")
+    skills: list[str] | None = Field(default=None, description="Optional skill whitelist (None=all enabled, []=none)")
    soul: str = Field(default="", description="SOUL.md content — agent personality and behavioral guardrails")


@@ -49,6 +53,7 @@ class AgentUpdateRequest(BaseModel):
    description: str | None = Field(default=None, description="Updated description")
    model: str | None = Field(default=None, description="Updated model override")
    tool_groups: list[str] | None = Field(default=None, description="Updated tool group whitelist")
+    skills: list[str] | None = Field(default=None, description="Updated skill whitelist (None=all, []=none)")
    soul: str | None = Field(default=None, description="Updated SOUL.md content")


@@ -73,6 +78,15 @@ def _normalize_agent_name(name: str) -> str:
    return name.lower()


+def _require_agents_api_enabled(app_config: AppConfig) -> None:
+    """Reject access unless the custom-agent management API is explicitly enabled."""
+    if not app_config.agents_api.enabled:
+        raise HTTPException(
+            status_code=403,
+            detail=("Custom-agent management API is disabled. Set agents_api.enabled=true to expose agent and user-profile routes over HTTP."),
+        )
+
+
 def _agent_config_to_response(agent_cfg: AgentConfig, include_soul: bool = False) -> AgentResponse:
    """Convert AgentConfig to AgentResponse."""
    soul: str | None = None
@@ -84,6 +98,7 @@ def _agent_config_to_response(agent_cfg: AgentConfig, include_soul: bool = False
        description=agent_cfg.description,
        model=agent_cfg.model,
        tool_groups=agent_cfg.tool_groups,
+        skills=agent_cfg.skills,
        soul=soul,
    )

@@ -94,12 +109,14 @@ def _agent_config_to_response(agent_cfg: AgentConfig, include_soul: bool = False
    summary="List Custom Agents",
    description="List all custom agents available in the agents directory, including their soul content.",
 )
-async def list_agents() -> AgentsListResponse:
+async def list_agents(app_config: AppConfig = Depends(get_config)) -> AgentsListResponse:
    """List all custom agents.

    Returns:
        List of all custom agents with their metadata and soul content.
    """
+    _require_agents_api_enabled(app_config)
+
    try:
        agents = list_custom_agents()
        return AgentsListResponse(agents=[_agent_config_to_response(a, include_soul=True) for a in agents])
@@ -125,6 +142,7 @@ async def check_agent_name(name: str) -> dict:
    Raises:
        HTTPException: 422 if the name is invalid.
    """
+    _require_agents_api_enabled(app_config)
    _validate_agent_name(name)
    normalized = _normalize_agent_name(name)
    available = not get_paths().agent_dir(normalized).exists()
@@ -137,7 +155,7 @@ async def check_agent_name(name: str) -> dict:
    summary="Get Custom Agent",
    description="Retrieve details and SOUL.md content for a specific custom agent.",
 )
-async def get_agent(name: str) -> AgentResponse:
+async def get_agent(name: str, app_config: AppConfig = Depends(get_config)) -> AgentResponse:
    """Get a specific custom agent by name.

    Args:
@@ -149,6 +167,7 @@ async def get_agent(name: str) -> AgentResponse:
    Raises:
        HTTPException: 404 if agent not found.
    """
+    _require_agents_api_enabled(app_config)
    _validate_agent_name(name)
    name = _normalize_agent_name(name)

@@ -169,7 +188,7 @@ async def get_agent(name: str) -> AgentResponse:
    summary="Create Custom Agent",
    description="Create a new custom agent with its config and SOUL.md.",
 )
-async def create_agent_endpoint(request: AgentCreateRequest) -> AgentResponse:
+async def create_agent_endpoint(request: AgentCreateRequest, app_config: AppConfig = Depends(get_config)) -> AgentResponse:
    """Create a new custom agent.

    Args:
@@ -181,6 +200,7 @@ async def create_agent_endpoint(request: AgentCreateRequest) -> AgentResponse:
    Raises:
        HTTPException: 409 if agent already exists, 422 if name is invalid.
    """
+    _require_agents_api_enabled(app_config)
    _validate_agent_name(request.name)
    normalized_name = _normalize_agent_name(request.name)

@@ -200,6 +220,8 @@ async def create_agent_endpoint(request: AgentCreateRequest) -> AgentResponse:
            config_data["model"] = request.model
        if request.tool_groups is not None:
            config_data["tool_groups"] = request.tool_groups
+        if request.skills is not None:
+            config_data["skills"] = request.skills

        config_file = agent_dir / "config.yaml"
        with open(config_file, "w", encoding="utf-8") as f:
@@ -230,7 +252,7 @@ async def create_agent_endpoint(request: AgentCreateRequest) -> AgentResponse:
    summary="Update Custom Agent",
    description="Update an existing custom agent's config and/or SOUL.md.",
 )
-async def update_agent(name: str, request: AgentUpdateRequest) -> AgentResponse:
+async def update_agent(name: str, request: AgentUpdateRequest, app_config: AppConfig = Depends(get_config)) -> AgentResponse:
    """Update an existing custom agent.

    Args:
@@ -243,6 +265,7 @@ async def update_agent(name: str, request: AgentUpdateRequest) -> AgentResponse:
    Raises:
        HTTPException: 404 if agent not found.
    """
+    _require_agents_api_enabled(app_config)
    _validate_agent_name(name)
    name = _normalize_agent_name(name)

@@ -255,21 +278,32 @@ async def update_agent(name: str, request: AgentUpdateRequest) -> AgentResponse:

    try:
        # Update config if any config fields changed
-        config_changed = any(v is not None for v in [request.description, request.model, request.tool_groups])
+        # Use model_fields_set to distinguish "field omitted" from "explicitly set to null".
+        # This is critical for skills where None means "inherit all" (not "don't change").
+        fields_set = request.model_fields_set
+        config_changed = bool(fields_set & {"description", "model", "tool_groups", "skills"})

        if config_changed:
            updated: dict = {
                "name": agent_cfg.name,
-                "description": request.description if request.description is not None else agent_cfg.description,
+                "description": request.description if "description" in fields_set else agent_cfg.description,
            }
-            new_model = request.model if request.model is not None else agent_cfg.model
+            new_model = request.model if "model" in fields_set else agent_cfg.model
            if new_model is not None:
                updated["model"] = new_model

-            new_tool_groups = request.tool_groups if request.tool_groups is not None else agent_cfg.tool_groups
+            new_tool_groups = request.tool_groups if "tool_groups" in fields_set else agent_cfg.tool_groups
            if new_tool_groups is not None:
                updated["tool_groups"] = new_tool_groups

+            # skills: None = inherit all, [] = no skills, ["a","b"] = whitelist
+            if "skills" in fields_set:
+                new_skills = request.skills
+            else:
+                new_skills = agent_cfg.skills
+            if new_skills is not None:
+                updated["skills"] = new_skills
+
            config_file = agent_dir / "config.yaml"
            with open(config_file, "w", encoding="utf-8") as f:
                yaml.dump(updated, f, default_flow_style=False, allow_unicode=True)
@@ -309,12 +343,14 @@ class UserProfileUpdateRequest(BaseModel):
    summary="Get User Profile",
    description="Read the global USER.md file that is injected into all custom agents.",
 )
-async def get_user_profile() -> UserProfileResponse:
+async def get_user_profile(app_config: AppConfig = Depends(get_config)) -> UserProfileResponse:
    """Return the current USER.md content.

    Returns:
        UserProfileResponse with content=None if USER.md does not exist yet.
    """
+    _require_agents_api_enabled(app_config)
+
    try:
        user_md_path = get_paths().user_md_file
        if not user_md_path.exists():
@@ -332,7 +368,7 @@ async def get_user_profile() -> UserProfileResponse:
    summary="Update User Profile",
    description="Write the global USER.md file that is injected into all custom agents.",
 )
-async def update_user_profile(request: UserProfileUpdateRequest) -> UserProfileResponse:
+async def update_user_profile(request: UserProfileUpdateRequest, app_config: AppConfig = Depends(get_config)) -> UserProfileResponse:
    """Create or overwrite the global USER.md.

    Args:
@@ -341,6 +377,8 @@ async def update_user_profile(request: UserProfileUpdateRequest) -> UserProfileR
    Returns:
        UserProfileResponse with the saved content.
    """
+    _require_agents_api_enabled(app_config)
+
    try:
        paths = get_paths()
        paths.base_dir.mkdir(parents=True, exist_ok=True)
@@ -358,7 +396,7 @@ async def update_user_profile(request: UserProfileUpdateRequest) -> UserProfileR
    summary="Delete Custom Agent",
    description="Delete a custom agent and all its files (config, SOUL.md, memory).",
 )
-async def delete_agent(name: str) -> None:
+async def delete_agent(name: str, app_config: AppConfig = Depends(get_config)) -> None:
    """Delete a custom agent.

    Args:
@@ -367,6 +405,7 @@ async def delete_agent(name: str) -> None:
    Raises:
        HTTPException: 404 if agent not found.
    """
+    _require_agents_api_enabled(app_config)
    _validate_agent_name(name)
    name = _normalize_agent_name(name)

@@ -7,6 +7,7 @@ from urllib.parse import quote
 from fastapi import APIRouter, HTTPException, Request
 from fastapi.responses import FileResponse, PlainTextResponse, Response

+from app.gateway.authz import require_permission
 from app.gateway.path_utils import resolve_thread_virtual_path

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

@@ -0,0 +1,459 @@
+"""Authentication endpoints."""
+
+import logging
+import os
+import time
+from ipaddress import ip_address, ip_network
+
+from fastapi import APIRouter, Depends, HTTPException, Request, Response, status
+from fastapi.security import OAuth2PasswordRequestForm
+from pydantic import BaseModel, EmailStr, Field, field_validator
+
+from app.gateway.auth import (
+    UserResponse,
+    create_access_token,
+)
+from app.gateway.auth.config import get_auth_config
+from app.gateway.auth.errors import AuthErrorCode, AuthErrorResponse
+from app.gateway.csrf_middleware import is_secure_request
+from app.gateway.deps import get_current_user_from_request, get_local_provider
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/api/v1/auth", tags=["auth"])
+
+
+# ── Request/Response Models ──────────────────────────────────────────────
+
+
+class LoginResponse(BaseModel):
+    """Response model for login — token only lives in HttpOnly cookie."""
+
+    expires_in: int  # seconds
+    needs_setup: bool = False
+
+
+# Top common-password blocklist. Drawn from the public SecLists "10k worst
+# passwords" set, lowercased + length>=8 only (shorter ones already fail
+# the min_length check). Kept tight on purpose: this is the **lower bound**
+# defense, not a full HIBP / passlib check, and runs in-process per request.
+_COMMON_PASSWORDS: frozenset[str] = frozenset(
+    {
+        "password",
+        "password1",
+        "password12",
+        "password123",
+        "password1234",
+        "12345678",
+        "123456789",
+        "1234567890",
+        "qwerty12",
+        "qwertyui",
+        "qwerty123",
+        "abc12345",
+        "abcd1234",
+        "iloveyou",
+        "letmein1",
+        "welcome1",
+        "welcome123",
+        "admin123",
+        "administrator",
+        "passw0rd",
+        "p@ssw0rd",
+        "monkey12",
+        "trustno1",
+        "sunshine",
+        "princess",
+        "football",
+        "baseball",
+        "superman",
+        "batman123",
+        "starwars",
+        "dragon123",
+        "master123",
+        "shadow12",
+        "michael1",
+        "jennifer",
+        "computer",
+    }
+)
+
+
+def _password_is_common(password: str) -> bool:
+    """Case-insensitive blocklist check.
+
+    Lowercases the input so trivial mutations like ``Password`` /
+    ``PASSWORD`` are also rejected. Does not normalize digit substitutions
+    (``p@ssw0rd`` is included as a literal entry instead) — keeping the
+    rule cheap and predictable.
+    """
+    return password.lower() in _COMMON_PASSWORDS
+
+
+def _validate_strong_password(value: str) -> str:
+    """Pydantic field-validator body shared by Register + ChangePassword.
+
+    Constraint = function, not type-level mixin. The two request models
+    have no "is-a" relationship; they only share the password-strength
+    rule. Lifting it into a free function lets each model bind it via
+    ``@field_validator(field_name)`` without inheritance gymnastics.
+    """
+    if _password_is_common(value):
+        raise ValueError("Password is too common; choose a stronger password.")
+    return value
+
+
+class RegisterRequest(BaseModel):
+    """Request model for user registration."""
+
+    email: EmailStr
+    password: str = Field(..., min_length=8)
+
+    _strong_password = field_validator("password")(classmethod(lambda cls, v: _validate_strong_password(v)))
+
+
+class ChangePasswordRequest(BaseModel):
+    """Request model for password change (also handles setup flow)."""
+
+    current_password: str
+    new_password: str = Field(..., min_length=8)
+    new_email: EmailStr | None = None
+
+    _strong_password = field_validator("new_password")(classmethod(lambda cls, v: _validate_strong_password(v)))
+
+
+class MessageResponse(BaseModel):
+    """Generic message response."""
+
+    message: str
+
+
+# ── Helpers ───────────────────────────────────────────────────────────────
+
+
+def _set_session_cookie(response: Response, token: str, request: Request) -> None:
+    """Set the access_token HttpOnly cookie on the response."""
+    config = get_auth_config()
+    is_https = is_secure_request(request)
+    response.set_cookie(
+        key="access_token",
+        value=token,
+        httponly=True,
+        secure=is_https,
+        samesite="lax",
+        max_age=config.token_expiry_days * 24 * 3600 if is_https else None,
+    )
+
+
+# ── Rate Limiting ────────────────────────────────────────────────────────
+# In-process dict — not shared across workers. Sufficient for single-worker deployments.
+
+_MAX_LOGIN_ATTEMPTS = 5
+_LOCKOUT_SECONDS = 300  # 5 minutes
+
+# ip → (fail_count, lock_until_timestamp)
+_login_attempts: dict[str, tuple[int, float]] = {}
+
+
+def _trusted_proxies() -> list:
+    """Parse ``AUTH_TRUSTED_PROXIES`` env var into a list of ip_network objects.
+
+    Comma-separated CIDR or single-IP entries. Empty / unset = no proxy is
+    trusted (direct mode). Invalid entries are skipped with a logger warning.
+    Read live so env-var overrides take effect immediately and tests can
+    ``monkeypatch.setenv`` without poking a module-level cache.
+    """
+    raw = os.getenv("AUTH_TRUSTED_PROXIES", "").strip()
+    if not raw:
+        return []
+    nets = []
+    for entry in raw.split(","):
+        entry = entry.strip()
+        if not entry:
+            continue
+        try:
+            nets.append(ip_network(entry, strict=False))
+        except ValueError:
+            logger.warning("AUTH_TRUSTED_PROXIES: ignoring invalid entry %r", entry)
+    return nets
+
+
+def _get_client_ip(request: Request) -> str:
+    """Extract the real client IP for rate limiting.
+
+    Trust model:
+
+    - The TCP peer (``request.client.host``) is always the baseline. It is
+      whatever the kernel reports as the connecting socket — unforgeable
+      by the client itself.
+    - ``X-Real-IP`` is **only** honored if the TCP peer is in the
+      ``AUTH_TRUSTED_PROXIES`` allowlist (set via env var, comma-separated
+      CIDR or single IPs). When set, the gateway is assumed to be behind a
+      reverse proxy (nginx, Cloudflare, ALB, …) that overwrites
+      ``X-Real-IP`` with the original client address.
+    - With no ``AUTH_TRUSTED_PROXIES`` set, ``X-Real-IP`` is silently
+      ignored — closing the bypass where any client could rotate the
+      header to dodge per-IP rate limits in dev / direct-gateway mode.
+
+    ``X-Forwarded-For`` is intentionally NOT used because it is naturally
+    client-controlled at the *first* hop and the trust chain is harder to
+    audit per-request.
+    """
+    peer_host = request.client.host if request.client else None
+
+    trusted = _trusted_proxies()
+    if trusted and peer_host:
+        try:
+            peer_ip = ip_address(peer_host)
+            if any(peer_ip in net for net in trusted):
+                real_ip = request.headers.get("x-real-ip", "").strip()
+                if real_ip:
+                    return real_ip
+        except ValueError:
+            # peer_host wasn't a parseable IP (e.g. "unknown") — fall through
+            pass
+
+    return peer_host or "unknown"
+
+
+def _check_rate_limit(ip: str) -> None:
+    """Raise 429 if the IP is currently locked out."""
+    record = _login_attempts.get(ip)
+    if record is None:
+        return
+    fail_count, lock_until = record
+    if fail_count >= _MAX_LOGIN_ATTEMPTS:
+        if time.time() < lock_until:
+            raise HTTPException(
+                status_code=429,
+                detail="Too many login attempts. Try again later.",
+            )
+        del _login_attempts[ip]
+
+
+_MAX_TRACKED_IPS = 10000
+
+
+def _record_login_failure(ip: str) -> None:
+    """Record a failed login attempt for the given IP."""
+    # Evict expired lockouts when dict grows too large
+    if len(_login_attempts) >= _MAX_TRACKED_IPS:
+        now = time.time()
+        expired = [k for k, (c, t) in _login_attempts.items() if c >= _MAX_LOGIN_ATTEMPTS and now >= t]
+        for k in expired:
+            del _login_attempts[k]
+        # If still too large, evict cheapest-to-lose half: below-threshold
+        # IPs (lock_until=0.0) sort first, then earliest-expiring lockouts.
+        if len(_login_attempts) >= _MAX_TRACKED_IPS:
+            by_time = sorted(_login_attempts.items(), key=lambda kv: kv[1][1])
+            for k, _ in by_time[: len(by_time) // 2]:
+                del _login_attempts[k]
+
+    record = _login_attempts.get(ip)
+    if record is None:
+        _login_attempts[ip] = (1, 0.0)
+    else:
+        new_count = record[0] + 1
+        lock_until = time.time() + _LOCKOUT_SECONDS if new_count >= _MAX_LOGIN_ATTEMPTS else 0.0
+        _login_attempts[ip] = (new_count, lock_until)
+
+
+def _record_login_success(ip: str) -> None:
+    """Clear failure counter for the given IP on successful login."""
+    _login_attempts.pop(ip, None)
+
+
+# ── Endpoints ─────────────────────────────────────────────────────────────
+
+
+@router.post("/login/local", response_model=LoginResponse)
+async def login_local(
+    request: Request,
+    response: Response,
+    form_data: OAuth2PasswordRequestForm = Depends(),
+):
+    """Local email/password login."""
+    client_ip = _get_client_ip(request)
+    _check_rate_limit(client_ip)
+
+    user = await get_local_provider().authenticate({"email": form_data.username, "password": form_data.password})
+
+    if user is None:
+        _record_login_failure(client_ip)
+        raise HTTPException(
+            status_code=status.HTTP_401_UNAUTHORIZED,
+            detail=AuthErrorResponse(code=AuthErrorCode.INVALID_CREDENTIALS, message="Incorrect email or password").model_dump(),
+        )
+
+    _record_login_success(client_ip)
+    token = create_access_token(str(user.id), token_version=user.token_version)
+    _set_session_cookie(response, token, request)
+
+    return LoginResponse(
+        expires_in=get_auth_config().token_expiry_days * 24 * 3600,
+        needs_setup=user.needs_setup,
+    )
+
+
+@router.post("/register", response_model=UserResponse, status_code=status.HTTP_201_CREATED)
+async def register(request: Request, response: Response, body: RegisterRequest):
+    """Register a new user account (always 'user' role).
+
+    Admin is auto-created on first boot. This endpoint creates regular users.
+    Auto-login by setting the session cookie.
+    """
+    try:
+        user = await get_local_provider().create_user(email=body.email, password=body.password, system_role="user")
+    except ValueError:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=AuthErrorResponse(code=AuthErrorCode.EMAIL_ALREADY_EXISTS, message="Email already registered").model_dump(),
+        )
+
+    token = create_access_token(str(user.id), token_version=user.token_version)
+    _set_session_cookie(response, token, request)
+
+    return UserResponse(id=str(user.id), email=user.email, system_role=user.system_role)
+
+
+@router.post("/logout", response_model=MessageResponse)
+async def logout(request: Request, response: Response):
+    """Logout current user by clearing the cookie."""
+    response.delete_cookie(key="access_token", secure=is_secure_request(request), samesite="lax")
+    return MessageResponse(message="Successfully logged out")
+
+
+@router.post("/change-password", response_model=MessageResponse)
+async def change_password(request: Request, response: Response, body: ChangePasswordRequest):
+    """Change password for the currently authenticated user.
+
+    Also handles the first-boot setup flow:
+    - If new_email is provided, updates email (checks uniqueness)
+    - If user.needs_setup is True and new_email is given, clears needs_setup
+    - Always increments token_version to invalidate old sessions
+    - Re-issues session cookie with new token_version
+    """
+    from app.gateway.auth.password import hash_password_async, verify_password_async
+
+    user = await get_current_user_from_request(request)
+
+    if user.password_hash is None:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=AuthErrorResponse(code=AuthErrorCode.INVALID_CREDENTIALS, message="OAuth users cannot change password").model_dump())
+
+    if not await verify_password_async(body.current_password, user.password_hash):
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=AuthErrorResponse(code=AuthErrorCode.INVALID_CREDENTIALS, message="Current password is incorrect").model_dump())
+
+    provider = get_local_provider()
+
+    # Update email if provided
+    if body.new_email is not None:
+        existing = await provider.get_user_by_email(body.new_email)
+        if existing and str(existing.id) != str(user.id):
+            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=AuthErrorResponse(code=AuthErrorCode.EMAIL_ALREADY_EXISTS, message="Email already in use").model_dump())
+        user.email = body.new_email
+
+    # Update password + bump version
+    user.password_hash = await hash_password_async(body.new_password)
+    user.token_version += 1
+
+    # Clear setup flag if this is the setup flow
+    if user.needs_setup and body.new_email is not None:
+        user.needs_setup = False
+
+    await provider.update_user(user)
+
+    # Re-issue cookie with new token_version
+    token = create_access_token(str(user.id), token_version=user.token_version)
+    _set_session_cookie(response, token, request)
+
+    return MessageResponse(message="Password changed successfully")
+
+
+@router.get("/me", response_model=UserResponse)
+async def get_me(request: Request):
+    """Get current authenticated user info."""
+    user = await get_current_user_from_request(request)
+    return UserResponse(id=str(user.id), email=user.email, system_role=user.system_role, needs_setup=user.needs_setup)
+
+
+@router.get("/setup-status")
+async def setup_status():
+    """Check if an admin account exists. Returns needs_setup=True when no admin exists."""
+    admin_count = await get_local_provider().count_admin_users()
+    return {"needs_setup": admin_count == 0}
+
+
+class InitializeAdminRequest(BaseModel):
+    """Request model for first-boot admin account creation."""
+
+    email: EmailStr
+    password: str = Field(..., min_length=8)
+
+    _strong_password = field_validator("password")(classmethod(lambda cls, v: _validate_strong_password(v)))
+
+
+@router.post("/initialize", response_model=UserResponse, status_code=status.HTTP_201_CREATED)
+async def initialize_admin(request: Request, response: Response, body: InitializeAdminRequest):
+    """Create the first admin account on initial system setup.
+
+    Only callable when no admin exists. Returns 409 Conflict if an admin
+    already exists.
+
+    On success, the admin account is created with ``needs_setup=False`` and
+    the session cookie is set.
+    """
+    admin_count = await get_local_provider().count_admin_users()
+    if admin_count > 0:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=AuthErrorResponse(code=AuthErrorCode.SYSTEM_ALREADY_INITIALIZED, message="System already initialized").model_dump(),
+        )
+
+    try:
+        user = await get_local_provider().create_user(email=body.email, password=body.password, system_role="admin", needs_setup=False)
+    except ValueError:
+        # DB unique-constraint race: another concurrent request beat us.
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=AuthErrorResponse(code=AuthErrorCode.SYSTEM_ALREADY_INITIALIZED, message="System already initialized").model_dump(),
+        )
+
+    token = create_access_token(str(user.id), token_version=user.token_version)
+    _set_session_cookie(response, token, request)
+
+    return UserResponse(id=str(user.id), email=user.email, system_role=user.system_role)
+
+
+# ── OAuth Endpoints (Future/Placeholder) ─────────────────────────────────
+
+
+@router.get("/oauth/{provider}")
+async def oauth_login(provider: str):
+    """Initiate OAuth login flow.
+
+    Redirects to the OAuth provider's authorization URL.
+    Currently a placeholder - requires OAuth provider implementation.
+    """
+    if provider not in ["github", "google"]:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=f"Unsupported OAuth provider: {provider}",
+        )
+
+    raise HTTPException(
+        status_code=status.HTTP_501_NOT_IMPLEMENTED,
+        detail="OAuth login not yet implemented",
+    )
+
+
+@router.get("/callback/{provider}")
+async def oauth_callback(provider: str, code: str, state: str):
+    """OAuth callback endpoint.
+
+    Handles the OAuth provider's callback after user authorization.
+    Currently a placeholder.
+    """
+    raise HTTPException(
+        status_code=status.HTTP_501_NOT_IMPLEMENTED,
+        detail="OAuth callback not yet implemented",
+    )
@@ -0,0 +1,188 @@
+"""Feedback endpoints — create, list, stats, delete.
+
+Allows users to submit thumbs-up/down feedback on runs,
+optionally scoped to a specific message.
+"""
+
+from __future__ import annotations
+
+import logging
+from typing import Any
+
+from fastapi import APIRouter, HTTPException, Request
+from pydantic import BaseModel, Field
+
+from app.gateway.authz import require_permission
+from app.gateway.deps import get_current_user, get_feedback_repo, get_run_store
+
+logger = logging.getLogger(__name__)
+router = APIRouter(prefix="/api/threads", tags=["feedback"])
+
+
+# ---------------------------------------------------------------------------
+# Request / response models
+# ---------------------------------------------------------------------------
+
+
+class FeedbackCreateRequest(BaseModel):
+    rating: int = Field(..., description="Feedback rating: +1 (positive) or -1 (negative)")
+    comment: str | None = Field(default=None, description="Optional text feedback")
+    message_id: str | None = Field(default=None, description="Optional: scope feedback to a specific message")
+
+
+class FeedbackUpsertRequest(BaseModel):
+    rating: int = Field(..., description="Feedback rating: +1 (positive) or -1 (negative)")
+    comment: str | None = Field(default=None, description="Optional text feedback")
+
+
+class FeedbackResponse(BaseModel):
+    feedback_id: str
+    run_id: str
+    thread_id: str
+    user_id: str | None = None
+    message_id: str | None = None
+    rating: int
+    comment: str | None = None
+    created_at: str = ""
+
+
+class FeedbackStatsResponse(BaseModel):
+    run_id: str
+    total: int = 0
+    positive: int = 0
+    negative: int = 0
+
+
+# ---------------------------------------------------------------------------
+# Endpoints
+# ---------------------------------------------------------------------------
+
+
+@router.put("/{thread_id}/runs/{run_id}/feedback", response_model=FeedbackResponse)
+@require_permission("threads", "write", owner_check=True, require_existing=True)
+async def upsert_feedback(
+    thread_id: str,
+    run_id: str,
+    body: FeedbackUpsertRequest,
+    request: Request,
+) -> dict[str, Any]:
+    """Create or update feedback for a run (idempotent)."""
+    if body.rating not in (1, -1):
+        raise HTTPException(status_code=400, detail="rating must be +1 or -1")
+
+    user_id = await get_current_user(request)
+
+    run_store = get_run_store(request)
+    run = await run_store.get(run_id)
+    if run is None:
+        raise HTTPException(status_code=404, detail=f"Run {run_id} not found")
+    if run.get("thread_id") != thread_id:
+        raise HTTPException(status_code=404, detail=f"Run {run_id} not found in thread {thread_id}")
+
+    feedback_repo = get_feedback_repo(request)
+    return await feedback_repo.upsert(
+        run_id=run_id,
+        thread_id=thread_id,
+        rating=body.rating,
+        user_id=user_id,
+        comment=body.comment,
+    )
+
+
+@router.delete("/{thread_id}/runs/{run_id}/feedback")
+@require_permission("threads", "delete", owner_check=True, require_existing=True)
+async def delete_run_feedback(
+    thread_id: str,
+    run_id: str,
+    request: Request,
+) -> dict[str, bool]:
+    """Delete the current user's feedback for a run."""
+    user_id = await get_current_user(request)
+    feedback_repo = get_feedback_repo(request)
+    deleted = await feedback_repo.delete_by_run(
+        thread_id=thread_id,
+        run_id=run_id,
+        user_id=user_id,
+    )
+    if not deleted:
+        raise HTTPException(status_code=404, detail="No feedback found for this run")
+    return {"success": True}
+
+
+@router.post("/{thread_id}/runs/{run_id}/feedback", response_model=FeedbackResponse)
+@require_permission("threads", "write", owner_check=True, require_existing=True)
+async def create_feedback(
+    thread_id: str,
+    run_id: str,
+    body: FeedbackCreateRequest,
+    request: Request,
+) -> dict[str, Any]:
+    """Submit feedback (thumbs-up/down) for a run."""
+    if body.rating not in (1, -1):
+        raise HTTPException(status_code=400, detail="rating must be +1 or -1")
+
+    user_id = await get_current_user(request)
+
+    # Validate run exists and belongs to thread
+    run_store = get_run_store(request)
+    run = await run_store.get(run_id)
+    if run is None:
+        raise HTTPException(status_code=404, detail=f"Run {run_id} not found")
+    if run.get("thread_id") != thread_id:
+        raise HTTPException(status_code=404, detail=f"Run {run_id} not found in thread {thread_id}")
+
+    feedback_repo = get_feedback_repo(request)
+    return await feedback_repo.create(
+        run_id=run_id,
+        thread_id=thread_id,
+        rating=body.rating,
+        user_id=user_id,
+        message_id=body.message_id,
+        comment=body.comment,
+    )
+
+
+@router.get("/{thread_id}/runs/{run_id}/feedback", response_model=list[FeedbackResponse])
+@require_permission("threads", "read", owner_check=True)
+async def list_feedback(
+    thread_id: str,
+    run_id: str,
+    request: Request,
+) -> list[dict[str, Any]]:
+    """List all feedback for a run."""
+    feedback_repo = get_feedback_repo(request)
+    return await feedback_repo.list_by_run(thread_id, run_id)
+
+
+@router.get("/{thread_id}/runs/{run_id}/feedback/stats", response_model=FeedbackStatsResponse)
+@require_permission("threads", "read", owner_check=True)
+async def feedback_stats(
+    thread_id: str,
+    run_id: str,
+    request: Request,
+) -> dict[str, Any]:
+    """Get aggregated feedback stats (positive/negative counts) for a run."""
+    feedback_repo = get_feedback_repo(request)
+    return await feedback_repo.aggregate_by_run(thread_id, run_id)
+
+
+@router.delete("/{thread_id}/runs/{run_id}/feedback/{feedback_id}")
+@require_permission("threads", "delete", owner_check=True, require_existing=True)
+async def delete_feedback(
+    thread_id: str,
+    run_id: str,
+    feedback_id: str,
+    request: Request,
+) -> dict[str, bool]:
+    """Delete a feedback record."""
+    feedback_repo = get_feedback_repo(request)
+    # Verify feedback belongs to the specified thread/run before deleting
+    existing = await feedback_repo.get(feedback_id)
+    if existing is None:
+        raise HTTPException(status_code=404, detail=f"Feedback {feedback_id} not found")
+    if existing.get("thread_id") != thread_id or existing.get("run_id") != run_id:
+        raise HTTPException(status_code=404, detail=f"Feedback {feedback_id} not found in run {run_id}")
+    deleted = await feedback_repo.delete(feedback_id)
+    if not deleted:
+        raise HTTPException(status_code=404, detail=f"Feedback {feedback_id} not found")
+    return {"success": True}
@@ -3,10 +3,12 @@ import logging
 from pathlib import Path
 from typing import Literal

-from fastapi import APIRouter, HTTPException
+from fastapi import APIRouter, Depends, HTTPException, Request
 from pydantic import BaseModel, Field

-from deerflow.config.extensions_config import ExtensionsConfig, get_extensions_config, reload_extensions_config
+from app.gateway.deps import get_config
+from deerflow.config.app_config import AppConfig
+from deerflow.config.extensions_config import ExtensionsConfig

 logger = logging.getLogger(__name__)
 router = APIRouter(prefix="/api", tags=["mcp"])
@@ -69,7 +71,7 @@ class McpConfigUpdateRequest(BaseModel):
    summary="Get MCP Configuration",
    description="Retrieve the current Model Context Protocol (MCP) server configurations.",
 )
-async def get_mcp_configuration() -> McpConfigResponse:
+async def get_mcp_configuration(config: AppConfig = Depends(get_config)) -> McpConfigResponse:
    """Get the current MCP configuration.

    Returns:
@@ -90,9 +92,9 @@ async def get_mcp_configuration() -> McpConfigResponse:
        }
        ```
    """
-    config = get_extensions_config()
+    ext = config.extensions

-    return McpConfigResponse(mcp_servers={name: McpServerConfigResponse(**server.model_dump()) for name, server in config.mcp_servers.items()})
+    return McpConfigResponse(mcp_servers={name: McpServerConfigResponse(**server.model_dump()) for name, server in ext.mcp_servers.items()})


@router.put(
@@ -101,7 +103,11 @@ async def get_mcp_configuration() -> McpConfigResponse:
    summary="Update MCP Configuration",
    description="Update Model Context Protocol (MCP) server configurations and save to file.",
 )
-async def update_mcp_configuration(request: McpConfigUpdateRequest) -> McpConfigResponse:
+async def update_mcp_configuration(
+    request: McpConfigUpdateRequest,
+    http_request: Request,
+    config: AppConfig = Depends(get_config),
+) -> McpConfigResponse:
    """Update the MCP configuration.

    This will:
@@ -142,13 +148,13 @@ async def update_mcp_configuration(request: McpConfigUpdateRequest) -> McpConfig
            config_path = Path.cwd().parent / "extensions_config.json"
            logger.info(f"No existing extensions config found. Creating new config at: {config_path}")

-        # Load current config to preserve skills configuration
-        current_config = get_extensions_config()
+        # Use injected config to preserve skills configuration
+        current_ext = config.extensions

        # Convert request to dict format for JSON serialization
        config_data = {
            "mcpServers": {name: server.model_dump() for name, server in request.mcp_servers.items()},
-            "skills": {name: {"enabled": skill.enabled} for name, skill in current_config.skills.items()},
+            "skills": {name: {"enabled": skill.enabled} for name, skill in current_ext.skills.items()},
        }

        # Write the configuration to file
@@ -160,9 +166,11 @@ async def update_mcp_configuration(request: McpConfigUpdateRequest) -> McpConfig
        # NOTE: No need to reload/reset cache here - LangGraph Server (separate process)
        # will detect config file changes via mtime and reinitialize MCP tools automatically

-        # Reload the configuration and update the global cache
-        reloaded_config = reload_extensions_config()
-        return McpConfigResponse(mcp_servers={name: McpServerConfigResponse(**server.model_dump()) for name, server in reloaded_config.mcp_servers.items()})
+        # Reload the configuration and swap ``app.state.config`` so subsequent
+        # ``Depends(get_config)`` calls see the refreshed value.
+        reloaded = AppConfig.from_file()
+        http_request.app.state.config = reloaded
+        return McpConfigResponse(mcp_servers={name: McpServerConfigResponse(**server.model_dump()) for name, server in reloaded.extensions.mcp_servers.items()})

    except Exception as e:
        logger.error(f"Failed to update MCP configuration: {e}", exc_info=True)
@@ -1,8 +1,9 @@
 """Memory API router for retrieving and managing global memory data."""

-from fastapi import APIRouter, HTTPException
+from fastapi import APIRouter, Depends, HTTPException
 from pydantic import BaseModel, Field

+from app.gateway.deps import get_config
 from deerflow.agents.memory.updater import (
    clear_memory_data,
    create_memory_fact,
@@ -12,7 +13,8 @@ from deerflow.agents.memory.updater import (
    reload_memory_data,
    update_memory_fact,
 )
-from deerflow.config.memory_config import get_memory_config
+from deerflow.config.app_config import AppConfig
+from deerflow.runtime.user_context import get_effective_user_id

 router = APIRouter(prefix="/api", tags=["memory"])

@@ -113,7 +115,7 @@ class MemoryStatusResponse(BaseModel):
    summary="Get Memory Data",
    description="Retrieve the current global memory data including user context, history, and facts.",
 )
-async def get_memory() -> MemoryResponse:
+async def get_memory(app_config: AppConfig = Depends(get_config)) -> MemoryResponse:
    """Get the current global memory data.

    Returns:
@@ -147,7 +149,7 @@ async def get_memory() -> MemoryResponse:
        }
        ```
    """
-    memory_data = get_memory_data()
+    memory_data = get_memory_data(app_config.memory, user_id=get_effective_user_id())
    return MemoryResponse(**memory_data)


@@ -158,7 +160,7 @@ async def get_memory() -> MemoryResponse:
    summary="Reload Memory Data",
    description="Reload memory data from the storage file, refreshing the in-memory cache.",
 )
-async def reload_memory() -> MemoryResponse:
+async def reload_memory(app_config: AppConfig = Depends(get_config)) -> MemoryResponse:
    """Reload memory data from file.

    This forces a reload of the memory data from the storage file,
@@ -167,7 +169,7 @@ async def reload_memory() -> MemoryResponse:
    Returns:
        The reloaded memory data.
    """
-    memory_data = reload_memory_data()
+    memory_data = reload_memory_data(app_config.memory, user_id=get_effective_user_id())
    return MemoryResponse(**memory_data)


@@ -178,10 +180,10 @@ async def reload_memory() -> MemoryResponse:
    summary="Clear All Memory Data",
    description="Delete all saved memory data and reset the memory structure to an empty state.",
 )
-async def clear_memory() -> MemoryResponse:
+async def clear_memory(app_config: AppConfig = Depends(get_config)) -> MemoryResponse:
    """Clear all persisted memory data."""
    try:
-        memory_data = clear_memory_data()
+        memory_data = clear_memory_data(app_config.memory, user_id=get_effective_user_id())
    except OSError as exc:
        raise HTTPException(status_code=500, detail="Failed to clear memory data.") from exc

@@ -195,13 +197,15 @@ async def clear_memory() -> MemoryResponse:
    summary="Create Memory Fact",
    description="Create a single saved memory fact manually.",
 )
-async def create_memory_fact_endpoint(request: FactCreateRequest) -> MemoryResponse:
+async def create_memory_fact_endpoint(request: FactCreateRequest, app_config: AppConfig = Depends(get_config)) -> MemoryResponse:
    """Create a single fact manually."""
    try:
        memory_data = create_memory_fact(
+            app_config.memory,
            content=request.content,
            category=request.category,
            confidence=request.confidence,
+            user_id=get_effective_user_id(),
        )
    except ValueError as exc:
        raise _map_memory_fact_value_error(exc) from exc
@@ -218,10 +222,10 @@ async def create_memory_fact_endpoint(request: FactCreateRequest) -> MemoryRespo
    summary="Delete Memory Fact",
    description="Delete a single saved memory fact by its fact id.",
 )
-async def delete_memory_fact_endpoint(fact_id: str) -> MemoryResponse:
+async def delete_memory_fact_endpoint(fact_id: str, app_config: AppConfig = Depends(get_config)) -> MemoryResponse:
    """Delete a single fact from memory by fact id."""
    try:
-        memory_data = delete_memory_fact(fact_id)
+        memory_data = delete_memory_fact(app_config.memory, fact_id, user_id=get_effective_user_id())
    except KeyError as exc:
        raise HTTPException(status_code=404, detail=f"Memory fact '{fact_id}' not found.") from exc
    except OSError as exc:
@@ -237,14 +241,16 @@ async def delete_memory_fact_endpoint(fact_id: str) -> MemoryResponse:
    summary="Patch Memory Fact",
    description="Partially update a single saved memory fact by its fact id while preserving omitted fields.",
 )
-async def update_memory_fact_endpoint(fact_id: str, request: FactPatchRequest) -> MemoryResponse:
+async def update_memory_fact_endpoint(fact_id: str, request: FactPatchRequest, app_config: AppConfig = Depends(get_config)) -> MemoryResponse:
    """Partially update a single fact manually."""
    try:
        memory_data = update_memory_fact(
+            app_config.memory,
            fact_id=fact_id,
            content=request.content,
            category=request.category,
            confidence=request.confidence,
+            user_id=get_effective_user_id(),
        )
    except ValueError as exc:
        raise _map_memory_fact_value_error(exc) from exc
@@ -263,9 +269,9 @@ async def update_memory_fact_endpoint(fact_id: str, request: FactPatchRequest) -
    summary="Export Memory Data",
    description="Export the current global memory data as JSON for backup or transfer.",
 )
-async def export_memory() -> MemoryResponse:
+async def export_memory(app_config: AppConfig = Depends(get_config)) -> MemoryResponse:
    """Export the current memory data."""
-    memory_data = get_memory_data()
+    memory_data = get_memory_data(app_config.memory, user_id=get_effective_user_id())
    return MemoryResponse(**memory_data)


@@ -276,10 +282,10 @@ async def export_memory() -> MemoryResponse:
    summary="Import Memory Data",
    description="Import and overwrite the current global memory data from a JSON payload.",
 )
-async def import_memory(request: MemoryResponse) -> MemoryResponse:
+async def import_memory(request: MemoryResponse, app_config: AppConfig = Depends(get_config)) -> MemoryResponse:
    """Import and persist memory data."""
    try:
-        memory_data = import_memory_data(request.model_dump())
+        memory_data = import_memory_data(app_config.memory, request.model_dump(), user_id=get_effective_user_id())
    except OSError as exc:
        raise HTTPException(status_code=500, detail="Failed to import memory data.") from exc

@@ -292,7 +298,9 @@ async def import_memory(request: MemoryResponse) -> MemoryResponse:
    summary="Get Memory Configuration",
    description="Retrieve the current memory system configuration.",
 )
-async def get_memory_config_endpoint() -> MemoryConfigResponse:
+async def get_memory_config_endpoint(
+    app_config: AppConfig = Depends(get_config),
+) -> MemoryConfigResponse:
    """Get the memory system configuration.

    Returns:
@@ -311,7 +319,7 @@ async def get_memory_config_endpoint() -> MemoryConfigResponse:
        }
        ```
    """
-    config = get_memory_config()
+    config = app_config.memory
    return MemoryConfigResponse(
        enabled=config.enabled,
        storage_path=config.storage_path,
@@ -330,14 +338,16 @@ async def get_memory_config_endpoint() -> MemoryConfigResponse:
    summary="Get Memory Status",
    description="Retrieve both memory configuration and current data in a single request.",
 )
-async def get_memory_status() -> MemoryStatusResponse:
+async def get_memory_status(
+    app_config: AppConfig = Depends(get_config),
+) -> MemoryStatusResponse:
    """Get the memory system status including configuration and data.

    Returns:
        Combined memory configuration and current data.
    """
-    config = get_memory_config()
-    memory_data = get_memory_data()
+    config = app_config.memory
+    memory_data = get_memory_data(config, user_id=get_effective_user_id())

    return MemoryStatusResponse(
        config=MemoryConfigResponse(
@@ -1,7 +1,8 @@
-from fastapi import APIRouter, HTTPException
+from fastapi import APIRouter, Depends, HTTPException
 from pydantic import BaseModel, Field

-from deerflow.config import get_app_config
+from app.gateway.deps import get_config
+from deerflow.config.app_config import AppConfig

 router = APIRouter(prefix="/api", tags=["models"])

@@ -17,10 +18,17 @@ class ModelResponse(BaseModel):
    supports_reasoning_effort: bool = Field(default=False, description="Whether model supports reasoning effort")


+class TokenUsageResponse(BaseModel):
+    """Token usage display configuration."""
+
+    enabled: bool = Field(default=False, description="Whether token usage display is enabled")
+
+
 class ModelsListResponse(BaseModel):
    """Response model for listing all models."""

    models: list[ModelResponse]
+    token_usage: TokenUsageResponse


@router.get(
@@ -29,14 +37,14 @@ class ModelsListResponse(BaseModel):
    summary="List All Models",
    description="Retrieve a list of all available AI models configured in the system.",
 )
-async def list_models() -> ModelsListResponse:
+async def list_models(config: AppConfig = Depends(get_config)) -> ModelsListResponse:
    """List all available models from configuration.

    Returns model information suitable for frontend display,
    excluding sensitive fields like API keys and internal configuration.

    Returns:
-        A list of all configured models with their metadata.
+        A list of all configured models with their metadata and token usage display settings.

    Example Response:
        ```json
@@ -44,21 +52,27 @@ async def list_models() -> ModelsListResponse:
            "models": [
                {
                    "name": "gpt-4",
+                    "model": "gpt-4",
                    "display_name": "GPT-4",
                    "description": "OpenAI GPT-4 model",
-                    "supports_thinking": false
+                    "supports_thinking": false,
+                    "supports_reasoning_effort": false
                },
                {
                    "name": "claude-3-opus",
+                    "model": "claude-3-opus",
                    "display_name": "Claude 3 Opus",
                    "description": "Anthropic Claude 3 Opus model",
-                    "supports_thinking": true
+                    "supports_thinking": true,
+                    "supports_reasoning_effort": false
                }
-            ]
+            ],
+            "token_usage": {
+                "enabled": true
+            }
        }
        ```
    """
-    config = get_app_config()
    models = [
        ModelResponse(
            name=model.name,
@@ -70,7 +84,10 @@ async def list_models() -> ModelsListResponse:
        )
        for model in config.models
    ]
-    return ModelsListResponse(models=models)
+    return ModelsListResponse(
+        models=models,
+        token_usage=TokenUsageResponse(enabled=config.token_usage.enabled),
+    )


@router.get(
@@ -79,7 +96,7 @@ async def list_models() -> ModelsListResponse:
    summary="Get Model Details",
    description="Retrieve detailed information about a specific AI model by its name.",
 )
-async def get_model(model_name: str) -> ModelResponse:
+async def get_model(model_name: str, config: AppConfig = Depends(get_config)) -> ModelResponse:
    """Get a specific model by name.

    Args:
@@ -101,7 +118,6 @@ async def get_model(model_name: str) -> ModelResponse:
        }
        ```
    """
-    config = get_app_config()
    model = config.get_model_config(model_name)
    if model is None:
        raise HTTPException(status_code=404, detail=f"Model '{model_name}' not found")
@@ -11,10 +11,11 @@ import asyncio
 import logging
 import uuid

-from fastapi import APIRouter, Request
+from fastapi import APIRouter, HTTPException, Query, Request
 from fastapi.responses import StreamingResponse

-from app.gateway.deps import get_checkpointer, get_run_manager, get_stream_bridge
+from app.gateway.authz import require_permission
+from app.gateway.deps import get_checkpointer, get_feedback_repo, get_run_event_store, get_run_manager, get_run_store, get_stream_bridge
 from app.gateway.routers.thread_runs import RunCreateRequest
 from app.gateway.services import sse_consumer, start_run
 from deerflow.runtime import serialize_channel_values
@@ -85,3 +86,57 @@ async def stateless_wait(body: RunCreateRequest, request: Request) -> dict:
        logger.exception("Failed to fetch final state for run %s", record.run_id)

    return {"status": record.status.value, "error": record.error}
+
+
+# ---------------------------------------------------------------------------
+# Run-scoped read endpoints
+# ---------------------------------------------------------------------------
+
+
+async def _resolve_run(run_id: str, request: Request) -> dict:
+    """Fetch run by run_id with user ownership check. Raises 404 if not found."""
+    run_store = get_run_store(request)
+    record = await run_store.get(run_id)  # user_id=AUTO filters by contextvar
+    if record is None:
+        raise HTTPException(status_code=404, detail=f"Run {run_id} not found")
+    return record
+
+
+@router.get("/{run_id}/messages")
+@require_permission("runs", "read")
+async def run_messages(
+    run_id: str,
+    request: Request,
+    limit: int = Query(default=50, le=200, ge=1),
+    before_seq: int | None = Query(default=None),
+    after_seq: int | None = Query(default=None),
+) -> dict:
+    """Return paginated messages for a run (cursor-based).
+
+    Pagination:
+    - after_seq: messages with seq > after_seq (forward)
+    - before_seq: messages with seq < before_seq (backward)
+    - neither: latest messages
+
+    Response: { data: [...], has_more: bool }
+    """
+    run = await _resolve_run(run_id, request)
+    event_store = get_run_event_store(request)
+    rows = await event_store.list_messages_by_run(
+        run["thread_id"], run_id,
+        limit=limit + 1,
+        before_seq=before_seq,
+        after_seq=after_seq,
+    )
+    has_more = len(rows) > limit
+    data = rows[:limit] if has_more else rows
+    return {"data": data, "has_more": has_more}
+
+
+@router.get("/{run_id}/feedback")
+@require_permission("runs", "read")
+async def run_feedback(run_id: str, request: Request) -> list[dict]:
+    """Return all feedback for a run."""
+    run = await _resolve_run(run_id, request)
+    feedback_repo = get_feedback_repo(request)
+    return await feedback_repo.list_by_run(run["thread_id"], run_id)
@@ -1,14 +1,17 @@
+import errno
 import json
 import logging
 import shutil
 from pathlib import Path

-from fastapi import APIRouter, HTTPException
+from fastapi import APIRouter, Depends, HTTPException, Request
 from pydantic import BaseModel, Field

+from app.gateway.deps import get_config
 from app.gateway.path_utils import resolve_thread_virtual_path
 from deerflow.agents.lead_agent.prompt import refresh_skills_system_prompt_cache_async
-from deerflow.config.extensions_config import ExtensionsConfig, SkillStateConfig, get_extensions_config, reload_extensions_config
+from deerflow.config.app_config import AppConfig
+from deerflow.config.extensions_config import ExtensionsConfig
 from deerflow.skills import Skill, load_skills
 from deerflow.skills.installer import SkillAlreadyExistsError, install_skill_from_archive
 from deerflow.skills.manager import (
@@ -100,9 +103,9 @@ def _skill_to_response(skill: Skill) -> SkillResponse:
    summary="List All Skills",
    description="Retrieve a list of all available skills from both public and custom directories.",
 )
-async def list_skills() -> SkillsListResponse:
+async def list_skills(app_config: AppConfig = Depends(get_config)) -> SkillsListResponse:
    try:
-        skills = load_skills(enabled_only=False)
+        skills = load_skills(app_config, enabled_only=False)
        return SkillsListResponse(skills=[_skill_to_response(skill) for skill in skills])
    except Exception as e:
        logger.error(f"Failed to load skills: {e}", exc_info=True)
@@ -115,11 +118,11 @@ async def list_skills() -> SkillsListResponse:
    summary="Install Skill",
    description="Install a skill from a .skill file (ZIP archive) located in the thread's user-data directory.",
 )
-async def install_skill(request: SkillInstallRequest) -> SkillInstallResponse:
+async def install_skill(request: SkillInstallRequest, app_config: AppConfig = Depends(get_config)) -> SkillInstallResponse:
    try:
        skill_file_path = resolve_thread_virtual_path(request.thread_id, request.path)
        result = install_skill_from_archive(skill_file_path)
-        await refresh_skills_system_prompt_cache_async()
+        await refresh_skills_system_prompt_cache_async(app_config)
        return SkillInstallResponse(**result)
    except FileNotFoundError as e:
        raise HTTPException(status_code=404, detail=str(e))
@@ -135,9 +138,9 @@ async def install_skill(request: SkillInstallRequest) -> SkillInstallResponse:


@router.get("/skills/custom", response_model=SkillsListResponse, summary="List Custom Skills")
-async def list_custom_skills() -> SkillsListResponse:
+async def list_custom_skills(app_config: AppConfig = Depends(get_config)) -> SkillsListResponse:
    try:
-        skills = [skill for skill in load_skills(enabled_only=False) if skill.category == "custom"]
+        skills = [skill for skill in load_skills(app_config, enabled_only=False) if skill.category == "custom"]
        return SkillsListResponse(skills=[_skill_to_response(skill) for skill in skills])
    except Exception as e:
        logger.error("Failed to list custom skills: %s", e, exc_info=True)
@@ -145,13 +148,13 @@ async def list_custom_skills() -> SkillsListResponse:


@router.get("/skills/custom/{skill_name}", response_model=CustomSkillContentResponse, summary="Get Custom Skill Content")
-async def get_custom_skill(skill_name: str) -> CustomSkillContentResponse:
+async def get_custom_skill(skill_name: str, app_config: AppConfig = Depends(get_config)) -> CustomSkillContentResponse:
    try:
-        skills = load_skills(enabled_only=False)
+        skills = load_skills(app_config, enabled_only=False)
        skill = next((s for s in skills if s.name == skill_name and s.category == "custom"), None)
        if skill is None:
            raise HTTPException(status_code=404, detail=f"Custom skill '{skill_name}' not found")
-        return CustomSkillContentResponse(**_skill_to_response(skill).model_dump(), content=read_custom_skill_content(skill_name))
+        return CustomSkillContentResponse(**_skill_to_response(skill).model_dump(), content=read_custom_skill_content(skill_name, app_config))
    except HTTPException:
        raise
    except Exception as e:
@@ -160,14 +163,18 @@ async def get_custom_skill(skill_name: str) -> CustomSkillContentResponse:


@router.put("/skills/custom/{skill_name}", response_model=CustomSkillContentResponse, summary="Edit Custom Skill")
-async def update_custom_skill(skill_name: str, request: CustomSkillUpdateRequest) -> CustomSkillContentResponse:
+async def update_custom_skill(
+    skill_name: str,
+    request: CustomSkillUpdateRequest,
+    app_config: AppConfig = Depends(get_config),
+) -> CustomSkillContentResponse:
    try:
-        ensure_custom_skill_is_editable(skill_name)
+        ensure_custom_skill_is_editable(skill_name, app_config)
        validate_skill_markdown_content(skill_name, request.content)
-        scan = await scan_skill_content(request.content, executable=False, location=f"{skill_name}/SKILL.md")
+        scan = await scan_skill_content(app_config, request.content, executable=False, location=f"{skill_name}/SKILL.md")
        if scan.decision == "block":
            raise HTTPException(status_code=400, detail=f"Security scan blocked the edit: {scan.reason}")
-        skill_file = get_custom_skill_dir(skill_name) / "SKILL.md"
+        skill_file = get_custom_skill_dir(skill_name, app_config) / "SKILL.md"
        prev_content = skill_file.read_text(encoding="utf-8")
        atomic_write(skill_file, request.content)
        append_history(
@@ -181,9 +188,10 @@ async def update_custom_skill(skill_name: str, request: CustomSkillUpdateRequest
                "new_content": request.content,
                "scanner": {"decision": scan.decision, "reason": scan.reason},
            },
+            app_config,
        )
-        await refresh_skills_system_prompt_cache_async()
-        return await get_custom_skill(skill_name)
+        await refresh_skills_system_prompt_cache_async(app_config)
+        return await get_custom_skill(skill_name, app_config)
    except HTTPException:
        raise
    except FileNotFoundError as e:
@@ -196,25 +204,31 @@ async def update_custom_skill(skill_name: str, request: CustomSkillUpdateRequest


@router.delete("/skills/custom/{skill_name}", summary="Delete Custom Skill")
-async def delete_custom_skill(skill_name: str) -> dict[str, bool]:
+async def delete_custom_skill(skill_name: str, app_config: AppConfig = Depends(get_config)) -> dict[str, bool]:
    try:
-        ensure_custom_skill_is_editable(skill_name)
-        skill_dir = get_custom_skill_dir(skill_name)
-        prev_content = read_custom_skill_content(skill_name)
-        append_history(
-            skill_name,
-            {
-                "action": "human_delete",
-                "author": "human",
-                "thread_id": None,
-                "file_path": "SKILL.md",
-                "prev_content": prev_content,
-                "new_content": None,
-                "scanner": {"decision": "allow", "reason": "Deletion requested."},
-            },
-        )
+        ensure_custom_skill_is_editable(skill_name, app_config)
+        skill_dir = get_custom_skill_dir(skill_name, app_config)
+        prev_content = read_custom_skill_content(skill_name, app_config)
+        try:
+            append_history(
+                skill_name,
+                {
+                    "action": "human_delete",
+                    "author": "human",
+                    "thread_id": None,
+                    "file_path": "SKILL.md",
+                    "prev_content": prev_content,
+                    "new_content": None,
+                    "scanner": {"decision": "allow", "reason": "Deletion requested."},
+                },
+                app_config,
+            )
+        except OSError as e:
+            if not isinstance(e, PermissionError) and e.errno not in {errno.EACCES, errno.EPERM, errno.EROFS}:
+                raise
+            logger.warning("Skipping delete history write for custom skill %s due to readonly/permission failure; continuing with skill directory removal: %s", skill_name, e)
        shutil.rmtree(skill_dir)
-        await refresh_skills_system_prompt_cache_async()
+        await refresh_skills_system_prompt_cache_async(app_config)
        return {"success": True}
    except FileNotFoundError as e:
        raise HTTPException(status_code=404, detail=str(e))
@@ -226,11 +240,11 @@ async def delete_custom_skill(skill_name: str) -> dict[str, bool]:


@router.get("/skills/custom/{skill_name}/history", response_model=CustomSkillHistoryResponse, summary="Get Custom Skill History")
-async def get_custom_skill_history(skill_name: str) -> CustomSkillHistoryResponse:
+async def get_custom_skill_history(skill_name: str, app_config: AppConfig = Depends(get_config)) -> CustomSkillHistoryResponse:
    try:
-        if not custom_skill_exists(skill_name) and not get_skill_history_file(skill_name).exists():
+        if not custom_skill_exists(skill_name, app_config) and not get_skill_history_file(skill_name, app_config).exists():
            raise HTTPException(status_code=404, detail=f"Custom skill '{skill_name}' not found")
-        return CustomSkillHistoryResponse(history=read_history(skill_name))
+        return CustomSkillHistoryResponse(history=read_history(skill_name, app_config))
    except HTTPException:
        raise
    except Exception as e:
@@ -239,11 +253,15 @@ async def get_custom_skill_history(skill_name: str) -> CustomSkillHistoryRespons


@router.post("/skills/custom/{skill_name}/rollback", response_model=CustomSkillContentResponse, summary="Rollback Custom Skill")
-async def rollback_custom_skill(skill_name: str, request: SkillRollbackRequest) -> CustomSkillContentResponse:
+async def rollback_custom_skill(
+    skill_name: str,
+    request: SkillRollbackRequest,
+    app_config: AppConfig = Depends(get_config),
+) -> CustomSkillContentResponse:
    try:
-        if not custom_skill_exists(skill_name) and not get_skill_history_file(skill_name).exists():
+        if not custom_skill_exists(skill_name, app_config) and not get_skill_history_file(skill_name, app_config).exists():
            raise HTTPException(status_code=404, detail=f"Custom skill '{skill_name}' not found")
-        history = read_history(skill_name)
+        history = read_history(skill_name, app_config)
        if not history:
            raise HTTPException(status_code=400, detail=f"Custom skill '{skill_name}' has no history")
        record = history[request.history_index]
@@ -251,8 +269,8 @@ async def rollback_custom_skill(skill_name: str, request: SkillRollbackRequest)
        if target_content is None:
            raise HTTPException(status_code=400, detail="Selected history entry has no previous content to roll back to")
        validate_skill_markdown_content(skill_name, target_content)
-        scan = await scan_skill_content(target_content, executable=False, location=f"{skill_name}/SKILL.md")
-        skill_file = get_custom_skill_file(skill_name)
+        scan = await scan_skill_content(app_config, target_content, executable=False, location=f"{skill_name}/SKILL.md")
+        skill_file = get_custom_skill_file(skill_name, app_config)
        current_content = skill_file.read_text(encoding="utf-8") if skill_file.exists() else None
        history_entry = {
            "action": "rollback",
@@ -265,12 +283,12 @@ async def rollback_custom_skill(skill_name: str, request: SkillRollbackRequest)
            "scanner": {"decision": scan.decision, "reason": scan.reason},
        }
        if scan.decision == "block":
-            append_history(skill_name, history_entry)
+            append_history(skill_name, history_entry, app_config)
            raise HTTPException(status_code=400, detail=f"Rollback blocked by security scanner: {scan.reason}")
        atomic_write(skill_file, target_content)
-        append_history(skill_name, history_entry)
-        await refresh_skills_system_prompt_cache_async()
-        return await get_custom_skill(skill_name)
+        append_history(skill_name, history_entry, app_config)
+        await refresh_skills_system_prompt_cache_async(app_config)
+        return await get_custom_skill(skill_name, app_config)
    except HTTPException:
        raise
    except IndexError:
@@ -290,9 +308,9 @@ async def rollback_custom_skill(skill_name: str, request: SkillRollbackRequest)
    summary="Get Skill Details",
    description="Retrieve detailed information about a specific skill by its name.",
 )
-async def get_skill(skill_name: str) -> SkillResponse:
+async def get_skill(skill_name: str, app_config: AppConfig = Depends(get_config)) -> SkillResponse:
    try:
-        skills = load_skills(enabled_only=False)
+        skills = load_skills(app_config, enabled_only=False)
        skill = next((s for s in skills if s.name == skill_name), None)

        if skill is None:
@@ -312,9 +330,14 @@ async def get_skill(skill_name: str) -> SkillResponse:
    summary="Update Skill",
    description="Update a skill's enabled status by modifying the extensions_config.json file.",
 )
-async def update_skill(skill_name: str, request: SkillUpdateRequest) -> SkillResponse:
+async def update_skill(
+    skill_name: str,
+    request: SkillUpdateRequest,
+    http_request: Request,
+    app_config: AppConfig = Depends(get_config),
+) -> SkillResponse:
    try:
-        skills = load_skills(enabled_only=False)
+        skills = load_skills(app_config, enabled_only=False)
        skill = next((s for s in skills if s.name == skill_name), None)

        if skill is None:
@@ -325,22 +348,29 @@ async def update_skill(skill_name: str, request: SkillUpdateRequest) -> SkillRes
            config_path = Path.cwd().parent / "extensions_config.json"
            logger.info(f"No existing extensions config found. Creating new config at: {config_path}")

-        extensions_config = get_extensions_config()
-        extensions_config.skills[skill_name] = SkillStateConfig(enabled=request.enabled)
+        # Do not mutate the frozen AppConfig in place. Compose the new skills
+        # state in a fresh dict, write to disk, and reload AppConfig below so
+        # every subsequent Depends(get_config) sees the refreshed snapshot.
+        ext = app_config.extensions
+        updated_skills = {name: {"enabled": skill_config.enabled} for name, skill_config in ext.skills.items()}
+        updated_skills[skill_name] = {"enabled": request.enabled}

        config_data = {
-            "mcpServers": {name: server.model_dump() for name, server in extensions_config.mcp_servers.items()},
-            "skills": {name: {"enabled": skill_config.enabled} for name, skill_config in extensions_config.skills.items()},
+            "mcpServers": {name: server.model_dump() for name, server in ext.mcp_servers.items()},
+            "skills": updated_skills,
        }

        with open(config_path, "w", encoding="utf-8") as f:
            json.dump(config_data, f, indent=2)

        logger.info(f"Skills configuration updated and saved to: {config_path}")
-        reload_extensions_config()
-        await refresh_skills_system_prompt_cache_async()
+        # Reload AppConfig and swap ``app.state.config`` so subsequent
+        # ``Depends(get_config)`` sees the refreshed value.
+        reloaded = AppConfig.from_file()
+        http_request.app.state.config = reloaded
+        await refresh_skills_system_prompt_cache_async(reloaded)

-        skills = load_skills(enabled_only=False)
+        skills = load_skills(reloaded, enabled_only=False)
        updated_skill = next((s for s in skills if s.name == skill_name), None)

        if updated_skill is None:
@@ -1,10 +1,13 @@
 import json
 import logging

-from fastapi import APIRouter
+from fastapi import APIRouter, Depends, Request
 from langchain_core.messages import HumanMessage, SystemMessage
 from pydantic import BaseModel, Field

+from app.gateway.authz import require_permission
+from app.gateway.deps import get_config
+from deerflow.config.app_config import AppConfig
 from deerflow.models import create_chat_model

 logger = logging.getLogger(__name__)
@@ -98,12 +101,13 @@ def _format_conversation(messages: list[SuggestionMessage]) -> str:
    summary="Generate Follow-up Questions",
    description="Generate short follow-up questions a user might ask next, based on recent conversation context.",
 )
-async def generate_suggestions(thread_id: str, request: SuggestionsRequest) -> SuggestionsResponse:
-    if not request.messages:
+@require_permission("threads", "read", owner_check=True)
+async def generate_suggestions(thread_id: str, body: SuggestionsRequest, request: Request, app_config: AppConfig = Depends(get_config)) -> SuggestionsResponse:
+    if not body.messages:
        return SuggestionsResponse(suggestions=[])

-    n = request.n
-    conversation = _format_conversation(request.messages)
+    n = body.n
+    conversation = _format_conversation(body.messages)
    if not conversation:
        return SuggestionsResponse(suggestions=[])

@@ -120,8 +124,8 @@ async def generate_suggestions(thread_id: str, request: SuggestionsRequest) -> S
    user_content = f"Conversation Context:\n{conversation}\n\nGenerate {n} follow-up questions"

    try:
-        model = create_chat_model(name=request.model_name, thinking_enabled=False)
-        response = await model.ainvoke([SystemMessage(content=system_instruction), HumanMessage(content=user_content)])
+        model = create_chat_model(name=body.model_name, thinking_enabled=False, app_config=app_config)
+        response = await model.ainvoke([SystemMessage(content=system_instruction), HumanMessage(content=user_content)], config={"run_name": "suggest_agent"})
        raw = _extract_response_text(response.content)
        suggestions = _parse_json_string_list(raw) or []
        cleaned = [s.replace("\n", " ").strip() for s in suggestions if s.strip()]
@@ -19,7 +19,8 @@ from fastapi import APIRouter, HTTPException, Query, Request
 from fastapi.responses import Response, StreamingResponse
 from pydantic import BaseModel, Field

-from app.gateway.deps import get_checkpointer, get_run_manager, get_stream_bridge
+from app.gateway.authz import require_permission
+from app.gateway.deps import get_checkpointer, get_current_user, get_feedback_repo, get_run_event_store, get_run_manager, get_run_store, get_stream_bridge
 from app.gateway.services import sse_consumer, start_run
 from deerflow.runtime import RunRecord, serialize_channel_values

@@ -53,6 +54,7 @@ class RunCreateRequest(BaseModel):
    after_seconds: float | None = Field(default=None, description="Delayed execution")
    if_not_exists: Literal["reject", "create"] = Field(default="create", description="Thread creation policy")
    feedback_keys: list[str] | None = Field(default=None, description="LangSmith feedback keys")
+    follow_up_to_run_id: str | None = Field(default=None, description="Run ID this message follows up on. Auto-detected from latest successful run if not provided.")


 class RunResponse(BaseModel):
@@ -92,6 +94,7 @@ def _record_to_response(record: RunRecord) -> RunResponse:


@router.post("/{thread_id}/runs", response_model=RunResponse)
+@require_permission("runs", "create", owner_check=True, require_existing=True)
 async def create_run(thread_id: str, body: RunCreateRequest, request: Request) -> RunResponse:
    """Create a background run (returns immediately)."""
    record = await start_run(body, thread_id, request)
@@ -99,6 +102,7 @@ async def create_run(thread_id: str, body: RunCreateRequest, request: Request) -


@router.post("/{thread_id}/runs/stream")
+@require_permission("runs", "create", owner_check=True, require_existing=True)
 async def stream_run(thread_id: str, body: RunCreateRequest, request: Request) -> StreamingResponse:
    """Create a run and stream events via SSE.

@@ -126,6 +130,7 @@ async def stream_run(thread_id: str, body: RunCreateRequest, request: Request) -


@router.post("/{thread_id}/runs/wait", response_model=dict)
+@require_permission("runs", "create", owner_check=True, require_existing=True)
 async def wait_run(thread_id: str, body: RunCreateRequest, request: Request) -> dict:
    """Create a run and block until it completes, returning the final state."""
    record = await start_run(body, thread_id, request)
@@ -151,6 +156,7 @@ async def wait_run(thread_id: str, body: RunCreateRequest, request: Request) ->


@router.get("/{thread_id}/runs", response_model=list[RunResponse])
+@require_permission("runs", "read", owner_check=True)
 async def list_runs(thread_id: str, request: Request) -> list[RunResponse]:
    """List all runs for a thread."""
    run_mgr = get_run_manager(request)
@@ -159,6 +165,7 @@ async def list_runs(thread_id: str, request: Request) -> list[RunResponse]:


@router.get("/{thread_id}/runs/{run_id}", response_model=RunResponse)
+@require_permission("runs", "read", owner_check=True)
 async def get_run(thread_id: str, run_id: str, request: Request) -> RunResponse:
    """Get details of a specific run."""
    run_mgr = get_run_manager(request)
@@ -169,6 +176,7 @@ async def get_run(thread_id: str, run_id: str, request: Request) -> RunResponse:


@router.post("/{thread_id}/runs/{run_id}/cancel")
+@require_permission("runs", "cancel", owner_check=True, require_existing=True)
 async def cancel_run(
    thread_id: str,
    run_id: str,
@@ -206,6 +214,7 @@ async def cancel_run(


@router.get("/{thread_id}/runs/{run_id}/join")
+@require_permission("runs", "read", owner_check=True)
 async def join_run(thread_id: str, run_id: str, request: Request) -> StreamingResponse:
    """Join an existing run's SSE stream."""
    bridge = get_stream_bridge(request)
@@ -226,6 +235,7 @@ async def join_run(thread_id: str, run_id: str, request: Request) -> StreamingRe


@router.api_route("/{thread_id}/runs/{run_id}/stream", methods=["GET", "POST"], response_model=None)
+@require_permission("runs", "read", owner_check=True)
 async def stream_existing_run(
    thread_id: str,
    run_id: str,
@@ -265,3 +275,99 @@ async def stream_existing_run(
            "X-Accel-Buffering": "no",
        },
    )
+
+
+# ---------------------------------------------------------------------------
+# Messages / Events / Token usage endpoints
+# ---------------------------------------------------------------------------
+
+
+@router.get("/{thread_id}/messages")
+@require_permission("runs", "read", owner_check=True)
+async def list_thread_messages(
+    thread_id: str,
+    request: Request,
+    limit: int = Query(default=50, le=200),
+    before_seq: int | None = Query(default=None),
+    after_seq: int | None = Query(default=None),
+) -> list[dict]:
+    """Return displayable messages for a thread (across all runs), with feedback attached."""
+    event_store = get_run_event_store(request)
+    messages = await event_store.list_messages(thread_id, limit=limit, before_seq=before_seq, after_seq=after_seq)
+
+    # Attach feedback to the last AI message of each run
+    feedback_repo = get_feedback_repo(request)
+    user_id = await get_current_user(request)
+    feedback_map = await feedback_repo.list_by_thread_grouped(thread_id, user_id=user_id)
+
+    # Find the last ai_message per run_id
+    last_ai_per_run: dict[str, int] = {}  # run_id -> index in messages list
+    for i, msg in enumerate(messages):
+        if msg.get("event_type") == "ai_message":
+            last_ai_per_run[msg["run_id"]] = i
+
+    # Attach feedback field
+    last_ai_indices = set(last_ai_per_run.values())
+    for i, msg in enumerate(messages):
+        if i in last_ai_indices:
+            run_id = msg["run_id"]
+            fb = feedback_map.get(run_id)
+            msg["feedback"] = {
+                "feedback_id": fb["feedback_id"],
+                "rating": fb["rating"],
+                "comment": fb.get("comment"),
+            } if fb else None
+        else:
+            msg["feedback"] = None
+
+    return messages
+
+
+@router.get("/{thread_id}/runs/{run_id}/messages")
+@require_permission("runs", "read", owner_check=True)
+async def list_run_messages(
+    thread_id: str,
+    run_id: str,
+    request: Request,
+    limit: int = Query(default=50, le=200, ge=1),
+    before_seq: int | None = Query(default=None),
+    after_seq: int | None = Query(default=None),
+) -> dict:
+    """Return paginated messages for a specific run.
+
+    Response: { data: [...], has_more: bool }
+    """
+    event_store = get_run_event_store(request)
+    rows = await event_store.list_messages_by_run(
+        thread_id, run_id,
+        limit=limit + 1,
+        before_seq=before_seq,
+        after_seq=after_seq,
+    )
+    has_more = len(rows) > limit
+    data = rows[:limit] if has_more else rows
+    return {"data": data, "has_more": has_more}
+
+
+@router.get("/{thread_id}/runs/{run_id}/events")
+@require_permission("runs", "read", owner_check=True)
+async def list_run_events(
+    thread_id: str,
+    run_id: str,
+    request: Request,
+    event_types: str | None = Query(default=None),
+    limit: int = Query(default=500, le=2000),
+) -> list[dict]:
+    """Return the full event stream for a run (debug/audit)."""
+    event_store = get_run_event_store(request)
+    types = event_types.split(",") if event_types else None
+    return await event_store.list_events(thread_id, run_id, event_types=types, limit=limit)
+
+
+@router.get("/{thread_id}/token-usage")
+@require_permission("threads", "read", owner_check=True)
+async def thread_token_usage(thread_id: str, request: Request) -> dict:
+    """Thread-level token usage aggregation."""
+    run_store = get_run_store(request)
+    agg = await run_store.aggregate_tokens_by_thread(thread_id)
+    return {"thread_id": thread_id, **agg}
@@ -13,28 +13,41 @@ matching the LangGraph Platform wire format expected by the
 from __future__ import annotations

 import logging
+import re
 import time
 import uuid
 from typing import Any

 from fastapi import APIRouter, HTTPException, Request
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, field_validator

-from app.gateway.deps import get_checkpointer, get_store
+from app.gateway.authz import require_permission
+from app.gateway.deps import get_checkpointer
+from app.gateway.utils import sanitize_log_param
 from deerflow.config.paths import Paths, get_paths
 from deerflow.runtime import serialize_channel_values
-
-# ---------------------------------------------------------------------------
-# Store namespace
-# ---------------------------------------------------------------------------
-
-THREADS_NS: tuple[str, ...] = ("threads",)
-"""Namespace used by the Store for thread metadata records."""
+from deerflow.runtime.user_context import get_effective_user_id

 logger = logging.getLogger(__name__)
 router = APIRouter(prefix="/api/threads", tags=["threads"])


+# Metadata keys that the server controls; clients are not allowed to set
+# them. Pydantic ``@field_validator("metadata")`` strips them on every
+# inbound model below so a malicious client cannot reflect a forged
+# owner identity through the API surface. Defense-in-depth — the
+# row-level invariant is still ``threads_meta.user_id`` populated from
+# the auth contextvar; this list closes the metadata-blob echo gap.
+_SERVER_RESERVED_METADATA_KEYS: frozenset[str] = frozenset({"owner_id", "user_id"})
+
+
+def _strip_reserved_metadata(metadata: dict[str, Any] | None) -> dict[str, Any]:
+    """Return ``metadata`` with server-controlled keys removed."""
+    if not metadata:
+        return metadata or {}
+    return {k: v for k, v in metadata.items() if k not in _SERVER_RESERVED_METADATA_KEYS}
+
+
 # ---------------------------------------------------------------------------
 # Response / request models
 # ---------------------------------------------------------------------------
@@ -63,8 +76,11 @@ class ThreadCreateRequest(BaseModel):
    """Request body for creating a thread."""

    thread_id: str | None = Field(default=None, description="Optional thread ID (auto-generated if omitted)")
+    assistant_id: str | None = Field(default=None, description="Associate thread with an assistant")
    metadata: dict[str, Any] = Field(default_factory=dict, description="Initial metadata")

+    _strip_reserved = field_validator("metadata")(classmethod(lambda cls, v: _strip_reserved_metadata(v)))
+

 class ThreadSearchRequest(BaseModel):
    """Request body for searching threads."""
@@ -93,6 +109,8 @@ class ThreadPatchRequest(BaseModel):

    metadata: dict[str, Any] = Field(default_factory=dict, description="Metadata to merge")

+    _strip_reserved = field_validator("metadata")(classmethod(lambda cls, v: _strip_reserved_metadata(v)))
+

 class ThreadStateUpdateRequest(BaseModel):
    """Request body for updating thread state (human-in-the-loop resume)."""
@@ -126,70 +144,25 @@ class ThreadHistoryRequest(BaseModel):
 # ---------------------------------------------------------------------------


-def _delete_thread_data(thread_id: str, paths: Paths | None = None) -> ThreadDeleteResponse:
+def _delete_thread_data(thread_id: str, paths: Paths | None = None, *, user_id: str | None = None) -> ThreadDeleteResponse:
    """Delete local persisted filesystem data for a thread."""
    path_manager = paths or get_paths()
    try:
-        path_manager.delete_thread_dir(thread_id)
+        path_manager.delete_thread_dir(thread_id, user_id=user_id)
    except ValueError as exc:
        raise HTTPException(status_code=422, detail=str(exc)) from exc
    except FileNotFoundError:
        # Not critical — thread data may not exist on disk
-        logger.debug("No local thread data to delete for %s", thread_id)
+        logger.debug("No local thread data to delete for %s", sanitize_log_param(thread_id))
        return ThreadDeleteResponse(success=True, message=f"No local data for {thread_id}")
    except Exception as exc:
-        logger.exception("Failed to delete thread data for %s", thread_id)
+        logger.exception("Failed to delete thread data for %s", sanitize_log_param(thread_id))
        raise HTTPException(status_code=500, detail="Failed to delete local thread data.") from exc

-    logger.info("Deleted local thread data for %s", thread_id)
+    logger.info("Deleted local thread data for %s", sanitize_log_param(thread_id))
    return ThreadDeleteResponse(success=True, message=f"Deleted local thread data for {thread_id}")


-async def _store_get(store, thread_id: str) -> dict | None:
-    """Fetch a thread record from the Store; returns ``None`` if absent."""
-    item = await store.aget(THREADS_NS, thread_id)
-    return item.value if item is not None else None
-
-
-async def _store_put(store, record: dict) -> None:
-    """Write a thread record to the Store."""
-    await store.aput(THREADS_NS, record["thread_id"], record)
-
-
-async def _store_upsert(store, thread_id: str, *, metadata: dict | None = None, values: dict | None = None) -> None:
-    """Create or refresh a thread record in the Store.
-
-    On creation the record is written with ``status="idle"``.  On update only
-    ``updated_at`` (and optionally ``metadata`` / ``values``) are changed so
-    that existing fields are preserved.
-
-    ``values`` carries the agent-state snapshot exposed to the frontend
-    (currently just ``{"title": "..."}``).
-    """
-    now = time.time()
-    existing = await _store_get(store, thread_id)
-    if existing is None:
-        await _store_put(
-            store,
-            {
-                "thread_id": thread_id,
-                "status": "idle",
-                "created_at": now,
-                "updated_at": now,
-                "metadata": metadata or {},
-                "values": values or {},
-            },
-        )
-    else:
-        val = dict(existing)
-        val["updated_at"] = now
-        if metadata:
-            val.setdefault("metadata", {}).update(metadata)
-        if values:
-            val.setdefault("values", {}).update(values)
-        await _store_put(store, val)
-
-
 def _derive_thread_status(checkpoint_tuple) -> str:
    """Derive thread status from checkpoint metadata."""
    if checkpoint_tuple is None:
@@ -215,22 +188,18 @@ def _derive_thread_status(checkpoint_tuple) -> str:


@router.delete("/{thread_id}", response_model=ThreadDeleteResponse)
+@require_permission("threads", "delete", owner_check=True, require_existing=True)
 async def delete_thread_data(thread_id: str, request: Request) -> ThreadDeleteResponse:
    """Delete local persisted filesystem data for a thread.

    Cleans DeerFlow-managed thread directories, removes checkpoint data,
-    and removes the thread record from the Store.
+    and removes the thread_meta row from the configured ThreadMetaStore
+    (sqlite or memory).
    """
-    # Clean local filesystem
-    response = _delete_thread_data(thread_id)
+    from app.gateway.deps import get_thread_store

-    # Remove from Store (best-effort)
-    store = get_store(request)
-    if store is not None:
-        try:
-            await store.adelete(THREADS_NS, thread_id)
-        except Exception:
-            logger.debug("Could not delete store record for thread %s (not critical)", thread_id)
+    # Clean local filesystem
+    response = _delete_thread_data(thread_id, user_id=get_effective_user_id())

    # Remove checkpoints (best-effort)
    checkpointer = getattr(request.app.state, "checkpointer", None)
@@ -239,7 +208,15 @@ async def delete_thread_data(thread_id: str, request: Request) -> ThreadDeleteRe
            if hasattr(checkpointer, "adelete_thread"):
                await checkpointer.adelete_thread(thread_id)
        except Exception:
-            logger.debug("Could not delete checkpoints for thread %s (not critical)", thread_id)
+            logger.debug("Could not delete checkpoints for thread %s (not critical)", sanitize_log_param(thread_id))
+
+    # Remove thread_meta row (best-effort) — required for sqlite backend
+    # so the deleted thread no longer appears in /threads/search.
+    try:
+        thread_store = get_thread_store(request)
+        await thread_store.delete(thread_id)
+    except Exception:
+        logger.debug("Could not delete thread_meta for %s (not critical)", sanitize_log_param(thread_id))

    return response

@@ -248,43 +225,40 @@ async def delete_thread_data(thread_id: str, request: Request) -> ThreadDeleteRe
 async def create_thread(body: ThreadCreateRequest, request: Request) -> ThreadResponse:
    """Create a new thread.

-    The thread record is written to the Store (for fast listing) and an
-    empty checkpoint is written to the checkpointer (for state reads).
+    Writes a thread_meta record (so the thread appears in /threads/search)
+    and an empty checkpoint (so state endpoints work immediately).
    Idempotent: returns the existing record when ``thread_id`` already exists.
    """
-    store = get_store(request)
+    from app.gateway.deps import get_thread_store
+
    checkpointer = get_checkpointer(request)
+    thread_store = get_thread_store(request)
    thread_id = body.thread_id or str(uuid.uuid4())
    now = time.time()
+    # ``body.metadata`` is already stripped of server-reserved keys by
+    # ``ThreadCreateRequest._strip_reserved`` — see the model definition.

-    # Idempotency: return existing record from Store when already present
-    if store is not None:
-        existing_record = await _store_get(store, thread_id)
-        if existing_record is not None:
-            return ThreadResponse(
-                thread_id=thread_id,
-                status=existing_record.get("status", "idle"),
-                created_at=str(existing_record.get("created_at", "")),
-                updated_at=str(existing_record.get("updated_at", "")),
-                metadata=existing_record.get("metadata", {}),
-            )
+    # Idempotency: return existing record when already present
+    existing_record = await thread_store.get(thread_id)
+    if existing_record is not None:
+        return ThreadResponse(
+            thread_id=thread_id,
+            status=existing_record.get("status", "idle"),
+            created_at=str(existing_record.get("created_at", "")),
+            updated_at=str(existing_record.get("updated_at", "")),
+            metadata=existing_record.get("metadata", {}),
+        )

-    # Write thread record to Store
-    if store is not None:
-        try:
-            await _store_put(
-                store,
-                {
-                    "thread_id": thread_id,
-                    "status": "idle",
-                    "created_at": now,
-                    "updated_at": now,
-                    "metadata": body.metadata,
-                },
-            )
-        except Exception:
-            logger.exception("Failed to write thread %s to store", thread_id)
-            raise HTTPException(status_code=500, detail="Failed to create thread")
+    # Write thread_meta so the thread appears in /threads/search immediately
+    try:
+        await thread_store.create(
+            thread_id,
+            assistant_id=getattr(body, "assistant_id", None),
+            metadata=body.metadata,
+        )
+    except Exception:
+        logger.exception("Failed to write thread_meta for %s", sanitize_log_param(thread_id))
+        raise HTTPException(status_code=500, detail="Failed to create thread")

    # Write an empty checkpoint so state endpoints work immediately
    config = {"configurable": {"thread_id": thread_id, "checkpoint_ns": ""}}
@@ -301,10 +275,10 @@ async def create_thread(body: ThreadCreateRequest, request: Request) -> ThreadRe
        }
        await checkpointer.aput(config, empty_checkpoint(), ckpt_metadata, {})
    except Exception:
-        logger.exception("Failed to create checkpoint for thread %s", thread_id)
+        logger.exception("Failed to create checkpoint for thread %s", sanitize_log_param(thread_id))
        raise HTTPException(status_code=500, detail="Failed to create thread")

-    logger.info("Thread created: %s", thread_id)
+    logger.info("Thread created: %s", sanitize_log_param(thread_id))
    return ThreadResponse(
        thread_id=thread_id,
        status="idle",
@@ -318,166 +292,91 @@ async def create_thread(body: ThreadCreateRequest, request: Request) -> ThreadRe
 async def search_threads(body: ThreadSearchRequest, request: Request) -> list[ThreadResponse]:
    """Search and list threads.

-    Two-phase approach:
-
-    **Phase 1 — Store (fast path, O(threads))**: returns threads that were
-    created or run through this Gateway.  Store records are tiny metadata
-    dicts so fetching all of them at once is cheap.
-
-    **Phase 2 — Checkpointer supplement (lazy migration)**: threads that
-    were created directly by LangGraph Server (and therefore absent from the
-    Store) are discovered here by iterating the shared checkpointer.  Any
-    newly found thread is immediately written to the Store so that the next
-    search skips Phase 2 for that thread — the Store converges to a full
-    index over time without a one-shot migration job.
+    Delegates to the configured ThreadMetaStore implementation
+    (SQL-backed for sqlite/postgres, Store-backed for memory mode).
    """
-    store = get_store(request)
-    checkpointer = get_checkpointer(request)
+    from app.gateway.deps import get_thread_store

-    # -----------------------------------------------------------------------
-    # Phase 1: Store
-    # -----------------------------------------------------------------------
-    merged: dict[str, ThreadResponse] = {}
-
-    if store is not None:
-        try:
-            items = await store.asearch(THREADS_NS, limit=10_000)
-        except Exception:
-            logger.warning("Store search failed — falling back to checkpointer only", exc_info=True)
-            items = []
-
-        for item in items:
-            val = item.value
-            merged[val["thread_id"]] = ThreadResponse(
-                thread_id=val["thread_id"],
-                status=val.get("status", "idle"),
-                created_at=str(val.get("created_at", "")),
-                updated_at=str(val.get("updated_at", "")),
-                metadata=val.get("metadata", {}),
-                values=val.get("values", {}),
-            )
-
-    # -----------------------------------------------------------------------
-    # Phase 2: Checkpointer supplement
-    # Discovers threads not yet in the Store (e.g. created by LangGraph
-    # Server) and lazily migrates them so future searches skip this phase.
-    # -----------------------------------------------------------------------
-    try:
-        async for checkpoint_tuple in checkpointer.alist(None):
-            cfg = getattr(checkpoint_tuple, "config", {})
-            thread_id = cfg.get("configurable", {}).get("thread_id")
-            if not thread_id or thread_id in merged:
-                continue
-
-            # Skip sub-graph checkpoints (checkpoint_ns is non-empty for those)
-            if cfg.get("configurable", {}).get("checkpoint_ns", ""):
-                continue
-
-            ckpt_meta = getattr(checkpoint_tuple, "metadata", {}) or {}
-            # Strip LangGraph internal keys from the user-visible metadata dict
-            user_meta = {k: v for k, v in ckpt_meta.items() if k not in ("created_at", "updated_at", "step", "source", "writes", "parents")}
-
-            # Extract state values (title) from the checkpoint's channel_values
-            checkpoint_data = getattr(checkpoint_tuple, "checkpoint", {}) or {}
-            channel_values = checkpoint_data.get("channel_values", {})
-            ckpt_values = {}
-            if title := channel_values.get("title"):
-                ckpt_values["title"] = title
-
-            thread_resp = ThreadResponse(
-                thread_id=thread_id,
-                status=_derive_thread_status(checkpoint_tuple),
-                created_at=str(ckpt_meta.get("created_at", "")),
-                updated_at=str(ckpt_meta.get("updated_at", ckpt_meta.get("created_at", ""))),
-                metadata=user_meta,
-                values=ckpt_values,
-            )
-            merged[thread_id] = thread_resp
-
-            # Lazy migration — write to Store so the next search finds it there
-            if store is not None:
-                try:
-                    await _store_upsert(store, thread_id, metadata=user_meta, values=ckpt_values or None)
-                except Exception:
-                    logger.debug("Failed to migrate thread %s to store (non-fatal)", thread_id)
-    except Exception:
-        logger.exception("Checkpointer scan failed during thread search")
-        # Don't raise — return whatever was collected from Store + partial scan
-
-    # -----------------------------------------------------------------------
-    # Phase 3: Filter → sort → paginate
-    # -----------------------------------------------------------------------
-    results = list(merged.values())
-
-    if body.metadata:
-        results = [r for r in results if all(r.metadata.get(k) == v for k, v in body.metadata.items())]
-
-    if body.status:
-        results = [r for r in results if r.status == body.status]
-
-    results.sort(key=lambda r: r.updated_at, reverse=True)
-    return results[body.offset : body.offset + body.limit]
+    repo = get_thread_store(request)
+    rows = await repo.search(
+        metadata=body.metadata or None,
+        status=body.status,
+        limit=body.limit,
+        offset=body.offset,
+    )
+    return [
+        ThreadResponse(
+            thread_id=r["thread_id"],
+            status=r.get("status", "idle"),
+            created_at=r.get("created_at", ""),
+            updated_at=r.get("updated_at", ""),
+            metadata=r.get("metadata", {}),
+            values={"title": r["display_name"]} if r.get("display_name") else {},
+            interrupts={},
+        )
+        for r in rows
+    ]


@router.patch("/{thread_id}", response_model=ThreadResponse)
+@require_permission("threads", "write", owner_check=True, require_existing=True)
 async def patch_thread(thread_id: str, body: ThreadPatchRequest, request: Request) -> ThreadResponse:
    """Merge metadata into a thread record."""
-    store = get_store(request)
-    if store is None:
-        raise HTTPException(status_code=503, detail="Store not available")
+    from app.gateway.deps import get_thread_store

-    record = await _store_get(store, thread_id)
+    thread_store = get_thread_store(request)
+    record = await thread_store.get(thread_id)
    if record is None:
        raise HTTPException(status_code=404, detail=f"Thread {thread_id} not found")

-    now = time.time()
-    updated = dict(record)
-    updated.setdefault("metadata", {}).update(body.metadata)
-    updated["updated_at"] = now
-
+    # ``body.metadata`` already stripped by ``ThreadPatchRequest._strip_reserved``.
    try:
-        await _store_put(store, updated)
+        await thread_store.update_metadata(thread_id, body.metadata)
    except Exception:
-        logger.exception("Failed to patch thread %s", thread_id)
+        logger.exception("Failed to patch thread %s", sanitize_log_param(thread_id))
        raise HTTPException(status_code=500, detail="Failed to update thread")

+    # Re-read to get the merged metadata + refreshed updated_at
+    record = await thread_store.get(thread_id) or record
    return ThreadResponse(
        thread_id=thread_id,
-        status=updated.get("status", "idle"),
-        created_at=str(updated.get("created_at", "")),
-        updated_at=str(now),
-        metadata=updated.get("metadata", {}),
+        status=record.get("status", "idle"),
+        created_at=str(record.get("created_at", "")),
+        updated_at=str(record.get("updated_at", "")),
+        metadata=record.get("metadata", {}),
    )


@router.get("/{thread_id}", response_model=ThreadResponse)
+@require_permission("threads", "read", owner_check=True)
 async def get_thread(thread_id: str, request: Request) -> ThreadResponse:
    """Get thread info.

-    Reads metadata from the Store and derives the accurate execution
-    status from the checkpointer.  Falls back to the checkpointer alone
-    for threads that pre-date Store adoption (backward compat).
+    Reads metadata from the ThreadMetaStore and derives the accurate
+    execution status from the checkpointer.  Falls back to the checkpointer
+    alone for threads that pre-date ThreadMetaStore adoption (backward compat).
    """
-    store = get_store(request)
+    from app.gateway.deps import get_thread_store
+
+    thread_store = get_thread_store(request)
    checkpointer = get_checkpointer(request)

-    record: dict | None = None
-    if store is not None:
-        record = await _store_get(store, thread_id)
+    record: dict | None = await thread_store.get(thread_id)

    # Derive accurate status from the checkpointer
    config = {"configurable": {"thread_id": thread_id, "checkpoint_ns": ""}}
    try:
        checkpoint_tuple = await checkpointer.aget_tuple(config)
    except Exception:
-        logger.exception("Failed to get checkpoint for thread %s", thread_id)
+        logger.exception("Failed to get checkpoint for thread %s", sanitize_log_param(thread_id))
        raise HTTPException(status_code=500, detail="Failed to get thread")

    if record is None and checkpoint_tuple is None:
        raise HTTPException(status_code=404, detail=f"Thread {thread_id} not found")

-    # If the thread exists in the checkpointer but not the store (e.g. legacy
-    # data), synthesize a minimal store record from the checkpoint metadata.
+    # If the thread exists in the checkpointer but not in thread_meta (e.g.
+    # legacy data created before thread_meta adoption), synthesize a minimal
+    # record from the checkpoint metadata.
    if record is None and checkpoint_tuple is not None:
        ckpt_meta = getattr(checkpoint_tuple, "metadata", {}) or {}
        record = {
@@ -505,7 +404,9 @@ async def get_thread(thread_id: str, request: Request) -> ThreadResponse:
    )


+# ---------------------------------------------------------------------------
@router.get("/{thread_id}/state", response_model=ThreadStateResponse)
+@require_permission("threads", "read", owner_check=True)
 async def get_thread_state(thread_id: str, request: Request) -> ThreadStateResponse:
    """Get the latest state snapshot for a thread.

@@ -518,7 +419,7 @@ async def get_thread_state(thread_id: str, request: Request) -> ThreadStateRespo
    try:
        checkpoint_tuple = await checkpointer.aget_tuple(config)
    except Exception:
-        logger.exception("Failed to get state for thread %s", thread_id)
+        logger.exception("Failed to get state for thread %s", sanitize_log_param(thread_id))
        raise HTTPException(status_code=500, detail="Failed to get thread state")

    if checkpoint_tuple is None:
@@ -542,8 +443,10 @@ async def get_thread_state(thread_id: str, request: Request) -> ThreadStateRespo
    next_tasks = [t.name for t in tasks_raw if hasattr(t, "name")]
    tasks = [{"id": getattr(t, "id", ""), "name": getattr(t, "name", "")} for t in tasks_raw]

+    values = serialize_channel_values(channel_values)
+
    return ThreadStateResponse(
-        values=serialize_channel_values(channel_values),
+        values=values,
        next=next_tasks,
        metadata=metadata,
        checkpoint={"id": checkpoint_id, "ts": str(metadata.get("created_at", ""))},
@@ -555,15 +458,19 @@ async def get_thread_state(thread_id: str, request: Request) -> ThreadStateRespo


@router.post("/{thread_id}/state", response_model=ThreadStateResponse)
+@require_permission("threads", "write", owner_check=True, require_existing=True)
 async def update_thread_state(thread_id: str, body: ThreadStateUpdateRequest, request: Request) -> ThreadStateResponse:
    """Update thread state (e.g. for human-in-the-loop resume or title rename).

    Writes a new checkpoint that merges *body.values* into the latest
-    channel values, then syncs any updated ``title`` field back to the Store
-    so that ``/threads/search`` reflects the change immediately.
+    channel values, then syncs any updated ``title`` field through the
+    ThreadMetaStore abstraction so that ``/threads/search`` reflects the
+    change immediately in both sqlite and memory backends.
    """
+    from app.gateway.deps import get_thread_store
+
    checkpointer = get_checkpointer(request)
-    store = get_store(request)
+    thread_store = get_thread_store(request)

    # checkpoint_ns must be present in the config for aput — default to ""
    # (the root graph namespace).  checkpoint_id is optional; omitting it
@@ -580,7 +487,7 @@ async def update_thread_state(thread_id: str, body: ThreadStateUpdateRequest, re
    try:
        checkpoint_tuple = await checkpointer.aget_tuple(read_config)
    except Exception:
-        logger.exception("Failed to get state for thread %s", thread_id)
+        logger.exception("Failed to get state for thread %s", sanitize_log_param(thread_id))
        raise HTTPException(status_code=500, detail="Failed to get thread state")

    if checkpoint_tuple is None:
@@ -614,19 +521,22 @@ async def update_thread_state(thread_id: str, body: ThreadStateUpdateRequest, re
    try:
        new_config = await checkpointer.aput(write_config, checkpoint, metadata, {})
    except Exception:
-        logger.exception("Failed to update state for thread %s", thread_id)
+        logger.exception("Failed to update state for thread %s", sanitize_log_param(thread_id))
        raise HTTPException(status_code=500, detail="Failed to update thread state")

    new_checkpoint_id: str | None = None
    if isinstance(new_config, dict):
        new_checkpoint_id = new_config.get("configurable", {}).get("checkpoint_id")

-    # Sync title changes to the Store so /threads/search reflects them immediately.
-    if store is not None and body.values and "title" in body.values:
-        try:
-            await _store_upsert(store, thread_id, values={"title": body.values["title"]})
-        except Exception:
-            logger.debug("Failed to sync title to store for thread %s (non-fatal)", thread_id)
+    # Sync title changes through the ThreadMetaStore abstraction so /threads/search
+    # reflects them immediately in both sqlite and memory backends.
+    if body.values and "title" in body.values:
+        new_title = body.values["title"]
+        if new_title:  # Skip empty strings and None
+            try:
+                await thread_store.update_display_name(thread_id, new_title)
+            except Exception:
+                logger.debug("Failed to sync title to thread_meta for %s (non-fatal)", sanitize_log_param(thread_id))

    return ThreadStateResponse(
        values=serialize_channel_values(channel_values),
@@ -638,8 +548,16 @@ async def update_thread_state(thread_id: str, body: ThreadStateUpdateRequest, re


@router.post("/{thread_id}/history", response_model=list[HistoryEntry])
+@require_permission("threads", "read", owner_check=True)
 async def get_thread_history(thread_id: str, body: ThreadHistoryRequest, request: Request) -> list[HistoryEntry]:
-    """Get checkpoint history for a thread."""
+    """Get checkpoint history for a thread.
+
+    Messages are read from the checkpointer's channel values (the
+    authoritative source) and serialized via
+    :func:`~deerflow.runtime.serialization.serialize_channel_values`.
+    Only the latest (first) checkpoint carries the ``messages`` key to
+    avoid duplicating them across every entry.
+    """
    checkpointer = get_checkpointer(request)

    config: dict[str, Any] = {"configurable": {"thread_id": thread_id}}
@@ -647,6 +565,7 @@ async def get_thread_history(thread_id: str, body: ThreadHistoryRequest, request
        config["configurable"]["checkpoint_id"] = body.before

    entries: list[HistoryEntry] = []
+    is_latest_checkpoint = True
    try:
        async for checkpoint_tuple in checkpointer.alist(config, limit=body.limit):
            ckpt_config = getattr(checkpoint_tuple, "config", {})
@@ -661,22 +580,42 @@ async def get_thread_history(thread_id: str, body: ThreadHistoryRequest, request

            channel_values = checkpoint.get("channel_values", {})

+            # Build values from checkpoint channel_values
+            values: dict[str, Any] = {}
+            if title := channel_values.get("title"):
+                values["title"] = title
+            if thread_data := channel_values.get("thread_data"):
+                values["thread_data"] = thread_data
+
+            # Attach messages only to the latest checkpoint entry.
+            if is_latest_checkpoint:
+                messages = channel_values.get("messages")
+                if messages:
+                    values["messages"] = serialize_channel_values({"messages": messages}).get("messages", [])
+            is_latest_checkpoint = False
+
            # Derive next tasks
            tasks_raw = getattr(checkpoint_tuple, "tasks", []) or []
            next_tasks = [t.name for t in tasks_raw if hasattr(t, "name")]

+            # Strip LangGraph internal keys from metadata
+            user_meta = {k: v for k, v in metadata.items() if k not in ("created_at", "updated_at", "step", "source", "writes", "parents")}
+            # Keep step for ordering context
+            if "step" in metadata:
+                user_meta["step"] = metadata["step"]
+
            entries.append(
                HistoryEntry(
                    checkpoint_id=checkpoint_id,
                    parent_checkpoint_id=parent_id,
-                    metadata=metadata,
-                    values=serialize_channel_values(channel_values),
+                    metadata=user_meta,
+                    values=values,
                    created_at=str(metadata.get("created_at", "")),
                    next=next_tasks,
                )
            )
    except Exception:
-        logger.exception("Failed to get history for thread %s", thread_id)
+        logger.exception("Failed to get history for thread %s", sanitize_log_param(thread_id))
        raise HTTPException(status_code=500, detail="Failed to get thread history")

    return entries
@@ -4,11 +4,15 @@ import logging
 import os
 import stat

-from fastapi import APIRouter, File, HTTPException, UploadFile
+from fastapi import APIRouter, Depends, File, HTTPException, Request, UploadFile
 from pydantic import BaseModel

+from app.gateway.authz import require_permission
+from app.gateway.deps import get_config
+from deerflow.config.app_config import AppConfig
 from deerflow.config.paths import get_paths
-from deerflow.sandbox.sandbox_provider import get_sandbox_provider
+from deerflow.runtime.user_context import get_effective_user_id
+from deerflow.sandbox.sandbox_provider import SandboxProvider, get_sandbox_provider
 from deerflow.uploads.manager import (
    PathTraversalError,
    delete_file_safe,
@@ -53,10 +57,40 @@ def _make_file_sandbox_writable(file_path: os.PathLike[str] | str) -> None:
    os.chmod(file_path, writable_mode, **chmod_kwargs)


+def _uses_thread_data_mounts(sandbox_provider: SandboxProvider) -> bool:
+    return bool(getattr(sandbox_provider, "uses_thread_data_mounts", False))
+
+
+def _get_uploads_config_value(app_config: AppConfig, key: str, default: object) -> object:
+    """Read a value from the uploads config, supporting dict and attribute access."""
+    uploads_cfg = getattr(app_config, "uploads", None)
+    if isinstance(uploads_cfg, dict):
+        return uploads_cfg.get(key, default)
+    return getattr(uploads_cfg, key, default)
+
+
+def _auto_convert_documents_enabled(app_config: AppConfig) -> bool:
+    """Return whether automatic host-side document conversion is enabled.
+
+    The secure default is disabled unless an operator explicitly opts in via
+    uploads.auto_convert_documents in config.yaml.
+    """
+    try:
+        raw = _get_uploads_config_value(app_config, "auto_convert_documents", False)
+        if isinstance(raw, str):
+            return raw.strip().lower() in {"1", "true", "yes", "on"}
+        return bool(raw)
+    except Exception:
+        return False
+
+
@router.post("", response_model=UploadResponse)
+@require_permission("threads", "write", owner_check=True, require_existing=True)
 async def upload_files(
    thread_id: str,
+    request: Request,
    files: list[UploadFile] = File(...),
+    app_config: AppConfig = Depends(get_config),
 ) -> UploadResponse:
    """Upload multiple files to a thread's uploads directory."""
    if not files:
@@ -66,12 +100,16 @@ async def upload_files(
        uploads_dir = ensure_uploads_dir(thread_id)
    except ValueError as e:
        raise HTTPException(status_code=400, detail=str(e))
-    sandbox_uploads = get_paths().sandbox_uploads_dir(thread_id)
+    sandbox_uploads = get_paths().sandbox_uploads_dir(thread_id, user_id=get_effective_user_id())
    uploaded_files = []

-    sandbox_provider = get_sandbox_provider()
-    sandbox_id = sandbox_provider.acquire(thread_id)
-    sandbox = sandbox_provider.get(sandbox_id)
+    sandbox_provider = get_sandbox_provider(app_config)
+    sync_to_sandbox = not _uses_thread_data_mounts(sandbox_provider)
+    sandbox = None
+    if sync_to_sandbox:
+        sandbox_id = sandbox_provider.acquire(thread_id)
+        sandbox = sandbox_provider.get(sandbox_id)
+    auto_convert_documents = _auto_convert_documents_enabled(app_config)

    for file in files:
        if not file.filename:
@@ -90,7 +128,7 @@ async def upload_files(

            virtual_path = upload_virtual_path(safe_filename)

-            if sandbox_id != "local":
+            if sync_to_sandbox and sandbox is not None:
                _make_file_sandbox_writable(file_path)
                sandbox.update_file(virtual_path, content)

@@ -105,12 +143,12 @@ async def upload_files(
            logger.info(f"Saved file: {safe_filename} ({len(content)} bytes) to {file_info['path']}")

            file_ext = file_path.suffix.lower()
-            if file_ext in CONVERTIBLE_EXTENSIONS:
+            if auto_convert_documents and file_ext in CONVERTIBLE_EXTENSIONS:
                md_path = await convert_file_to_markdown(file_path)
                if md_path:
                    md_virtual_path = upload_virtual_path(md_path.name)

-                    if sandbox_id != "local":
+                    if sync_to_sandbox and sandbox is not None:
                        _make_file_sandbox_writable(md_path)
                        sandbox.update_file(md_virtual_path, md_path.read_bytes())

@@ -133,7 +171,8 @@ async def upload_files(


@router.get("/list", response_model=dict)
-async def list_uploaded_files(thread_id: str) -> dict:
+@require_permission("threads", "read", owner_check=True)
+async def list_uploaded_files(thread_id: str, request: Request) -> dict:
    """List all files in a thread's uploads directory."""
    try:
        uploads_dir = get_uploads_dir(thread_id)
@@ -143,7 +182,7 @@ async def list_uploaded_files(thread_id: str) -> dict:
    enrich_file_listing(result, thread_id)

    # Gateway additionally includes the sandbox-relative path.
-    sandbox_uploads = get_paths().sandbox_uploads_dir(thread_id)
+    sandbox_uploads = get_paths().sandbox_uploads_dir(thread_id, user_id=get_effective_user_id())
    for f in result["files"]:
        f["path"] = str(sandbox_uploads / f["filename"])

@@ -151,7 +190,8 @@ async def list_uploaded_files(thread_id: str) -> dict:


@router.delete("/{filename}")
-async def delete_uploaded_file(thread_id: str, filename: str) -> dict:
+@require_permission("threads", "delete", owner_check=True, require_existing=True)
+async def delete_uploaded_file(thread_id: str, filename: str, request: Request) -> dict:
    """Delete a file from a thread's uploads directory."""
    try:
        uploads_dir = get_uploads_dir(thread_id)
@@ -8,16 +8,19 @@ frames, and consuming stream bridge events.  Router modules
 from __future__ import annotations

 import asyncio
+import dataclasses
 import json
 import logging
 import re
 import time
+from collections.abc import Mapping
 from typing import Any

 from fastapi import HTTPException, Request
 from langchain_core.messages import HumanMessage

-from app.gateway.deps import get_checkpointer, get_run_manager, get_store, get_stream_bridge
+from app.gateway.deps import get_run_context, get_run_manager, get_run_store, get_stream_bridge
+from app.gateway.utils import sanitize_log_param
 from deerflow.runtime import (
    END_SENTINEL,
    HEARTBEAT_SENTINEL,
@@ -101,9 +104,10 @@ def resolve_agent_factory(assistant_id: str | None):
    """Resolve the agent factory callable from config.

    Custom agents are implemented as ``lead_agent`` + an ``agent_name``
-    injected into ``configurable`` — see :func:`build_run_config`.  All
-    ``assistant_id`` values therefore map to the same factory; the routing
-    happens inside ``make_lead_agent`` when it reads ``cfg["agent_name"]``.
+    injected into ``configurable`` or ``context`` — see
+    :func:`build_run_config`.  All ``assistant_id`` values therefore map to the
+    same factory; the routing happens inside ``make_lead_agent`` when it reads
+    ``cfg["agent_name"]``.
    """
    from deerflow.agents.lead_agent.agent import make_lead_agent

@@ -120,10 +124,12 @@ def build_run_config(
    """Build a RunnableConfig dict for the agent.

    When *assistant_id* refers to a custom agent (anything other than
-    ``"lead_agent"`` / ``None``), the name is forwarded as
-    ``configurable["agent_name"]``.  ``make_lead_agent`` reads this key to
-    load the matching ``agents/<name>/SOUL.md`` and per-agent config —
-    without it the agent silently runs as the default lead agent.
+    ``"lead_agent"`` / ``None``), the name is forwarded as ``agent_name`` in
+    whichever runtime options container is active: ``context`` for
+    LangGraph >= 0.6.0 requests, otherwise ``configurable``.
+    ``make_lead_agent`` reads this key to load the matching
+    ``agents/<name>/SOUL.md`` and per-agent config — without it the agent
+    silently runs as the default lead agent.

    This mirrors the channel manager's ``_resolve_run_params`` logic so that
    the LangGraph Platform-compatible HTTP API and the IM channel path behave
@@ -142,7 +148,14 @@ def build_run_config(
                    thread_id,
                    list(request_config.get("configurable", {}).keys()),
                )
-            config["context"] = request_config["context"]
+            context_value = request_config["context"]
+            if context_value is None:
+                context = {}
+            elif isinstance(context_value, Mapping):
+                context = dict(context_value)
+            else:
+                raise ValueError("request config 'context' must be a mapping or null.")
+            config["context"] = context
        else:
            configurable = {"thread_id": thread_id}
            configurable.update(request_config.get("configurable", {}))
@@ -154,13 +167,19 @@ def build_run_config(
        config["configurable"] = {"thread_id": thread_id}

    # Inject custom agent name when the caller specified a non-default assistant.
-    # Honour an explicit configurable["agent_name"] in the request if already set.
-    if assistant_id and assistant_id != _DEFAULT_ASSISTANT_ID and "configurable" in config:
-        if "agent_name" not in config["configurable"]:
-            normalized = assistant_id.strip().lower().replace("_", "-")
-            if not normalized or not re.fullmatch(r"[a-z0-9-]+", normalized):
-                raise ValueError(f"Invalid assistant_id {assistant_id!r}: must contain only letters, digits, and hyphens after normalization.")
-            config["configurable"]["agent_name"] = normalized
+    # Honour an explicit agent_name in the active runtime options container.
+    if assistant_id and assistant_id != _DEFAULT_ASSISTANT_ID:
+        normalized = assistant_id.strip().lower().replace("_", "-")
+        if not normalized or not re.fullmatch(r"[a-z0-9-]+", normalized):
+            raise ValueError(f"Invalid assistant_id {assistant_id!r}: must contain only letters, digits, and hyphens after normalization.")
+        if "configurable" in config:
+            target = config["configurable"]
+        elif "context" in config:
+            target = config["context"]
+        else:
+            target = config.setdefault("configurable", {})
+        if target is not None and "agent_name" not in target:
+            target["agent_name"] = normalized
    if metadata:
        config.setdefault("metadata", {}).update(metadata)
    return config
@@ -171,71 +190,6 @@ def build_run_config(
 # ---------------------------------------------------------------------------


-async def _upsert_thread_in_store(store, thread_id: str, metadata: dict | None) -> None:
-    """Create or refresh the thread record in the Store.
-
-    Called from :func:`start_run` so that threads created via the stateless
-    ``/runs/stream`` endpoint (which never calls ``POST /threads``) still
-    appear in ``/threads/search`` results.
-    """
-    # Deferred import to avoid circular import with the threads router module.
-    from app.gateway.routers.threads import _store_upsert
-
-    try:
-        await _store_upsert(store, thread_id, metadata=metadata)
-    except Exception:
-        logger.warning("Failed to upsert thread %s in store (non-fatal)", thread_id)
-
-
-async def _sync_thread_title_after_run(
-    run_task: asyncio.Task,
-    thread_id: str,
-    checkpointer: Any,
-    store: Any,
-) -> None:
-    """Wait for *run_task* to finish, then persist the generated title to the Store.
-
-    TitleMiddleware writes the generated title to the LangGraph agent state
-    (checkpointer) but the Gateway's Store record is not updated automatically.
-    This coroutine closes that gap by reading the final checkpoint after the
-    run completes and syncing ``values.title`` into the Store record so that
-    subsequent ``/threads/search`` responses include the correct title.
-
-    Runs as a fire-and-forget :func:`asyncio.create_task`; failures are
-    logged at DEBUG level and never propagate.
-    """
-    # Wait for the background run task to complete (any outcome).
-    # asyncio.wait does not propagate task exceptions — it just returns
-    # when the task is done, cancelled, or failed.
-    await asyncio.wait({run_task})
-
-    # Deferred import to avoid circular import with the threads router module.
-    from app.gateway.routers.threads import _store_get, _store_put
-
-    try:
-        ckpt_config = {"configurable": {"thread_id": thread_id, "checkpoint_ns": ""}}
-        ckpt_tuple = await checkpointer.aget_tuple(ckpt_config)
-        if ckpt_tuple is None:
-            return
-
-        channel_values = ckpt_tuple.checkpoint.get("channel_values", {})
-        title = channel_values.get("title")
-        if not title:
-            return
-
-        existing = await _store_get(store, thread_id)
-        if existing is None:
-            return
-
-        updated = dict(existing)
-        updated.setdefault("values", {})["title"] = title
-        updated["updated_at"] = time.time()
-        await _store_put(store, updated)
-        logger.debug("Synced title %r for thread %s", title, thread_id)
-    except Exception:
-        logger.debug("Failed to sync title for thread %s (non-fatal)", thread_id, exc_info=True)
-
-
 async def start_run(
    body: Any,
    thread_id: str,
@@ -255,11 +209,25 @@ async def start_run(
    """
    bridge = get_stream_bridge(request)
    run_mgr = get_run_manager(request)
-    checkpointer = get_checkpointer(request)
-    store = get_store(request)
+    run_ctx = get_run_context(request)

    disconnect = DisconnectMode.cancel if body.on_disconnect == "cancel" else DisconnectMode.continue_

+    # Resolve follow_up_to_run_id: explicit from request, or auto-detect from latest successful run
+    follow_up_to_run_id = getattr(body, "follow_up_to_run_id", None)
+    if follow_up_to_run_id is None:
+        run_store = get_run_store(request)
+        try:
+            recent_runs = await run_store.list_by_thread(thread_id, limit=1)
+            if recent_runs and recent_runs[0].get("status") == "success":
+                follow_up_to_run_id = recent_runs[0]["run_id"]
+        except Exception:
+            pass  # Don't block run creation
+
+    # Enrich base context with per-run field
+    if follow_up_to_run_id:
+        run_ctx = dataclasses.replace(run_ctx, follow_up_to_run_id=follow_up_to_run_id)
+
    try:
        record = await run_mgr.create_or_reject(
            thread_id,
@@ -268,17 +236,28 @@ async def start_run(
            metadata=body.metadata or {},
            kwargs={"input": body.input, "config": body.config},
            multitask_strategy=body.multitask_strategy,
+            follow_up_to_run_id=follow_up_to_run_id,
        )
    except ConflictError as exc:
        raise HTTPException(status_code=409, detail=str(exc)) from exc
    except UnsupportedStrategyError as exc:
        raise HTTPException(status_code=501, detail=str(exc)) from exc

-    # Ensure the thread is visible in /threads/search, even for threads that
-    # were never explicitly created via POST /threads (e.g. stateless runs).
-    store = get_store(request)
-    if store is not None:
-        await _upsert_thread_in_store(store, thread_id, body.metadata)
+    # Upsert thread metadata so the thread appears in /threads/search,
+    # even for threads that were never explicitly created via POST /threads
+    # (e.g. stateless runs).
+    try:
+        existing = await run_ctx.thread_store.get(thread_id)
+        if existing is None:
+            await run_ctx.thread_store.create(
+                thread_id,
+                assistant_id=body.assistant_id,
+                metadata=body.metadata,
+            )
+        else:
+            await run_ctx.thread_store.update_status(thread_id, "running")
+    except Exception:
+        logger.warning("Failed to upsert thread_meta for %s (non-fatal)", sanitize_log_param(thread_id))

    agent_factory = resolve_agent_factory(body.assistant_id)
    graph_input = normalize_input(body.input)
@@ -298,6 +277,8 @@ async def start_run(
            "is_plan_mode",
            "subagent_enabled",
            "max_concurrent_subagents",
+            "agent_name",
+            "is_bootstrap",
        }
        configurable = config.setdefault("configurable", {})
        for key in _CONTEXT_CONFIGURABLE_KEYS:
@@ -311,8 +292,7 @@ async def start_run(
            bridge,
            run_mgr,
            record,
-            checkpointer=checkpointer,
-            store=store,
+            ctx=run_ctx,
            agent_factory=agent_factory,
            graph_input=graph_input,
            config=config,
@@ -324,11 +304,9 @@ async def start_run(
    )
    record.task = task

-    # After the run completes, sync the title generated by TitleMiddleware from
-    # the checkpointer into the Store record so that /threads/search returns the
-    # correct title instead of an empty values dict.
-    if store is not None:
-        asyncio.create_task(_sync_thread_title_after_run(task, thread_id, checkpointer, store))
+    # Title sync is handled by worker.py's finally block which reads the
+    # title from the checkpoint and calls thread_store.update_display_name
+    # after the run completes.

    return record

@@ -0,0 +1,6 @@
+"""Shared utility helpers for the Gateway layer."""
+
+
+def sanitize_log_param(value: str) -> str:
+    """Strip control characters to prevent log injection."""
+    return value.replace("\n", "").replace("\r", "").replace("\x00", "")
@@ -19,24 +19,78 @@ import asyncio
 import logging

 from dotenv import load_dotenv
-from langchain_core.messages import HumanMessage

-from deerflow.agents import make_lead_agent
+try:
+    from prompt_toolkit import PromptSession
+    from prompt_toolkit.history import InMemoryHistory
+
+    _HAS_PROMPT_TOOLKIT = True
+except ImportError:
+    _HAS_PROMPT_TOOLKIT = False

 load_dotenv()

-logging.basicConfig(
-    level=logging.INFO,
-    format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
-    datefmt="%Y-%m-%d %H:%M:%S",
-)
+_LOG_FMT = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+_LOG_DATEFMT = "%Y-%m-%d %H:%M:%S"
+
+
+def _logging_level_from_config(name: str) -> int:
+    """Map ``config.yaml`` ``log_level`` string to a ``logging`` level constant."""
+    mapping = logging.getLevelNamesMapping()
+    return mapping.get((name or "info").strip().upper(), logging.INFO)
+
+
+def _setup_logging(log_level: str) -> None:
+    """Send application logs to ``debug.log`` at *log_level*; do not print them on the console.
+
+    Idempotent: any pre-existing handlers on the root logger (e.g. installed by
+    ``logging.basicConfig`` in transitively imported modules) are removed so the
+    debug session output only lands in ``debug.log``.
+    """
+    level = _logging_level_from_config(log_level)
+    root = logging.root
+    for h in list(root.handlers):
+        root.removeHandler(h)
+        h.close()
+    root.setLevel(level)
+
+    file_handler = logging.FileHandler("debug.log", mode="a", encoding="utf-8")
+    file_handler.setLevel(level)
+    file_handler.setFormatter(logging.Formatter(_LOG_FMT, datefmt=_LOG_DATEFMT))
+    root.addHandler(file_handler)
+
+
+def _update_logging_level(log_level: str) -> None:
+    """Update the root logger and existing handlers to *log_level*."""
+    level = _logging_level_from_config(log_level)
+    root = logging.root
+    root.setLevel(level)
+    for handler in root.handlers:
+        handler.setLevel(level)


 async def main():
+    # Install file logging first so warnings emitted while loading config do not
+    # leak onto the interactive terminal via Python's lastResort handler.
+    _setup_logging("info")
+
+    from deerflow.config import get_app_config
+
+    app_config = get_app_config()
+    _update_logging_level(app_config.log_level)
+
+    # Delay the rest of the deerflow imports until *after* logging is installed
+    # so that any import-time side effects (e.g. deerflow.agents starts a
+    # background skill-loader thread on import) emit logs to debug.log instead
+    # of leaking onto the interactive terminal via Python's lastResort handler.
+    from langchain_core.messages import HumanMessage
+    from langgraph.runtime import Runtime
+
+    from deerflow.agents import make_lead_agent
+    from deerflow.mcp import initialize_mcp_tools
+
    # Initialize MCP tools at startup
    try:
-        from deerflow.mcp import initialize_mcp_tools
-
        await initialize_mcp_tools()
    except Exception as e:
        print(f"Warning: Failed to initialize MCP tools: {e}")
@@ -52,16 +106,27 @@ async def main():
        }
    }

+    runtime = Runtime(context={"thread_id": config["configurable"]["thread_id"]})
+    config["configurable"]["__pregel_runtime"] = runtime
+
    agent = make_lead_agent(config)

+    session = PromptSession(history=InMemoryHistory()) if _HAS_PROMPT_TOOLKIT else None
+
    print("=" * 50)
    print("Lead Agent Debug Mode")
    print("Type 'quit' or 'exit' to stop")
+    print(f"Logs: debug.log (log_level={app_config.log_level})")
+    if not _HAS_PROMPT_TOOLKIT:
+        print("Tip: `uv sync --group dev` to enable arrow-key & history support")
    print("=" * 50)

    while True:
        try:
-            user_input = input("\nYou: ").strip()
+            if session:
+                user_input = (await session.prompt_async("\nYou: ")).strip()
+            else:
+                user_input = input("\nYou: ").strip()
            if not user_input:
                continue
            if user_input.lower() in ("quit", "exit"):
@@ -70,15 +135,15 @@ async def main():

            # Invoke the agent
            state = {"messages": [HumanMessage(content=user_input)]}
-            result = await agent.ainvoke(state, config=config, context={"thread_id": "debug-thread-001"})
+            result = await agent.ainvoke(state, config=config)

            # Print the response
            if result.get("messages"):
                last_message = result["messages"][-1]
                print(f"\nAgent: {last_message.content}")

-        except KeyboardInterrupt:
-            print("\nInterrupted. Goodbye!")
+        except (KeyboardInterrupt, EOFError):
+            print("\nGoodbye!")
            break
        except Exception as e:
            print(f"\nError: {e}")
@@ -199,7 +199,7 @@ class ThreadState(AgentState):
 │   Built-in Tools    │  │  Configured Tools   │  │     MCP Tools       │
 │  (packages/harness/deerflow/tools/)       │  │  (config.yaml)      │  │  (extensions.json)  │
 ├─────────────────────┤  ├─────────────────────┤  ├─────────────────────┤
-│ - present_file      │  │ - web_search        │  │ - github            │
+│ - present_files     │  │ - web_search        │  │ - github            │
 │ - ask_clarification │  │ - web_fetch         │  │ - filesystem        │
 │ - view_image        │  │ - bash              │  │ - postgres          │
 │                     │  │ - read_file         │  │ - brave-search      │
@@ -0,0 +1,77 @@
+# Docker Test Gap (Section 七 7.4)
+
+This file documents the only **un-executed** test cases from
+`backend/docs/AUTH_TEST_PLAN.md` after the full release validation pass.
+
+## Why this gap exists
+
+The release validation environment (sg_dev: `10.251.229.92`) **does not have
+a Docker daemon installed**. The TC-DOCKER cases are container-runtime
+behavior tests that need an actual Docker engine to spin up
+`docker/docker-compose.yaml` services.
+
+```bash
+$ ssh sg_dev "which docker; docker --version"
+# (empty)
+# bash: docker: command not found
+```
+
+All other test plan sections were executed against either:
+- The local dev box (Mac, all services running locally), or
+- The deployed sg_dev instance (gateway + frontend + nginx via SSH tunnel)
+
+## Cases not executed
+
+| Case | Title | What it covers | Why not run |
+|---|---|---|---|
+| TC-DOCKER-01 | `users.db` volume persistence | Verify the `DEER_FLOW_HOME` bind mount survives container restart | needs `docker compose up` |
+| TC-DOCKER-02 | Session persistence across container restart | `AUTH_JWT_SECRET` env var keeps cookies valid after `docker compose down && up` | needs `docker compose down/up` |
+| TC-DOCKER-03 | Per-worker rate limiter divergence | Confirms in-process `_login_attempts` dict doesn't share state across `gunicorn` workers (4 by default in the compose file); known limitation, documented | needs multi-worker container |
+| TC-DOCKER-04 | IM channels skip AuthMiddleware | Verify Feishu/Slack/Telegram dispatchers run in-container against `http://langgraph:2024` without going through nginx | needs `docker logs` |
+| TC-DOCKER-05 | Admin credentials surfacing | **Updated post-simplify** — was "log scrape", now "0600 credential file in `DEER_FLOW_HOME`". The file-based behavior is already validated by TC-1.1 + TC-UPG-13 on sg_dev (non-Docker), so the only Docker-specific gap is verifying the volume mount carries the file out to the host | needs container + host volume |
+| TC-DOCKER-06 | Gateway-mode Docker deploy | `./scripts/deploy.sh --gateway` produces a 3-container topology (no `langgraph` container); same auth flow as standard mode | needs `docker compose --profile gateway` |
+
+## Coverage already provided by non-Docker tests
+
+The **auth-relevant** behavior in each Docker case is already exercised by
+the test cases that ran on sg_dev or local:
+
+| Docker case | Auth behavior covered by |
+|---|---|
+| TC-DOCKER-01 (volume persistence) | TC-REENT-01 on sg_dev (admin row survives gateway restart) — same SQLite file, just no container layer between |
+| TC-DOCKER-02 (session persistence) | TC-API-02/03/06 (cookie roundtrip), plus TC-REENT-04 (multi-cookie) — JWT verification is process-state-free, container restart is equivalent to `pkill uvicorn && uv run uvicorn` |
+| TC-DOCKER-03 (per-worker rate limit) | TC-GW-04 + TC-REENT-09 (single-worker rate limit + 5min expiry). The cross-worker divergence is an architectural property of the in-memory dict; no auth code path differs |
+| TC-DOCKER-04 (IM channels skip auth) | Code-level only: `app/channels/manager.py` uses `langgraph_sdk` directly with no cookie handling. The langgraph_auth handler is bypassed by going through SDK, not HTTP |
+| TC-DOCKER-05 (credential surfacing) | TC-1.1 on sg_dev (file at `~/deer-flow/backend/.deer-flow/admin_initial_credentials.txt`, mode 0600, password 22 chars) — the only Docker-unique step is whether the bind mount projects this path onto the host, which is a `docker compose` config check, not a runtime behavior change |
+| TC-DOCKER-06 (gateway-mode container) | Section 七 7.2 covered by TC-GW-01..05 + Section 二 (gateway-mode auth flow on sg_dev) — same Gateway code, container is just a packaging change |
+
+## Reproduction steps when Docker becomes available
+
+Anyone with `docker` + `docker compose` installed can reproduce the gap by
+running the test plan section verbatim. Pre-flight:
+
+```bash
+# Required on the host
+docker --version           # >=24.x
+docker compose version     # plugin >=2.x
+
+# Required env var (otherwise sessions reset on every container restart)
+echo "AUTH_JWT_SECRET=$(python3 -c 'import secrets; print(secrets.token_urlsafe(32))')" \
+  >> .env
+
+# Optional: pin DEER_FLOW_HOME to a stable host path
+echo "DEER_FLOW_HOME=$HOME/deer-flow-data" >> .env
+```
+
+Then run TC-DOCKER-01..06 from the test plan as written.
+
+## Decision log
+
+- **Not blocking the release.** The auth-relevant behavior in every Docker
+  case has an already-validated equivalent on bare metal. The gap is purely
+  about *container packaging* details (bind mounts, multi-worker, log
+  collection), not about whether the auth code paths work.
+- **TC-DOCKER-05 was updated in place** in `AUTH_TEST_PLAN.md` to reflect
+  the post-simplify reality (credentials file → 0600 file, no log leak).
+  The old "grep 'Password:' in docker logs" expectation would have failed
+  silently and given a false sense of coverage.
@@ -0,0 +1,129 @@
+# Authentication Upgrade Guide
+
+DeerFlow 内置了认证模块。本文档面向从无认证版本升级的用户。
+
+## 核心概念
+
+认证模块采用**始终强制**策略：
+
+- 首次启动时自动创建 admin 账号，随机密码打印到控制台日志
+- 认证从一开始就是强制的，无竞争窗口
+- 历史对话（升级前创建的 thread）自动迁移到 admin 名下
+
+## 升级步骤
+
+### 1. 更新代码
+
+```bash
+git pull origin main
+cd backend && make install
+```
+
+### 2. 首次启动
+
+```bash
+make dev
+```
+
+控制台会输出：
+
+```
+============================================================
+  Admin account created on first boot
+  Email:    admin@deerflow.dev
+  Password: aB3xK9mN_pQ7rT2w
+  Change it after login: Settings → Account
+============================================================
+```
+
+如果未登录就重启了服务，不用担心——只要 setup 未完成，每次启动都会重置密码并重新打印到控制台。
+
+### 3. 登录
+
+访问 `http://localhost:2026/login`，使用控制台输出的邮箱和密码登录。
+
+### 4. 修改密码
+
+登录后进入 Settings → Account → Change Password。
+
+### 5. 添加用户（可选）
+
+其他用户通过 `/login` 页面注册，自动获得 **user** 角色。每个用户只能看到自己的对话。
+
+## 安全机制
+
+| 机制 | 说明 |
+|------|------|
+| JWT HttpOnly Cookie | Token 不暴露给 JavaScript，防止 XSS 窃取 |
+| CSRF Double Submit Cookie | 所有 POST/PUT/DELETE 请求需携带 `X-CSRF-Token` |
+| bcrypt 密码哈希 | 密码不以明文存储 |
+| 多租户隔离 | 用户只能访问自己的 thread |
+| HTTPS 自适应 | 检测 `x-forwarded-proto`，自动设置 `Secure` cookie 标志 |
+
+## 常见操作
+
+### 忘记密码
+
+```bash
+cd backend
+
+# 重置 admin 密码
+python -m app.gateway.auth.reset_admin
+
+# 重置指定用户密码
+python -m app.gateway.auth.reset_admin --email user@example.com
+```
+
+会输出新的随机密码。
+
+### 完全重置
+
+删除用户数据库，重启后自动创建新 admin：
+
+```bash
+rm -f backend/.deer-flow/users.db
+# 重启服务，控制台输出新密码
+```
+
+## 数据存储
+
+| 文件 | 内容 |
+|------|------|
+| `.deer-flow/users.db` | SQLite 用户数据库（密码哈希、角色） |
+| `.env` 中的 `AUTH_JWT_SECRET` | JWT 签名密钥（未设置时自动生成临时密钥，重启后 session 失效） |
+
+### 生产环境建议
+
+```bash
+# 生成持久化 JWT 密钥，避免重启后所有用户需重新登录
+python -c "import secrets; print(secrets.token_urlsafe(32))"
+# 将输出添加到 .env：
+# AUTH_JWT_SECRET=<生成的密钥>
+```
+
+## API 端点
+
+| 端点 | 方法 | 说明 |
+|------|------|------|
+| `/api/v1/auth/login/local` | POST | 邮箱密码登录（OAuth2 form） |
+| `/api/v1/auth/register` | POST | 注册新用户（user 角色） |
+| `/api/v1/auth/logout` | POST | 登出（清除 cookie） |
+| `/api/v1/auth/me` | GET | 获取当前用户信息 |
+| `/api/v1/auth/change-password` | POST | 修改密码 |
+| `/api/v1/auth/setup-status` | GET | 检查 admin 是否存在 |
+
+## 兼容性
+
+- **标准模式**（`make dev`）：完全兼容，admin 自动创建
+- **Gateway 模式**（`make dev-pro`）：完全兼容
+- **Docker 部署**：完全兼容，`.deer-flow/users.db` 需持久化卷挂载
+- **IM 渠道**（Feishu/Slack/Telegram）：通过 LangGraph SDK 通信，不经过认证层
+- **DeerFlowClient**（嵌入式）：不经过 HTTP，不受认证影响
+
+## 故障排查
+
+| 症状 | 原因 | 解决 |
+|------|------|------|
+| 启动后没看到密码 | admin 已存在（非首次启动） | 用 `reset_admin` 重置，或删 `users.db` |
+| 登录后 POST 返回 403 | CSRF token 缺失 | 确认前端已更新 |
+| 重启后需要重新登录 | `AUTH_JWT_SECRET` 未持久化 | 在 `.env` 中设置固定密钥 |
@@ -2,12 +2,12 @@

 ## 概述

-DeerFlow 后端提供了完整的文件上传功能，支持多文件上传，并自动将 Office 文档和 PDF 转换为 Markdown 格式。
+DeerFlow 后端提供了完整的文件上传功能，支持多文件上传，并可选地将 Office 文档和 PDF 转换为 Markdown 格式。

 ## 功能特性

 - ✅ 支持多文件同时上传
- ✅ 自动转换文档为 Markdown（PDF、PPT、Excel、Word）
+- ✅ 可选地转换文档为 Markdown（PDF、PPT、Excel、Word）
 - ✅ 文件存储在线程隔离的目录中
 - ✅ Agent 自动感知已上传的文件
 - ✅ 支持文件列表查询和删除
@@ -86,7 +86,7 @@ DELETE /api/threads/{thread_id}/uploads/{filename}

 ## 支持的文档格式

-以下格式会自动转换为 Markdown：
+以下格式在显式启用 `uploads.auto_convert_documents: true` 时会自动转换为 Markdown：
 - PDF (`.pdf`)
 - PowerPoint (`.ppt`, `.pptx`)
 - Excel (`.xls`, `.xlsx`)
@@ -94,6 +94,8 @@ DELETE /api/threads/{thread_id}/uploads/{filename}

 转换后的 Markdown 文件会保存在同一目录下，文件名为原文件名 + `.md` 扩展名。

+默认情况下，自动转换是关闭的，以避免在网关主机上对不受信任的 Office/PDF 上传执行解析。只有在受信任部署中明确接受此风险时，才应将 `uploads.auto_convert_documents` 设置为 `true`。
+
 ## Agent 集成

 ### 自动文件列举
@@ -207,6 +209,7 @@ backend/.deer-flow/threads/
 - 最大文件大小：100MB（可在 nginx.conf 中配置 `client_max_body_size`）
 - 文件名安全性：系统会自动验证文件路径，防止目录遍历攻击
 - 线程隔离：每个线程的上传文件相互隔离，无法跨线程访问
+- 自动文档转换默认关闭；如需启用，需在 `config.yaml` 中显式设置 `uploads.auto_convert_documents: true`

 ## 技术实现

@@ -296,7 +296,7 @@ These are the tool names your provider will see in `request.tool_name`:
 | `web_search` | Web search query |
 | `web_fetch` | Fetch URL content |
 | `image_search` | Image search |
-| `present_file` | Present file to user |
+| `present_files` | Present file to user |
 | `view_image` | Display image |
 | `ask_clarification` | Ask user a question |
 | `task` | Delegate to subagent |
@@ -45,6 +45,41 @@ Example:
 }
 ```

+## Custom Tool Interceptors
+
+You can register custom interceptors that run before every MCP tool call. This is useful for injecting per-request headers (e.g., user auth tokens from the LangGraph execution context), logging, or metrics.
+
+Declare interceptors in `extensions_config.json` using the `mcpInterceptors` field:
+
+```json
+{
+  "mcpInterceptors": [
+    "my_package.mcp.auth:build_auth_interceptor"
+  ],
+  "mcpServers": { ... }
+}
+```
+
+Each entry is a Python import path in `module:variable` format (resolved via `resolve_variable`). The variable must be a **no-arg builder function** that returns an async interceptor compatible with `MultiServerMCPClient`’s `tool_interceptors` interface, or `None` to skip.
+
+Example interceptor that injects auth headers from LangGraph metadata:
+
+```python
+def build_auth_interceptor():
+    async def interceptor(request, handler):
+        from langgraph.config import get_config
+        metadata = get_config().get("metadata", {})
+        headers = dict(request.headers or {})
+        if token := metadata.get("auth_token"):
+            headers["X-Auth-Token"] = token
+        return await handler(request.override(headers=headers))
+    return interceptor
+```
+
+- A single string value is accepted and normalized to a one-element list.
+- Invalid paths or builder failures are logged as warnings without blocking other interceptors.
+- The builder return value must be `callable`; non-callable values are skipped with a warning.
+
 ## How It Works

 MCP servers expose tools that are automatically discovered and integrated into DeerFlow’s agent system at runtime. Once enabled, these tools become available to agents without additional code changes.
@@ -124,7 +124,7 @@ title:
 # checkpointer.py
 from langgraph.checkpoint.sqlite import SqliteSaver

-checkpointer = SqliteSaver.from_conn_string("checkpoints.db")
+checkpointer = SqliteSaver.from_conn_string("deerflow.db")
 ```

 ```json
@@ -11,6 +11,7 @@
 - [x] Add Plan Mode with TodoList middleware
 - [x] Add vision model support with ViewImageMiddleware
 - [x] Skills system with SKILL.md format
+- [x] Replace `time.sleep(5)` with `asyncio.sleep()` in `packages/harness/deerflow/tools/builtins/task_tool.py` (subagent polling)

 ## Planned Features

@@ -21,10 +22,9 @@
 - [ ] Support for more document formats in upload
 - [ ] Skill marketplace / remote skill installation
 - [ ] Optimize async concurrency in agent hot path (IM channels multi-task scenario)
-  - Replace `time.sleep(5)` with `asyncio.sleep()` in `packages/harness/deerflow/tools/builtins/task_tool.py` (subagent polling)
-  - Replace `subprocess.run()` with `asyncio.create_subprocess_shell()` in `packages/harness/deerflow/sandbox/local/local_sandbox.py`
+- [ ] Replace `subprocess.run()` with `asyncio.create_subprocess_shell()` in `packages/harness/deerflow/sandbox/local/local_sandbox.py`
  - Replace sync `requests` with `httpx.AsyncClient` in community tools (tavily, jina_ai, firecrawl, infoquest, image_search)
-  - Replace sync `model.invoke()` with async `model.ainvoke()` in title_middleware and memory updater
+  - [x] Replace sync `model.invoke()` with async `model.ainvoke()` in title_middleware and memory updater
  - Consider `asyncio.to_thread()` wrapper for remaining blocking file I/O
  - For production: use `langgraph up` (multi-worker) instead of `langgraph dev` (single-worker)

@@ -41,6 +41,13 @@ summarization:

  # Custom summary prompt (optional)
  summary_prompt: null
+
+  # Tool names treated as skill file reads for skill rescue
+  skill_file_read_tool_names:
+    - read_file
+    - read
+    - view
+    - cat
 ```

 ### Configuration Options
@@ -125,6 +132,26 @@ keep:
 - **Default**: `null` (uses LangChain's default prompt)
 - **Description**: Custom prompt template for generating summaries. The prompt should guide the model to extract the most important context.

+#### `preserve_recent_skill_count`
+- **Type**: Integer (≥ 0)
+- **Default**: `5`
+- **Description**: Number of most-recently-loaded skill files (tool results whose tool name is in `skill_file_read_tool_names` and whose target path is under `skills.container_path`, e.g. `/mnt/skills/...`) that are rescued from summarization. Prevents the agent from losing skill instructions after compression. Set to `0` to disable skill rescue entirely.
+
+#### `preserve_recent_skill_tokens`
+- **Type**: Integer (≥ 0)
+- **Default**: `25000`
+- **Description**: Total token budget reserved for rescued skill reads. Once this budget is exhausted, older skill bundles are allowed to be summarized.
+
+#### `preserve_recent_skill_tokens_per_skill`
+- **Type**: Integer (≥ 0)
+- **Default**: `5000`
+- **Description**: Per-skill token cap. Any individual skill read whose tool result exceeds this size is not rescued (it falls through to the summarizer like ordinary content).
+
+#### `skill_file_read_tool_names`
+- **Type**: List of strings
+- **Default**: `["read_file", "read", "view", "cat"]`
+- **Description**: Tool names treated as skill file reads during summarization rescue. A tool call is only eligible for skill rescue when its name appears in this list and its target path is under `skills.container_path`.
+
 **Default Prompt Behavior:**
 The default LangChain prompt instructs the model to:
 - Extract highest quality/most relevant context
@@ -147,6 +174,7 @@ The default LangChain prompt instructs the model to:
   - A single summary message is added
   - Recent messages are preserved
 6. **AI/Tool Pair Protection**: The system ensures AI messages and their corresponding tool messages stay together
+7. **Skill Rescue**: Before the summary is generated, the most recently loaded skill files (tool results whose tool name is in `skill_file_read_tool_names` and whose target path is under `skills.container_path`) are lifted out of the summarization set and prepended to the preserved tail. Selection walks newest-first under three budgets: `preserve_recent_skill_count`, `preserve_recent_skill_tokens`, and `preserve_recent_skill_tokens_per_skill`. The triggering AIMessage and all of its paired ToolMessages move together so tool_call ↔ tool_result pairing stays intact.

 ### Token Counting

@@ -8,6 +8,9 @@
  "graphs": {
    "lead_agent": "deerflow.agents:make_lead_agent"
  },
+  "auth": {
+    "path": "./app/gateway/langgraph_auth.py:auth"
+  },
  "checkpointer": {
    "path": "./packages/harness/deerflow/agents/checkpointer/async_provider.py:make_checkpointer"
  }
@@ -1,4 +1,3 @@
-from .checkpointer import get_checkpointer, make_checkpointer, reset_checkpointer
 from .factory import create_deerflow_agent
 from .features import Next, Prev, RuntimeFeatures
 from .lead_agent import make_lead_agent
@@ -18,7 +17,4 @@ __all__ = [
    "make_lead_agent",
    "SandboxState",
    "ThreadState",
-    "get_checkpointer",
-    "reset_checkpointer",
-    "make_checkpointer",
 ]
@@ -1,31 +1,42 @@
 import logging

 from langchain.agents import create_agent
-from langchain.agents.middleware import AgentMiddleware, SummarizationMiddleware
+from langchain.agents.middleware import AgentMiddleware
 from langchain_core.runnables import RunnableConfig
+from langgraph.graph.state import CompiledStateGraph

 from deerflow.agents.lead_agent.prompt import apply_prompt_template
+from deerflow.agents.memory.summarization_hook import memory_flush_hook
 from deerflow.agents.middlewares.clarification_middleware import ClarificationMiddleware
 from deerflow.agents.middlewares.loop_detection_middleware import LoopDetectionMiddleware
 from deerflow.agents.middlewares.memory_middleware import MemoryMiddleware
 from deerflow.agents.middlewares.subagent_limit_middleware import SubagentLimitMiddleware
+from deerflow.agents.middlewares.summarization_middleware import BeforeSummarizationHook, DeerFlowSummarizationMiddleware
 from deerflow.agents.middlewares.title_middleware import TitleMiddleware
 from deerflow.agents.middlewares.todo_middleware import TodoMiddleware
 from deerflow.agents.middlewares.token_usage_middleware import TokenUsageMiddleware
 from deerflow.agents.middlewares.tool_error_handling_middleware import build_lead_runtime_middlewares
 from deerflow.agents.middlewares.view_image_middleware import ViewImageMiddleware
 from deerflow.agents.thread_state import ThreadState
-from deerflow.config.agents_config import load_agent_config
-from deerflow.config.app_config import get_app_config
-from deerflow.config.summarization_config import get_summarization_config
+from deerflow.config.agents_config import load_agent_config, validate_agent_name
+from deerflow.config.app_config import AppConfig
+from deerflow.config.deer_flow_context import DeerFlowContext
 from deerflow.models import create_chat_model

 logger = logging.getLogger(__name__)


-def _resolve_model_name(requested_model_name: str | None = None) -> str:
+def _get_runtime_config(config: RunnableConfig) -> dict:
+    """Merge legacy configurable options with LangGraph runtime context."""
+    cfg = dict(config.get("configurable", {}) or {})
+    context = config.get("context", {}) or {}
+    if isinstance(context, dict):
+        cfg.update(context)
+    return cfg
+
+
+def _resolve_model_name(app_config: AppConfig, requested_model_name: str | None = None) -> str:
    """Resolve a runtime model name safely, falling back to default if invalid. Returns None if no models are configured."""
-    app_config = get_app_config()
    default_model_name = app_config.models[0].name if app_config.models else None
    if default_model_name is None:
        raise ValueError("No chat models are configured. Please configure at least one model in config.yaml.")
@@ -38,9 +49,9 @@ def _resolve_model_name(requested_model_name: str | None = None) -> str:
    return default_model_name


-def _create_summarization_middleware() -> SummarizationMiddleware | None:
+def _create_summarization_middleware(app_config: AppConfig) -> DeerFlowSummarizationMiddleware | None:
    """Create and configure the summarization middleware from config."""
-    config = get_summarization_config()
+    config = app_config.summarization

    if not config.enabled:
        return None
@@ -56,13 +67,15 @@ def _create_summarization_middleware() -> SummarizationMiddleware | None:
    # Prepare keep parameter
    keep = config.keep.to_tuple()

-    # Prepare model parameter
+    # Prepare model parameter.
+    # Bind "middleware:summarize" tag so RunJournal identifies these LLM calls
+    # as middleware rather than lead_agent (SummarizationMiddleware is a
+    # LangChain built-in, so we tag the model at creation time).
    if config.model_name:
-        model = create_chat_model(name=config.model_name, thinking_enabled=False)
+        model = create_chat_model(name=config.model_name, thinking_enabled=False, app_config=app_config)
    else:
-        # Use a lightweight model for summarization to save costs
-        # Falls back to default model if not explicitly specified
-        model = create_chat_model(thinking_enabled=False)
+        model = create_chat_model(thinking_enabled=False, app_config=app_config)
+    model = model.with_config(tags=["middleware:summarize"])

    # Prepare kwargs
    kwargs = {
@@ -77,7 +90,28 @@ def _create_summarization_middleware() -> SummarizationMiddleware | None:
    if config.summary_prompt is not None:
        kwargs["summary_prompt"] = config.summary_prompt

-    return SummarizationMiddleware(**kwargs)
+    hooks: list[BeforeSummarizationHook] = []
+    if app_config.memory.enabled:
+        hooks.append(memory_flush_hook)
+
+    # The logic below relies on two assumptions holding true: this factory is
+    # the sole entry point for DeerFlowSummarizationMiddleware, and the runtime
+    # config is not expected to change after startup.
+    try:
+        skills_container_path = app_config.skills.container_path or "/mnt/skills"
+    except Exception:
+        logger.exception("Failed to resolve skills container path; falling back to default")
+        skills_container_path = "/mnt/skills"
+
+    return DeerFlowSummarizationMiddleware(
+        **kwargs,
+        skills_container_path=skills_container_path,
+        skill_file_read_tool_names=config.skill_file_read_tool_names,
+        before_summarization=hooks,
+        preserve_recent_skill_count=config.preserve_recent_skill_count,
+        preserve_recent_skill_tokens=config.preserve_recent_skill_tokens,
+        preserve_recent_skill_tokens_per_skill=config.preserve_recent_skill_tokens_per_skill,
+    )


 def _create_todo_list_middleware(is_plan_mode: bool) -> TodoMiddleware | None:
@@ -205,10 +239,18 @@ Being proactive with task management demonstrates thoroughness and ensures all r
 # ViewImageMiddleware should be before ClarificationMiddleware to inject image details before LLM
 # ToolErrorHandlingMiddleware should be before ClarificationMiddleware to convert tool exceptions to ToolMessages
 # ClarificationMiddleware should be last to intercept clarification requests after model calls
-def _build_middlewares(config: RunnableConfig, model_name: str | None, agent_name: str | None = None, custom_middlewares: list[AgentMiddleware] | None = None):
+def _build_middlewares(
+    app_config: AppConfig,
+    config: RunnableConfig,
+    *,
+    model_name: str | None,
+    agent_name: str | None = None,
+    custom_middlewares: list[AgentMiddleware] | None = None,
+):
    """Build middleware chain based on runtime configuration.

    Args:
+        app_config: Resolved application config.
        config: Runtime configuration containing configurable options like is_plan_mode.
        agent_name: If provided, MemoryMiddleware will use per-agent memory storage.
        custom_middlewares: Optional list of custom middlewares to inject into the chain.
@@ -216,21 +258,22 @@ def _build_middlewares(config: RunnableConfig, model_name: str | None, agent_nam
    Returns:
        List of middleware instances.
    """
-    middlewares = build_lead_runtime_middlewares(lazy_init=True)
+    middlewares = build_lead_runtime_middlewares(app_config=app_config, lazy_init=True)

    # Add summarization middleware if enabled
-    summarization_middleware = _create_summarization_middleware()
+    summarization_middleware = _create_summarization_middleware(app_config)
    if summarization_middleware is not None:
        middlewares.append(summarization_middleware)

    # Add TodoList middleware if plan mode is enabled
-    is_plan_mode = config.get("configurable", {}).get("is_plan_mode", False)
+    cfg = _get_runtime_config(config)
+    is_plan_mode = cfg.get("is_plan_mode", False)
    todo_list_middleware = _create_todo_list_middleware(is_plan_mode)
    if todo_list_middleware is not None:
        middlewares.append(todo_list_middleware)

    # Add TokenUsageMiddleware when token_usage tracking is enabled
-    if get_app_config().token_usage.enabled:
+    if app_config.token_usage.enabled:
        middlewares.append(TokenUsageMiddleware())

    # Add TitleMiddleware
@@ -241,7 +284,6 @@ def _build_middlewares(config: RunnableConfig, model_name: str | None, agent_nam

    # Add ViewImageMiddleware only if the current model supports vision.
    # Use the resolved runtime model_name from make_lead_agent to avoid stale config values.
-    app_config = get_app_config()
    model_config = app_config.get_model_config(model_name) if model_name else None
    if model_config is not None and model_config.supports_vision:
        middlewares.append(ViewImageMiddleware())
@@ -253,9 +295,9 @@ def _build_middlewares(config: RunnableConfig, model_name: str | None, agent_nam
        middlewares.append(DeferredToolFilterMiddleware())

    # Add SubagentLimitMiddleware to truncate excess parallel task calls
-    subagent_enabled = config.get("configurable", {}).get("subagent_enabled", False)
+    subagent_enabled = cfg.get("subagent_enabled", False)
    if subagent_enabled:
-        max_concurrent_subagents = config.get("configurable", {}).get("max_concurrent_subagents", 3)
+        max_concurrent_subagents = cfg.get("max_concurrent_subagents", 3)
        middlewares.append(SubagentLimitMiddleware(max_concurrent=max_concurrent_subagents))

    # LoopDetectionMiddleware — detect and break repetitive tool call loops
@@ -270,12 +312,33 @@ def _build_middlewares(config: RunnableConfig, model_name: str | None, agent_nam
    return middlewares


-def make_lead_agent(config: RunnableConfig):
+def make_lead_agent(
+    config: RunnableConfig,
+    app_config: AppConfig | None = None,
+) -> CompiledStateGraph:
+    """Build the lead agent from runtime config.
+
+    Args:
+        config: LangGraph ``RunnableConfig`` carrying per-invocation options
+            (``thinking_enabled``, ``model_name``, ``is_plan_mode``, etc.).
+        app_config: Resolved application config. Required for in-process
+            entry points (DeerFlowClient, Gateway Worker). When omitted we
+            are being called via ``langgraph.json`` registration and reload
+            from disk — the LangGraph Server bootstrap path has no other
+            way to thread the value.
+    """
    # Lazy import to avoid circular dependency
    from deerflow.tools import get_available_tools
    from deerflow.tools.builtins import setup_agent

-    cfg = config.get("configurable", {})
+    if app_config is None:
+        # LangGraph Server registers ``make_lead_agent`` via ``langgraph.json``
+        # and hands us only a ``RunnableConfig``. Reload config from disk
+        # here — it's a pure function, equivalent to the process-global the
+        # old code path would have read.
+        app_config = AppConfig.from_file()
+
+    cfg = _get_runtime_config(config)

    thinking_enabled = cfg.get("thinking_enabled", True)
    reasoning_effort = cfg.get("reasoning_effort", None)
@@ -284,16 +347,15 @@ def make_lead_agent(config: RunnableConfig):
    subagent_enabled = cfg.get("subagent_enabled", False)
    max_concurrent_subagents = cfg.get("max_concurrent_subagents", 3)
    is_bootstrap = cfg.get("is_bootstrap", False)
-    agent_name = cfg.get("agent_name")
+    agent_name = validate_agent_name(cfg.get("agent_name"))

    agent_config = load_agent_config(agent_name) if not is_bootstrap else None
    # Custom agent model from agent config (if any), or None to let _resolve_model_name pick the default
    agent_model_name = agent_config.model if agent_config and agent_config.model else None

    # Final model name resolution: request → agent config → global default, with fallback for unknown names
-    model_name = _resolve_model_name(requested_model_name or agent_model_name)
+    model_name = _resolve_model_name(app_config, requested_model_name or agent_model_name)

-    app_config = get_app_config()
    model_config = app_config.get_model_config(model_name)

    if model_config is None:
@@ -325,26 +387,30 @@ def make_lead_agent(config: RunnableConfig):
            "reasoning_effort": reasoning_effort,
            "is_plan_mode": is_plan_mode,
            "subagent_enabled": subagent_enabled,
+            "tool_groups": agent_config.tool_groups if agent_config else None,
+            "available_skills": ["bootstrap"] if is_bootstrap else (agent_config.skills if agent_config and agent_config.skills is not None else None),
        }
    )

    if is_bootstrap:
        # Special bootstrap agent with minimal prompt for initial custom agent creation flow
        return create_agent(
-            model=create_chat_model(name=model_name, thinking_enabled=thinking_enabled),
-            tools=get_available_tools(model_name=model_name, subagent_enabled=subagent_enabled) + [setup_agent],
-            middleware=_build_middlewares(config, model_name=model_name),
-            system_prompt=apply_prompt_template(subagent_enabled=subagent_enabled, max_concurrent_subagents=max_concurrent_subagents, available_skills=set(["bootstrap"])),
+            model=create_chat_model(name=model_name, thinking_enabled=thinking_enabled, app_config=app_config),
+            tools=get_available_tools(model_name=model_name, subagent_enabled=subagent_enabled, app_config=app_config) + [setup_agent],
+            middleware=_build_middlewares(app_config, config, model_name=model_name),
+            system_prompt=apply_prompt_template(app_config, subagent_enabled=subagent_enabled, max_concurrent_subagents=max_concurrent_subagents, available_skills=set(["bootstrap"])),
            state_schema=ThreadState,
+            context_schema=DeerFlowContext,
        )

    # Default lead agent (unchanged behavior)
    return create_agent(
-        model=create_chat_model(name=model_name, thinking_enabled=thinking_enabled, reasoning_effort=reasoning_effort),
-        tools=get_available_tools(model_name=model_name, groups=agent_config.tool_groups if agent_config else None, subagent_enabled=subagent_enabled),
-        middleware=_build_middlewares(config, model_name=model_name, agent_name=agent_name),
+        model=create_chat_model(name=model_name, thinking_enabled=thinking_enabled, reasoning_effort=reasoning_effort, app_config=app_config),
+        tools=get_available_tools(model_name=model_name, groups=agent_config.tool_groups if agent_config else None, subagent_enabled=subagent_enabled, app_config=app_config),
+        middleware=_build_middlewares(app_config, config, model_name=model_name, agent_name=agent_name),
        system_prompt=apply_prompt_template(
-            subagent_enabled=subagent_enabled, max_concurrent_subagents=max_concurrent_subagents, agent_name=agent_name, available_skills=set(agent_config.skills) if agent_config and agent_config.skills is not None else None
+            app_config, subagent_enabled=subagent_enabled, max_concurrent_subagents=max_concurrent_subagents, agent_name=agent_name, available_skills=set(agent_config.skills) if agent_config and agent_config.skills is not None else None
        ),
        state_schema=ThreadState,
+        context_schema=DeerFlowContext,
    )
@@ -5,6 +5,7 @@ from datetime import datetime
 from functools import lru_cache

 from deerflow.config.agents_config import load_agent_soul
+from deerflow.config.app_config import AppConfig
 from deerflow.skills import load_skills
 from deerflow.skills.types import Skill
 from deerflow.subagents import get_available_subagent_names
@@ -19,19 +20,20 @@ _enabled_skills_refresh_version = 0
 _enabled_skills_refresh_event = threading.Event()


-def _load_enabled_skills_sync() -> list[Skill]:
-    return list(load_skills(enabled_only=True))
+def _load_enabled_skills_sync(app_config: AppConfig | None) -> list[Skill]:
+    return list(load_skills(app_config, enabled_only=True))


-def _start_enabled_skills_refresh_thread() -> None:
+def _start_enabled_skills_refresh_thread(app_config: AppConfig | None) -> None:
    threading.Thread(
        target=_refresh_enabled_skills_cache_worker,
+        args=(app_config,),
        name="deerflow-enabled-skills-loader",
        daemon=True,
    ).start()


-def _refresh_enabled_skills_cache_worker() -> None:
+def _refresh_enabled_skills_cache_worker(app_config: AppConfig | None) -> None:
    global _enabled_skills_cache, _enabled_skills_refresh_active

    while True:
@@ -39,8 +41,8 @@ def _refresh_enabled_skills_cache_worker() -> None:
            target_version = _enabled_skills_refresh_version

        try:
-            skills = _load_enabled_skills_sync()
-        except Exception:
+            skills = _load_enabled_skills_sync(app_config)
+        except (OSError, ImportError):
            logger.exception("Failed to load enabled skills for prompt injection")
            skills = []

@@ -56,7 +58,7 @@ def _refresh_enabled_skills_cache_worker() -> None:
            _enabled_skills_cache = None


-def _ensure_enabled_skills_cache() -> threading.Event:
+def _ensure_enabled_skills_cache(app_config: AppConfig | None) -> threading.Event:
    global _enabled_skills_refresh_active

    with _enabled_skills_lock:
@@ -68,11 +70,11 @@ def _ensure_enabled_skills_cache() -> threading.Event:
        _enabled_skills_refresh_active = True
        _enabled_skills_refresh_event.clear()

-    _start_enabled_skills_refresh_thread()
+    _start_enabled_skills_refresh_thread(app_config)
    return _enabled_skills_refresh_event


-def _invalidate_enabled_skills_cache() -> threading.Event:
+def _invalidate_enabled_skills_cache(app_config: AppConfig | None) -> threading.Event:
    global _enabled_skills_cache, _enabled_skills_refresh_active, _enabled_skills_refresh_version

    _get_cached_skills_prompt_section.cache_clear()
@@ -84,30 +86,30 @@ def _invalidate_enabled_skills_cache() -> threading.Event:
            return _enabled_skills_refresh_event
        _enabled_skills_refresh_active = True

-    _start_enabled_skills_refresh_thread()
+    _start_enabled_skills_refresh_thread(app_config)
    return _enabled_skills_refresh_event


-def prime_enabled_skills_cache() -> None:
-    _ensure_enabled_skills_cache()
+def prime_enabled_skills_cache(app_config: AppConfig | None = None) -> None:
+    _ensure_enabled_skills_cache(app_config)


-def warm_enabled_skills_cache(timeout_seconds: float = _ENABLED_SKILLS_REFRESH_WAIT_TIMEOUT_SECONDS) -> bool:
-    if _ensure_enabled_skills_cache().wait(timeout=timeout_seconds):
+def warm_enabled_skills_cache(app_config: AppConfig | None = None, timeout_seconds: float = _ENABLED_SKILLS_REFRESH_WAIT_TIMEOUT_SECONDS) -> bool:
+    if _ensure_enabled_skills_cache(app_config).wait(timeout=timeout_seconds):
        return True

    logger.warning("Timed out waiting %.1fs for enabled skills cache warm-up", timeout_seconds)
    return False


-def _get_enabled_skills():
+def _get_enabled_skills(app_config: AppConfig | None = None):
    with _enabled_skills_lock:
        cached = _enabled_skills_cache

    if cached is not None:
        return list(cached)

-    _ensure_enabled_skills_cache()
+    _ensure_enabled_skills_cache(app_config)
    return []


@@ -115,12 +117,12 @@ def _skill_mutability_label(category: str) -> str:
    return "[custom, editable]" if category == "custom" else "[built-in]"


-def clear_skills_system_prompt_cache() -> None:
-    _invalidate_enabled_skills_cache()
+def clear_skills_system_prompt_cache(app_config: AppConfig | None = None) -> None:
+    _invalidate_enabled_skills_cache(app_config)


-async def refresh_skills_system_prompt_cache_async() -> None:
-    await asyncio.to_thread(_invalidate_enabled_skills_cache().wait)
+async def refresh_skills_system_prompt_cache_async(app_config: AppConfig | None = None) -> None:
+    await asyncio.to_thread(_invalidate_enabled_skills_cache(app_config).wait)


 def _reset_skills_system_prompt_cache_state() -> None:
@@ -134,10 +136,10 @@ def _reset_skills_system_prompt_cache_state() -> None:
        _enabled_skills_refresh_event.clear()


-def _refresh_enabled_skills_cache() -> None:
+def _refresh_enabled_skills_cache(app_config: AppConfig | None = None) -> None:
    """Backward-compatible test helper for direct synchronous reload."""
    try:
-        skills = _load_enabled_skills_sync()
+        skills = _load_enabled_skills_sync(app_config)
    except Exception:
        logger.exception("Failed to load enabled skills for prompt injection")
        skills = []
@@ -164,23 +166,53 @@ Skip simple one-off tasks.
 """


-def _build_subagent_section(max_concurrent: int) -> str:
+def _build_available_subagents_description(available_names: list[str], bash_available: bool, app_config: AppConfig) -> str:
+    """Dynamically build subagent type descriptions from registry.
+
+    Mirrors Codex's pattern where agent_type_description is dynamically generated
+    from all registered roles, so the LLM knows about every available type.
+    """
+    # Built-in descriptions (kept for backward compatibility with existing prompt quality)
+    builtin_descriptions = {
+        "general-purpose": "For ANY non-trivial task - web research, code exploration, file operations, analysis, etc.",
+        "bash": (
+            "For command execution (git, build, test, deploy operations)" if bash_available else "Not available in the current sandbox configuration. Use direct file/web tools or switch to AioSandboxProvider for isolated shell access."
+        ),
+    }
+
+    # Lazy import moved outside loop to avoid repeated import overhead
+    from deerflow.subagents.registry import get_subagent_config
+
+    lines = []
+    for name in available_names:
+        if name in builtin_descriptions:
+            lines.append(f"- **{name}**: {builtin_descriptions[name]}")
+        else:
+            config = get_subagent_config(name, app_config)
+            if config is not None:
+                desc = config.description.split("\n")[0].strip()  # First line only for brevity
+                lines.append(f"- **{name}**: {desc}")
+
+    return "\n".join(lines)
+
+
+def _build_subagent_section(max_concurrent: int, app_config: AppConfig) -> str:
    """Build the subagent system prompt section with dynamic concurrency limit.

    Args:
        max_concurrent: Maximum number of concurrent subagent calls allowed per response.
+        app_config: Application config used to gate bash availability.

    Returns:
        Formatted subagent section string.
    """
    n = max_concurrent
-    bash_available = "bash" in get_available_subagent_names()
-    available_subagents = (
-        "- **general-purpose**: For ANY non-trivial task - web research, code exploration, file operations, analysis, etc.\n- **bash**: For command execution (git, build, test, deploy operations)"
-        if bash_available
-        else "- **general-purpose**: For ANY non-trivial task - web research, code exploration, file operations, analysis, etc.\n"
-        "- **bash**: Not available in the current sandbox configuration. Use direct file/web tools or switch to AioSandboxProvider for isolated shell access."
-    )
+    available_names = get_available_subagent_names(app_config)
+    bash_available = "bash" in available_names
+
+    # Dynamically build subagent type descriptions from registry (aligned with Codex's
+    # agent_type_description pattern where all registered roles are listed in the tool spec).
+    available_subagents = _build_available_subagents_description(available_names, bash_available, app_config)
    direct_tool_examples = "bash, ls, read_file, web_search, etc." if bash_available else "ls, read_file, web_search, etc."
    direct_execution_example = (
        '# User asks: "Run the tests"\n# Thinking: Cannot decompose into parallel sub-tasks\n# → Execute directly\n\nbash("npm test")  # Direct execution, not task()'
@@ -420,7 +452,7 @@ You: "Deploying to staging..." [proceed]
 - Treat `/mnt/user-data/workspace` as your default current working directory for coding and file-editing tasks
 - When writing scripts or commands that create/read files from the workspace, prefer relative paths such as `hello.txt`, `../uploads/data.csv`, and `../outputs/report.md`
 - Avoid hardcoding `/mnt/user-data/...` inside generated scripts when a relative path from the workspace is enough
- Final deliverables must be copied to `/mnt/user-data/outputs` and presented using `present_file` tool
+- Final deliverables must be copied to `/mnt/user-data/outputs` and presented using `present_files` tool
 {acp_section}
 </working_directory>

@@ -507,36 +539,34 @@ combined with a FastAPI gateway for REST API access [citation:FastAPI](https://f
 """


-def _get_memory_context(agent_name: str | None = None) -> str:
+def _get_memory_context(app_config: AppConfig, agent_name: str | None = None) -> str:
    """Get memory context for injection into system prompt.

-    Args:
-        agent_name: If provided, loads per-agent memory. If None, loads global memory.
-
-    Returns:
-        Formatted memory context string wrapped in XML tags, or empty string if disabled.
+    Returns an empty string when memory is disabled or the stored memory file
+    cannot be read/parsed. A corrupt memory.json degrades the prompt to
+    no-memory; it never kills the agent.
    """
+    from deerflow.agents.memory import format_memory_for_injection, get_memory_data
+    from deerflow.runtime.user_context import get_effective_user_id
+
+    memory_config = app_config.memory
+    if not memory_config.enabled or not memory_config.injection_enabled:
+        return ""
+
    try:
-        from deerflow.agents.memory import format_memory_for_injection, get_memory_data
-        from deerflow.config.memory_config import get_memory_config
+        memory_data = get_memory_data(memory_config, agent_name, user_id=get_effective_user_id())
+    except (OSError, ValueError, UnicodeDecodeError):
+        logger.exception("Failed to load memory data for prompt injection")
+        return ""

-        config = get_memory_config()
-        if not config.enabled or not config.injection_enabled:
-            return ""
+    memory_content = format_memory_for_injection(memory_data, max_tokens=memory_config.max_injection_tokens)
+    if not memory_content.strip():
+        return ""

-        memory_data = get_memory_data(agent_name)
-        memory_content = format_memory_for_injection(memory_data, max_tokens=config.max_injection_tokens)
-
-        if not memory_content.strip():
-            return ""
-
-        return f"""<memory>
+    return f"""<memory>
 {memory_content}
 </memory>
 """
-    except Exception as e:
-        logger.error("Failed to load memory context: %s", e)
-        return ""


@lru_cache(maxsize=32)
@@ -571,19 +601,12 @@ You have access to skills that provide optimized workflows for specific tasks. E
 </skill_system>"""


-def get_skills_prompt_section(available_skills: set[str] | None = None) -> str:
+def get_skills_prompt_section(app_config: AppConfig, available_skills: set[str] | None = None) -> str:
    """Generate the skills prompt section with available skills list."""
-    skills = _get_enabled_skills()
+    skills = _get_enabled_skills(app_config)

-    try:
-        from deerflow.config import get_app_config
-
-        config = get_app_config()
-        container_base_path = config.skills.container_path
-        skill_evolution_enabled = config.skill_evolution.enabled
-    except Exception:
-        container_base_path = "/mnt/skills"
-        skill_evolution_enabled = False
+    container_base_path = app_config.skills.container_path
+    skill_evolution_enabled = app_config.skill_evolution.enabled

    if not skills and not skill_evolution_enabled:
        return ""
@@ -607,7 +630,7 @@ def get_agent_soul(agent_name: str | None) -> str:
    return ""


-def get_deferred_tools_prompt_section() -> str:
+def get_deferred_tools_prompt_section(app_config: AppConfig) -> str:
    """Generate <available-deferred-tools> block for the system prompt.

    Lists only deferred tool names so the agent knows what exists
@@ -616,12 +639,7 @@ def get_deferred_tools_prompt_section() -> str:
    """
    from deerflow.tools.builtins.tool_search import get_deferred_registry

-    try:
-        from deerflow.config import get_app_config
-
-        if not get_app_config().tool_search.enabled:
-            return ""
-    except Exception:
+    if not app_config.tool_search.enabled:
        return ""

    registry = get_deferred_registry()
@@ -632,15 +650,9 @@ def get_deferred_tools_prompt_section() -> str:
    return f"<available-deferred-tools>\n{names}\n</available-deferred-tools>"


-def _build_acp_section() -> str:
+def _build_acp_section(app_config: AppConfig) -> str:
    """Build the ACP agent prompt section, only if ACP agents are configured."""
-    try:
-        from deerflow.config.acp_config import get_acp_agents
-
-        agents = get_acp_agents()
-        if not agents:
-            return ""
-    except Exception:
+    if not app_config.acp_agents:
        return ""

    return (
@@ -648,19 +660,13 @@ def _build_acp_section() -> str:
        "- ACP agents (e.g. codex, claude_code) run in their own independent workspace — NOT in `/mnt/user-data/`\n"
        "- When writing prompts for ACP agents, describe the task only — do NOT reference `/mnt/user-data` paths\n"
        "- ACP agent results are accessible at `/mnt/acp-workspace/` (read-only) — use `ls`, `read_file`, or `bash cp` to retrieve output files\n"
-        "- To deliver ACP output to the user: copy from `/mnt/acp-workspace/<file>` to `/mnt/user-data/outputs/<file>`, then use `present_file`"
+        "- To deliver ACP output to the user: copy from `/mnt/acp-workspace/<file>` to `/mnt/user-data/outputs/<file>`, then use `present_files`"
    )


-def _build_custom_mounts_section() -> str:
+def _build_custom_mounts_section(app_config: AppConfig) -> str:
    """Build a prompt section for explicitly configured sandbox mounts."""
-    try:
-        from deerflow.config import get_app_config
-
-        mounts = get_app_config().sandbox.mounts or []
-    except Exception:
-        logger.exception("Failed to load configured sandbox mounts for the lead-agent prompt")
-        return ""
+    mounts = app_config.sandbox.mounts or []

    if not mounts:
        return ""
@@ -674,13 +680,20 @@ def _build_custom_mounts_section() -> str:
    return f"\n**Custom Mounted Directories:**\n{mounts_list}\n- If the user needs files outside `/mnt/user-data`, use these absolute container paths directly when they match the requested directory"


-def apply_prompt_template(subagent_enabled: bool = False, max_concurrent_subagents: int = 3, *, agent_name: str | None = None, available_skills: set[str] | None = None) -> str:
+def apply_prompt_template(
+    app_config: AppConfig,
+    subagent_enabled: bool = False,
+    max_concurrent_subagents: int = 3,
+    *,
+    agent_name: str | None = None,
+    available_skills: set[str] | None = None,
+) -> str:
    # Get memory context
-    memory_context = _get_memory_context(agent_name)
+    memory_context = _get_memory_context(app_config, agent_name)

    # Include subagent section only if enabled (from runtime parameter)
    n = max_concurrent_subagents
-    subagent_section = _build_subagent_section(n) if subagent_enabled else ""
+    subagent_section = _build_subagent_section(n, app_config) if subagent_enabled else ""

    # Add subagent reminder to critical_reminders if enabled
    subagent_reminder = (
@@ -701,14 +714,14 @@ def apply_prompt_template(subagent_enabled: bool = False, max_concurrent_subagen
    )

    # Get skills section
-    skills_section = get_skills_prompt_section(available_skills)
+    skills_section = get_skills_prompt_section(app_config, available_skills)

    # Get deferred tools section (tool_search)
-    deferred_tools_section = get_deferred_tools_prompt_section()
+    deferred_tools_section = get_deferred_tools_prompt_section(app_config)

    # Build ACP agent section only if ACP agents are configured
-    acp_section = _build_acp_section()
-    custom_mounts_section = _build_custom_mounts_section()
+    acp_section = _build_acp_section(app_config)
+    custom_mounts_section = _build_custom_mounts_section(app_config)
    acp_and_mounts_section = "\n".join(section for section in (acp_section, custom_mounts_section) if section)

    # Format the prompt with dynamic skills and memory
@@ -0,0 +1,109 @@
+"""Shared helpers for turning conversations into memory update inputs."""
+
+from __future__ import annotations
+
+import re
+from copy import copy
+from typing import Any
+
+_UPLOAD_BLOCK_RE = re.compile(r"<uploaded_files>[\s\S]*?</uploaded_files>\n*", re.IGNORECASE)
+_CORRECTION_PATTERNS = (
+    re.compile(r"\bthat(?:'s| is) (?:wrong|incorrect)\b", re.IGNORECASE),
+    re.compile(r"\byou misunderstood\b", re.IGNORECASE),
+    re.compile(r"\btry again\b", re.IGNORECASE),
+    re.compile(r"\bredo\b", re.IGNORECASE),
+    re.compile(r"不对"),
+    re.compile(r"你理解错了"),
+    re.compile(r"你理解有误"),
+    re.compile(r"重试"),
+    re.compile(r"重新来"),
+    re.compile(r"换一种"),
+    re.compile(r"改用"),
+)
+_REINFORCEMENT_PATTERNS = (
+    re.compile(r"\byes[,.]?\s+(?:exactly|perfect|that(?:'s| is) (?:right|correct|it))\b", re.IGNORECASE),
+    re.compile(r"\bperfect(?:[.!?]|$)", re.IGNORECASE),
+    re.compile(r"\bexactly\s+(?:right|correct)\b", re.IGNORECASE),
+    re.compile(r"\bthat(?:'s| is)\s+(?:exactly\s+)?(?:right|correct|what i (?:wanted|needed|meant))\b", re.IGNORECASE),
+    re.compile(r"\bkeep\s+(?:doing\s+)?that\b", re.IGNORECASE),
+    re.compile(r"\bjust\s+(?:like\s+)?(?:that|this)\b", re.IGNORECASE),
+    re.compile(r"\bthis is (?:great|helpful)\b(?:[.!?]|$)", re.IGNORECASE),
+    re.compile(r"\bthis is what i wanted\b(?:[.!?]|$)", re.IGNORECASE),
+    re.compile(r"对[，,]?\s*就是这样(?:[。！？!?.]|$)"),
+    re.compile(r"完全正确(?:[。！？!?.]|$)"),
+    re.compile(r"(?:对[，,]?\s*)?就是这个意思(?:[。！？!?.]|$)"),
+    re.compile(r"正是我想要的(?:[。！？!?.]|$)"),
+    re.compile(r"继续保持(?:[。！？!?.]|$)"),
+)
+
+
+def extract_message_text(message: Any) -> str:
+    """Extract plain text from message content for filtering and signal detection."""
+    content = getattr(message, "content", "")
+    if isinstance(content, list):
+        text_parts: list[str] = []
+        for part in content:
+            if isinstance(part, str):
+                text_parts.append(part)
+            elif isinstance(part, dict):
+                text_val = part.get("text")
+                if isinstance(text_val, str):
+                    text_parts.append(text_val)
+        return " ".join(text_parts)
+    return str(content)
+
+
+def filter_messages_for_memory(messages: list[Any]) -> list[Any]:
+    """Keep only user inputs and final assistant responses for memory updates."""
+    filtered = []
+    skip_next_ai = False
+    for msg in messages:
+        msg_type = getattr(msg, "type", None)
+
+        if msg_type == "human":
+            content_str = extract_message_text(msg)
+            if "<uploaded_files>" in content_str:
+                stripped = _UPLOAD_BLOCK_RE.sub("", content_str).strip()
+                if not stripped:
+                    skip_next_ai = True
+                    continue
+                clean_msg = copy(msg)
+                clean_msg.content = stripped
+                filtered.append(clean_msg)
+                skip_next_ai = False
+            else:
+                filtered.append(msg)
+                skip_next_ai = False
+        elif msg_type == "ai":
+            tool_calls = getattr(msg, "tool_calls", None)
+            if not tool_calls:
+                if skip_next_ai:
+                    skip_next_ai = False
+                    continue
+                filtered.append(msg)
+
+    return filtered
+
+
+def detect_correction(messages: list[Any]) -> bool:
+    """Detect explicit user corrections in recent conversation turns."""
+    recent_user_msgs = [msg for msg in messages[-6:] if getattr(msg, "type", None) == "human"]
+
+    for msg in recent_user_msgs:
+        content = extract_message_text(msg).strip()
+        if content and any(pattern.search(content) for pattern in _CORRECTION_PATTERNS):
+            return True
+
+    return False
+
+
+def detect_reinforcement(messages: list[Any]) -> bool:
+    """Detect explicit positive reinforcement signals in recent conversation turns."""
+    recent_user_msgs = [msg for msg in messages[-6:] if getattr(msg, "type", None) == "human"]
+
+    for msg in recent_user_msgs:
+        content = extract_message_text(msg).strip()
+        if content and any(pattern.search(content) for pattern in _REINFORCEMENT_PATTERNS):
+            return True
+
+    return False
@@ -7,11 +7,17 @@ from dataclasses import dataclass, field
 from datetime import UTC, datetime
 from typing import Any

-from deerflow.config.memory_config import get_memory_config
+from deerflow.config.app_config import AppConfig

 logger = logging.getLogger(__name__)


+# Module-level config pointer set by the middleware that owns the queue.
+# The queue runs on a background Timer thread where ``Runtime`` and FastAPI
+# request context are not accessible; the enqueuer (which does have runtime
+# context) is responsible for plumbing ``AppConfig`` through ``add()``.
+
+
@dataclass
 class ConversationContext:
    """Context for a conversation to be processed for memory update."""
@@ -20,6 +26,7 @@ class ConversationContext:
    messages: list[Any]
    timestamp: datetime = field(default_factory=lambda: datetime.now(UTC))
    agent_name: str | None = None
+    user_id: str | None = None
    correction_detected: bool = False
    reinforcement_detected: bool = False

@@ -30,10 +37,21 @@ class MemoryUpdateQueue:
    This queue collects conversation contexts and processes them after
    a configurable debounce period. Multiple conversations received within
    the debounce window are batched together.
+
+    The queue captures an ``AppConfig`` reference at construction time and
+    reuses it for the MemoryUpdater it spawns. Callers must construct a
+    fresh queue when the config changes rather than reaching into a global.
    """

-    def __init__(self):
-        """Initialize the memory update queue."""
+    def __init__(self, app_config: AppConfig):
+        """Initialize the memory update queue.
+
+        Args:
+            app_config: Application config. The queue reads its own
+                ``memory`` section for debounce timing and hands the full
+                config to :class:`MemoryUpdater`.
+        """
+        self._app_config = app_config
        self._queue: list[ConversationContext] = []
        self._lock = threading.Lock()
        self._timer: threading.Timer | None = None
@@ -44,65 +62,103 @@ class MemoryUpdateQueue:
        thread_id: str,
        messages: list[Any],
        agent_name: str | None = None,
+        user_id: str | None = None,
        correction_detected: bool = False,
        reinforcement_detected: bool = False,
    ) -> None:
-        """Add a conversation to the update queue.
-
-        Args:
-            thread_id: The thread ID.
-            messages: The conversation messages.
-            agent_name: If provided, memory is stored per-agent. If None, uses global memory.
-            correction_detected: Whether recent turns include an explicit correction signal.
-            reinforcement_detected: Whether recent turns include a positive reinforcement signal.
-        """
-        config = get_memory_config()
+        """Add a conversation to the update queue."""
+        config = self._app_config.memory
        if not config.enabled:
            return

        with self._lock:
-            existing_context = next(
-                (context for context in self._queue if context.thread_id == thread_id),
-                None,
-            )
-            merged_correction_detected = correction_detected or (existing_context.correction_detected if existing_context is not None else False)
-            merged_reinforcement_detected = reinforcement_detected or (existing_context.reinforcement_detected if existing_context is not None else False)
-            context = ConversationContext(
+            self._enqueue_locked(
                thread_id=thread_id,
                messages=messages,
                agent_name=agent_name,
-                correction_detected=merged_correction_detected,
-                reinforcement_detected=merged_reinforcement_detected,
+                user_id=user_id,
+                correction_detected=correction_detected,
+                reinforcement_detected=reinforcement_detected,
            )
-
-            # Check if this thread already has a pending update
-            # If so, replace it with the newer one
-            self._queue = [c for c in self._queue if c.thread_id != thread_id]
-            self._queue.append(context)
-
-            # Reset or start the debounce timer
            self._reset_timer()

        logger.info("Memory update queued for thread %s, queue size: %d", thread_id, len(self._queue))

+    def add_nowait(
+        self,
+        thread_id: str,
+        messages: list[Any],
+        agent_name: str | None = None,
+        user_id: str | None = None,
+        correction_detected: bool = False,
+        reinforcement_detected: bool = False,
+    ) -> None:
+        """Add a conversation and start processing immediately in the background."""
+        config = self._app_config.memory
+        if not config.enabled:
+            return
+
+        with self._lock:
+            self._enqueue_locked(
+                thread_id=thread_id,
+                messages=messages,
+                agent_name=agent_name,
+                user_id=user_id,
+                correction_detected=correction_detected,
+                reinforcement_detected=reinforcement_detected,
+            )
+            self._schedule_timer(0)
+
+        logger.info("Memory update queued for immediate processing on thread %s, queue size: %d", thread_id, len(self._queue))
+
+    def _enqueue_locked(
+        self,
+        *,
+        thread_id: str,
+        messages: list[Any],
+        agent_name: str | None,
+        user_id: str | None = None,
+        correction_detected: bool,
+        reinforcement_detected: bool,
+    ) -> None:
+        existing_context = next(
+            (context for context in self._queue if context.thread_id == thread_id),
+            None,
+        )
+        merged_correction_detected = correction_detected or (existing_context.correction_detected if existing_context is not None else False)
+        merged_reinforcement_detected = reinforcement_detected or (existing_context.reinforcement_detected if existing_context is not None else False)
+        context = ConversationContext(
+            thread_id=thread_id,
+            messages=messages,
+            agent_name=agent_name,
+            user_id=user_id,
+            correction_detected=merged_correction_detected,
+            reinforcement_detected=merged_reinforcement_detected,
+        )
+
+        self._queue = [c for c in self._queue if c.thread_id != thread_id]
+        self._queue.append(context)
+
    def _reset_timer(self) -> None:
        """Reset the debounce timer."""
-        config = get_memory_config()
+        config = self._app_config.memory
+        self._schedule_timer(config.debounce_seconds)

+        logger.debug("Memory update timer set for %ss", config.debounce_seconds)
+
+    def _schedule_timer(self, delay_seconds: float) -> None:
+        """Schedule queue processing after the provided delay."""
        # Cancel existing timer if any
        if self._timer is not None:
            self._timer.cancel()

-        # Start new timer
        self._timer = threading.Timer(
-            config.debounce_seconds,
+            delay_seconds,
            self._process_queue,
        )
        self._timer.daemon = True
        self._timer.start()

-        logger.debug("Memory update timer set for %ss", config.debounce_seconds)
-
    def _process_queue(self) -> None:
        """Process all queued conversation contexts."""
        # Import here to avoid circular dependency
@@ -110,8 +166,8 @@ class MemoryUpdateQueue:

        with self._lock:
            if self._processing:
-                # Already processing, reschedule
-                self._reset_timer()
+                # Preserve immediate flush semantics even if another worker is active.
+                self._schedule_timer(0)
                return

            if not self._queue:
@@ -125,7 +181,7 @@ class MemoryUpdateQueue:
        logger.info("Processing %d queued memory updates", len(contexts_to_process))

        try:
-            updater = MemoryUpdater()
+            updater = MemoryUpdater(self._app_config)

            for context in contexts_to_process:
                try:
@@ -136,6 +192,7 @@ class MemoryUpdateQueue:
                        agent_name=context.agent_name,
                        correction_detected=context.correction_detected,
                        reinforcement_detected=context.reinforcement_detected,
+                        user_id=context.user_id,
                    )
                    if success:
                        logger.info("Memory updated successfully for thread %s", context.thread_id)
@@ -164,6 +221,13 @@ class MemoryUpdateQueue:

        self._process_queue()

+    def flush_nowait(self) -> None:
+        """Start queue processing immediately in a background thread."""
+        with self._lock:
+            # Daemon thread: queued messages may be lost if the process exits
+            # before _process_queue completes. Acceptable for best-effort memory updates.
+            self._schedule_timer(0)
+
    def clear(self) -> None:
        """Clear the queue without processing.

@@ -189,31 +253,35 @@ class MemoryUpdateQueue:
            return self._processing


-# Global singleton instance
-_memory_queue: MemoryUpdateQueue | None = None
+# Queues keyed by ``id(AppConfig)`` so tests and multi-client setups with
+# distinct configs do not share a debounce queue.
+_memory_queues: dict[int, MemoryUpdateQueue] = {}
 _queue_lock = threading.Lock()


-def get_memory_queue() -> MemoryUpdateQueue:
-    """Get the global memory update queue singleton.
-
-    Returns:
-        The memory update queue instance.
-    """
-    global _memory_queue
+def get_memory_queue(app_config: AppConfig) -> MemoryUpdateQueue:
+    """Get or create the memory update queue for the given app config."""
+    key = id(app_config)
    with _queue_lock:
-        if _memory_queue is None:
-            _memory_queue = MemoryUpdateQueue()
-        return _memory_queue
+        queue = _memory_queues.get(key)
+        if queue is None:
+            queue = MemoryUpdateQueue(app_config)
+            _memory_queues[key] = queue
+        return queue


-def reset_memory_queue() -> None:
-    """Reset the global memory queue.
+def reset_memory_queue(app_config: AppConfig | None = None) -> None:
+    """Reset memory queue(s).

-    This is useful for testing.
+    Pass an ``app_config`` to reset only its queue, or omit to reset all
+    (useful at test teardown).
    """
-    global _memory_queue
    with _queue_lock:
-        if _memory_queue is not None:
-            _memory_queue.clear()
-        _memory_queue = None
+        if app_config is not None:
+            queue = _memory_queues.pop(id(app_config), None)
+            if queue is not None:
+                queue.clear()
+            return
+        for queue in _memory_queues.values():
+            queue.clear()
+        _memory_queues.clear()
@@ -4,12 +4,13 @@ import abc
 import json
 import logging
 import threading
+import uuid
 from datetime import UTC, datetime
 from pathlib import Path
 from typing import Any

 from deerflow.config.agents_config import AGENT_NAME_PATTERN
-from deerflow.config.memory_config import get_memory_config
+from deerflow.config.memory_config import MemoryConfig
 from deerflow.config.paths import get_paths

 logger = logging.getLogger(__name__)
@@ -43,17 +44,17 @@ class MemoryStorage(abc.ABC):
    """Abstract base class for memory storage providers."""

    @abc.abstractmethod
-    def load(self, agent_name: str | None = None) -> dict[str, Any]:
+    def load(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
        """Load memory data for the given agent."""
        pass

    @abc.abstractmethod
-    def reload(self, agent_name: str | None = None) -> dict[str, Any]:
+    def reload(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
        """Force reload memory data for the given agent."""
        pass

    @abc.abstractmethod
-    def save(self, memory_data: dict[str, Any], agent_name: str | None = None) -> bool:
+    def save(self, memory_data: dict[str, Any], agent_name: str | None = None, *, user_id: str | None = None) -> bool:
        """Save memory data for the given agent."""
        pass

@@ -61,11 +62,20 @@ class MemoryStorage(abc.ABC):
 class FileMemoryStorage(MemoryStorage):
    """File-based memory storage provider."""

-    def __init__(self):
-        """Initialize the file memory storage."""
-        # Per-agent memory cache: keyed by agent_name (None = global)
+    def __init__(self, memory_config: MemoryConfig):
+        """Initialize the file memory storage.
+
+        Args:
+            memory_config: Memory configuration (storage_path etc.). Stored on
+                the instance so per-request lookups don't need to reach for
+                ambient state.
+        """
+        self._memory_config = memory_config
+        # Per-user/agent memory cache: keyed by (user_id, agent_name) tuple (None = global)
        # Value: (memory_data, file_mtime)
-        self._memory_cache: dict[str | None, tuple[dict[str, Any], float | None]] = {}
+        self._memory_cache: dict[tuple[str | None, str | None], tuple[dict[str, Any], float | None]] = {}
+        # Guards all reads and writes to _memory_cache across concurrent callers.
+        self._cache_lock = threading.Lock()

    def _validate_agent_name(self, agent_name: str) -> None:
        """Validate that the agent name is safe to use in filesystem paths.
@@ -78,21 +88,28 @@ class FileMemoryStorage(MemoryStorage):
        if not AGENT_NAME_PATTERN.match(agent_name):
            raise ValueError(f"Invalid agent name {agent_name!r}: names must match {AGENT_NAME_PATTERN.pattern}")

-    def _get_memory_file_path(self, agent_name: str | None = None) -> Path:
+    def _get_memory_file_path(self, agent_name: str | None = None, *, user_id: str | None = None) -> Path:
        """Get the path to the memory file."""
+        config = self._memory_config
+        if user_id is not None:
+            if agent_name is not None:
+                self._validate_agent_name(agent_name)
+                return get_paths().user_agent_memory_file(user_id, agent_name)
+            if config.storage_path and Path(config.storage_path).is_absolute():
+                return Path(config.storage_path)
+            return get_paths().user_memory_file(user_id)
+        # Legacy: no user_id
        if agent_name is not None:
            self._validate_agent_name(agent_name)
            return get_paths().agent_memory_file(agent_name)
-
-        config = get_memory_config()
        if config.storage_path:
            p = Path(config.storage_path)
            return p if p.is_absolute() else get_paths().base_dir / p
        return get_paths().memory_file

-    def _load_memory_from_file(self, agent_name: str | None = None) -> dict[str, Any]:
+    def _load_memory_from_file(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
        """Load memory data from file."""
-        file_path = self._get_memory_file_path(agent_name)
+        file_path = self._get_memory_file_path(agent_name, user_id=user_id)

        if not file_path.exists():
            return create_empty_memory()
@@ -105,46 +122,55 @@ class FileMemoryStorage(MemoryStorage):
            logger.warning("Failed to load memory file: %s", e)
            return create_empty_memory()

-    def load(self, agent_name: str | None = None) -> dict[str, Any]:
+    def load(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
        """Load memory data (cached with file modification time check)."""
-        file_path = self._get_memory_file_path(agent_name)
+        file_path = self._get_memory_file_path(agent_name, user_id=user_id)

        try:
            current_mtime = file_path.stat().st_mtime if file_path.exists() else None
        except OSError:
            current_mtime = None

-        cached = self._memory_cache.get(agent_name)
+        cache_key = (user_id, agent_name)
+        with self._cache_lock:
+            cached = self._memory_cache.get(cache_key)
+            if cached is not None and cached[1] == current_mtime:
+                return cached[0]

-        if cached is None or cached[1] != current_mtime:
-            memory_data = self._load_memory_from_file(agent_name)
-            self._memory_cache[agent_name] = (memory_data, current_mtime)
-            return memory_data
+        memory_data = self._load_memory_from_file(agent_name, user_id=user_id)

-        return cached[0]
+        with self._cache_lock:
+            self._memory_cache[cache_key] = (memory_data, current_mtime)

-    def reload(self, agent_name: str | None = None) -> dict[str, Any]:
+        return memory_data
+
+    def reload(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
        """Reload memory data from file, forcing cache invalidation."""
-        file_path = self._get_memory_file_path(agent_name)
-        memory_data = self._load_memory_from_file(agent_name)
+        file_path = self._get_memory_file_path(agent_name, user_id=user_id)
+        memory_data = self._load_memory_from_file(agent_name, user_id=user_id)

        try:
            mtime = file_path.stat().st_mtime if file_path.exists() else None
        except OSError:
            mtime = None

-        self._memory_cache[agent_name] = (memory_data, mtime)
+        cache_key = (user_id, agent_name)
+        with self._cache_lock:
+            self._memory_cache[cache_key] = (memory_data, mtime)
        return memory_data

-    def save(self, memory_data: dict[str, Any], agent_name: str | None = None) -> bool:
+    def save(self, memory_data: dict[str, Any], agent_name: str | None = None, *, user_id: str | None = None) -> bool:
        """Save memory data to file and update cache."""
-        file_path = self._get_memory_file_path(agent_name)
+        file_path = self._get_memory_file_path(agent_name, user_id=user_id)

        try:
            file_path.parent.mkdir(parents=True, exist_ok=True)
-            memory_data["lastUpdated"] = utc_now_iso_z()
+            # Shallow-copy before adding lastUpdated so the caller's dict is not
+            # mutated as a side-effect, and the cache reference is not silently
+            # updated before the file write succeeds.
+            memory_data = {**memory_data, "lastUpdated": utc_now_iso_z()}

-            temp_path = file_path.with_suffix(".tmp")
+            temp_path = file_path.with_suffix(f".{uuid.uuid4().hex}.tmp")
            with open(temp_path, "w", encoding="utf-8") as f:
                json.dump(memory_data, f, indent=2, ensure_ascii=False)

@@ -155,7 +181,9 @@ class FileMemoryStorage(MemoryStorage):
            except OSError:
                mtime = None

-            self._memory_cache[agent_name] = (memory_data, mtime)
+            cache_key = (user_id, agent_name)
+            with self._cache_lock:
+                self._memory_cache[cache_key] = (memory_data, mtime)
            logger.info("Memory saved to %s", file_path)
            return True
        except OSError as e:
@@ -163,23 +191,31 @@ class FileMemoryStorage(MemoryStorage):
            return False


-_storage_instance: MemoryStorage | None = None
+# Instances keyed by (storage_class_path, id(memory_config)) so tests can
+# construct isolated storages and multi-client setups with different configs
+# don't collide on a single process-wide singleton.
+_storage_instances: dict[tuple[str, int], MemoryStorage] = {}
 _storage_lock = threading.Lock()


-def get_memory_storage() -> MemoryStorage:
-    """Get the configured memory storage instance."""
-    global _storage_instance
-    if _storage_instance is not None:
-        return _storage_instance
+def get_memory_storage(memory_config: MemoryConfig) -> MemoryStorage:
+    """Get the configured memory storage instance.
+
+    Caches one instance per ``(storage_class, memory_config)`` pair. In
+    single-config deployments this collapses to one instance; in multi-client
+    or test scenarios each config gets its own storage.
+    """
+    key = (memory_config.storage_class, id(memory_config))
+    existing = _storage_instances.get(key)
+    if existing is not None:
+        return existing

    with _storage_lock:
-        if _storage_instance is not None:
-            return _storage_instance
-
-        config = get_memory_config()
-        storage_class_path = config.storage_class
+        existing = _storage_instances.get(key)
+        if existing is not None:
+            return existing

+        storage_class_path = memory_config.storage_class
        try:
            module_path, class_name = storage_class_path.rsplit(".", 1)
            import importlib
@@ -193,13 +229,14 @@ def get_memory_storage() -> MemoryStorage:
            if not issubclass(storage_class, MemoryStorage):
                raise TypeError(f"Configured memory storage '{storage_class_path}' is not a subclass of MemoryStorage")

-            _storage_instance = storage_class()
+            instance = storage_class(memory_config)
        except Exception as e:
            logger.error(
                "Failed to load memory storage %s, falling back to FileMemoryStorage: %s",
                storage_class_path,
                e,
            )
-            _storage_instance = FileMemoryStorage()
+            instance = FileMemoryStorage(memory_config)

-    return _storage_instance
+        _storage_instances[key] = instance
+        return instance
@@ -0,0 +1,38 @@
+"""Hooks fired before summarization removes messages from state."""
+
+from __future__ import annotations
+
+from deerflow.agents.memory.message_processing import detect_correction, detect_reinforcement, filter_messages_for_memory
+from deerflow.agents.memory.queue import get_memory_queue
+from deerflow.agents.middlewares.summarization_middleware import SummarizationEvent
+from deerflow.config.app_config import AppConfig
+
+
+def memory_flush_hook(event: SummarizationEvent) -> None:
+    """Flush messages about to be summarized into the memory queue.
+
+    Reads ``AppConfig`` from disk on every invocation. This hook is fired by
+    ``SummarizationMiddleware`` which has no ergonomic way to thread an
+    explicit ``app_config`` through; ``AppConfig.from_file()`` is a pure load
+    so the cost is acceptable for this rare pre-summarization callback.
+    """
+    app_config = AppConfig.from_file()
+    if not app_config.memory.enabled or not event.thread_id:
+        return
+
+    filtered_messages = filter_messages_for_memory(list(event.messages_to_summarize))
+    user_messages = [message for message in filtered_messages if getattr(message, "type", None) == "human"]
+    assistant_messages = [message for message in filtered_messages if getattr(message, "type", None) == "ai"]
+    if not user_messages or not assistant_messages:
+        return
+
+    correction_detected = detect_correction(filtered_messages)
+    reinforcement_detected = not correction_detected and detect_reinforcement(filtered_messages)
+    queue = get_memory_queue(app_config)
+    queue.add_nowait(
+        thread_id=event.thread_id,
+        messages=filtered_messages,
+        agent_name=event.agent_name,
+        correction_detected=correction_detected,
+        reinforcement_detected=reinforcement_detected,
+    )
@@ -1,10 +1,15 @@
 """Memory updater for reading, writing, and updating memory data."""

+import asyncio
+import atexit
+import concurrent.futures
+import copy
 import json
 import logging
 import math
 import re
 import uuid
+from collections.abc import Awaitable
 from typing import Any

 from deerflow.agents.memory.prompt import (
@@ -16,55 +21,51 @@ from deerflow.agents.memory.storage import (
    get_memory_storage,
    utc_now_iso_z,
 )
-from deerflow.config.memory_config import get_memory_config
+from deerflow.config.app_config import AppConfig
+from deerflow.config.memory_config import MemoryConfig
 from deerflow.models import create_chat_model

 logger = logging.getLogger(__name__)

+_SYNC_MEMORY_UPDATER_EXECUTOR = concurrent.futures.ThreadPoolExecutor(
+    max_workers=4,
+    thread_name_prefix="memory-updater-sync",
+)
+atexit.register(lambda: _SYNC_MEMORY_UPDATER_EXECUTOR.shutdown(wait=False))
+

 def _create_empty_memory() -> dict[str, Any]:
    """Backward-compatible wrapper around the storage-layer empty-memory factory."""
    return create_empty_memory()


-def _save_memory_to_file(memory_data: dict[str, Any], agent_name: str | None = None) -> bool:
-    """Backward-compatible wrapper around the configured memory storage save path."""
-    return get_memory_storage().save(memory_data, agent_name)
+def _save_memory_to_file(memory_config: MemoryConfig, memory_data: dict[str, Any], agent_name: str | None = None, *, user_id: str | None = None) -> bool:
+    """Save via the configured memory storage."""
+    return get_memory_storage(memory_config).save(memory_data, agent_name, user_id=user_id)


-def get_memory_data(agent_name: str | None = None) -> dict[str, Any]:
+def get_memory_data(memory_config: MemoryConfig, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
    """Get the current memory data via storage provider."""
-    return get_memory_storage().load(agent_name)
+    return get_memory_storage(memory_config).load(agent_name, user_id=user_id)


-def reload_memory_data(agent_name: str | None = None) -> dict[str, Any]:
+def reload_memory_data(memory_config: MemoryConfig, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
    """Reload memory data via storage provider."""
-    return get_memory_storage().reload(agent_name)
+    return get_memory_storage(memory_config).reload(agent_name, user_id=user_id)


-def import_memory_data(memory_data: dict[str, Any], agent_name: str | None = None) -> dict[str, Any]:
-    """Persist imported memory data via storage provider.
-
-    Args:
-        memory_data: Full memory payload to persist.
-        agent_name: If provided, imports into per-agent memory.
-
-    Returns:
-        The saved memory data after storage normalization.
-
-    Raises:
-        OSError: If persisting the imported memory fails.
-    """
-    storage = get_memory_storage()
-    if not storage.save(memory_data, agent_name):
+def import_memory_data(memory_config: MemoryConfig, memory_data: dict[str, Any], agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
+    """Persist imported memory data via storage provider."""
+    storage = get_memory_storage(memory_config)
+    if not storage.save(memory_data, agent_name, user_id=user_id):
        raise OSError("Failed to save imported memory data")
-    return storage.load(agent_name)
+    return storage.load(agent_name, user_id=user_id)


-def clear_memory_data(agent_name: str | None = None) -> dict[str, Any]:
+def clear_memory_data(memory_config: MemoryConfig, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
    """Clear all stored memory data and persist an empty structure."""
    cleared_memory = create_empty_memory()
-    if not _save_memory_to_file(cleared_memory, agent_name):
+    if not _save_memory_to_file(memory_config, cleared_memory, agent_name, user_id=user_id):
        raise OSError("Failed to save cleared memory data")
    return cleared_memory

@@ -77,10 +78,13 @@ def _validate_confidence(confidence: float) -> float:


 def create_memory_fact(
+    memory_config: MemoryConfig,
    content: str,
    category: str = "context",
    confidence: float = 0.5,
    agent_name: str | None = None,
+    *,
+    user_id: str | None = None,
 ) -> dict[str, Any]:
    """Create a new fact and persist the updated memory data."""
    normalized_content = content.strip()
@@ -90,7 +94,7 @@ def create_memory_fact(
    normalized_category = category.strip() or "context"
    validated_confidence = _validate_confidence(confidence)
    now = utc_now_iso_z()
-    memory_data = get_memory_data(agent_name)
+    memory_data = get_memory_data(memory_config, agent_name, user_id=user_id)
    updated_memory = dict(memory_data)
    facts = list(memory_data.get("facts", []))
    facts.append(
@@ -105,15 +109,15 @@ def create_memory_fact(
    )
    updated_memory["facts"] = facts

-    if not _save_memory_to_file(updated_memory, agent_name):
+    if not _save_memory_to_file(memory_config, updated_memory, agent_name, user_id=user_id):
        raise OSError("Failed to save memory data after creating fact")

    return updated_memory


-def delete_memory_fact(fact_id: str, agent_name: str | None = None) -> dict[str, Any]:
+def delete_memory_fact(memory_config: MemoryConfig, fact_id: str, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
    """Delete a fact by its id and persist the updated memory data."""
-    memory_data = get_memory_data(agent_name)
+    memory_data = get_memory_data(memory_config, agent_name, user_id=user_id)
    facts = memory_data.get("facts", [])
    updated_facts = [fact for fact in facts if fact.get("id") != fact_id]
    if len(updated_facts) == len(facts):
@@ -122,21 +126,24 @@ def delete_memory_fact(fact_id: str, agent_name: str | None = None) -> dict[str,
    updated_memory = dict(memory_data)
    updated_memory["facts"] = updated_facts

-    if not _save_memory_to_file(updated_memory, agent_name):
+    if not _save_memory_to_file(memory_config, updated_memory, agent_name, user_id=user_id):
        raise OSError(f"Failed to save memory data after deleting fact '{fact_id}'")

    return updated_memory


 def update_memory_fact(
+    memory_config: MemoryConfig,
    fact_id: str,
    content: str | None = None,
    category: str | None = None,
    confidence: float | None = None,
    agent_name: str | None = None,
+    *,
+    user_id: str | None = None,
 ) -> dict[str, Any]:
    """Update an existing fact and persist the updated memory data."""
-    memory_data = get_memory_data(agent_name)
+    memory_data = get_memory_data(memory_config, agent_name, user_id=user_id)
    updated_memory = dict(memory_data)
    updated_facts: list[dict[str, Any]] = []
    found = False
@@ -163,7 +170,7 @@ def update_memory_fact(

    updated_memory["facts"] = updated_facts

-    if not _save_memory_to_file(updated_memory, agent_name):
+    if not _save_memory_to_file(memory_config, updated_memory, agent_name, user_id=user_id):
        raise OSError(f"Failed to save memory data after updating fact '{fact_id}'")

    return updated_memory
@@ -206,6 +213,39 @@ def _extract_text(content: Any) -> str:
    return str(content)


+def _run_async_update_sync(coro: Awaitable[bool]) -> bool:
+    """Run an async memory update from sync code, including nested-loop contexts."""
+    handed_off = False
+
+    try:
+        try:
+            loop = asyncio.get_running_loop()
+        except RuntimeError:
+            loop = None
+
+        if loop is not None and loop.is_running():
+            future = _SYNC_MEMORY_UPDATER_EXECUTOR.submit(asyncio.run, coro)
+            handed_off = True
+            return future.result()
+
+        handed_off = True
+        return asyncio.run(coro)
+    except Exception:
+        if not handed_off:
+            close = getattr(coro, "close", None)
+            if callable(close):
+                try:
+                    close()
+                except Exception:
+                    logger.debug(
+                        "Failed to close un-awaited memory update coroutine",
+                        exc_info=True,
+                    )
+
+        logger.exception("Failed to run async memory update from sync context")
+        return False
+
+
 # Matches sentences that describe a file-upload *event* rather than general
 # file-related work.  Deliberately narrow to avoid removing legitimate facts
 # such as "User works with CSV files" or "prefers PDF export".
@@ -255,19 +295,141 @@ def _fact_content_key(content: Any) -> str | None:
 class MemoryUpdater:
    """Updates memory using LLM based on conversation context."""

-    def __init__(self, model_name: str | None = None):
+    def __init__(self, app_config: AppConfig, model_name: str | None = None):
        """Initialize the memory updater.

        Args:
+            app_config: Application config (the updater needs both ``memory``
+                section for behavior and the full config for ``create_chat_model``).
            model_name: Optional model name to use. If None, uses config or default.
        """
+        self._app_config = app_config
        self._model_name = model_name

+    @property
+    def _memory_config(self) -> MemoryConfig:
+        return self._app_config.memory
+
    def _get_model(self):
        """Get the model for memory updates."""
-        config = get_memory_config()
-        model_name = self._model_name or config.model_name
-        return create_chat_model(name=model_name, thinking_enabled=False)
+        model_name = self._model_name or self._memory_config.model_name
+        return create_chat_model(name=model_name, thinking_enabled=False, app_config=self._app_config)
+
+    def _build_correction_hint(
+        self,
+        correction_detected: bool,
+        reinforcement_detected: bool,
+    ) -> str:
+        """Build optional prompt hints for correction and reinforcement signals."""
+        correction_hint = ""
+        if correction_detected:
+            correction_hint = (
+                "IMPORTANT: Explicit correction signals were detected in this conversation. "
+                "Pay special attention to what the agent got wrong, what the user corrected, "
+                "and record the correct approach as a fact with category "
+                '"correction" and confidence >= 0.95 when appropriate.'
+            )
+        if reinforcement_detected:
+            reinforcement_hint = (
+                "IMPORTANT: Positive reinforcement signals were detected in this conversation. "
+                "The user explicitly confirmed the agent's approach was correct or helpful. "
+                "Record the confirmed approach, style, or preference as a fact with category "
+                '"preference" or "behavior" and confidence >= 0.9 when appropriate.'
+            )
+            correction_hint = (correction_hint + "\n" + reinforcement_hint).strip() if correction_hint else reinforcement_hint
+
+        return correction_hint
+
+    def _prepare_update_prompt(
+        self,
+        messages: list[Any],
+        agent_name: str | None,
+        correction_detected: bool,
+        reinforcement_detected: bool,
+        user_id: str | None = None,
+    ) -> tuple[dict[str, Any], str] | None:
+        """Load memory and build the update prompt for a conversation."""
+        config = self._memory_config
+        if not config.enabled or not messages:
+            return None
+
+        current_memory = get_memory_data(config, agent_name, user_id=user_id)
+        conversation_text = format_conversation_for_update(messages)
+        if not conversation_text.strip():
+            return None
+
+        correction_hint = self._build_correction_hint(
+            correction_detected=correction_detected,
+            reinforcement_detected=reinforcement_detected,
+        )
+        prompt = MEMORY_UPDATE_PROMPT.format(
+            current_memory=json.dumps(current_memory, indent=2),
+            conversation=conversation_text,
+            correction_hint=correction_hint,
+        )
+        return current_memory, prompt
+
+    def _finalize_update(
+        self,
+        current_memory: dict[str, Any],
+        response_content: Any,
+        thread_id: str | None,
+        agent_name: str | None,
+        user_id: str | None = None,
+    ) -> bool:
+        """Parse the model response, apply updates, and persist memory."""
+        response_text = _extract_text(response_content).strip()
+
+        if response_text.startswith("```"):
+            lines = response_text.split("\n")
+            response_text = "\n".join(lines[1:-1] if lines[-1] == "```" else lines[1:])
+
+        update_data = json.loads(response_text)
+        # Deep-copy before in-place mutation so a subsequent save() failure
+        # cannot corrupt the still-cached original object reference.
+        updated_memory = self._apply_updates(copy.deepcopy(current_memory), update_data, thread_id)
+        updated_memory = _strip_upload_mentions_from_memory(updated_memory)
+        return get_memory_storage(self._memory_config).save(updated_memory, agent_name, user_id=user_id)
+
+    async def aupdate_memory(
+        self,
+        messages: list[Any],
+        thread_id: str | None = None,
+        agent_name: str | None = None,
+        correction_detected: bool = False,
+        reinforcement_detected: bool = False,
+        user_id: str | None = None,
+    ) -> bool:
+        """Update memory asynchronously based on conversation messages."""
+        try:
+            prepared = await asyncio.to_thread(
+                self._prepare_update_prompt,
+                messages=messages,
+                agent_name=agent_name,
+                correction_detected=correction_detected,
+                reinforcement_detected=reinforcement_detected,
+                user_id=user_id,
+            )
+            if prepared is None:
+                return False
+
+            current_memory, prompt = prepared
+            model = self._get_model()
+            response = await model.ainvoke(prompt, config={"run_name": "memory_agent"})
+            return await asyncio.to_thread(
+                self._finalize_update,
+                current_memory=current_memory,
+                response_content=response.content,
+                thread_id=thread_id,
+                agent_name=agent_name,
+                user_id=user_id,
+            )
+        except json.JSONDecodeError as e:
+            logger.warning("Failed to parse LLM response for memory update: %s", e)
+            return False
+        except Exception as e:
+            logger.exception("Memory update failed: %s", e)
+            return False

    def update_memory(
        self,
@@ -276,8 +438,9 @@ class MemoryUpdater:
        agent_name: str | None = None,
        correction_detected: bool = False,
        reinforcement_detected: bool = False,
+        user_id: str | None = None,
    ) -> bool:
-        """Update memory based on conversation messages.
+        """Synchronously update memory via the async updater path.

        Args:
            messages: List of conversation messages.
@@ -285,11 +448,12 @@ class MemoryUpdater:
            agent_name: If provided, updates per-agent memory. If None, updates global memory.
            correction_detected: Whether recent turns include an explicit correction signal.
            reinforcement_detected: Whether recent turns include a positive reinforcement signal.
+            user_id: If provided, scopes memory to a specific user.

        Returns:
            True if update was successful, False otherwise.
        """
-        config = get_memory_config()
+        config = self._memory_config
        if not config.enabled:
            return False

@@ -298,7 +462,7 @@ class MemoryUpdater:

        try:
            # Get current memory
-            current_memory = get_memory_data(agent_name)
+            current_memory = get_memory_data(config, agent_name, user_id=user_id)

            # Format conversation for prompt
            conversation_text = format_conversation_for_update(messages)
@@ -353,7 +517,7 @@ class MemoryUpdater:
            updated_memory = _strip_upload_mentions_from_memory(updated_memory)

            # Save
-            return get_memory_storage().save(updated_memory, agent_name)
+            return get_memory_storage(config).save(updated_memory, agent_name, user_id=user_id)

        except json.JSONDecodeError as e:
            logger.warning("Failed to parse LLM response for memory update: %s", e)
@@ -378,7 +542,7 @@ class MemoryUpdater:
        Returns:
            Updated memory data.
        """
-        config = get_memory_config()
+        config = self._memory_config
        now = utc_now_iso_z()

        # Update user sections
@@ -455,6 +619,7 @@ def update_memory_from_conversation(
    agent_name: str | None = None,
    correction_detected: bool = False,
    reinforcement_detected: bool = False,
+    user_id: str | None = None,
 ) -> bool:
    """Convenience function to update memory from a conversation.

@@ -464,9 +629,10 @@ def update_memory_from_conversation(
        agent_name: If provided, updates per-agent memory. If None, updates global memory.
        correction_detected: Whether recent turns include an explicit correction signal.
        reinforcement_detected: Whether recent turns include a positive reinforcement signal.
+        user_id: If provided, scopes memory to a specific user.

    Returns:
        True if successful, False otherwise.
    """
    updater = MemoryUpdater()
-    return updater.update_memory(messages, thread_id, agent_name, correction_detected, reinforcement_detected)
+    return updater.update_memory(messages, thread_id, agent_name, correction_detected, reinforcement_detected, user_id=user_id)
@@ -3,6 +3,7 @@
 import json
 import logging
 from collections.abc import Callable
+from hashlib import sha256
 from typing import override

 from langchain.agents import AgentState
@@ -36,6 +37,13 @@ class ClarificationMiddleware(AgentMiddleware[ClarificationMiddlewareState]):

    state_schema = ClarificationMiddlewareState

+    def _stable_message_id(self, tool_call_id: str, formatted_message: str) -> str:
+        """Build a deterministic message ID so retried clarification calls replace, not append."""
+        if tool_call_id:
+            return f"clarification:{tool_call_id}"
+        digest = sha256(formatted_message.encode("utf-8")).hexdigest()[:16]
+        return f"clarification:{digest}"
+
    def _is_chinese(self, text: str) -> bool:
        """Check if text contains Chinese characters.

@@ -131,6 +139,7 @@ class ClarificationMiddleware(AgentMiddleware[ClarificationMiddlewareState]):
        # Create a ToolMessage with the formatted question
        # This will be added to the message history
        tool_message = ToolMessage(
+            id=self._stable_message_id(tool_call_id, formatted_message),
            content=formatted_message,
            tool_call_id=tool_call_id,
            name="ask_clarification",
@@ -13,6 +13,7 @@ at the correct positions (immediately after each dangling AIMessage), not append
 to the end of the message list as before_model + add_messages reducer would do.
 """

+import json
 import logging
 from collections.abc import Awaitable, Callable
 from typing import override
@@ -33,6 +34,44 @@ class DanglingToolCallMiddleware(AgentMiddleware[AgentState]):
    offending AIMessage so the LLM receives a well-formed conversation.
    """

+    @staticmethod
+    def _message_tool_calls(msg) -> list[dict]:
+        """Return normalized tool calls from structured fields or raw provider payloads."""
+        tool_calls = getattr(msg, "tool_calls", None) or []
+        if tool_calls:
+            return list(tool_calls)
+
+        raw_tool_calls = (getattr(msg, "additional_kwargs", None) or {}).get("tool_calls") or []
+        normalized: list[dict] = []
+        for raw_tc in raw_tool_calls:
+            if not isinstance(raw_tc, dict):
+                continue
+
+            function = raw_tc.get("function")
+            name = raw_tc.get("name")
+            if not name and isinstance(function, dict):
+                name = function.get("name")
+
+            args = raw_tc.get("args", {})
+            if not args and isinstance(function, dict):
+                raw_args = function.get("arguments")
+                if isinstance(raw_args, str):
+                    try:
+                        parsed_args = json.loads(raw_args)
+                    except (TypeError, ValueError, json.JSONDecodeError):
+                        parsed_args = {}
+                    args = parsed_args if isinstance(parsed_args, dict) else {}
+
+            normalized.append(
+                {
+                    "id": raw_tc.get("id"),
+                    "name": name or "unknown",
+                    "args": args if isinstance(args, dict) else {},
+                }
+            )
+
+        return normalized
+
    def _build_patched_messages(self, messages: list) -> list | None:
        """Return a new message list with patches inserted at the correct positions.

@@ -51,7 +90,7 @@ class DanglingToolCallMiddleware(AgentMiddleware[AgentState]):
        for msg in messages:
            if getattr(msg, "type", None) != "ai":
                continue
-            for tc in getattr(msg, "tool_calls", None) or []:
+            for tc in self._message_tool_calls(msg):
                tc_id = tc.get("id")
                if tc_id and tc_id not in existing_tool_msg_ids:
                    needs_patch = True
@@ -70,7 +109,7 @@ class DanglingToolCallMiddleware(AgentMiddleware[AgentState]):
            patched.append(msg)
            if getattr(msg, "type", None) != "ai":
                continue
-            for tc in getattr(msg, "tool_calls", None) or []:
+            for tc in self._message_tool_calls(msg):
                tc_id = tc.get("id")
                if tc_id and tc_id not in existing_tool_msg_ids and tc_id not in patched_ids:
                    patched.append(
@@ -16,6 +16,9 @@ from typing import override
 from langchain.agents import AgentState
 from langchain.agents.middleware import AgentMiddleware
 from langchain.agents.middleware.types import ModelCallResult, ModelRequest, ModelResponse
+from langchain_core.messages import ToolMessage
+from langgraph.prebuilt.tool_node import ToolCallRequest
+from langgraph.types import Command

 logger = logging.getLogger(__name__)

@@ -35,7 +38,7 @@ class DeferredToolFilterMiddleware(AgentMiddleware[AgentState]):
        if not registry:
            return request

-        deferred_names = {e.name for e in registry.entries}
+        deferred_names = registry.deferred_names
        active_tools = [t for t in request.tools if getattr(t, "name", None) not in deferred_names]

        if len(active_tools) < len(request.tools):
@@ -43,6 +46,28 @@ class DeferredToolFilterMiddleware(AgentMiddleware[AgentState]):

        return request.override(tools=active_tools)

+    def _blocked_tool_message(self, request: ToolCallRequest) -> ToolMessage | None:
+        from deerflow.tools.builtins.tool_search import get_deferred_registry
+
+        registry = get_deferred_registry()
+        if not registry:
+            return None
+
+        tool_name = str(request.tool_call.get("name") or "")
+        if not tool_name:
+            return None
+
+        if not registry.contains(tool_name):
+            return None
+
+        tool_call_id = str(request.tool_call.get("id") or "missing_tool_call_id")
+        return ToolMessage(
+            content=(f"Error: Tool '{tool_name}' is deferred and has not been promoted yet. Call tool_search first to expose and promote this tool's schema, then retry."),
+            tool_call_id=tool_call_id,
+            name=tool_name,
+            status="error",
+        )
+
    @override
    def wrap_model_call(
        self,
@@ -51,6 +76,17 @@ class DeferredToolFilterMiddleware(AgentMiddleware[AgentState]):
    ) -> ModelCallResult:
        return handler(self._filter_tools(request))

+    @override
+    def wrap_tool_call(
+        self,
+        request: ToolCallRequest,
+        handler: Callable[[ToolCallRequest], ToolMessage | Command],
+    ) -> ToolMessage | Command:
+        blocked = self._blocked_tool_message(request)
+        if blocked is not None:
+            return blocked
+        return handler(request)
+
    @override
    async def awrap_model_call(
        self,
@@ -58,3 +94,14 @@ class DeferredToolFilterMiddleware(AgentMiddleware[AgentState]):
        handler: Callable[[ModelRequest], Awaitable[ModelResponse]],
    ) -> ModelCallResult:
        return await handler(self._filter_tools(request))
+
+    @override
+    async def awrap_tool_call(
+        self,
+        request: ToolCallRequest,
+        handler: Callable[[ToolCallRequest], Awaitable[ToolMessage | Command]],
+    ) -> ToolMessage | Command:
+        blocked = self._blocked_tool_message(request)
+        if blocked is not None:
+            return blocked
+        return await handler(request)
@@ -4,6 +4,7 @@ from __future__ import annotations

 import asyncio
 import logging
+import threading
 import time
 from collections.abc import Awaitable, Callable
 from email.utils import parsedate_to_datetime
@@ -19,6 +20,8 @@ from langchain.agents.middleware.types import (
 from langchain_core.messages import AIMessage
 from langgraph.errors import GraphBubbleUp

+from deerflow.config.app_config import AppConfig
+
 logger = logging.getLogger(__name__)

 _RETRIABLE_STATUS_CODES = {408, 409, 425, 429, 500, 502, 503, 504}
@@ -67,6 +70,80 @@ class LLMErrorHandlingMiddleware(AgentMiddleware[AgentState]):
    retry_base_delay_ms: int = 1000
    retry_cap_delay_ms: int = 8000

+    circuit_failure_threshold: int = 5
+    circuit_recovery_timeout_sec: int = 60
+
+    def __init__(self, **kwargs: Any) -> None:
+        super().__init__(**kwargs)
+
+        # Load Circuit Breaker configs from app config if available, fall back to defaults
+        try:
+            app_config = AppConfig.from_file()
+            self.circuit_failure_threshold = app_config.circuit_breaker.failure_threshold
+            self.circuit_recovery_timeout_sec = app_config.circuit_breaker.recovery_timeout_sec
+        except (FileNotFoundError, RuntimeError):
+            # Gracefully fall back to class defaults in test environments
+            pass
+
+        # Circuit Breaker state
+        self._circuit_lock = threading.Lock()
+        self._circuit_failure_count = 0
+        self._circuit_open_until = 0.0
+        self._circuit_state = "closed"
+        self._circuit_probe_in_flight = False
+
+    def _check_circuit(self) -> bool:
+        """Returns True if circuit is OPEN (fast fail), False otherwise."""
+        with self._circuit_lock:
+            now = time.time()
+
+            if self._circuit_state == "open":
+                if now < self._circuit_open_until:
+                    return True
+                self._circuit_state = "half_open"
+                self._circuit_probe_in_flight = False
+
+            if self._circuit_state == "half_open":
+                if self._circuit_probe_in_flight:
+                    return True
+                self._circuit_probe_in_flight = True
+                return False
+
+            return False
+
+    def _record_success(self) -> None:
+        with self._circuit_lock:
+            if self._circuit_state != "closed" or self._circuit_failure_count > 0:
+                logger.info("Circuit breaker reset (Closed). LLM service recovered.")
+            self._circuit_failure_count = 0
+            self._circuit_open_until = 0.0
+            self._circuit_state = "closed"
+            self._circuit_probe_in_flight = False
+
+    def _record_failure(self) -> None:
+        with self._circuit_lock:
+            if self._circuit_state == "half_open":
+                self._circuit_open_until = time.time() + self.circuit_recovery_timeout_sec
+                self._circuit_state = "open"
+                self._circuit_probe_in_flight = False
+                logger.error(
+                    "Circuit breaker probe failed (Open). Will probe again after %ds.",
+                    self.circuit_recovery_timeout_sec,
+                )
+                return
+
+            self._circuit_failure_count += 1
+            if self._circuit_failure_count >= self.circuit_failure_threshold:
+                self._circuit_open_until = time.time() + self.circuit_recovery_timeout_sec
+                if self._circuit_state != "open":
+                    self._circuit_state = "open"
+                    self._circuit_probe_in_flight = False
+                    logger.error(
+                        "Circuit breaker tripped (Open). Threshold reached (%d). Will probe after %ds.",
+                        self.circuit_failure_threshold,
+                        self.circuit_recovery_timeout_sec,
+                    )
+
    def _classify_error(self, exc: BaseException) -> tuple[bool, str]:
        detail = _extract_error_detail(exc)
        lowered = detail.lower()
@@ -83,6 +160,8 @@ class LLMErrorHandlingMiddleware(AgentMiddleware[AgentState]):
            "APITimeoutError",
            "APIConnectionError",
            "InternalServerError",
+            "ReadError",  # httpx.ReadError: connection dropped mid-stream
+            "RemoteProtocolError",  # httpx: server closed connection unexpectedly
        }:
            return True, "transient"
        if status_code in _RETRIABLE_STATUS_CODES:
@@ -104,6 +183,9 @@ class LLMErrorHandlingMiddleware(AgentMiddleware[AgentState]):
        reason_text = "provider is busy" if reason == "busy" else "provider request failed temporarily"
        return f"LLM request retry {attempt}/{self.retry_max_attempts}: {reason_text}. Retrying in {seconds}s."

+    def _build_circuit_breaker_message(self) -> str:
+        return "The configured LLM provider is currently unavailable due to continuous failures. Circuit breaker is engaged to protect the system. Please wait a moment before trying again."
+
    def _build_user_message(self, exc: BaseException, reason: str) -> str:
        detail = _extract_error_detail(exc)
        if reason == "quota":
@@ -138,12 +220,20 @@ class LLMErrorHandlingMiddleware(AgentMiddleware[AgentState]):
        request: ModelRequest,
        handler: Callable[[ModelRequest], ModelResponse],
    ) -> ModelCallResult:
+        if self._check_circuit():
+            return AIMessage(content=self._build_circuit_breaker_message())
+
        attempt = 1
        while True:
            try:
-                return handler(request)
+                response = handler(request)
+                self._record_success()
+                return response
            except GraphBubbleUp:
                # Preserve LangGraph control-flow signals (interrupt/pause/resume).
+                with self._circuit_lock:
+                    if self._circuit_state == "half_open":
+                        self._circuit_probe_in_flight = False
                raise
            except Exception as exc:
                retriable, reason = self._classify_error(exc)
@@ -166,6 +256,8 @@ class LLMErrorHandlingMiddleware(AgentMiddleware[AgentState]):
                    _extract_error_detail(exc),
                    exc_info=exc,
                )
+                if retriable:
+                    self._record_failure()
                return AIMessage(content=self._build_user_message(exc, reason))

    @override
@@ -174,12 +266,20 @@ class LLMErrorHandlingMiddleware(AgentMiddleware[AgentState]):
        request: ModelRequest,
        handler: Callable[[ModelRequest], Awaitable[ModelResponse]],
    ) -> ModelCallResult:
+        if self._check_circuit():
+            return AIMessage(content=self._build_circuit_breaker_message())
+
        attempt = 1
        while True:
            try:
-                return await handler(request)
+                response = await handler(request)
+                self._record_success()
+                return response
            except GraphBubbleUp:
                # Preserve LangGraph control-flow signals (interrupt/pause/resume).
+                with self._circuit_lock:
+                    if self._circuit_state == "half_open":
+                        self._circuit_probe_in_flight = False
                raise
            except Exception as exc:
                retriable, reason = self._classify_error(exc)
@@ -202,6 +302,8 @@ class LLMErrorHandlingMiddleware(AgentMiddleware[AgentState]):
                    _extract_error_detail(exc),
                    exc_info=exc,
                )
+                if retriable:
+                    self._record_failure()
                return AIMessage(content=self._build_user_message(exc, reason))


@@ -17,6 +17,7 @@ import json
 import logging
 import threading
 from collections import OrderedDict, defaultdict
+from copy import deepcopy
 from typing import override

 from langchain.agents import AgentState
@@ -24,6 +25,8 @@ from langchain.agents.middleware import AgentMiddleware
 from langchain_core.messages import HumanMessage
 from langgraph.runtime import Runtime

+from deerflow.config.deer_flow_context import DeerFlowContext
+
 logger = logging.getLogger(__name__)

 # Defaults — can be overridden via constructor
@@ -31,6 +34,8 @@ _DEFAULT_WARN_THRESHOLD = 3  # inject warning after 3 identical calls
 _DEFAULT_HARD_LIMIT = 5  # force-stop after 5 identical calls
 _DEFAULT_WINDOW_SIZE = 20  # track last N tool calls
 _DEFAULT_MAX_TRACKED_THREADS = 100  # LRU eviction limit
+_DEFAULT_TOOL_FREQ_WARN = 30  # warn after 30 calls to the same tool type
+_DEFAULT_TOOL_FREQ_HARD_LIMIT = 50  # force-stop after 50 calls to the same tool type


 def _normalize_tool_call_args(raw_args: object) -> tuple[dict, str | None]:
@@ -125,8 +130,14 @@ def _hash_tool_calls(tool_calls: list[dict]) -> str:

 _WARNING_MSG = "[LOOP DETECTED] You are repeating the same tool calls. Stop calling tools and produce your final answer now. If you cannot complete the task, summarize what you accomplished so far."

+_TOOL_FREQ_WARNING_MSG = (
+    "[LOOP DETECTED] You have called {tool_name} {count} times without producing a final answer. Stop calling tools and produce your final answer now. If you cannot complete the task, summarize what you accomplished so far."
+)
+
 _HARD_STOP_MSG = "[FORCED STOP] Repeated tool calls exceeded the safety limit. Producing final answer with results collected so far."

+_TOOL_FREQ_HARD_STOP_MSG = "[FORCED STOP] Tool {tool_name} called {count} times — exceeded the per-tool safety limit. Producing final answer with results collected so far."
+

 class LoopDetectionMiddleware(AgentMiddleware[AgentState]):
    """Detects and breaks repetitive tool call loops.
@@ -140,6 +151,12 @@ class LoopDetectionMiddleware(AgentMiddleware[AgentState]):
            Default: 20.
        max_tracked_threads: Maximum number of threads to track before
            evicting the least recently used. Default: 100.
+        tool_freq_warn: Number of calls to the same tool *type* (regardless
+            of arguments) before injecting a frequency warning. Catches
+            cross-file read loops that hash-based detection misses.
+            Default: 30.
+        tool_freq_hard_limit: Number of calls to the same tool type before
+            forcing a stop. Default: 50.
    """

    def __init__(
@@ -148,23 +165,27 @@ class LoopDetectionMiddleware(AgentMiddleware[AgentState]):
        hard_limit: int = _DEFAULT_HARD_LIMIT,
        window_size: int = _DEFAULT_WINDOW_SIZE,
        max_tracked_threads: int = _DEFAULT_MAX_TRACKED_THREADS,
+        tool_freq_warn: int = _DEFAULT_TOOL_FREQ_WARN,
+        tool_freq_hard_limit: int = _DEFAULT_TOOL_FREQ_HARD_LIMIT,
    ):
        super().__init__()
        self.warn_threshold = warn_threshold
        self.hard_limit = hard_limit
        self.window_size = window_size
        self.max_tracked_threads = max_tracked_threads
+        self.tool_freq_warn = tool_freq_warn
+        self.tool_freq_hard_limit = tool_freq_hard_limit
        self._lock = threading.Lock()
        # Per-thread tracking using OrderedDict for LRU eviction
        self._history: OrderedDict[str, list[str]] = OrderedDict()
        self._warned: dict[str, set[str]] = defaultdict(set)
+        # Per-thread, per-tool-type cumulative call counts
+        self._tool_freq: dict[str, dict[str, int]] = defaultdict(lambda: defaultdict(int))
+        self._tool_freq_warned: dict[str, set[str]] = defaultdict(set)

-    def _get_thread_id(self, runtime: Runtime) -> str:
+    def _get_thread_id(self, runtime: Runtime[DeerFlowContext]) -> str:
        """Extract thread_id from runtime context for per-thread tracking."""
-        thread_id = runtime.context.get("thread_id") if runtime.context else None
-        if thread_id:
-            return thread_id
-        return "default"
+        return runtime.context.thread_id or "default"

    def _evict_if_needed(self) -> None:
        """Evict least recently used threads if over the limit.
@@ -174,11 +195,19 @@ class LoopDetectionMiddleware(AgentMiddleware[AgentState]):
        while len(self._history) > self.max_tracked_threads:
            evicted_id, _ = self._history.popitem(last=False)
            self._warned.pop(evicted_id, None)
+            self._tool_freq.pop(evicted_id, None)
+            self._tool_freq_warned.pop(evicted_id, None)
            logger.debug("Evicted loop tracking for thread %s (LRU)", evicted_id)

    def _track_and_check(self, state: AgentState, runtime: Runtime) -> tuple[str | None, bool]:
        """Track tool calls and check for loops.

+        Two detection layers:
+          1. **Hash-based** (existing): catches identical tool call sets.
+          2. **Frequency-based** (new): catches the same *tool type* being
+             called many times with varying arguments (e.g. ``read_file``
+             on 40 different files).
+
        Returns:
            (warning_message_or_none, should_hard_stop)
        """
@@ -213,6 +242,7 @@ class LoopDetectionMiddleware(AgentMiddleware[AgentState]):
            count = history.count(call_hash)
            tool_names = [tc.get("name", "?") for tc in tool_calls]

+            # --- Layer 1: hash-based (identical call sets) ---
            if count >= self.hard_limit:
                logger.error(
                    "Loop hard limit reached — forcing stop",
@@ -239,8 +269,40 @@ class LoopDetectionMiddleware(AgentMiddleware[AgentState]):
                        },
                    )
                    return _WARNING_MSG, False
-                # Warning already injected for this hash — suppress
-                return None, False
+
+            # --- Layer 2: per-tool-type frequency ---
+            freq = self._tool_freq[thread_id]
+            for tc in tool_calls:
+                name = tc.get("name", "")
+                if not name:
+                    continue
+                freq[name] += 1
+                tc_count = freq[name]
+
+                if tc_count >= self.tool_freq_hard_limit:
+                    logger.error(
+                        "Tool frequency hard limit reached — forcing stop",
+                        extra={
+                            "thread_id": thread_id,
+                            "tool_name": name,
+                            "count": tc_count,
+                        },
+                    )
+                    return _TOOL_FREQ_HARD_STOP_MSG.format(tool_name=name, count=tc_count), True
+
+                if tc_count >= self.tool_freq_warn:
+                    warned = self._tool_freq_warned[thread_id]
+                    if name not in warned:
+                        warned.add(name)
+                        logger.warning(
+                            "Tool frequency warning — too many calls to same tool type",
+                            extra={
+                                "thread_id": thread_id,
+                                "tool_name": name,
+                                "count": tc_count,
+                            },
+                        )
+                        return _TOOL_FREQ_WARNING_MSG.format(tool_name=name, count=tc_count), False

        return None, False

@@ -261,6 +323,26 @@ class LoopDetectionMiddleware(AgentMiddleware[AgentState]):
        # Fallback: coerce unexpected types to str to avoid TypeError
        return str(content) + f"\n\n{text}"

+    @staticmethod
+    def _build_hard_stop_update(last_msg, content: str | list) -> dict:
+        """Clear tool-call metadata so forced-stop messages serialize as plain assistant text."""
+        update = {
+            "tool_calls": [],
+            "content": content,
+        }
+
+        additional_kwargs = dict(getattr(last_msg, "additional_kwargs", {}) or {})
+        for key in ("tool_calls", "function_call"):
+            additional_kwargs.pop(key, None)
+        update["additional_kwargs"] = additional_kwargs
+
+        response_metadata = deepcopy(getattr(last_msg, "response_metadata", {}) or {})
+        if response_metadata.get("finish_reason") == "tool_calls":
+            response_metadata["finish_reason"] = "stop"
+        update["response_metadata"] = response_metadata
+
+        return update
+
    def _apply(self, state: AgentState, runtime: Runtime) -> dict | None:
        warning, hard_stop = self._track_and_check(state, runtime)

@@ -268,12 +350,8 @@ class LoopDetectionMiddleware(AgentMiddleware[AgentState]):
            # Strip tool_calls from the last AIMessage to force text output
            messages = state.get("messages", [])
            last_msg = messages[-1]
-            stripped_msg = last_msg.model_copy(
-                update={
-                    "tool_calls": [],
-                    "content": self._append_text(last_msg.content, _HARD_STOP_MSG),
-                }
-            )
+            content = self._append_text(last_msg.content, warning or _HARD_STOP_MSG)
+            stripped_msg = last_msg.model_copy(update=self._build_hard_stop_update(last_msg, content))
            return {"messages": [stripped_msg]}

        if warning:
@@ -288,11 +366,11 @@ class LoopDetectionMiddleware(AgentMiddleware[AgentState]):
        return None

    @override
-    def after_model(self, state: AgentState, runtime: Runtime) -> dict | None:
+    def after_model(self, state: AgentState, runtime: Runtime[DeerFlowContext]) -> dict | None:
        return self._apply(state, runtime)

    @override
-    async def aafter_model(self, state: AgentState, runtime: Runtime) -> dict | None:
+    async def aafter_model(self, state: AgentState, runtime: Runtime[DeerFlowContext]) -> dict | None:
        return self._apply(state, runtime)

    def reset(self, thread_id: str | None = None) -> None:
@@ -301,6 +379,10 @@ class LoopDetectionMiddleware(AgentMiddleware[AgentState]):
            if thread_id:
                self._history.pop(thread_id, None)
                self._warned.pop(thread_id, None)
+                self._tool_freq.pop(thread_id, None)
+                self._tool_freq_warned.pop(thread_id, None)
            else:
                self._history.clear()
                self._warned.clear()
+                self._tool_freq.clear()
+                self._tool_freq_warned.clear()
@@ -1,50 +1,19 @@
 """Middleware for memory mechanism."""

 import logging
-import re
-from typing import Any, override
+from typing import override

 from langchain.agents import AgentState
 from langchain.agents.middleware import AgentMiddleware
-from langgraph.config import get_config
 from langgraph.runtime import Runtime

+from deerflow.agents.memory.message_processing import detect_correction, detect_reinforcement, filter_messages_for_memory
 from deerflow.agents.memory.queue import get_memory_queue
-from deerflow.config.memory_config import get_memory_config
+from deerflow.config.deer_flow_context import DeerFlowContext
+from deerflow.runtime.user_context import get_effective_user_id

 logger = logging.getLogger(__name__)

-_UPLOAD_BLOCK_RE = re.compile(r"<uploaded_files>[\s\S]*?</uploaded_files>\n*", re.IGNORECASE)
-_CORRECTION_PATTERNS = (
-    re.compile(r"\bthat(?:'s| is) (?:wrong|incorrect)\b", re.IGNORECASE),
-    re.compile(r"\byou misunderstood\b", re.IGNORECASE),
-    re.compile(r"\btry again\b", re.IGNORECASE),
-    re.compile(r"\bredo\b", re.IGNORECASE),
-    re.compile(r"不对"),
-    re.compile(r"你理解错了"),
-    re.compile(r"你理解有误"),
-    re.compile(r"重试"),
-    re.compile(r"重新来"),
-    re.compile(r"换一种"),
-    re.compile(r"改用"),
-)
-
-_REINFORCEMENT_PATTERNS = (
-    re.compile(r"\byes[,.]?\s+(?:exactly|perfect|that(?:'s| is) (?:right|correct|it))\b", re.IGNORECASE),
-    re.compile(r"\bperfect(?:[.!?]|$)", re.IGNORECASE),
-    re.compile(r"\bexactly\s+(?:right|correct)\b", re.IGNORECASE),
-    re.compile(r"\bthat(?:'s| is)\s+(?:exactly\s+)?(?:right|correct|what i (?:wanted|needed|meant))\b", re.IGNORECASE),
-    re.compile(r"\bkeep\s+(?:doing\s+)?that\b", re.IGNORECASE),
-    re.compile(r"\bjust\s+(?:like\s+)?(?:that|this)\b", re.IGNORECASE),
-    re.compile(r"\bthis is (?:great|helpful)\b(?:[.!?]|$)", re.IGNORECASE),
-    re.compile(r"\bthis is what i wanted\b(?:[.!?]|$)", re.IGNORECASE),
-    re.compile(r"对[，,]?\s*就是这样(?:[。！？!?.]|$)"),
-    re.compile(r"完全正确(?:[。！？!?.]|$)"),
-    re.compile(r"(?:对[，,]?\s*)?就是这个意思(?:[。！？!?.]|$)"),
-    re.compile(r"正是我想要的(?:[。！？!?.]|$)"),
-    re.compile(r"继续保持(?:[。！？!?.]|$)"),
-)
-

 class MemoryMiddlewareState(AgentState):
    """Compatible with the `ThreadState` schema."""
@@ -52,125 +21,6 @@ class MemoryMiddlewareState(AgentState):
    pass


-def _extract_message_text(message: Any) -> str:
-    """Extract plain text from message content for filtering and signal detection."""
-    content = getattr(message, "content", "")
-    if isinstance(content, list):
-        text_parts: list[str] = []
-        for part in content:
-            if isinstance(part, str):
-                text_parts.append(part)
-            elif isinstance(part, dict):
-                text_val = part.get("text")
-                if isinstance(text_val, str):
-                    text_parts.append(text_val)
-        return " ".join(text_parts)
-    return str(content)
-
-
-def _filter_messages_for_memory(messages: list[Any]) -> list[Any]:
-    """Filter messages to keep only user inputs and final assistant responses.
-
-    This filters out:
-    - Tool messages (intermediate tool call results)
-    - AI messages with tool_calls (intermediate steps, not final responses)
-    - The <uploaded_files> block injected by UploadsMiddleware into human messages
-      (file paths are session-scoped and must not persist in long-term memory).
-      The user's actual question is preserved; only turns whose content is entirely
-      the upload block (nothing remains after stripping) are dropped along with
-      their paired assistant response.
-
-    Only keeps:
-    - Human messages (with the ephemeral upload block removed)
-    - AI messages without tool_calls (final assistant responses), unless the
-      paired human turn was upload-only and had no real user text.
-
-    Args:
-        messages: List of all conversation messages.
-
-    Returns:
-        Filtered list containing only user inputs and final assistant responses.
-    """
-    filtered = []
-    skip_next_ai = False
-    for msg in messages:
-        msg_type = getattr(msg, "type", None)
-
-        if msg_type == "human":
-            content_str = _extract_message_text(msg)
-            if "<uploaded_files>" in content_str:
-                # Strip the ephemeral upload block; keep the user's real question.
-                stripped = _UPLOAD_BLOCK_RE.sub("", content_str).strip()
-                if not stripped:
-                    # Nothing left — the entire turn was upload bookkeeping;
-                    # skip it and the paired assistant response.
-                    skip_next_ai = True
-                    continue
-                # Rebuild the message with cleaned content so the user's question
-                # is still available for memory summarisation.
-                from copy import copy
-
-                clean_msg = copy(msg)
-                clean_msg.content = stripped
-                filtered.append(clean_msg)
-                skip_next_ai = False
-            else:
-                filtered.append(msg)
-                skip_next_ai = False
-        elif msg_type == "ai":
-            tool_calls = getattr(msg, "tool_calls", None)
-            if not tool_calls:
-                if skip_next_ai:
-                    skip_next_ai = False
-                    continue
-                filtered.append(msg)
-        # Skip tool messages and AI messages with tool_calls
-
-    return filtered
-
-
-def detect_correction(messages: list[Any]) -> bool:
-    """Detect explicit user corrections in recent conversation turns.
-
-    The queue keeps only one pending context per thread, so callers pass the
-    latest filtered message list. Checking only recent user turns keeps signal
-    detection conservative while avoiding stale corrections from long histories.
-    """
-    recent_user_msgs = [msg for msg in messages[-6:] if getattr(msg, "type", None) == "human"]
-
-    for msg in recent_user_msgs:
-        content = _extract_message_text(msg).strip()
-        if not content:
-            continue
-        if any(pattern.search(content) for pattern in _CORRECTION_PATTERNS):
-            return True
-
-    return False
-
-
-def detect_reinforcement(messages: list[Any]) -> bool:
-    """Detect explicit positive reinforcement signals in recent conversation turns.
-
-    Complements detect_correction() by identifying when the user confirms the
-    agent's approach was correct. This allows the memory system to record what
-    worked well, not just what went wrong.
-
-    The queue keeps only one pending context per thread, so callers pass the
-    latest filtered message list. Checking only recent user turns keeps signal
-    detection conservative while avoiding stale signals from long histories.
-    """
-    recent_user_msgs = [msg for msg in messages[-6:] if getattr(msg, "type", None) == "human"]
-
-    for msg in recent_user_msgs:
-        content = _extract_message_text(msg).strip()
-        if not content:
-            continue
-        if any(pattern.search(content) for pattern in _REINFORCEMENT_PATTERNS):
-            return True
-
-    return False
-
-
 class MemoryMiddleware(AgentMiddleware[MemoryMiddlewareState]):
    """Middleware that queues conversation for memory update after agent execution.

@@ -193,7 +43,7 @@ class MemoryMiddleware(AgentMiddleware[MemoryMiddlewareState]):
        self._agent_name = agent_name

    @override
-    def after_agent(self, state: MemoryMiddlewareState, runtime: Runtime) -> dict | None:
+    def after_agent(self, state: MemoryMiddlewareState, runtime: Runtime[DeerFlowContext]) -> dict | None:
        """Queue conversation for memory update after agent completes.

        Args:
@@ -203,15 +53,11 @@ class MemoryMiddleware(AgentMiddleware[MemoryMiddlewareState]):
        Returns:
            None (no state changes needed from this middleware).
        """
-        config = get_memory_config()
-        if not config.enabled:
+        memory_config = runtime.context.app_config.memory
+        if not memory_config.enabled:
            return None

-        # Get thread ID from runtime context first, then fall back to LangGraph's configurable metadata
-        thread_id = runtime.context.get("thread_id") if runtime.context else None
-        if thread_id is None:
-            config_data = get_config()
-            thread_id = config_data.get("configurable", {}).get("thread_id")
+        thread_id = runtime.context.thread_id
        if not thread_id:
            logger.debug("No thread_id in context, skipping memory update")
            return None
@@ -223,7 +69,7 @@ class MemoryMiddleware(AgentMiddleware[MemoryMiddlewareState]):
            return None

        # Filter to only keep user inputs and final assistant responses
-        filtered_messages = _filter_messages_for_memory(messages)
+        filtered_messages = filter_messages_for_memory(messages)

        # Only queue if there's meaningful conversation
        # At minimum need one user message and one assistant response
@@ -236,11 +82,16 @@ class MemoryMiddleware(AgentMiddleware[MemoryMiddlewareState]):
        # Queue the filtered conversation for memory update
        correction_detected = detect_correction(filtered_messages)
        reinforcement_detected = not correction_detected and detect_reinforcement(filtered_messages)
-        queue = get_memory_queue()
+        # Capture user_id at enqueue time while the request context is still alive.
+        # threading.Timer fires on a different thread where ContextVar values are not
+        # propagated, so we must store user_id explicitly in ConversationContext.
+        user_id = get_effective_user_id()
+        queue = get_memory_queue(runtime.context.app_config)
        queue.add(
            thread_id=thread_id,
            messages=filtered_messages,
            agent_name=self._agent_name,
+            user_id=user_id,
            correction_detected=correction_detected,
            reinforcement_detected=reinforcement_detected,
        )
@@ -0,0 +1,347 @@
+"""Summarization middleware extensions for DeerFlow."""
+
+from __future__ import annotations
+
+import logging
+from collections.abc import Collection
+from dataclasses import dataclass
+from typing import Any, Protocol, runtime_checkable
+
+from langchain.agents import AgentState
+from langchain.agents.middleware import SummarizationMiddleware
+from langchain_core.messages import AIMessage, AnyMessage, RemoveMessage, ToolMessage
+from langgraph.config import get_config
+from langgraph.graph.message import REMOVE_ALL_MESSAGES
+from langgraph.runtime import Runtime
+
+logger = logging.getLogger(__name__)
+
+
+@dataclass(frozen=True)
+class SummarizationEvent:
+    """Context emitted before conversation history is summarized away."""
+
+    messages_to_summarize: tuple[AnyMessage, ...]
+    preserved_messages: tuple[AnyMessage, ...]
+    thread_id: str | None
+    agent_name: str | None
+    runtime: Runtime
+
+
+@runtime_checkable
+class BeforeSummarizationHook(Protocol):
+    """Hook invoked before summarization removes messages from state."""
+
+    def __call__(self, event: SummarizationEvent) -> None: ...
+
+
+def _resolve_thread_id(runtime: Runtime) -> str | None:
+    """Resolve the current thread ID from runtime context or LangGraph config."""
+    thread_id = runtime.context.get("thread_id") if runtime.context else None
+    if thread_id is None:
+        try:
+            config_data = get_config()
+        except RuntimeError:
+            return None
+        thread_id = config_data.get("configurable", {}).get("thread_id")
+    return thread_id
+
+
+def _resolve_agent_name(runtime: Runtime) -> str | None:
+    """Resolve the current agent name from runtime context or LangGraph config."""
+    agent_name = runtime.context.get("agent_name") if runtime.context else None
+    if agent_name is None:
+        try:
+            config_data = get_config()
+        except RuntimeError:
+            return None
+        agent_name = config_data.get("configurable", {}).get("agent_name")
+    return agent_name
+
+
+def _tool_call_path(tool_call: dict[str, Any]) -> str | None:
+    """Best-effort extraction of a file path argument from a read_file-like tool call."""
+    args = tool_call.get("args") or {}
+    if not isinstance(args, dict):
+        return None
+    for key in ("path", "file_path", "filepath"):
+        value = args.get(key)
+        if isinstance(value, str) and value:
+            return value
+    return None
+
+
+def _clone_ai_message(
+    message: AIMessage,
+    tool_calls: list[dict[str, Any]],
+    *,
+    content: Any | None = None,
+) -> AIMessage:
+    """Clone an AIMessage while replacing its tool_calls list and optional content."""
+    update: dict[str, Any] = {"tool_calls": tool_calls}
+    if content is not None:
+        update["content"] = content
+    return message.model_copy(update=update)
+
+
+@dataclass
+class _SkillBundle:
+    """Skill-related tool calls and tool results associated with one AIMessage."""
+
+    ai_index: int
+    skill_tool_indices: tuple[int, ...]
+    skill_tool_call_ids: frozenset[str]
+    skill_tool_tokens: int
+    skill_key: str
+
+
+class DeerFlowSummarizationMiddleware(SummarizationMiddleware):
+    """Summarization middleware with pre-compression hook dispatch and skill rescue."""
+
+    def __init__(
+        self,
+        *args,
+        skills_container_path: str | None = None,
+        skill_file_read_tool_names: Collection[str] | None = None,
+        before_summarization: list[BeforeSummarizationHook] | None = None,
+        preserve_recent_skill_count: int = 5,
+        preserve_recent_skill_tokens: int = 25_000,
+        preserve_recent_skill_tokens_per_skill: int = 5_000,
+        **kwargs,
+    ) -> None:
+        super().__init__(*args, **kwargs)
+        self._skills_container_path = skills_container_path or "/mnt/skills"
+        self._skill_file_read_tool_names = frozenset(skill_file_read_tool_names or {"read_file", "read", "view", "cat"})
+        self._before_summarization_hooks = before_summarization or []
+        self._preserve_recent_skill_count = max(0, preserve_recent_skill_count)
+        self._preserve_recent_skill_tokens = max(0, preserve_recent_skill_tokens)
+        self._preserve_recent_skill_tokens_per_skill = max(0, preserve_recent_skill_tokens_per_skill)
+
+    def before_model(self, state: AgentState, runtime: Runtime) -> dict | None:
+        return self._maybe_summarize(state, runtime)
+
+    async def abefore_model(self, state: AgentState, runtime: Runtime) -> dict | None:
+        return await self._amaybe_summarize(state, runtime)
+
+    def _maybe_summarize(self, state: AgentState, runtime: Runtime) -> dict | None:
+        messages = state["messages"]
+        self._ensure_message_ids(messages)
+
+        total_tokens = self.token_counter(messages)
+        if not self._should_summarize(messages, total_tokens):
+            return None
+
+        cutoff_index = self._determine_cutoff_index(messages)
+        if cutoff_index <= 0:
+            return None
+
+        messages_to_summarize, preserved_messages = self._partition_with_skill_rescue(messages, cutoff_index)
+        self._fire_hooks(messages_to_summarize, preserved_messages, runtime)
+        summary = self._create_summary(messages_to_summarize)
+        new_messages = self._build_new_messages(summary)
+
+        return {
+            "messages": [
+                RemoveMessage(id=REMOVE_ALL_MESSAGES),
+                *new_messages,
+                *preserved_messages,
+            ]
+        }
+
+    async def _amaybe_summarize(self, state: AgentState, runtime: Runtime) -> dict | None:
+        messages = state["messages"]
+        self._ensure_message_ids(messages)
+
+        total_tokens = self.token_counter(messages)
+        if not self._should_summarize(messages, total_tokens):
+            return None
+
+        cutoff_index = self._determine_cutoff_index(messages)
+        if cutoff_index <= 0:
+            return None
+
+        messages_to_summarize, preserved_messages = self._partition_with_skill_rescue(messages, cutoff_index)
+        self._fire_hooks(messages_to_summarize, preserved_messages, runtime)
+        summary = await self._acreate_summary(messages_to_summarize)
+        new_messages = self._build_new_messages(summary)
+
+        return {
+            "messages": [
+                RemoveMessage(id=REMOVE_ALL_MESSAGES),
+                *new_messages,
+                *preserved_messages,
+            ]
+        }
+
+    def _partition_with_skill_rescue(
+        self,
+        messages: list[AnyMessage],
+        cutoff_index: int,
+    ) -> tuple[list[AnyMessage], list[AnyMessage]]:
+        """Partition like the parent, then rescue recently-loaded skill bundles."""
+        to_summarize, preserved = self._partition_messages(messages, cutoff_index)
+
+        if self._preserve_recent_skill_count == 0 or self._preserve_recent_skill_tokens == 0 or not to_summarize:
+            return to_summarize, preserved
+
+        try:
+            bundles = self._find_skill_bundles(to_summarize, self._skills_container_path)
+        except Exception:
+            logger.exception("Skill-preserving summarization rescue failed; falling back to default partition")
+            return to_summarize, preserved
+
+        if not bundles:
+            return to_summarize, preserved
+
+        rescue_bundles = self._select_bundles_to_rescue(bundles)
+        if not rescue_bundles:
+            return to_summarize, preserved
+
+        bundles_by_ai_index = {bundle.ai_index: bundle for bundle in rescue_bundles}
+        rescue_tool_indices = {idx for bundle in rescue_bundles for idx in bundle.skill_tool_indices}
+        rescued: list[AnyMessage] = []
+        remaining: list[AnyMessage] = []
+        for i, msg in enumerate(to_summarize):
+            bundle = bundles_by_ai_index.get(i)
+            if bundle is not None and isinstance(msg, AIMessage):
+                rescued_tool_calls = [tc for tc in msg.tool_calls if tc.get("id") in bundle.skill_tool_call_ids]
+                remaining_tool_calls = [tc for tc in msg.tool_calls if tc.get("id") not in bundle.skill_tool_call_ids]
+
+                if rescued_tool_calls:
+                    rescued.append(_clone_ai_message(msg, rescued_tool_calls, content=""))
+                if remaining_tool_calls or msg.content:
+                    remaining.append(_clone_ai_message(msg, remaining_tool_calls))
+                continue
+
+            if i in rescue_tool_indices:
+                rescued.append(msg)
+                continue
+
+            remaining.append(msg)
+
+        return remaining, rescued + preserved
+
+    def _find_skill_bundles(
+        self,
+        messages: list[AnyMessage],
+        skills_root: str,
+    ) -> list[_SkillBundle]:
+        """Locate AIMessage + paired ToolMessage groups that load skill files."""
+        bundles: list[_SkillBundle] = []
+        n = len(messages)
+        i = 0
+        while i < n:
+            msg = messages[i]
+            if not (isinstance(msg, AIMessage) and msg.tool_calls):
+                i += 1
+                continue
+
+            tool_calls = list(msg.tool_calls)
+            skill_paths_by_id: dict[str, str] = {}
+            for tc in tool_calls:
+                if self._is_skill_tool_call(tc, skills_root):
+                    tc_id = tc.get("id")
+                    path = _tool_call_path(tc)
+                    if tc_id and path:
+                        skill_paths_by_id[tc_id] = path
+
+            if not skill_paths_by_id:
+                i += 1
+                continue
+
+            skill_tool_tokens = 0
+            skill_key_parts: list[str] = []
+            skill_tool_indices: list[int] = []
+            matched_skill_call_ids: set[str] = set()
+
+            j = i + 1
+            while j < n and isinstance(messages[j], ToolMessage):
+                j += 1
+
+            for k in range(i + 1, j):
+                tool_msg = messages[k]
+                if isinstance(tool_msg, ToolMessage) and tool_msg.tool_call_id in skill_paths_by_id:
+                    skill_tool_tokens += self.token_counter([tool_msg])
+                    skill_key_parts.append(skill_paths_by_id[tool_msg.tool_call_id])
+                    skill_tool_indices.append(k)
+                    matched_skill_call_ids.add(tool_msg.tool_call_id)
+
+            if not skill_tool_indices:
+                i = j
+                continue
+
+            bundles.append(
+                _SkillBundle(
+                    ai_index=i,
+                    skill_tool_indices=tuple(skill_tool_indices),
+                    skill_tool_call_ids=frozenset(matched_skill_call_ids),
+                    skill_tool_tokens=skill_tool_tokens,
+                    skill_key="|".join(sorted(skill_key_parts)),
+                )
+            )
+            i = j
+
+        return bundles
+
+    def _select_bundles_to_rescue(self, bundles: list[_SkillBundle]) -> list[_SkillBundle]:
+        """Pick bundles to keep, walking newest-first under count/token budgets."""
+        selected: list[_SkillBundle] = []
+        if not bundles:
+            return selected
+
+        seen_skill_keys: set[str] = set()
+        total_tokens = 0
+        kept = 0
+
+        for bundle in reversed(bundles):
+            if kept >= self._preserve_recent_skill_count:
+                break
+            if bundle.skill_key in seen_skill_keys:
+                continue
+            if bundle.skill_tool_tokens > self._preserve_recent_skill_tokens_per_skill:
+                continue
+            if total_tokens + bundle.skill_tool_tokens > self._preserve_recent_skill_tokens:
+                continue
+
+            selected.append(bundle)
+            total_tokens += bundle.skill_tool_tokens
+            kept += 1
+            seen_skill_keys.add(bundle.skill_key)
+
+        selected.reverse()
+        return selected
+
+    def _is_skill_tool_call(self, tool_call: dict[str, Any], skills_root: str) -> bool:
+        """Return True when ``tool_call`` reads a file under the configured skills root."""
+        name = tool_call.get("name") or ""
+        if name not in self._skill_file_read_tool_names:
+            return False
+        path = _tool_call_path(tool_call)
+        if not path:
+            return False
+        normalized_root = skills_root.rstrip("/")
+        return path == normalized_root or path.startswith(normalized_root + "/")
+
+    def _fire_hooks(
+        self,
+        messages_to_summarize: list[AnyMessage],
+        preserved_messages: list[AnyMessage],
+        runtime: Runtime,
+    ) -> None:
+        if not self._before_summarization_hooks:
+            return
+
+        event = SummarizationEvent(
+            messages_to_summarize=tuple(messages_to_summarize),
+            preserved_messages=tuple(preserved_messages),
+            thread_id=_resolve_thread_id(runtime),
+            agent_name=_resolve_agent_name(runtime),
+            runtime=runtime,
+        )
+
+        for hook in self._before_summarization_hooks:
+            try:
+                hook(event)
+            except Exception:
+                hook_name = getattr(hook, "__name__", None) or type(hook).__name__
+                logger.exception("before_summarization hook %s failed", hook_name)
@@ -3,11 +3,12 @@ from typing import NotRequired, override

 from langchain.agents import AgentState
 from langchain.agents.middleware import AgentMiddleware
-from langgraph.config import get_config
 from langgraph.runtime import Runtime

 from deerflow.agents.thread_state import ThreadDataState
+from deerflow.config.deer_flow_context import DeerFlowContext
 from deerflow.config.paths import Paths, get_paths
+from deerflow.runtime.user_context import get_effective_user_id

 logger = logging.getLogger(__name__)

@@ -46,50 +47,50 @@ class ThreadDataMiddleware(AgentMiddleware[ThreadDataMiddlewareState]):
        self._paths = Paths(base_dir) if base_dir else get_paths()
        self._lazy_init = lazy_init

-    def _get_thread_paths(self, thread_id: str) -> dict[str, str]:
+    def _get_thread_paths(self, thread_id: str, user_id: str | None = None) -> dict[str, str]:
        """Get the paths for a thread's data directories.

        Args:
            thread_id: The thread ID.
+            user_id: Optional user ID for per-user path isolation.

        Returns:
            Dictionary with workspace_path, uploads_path, and outputs_path.
        """
        return {
-            "workspace_path": str(self._paths.sandbox_work_dir(thread_id)),
-            "uploads_path": str(self._paths.sandbox_uploads_dir(thread_id)),
-            "outputs_path": str(self._paths.sandbox_outputs_dir(thread_id)),
+            "workspace_path": str(self._paths.sandbox_work_dir(thread_id, user_id=user_id)),
+            "uploads_path": str(self._paths.sandbox_uploads_dir(thread_id, user_id=user_id)),
+            "outputs_path": str(self._paths.sandbox_outputs_dir(thread_id, user_id=user_id)),
        }

-    def _create_thread_directories(self, thread_id: str) -> dict[str, str]:
+    def _create_thread_directories(self, thread_id: str, user_id: str | None = None) -> dict[str, str]:
        """Create the thread data directories.

        Args:
            thread_id: The thread ID.
+            user_id: Optional user ID for per-user path isolation.

        Returns:
            Dictionary with the created directory paths.
        """
-        self._paths.ensure_thread_dirs(thread_id)
-        return self._get_thread_paths(thread_id)
+        self._paths.ensure_thread_dirs(thread_id, user_id=user_id)
+        return self._get_thread_paths(thread_id, user_id=user_id)

    @override
-    def before_agent(self, state: ThreadDataMiddlewareState, runtime: Runtime) -> dict | None:
-        context = runtime.context or {}
-        thread_id = context.get("thread_id")
-        if thread_id is None:
-            config = get_config()
-            thread_id = config.get("configurable", {}).get("thread_id")
+    def before_agent(self, state: ThreadDataMiddlewareState, runtime: Runtime[DeerFlowContext]) -> dict | None:
+        thread_id = runtime.context.thread_id

-        if thread_id is None:
+        if not thread_id:
            raise ValueError("Thread ID is required in runtime context or config.configurable")

+        user_id = get_effective_user_id()
+
        if self._lazy_init:
            # Lazy initialization: only compute paths, don't create directories
-            paths = self._get_thread_paths(thread_id)
+            paths = self._get_thread_paths(thread_id, user_id=user_id)
        else:
            # Eager initialization: create directories immediately
-            paths = self._create_thread_directories(thread_id)
+            paths = self._create_thread_directories(thread_id, user_id=user_id)
            logger.debug("Created thread data directories for thread %s", thread_id)

        return {
@@ -1,13 +1,17 @@
 """Middleware for automatic thread title generation."""

 import logging
-from typing import NotRequired, override
+import re
+from typing import Any, NotRequired, override

 from langchain.agents import AgentState
 from langchain.agents.middleware import AgentMiddleware
+from langgraph.config import get_config
 from langgraph.runtime import Runtime

-from deerflow.config.title_config import get_title_config
+from deerflow.config.app_config import AppConfig
+from deerflow.config.deer_flow_context import DeerFlowContext
+from deerflow.config.title_config import TitleConfig
 from deerflow.models import create_chat_model

 logger = logging.getLogger(__name__)
@@ -43,10 +47,9 @@ class TitleMiddleware(AgentMiddleware[TitleMiddlewareState]):

        return ""

-    def _should_generate_title(self, state: TitleMiddlewareState) -> bool:
+    def _should_generate_title(self, state: TitleMiddlewareState, title_config: TitleConfig) -> bool:
        """Check if we should generate a title for this thread."""
-        config = get_title_config()
-        if not config.enabled:
+        if not title_config.enabled:
            return False

        # Check if thread already has a title in state
@@ -65,74 +68,90 @@ class TitleMiddleware(AgentMiddleware[TitleMiddlewareState]):
        # Generate title after first complete exchange
        return len(user_messages) == 1 and len(assistant_messages) >= 1

-    def _build_title_prompt(self, state: TitleMiddlewareState) -> tuple[str, str]:
+    def _build_title_prompt(self, state: TitleMiddlewareState, title_config: TitleConfig) -> tuple[str, str]:
        """Extract user/assistant messages and build the title prompt.

        Returns (prompt_string, user_msg) so callers can use user_msg as fallback.
        """
-        config = get_title_config()
        messages = state.get("messages", [])

        user_msg_content = next((m.content for m in messages if m.type == "human"), "")
        assistant_msg_content = next((m.content for m in messages if m.type == "ai"), "")

        user_msg = self._normalize_content(user_msg_content)
-        assistant_msg = self._normalize_content(assistant_msg_content)
+        assistant_msg = self._strip_think_tags(self._normalize_content(assistant_msg_content))

-        prompt = config.prompt_template.format(
-            max_words=config.max_words,
+        prompt = title_config.prompt_template.format(
+            max_words=title_config.max_words,
            user_msg=user_msg[:500],
            assistant_msg=assistant_msg[:500],
        )
        return prompt, user_msg

-    def _parse_title(self, content: object) -> str:
-        """Normalize model output into a clean title string."""
-        config = get_title_config()
-        title_content = self._normalize_content(content)
-        title = title_content.strip().strip('"').strip("'")
-        return title[: config.max_chars] if len(title) > config.max_chars else title
+    def _strip_think_tags(self, text: str) -> str:
+        """Remove <think>...</think> blocks emitted by reasoning models (e.g. minimax, DeepSeek-R1)."""
+        return re.sub(r"<think>[\s\S]*?</think>", "", text, flags=re.IGNORECASE).strip()

-    def _fallback_title(self, user_msg: str) -> str:
-        config = get_title_config()
-        fallback_chars = min(config.max_chars, 50)
+    def _parse_title(self, content: object, title_config: TitleConfig) -> str:
+        """Normalize model output into a clean title string."""
+        title_content = self._normalize_content(content)
+        title_content = self._strip_think_tags(title_content)
+        title = title_content.strip().strip('"').strip("'")
+        return title[: title_config.max_chars] if len(title) > title_config.max_chars else title
+
+    def _fallback_title(self, user_msg: str, title_config: TitleConfig) -> str:
+        fallback_chars = min(title_config.max_chars, 50)
        if len(user_msg) > fallback_chars:
            return user_msg[:fallback_chars].rstrip() + "..."
        return user_msg if user_msg else "New Conversation"

-    def _generate_title_result(self, state: TitleMiddlewareState) -> dict | None:
+    def _get_runnable_config(self) -> dict[str, Any]:
+        """Inherit the parent RunnableConfig and add middleware tag.
+
+        This ensures RunJournal identifies LLM calls from this middleware
+        as ``middleware:title`` instead of ``lead_agent``.
+        """
+        try:
+            parent = get_config()
+        except Exception:
+            parent = {}
+        config = {**parent}
+        config["tags"] = [*(config.get("tags") or []), "middleware:title"]
+        return config
+
+    def _generate_title_result(self, state: TitleMiddlewareState, title_config: TitleConfig) -> dict | None:
        """Generate a local fallback title without blocking on an LLM call."""
-        if not self._should_generate_title(state):
+        if not self._should_generate_title(state, title_config):
            return None

-        _, user_msg = self._build_title_prompt(state)
-        return {"title": self._fallback_title(user_msg)}
+        _, user_msg = self._build_title_prompt(state, title_config)
+        return {"title": self._fallback_title(user_msg, title_config)}

-    async def _agenerate_title_result(self, state: TitleMiddlewareState) -> dict | None:
+    async def _agenerate_title_result(self, state: TitleMiddlewareState, app_config: AppConfig) -> dict | None:
        """Generate a title asynchronously and fall back locally on failure."""
-        if not self._should_generate_title(state):
+        title_config = app_config.title
+        if not self._should_generate_title(state, title_config):
            return None

-        config = get_title_config()
-        prompt, user_msg = self._build_title_prompt(state)
+        prompt, user_msg = self._build_title_prompt(state, title_config)

        try:
-            if config.model_name:
-                model = create_chat_model(name=config.model_name, thinking_enabled=False)
+            if title_config.model_name:
+                model = create_chat_model(name=title_config.model_name, thinking_enabled=False, app_config=app_config)
            else:
-                model = create_chat_model(thinking_enabled=False)
-            response = await model.ainvoke(prompt)
-            title = self._parse_title(response.content)
+                model = create_chat_model(thinking_enabled=False, app_config=app_config)
+            response = await model.ainvoke(prompt, config=self._get_runnable_config())
+            title = self._parse_title(response.content, title_config)
            if title:
                return {"title": title}
        except Exception:
            logger.debug("Failed to generate async title; falling back to local title", exc_info=True)
-        return {"title": self._fallback_title(user_msg)}
+        return {"title": self._fallback_title(user_msg, title_config)}

    @override
-    def after_model(self, state: TitleMiddlewareState, runtime: Runtime) -> dict | None:
-        return self._generate_title_result(state)
+    def after_model(self, state: TitleMiddlewareState, runtime: Runtime[DeerFlowContext]) -> dict | None:
+        return self._generate_title_result(state, runtime.context.app_config.title)

    @override
-    async def aafter_model(self, state: TitleMiddlewareState, runtime: Runtime) -> dict | None:
-        return await self._agenerate_title_result(state)
+    async def aafter_model(self, state: TitleMiddlewareState, runtime: Runtime[DeerFlowContext]) -> dict | None:
+        return await self._agenerate_title_result(state, runtime.context.app_config)
@@ -1,9 +1,14 @@
-"""Middleware that extends TodoListMiddleware with context-loss detection.
+"""Middleware that extends TodoListMiddleware with context-loss detection and premature-exit prevention.

 When the message history is truncated (e.g., by SummarizationMiddleware), the
 original `write_todos` tool call and its ToolMessage can be scrolled out of the
 active context window. This middleware detects that situation and injects a
 reminder message so the model still knows about the outstanding todo list.
+
+Additionally, this middleware prevents the agent from exiting the loop while
+there are still incomplete todo items. When the model produces a final response
+(no tool calls) but todos are not yet complete, the middleware injects a reminder
+and jumps back to the model node to force continued engagement.
 """

 from __future__ import annotations
@@ -12,6 +17,7 @@ from typing import Any, override

 from langchain.agents.middleware import TodoListMiddleware
 from langchain.agents.middleware.todo import PlanningState, Todo
+from langchain.agents.middleware.types import hook_config
 from langchain_core.messages import AIMessage, HumanMessage
 from langgraph.runtime import Runtime

@@ -34,6 +40,11 @@ def _reminder_in_messages(messages: list[Any]) -> bool:
    return False


+def _completion_reminder_count(messages: list[Any]) -> int:
+    """Return the number of todo_completion_reminder HumanMessages in *messages*."""
+    return sum(1 for msg in messages if isinstance(msg, HumanMessage) and getattr(msg, "name", None) == "todo_completion_reminder")
+
+
 def _format_todos(todos: list[Todo]) -> str:
    """Format a list of Todo items into a human-readable string."""
    lines: list[str] = []
@@ -57,7 +68,7 @@ class TodoMiddleware(TodoListMiddleware):
    def before_model(
        self,
        state: PlanningState,
-        runtime: Runtime,  # noqa: ARG002
+        runtime: Runtime,
    ) -> dict[str, Any] | None:
        """Inject a todo-list reminder when write_todos has left the context window."""
        todos: list[Todo] = state.get("todos") or []  # type: ignore[assignment]
@@ -98,3 +109,71 @@ class TodoMiddleware(TodoListMiddleware):
    ) -> dict[str, Any] | None:
        """Async version of before_model."""
        return self.before_model(state, runtime)
+
+    # Maximum number of completion reminders before allowing the agent to exit.
+    # This prevents infinite loops when the agent cannot make further progress.
+    _MAX_COMPLETION_REMINDERS = 2
+
+    @hook_config(can_jump_to=["model"])
+    @override
+    def after_model(
+        self,
+        state: PlanningState,
+        runtime: Runtime,
+    ) -> dict[str, Any] | None:
+        """Prevent premature agent exit when todo items are still incomplete.
+
+        In addition to the base class check for parallel ``write_todos`` calls,
+        this override intercepts model responses that have no tool calls while
+        there are still incomplete todo items. It injects a reminder
+        ``HumanMessage`` and jumps back to the model node so the agent
+        continues working through the todo list.
+
+        A retry cap of ``_MAX_COMPLETION_REMINDERS`` (default 2) prevents
+        infinite loops when the agent cannot make further progress.
+        """
+        # 1. Preserve base class logic (parallel write_todos detection).
+        base_result = super().after_model(state, runtime)
+        if base_result is not None:
+            return base_result
+
+        # 2. Only intervene when the agent wants to exit (no tool calls).
+        messages = state.get("messages") or []
+        last_ai = next((m for m in reversed(messages) if isinstance(m, AIMessage)), None)
+        if not last_ai or last_ai.tool_calls:
+            return None
+
+        # 3. Allow exit when all todos are completed or there are no todos.
+        todos: list[Todo] = state.get("todos") or []  # type: ignore[assignment]
+        if not todos or all(t.get("status") == "completed" for t in todos):
+            return None
+
+        # 4. Enforce a reminder cap to prevent infinite re-engagement loops.
+        if _completion_reminder_count(messages) >= self._MAX_COMPLETION_REMINDERS:
+            return None
+
+        # 5. Inject a reminder and force the agent back to the model.
+        incomplete = [t for t in todos if t.get("status") != "completed"]
+        incomplete_text = "\n".join(f"- [{t.get('status', 'pending')}] {t.get('content', '')}" for t in incomplete)
+        reminder = HumanMessage(
+            name="todo_completion_reminder",
+            content=(
+                "<system_reminder>\n"
+                "You have incomplete todo items that must be finished before giving your final response:\n\n"
+                f"{incomplete_text}\n\n"
+                "Please continue working on these tasks. Call `write_todos` to mark items as completed "
+                "as you finish them, and only respond when all items are done.\n"
+                "</system_reminder>"
+            ),
+        )
+        return {"jump_to": "model", "messages": [reminder]}
+
+    @override
+    @hook_config(can_jump_to=["model"])
+    async def aafter_model(
+        self,
+        state: PlanningState,
+        runtime: Runtime,
+    ) -> dict[str, Any] | None:
+        """Async version of after_model."""
+        return self.after_model(state, runtime)
@@ -1,8 +1,10 @@
 """Tool error handling middleware and shared runtime middleware builders."""

+from __future__ import annotations
+
 import logging
 from collections.abc import Awaitable, Callable
-from typing import override
+from typing import TYPE_CHECKING, override

 from langchain.agents import AgentState
 from langchain.agents.middleware import AgentMiddleware
@@ -11,6 +13,9 @@ from langgraph.errors import GraphBubbleUp
 from langgraph.prebuilt.tool_node import ToolCallRequest
 from langgraph.types import Command

+if TYPE_CHECKING:
+    from deerflow.config.app_config import AppConfig
+
 logger = logging.getLogger(__name__)

 _MISSING_TOOL_CALL_ID = "missing_tool_call_id"
@@ -67,6 +72,7 @@ class ToolErrorHandlingMiddleware(AgentMiddleware[AgentState]):

 def _build_runtime_middlewares(
    *,
+    app_config: "AppConfig",
    include_uploads: bool,
    include_dangling_tool_call_patch: bool,
    lazy_init: bool = True,
@@ -94,9 +100,7 @@ def _build_runtime_middlewares(
    middlewares.append(LLMErrorHandlingMiddleware())

    # Guardrail middleware (if configured)
-    from deerflow.config.guardrails_config import get_guardrails_config
-
-    guardrails_config = get_guardrails_config()
+    guardrails_config = app_config.guardrails
    if guardrails_config.enabled and guardrails_config.provider:
        import inspect

@@ -125,9 +129,10 @@ def _build_runtime_middlewares(
    return middlewares


-def build_lead_runtime_middlewares(*, lazy_init: bool = True) -> list[AgentMiddleware]:
+def build_lead_runtime_middlewares(*, app_config: "AppConfig", lazy_init: bool = True) -> list[AgentMiddleware]:
    """Middlewares shared by lead agent runtime before lead-only middlewares."""
    return _build_runtime_middlewares(
+        app_config=app_config,
        include_uploads=True,
        include_dangling_tool_call_patch=True,
        lazy_init=lazy_init,
@@ -9,7 +9,9 @@ from langchain.agents.middleware import AgentMiddleware
 from langchain_core.messages import HumanMessage
 from langgraph.runtime import Runtime

+from deerflow.config.deer_flow_context import DeerFlowContext
 from deerflow.config.paths import Paths, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.utils.file_conversion import extract_outline

 logger = logging.getLogger(__name__)
@@ -184,7 +186,7 @@ class UploadsMiddleware(AgentMiddleware[UploadsMiddlewareState]):
        return files if files else None

    @override
-    def before_agent(self, state: UploadsMiddlewareState, runtime: Runtime) -> dict | None:
+    def before_agent(self, state: UploadsMiddlewareState, runtime: Runtime[DeerFlowContext]) -> dict | None:
        """Inject uploaded files information before agent execution.

        New files come from the current message's additional_kwargs.files.
@@ -213,15 +215,8 @@ class UploadsMiddleware(AgentMiddleware[UploadsMiddlewareState]):
            return None

        # Resolve uploads directory for existence checks
-        thread_id = (runtime.context or {}).get("thread_id")
-        if thread_id is None:
-            try:
-                from langgraph.config import get_config
-
-                thread_id = get_config().get("configurable", {}).get("thread_id")
-            except RuntimeError:
-                pass  # get_config() raises outside a runnable context (e.g. unit tests)
-        uploads_dir = self._paths.sandbox_uploads_dir(thread_id) if thread_id else None
+        thread_id = runtime.context.thread_id
+        uploads_dir = self._paths.sandbox_uploads_dir(thread_id, user_id=get_effective_user_id()) if thread_id else None

        # Get newly uploaded files from the current message's additional_kwargs.files
        new_files = self._files_from_kwargs(last_message, uploads_dir) or []
@@ -262,21 +257,25 @@ class UploadsMiddleware(AgentMiddleware[UploadsMiddlewareState]):
        files_message = self._create_files_message(new_files, historical_files)

        # Extract original content - handle both string and list formats
-        original_content = ""
-        if isinstance(last_message.content, str):
-            original_content = last_message.content
-        elif isinstance(last_message.content, list):
-            text_parts = []
-            for block in last_message.content:
-                if isinstance(block, dict) and block.get("type") == "text":
-                    text_parts.append(block.get("text", ""))
-            original_content = "\n".join(text_parts)
+        original_content = last_message.content
+        if isinstance(original_content, str):
+            # Simple case: string content, just prepend files message
+            updated_content = f"{files_message}\n\n{original_content}"
+        elif isinstance(original_content, list):
+            # Complex case: list content (multimodal), preserve all blocks
+            # Prepend files message as the first text block
+            files_block = {"type": "text", "text": f"{files_message}\n\n"}
+            # Keep all original blocks (including images)
+            updated_content = [files_block, *original_content]
+        else:
+            # Other types, preserve as-is
+            updated_content = original_content

        # Create new message with combined content.
        # Preserve additional_kwargs (including files metadata) so the frontend
        # can read structured file info from the streamed message.
        updated_message = HumanMessage(
-            content=f"{files_message}\n\n{original_content}",
+            content=updated_content,
            id=last_message.id,
            additional_kwargs=last_message.additional_kwargs,
        )
@@ -36,10 +36,12 @@ from deerflow.agents.lead_agent.agent import _build_middlewares
 from deerflow.agents.lead_agent.prompt import apply_prompt_template
 from deerflow.agents.thread_state import ThreadState
 from deerflow.config.agents_config import AGENT_NAME_PATTERN
-from deerflow.config.app_config import get_app_config, reload_app_config
-from deerflow.config.extensions_config import ExtensionsConfig, SkillStateConfig, get_extensions_config, reload_extensions_config
+from deerflow.config.app_config import AppConfig
+from deerflow.config.deer_flow_context import DeerFlowContext
+from deerflow.config.extensions_config import ExtensionsConfig
 from deerflow.config.paths import get_paths
 from deerflow.models import create_chat_model
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.skills.installer import install_skill_from_archive
 from deerflow.uploads.manager import (
    claim_unique_filename,
@@ -115,6 +117,7 @@ class DeerFlowClient:
        config_path: str | None = None,
        checkpointer=None,
        *,
+        config: AppConfig | None = None,
        model_name: str | None = None,
        thinking_enabled: bool = True,
        subagent_enabled: bool = False,
@@ -129,9 +132,14 @@ class DeerFlowClient:

        Args:
            config_path: Path to config.yaml. Uses default resolution if None.
+                Ignored when ``config`` is provided.
            checkpointer: LangGraph checkpointer instance for state persistence.
                Required for multi-turn conversations on the same thread_id.
                Without a checkpointer, each call is stateless.
+            config: Optional pre-constructed AppConfig. When provided, it takes
+                precedence over ``config_path`` and no file is read. Enables
+                multi-client isolation: two clients with different configs can
+                coexist in the same process without touching process-global state.
            model_name: Override the default model name from config.
            thinking_enabled: Enable model's extended thinking.
            subagent_enabled: Enable subagent delegation.
@@ -140,9 +148,18 @@ class DeerFlowClient:
            available_skills: Optional set of skill names to make available. If None (default), all scanned skills are available.
            middlewares: Optional list of custom middlewares to inject into the agent.
        """
-        if config_path is not None:
-            reload_app_config(config_path)
-        self._app_config = get_app_config()
+        # Constructor-captured config: the client owns its AppConfig for its lifetime.
+        # Multiple clients with different configs do not contend.
+        #
+        # Priority: explicit ``config=`` > explicit ``config_path=`` > ``AppConfig.from_file()``
+        # with default path resolution. There is no ambient global fallback; if
+        # config.yaml cannot be located, ``from_file`` raises loudly.
+        if config is not None:
+            self._app_config = config
+        elif config_path is not None:
+            self._app_config = AppConfig.from_file(config_path)
+        else:
+            self._app_config = AppConfig.from_file()

        if agent_name is not None and not AGENT_NAME_PATTERN.match(agent_name):
            raise ValueError(f"Invalid agent name '{agent_name}'. Must match pattern: {AGENT_NAME_PATTERN.pattern}")
@@ -170,6 +187,15 @@ class DeerFlowClient:
        self._agent = None
        self._agent_config_key = None

+    def _reload_config(self) -> None:
+        """Reload config from file and refresh the cached reference.
+
+        Only the client's own ``_app_config`` is rebuilt. Other clients
+        and the process-global are untouched, so multi-client coexistence
+        survives reload.
+        """
+        self._app_config = AppConfig.from_file()
+
    # ------------------------------------------------------------------
    # Internal helpers
    # ------------------------------------------------------------------
@@ -227,10 +253,11 @@ class DeerFlowClient:
        max_concurrent_subagents = cfg.get("max_concurrent_subagents", 3)

        kwargs: dict[str, Any] = {
-            "model": create_chat_model(name=model_name, thinking_enabled=thinking_enabled),
+            "model": create_chat_model(name=model_name, thinking_enabled=thinking_enabled, app_config=self._app_config),
            "tools": self._get_tools(model_name=model_name, subagent_enabled=subagent_enabled),
-            "middleware": _build_middlewares(config, model_name=model_name, agent_name=self._agent_name, custom_middlewares=self._middlewares),
+            "middleware": _build_middlewares(self._app_config, config, model_name=model_name, agent_name=self._agent_name, custom_middlewares=self._middlewares),
            "system_prompt": apply_prompt_template(
+                self._app_config,
                subagent_enabled=subagent_enabled,
                max_concurrent_subagents=max_concurrent_subagents,
                agent_name=self._agent_name,
@@ -240,9 +267,9 @@ class DeerFlowClient:
        }
        checkpointer = self._checkpointer
        if checkpointer is None:
-            from deerflow.agents.checkpointer import get_checkpointer
+            from deerflow.runtime.checkpointer import get_checkpointer

-            checkpointer = get_checkpointer()
+            checkpointer = get_checkpointer(self._app_config)
        if checkpointer is not None:
            kwargs["checkpointer"] = checkpointer

@@ -250,12 +277,11 @@ class DeerFlowClient:
        self._agent_config_key = key
        logger.info("Agent created: agent_name=%s, model=%s, thinking=%s", self._agent_name, model_name, thinking_enabled)

-    @staticmethod
-    def _get_tools(*, model_name: str | None, subagent_enabled: bool):
+    def _get_tools(self, *, model_name: str | None, subagent_enabled: bool):
        """Lazy import to avoid circular dependency at module level."""
        from deerflow.tools import get_available_tools

-        return get_available_tools(model_name=model_name, subagent_enabled=subagent_enabled)
+        return get_available_tools(model_name=model_name, subagent_enabled=subagent_enabled, app_config=self._app_config)

    @staticmethod
    def _serialize_tool_calls(tool_calls) -> list[dict]:
@@ -374,9 +400,9 @@ class DeerFlowClient:
        """
        checkpointer = self._checkpointer
        if checkpointer is None:
-            from deerflow.agents.checkpointer.provider import get_checkpointer
+            from deerflow.runtime.checkpointer.provider import get_checkpointer

-            checkpointer = get_checkpointer()
+            checkpointer = get_checkpointer(self._app_config)

        thread_info_map = {}

@@ -429,9 +455,9 @@ class DeerFlowClient:
        """
        checkpointer = self._checkpointer
        if checkpointer is None:
-            from deerflow.agents.checkpointer.provider import get_checkpointer
+            from deerflow.runtime.checkpointer.provider import get_checkpointer

-            checkpointer = get_checkpointer()
+            checkpointer = get_checkpointer(self._app_config)

        config = {"configurable": {"thread_id": thread_id}}
        checkpoints = []
@@ -551,9 +577,7 @@ class DeerFlowClient:
        self._ensure_agent(config)

        state: dict[str, Any] = {"messages": [HumanMessage(content=message)]}
-        context = {"thread_id": thread_id}
-        if self._agent_name:
-            context["agent_name"] = self._agent_name
+        context = DeerFlowContext(app_config=self._app_config, thread_id=thread_id, agent_name=self._agent_name)

        seen_ids: set[str] = set()
        # Cross-mode handoff: ids already streamed via LangGraph ``messages``
@@ -722,6 +746,10 @@ class DeerFlowClient:
            Dict with "models" key containing list of model info dicts,
            matching the Gateway API ``ModelsListResponse`` schema.
        """
+        token_usage_enabled = getattr(getattr(self._app_config, "token_usage", None), "enabled", False)
+        if not isinstance(token_usage_enabled, bool):
+            token_usage_enabled = False
+
        return {
            "models": [
                {
@@ -733,7 +761,8 @@ class DeerFlowClient:
                    "supports_reasoning_effort": getattr(model, "supports_reasoning_effort", False),
                }
                for model in self._app_config.models
-            ]
+            ],
+            "token_usage": {"enabled": token_usage_enabled},
        }

    def list_skills(self, enabled_only: bool = False) -> dict:
@@ -757,7 +786,7 @@ class DeerFlowClient:
                    "category": s.category,
                    "enabled": s.enabled,
                }
-                for s in load_skills(enabled_only=enabled_only)
+                for s in load_skills(self._app_config, enabled_only=enabled_only)
            ]
        }

@@ -769,19 +798,19 @@ class DeerFlowClient:
        """
        from deerflow.agents.memory.updater import get_memory_data

-        return get_memory_data()
+        return get_memory_data(self._app_config.memory, user_id=get_effective_user_id())

    def export_memory(self) -> dict:
        """Export current memory data for backup or transfer."""
        from deerflow.agents.memory.updater import get_memory_data

-        return get_memory_data()
+        return get_memory_data(self._app_config.memory, user_id=get_effective_user_id())

    def import_memory(self, memory_data: dict) -> dict:
        """Import and persist full memory data."""
        from deerflow.agents.memory.updater import import_memory_data

-        return import_memory_data(memory_data)
+        return import_memory_data(self._app_config.memory, memory_data, user_id=get_effective_user_id())

    def get_model(self, name: str) -> dict | None:
        """Get a specific model's configuration by name.
@@ -816,8 +845,8 @@ class DeerFlowClient:
            Dict with "mcp_servers" key mapping server name to config,
            matching the Gateway API ``McpConfigResponse`` schema.
        """
-        config = get_extensions_config()
-        return {"mcp_servers": {name: server.model_dump() for name, server in config.mcp_servers.items()}}
+        ext = self._app_config.extensions
+        return {"mcp_servers": {name: server.model_dump() for name, server in ext.mcp_servers.items()}}

    def update_mcp_config(self, mcp_servers: dict[str, dict]) -> dict:
        """Update MCP server configurations.
@@ -839,18 +868,19 @@ class DeerFlowClient:
        if config_path is None:
            raise FileNotFoundError("Cannot locate extensions_config.json. Set DEER_FLOW_EXTENSIONS_CONFIG_PATH or ensure it exists in the project root.")

-        current_config = get_extensions_config()
+        current_ext = self._app_config.extensions

        config_data = {
            "mcpServers": mcp_servers,
-            "skills": {name: {"enabled": skill.enabled} for name, skill in current_config.skills.items()},
+            "skills": {name: {"enabled": skill.enabled} for name, skill in current_ext.skills.items()},
        }

        self._atomic_write_json(config_path, config_data)

        self._agent = None
        self._agent_config_key = None
-        reloaded = reload_extensions_config()
+        self._reload_config()
+        reloaded = self._app_config.extensions
        return {"mcp_servers": {name: server.model_dump() for name, server in reloaded.mcp_servers.items()}}

    # ------------------------------------------------------------------
@@ -868,7 +898,7 @@ class DeerFlowClient:
        """
        from deerflow.skills.loader import load_skills

-        skill = next((s for s in load_skills(enabled_only=False) if s.name == name), None)
+        skill = next((s for s in load_skills(self._app_config, enabled_only=False) if s.name == name), None)
        if skill is None:
            return None
        return {
@@ -895,7 +925,7 @@ class DeerFlowClient:
        """
        from deerflow.skills.loader import load_skills

-        skills = load_skills(enabled_only=False)
+        skills = load_skills(self._app_config, enabled_only=False)
        skill = next((s for s in skills if s.name == name), None)
        if skill is None:
            raise ValueError(f"Skill '{name}' not found")
@@ -904,21 +934,25 @@ class DeerFlowClient:
        if config_path is None:
            raise FileNotFoundError("Cannot locate extensions_config.json. Set DEER_FLOW_EXTENSIONS_CONFIG_PATH or ensure it exists in the project root.")

-        extensions_config = get_extensions_config()
-        extensions_config.skills[name] = SkillStateConfig(enabled=enabled)
+        # Do not mutate self._app_config (frozen value). Compose the new
+        # skills state in a fresh dict, write it to disk, and let _reload_config()
+        # below rebuild AppConfig from the updated file.
+        ext = self._app_config.extensions
+        new_skills = {n: {"enabled": sc.enabled} for n, sc in ext.skills.items()}
+        new_skills[name] = {"enabled": enabled}

        config_data = {
-            "mcpServers": {n: s.model_dump() for n, s in extensions_config.mcp_servers.items()},
-            "skills": {n: {"enabled": sc.enabled} for n, sc in extensions_config.skills.items()},
+            "mcpServers": {n: s.model_dump() for n, s in ext.mcp_servers.items()},
+            "skills": new_skills,
        }

        self._atomic_write_json(config_path, config_data)

        self._agent = None
        self._agent_config_key = None
-        reload_extensions_config()
+        self._reload_config()

-        updated = next((s for s in load_skills(enabled_only=False) if s.name == name), None)
+        updated = next((s for s in load_skills(self._app_config, enabled_only=False) if s.name == name), None)
        if updated is None:
            raise RuntimeError(f"Skill '{name}' disappeared after update")
        return {
@@ -956,25 +990,25 @@ class DeerFlowClient:
        """
        from deerflow.agents.memory.updater import reload_memory_data

-        return reload_memory_data()
+        return reload_memory_data(self._app_config.memory, user_id=get_effective_user_id())

    def clear_memory(self) -> dict:
        """Clear all persisted memory data."""
        from deerflow.agents.memory.updater import clear_memory_data

-        return clear_memory_data()
+        return clear_memory_data(self._app_config.memory, user_id=get_effective_user_id())

    def create_memory_fact(self, content: str, category: str = "context", confidence: float = 0.5) -> dict:
        """Create a single fact manually."""
        from deerflow.agents.memory.updater import create_memory_fact

-        return create_memory_fact(content=content, category=category, confidence=confidence)
+        return create_memory_fact(self._app_config.memory, content=content, category=category, confidence=confidence)

    def delete_memory_fact(self, fact_id: str) -> dict:
        """Delete a single fact from memory by fact id."""
        from deerflow.agents.memory.updater import delete_memory_fact

-        return delete_memory_fact(fact_id)
+        return delete_memory_fact(self._app_config.memory, fact_id)

    def update_memory_fact(
        self,
@@ -987,6 +1021,7 @@ class DeerFlowClient:
        from deerflow.agents.memory.updater import update_memory_fact

        return update_memory_fact(
+            self._app_config.memory,
            fact_id=fact_id,
            content=content,
            category=category,
@@ -999,9 +1034,7 @@ class DeerFlowClient:
        Returns:
            Memory config dict.
        """
-        from deerflow.config.memory_config import get_memory_config
-
-        config = get_memory_config()
+        config = self._app_config.memory
        return {
            "enabled": config.enabled,
            "storage_path": config.storage_path,
@@ -1179,7 +1212,7 @@ class DeerFlowClient:
            ValueError: If the path is invalid.
        """
        try:
-            actual = get_paths().resolve_virtual_path(thread_id, path)
+            actual = get_paths().resolve_virtual_path(thread_id, path, user_id=get_effective_user_id())
        except ValueError as exc:
            if "traversal" in str(exc):
                from deerflow.uploads.manager import PathTraversalError
@@ -25,8 +25,9 @@ except ImportError:  # pragma: no cover - Windows fallback
    fcntl = None  # type: ignore[assignment]
    import msvcrt

-from deerflow.config import get_app_config
+from deerflow.config.app_config import AppConfig
 from deerflow.config.paths import VIRTUAL_PATH_PREFIX, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.sandbox.sandbox import Sandbox
 from deerflow.sandbox.sandbox_provider import SandboxProvider

@@ -89,7 +90,8 @@ class AioSandboxProvider(SandboxProvider):
          API_KEY: $MY_API_KEY
    """

-    def __init__(self):
+    def __init__(self, app_config: "AppConfig"):
+        self._app_config = app_config
        self._lock = threading.Lock()
        self._sandboxes: dict[str, AioSandbox] = {}  # sandbox_id -> AioSandbox instance
        self._sandbox_infos: dict[str, SandboxInfo] = {}  # sandbox_id -> SandboxInfo (for destroy)
@@ -119,6 +121,16 @@ class AioSandboxProvider(SandboxProvider):
        if self._config.get("idle_timeout", DEFAULT_IDLE_TIMEOUT) > 0:
            self._start_idle_checker()

+    @property
+    def uses_thread_data_mounts(self) -> bool:
+        """Whether thread workspace/uploads/outputs are visible via mounts.
+
+        Local container backends bind-mount the thread data directories, so files
+        written by the gateway are already visible when the sandbox starts.
+        Remote backends may require explicit file sync.
+        """
+        return isinstance(self._backend, LocalContainerBackend)
+
    # ── Factory methods ──────────────────────────────────────────────────

    def _create_backend(self) -> SandboxBackend:
@@ -148,8 +160,7 @@ class AioSandboxProvider(SandboxProvider):

    def _load_config(self) -> dict:
        """Load sandbox configuration from app config."""
-        config = get_app_config()
-        sandbox_config = config.sandbox
+        sandbox_config = self._app_config.sandbox

        idle_timeout = getattr(sandbox_config, "idle_timeout", None)
        replicas = getattr(sandbox_config, "replicas", None)
@@ -260,28 +271,27 @@ class AioSandboxProvider(SandboxProvider):
        mounted Docker socket (DooD), the host Docker daemon can resolve the paths.
        """
        paths = get_paths()
-        paths.ensure_thread_dirs(thread_id)
+        user_id = get_effective_user_id()
+        paths.ensure_thread_dirs(thread_id, user_id=user_id)

        return [
-            (paths.host_sandbox_work_dir(thread_id), f"{VIRTUAL_PATH_PREFIX}/workspace", False),
-            (paths.host_sandbox_uploads_dir(thread_id), f"{VIRTUAL_PATH_PREFIX}/uploads", False),
-            (paths.host_sandbox_outputs_dir(thread_id), f"{VIRTUAL_PATH_PREFIX}/outputs", False),
+            (paths.host_sandbox_work_dir(thread_id, user_id=user_id), f"{VIRTUAL_PATH_PREFIX}/workspace", False),
+            (paths.host_sandbox_uploads_dir(thread_id, user_id=user_id), f"{VIRTUAL_PATH_PREFIX}/uploads", False),
+            (paths.host_sandbox_outputs_dir(thread_id, user_id=user_id), f"{VIRTUAL_PATH_PREFIX}/outputs", False),
            # ACP workspace: read-only inside the sandbox (lead agent reads results;
            # the ACP subprocess writes from the host side, not from within the container).
-            (paths.host_acp_workspace_dir(thread_id), "/mnt/acp-workspace", True),
+            (paths.host_acp_workspace_dir(thread_id, user_id=user_id), "/mnt/acp-workspace", True),
        ]

-    @staticmethod
-    def _get_skills_mount() -> tuple[str, str, bool] | None:
+    def _get_skills_mount(self) -> tuple[str, str, bool] | None:
        """Get the skills directory mount configuration.

        Mount source uses DEER_FLOW_HOST_SKILLS_PATH when running inside Docker (DooD)
        so the host Docker daemon can resolve the path.
        """
        try:
-            config = get_app_config()
-            skills_path = config.skills.get_skills_path()
-            container_path = config.skills.container_path
+            skills_path = self._app_config.skills.get_skills_path()
+            container_path = self._app_config.skills.container_path

            if skills_path.exists():
                # When running inside Docker with DooD, use host-side skills path.
@@ -480,8 +490,9 @@ class AioSandboxProvider(SandboxProvider):
        across multiple processes, preventing container-name conflicts.
        """
        paths = get_paths()
-        paths.ensure_thread_dirs(thread_id)
-        lock_path = paths.thread_dir(thread_id) / f"{sandbox_id}.lock"
+        user_id = get_effective_user_id()
+        paths.ensure_thread_dirs(thread_id, user_id=user_id)
+        lock_path = paths.thread_dir(thread_id, user_id=user_id) / f"{sandbox_id}.lock"

        with open(lock_path, "a", encoding="utf-8") as lock_file:
            locked = False
@@ -5,9 +5,9 @@ Web Search Tool - Search the web using DuckDuckGo (no API key required).
 import json
 import logging

-from langchain.tools import tool
+from langchain.tools import ToolRuntime, tool

-from deerflow.config import get_app_config
+from deerflow.config.deer_flow_context import resolve_context

 logger = logging.getLogger(__name__)

@@ -55,6 +55,7 @@ def _search_text(
@tool("web_search", parse_docstring=True)
 def web_search_tool(
    query: str,
+    runtime: ToolRuntime,
    max_results: int = 5,
 ) -> str:
    """Search the web for information. Use this tool to find current information, news, articles, and facts from the internet.
@@ -63,11 +64,11 @@ def web_search_tool(
        query: Search keywords describing what you want to find. Be specific for better results.
        max_results: Maximum number of results to return. Default is 5.
    """
-    config = get_app_config().get_tool_config("web_search")
+    tool_config = resolve_context(runtime).app_config.get_tool_config("web_search")

    # Override max_results from config if set
-    if config is not None and "max_results" in config.model_extra:
-        max_results = config.model_extra.get("max_results", max_results)
+    if tool_config is not None and "max_results" in tool_config.model_extra:
+        max_results = tool_config.model_extra.get("max_results", max_results)

    results = _search_text(
        query=query,
@@ -1,37 +1,39 @@
 import json

 from exa_py import Exa
-from langchain.tools import tool
+from langchain.tools import ToolRuntime, tool

-from deerflow.config import get_app_config
+from deerflow.config.app_config import AppConfig
+from deerflow.config.deer_flow_context import resolve_context


-def _get_exa_client(tool_name: str = "web_search") -> Exa:
-    config = get_app_config().get_tool_config(tool_name)
+def _get_exa_client(app_config: AppConfig, tool_name: str = "web_search") -> Exa:
+    tool_config = app_config.get_tool_config(tool_name)
    api_key = None
-    if config is not None and "api_key" in config.model_extra:
-        api_key = config.model_extra.get("api_key")
+    if tool_config is not None and "api_key" in tool_config.model_extra:
+        api_key = tool_config.model_extra.get("api_key")
    return Exa(api_key=api_key)


@tool("web_search", parse_docstring=True)
-def web_search_tool(query: str) -> str:
+def web_search_tool(query: str, runtime: ToolRuntime) -> str:
    """Search the web.

    Args:
        query: The query to search for.
    """
    try:
-        config = get_app_config().get_tool_config("web_search")
+        app_config = resolve_context(runtime).app_config
+        tool_config = app_config.get_tool_config("web_search")
        max_results = 5
        search_type = "auto"
        contents_max_characters = 1000
-        if config is not None:
-            max_results = config.model_extra.get("max_results", max_results)
-            search_type = config.model_extra.get("search_type", search_type)
-            contents_max_characters = config.model_extra.get("contents_max_characters", contents_max_characters)
+        if tool_config is not None:
+            max_results = tool_config.model_extra.get("max_results", max_results)
+            search_type = tool_config.model_extra.get("search_type", search_type)
+            contents_max_characters = tool_config.model_extra.get("contents_max_characters", contents_max_characters)

-        client = _get_exa_client()
+        client = _get_exa_client(app_config)
        res = client.search(
            query,
            type=search_type,
@@ -54,7 +56,7 @@ def web_search_tool(query: str) -> str:


@tool("web_fetch", parse_docstring=True)
-def web_fetch_tool(url: str) -> str:
+def web_fetch_tool(url: str, runtime: ToolRuntime) -> str:
    """Fetch the contents of a web page at a given URL.
    Only fetch EXACT URLs that have been provided directly by the user or have been returned in results from the web_search and web_fetch tools.
    This tool can NOT access content that requires authentication, such as private Google Docs or pages behind login walls.
@@ -65,7 +67,7 @@ def web_fetch_tool(url: str) -> str:
        url: The URL to fetch the contents of.
    """
    try:
-        client = _get_exa_client("web_fetch")
+        client = _get_exa_client(resolve_context(runtime).app_config, "web_fetch")
        res = client.get_contents([url], text={"max_characters": 4096})

        if res.results:
@@ -1,33 +1,35 @@
 import json

 from firecrawl import FirecrawlApp
-from langchain.tools import tool
+from langchain.tools import ToolRuntime, tool

-from deerflow.config import get_app_config
+from deerflow.config.app_config import AppConfig
+from deerflow.config.deer_flow_context import resolve_context


-def _get_firecrawl_client(tool_name: str = "web_search") -> FirecrawlApp:
-    config = get_app_config().get_tool_config(tool_name)
+def _get_firecrawl_client(app_config: AppConfig, tool_name: str = "web_search") -> FirecrawlApp:
+    tool_config = app_config.get_tool_config(tool_name)
    api_key = None
-    if config is not None and "api_key" in config.model_extra:
-        api_key = config.model_extra.get("api_key")
+    if tool_config is not None and "api_key" in tool_config.model_extra:
+        api_key = tool_config.model_extra.get("api_key")
    return FirecrawlApp(api_key=api_key)  # type: ignore[arg-type]


@tool("web_search", parse_docstring=True)
-def web_search_tool(query: str) -> str:
+def web_search_tool(query: str, runtime: ToolRuntime) -> str:
    """Search the web.

    Args:
        query: The query to search for.
    """
    try:
-        config = get_app_config().get_tool_config("web_search")
+        app_config = resolve_context(runtime).app_config
+        tool_config = app_config.get_tool_config("web_search")
        max_results = 5
-        if config is not None:
-            max_results = config.model_extra.get("max_results", max_results)
+        if tool_config is not None:
+            max_results = tool_config.model_extra.get("max_results", max_results)

-        client = _get_firecrawl_client("web_search")
+        client = _get_firecrawl_client(app_config, "web_search")
        result = client.search(query, limit=max_results)

        # result.web contains list of SearchResultWeb objects
@@ -47,7 +49,7 @@ def web_search_tool(query: str) -> str:


@tool("web_fetch", parse_docstring=True)
-def web_fetch_tool(url: str) -> str:
+def web_fetch_tool(url: str, runtime: ToolRuntime) -> str:
    """Fetch the contents of a web page at a given URL.
    Only fetch EXACT URLs that have been provided directly by the user or have been returned in results from the web_search and web_fetch tools.
    This tool can NOT access content that requires authentication, such as private Google Docs or pages behind login walls.
@@ -58,7 +60,8 @@ def web_fetch_tool(url: str) -> str:
        url: The URL to fetch the contents of.
    """
    try:
-        client = _get_firecrawl_client("web_fetch")
+        app_config = resolve_context(runtime).app_config
+        client = _get_firecrawl_client(app_config, "web_fetch")
        result = client.scrape(url, formats=["markdown"])

        markdown_content = result.markdown or ""
@@ -5,9 +5,9 @@ Image Search Tool - Search images using DuckDuckGo for reference in image genera
 import json
 import logging

-from langchain.tools import tool
+from langchain.tools import ToolRuntime, tool

-from deerflow.config import get_app_config
+from deerflow.config.deer_flow_context import resolve_context

 logger = logging.getLogger(__name__)

@@ -77,6 +77,7 @@ def _search_images(
@tool("image_search", parse_docstring=True)
 def image_search_tool(
    query: str,
+    runtime: ToolRuntime,
    max_results: int = 5,
    size: str | None = None,
    type_image: str | None = None,
@@ -99,11 +100,11 @@ def image_search_tool(
        type_image: Image type filter. Options: "photo", "clipart", "gif", "transparent", "line". Use "photo" for realistic references.
        layout: Layout filter. Options: "Square", "Tall", "Wide". Choose based on your generation needs.
    """
-    config = get_app_config().get_tool_config("image_search")
+    tool_config = resolve_context(runtime).app_config.get_tool_config("image_search")

    # Override max_results from config if set
-    if config is not None and "max_results" in config.model_extra:
-        max_results = config.model_extra.get("max_results", max_results)
+    if tool_config is not None and "max_results" in tool_config.model_extra:
+        max_results = tool_config.model_extra.get("max_results", max_results)

    results = _search_images(
        query=query,
@@ -1,6 +1,7 @@
-from langchain.tools import tool
+from langchain.tools import ToolRuntime, tool

-from deerflow.config import get_app_config
+from deerflow.config.app_config import AppConfig
+from deerflow.config.deer_flow_context import resolve_context
 from deerflow.utils.readability import ReadabilityExtractor

 from .infoquest_client import InfoQuestClient
@@ -8,13 +9,13 @@ from .infoquest_client import InfoQuestClient
 readability_extractor = ReadabilityExtractor()


-def _get_infoquest_client() -> InfoQuestClient:
-    search_config = get_app_config().get_tool_config("web_search")
+def _get_infoquest_client(app_config: AppConfig) -> InfoQuestClient:
+    search_config = app_config.get_tool_config("web_search")
    search_time_range = -1
    if search_config is not None and "search_time_range" in search_config.model_extra:
        search_time_range = search_config.model_extra.get("search_time_range")

-    fetch_config = get_app_config().get_tool_config("web_fetch")
+    fetch_config = app_config.get_tool_config("web_fetch")
    fetch_time = -1
    if fetch_config is not None and "fetch_time" in fetch_config.model_extra:
        fetch_time = fetch_config.model_extra.get("fetch_time")
@@ -25,7 +26,7 @@ def _get_infoquest_client() -> InfoQuestClient:
    if fetch_config is not None and "navigation_timeout" in fetch_config.model_extra:
        navigation_timeout = fetch_config.model_extra.get("navigation_timeout")

-    image_search_config = get_app_config().get_tool_config("image_search")
+    image_search_config = app_config.get_tool_config("image_search")
    image_search_time_range = -1
    if image_search_config is not None and "image_search_time_range" in image_search_config.model_extra:
        image_search_time_range = image_search_config.model_extra.get("image_search_time_range")
@@ -44,19 +45,18 @@ def _get_infoquest_client() -> InfoQuestClient:


@tool("web_search", parse_docstring=True)
-def web_search_tool(query: str) -> str:
+def web_search_tool(query: str, runtime: ToolRuntime) -> str:
    """Search the web.

    Args:
        query: The query to search for.
    """
-
-    client = _get_infoquest_client()
+    client = _get_infoquest_client(resolve_context(runtime).app_config)
    return client.web_search(query)


@tool("web_fetch", parse_docstring=True)
-def web_fetch_tool(url: str) -> str:
+def web_fetch_tool(url: str, runtime: ToolRuntime) -> str:
    """Fetch the contents of a web page at a given URL.
    Only fetch EXACT URLs that have been provided directly by the user or have been returned in results from the web_search and web_fetch tools.
    This tool can NOT access content that requires authentication, such as private Google Docs or pages behind login walls.
@@ -66,7 +66,7 @@ def web_fetch_tool(url: str) -> str:
    Args:
        url: The URL to fetch the contents of.
    """
-    client = _get_infoquest_client()
+    client = _get_infoquest_client(resolve_context(runtime).app_config)
    result = client.fetch(url)
    if result.startswith("Error: "):
        return result
@@ -75,7 +75,7 @@ def web_fetch_tool(url: str) -> str:


@tool("image_search", parse_docstring=True)
-def image_search_tool(query: str) -> str:
+def image_search_tool(query: str, runtime: ToolRuntime) -> str:
    """Search for images online. Use this tool BEFORE image generation to find reference images for characters, portraits, objects, scenes, or any content requiring visual accuracy.

    **When to use:**
@@ -89,5 +89,5 @@ def image_search_tool(query: str) -> str:
    Args:
        query: The query to search for images.
    """
-    client = _get_infoquest_client()
+    client = _get_infoquest_client(resolve_context(runtime).app_config)
    return client.image_search(query)
@@ -38,6 +38,6 @@ class JinaClient:

            return response.text
        except Exception as e:
-            error_message = f"Request to Jina API failed: {str(e)}"
-            logger.exception(error_message)
+            error_message = f"Request to Jina API failed: {type(e).__name__}: {e}"
+            logger.warning(error_message)
            return f"Error: {error_message}"
@@ -1,14 +1,16 @@
-from langchain.tools import tool
+import asyncio
+
+from langchain.tools import ToolRuntime, tool

 from deerflow.community.jina_ai.jina_client import JinaClient
-from deerflow.config import get_app_config
+from deerflow.config.deer_flow_context import resolve_context
 from deerflow.utils.readability import ReadabilityExtractor

 readability_extractor = ReadabilityExtractor()


@tool("web_fetch", parse_docstring=True)
-async def web_fetch_tool(url: str) -> str:
+async def web_fetch_tool(url: str, runtime: ToolRuntime) -> str:
    """Fetch the contents of a web page at a given URL.
    Only fetch EXACT URLs that have been provided directly by the user or have been returned in results from the web_search and web_fetch tools.
    This tool can NOT access content that requires authentication, such as private Google Docs or pages behind login walls.
@@ -20,11 +22,11 @@ async def web_fetch_tool(url: str) -> str:
    """
    jina_client = JinaClient()
    timeout = 10
-    config = get_app_config().get_tool_config("web_fetch")
-    if config is not None and "timeout" in config.model_extra:
-        timeout = config.model_extra.get("timeout")
+    tool_config = resolve_context(runtime).app_config.get_tool_config("web_fetch")
+    if tool_config is not None and "timeout" in tool_config.model_extra:
+        timeout = tool_config.model_extra.get("timeout")
    html_content = await jina_client.crawl(url, return_format="html", timeout=timeout)
    if isinstance(html_content, str) and html_content.startswith("Error:"):
        return html_content
-    article = readability_extractor.extract_article(html_content)
+    article = await asyncio.to_thread(readability_extractor.extract_article, html_content)
    return article.to_markdown()[:4096]
@@ -1,32 +1,34 @@
 import json

-from langchain.tools import tool
+from langchain.tools import ToolRuntime, tool
 from tavily import TavilyClient

-from deerflow.config import get_app_config
+from deerflow.config.app_config import AppConfig
+from deerflow.config.deer_flow_context import resolve_context


-def _get_tavily_client() -> TavilyClient:
-    config = get_app_config().get_tool_config("web_search")
+def _get_tavily_client(app_config: AppConfig) -> TavilyClient:
+    tool_config = app_config.get_tool_config("web_search")
    api_key = None
-    if config is not None and "api_key" in config.model_extra:
-        api_key = config.model_extra.get("api_key")
+    if tool_config is not None and "api_key" in tool_config.model_extra:
+        api_key = tool_config.model_extra.get("api_key")
    return TavilyClient(api_key=api_key)


@tool("web_search", parse_docstring=True)
-def web_search_tool(query: str) -> str:
+def web_search_tool(query: str, runtime: ToolRuntime) -> str:
    """Search the web.

    Args:
        query: The query to search for.
    """
-    config = get_app_config().get_tool_config("web_search")
+    app_config = resolve_context(runtime).app_config
+    tool_config = app_config.get_tool_config("web_search")
    max_results = 5
-    if config is not None and "max_results" in config.model_extra:
-        max_results = config.model_extra.get("max_results")
+    if tool_config is not None and "max_results" in tool_config.model_extra:
+        max_results = tool_config.model_extra.get("max_results")

-    client = _get_tavily_client()
+    client = _get_tavily_client(app_config)
    res = client.search(query, max_results=max_results)
    normalized_results = [
        {
@@ -41,7 +43,7 @@ def web_search_tool(query: str) -> str:


@tool("web_fetch", parse_docstring=True)
-def web_fetch_tool(url: str) -> str:
+def web_fetch_tool(url: str, runtime: ToolRuntime) -> str:
    """Fetch the contents of a web page at a given URL.
    Only fetch EXACT URLs that have been provided directly by the user or have been returned in results from the web_search and web_fetch tools.
    This tool can NOT access content that requires authentication, such as private Google Docs or pages behind login walls.
@@ -51,7 +53,8 @@ def web_fetch_tool(url: str) -> str:
    Args:
        url: The URL to fetch the contents of.
    """
-    client = _get_tavily_client()
+    app_config = resolve_context(runtime).app_config
+    client = _get_tavily_client(app_config)
    res = client.extract([url])
    if "failed_results" in res and len(res["failed_results"]) > 0:
        return f"Error: {res['failed_results'][0]['error']}"
@@ -1,6 +1,6 @@
-from .app_config import get_app_config
-from .extensions_config import ExtensionsConfig, get_extensions_config
-from .memory_config import MemoryConfig, get_memory_config
+from .app_config import AppConfig
+from .extensions_config import ExtensionsConfig
+from .memory_config import MemoryConfig
 from .paths import Paths, get_paths
 from .skill_evolution_config import SkillEvolutionConfig
 from .skills_config import SkillsConfig
@@ -13,18 +13,16 @@ from .tracing_config import (
 )

 __all__ = [
-    "get_app_config",
-    "SkillEvolutionConfig",
-    "Paths",
-    "get_paths",
-    "SkillsConfig",
+    "AppConfig",
    "ExtensionsConfig",
-    "get_extensions_config",
    "MemoryConfig",
-    "get_memory_config",
-    "get_tracing_config",
-    "get_explicitly_enabled_tracing_providers",
+    "Paths",
+    "SkillEvolutionConfig",
+    "SkillsConfig",
    "get_enabled_tracing_providers",
+    "get_explicitly_enabled_tracing_providers",
+    "get_paths",
+    "get_tracing_config",
    "is_tracing_enabled",
    "validate_enabled_tracing_providers",
 ]
@@ -1,16 +1,13 @@
 """ACP (Agent Client Protocol) agent configuration loaded from config.yaml."""

-import logging
-from collections.abc import Mapping
-
-from pydantic import BaseModel, Field
-
-logger = logging.getLogger(__name__)
+from pydantic import BaseModel, ConfigDict, Field


 class ACPAgentConfig(BaseModel):
    """Configuration for a single ACP-compatible agent."""

+    model_config = ConfigDict(frozen=True)
+
    command: str = Field(description="Command to launch the ACP agent subprocess")
    args: list[str] = Field(default_factory=list, description="Additional command arguments")
    env: dict[str, str] = Field(default_factory=dict, description="Environment variables to inject into the agent subprocess. Values starting with $ are resolved from host environment variables.")
@@ -24,28 +21,3 @@ class ACPAgentConfig(BaseModel):
            "are denied — the agent must be configured to operate without requesting permissions."
        ),
    )
-
-
-_acp_agents: dict[str, ACPAgentConfig] = {}
-
-
-def get_acp_agents() -> dict[str, ACPAgentConfig]:
-    """Get the currently configured ACP agents.
-
-    Returns:
-        Mapping of agent name -> ACPAgentConfig.  Empty dict if no ACP agents are configured.
-    """
-    return _acp_agents
-
-
-def load_acp_config_from_dict(config_dict: Mapping[str, Mapping[str, object]] | None) -> None:
-    """Load ACP agent configuration from a dictionary (typically from config.yaml).
-
-    Args:
-        config_dict: Mapping of agent name -> config fields.
-    """
-    global _acp_agents
-    if config_dict is None:
-        config_dict = {}
-    _acp_agents = {name: ACPAgentConfig(**cfg) for name, cfg in config_dict.items()}
-    logger.info("ACP config loaded: %d agent(s): %s", len(_acp_agents), list(_acp_agents.keys()))
@@ -0,0 +1,14 @@
+"""Configuration for the custom agents management API."""
+
+from pydantic import BaseModel, ConfigDict, Field
+
+
+class AgentsApiConfig(BaseModel):
+    """Configuration for custom-agent and user-profile management routes."""
+
+    model_config = ConfigDict(frozen=True)
+
+    enabled: bool = Field(
+        default=False,
+        description=("Whether to expose the custom-agent management API over HTTP. When disabled, the gateway rejects read/write access to custom agent SOUL.md, config, and USER.md prompt-management routes."),
+    )
@@ -5,7 +5,7 @@ import re
 from typing import Any

 import yaml
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict

 from deerflow.config.paths import get_paths

@@ -15,9 +15,22 @@ SOUL_FILENAME = "SOUL.md"
 AGENT_NAME_PATTERN = re.compile(r"^[A-Za-z0-9-]+$")


+def validate_agent_name(name: str | None) -> str | None:
+    """Validate a custom agent name before using it in filesystem paths."""
+    if name is None:
+        return None
+    if not isinstance(name, str):
+        raise ValueError("Invalid agent name. Expected a string or None.")
+    if not AGENT_NAME_PATTERN.fullmatch(name):
+        raise ValueError(f"Invalid agent name '{name}'. Must match pattern: {AGENT_NAME_PATTERN.pattern}")
+    return name
+
+
 class AgentConfig(BaseModel):
    """Configuration for a custom agent."""

+    model_config = ConfigDict(frozen=True)
+
    name: str
    description: str = ""
    model: str | None = None
@@ -46,8 +59,7 @@ def load_agent_config(name: str | None) -> AgentConfig | None:
    if name is None:
        return None

-    if not AGENT_NAME_PATTERN.match(name):
-        raise ValueError(f"Invalid agent name '{name}'. Must match pattern: {AGENT_NAME_PATTERN.pattern}")
+    name = validate_agent_name(name)
    agent_dir = get_paths().agent_dir(name)
    config_file = agent_dir / "config.yaml"

@@ -1,6 +1,7 @@
+from __future__ import annotations
+
 import logging
 import os
-from contextvars import ContextVar
 from pathlib import Path
 from typing import Any, Self

@@ -8,28 +9,38 @@ import yaml
 from dotenv import load_dotenv
 from pydantic import BaseModel, ConfigDict, Field

-from deerflow.config.acp_config import load_acp_config_from_dict
-from deerflow.config.checkpointer_config import CheckpointerConfig, load_checkpointer_config_from_dict
+from deerflow.config.acp_config import ACPAgentConfig
+from deerflow.config.agents_api_config import AgentsApiConfig
+from deerflow.config.checkpointer_config import CheckpointerConfig
+from deerflow.config.database_config import DatabaseConfig
 from deerflow.config.extensions_config import ExtensionsConfig
-from deerflow.config.guardrails_config import GuardrailsConfig, load_guardrails_config_from_dict
-from deerflow.config.memory_config import MemoryConfig, load_memory_config_from_dict
+from deerflow.config.guardrails_config import GuardrailsConfig
+from deerflow.config.memory_config import MemoryConfig
 from deerflow.config.model_config import ModelConfig
+from deerflow.config.run_events_config import RunEventsConfig
 from deerflow.config.sandbox_config import SandboxConfig
 from deerflow.config.skill_evolution_config import SkillEvolutionConfig
 from deerflow.config.skills_config import SkillsConfig
-from deerflow.config.stream_bridge_config import StreamBridgeConfig, load_stream_bridge_config_from_dict
-from deerflow.config.subagents_config import SubagentsAppConfig, load_subagents_config_from_dict
-from deerflow.config.summarization_config import SummarizationConfig, load_summarization_config_from_dict
-from deerflow.config.title_config import TitleConfig, load_title_config_from_dict
+from deerflow.config.stream_bridge_config import StreamBridgeConfig
+from deerflow.config.subagents_config import SubagentsAppConfig
+from deerflow.config.summarization_config import SummarizationConfig
+from deerflow.config.title_config import TitleConfig
 from deerflow.config.token_usage_config import TokenUsageConfig
 from deerflow.config.tool_config import ToolConfig, ToolGroupConfig
-from deerflow.config.tool_search_config import ToolSearchConfig, load_tool_search_config_from_dict
+from deerflow.config.tool_search_config import ToolSearchConfig

 load_dotenv()

 logger = logging.getLogger(__name__)


+class CircuitBreakerConfig(BaseModel):
+    """Configuration for the LLM Circuit Breaker."""
+
+    failure_threshold: int = Field(default=5, description="Number of consecutive failures before tripping the circuit")
+    recovery_timeout_sec: int = Field(default=60, description="Time in seconds before attempting to recover the circuit")
+
+
 def _default_config_candidates() -> tuple[Path, ...]:
    """Return deterministic config.yaml locations without relying on cwd."""
    backend_dir = Path(__file__).resolve().parents[4]
@@ -53,11 +64,16 @@ class AppConfig(BaseModel):
    title: TitleConfig = Field(default_factory=TitleConfig, description="Automatic title generation configuration")
    summarization: SummarizationConfig = Field(default_factory=SummarizationConfig, description="Conversation summarization configuration")
    memory: MemoryConfig = Field(default_factory=MemoryConfig, description="Memory subsystem configuration")
+    agents_api: AgentsApiConfig = Field(default_factory=AgentsApiConfig, description="Custom-agent management API configuration")
    subagents: SubagentsAppConfig = Field(default_factory=SubagentsAppConfig, description="Subagent runtime configuration")
    guardrails: GuardrailsConfig = Field(default_factory=GuardrailsConfig, description="Guardrail middleware configuration")
-    model_config = ConfigDict(extra="allow", frozen=False)
+    circuit_breaker: CircuitBreakerConfig = Field(default_factory=CircuitBreakerConfig, description="LLM circuit breaker configuration")
+    database: DatabaseConfig = Field(default_factory=DatabaseConfig, description="Unified database backend configuration")
+    run_events: RunEventsConfig = Field(default_factory=RunEventsConfig, description="Run event storage configuration")
+    model_config = ConfigDict(extra="allow", frozen=True)
    checkpointer: CheckpointerConfig | None = Field(default=None, description="Checkpointer configuration")
    stream_bridge: StreamBridgeConfig | None = Field(default=None, description="Stream bridge configuration")
+    acp_agents: dict[str, ACPAgentConfig] = Field(default_factory=dict, description="ACP agent configurations keyed by agent name")

    @classmethod
    def resolve_config_path(cls, config_path: str | None = None) -> Path:
@@ -105,41 +121,6 @@ class AppConfig(BaseModel):

        config_data = cls.resolve_env_variables(config_data)

-        # Load title config if present
-        if "title" in config_data:
-            load_title_config_from_dict(config_data["title"])
-
-        # Load summarization config if present
-        if "summarization" in config_data:
-            load_summarization_config_from_dict(config_data["summarization"])
-
-        # Load memory config if present
-        if "memory" in config_data:
-            load_memory_config_from_dict(config_data["memory"])
-
-        # Load subagents config if present
-        if "subagents" in config_data:
-            load_subagents_config_from_dict(config_data["subagents"])
-
-        # Load tool_search config if present
-        if "tool_search" in config_data:
-            load_tool_search_config_from_dict(config_data["tool_search"])
-
-        # Load guardrails config if present
-        if "guardrails" in config_data:
-            load_guardrails_config_from_dict(config_data["guardrails"])
-
-        # Load checkpointer config if present
-        if "checkpointer" in config_data:
-            load_checkpointer_config_from_dict(config_data["checkpointer"])
-
-        # Load stream bridge config if present
-        if "stream_bridge" in config_data:
-            load_stream_bridge_config_from_dict(config_data["stream_bridge"])
-
-        # Always refresh ACP agent config so removed entries do not linger across reloads.
-        load_acp_config_from_dict(config_data.get("acp_agents", {}))
-
        # Load extensions config separately (it's in a different file)
        extensions_config = ExtensionsConfig.from_file()
        config_data["extensions"] = extensions_config.model_dump()
@@ -250,130 +231,8 @@ class AppConfig(BaseModel):
        """
        return next((group for group in self.tool_groups if group.name == name), None)

-
-_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:
-    """Reload the config from file and update the cached instance.
-
-    This is useful when the config file has been modified and you want
-    to pick up the changes without restarting the application.
-
-    Args:
-        config_path: Optional path to config file. If not provided,
-                     uses the default resolution strategy.
-
-    Returns:
-        The newly loaded AppConfig instance.
-    """
-    return _load_and_cache_app_config(config_path)
-
-
-def reset_app_config() -> None:
-    """Reset the cached config instance.
-
-    This clears the singleton cache, causing the next call to
-    `get_app_config()` to reload from file. Useful for testing
-    or when switching between different configurations.
-    """
-    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:
-    """Set a custom config instance.
-
-    This allows injecting a custom or mock config for testing purposes.
-
-    Args:
-        config: The AppConfig instance to use.
-    """
-    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)
+    # AppConfig is a pure value object: construct with ``from_file()``, pass around.
+    # Composition roots that hold the resolved instance:
+    #   - Gateway:   ``app.state.config`` via ``Depends(get_config)``
+    #   - Client:    ``DeerFlowClient._app_config``
+    #   - Agent run: ``Runtime[DeerFlowContext].context.app_config``
@@ -2,7 +2,7 @@

 from typing import Literal

-from pydantic import BaseModel, Field
+from pydantic import BaseModel, ConfigDict, Field

 CheckpointerType = Literal["memory", "sqlite", "postgres"]

@@ -10,6 +10,8 @@ CheckpointerType = Literal["memory", "sqlite", "postgres"]
 class CheckpointerConfig(BaseModel):
    """Configuration for LangGraph state persistence checkpointer."""

+    model_config = ConfigDict(frozen=True)
+
    type: CheckpointerType = Field(
        description="Checkpointer backend type. "
        "'memory' is in-process only (lost on restart). "
@@ -23,24 +25,3 @@ class CheckpointerConfig(BaseModel):
        "For sqlite, use a file path like '.deer-flow/checkpoints.db' or ':memory:' for in-memory. "
        "For postgres, use a DSN like 'postgresql://user:pass@localhost:5432/db'.",
    )
-
-
-# Global configuration instance — None means no checkpointer is configured.
-_checkpointer_config: CheckpointerConfig | None = None
-
-
-def get_checkpointer_config() -> CheckpointerConfig | None:
-    """Get the current checkpointer configuration, or None if not configured."""
-    return _checkpointer_config
-
-
-def set_checkpointer_config(config: CheckpointerConfig | None) -> None:
-    """Set the checkpointer configuration."""
-    global _checkpointer_config
-    _checkpointer_config = config
-
-
-def load_checkpointer_config_from_dict(config_dict: dict) -> None:
-    """Load checkpointer configuration from a dictionary."""
-    global _checkpointer_config
-    _checkpointer_config = CheckpointerConfig(**config_dict)
@@ -0,0 +1,103 @@
+"""Unified database backend configuration.
+
+Controls BOTH the LangGraph checkpointer and the DeerFlow application
+persistence layer (runs, threads metadata, users, etc.). The user
+configures one backend; the system handles physical separation details.
+
+SQLite mode: checkpointer and app share a single .db file
+({sqlite_dir}/deerflow.db) with WAL journal mode enabled on every
+connection. WAL allows concurrent readers and a single writer without
+blocking, making a unified file safe for both workloads.  Writers
+that contend for the lock wait via the default 5-second sqlite3
+busy timeout rather than failing immediately.
+
+Postgres mode: both use the same database URL but maintain independent
+connection pools with different lifecycles.
+
+Memory mode: checkpointer uses MemorySaver, app uses in-memory stores.
+No database is initialized.
+
+Sensitive values (postgres_url) should use $VAR syntax in config.yaml
+to reference environment variables from .env:
+
+    database:
+      backend: postgres
+      postgres_url: $DATABASE_URL
+
+The $VAR resolution is handled by AppConfig.resolve_env_variables()
+before this config is instantiated -- DatabaseConfig itself does not
+need to do any environment variable processing.
+"""
+
+from __future__ import annotations
+
+import os
+from typing import Literal
+
+from pydantic import BaseModel, ConfigDict, Field
+
+
+class DatabaseConfig(BaseModel):
+    model_config = ConfigDict(frozen=True)
+    backend: Literal["memory", "sqlite", "postgres"] = Field(
+        default="memory",
+        description=("Storage backend for both checkpointer and application data. 'memory' for development (no persistence across restarts), 'sqlite' for single-node deployment, 'postgres' for production multi-node deployment."),
+    )
+    sqlite_dir: str = Field(
+        default=".deer-flow/data",
+        description=("Directory for the SQLite database file. Both checkpointer and application data share {sqlite_dir}/deerflow.db."),
+    )
+    postgres_url: str = Field(
+        default="",
+        description=(
+            "PostgreSQL connection URL, shared by checkpointer and app. "
+            "Use $DATABASE_URL in config.yaml to reference .env. "
+            "Example: postgresql://user:pass@host:5432/deerflow "
+            "(the +asyncpg driver suffix is added automatically where needed)."
+        ),
+    )
+    echo_sql: bool = Field(
+        default=False,
+        description="Echo all SQL statements to log (debug only).",
+    )
+    pool_size: int = Field(
+        default=5,
+        description="Connection pool size for the app ORM engine (postgres only).",
+    )
+
+    # -- Derived helpers (not user-configured) --
+
+    @property
+    def _resolved_sqlite_dir(self) -> str:
+        """Resolve sqlite_dir to an absolute path (relative to CWD)."""
+        from pathlib import Path
+
+        return str(Path(self.sqlite_dir).resolve())
+
+    @property
+    def sqlite_path(self) -> str:
+        """Unified SQLite file path shared by checkpointer and app."""
+        return os.path.join(self._resolved_sqlite_dir, "deerflow.db")
+
+    # Backward-compatible aliases
+    @property
+    def checkpointer_sqlite_path(self) -> str:
+        """SQLite file path for the LangGraph checkpointer (alias for sqlite_path)."""
+        return self.sqlite_path
+
+    @property
+    def app_sqlite_path(self) -> str:
+        """SQLite file path for application ORM data (alias for sqlite_path)."""
+        return self.sqlite_path
+
+    @property
+    def app_sqlalchemy_url(self) -> str:
+        """SQLAlchemy async URL for the application ORM engine."""
+        if self.backend == "sqlite":
+            return f"sqlite+aiosqlite:///{self.sqlite_path}"
+        if self.backend == "postgres":
+            url = self.postgres_url
+            if url.startswith("postgresql://"):
+                url = url.replace("postgresql://", "postgresql+asyncpg://", 1)
+            return url
+        raise ValueError(f"No SQLAlchemy URL for backend={self.backend!r}")
@@ -0,0 +1,55 @@
+"""Per-invocation context for DeerFlow agent execution.
+
+Injected via LangGraph Runtime. Middleware and tools access this
+via Runtime[DeerFlowContext] parameters, through resolve_context().
+"""
+
+from __future__ import annotations
+
+import logging
+from dataclasses import dataclass
+from typing import TYPE_CHECKING, Any
+
+if TYPE_CHECKING:
+    from deerflow.config.app_config import AppConfig
+
+logger = logging.getLogger(__name__)
+
+
+@dataclass(frozen=True)
+class DeerFlowContext:
+    """Typed, immutable, per-invocation context injected via LangGraph Runtime.
+
+    Fields are all known at run start and never change during execution.
+    Mutable runtime state (e.g. sandbox_id) flows through ThreadState, not here.
+    """
+
+    app_config: AppConfig
+    thread_id: str
+    agent_name: str | None = None
+
+
+def resolve_context(runtime: Any) -> DeerFlowContext:
+    """Return the typed DeerFlowContext that the runtime carries.
+
+    Gateway mode (``DeerFlowClient``, ``run_agent``) always attaches a typed
+    ``DeerFlowContext`` via ``agent.astream(context=...)``; the LangGraph
+    Server path uses ``langgraph.json`` registration where the top-level
+    ``make_lead_agent`` loads ``AppConfig`` from disk itself, so we still
+    arrive here with a typed context.
+
+    Only the dict/None shapes that legacy tests used to exercise would fall
+    through this function; we now reject them loudly instead of papering
+    over the missing context with an ambient ``AppConfig`` lookup.
+    """
+    ctx = getattr(runtime, "context", None)
+    if isinstance(ctx, DeerFlowContext):
+        return ctx
+
+    raise RuntimeError(
+        "resolve_context: runtime.context is not a DeerFlowContext "
+        "(got type %s). Every entry point must attach one at invoke time — "
+        "Gateway/Client via agent.astream(context=DeerFlowContext(...)), "
+        "LangGraph Server via the make_lead_agent boundary that loads "
+        "AppConfig.from_file()." % type(ctx).__name__
+    )
--- a/Show More
+++ b/Show More