# AGENTS.md

This file provides guidance to AI coding agents (Claude Code, Codex, and others) when working with code in this repository. It is the source of truth; the sibling `CLAUDE.md` imports it via `@AGENTS.md`.

## Project Overview

DeerFlow is a LangGraph-based AI super agent system with a full-stack architecture. The backend provides a "super agent" with sandbox execution, persistent memory, subagent delegation, and extensible tool integration - all operating in per-thread isolated environments.

**Architecture**:
- **Gateway API** (port 8001): REST API plus embedded LangGraph-compatible agent runtime
- **Frontend** (port 3000): Next.js web interface
- **Nginx** (port 2026): Unified reverse proxy entry point
- **Provisioner** (port 8002, optional in Docker dev): Started only when sandbox is configured for provisioner/Kubernetes mode

**Runtime**:
- `make dev`, Docker dev, and production all run the agent runtime in Gateway via `RunManager` + `run_agent()` + `StreamBridge` (`packages/harness/deerflow/runtime/`). Nginx exposes that runtime at `/api/langgraph/*` and rewrites it to Gateway's native `/api/*` routers.

**Project Structure**:
```
deer-flow/
├── Makefile                    # Root commands (check, install, dev, stop)
├── config.yaml                 # Main application configuration
├── extensions_config.json      # MCP servers and skills configuration
├── backend/                    # Backend application (this directory)
│   ├── Makefile               # Backend-only commands (dev, gateway, lint)
│   ├── langgraph.json         # LangGraph Studio graph configuration
│   ├── packages/
│   │   └── harness/           # deerflow-harness package (import: deerflow.*)
│   │       ├── pyproject.toml
│   │       └── deerflow/
│   │           ├── agents/            # LangGraph agent system
│   │           │   ├── lead_agent/    # Main agent (factory + system prompt)
│   │           │   ├── middlewares/   # middleware components (see Middleware Chain section)
│   │           │   ├── memory/        # Memory extraction, queue, prompts
│   │           │   └── thread_state.py # ThreadState schema
│   │           ├── sandbox/           # Sandbox execution system
│   │           │   ├── local/         # Local filesystem provider
│   │           │   ├── sandbox.py     # Abstract Sandbox interface
│   │           │   ├── tools.py       # bash, ls, read/write/str_replace
│   │           │   └── middleware.py  # Sandbox lifecycle management
│   │           ├── subagents/         # Subagent delegation system
│   │           │   ├── builtins/      # general-purpose, bash agents
│   │           │   ├── executor.py    # Background execution engine
│   │           │   └── registry.py    # Agent registry
│   │           ├── tools/builtins/    # Built-in tools (present_files, ask_clarification, view_image)
│   │           ├── mcp/               # MCP integration (tools, cache, client)
│   │           ├── models/            # Model factory with thinking/vision support
│   │           ├── skills/            # Skills discovery, loading, parsing
│   │           ├── config/            # Configuration system (app, model, sandbox, tool, etc.)
│   │           ├── community/         # Community tools (search/fetch/scrape, image search, AIO sandbox)
│   │           ├── reflection/        # Dynamic module loading (resolve_variable, resolve_class)
│   │           ├── utils/             # Utilities (network, readability)
│   │           └── client.py          # Embedded Python client (DeerFlowClient)
│   ├── app/                   # Application layer (import: app.*)
│   │   ├── gateway/           # FastAPI Gateway API
│   │   │   ├── app.py         # FastAPI application
│   │   │   └── routers/       # FastAPI route modules (models, mcp, memory, skills, uploads, threads, artifacts, agents, suggestions, channels)
│   │   └── channels/          # IM platform integrations
│   ├── tests/                 # Test suite
│   └── docs/                  # Documentation
├── frontend/                   # Next.js frontend application
└── skills/                     # Agent skills directory
    ├── public/                # Public skills (committed)
    └── custom/                # Custom skills (gitignored)
```

## Important Development Guidelines

### Documentation Update Policy
**CRITICAL: Always update README.md and AGENTS.md after every code change**

When making code changes, you MUST update the relevant documentation:
- Update `README.md` for user-facing changes (features, setup, usage instructions)
- Update `AGENTS.md` for development changes (architecture, commands, workflows, internal systems). `CLAUDE.md` imports it via `@AGENTS.md`, so editing `AGENTS.md` updates both.
- Keep documentation synchronized with the codebase at all times
- Ensure accuracy and timeliness of all documentation

## Commands

**Root directory** (for full application):
```bash
make check      # Check system requirements
make install    # Install all dependencies (frontend + backend)
make dev        # Start all services (Gateway + Frontend + Nginx), with config.yaml preflight
make start      # Start production services locally
make stop       # Stop all services
```

**Backend directory** (for backend development only):
```bash
make install            # Install backend dependencies
make dev                # Run Gateway API with reload (port 8001)
make gateway            # Run Gateway API only (port 8001)
make test               # Run all backend tests
make test-blocking-io   # Run strict Blockbuster runtime gate on tests/blocking_io/
make lint               # Lint with ruff
make format             # Format code with ruff
make migrate-rev MSG="..."  # Autogenerate a new alembic revision (see Schema Migrations section)
```

The `detect-blocking-io` target parses `app/`, `packages/harness/deerflow/`,
and `scripts/` with AST. By default it reports only blocking IO candidates that
are inside async code, reachable from async code in the same file, or reachable
from sync-only `AgentMiddleware` before/after hooks that LangGraph can execute
on the async graph path. It prints a concise summary and writes complete JSON
findings to `.deer-flow/blocking-io-findings.json` at the repository root
(both `make detect-blocking-io` from the repo root and `cd backend && make
detect-blocking-io` resolve to the same repo-root path). JSON findings include
`priority`, `location`, `blocking_call`, `event_loop_exposure`, `reason`, and
`code` for model-assisted or manual review. `priority` is a deterministic
review ordering from operation type, not proof of a bug. Bare-name same-file
calls are resolved by function name, so duplicate helper names in one file can
conservatively over-report async reachability. It is intentionally
informational and is not run from CI in this round.

For a diff-scoped view of the same findings, `scripts/scan_changed_blocking_io.py`
(repo root) reports findings on the added lines of `git diff <base>...HEAD`
plus findings new versus the merge base (so a new async caller exposing an
untouched sync helper in the same file is still reported) — used by the
`blocking-io-guard` skill (`.agent/skills/blocking-io-guard/`) as the
deterministic scope step before routing each candidate to a fix and/or a
`tests/blocking_io/` runtime anchor.

Regression tests related to Docker/provisioner behavior:
- `tests/test_docker_sandbox_mode_detection.py` (mode detection from `config.yaml`)
- `tests/test_provisioner_kubeconfig.py` (kubeconfig file/directory handling)

Blocking-IO runtime gate (`tests/blocking_io/`):
- Wraps every item under `tests/blocking_io/` with a strict Blockbuster
  context scoped to `app.*` and `deerflow.*` (see
  `tests/support/detectors/blocking_io_runtime.py`). Any sync blocking IO
  call whose stack passes through DeerFlow business code while running on
  the asyncio event loop raises `BlockingError` and fails the test.
- Regression anchors live there: `test_skills_load.py` (locks the
  `asyncio.to_thread` offload around `LocalSkillStorage.load_skills`, fix
  for #1917); `test_sqlite_lifespan.py` (locks the offload around
  SQLite path resolution plus `ensure_sqlite_parent_dir`, fix for #1912);
  `test_jsonl_run_event_store.py` (locks `JsonlRunEventStore`'s async
  API offloading its file IO via `asyncio.to_thread`, fix #3084); and
  `test_uploads_middleware.py` (locks `UploadsMiddleware.abefore_agent`
  offloading the uploads-directory scan off the event loop).
- `test_gate_smoke.py` is a meta-test asserting the gate actually catches
  unoffloaded blocking IO and that the `@pytest.mark.allow_blocking_io`
  opt-out works.
- Coverage boundary: the gate only sees code that test execution actually
  touches. Static AST coverage is a separate concern (out of scope for
  this PR).
- CI: runs on every PR via `.github/workflows/backend-blocking-io-tests.yml`,
  hard-fail.

Boundary check (harness → app import firewall):
- `tests/test_harness_boundary.py` — ensures `packages/harness/deerflow/` never imports from `app.*`

CI runs these regression tests for every pull request via [.github/workflows/backend-unit-tests.yml](../.github/workflows/backend-unit-tests.yml).

## Architecture

### Harness / App Split

The backend is split into two layers with a strict dependency direction:

- **Harness** (`packages/harness/deerflow/`): Publishable agent framework package (`deerflow-harness`). Import prefix: `deerflow.*`. Contains agent orchestration, tools, sandbox, models, MCP, skills, config — everything needed to build and run agents.
- **App** (`app/`): Unpublished application code. Import prefix: `app.*`. Contains the FastAPI Gateway API and IM channel integrations (Feishu, Slack, Telegram, DingTalk).

**Dependency rule**: App imports deerflow, but deerflow never imports app. This boundary is enforced by `tests/test_harness_boundary.py` which runs in CI.

**Import conventions**:
```python
# Harness internal
from deerflow.agents import make_lead_agent
from deerflow.models import create_chat_model

# App internal
from app.gateway.app import app
from app.channels.service import start_channel_service

# App → Harness (allowed)
from deerflow.config import get_app_config

# Harness → App (FORBIDDEN — enforced by test_harness_boundary.py)
# from app.gateway.routers.uploads import ...  # ← will fail CI
```

### Agent System

**Lead Agent** (`packages/harness/deerflow/agents/lead_agent/agent.py`):
- Entry point: `make_lead_agent(config: RunnableConfig)` registered in `langgraph.json`
- Dynamic model selection via `create_chat_model()` with thinking/vision support
- Tools loaded via `get_available_tools()` - combines sandbox, built-in, MCP, community, and subagent tools
- System prompt generated by `apply_prompt_template()` with skills, memory, and subagent instructions

**ThreadState** (`packages/harness/deerflow/agents/thread_state.py`):
- Extends `AgentState` with: `sandbox`, `thread_data`, `title`, `artifacts`, `todos`, `uploaded_files`, `viewed_images`
- Uses custom reducers: `merge_artifacts` (deduplicate), `merge_viewed_images` (merge/clear)

**Runtime Configuration** (via `config.configurable`):
- `thinking_enabled` - Enable model's extended thinking
- `model_name` - Select specific LLM model
- `is_plan_mode` - Enable TodoList middleware
- `subagent_enabled` - Enable task delegation tool

### Middleware Chain

Lead-agent middlewares are assembled in strict order across three functions: the shared base in `packages/harness/deerflow/agents/middlewares/tool_error_handling_middleware.py` (`_build_runtime_middlewares`, exposed via `build_lead_runtime_middlewares`), then the lead-only middlewares appended in `packages/harness/deerflow/agents/lead_agent/agent.py` (`build_middlewares`). Items marked *(optional)* are appended only when their config/runtime condition holds, so the live chain length varies.

**Shared runtime base** (`build_lead_runtime_middlewares`; subagents reuse most of this via `build_subagent_runtime_middlewares`):

1. **InputSanitizationMiddleware** - First, so it is the outermost `wrap_model_call` wrapper; every inner middleware (including LLM retries) sees sanitized messages
2. **ToolOutputBudgetMiddleware** - Caps tool output size (per app config) before it re-enters the model context
3. **UploadsMiddleware** - Tracks and injects newly uploaded files into conversation (lead agent only)
4. **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)
5. **SandboxMiddleware** - Acquires sandbox, stores `sandbox_id` in state
6. **DanglingToolCallMiddleware** - Injects placeholder ToolMessages for AIMessage tool_calls that lack responses (e.g., user interruption), preserving raw provider tool-call payloads in `additional_kwargs["tool_calls"]`
7. **LLMErrorHandlingMiddleware** - Normalizes provider/model invocation failures into recoverable assistant-facing errors before later stages run
8. **GuardrailMiddleware** - *(optional, if `guardrails.enabled`)* Pre-tool-call authorization via pluggable `GuardrailProvider`; returns an error ToolMessage on deny. Providers: built-in `AllowlistProvider` (zero deps), OAP policy providers (e.g. `aport-agent-guardrails`), or custom. See [docs/GUARDRAILS.md](docs/GUARDRAILS.md)
9. **SandboxAuditMiddleware** - Audits sandboxed shell/file operations for security logging before tool execution
10. **ToolErrorHandlingMiddleware** - Converts tool exceptions into error `ToolMessage`s so the run can continue instead of aborting

**Lead-only middlewares** (`build_middlewares`, appended after the base):

11. **DynamicContextMiddleware** - Injects the current date (and optionally memory) as a `<system-reminder>` into the first HumanMessage, keeping the base system prompt fully static for prefix-cache reuse
12. **SkillActivationMiddleware** - Detects strict `/skill-name task` syntax on the latest real user message, resolves only enabled and runtime-allowed skills, injects the `SKILL.md` body as hidden current-turn context, and records a `middleware:skill_activation` audit event
13. **SummarizationMiddleware** - *(optional, if enabled)* Context reduction when approaching token limits
14. **TodoListMiddleware** - *(optional, if `is_plan_mode`)* Task tracking with the `write_todos` tool
15. **TokenUsageMiddleware** - *(optional, if `token_usage.enabled`)* Records token usage metrics; subagent usage is merged back into the dispatching AIMessage by message position
16. **TitleMiddleware** - Auto-generates the thread title after the first complete exchange and normalizes structured message content before prompting the title model
17. **MemoryMiddleware** - Queues conversations for async memory update (filters to user + final AI responses)
18. **ViewImageMiddleware** - *(optional, if the model supports vision)* Injects base64 image data before the LLM call
19. **DeferredToolFilterMiddleware** - *(optional, if `tool_search.enabled`)* Hides deferred (MCP) tool schemas from the bound model until `tool_search` promotes them (reads per-thread promotions from `ThreadState.promoted`, hash-scoped)
20. **SystemMessageCoalescingMiddleware** - Merges every SystemMessage into a single leading SystemMessage per request; provider-agnostic fix for strict backends (vLLM/SGLang/Qwen/Anthropic) that reject non-leading system messages. Touches the per-request payload only (checkpoint state unchanged); on midnight crossings only the latest `dynamic_context_reminder` SystemMessage survives
21. **SubagentLimitMiddleware** - *(optional, if `subagent_enabled`)* Truncates excess `task` tool calls to enforce the `MAX_CONCURRENT_SUBAGENTS` limit
22. **LoopDetectionMiddleware** - *(optional, if `loop_detection.enabled`)* Detects repeated tool-call loops; hard-stop clears both structured `tool_calls` and raw provider tool-call metadata before forcing a final text answer
23. **TokenBudgetMiddleware** - *(optional, if `token_budget.enabled`)* Enforces per-run token limits
24. **Custom middlewares** - *(optional)* Any `custom_middlewares` passed to `build_middlewares` are injected here, before the safety/clarification tail
25. **SafetyFinishReasonMiddleware** - *(optional, if `safety_finish_reason.enabled`)* Suppresses tool execution when the provider safety-terminated the response (e.g. `finish_reason=content_filter`); registered after custom middlewares so LangChain's reverse-order `after_model` dispatch runs it first
26. **ClarificationMiddleware** - Intercepts `ask_clarification` tool calls, interrupts via `Command(goto=END)` (must be last)

### Configuration System

**Main Configuration** (`config.yaml`):

Setup: Copy `config.example.yaml` to `config.yaml` in the **project root** directory.

**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 or file content signature changes. The signature includes file metadata and a content digest, so Gateway and LangGraph reads stay aligned with `config.yaml` edits even on object-store or network mounts where mtime can remain stale.

**Config Hot-Reload Boundary**: Gateway dependencies route through `get_app_config()` on every request, so per-run fields like `models[*].max_tokens`, `summarization.*`, `title.*`, `memory.*`, `subagents.*`, `tools[*]`, and the agent system prompt pick up `config.yaml` edits on the next message. `AppConfig` is intentionally **not** cached on `app.state` — `lifespan()` keeps a local `startup_config` variable for one-shot bootstrap work and passes it to `langgraph_runtime(app, startup_config)`.

Infrastructure fields are **restart-required**. The authoritative list lives in `packages/harness/deerflow/config/reload_boundary.py::STARTUP_ONLY_FIELDS` and is mirrored by the standardised `"startup-only:"` prefix on the corresponding `Field(description=...)` in `AppConfig`, so IDE hover on those fields surfaces the reason inline (no need to context-switch into this table). Currently registered: `database`, `checkpointer`, `run_events`, `stream_bridge`, `sandbox`, `log_level`, `channels`, `channel_connections`. Adding a new restart-required field requires updating the registry; drift is pinned by `tests/test_reload_boundary.py`.

Configuration priority:
1. Explicit `config_path` argument
2. `DEER_FLOW_CONFIG_PATH` environment variable
3. `config.yaml` in current directory (backend/)
4. `config.yaml` in parent directory (project root - **recommended location**)

Config values starting with `$` are resolved as environment variables (e.g., `$OPENAI_API_KEY`).
`ModelConfig` also declares `use_responses_api` and `output_version` so OpenAI `/v1/responses` can be enabled explicitly while still using `langchain_openai:ChatOpenAI`.

**Extensions Configuration** (`extensions_config.json`):

MCP servers and skills are configured together in `extensions_config.json` in project root:

Configuration priority:
1. Explicit `config_path` argument
2. `DEER_FLOW_EXTENSIONS_CONFIG_PATH` environment variable
3. `extensions_config.json` in current directory (backend/)
4. `extensions_config.json` in parent directory (project root - **recommended location**)

### Gateway API (`app/gateway/`)

FastAPI application on port 8001 with health check at `GET /health`. Set `GATEWAY_ENABLE_DOCS=false` to disable `/docs`, `/redoc`, and `/openapi.json` in production (default: enabled).

CORS is same-origin by default when requests enter through nginx on port 2026. Split-origin or port-forwarded browser clients must opt in with `GATEWAY_CORS_ORIGINS` (comma-separated exact origins); Gateway `CORSMiddleware` and `CSRFMiddleware` both read that variable so browser CORS and auth-origin checks stay aligned.

**Routers**:

| Router | Endpoints |
|--------|-----------|
| **Models** (`/api/models`) | `GET /` - list models; `GET /{name}` - model details |
| **MCP** (`/api/mcp`) | `GET /config` - get config; `PUT /config` - update config (saves to extensions_config.json) |
| **Skills** (`/api/skills`) | `GET /` - list skills; `GET /{name}` - details; `PUT /{name}` - update enabled; `POST /install` - install from .skill archive (accepts standard optional frontmatter like `version`, `author`, `compatibility`) |
| **Memory** (`/api/memory`) | `GET /` - memory data; `POST /reload` - force reload; `GET /config` - config; `GET /status` - config + data |
| **Uploads** (`/api/threads/{id}/uploads`) | `POST /` - upload files (auto-converts PDF/PPT/Excel/Word); `GET /list` - list; `DELETE /{filename}` - delete |
| **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/suggestions`) | `GET /config` - returns global suggestions config boolean; `POST /threads/{id}/suggestions` - generate follow-up questions; rich list/block model content is normalized and inline reasoning (`<think>...</think>`, including unclosed/truncated blocks from reasoning models like MiniMax-M3) is stripped before JSON parsing |
| **Thread Runs** (`/api/threads/{id}/runs`) | `POST /` - create background run; `POST /stream` - create + SSE stream; `POST /wait` - create + block; `POST /regenerate/prepare` - prepare clean input + checkpoint metadata for regenerating the latest assistant answer; `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 |

**RunManager / RunStore contract**:
- `RunManager.get()` is async; direct callers must `await` it.
- When a persistent `RunStore` is configured, `get()` and `list_by_thread()` hydrate historical runs from the store. In-memory records win for the same `run_id` so task, abort, and stream-control state stays attached to active local runs.
- `cancel()` and `create_or_reject(..., multitask_strategy="interrupt"|"rollback")` persist interrupted status through `RunStore.update_status()`, matching normal `set_status()` transitions.
- Store-only hydrated runs are readable history. If the current worker has no in-memory task/control state for that run, cancellation APIs can return 409 because this worker cannot stop the task.
- `POST /wait` (both thread-scoped and `/api/runs/wait`) drains the stream bridge via `wait_for_run_completion()` instead of bare `await record.task`, so it honours the run's `on_disconnect` setting and cancels the background run on real client disconnect rather than returning a stale checkpoint (issue #3265).
- Thread-scoped run creation accepts `checkpoint` / `checkpoint_id`; Gateway validates the checkpoint belongs to the request thread before writing `checkpoint_id` / `checkpoint_ns` into `config.configurable` for LangGraph branching.

Proxied through nginx: `/api/langgraph/*` → Gateway LangGraph-compatible runtime, all other `/api/*` → Gateway REST APIs.

### Sandbox System (`packages/harness/deerflow/sandbox/`)

**Interface**: Abstract `Sandbox` with `execute_command`, `read_file`, `write_file`, `list_dir`
**Provider Pattern**: `SandboxProvider` with `acquire`, `acquire_async`, `get`, `release` lifecycle. Async agent/tool paths call async sandbox lifecycle hooks so Docker sandbox creation, discovery, cross-process locking, readiness polling, and release stay off the event loop.
**Implementations**:
- `LocalSandboxProvider` - Local filesystem execution. `acquire(thread_id)` returns a per-thread `LocalSandbox` (id `local:{thread_id}`) whose `path_mappings` resolve `/mnt/user-data/{workspace,uploads,outputs}` and `/mnt/acp-workspace` to that thread's host directories, so the public `Sandbox` API honours the `/mnt/user-data` contract uniformly with AIO. `acquire()` / `acquire(None)` keeps the legacy generic singleton (id `local`) for callers without a thread context. Per-thread sandboxes are held in an LRU cache (default 256 entries) guarded by a `threading.Lock`.
- `AioSandboxProvider` (`packages/harness/deerflow/community/`) - Docker-based isolation. Active-cache and warm-pool entries are checked with the backend during acquire/reuse; definitively dead containers are dropped from all in-process maps so the thread can discover or create a fresh sandbox instead of reusing a stale client. Backend health-check failures are treated as unknown, not dead; local discovery likewise treats an unverifiable container as not adoptable and falls through to create rather than failing acquire. `get()` remains an in-memory lookup for event-loop-safe tool paths.

**Virtual Path System**:
- Agent sees: `/mnt/user-data/{workspace,uploads,outputs}`, `/mnt/skills`
- Physical: `backend/.deer-flow/users/{user_id}/threads/{thread_id}/user-data/...`, `deer-flow/skills/`
- Translation: `LocalSandboxProvider` builds per-thread `PathMapping`s for the user-data prefixes at acquire time; `tools.py` keeps `replace_virtual_path()` / `replace_virtual_paths_in_command()` as a defense-in-depth layer (and for path validation). AIO has the directories volume-mounted at the same virtual paths inside its container, so both implementations accept `/mnt/user-data/...` natively.
- Detection: `is_local_sandbox()` accepts both `sandbox_id == "local"` (legacy / no-thread) and `sandbox_id.startswith("local:")` (per-thread)

**Sandbox Tools** (in `packages/harness/deerflow/sandbox/tools.py`):
- `bash` - Execute commands with path translation and error handling
- `ls` - Directory listing (tree format, max 2 levels)
- `read_file` - Read file contents with optional line range
- `write_file` - Write/append to files, creates directories; overwrites by default and exposes the `append` argument in the model-facing schema for end-of-file writes
- `str_replace` - Substring replacement (single or all occurrences); same-path serialization is scoped to `(sandbox.id, path)` so isolated sandboxes do not contend on identical virtual paths inside one process

### Subagent System (`packages/harness/deerflow/subagents/`)

**Built-in Agents**: `general-purpose` (all tools except `task`) and `bash` (command specialist)
**Execution**: Dual thread pool - `_scheduler_pool` (3 workers) + `_execution_pool` (3 workers)
**Concurrency**: `MAX_CONCURRENT_SUBAGENTS = 3` enforced by `SubagentLimitMiddleware` (truncates excess tool calls in `after_model`); default subagent timeout `subagents.timeout_seconds=1800` (30 min) and built-in `general-purpose` `max_turns=150` (raised from 100/15-min so deep-research subtasks stop hitting `GraphRecursionError` out of the box)
**Flow**: `task()` tool → `SubagentExecutor` → background thread → poll 5s → SSE events → result
**Events**: `task_started`, `task_running`, `task_completed`/`task_failed`/`task_timed_out`
**Deferred MCP tools** (if `tool_search.enabled`): `SubagentExecutor._build_initial_state` assembles deferral after policy filtering via the shared `assemble_deferred_tools` (fail-closed), appends the `tool_search` tool, injects the `<available-deferred-tools>` section into the subagent's `SystemMessage`, and threads the setup to `_create_agent`, which attaches `DeferredToolFilterMiddleware` through `build_subagent_runtime_middlewares(deferred_setup=...)`. Subagents thus withhold full MCP schemas until promotion, same as the lead agent; each task run gets a fresh `ThreadState` so promotion is isolated per run
**Checkpointer isolation**: Subagent graphs are compiled with `checkpointer=False` to avoid inheriting the parent run's checkpointer, since subagents are one-shot and never resume.

### Tool System (`packages/harness/deerflow/tools/`)

`get_available_tools(groups, include_mcp, model_name, subagent_enabled)` assembles:
1. **Config-defined tools** - Resolved from `config.yaml` via `resolve_variable()`
2. **MCP tools** - From enabled MCP servers (lazy initialized, cached with mtime invalidation)
3. **Built-in tools**:
   - `present_files` - Make output files visible to user (only `/mnt/user-data/outputs`)
   - `ask_clarification` - Request clarification (intercepted by ClarificationMiddleware → interrupts)
   - `view_image` - Read image as base64 (added only if model supports vision)
   - `setup_agent` - Bootstrap-only: persist a brand-new custom agent's `SOUL.md` and `config.yaml`. Bound only when `is_bootstrap=True`.
   - `update_agent` - Custom-agent-only: persist self-updates to the current agent's `SOUL.md` / `config.yaml` from inside a normal chat (partial update + atomic write). Bound when `agent_name` is set and `is_bootstrap=False`.
4. **Subagent tool** (if enabled):
   - `task` - Delegate to subagent (description, prompt, subagent_type)

**Community tools** (`packages/harness/deerflow/community/`): optional integrations, each in its own subpackage and wired through `config.yaml`. Documented examples:
- `tavily/` - Web search (5 results default) and web fetch (4KB limit)
- `jina_ai/` - Web fetch via Jina reader API with readability extraction
- `firecrawl/` - Web scraping via Firecrawl API
- `image_search/` - Image search
- `aio_sandbox/` - Docker-based isolation (`AioSandboxProvider`)

Additional providers also live here (`brave`, `browserless`, `ddg_search`, `exa`, `fastcrw`, `groundroute`, `infoquest`, `searxng`, `serper`); see each subpackage for specifics.

**ACP agent tools**:
- `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}/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/`)

- Uses `langchain-mcp-adapters` `MultiServerMCPClient` for multi-server management
- **Lazy initialization**: Tools loaded on first use via `get_cached_mcp_tools()`
- **Cache invalidation**: Detects config file changes via mtime comparison
- **Transports**: stdio (command-based), SSE, HTTP
- **OAuth (HTTP/SSE)**: Supports token endpoint flows (`client_credentials`, `refresh_token`) with automatic token refresh + Authorization header injection
- **Stdio file outputs**: Persistent stdio sessions are scoped by `user_id:thread_id`. For stdio transports only, DeerFlow pins the subprocess default `cwd` to the thread workspace and `TMPDIR`/`TMP`/`TEMP` to `workspace/.mcp/tmp/`, unless the operator explicitly configured `cwd` or temp env values. SSE/HTTP transports skip this filesystem prep entirely.
- **Stdio path translation**: MCP-returned local file references are not copied. If a `ResourceLink` or conservative free-text path resolves to an existing file inside the thread's mounted user-data tree, it is translated deterministically to `/mnt/user-data/...`; paths outside that tree remain unchanged.
- **Runtime updates**: Gateway API saves to extensions_config.json; the Gateway-embedded runtime detects changes via mtime

### Skills System (`packages/harness/deerflow/skills/`)

- **Location**: `deer-flow/skills/{public,custom}/`
- **Format**: Directory with `SKILL.md` (YAML frontmatter: name, description, license, allowed-tools)
- **Loading**: `load_skills()` recursively scans `skills/{public,custom}` for `SKILL.md`, parses metadata, and reads enabled state from extensions_config.json
- **Injection**: Enabled skills listed in agent system prompt with container paths
- **Slash activation**: `/skill-name task` loads that enabled skill's `SKILL.md` for the current model call only. The resolver rejects leading whitespace, missing separators, reserved channel commands (`/new`, `/help`, `/bootstrap`, `/status`, `/models`, `/memory`), disabled skills, and skills outside a custom agent's whitelist.
- **Installation**: `POST /api/skills/install` extracts .skill ZIP archive to custom/ directory

### Model Factory (`packages/harness/deerflow/models/factory.py`)

- `create_chat_model(name, thinking_enabled)` instantiates LLM from config via reflection
- Supports `thinking_enabled` flag with per-model `when_thinking_enabled` overrides
- Supports vLLM-style thinking toggles via `when_thinking_enabled.extra_body.chat_template_kwargs.enable_thinking` for Qwen reasoning models, while normalizing legacy `thinking` configs for backward compatibility
- Supports `supports_vision` flag for image understanding models
- Config values starting with `$` resolved as environment variables
- Missing provider modules surface actionable install hints from reflection resolvers (for example `uv add langchain-google-genai`)

### vLLM Provider (`packages/harness/deerflow/models/vllm_provider.py`)

- `VllmChatModel` subclasses `langchain_openai:ChatOpenAI` for vLLM 0.19.0 OpenAI-compatible endpoints
- Preserves vLLM's non-standard assistant `reasoning` field on full responses, streaming deltas, and follow-up tool-call turns
- Designed for configs that enable thinking through `extra_body.chat_template_kwargs.enable_thinking` on vLLM 0.19.0 Qwen reasoning models, while accepting the older `thinking` alias

### IM Channels System (`app/channels/`)

Bridges external messaging platforms (Feishu, Slack, Telegram, Discord, DingTalk) to the DeerFlow agent via Gateway's LangGraph-compatible API.

**Architecture**: Channels communicate with Gateway through the `langgraph-sdk` HTTP client (same as the frontend), ensuring threads are created and managed server-side. The internal SDK client injects process-local internal auth plus a matching CSRF cookie/header pair so Gateway accepts state-changing thread/run requests from channel workers without relying on browser session cookies.

**Components**:
- `message_bus.py` - Async pub/sub hub (`InboundMessage` → queue → dispatcher; `OutboundMessage` → callbacks → channels)
- `store.py` - JSON-file persistence mapping `channel_name:chat_id[:topic_id]` → `thread_id` (keys are `channel:chat` for root conversations and `channel:chat:topic` for threaded conversations)
- `manager.py` - Core dispatcher: creates threads via `client.threads.create()`, routes commands, keeps Slack/Discord on `client.runs.wait()`, and uses `client.runs.stream(["messages-tuple", "values"])` for Feishu/Telegram incremental outbound updates
- `base.py` - Abstract `Channel` base class (start/stop/send lifecycle)
- `service.py` - Manages lifecycle of all configured channels from `config.yaml`
- `slack.py` / `feishu.py` / `telegram.py` / `discord.py` / `dingtalk.py` - Platform-specific implementations (`feishu.py` tracks the running card `message_id` in memory and patches the same card in place; `telegram.py` registers the "Working on it..." placeholder as the stream target and edits it in place via `editMessageText`; `dingtalk.py` optionally uses AI Card streaming for in-place updates when `card_template_id` is configured)
- `app/gateway/routers/channel_connections.py` - Browser-facing user connection and disconnect APIs
- `deerflow.persistence.channel_connections` - SQL-backed user-owned connection, optional credential, connect state, and conversation store

**Message Flow**:
1. External platform -> Channel impl -> `MessageBus.publish_inbound()`
2. `ChannelManager._dispatch_loop()` consumes from queue
3. For user-owned channel connections, incoming messages carry `connection_id`, `owner_user_id`, and `workspace_id`; `owner_user_id` becomes the DeerFlow run `user_id`, while the raw platform user id remains `channel_user_id`
4. For chat: look up/create thread through Gateway's LangGraph-compatible API
5. Feishu/Telegram chat: `runs.stream()` → accumulate AI text → publish multiple outbound updates (`is_final=False`) → publish final outbound (`is_final=True`)
6. Slack/Discord chat: `runs.wait()` → extract final response → publish outbound
7. Feishu channel sends one running reply card up front, then patches the same card for each outbound update (card JSON sets `config.update_multi=true` for Feishu's patch API requirement)
8. Telegram streaming: the "Working on it..." placeholder message is registered as the stream target; non-final updates `editMessageText` it in place (channel-side throttle: 1s in private chats, 3s in groups due to Telegram's 20 msg/min group cap; 4096-char truncation; rate-limited updates dropped); the final update performs the last edit and splits >4096 texts into follow-up messages
9. DingTalk AI Card mode (when `card_template_id` configured): `runs.stream()` → create card with initial text → stream updates via `PUT /v1.0/card/streaming` → finalize on `is_final=True`. Falls back to `sampleMarkdown` if card creation or streaming fails
10. For commands (`/new`, `/status`, `/models`, `/memory`, `/help`): handle locally or query Gateway API
11. Outbound → channel callbacks → platform reply

**Owner-scoped file storage**: inbound files, uploads, and output artifacts are staged under the DeerFlow owner's bucket so they land where the agent run reads/writes (`users/{user_id}/threads/{thread_id}/user-data/{uploads,outputs}`). `ChannelManager._handle_chat` resolves the storage owner once via `_channel_storage_user_id(msg)` (sanitized owner id, falling back to `safe(msg.user_id)` for unbound auth-enabled channels — mirroring `_resolve_run_params`'s run identity; `None` only when no identity is available) and threads it as the `user_id=` kwarg through the file pipeline:
- `Channel.receive_file(msg, thread_id, user_id=...)` — owner-bound channels persist downloaded files under the owner's bucket instead of the default bucket
- `_ingest_inbound_files(...)` and the underlying `ensure_uploads_dir` / `get_uploads_dir` — owner-scoped via the same kwarg
- `_resolve_attachments` / `_prepare_artifact_delivery` — resolve output artifacts from the bound owner's bucket
The cached value is reused for both the blocking (`runs.wait`) and streaming (`_handle_streaming_chat`) paths, so uploads and artifact delivery always target the same bucket even if a channel returns a rewritten `InboundMessage` from `receive_file`. The bucket id matches the memory bucket resolved by `_resolve_memory_user_id` (both normalize through `make_safe_user_id`).

**Configuration** (`config.yaml` -> `channels`):
- `langgraph_url` - LangGraph-compatible Gateway API base URL (default: `http://localhost:8001/api`)
- `gateway_url` - Gateway API URL for auxiliary commands (default: `http://localhost:8001`)
- In Docker Compose, IM channels run inside the `gateway` container, so `localhost` points back to that container. Use `http://gateway:8001/api` for `langgraph_url` and `http://gateway:8001` for `gateway_url`, or set `DEER_FLOW_CHANNELS_LANGGRAPH_URL` / `DEER_FLOW_CHANNELS_GATEWAY_URL`.
- Per-channel configs: `feishu` (app_id, app_secret), `slack` (bot_token, app_token), `telegram` (bot_token), `dingtalk` (client_id, client_secret, optional `card_template_id` for AI Card streaming)

**User-owned channel connections** (`config.yaml` -> `channel_connections`):
- Disabled by default. It is a user-binding layer on top of the existing `channels.*` runtime config, not a replacement for provider bot credentials.
- No public IP, OAuth callback URL, or provider webhook route is required by the current implementation.
- Telegram uses a deep-link `/start <code>` flow over the existing long-polling worker. Slack, Discord, Feishu/Lark, DingTalk, WeChat, and WeCom use `/connect <code>` over their existing outbound channel workers.
- Frontend APIs: `GET /api/channels/providers`, `GET /api/channels/connections`, `POST /api/channels/{provider}/connect`, and `DELETE /api/channels/connections/{connection_id}`.
- Browser APIs remain protected by normal Gateway auth/CSRF. Provider messages arrive through the already-configured channel workers.
- Provider-level `connection_status` reflects the user's newest connection row. With no binding it is `not_connected`, except in auth-disabled local mode where a configured running channel reports `connected` because all channel messages already route to the default user.
- Slack replies use the configured operator bot token from `channels.slack` unless per-connection credentials are present; unreadable or corrupt stored credentials are treated as unavailable.
- Telegram, Slack, Discord, Feishu/Lark, DingTalk, WeChat, and WeCom workers resolve incoming platform identities to connection records before reaching `ChannelManager`.
- **Connect-code ordering vs `allowed_users`**: inbound workers consume a valid `/connect <code>` (or Telegram `/start <code>`) **before** applying the `allowed_users` filter, so a newly allowlisted-but-unbound user can bootstrap their first bind via the browser flow. Consequence: `allowed_users` is **not** a bind-time defense — any sender who possesses a valid code can consume it (not only allowlisted users). The bind security model rests on the code's confidentiality: `secrets.token_urlsafe(16)`, 600 s TTL, one-time `consume_oauth_state`, and codes surfaced only in the initiating browser (never echoed to chat). `allowed_users` still gates ordinary (non-bind) messages.
- **Single-active-owner transfer semantics**: an external identity is keyed by `(provider, external_account_id, workspace_id)`. The latest successful bind wins — `upsert_connection` revokes other owners' active rows for the same identity (ownership transfer). This invariant is enforced at the DB layer by the partial unique index `uq_channel_connection_active_identity` (`WHERE status != 'revoked'`), so concurrent connects from different owners cannot both end `connected`; the losing writer retries against the now-visible state. `find_connection_by_external_identity` therefore resolves deterministically.
- See `backend/docs/IM_CHANNEL_CONNECTIONS.md` for provider setup and operational notes.


### Memory System (`packages/harness/deerflow/agents/memory/`)

**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); 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

**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`
- Custom agent definitions (`SOUL.md` + `config.yaml`) are also per-user at `{base_dir}/users/{user_id}/agents/{agent_name}/`. The legacy shared layout `{base_dir}/agents/{agent_name}/` remains read-only fallback for unmigrated installations
- `user_id` is resolved via `get_effective_user_id()` from `deerflow.runtime.user_context`
- The `/api/memory*` endpoints resolve the owner through `_resolve_memory_user_id(request)`: trusted internal callers (IM channel workers carrying the `X-DeerFlow-Owner-User-Id` header, e.g. a bound `/memory` command) act for the connection owner; browser/API callers fall back to `get_effective_user_id()`. The header is only honored after `AuthMiddleware` validated the internal token, mirroring `get_trusted_internal_owner_user_id` used by the threads router
- 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`, `threads/`, and `agents/` into per-user layout. Supports `--dry-run` (preview changes) and `--user-id USER_ID` (assign unowned legacy data to a user, defaults to `default`).

**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), 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, 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

**Token counting** (`packages/harness/deerflow/agents/memory/prompt.py`):
- `_count_tokens` budgets the injection. In default `tiktoken` mode, the encoding is loaded lazily and cached.
- Failed tiktoken loads are cached with a timestamp. During the fixed cooldown (`_TIKTOKEN_RETRY_COOLDOWN_S`, 600s), callers fall back to char estimation immediately instead of re-triggering the blocking BPE download; after the cooldown, transient outages can self-heal without a restart.
- In-flight loads are cached as a LOADING sentinel so concurrent callers fall back instead of spawning more blocking threads.
- Set `memory.token_counting: char` to skip tiktoken entirely and use the network-free CJK-aware char estimate.

Focused regression coverage for the updater lives in `backend/tests/test_memory_updater.py`.

**Configuration** (`config.yaml` → `memory`):
- `enabled` / `injection_enabled` - Master switches
- `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)
- `max_injection_tokens` - Token limit for prompt injection (2000)
- `token_counting` - Token counting strategy for the injection budget: `tiktoken` (default, accurate but may download BPE data from a public endpoint on first use — can block for a long time in network-restricted environments, see issues #3402/#3429) or `char` (network-free CJK-aware char estimate, never touches tiktoken)

### Reflection System (`packages/harness/deerflow/reflection/`)

- `resolve_variable(path)` - Import module and return variable (e.g., `module.path:variable_name`)
- `resolve_class(path, base_class)` - Import and validate class against base class

### Schema Migrations (`packages/harness/deerflow/persistence/migrations/`)

DeerFlow's application tables (`runs`, `threads_meta`, `feedback`, `users`, `run_events`, plus the four `channel_*` tables) are owned by alembic via a **hybrid bootstrap** strategy. LangGraph's checkpointer tables (`checkpoints`, `checkpoint_blobs`, `checkpoint_writes`, `checkpoint_migrations`) live in the same database but are owned by LangGraph and excluded from alembic's view via `migrations/_env_filters.py::include_object`.

**Convention**: every ORM model change (new column, new table, new index) MUST ship as an alembic revision under `migrations/versions/`. The Gateway runs `alembic upgrade head` automatically on startup; users do not run `alembic` manually in production.

**Hybrid bootstrap** (`persistence/bootstrap.py::bootstrap_schema`, invoked from `persistence/engine.py::init_engine`):

| DB state                                  | Action                                  |
|-------------------------------------------|-----------------------------------------|
| empty (no DeerFlow tables)                | `create_all` + `alembic stamp head`     |
| legacy (DeerFlow tables, no `alembic_version`) | `create_all` (baseline tables only, backfill) + `alembic stamp 0001_baseline` + `upgrade head` |
| versioned (`alembic_version` row exists)  | `alembic upgrade head`                  |

The legacy branch handles pre-alembic databases that already have at least one DeerFlow-owned table. `create_all` runs first because stamping at `0001_baseline` makes alembic skip the baseline's own `create_table` DDL on the subsequent upgrade — so any baseline table introduced into `Base.metadata` after the user's DB was first provisioned (e.g. the `channel_*` tables from PR #1930 for users upgrading across multiple releases) would otherwise never be created, and the first request hitting that table would 500 with `no such table`. The backfill is **restricted to `_BASELINE_TABLE_NAMES`** so it does not also create tables that future revisions introduce — those revisions' own `op.create_table` would otherwise fail with `relation already exists`. A guard test pins `_BASELINE_TABLE_NAMES` against `0001_baseline.upgrade()`'s actual output, so editing 0001 to add or remove a table forces a matching update to the constant. Column-level shape (pre-#3658 vs post-#3658 vs manual-ALTER for `token_usage_by_model`) is answered by each `versions/*.py` revision via the idempotent helpers in `migrations/_helpers.py` (`safe_add_column` / `safe_drop_column`) which no-op when the change is already present and `logger.warning` on shape drift. **Adding a new ORM column / table only requires a new revision file — no edit to `bootstrap.py` is needed** *unless* the new revision adds a new baseline table (rare; only happens when a new model is part of the baseline rather than introduced by its own revision).

The empty-DB path keeps using `create_all` because `Base.metadata` is the only authoritative schema source — `create_all` renders both SQLite (JSON, type affinity) and Postgres (JSONB, partial indexes) correctly without anyone having to keep a hand-written baseline in lockstep. `0001_baseline.upgrade()` is therefore almost never executed in practice; it exists as a stamp target + chain root.

**Concurrency safety**: Postgres uses `pg_advisory_lock` to serialise concurrent Gateway instances. SQLite uses a per-engine `asyncio.Lock` for same-process startup and is best-effort across processes via SQLite's file-level write lock + `PRAGMA busy_timeout`; multi-instance deployments should use Postgres. Column revisions in `versions/` additionally use idempotent helpers (`_helpers.py::safe_add_column`, `safe_drop_column`) so repeated post-baseline changes and retries are no-ops when the change is already present.

**Authoring a new revision**:
```bash
cd backend && make migrate-rev MSG="add foo column to runs"
```
This invokes `alembic revision --autogenerate` against the live ORM models. Review the generated file under `migrations/versions/` and switch raw `op.add_column` / `op.drop_column` calls to the idempotent helpers from `_helpers.py` before committing. There is no `make migrate` / `make migrate-stamp` target on purpose — the only execution path is Gateway startup, which keeps operational mistakes off the table.

**Where things live**:
- `migrations/env.py` — alembic env, delegates filter to `_env_filters.py`, sets `render_as_batch=True` for SQLite ALTER support
- `migrations/_env_filters.py::include_object` — drops LangGraph checkpointer tables from alembic's view
- `migrations/_helpers.py` — `safe_add_column` / `safe_drop_column`
- `migrations/versions/0001_baseline.py` — chain root, matches the schema `create_all` produces from `Base.metadata`
- `migrations/versions/0002_runs_token_usage.py` — fixes issue #3682
- `persistence/bootstrap.py` — `bootstrap_schema(engine, backend=...)`, the three-branch decision + locking
- Tests: `tests/test_persistence_bootstrap.py` (branches), `tests/test_persistence_bootstrap_concurrency.py` (concurrency), `tests/test_persistence_bootstrap_regression.py` (issue #3682), `tests/test_persistence_migrations_env.py` (filter), `tests/blocking_io/test_persistence_bootstrap.py` (asyncio.to_thread anchor)

### Terminal Workbench / TUI (`packages/harness/deerflow/tui/`)

A terminal-native UI over the embedded harness, exposed as the `deerflow` console script (`[project.scripts]` in `packages/harness/pyproject.toml`). It is a UI shell over `DeerFlowClient` and does **not** fork agent behavior. `textual` is an optional dependency (`deerflow-harness[tui]`; also in the backend dev group); the console script degrades to headless help when it is absent. Full guide: [docs/TUI.md](docs/TUI.md).

**Module layout** (all layers except `app.py` are pure / Textual-free and unit-tested directly):
- `cli.py` — `plan_launch()` (pure launch-mode decision) + headless `--print` / `--json` + `main()` entry point. TTY → TUI, else headless help. Uses an **absolute** `from deerflow.tui.app import run_tui` so the `app.py` module name doesn't trip `test_harness_boundary.py` (which records relative import module names verbatim).
- `view_state.py` — `ViewState` + `reduce(state, action)`, the testable heart. Rows: user / assistant / tool / system. Title captured from `values` events.
- `runtime.py` — `translate(StreamEvent) -> [Action]` (pure) + `stream_actions()` which brackets a run with `RunStarted`/`RunEnded` and turns model errors into an `AssistantError` row.
- `message_format.py` / `command_registry.py` / `input_history.py` / `render.py` / `theme.py` — pure helpers (tool summaries, slash registry + `resolve()`, ↑/↓ history, Rich renderers).
- `app.py` — Textual `App`. Runs `DeerFlowClient.stream()` (sync) on a worker thread and marshals actions to the UI thread via `call_from_thread`. Slash palette + model/thread modal pickers; priority key bindings gated by `check_action` so they never steal keys from overlays or the composer.
- `session.py` / `persistence.py` — builds the client + checkpointer and the `ThreadMetaWriter`.

**Web UI visibility**: the Web UI lists threads from the `threads_meta` SQL table (user-scoped), not the checkpointer. `persistence.py` writes a `threads_meta` row under the default user (`"default"`) into the same DB the Gateway reads — via the harness-only `deerflow.persistence.engine.init_engine_from_config()` — so TUI sessions appear in the Web UI sidebar **without** running the Gateway. Best-effort: a no-op on the `memory` backend. All DB work runs on one long-lived background event loop (a SQLAlchemy async engine is bound to its creating loop).

**Tests**: `tests/test_tui_*.py` — pure layers via plain pytest, the app/palette/overlays via Textual's pilot harness with a fake in-process session, and `test_tui_persistence.py` for the `threads_meta` round-trip.

### Tracing System (`packages/harness/deerflow/tracing/`)

LangSmith and Langfuse are both supported. The wiring lives in two layers:

- `factory.py::build_tracing_callbacks()` — returns the LangChain `CallbackHandler` list for the providers currently enabled via env vars (`LANGSMITH_TRACING`, `LANGFUSE_TRACING`, etc.). The handlers are attached at the **graph invocation root** for in-graph runs (`make_lead_agent` and `DeerFlowClient.stream` both append them to `config["callbacks"]` before invoking the graph) so a single run produces one trace with all node / LLM / tool calls as child spans. Standalone callers — anything that invokes a model outside such a graph (e.g. `MemoryUpdater`) — keep `create_chat_model`'s default `attach_tracing=True`, which falls back to model-level callback attachment.
- `metadata.py::build_langfuse_trace_metadata()` — builds the Langfuse-reserved trace attributes for `RunnableConfig.metadata`. The Langfuse v4 `langchain.CallbackHandler` lifts these onto the root trace (see its `_parse_langfuse_trace_attributes`), but only when it sees `on_chain_start(parent_run_id=None)` — which is why the callbacks have to live at the graph root, not the model.

**Trace-attribute injection points**: both `runtime/runs/worker.py::run_agent` (gateway path) and `client.py::DeerFlowClient.stream` (embedded path) merge the metadata into `config["metadata"]` right before constructing the graph. `subagents/executor.py::_aexecute` does the same for every subagent run so subagent traces group under the parent thread's session card (carrying the parent `thread_id` → `langfuse_session_id`, the user_id captured at `task_tool` → `langfuse_user_id`, and a `subagent:<normalized-name>` trace name). Caller-supplied keys win via `setdefault`, so an external `session_id` override is preserved. Field mapping:

| Langfuse field         | Source                                       |
|-----------------------|----------------------------------------------|
| `langfuse_session_id` | LangGraph `thread_id`                         |
| `langfuse_user_id`    | `get_effective_user_id()` (`default` in no-auth); for subagents, captured from `runtime.context` at `task_tool` time via `resolve_runtime_user_id()` |
| `langfuse_trace_name` | `RunRecord.assistant_id` / client `agent_name` (defaults to `lead-agent`); for subagents, `subagent:<name>` (lowercased, `_` → `-`) |
| `langfuse_tags`       | `env:<DEER_FLOW_ENV>` + `model:<model_name>`  |

Returns `{}` when Langfuse is not in the enabled providers — LangSmith-only deployments are unaffected. Set `DEER_FLOW_ENV` (or `ENVIRONMENT`) to tag traces by deployment environment. Tests live in `tests/test_tracing_factory.py`, `tests/test_tracing_metadata.py`, `tests/test_worker_langfuse_metadata.py`, `tests/test_client_langfuse_metadata.py`, and `tests/test_subagent_executor.py::TestSubagentTracingWiring`.

### Config Schema

**`config.yaml`** key sections:
- `models[]` - LLM configs with `use` class path, `supports_thinking`, `supports_vision`, provider-specific fields
- vLLM reasoning models should use `deerflow.models.vllm_provider:VllmChatModel`; for Qwen-style parsers prefer `when_thinking_enabled.extra_body.chat_template_kwargs.enable_thinking`, and DeerFlow will also normalize the older `thinking` alias
- `tools[]` - Tool configs with `use` variable path and `group`
- `tool_groups[]` - Logical groupings for tools
- `sandbox.use` - Sandbox provider class path
- `skills.path` / `skills.container_path` - Host and container paths to skills directory
- `title` - Auto-title generation (enabled, max_words, max_chars, prompt_template)
- `summarization` - Context summarization (enabled, trigger conditions, keep policy)
- `subagents.enabled` - Master switch for subagent delegation
- `memory` - Memory system (enabled, storage_path, debounce_seconds, model_name, max_facts, fact_confidence_threshold, injection_enabled, max_injection_tokens)

**`extensions_config.json`**:
- `mcpServers` - Map of server name → config (enabled, type, command, args, env, url, headers, oauth, description)
- `skills` - Map of skill name → state (enabled)

Both can be modified at runtime via Gateway API endpoints or `DeerFlowClient` methods.

### Embedded Client (`packages/harness/deerflow/client.py`)

`DeerFlowClient` provides direct in-process access to all DeerFlow capabilities without HTTP services. All return types align with the Gateway API response schemas, so consumer code works identically in HTTP and embedded modes.

**Architecture**: Imports the same `deerflow` modules that Gateway API uses. Shares the same config files and data directories. No FastAPI dependency.

**Agent Conversation**:
- `chat(message, thread_id)` — synchronous, accumulates streaming deltas per message-id and returns the final AI text
- `stream(message, thread_id)` — subscribes to LangGraph `stream_mode=["values", "messages", "custom"]` and yields `StreamEvent`:
  - `"values"` — full state snapshot (title, messages, artifacts); AI text already delivered via `messages` mode is **not** re-synthesized here to avoid duplicate deliveries
  - `"messages-tuple"` — per-chunk update: for AI text this is a **delta** (concat per `id` to rebuild the full message); tool calls and tool results are emitted once each
  - `"custom"` — forwarded from `StreamWriter`
  - `"end"` — stream finished (carries cumulative `usage` counted once per message id)
- Agent created lazily via `create_agent()` + `build_middlewares()`, same as `make_lead_agent`
- Supports `checkpointer` parameter for state persistence across turns
- `reset_agent()` forces agent recreation (e.g. after memory or skill changes)
- See [docs/STREAMING.md](docs/STREAMING.md) for the full design: why Gateway and DeerFlowClient are parallel paths, LangGraph's `stream_mode` semantics, the per-id dedup invariants, and regression testing strategy

**Gateway Equivalent Methods** (replaces Gateway API):

| Category | Methods | Return format |
|----------|---------|---------------|
| Models | `list_models()`, `get_model(name)` | `{"models": [...]}`, `{name, display_name, ...}` |
| MCP | `get_mcp_config()`, `update_mcp_config(servers)` | `{"mcp_servers": {...}}` |
| Skills | `list_skills()`, `get_skill(name)`, `update_skill(name, enabled)`, `install_skill(path)` | `{"skills": [...]}` |
| Memory | `get_memory()`, `reload_memory()`, `get_memory_config()`, `get_memory_status()` | dict |
| Uploads | `upload_files(thread_id, files)`, `list_uploads(thread_id)`, `delete_upload(thread_id, filename)` | `{"success": true, "files": [...]}`, `{"files": [...], "count": N}` |
| Artifacts | `get_artifact(thread_id, path)` → `(bytes, mime_type)` | tuple |

**Key difference from Gateway**: Upload accepts local `Path` objects instead of HTTP `UploadFile`, rejects directory paths before copying, and reuses a single worker when document conversion must run inside an active event loop. Artifact returns `(bytes, mime_type)` instead of HTTP Response. The new Gateway-only thread cleanup route deletes `.deer-flow/threads/{thread_id}` after LangGraph thread deletion; there is no matching `DeerFlowClient` method yet. `update_mcp_config()` and `update_skill()` automatically invalidate the cached agent.

**Tests**: `tests/test_client.py` (77 unit tests including `TestGatewayConformance`), `tests/test_client_live.py` (live integration tests, requires config.yaml)

**Gateway Conformance Tests** (`TestGatewayConformance`): Validate that every dict-returning client method conforms to the corresponding Gateway Pydantic response model. Each test parses the client output through the Gateway model — if Gateway adds a required field that the client doesn't provide, Pydantic raises `ValidationError` and CI catches the drift. Covers: `ModelsListResponse`, `ModelResponse`, `SkillsListResponse`, `SkillResponse`, `SkillInstallResponse`, `McpConfigResponse`, `UploadResponse`, `MemoryConfigResponse`, `MemoryStatusResponse`.

## Development Workflow

### Test-Driven Development (TDD) — MANDATORY

**Every new feature or bug fix MUST be accompanied by unit tests. No exceptions.**

- Write tests in `backend/tests/` following the existing naming convention `test_<feature>.py`
- Run the full suite before and after your change: `make test`
- Tests must pass before a feature is considered complete
- For lightweight config/utility modules, prefer pure unit tests with no external dependencies
- If a module causes circular import issues in tests, add a `sys.modules` mock in `tests/conftest.py` (see existing example for `deerflow.subagents.executor`)

```bash
# Run all tests
make test

# Run a specific test file
PYTHONPATH=. uv run pytest tests/test_<feature>.py -v
```

### Running the Full Application

From the **project root** directory:
```bash
make dev
```

This starts all services and makes the application available at `http://localhost:2026`.

**All startup modes:**

| | **Local Foreground** | **Local Daemon** | **Docker Dev** | **Docker Prod** |
|---|---|---|---|---|
| **Dev** | `./scripts/serve.sh --dev`<br/>`make dev` | `./scripts/serve.sh --dev --daemon`<br/>`make dev-daemon` | `./scripts/docker.sh start`<br/>`make docker-start` | — |
| **Prod** | `./scripts/serve.sh --prod`<br/>`make start` | `./scripts/serve.sh --prod --daemon`<br/>`make start-daemon` | — | `./scripts/deploy.sh`<br/>`make up` |

| Action | Local | Docker Dev | Docker Prod |
|---|---|---|---|
| **Stop** | `./scripts/serve.sh --stop`<br/>`make stop` | `./scripts/docker.sh stop`<br/>`make docker-stop` | `./scripts/deploy.sh down`<br/>`make down` |
| **Restart** | `./scripts/serve.sh --restart [flags]` | `./scripts/docker.sh restart` | — |

**Nginx routing**:
- `/api/langgraph/*` → Gateway embedded runtime (8001), rewritten to `/api/*`
- `/api/*` (other) → Gateway API (8001)
- `/` (non-API) → Frontend (3000)

### Running Backend Services Separately

From the **backend** directory:

```bash
# Gateway API
make gateway
```

Direct access (without nginx):
- Gateway: `http://localhost:8001`

### Frontend Configuration

The frontend uses environment variables to connect to backend services:
- `NEXT_PUBLIC_LANGGRAPH_BASE_URL` - Defaults to `/api/langgraph` (through nginx)
- `NEXT_PUBLIC_BACKEND_BASE_URL` - Defaults to empty string (through nginx)

When using `make dev` from root, the frontend automatically connects through nginx.

## Key Features

### File Upload

Multi-file upload with automatic document conversion:
- Endpoint: `POST /api/threads/{thread_id}/uploads`
- Supports: PDF, PPT, Excel, Word documents (converted via `markitdown`)
- Rejects directory inputs before copying so uploads stay all-or-nothing
- Reuses one conversion worker per request when called from an active event loop
- Files stored in thread-isolated directories under the resolving user's bucket (`users/{user_id}/threads/{thread_id}/user-data/uploads`). For IM channels the owner is threaded explicitly via the `user_id=` kwarg (see IM Channels → Owner-scoped file storage); HTTP/embedded callers resolve it from `get_effective_user_id()`
- Duplicate filenames in a single upload request are auto-renamed with `_N` suffixes so later files do not truncate earlier files
- Agent receives uploaded file list via `UploadsMiddleware`

See [docs/FILE_UPLOAD.md](docs/FILE_UPLOAD.md) for details.

### Plan Mode

TodoList middleware for complex multi-step tasks:
- Controlled via runtime config: `config.configurable.is_plan_mode = True`
- Provides `write_todos` tool for task tracking
- One task in_progress at a time, real-time updates

See [docs/plan_mode_usage.md](docs/plan_mode_usage.md) for details.

### Context Summarization

Automatic conversation summarization when approaching token limits:
- Configured in `config.yaml` under `summarization` key
- Trigger types: tokens, messages, or fraction of max input
- Keeps recent messages while summarizing older ones

See [docs/summarization.md](docs/summarization.md) for details.

### Vision Support

For models with `supports_vision: true`:
- `ViewImageMiddleware` processes images in conversation
- `view_image_tool` added to agent's toolset
- Images automatically converted to base64 and injected into state

## Code Style

- Uses `ruff` for linting and formatting
- Line length: 240 characters
- Python 3.12+ with type hints
- Double quotes, space indentation

## Documentation

See `docs/` directory for detailed documentation:
- [CONFIGURATION.md](docs/CONFIGURATION.md) - Configuration options
- [ARCHITECTURE.md](docs/ARCHITECTURE.md) - Architecture details
- [API.md](docs/API.md) - API reference
- [SETUP.md](docs/SETUP.md) - Setup guide
- [FILE_UPLOAD.md](docs/FILE_UPLOAD.md) - File upload feature
- [PATH_EXAMPLES.md](docs/PATH_EXAMPLES.md) - Path types and usage
- [summarization.md](docs/summarization.md) - Context summarization
- [plan_mode_usage.md](docs/plan_mode_usage.md) - Plan mode with TodoList
