diff --git a/.env.example b/.env.example
index f443818b3..41d87a8c7 100644
--- a/.env.example
+++ b/.env.example
@@ -1,3 +1,6 @@
+# Serper API Key (Google Search) - https://serper.dev
+SERPER_API_KEY=your-serper-api-key
+
 # TAVILY API Key
 TAVILY_API_KEY=your-tavily-api-key
 
diff --git a/README.md b/README.md
index c67fdc005..0fc8f173e 100644
--- a/README.md
+++ b/README.md
@@ -251,7 +251,7 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) for detailed Docker development guide.
 
 If you prefer running services locally:
 
-Prerequisite: complete the "Configuration" steps above first (`make setup`). `make dev` requires a valid `config.yaml` in the project root (can be overridden via `DEER_FLOW_CONFIG_PATH`). Run `make doctor` to verify your setup before starting.
+Prerequisite: complete the "Configuration" steps above first (`make setup`). `make dev` requires a valid `config.yaml` in the project root. Set `DEER_FLOW_PROJECT_ROOT` to define that root explicitly, or `DEER_FLOW_CONFIG_PATH` to point at a specific config file. Runtime state defaults to `.deer-flow` under the project root and can be moved with `DEER_FLOW_HOME`; skills default to `skills/` under the project root and can be moved with `DEER_FLOW_SKILLS_PATH`. Run `make doctor` to verify your setup before starting.
 On Windows, run the local development flow from Git Bash. Native `cmd.exe` and PowerShell shells are not supported for the bash-based service scripts, and WSL is not guaranteed because some scripts rely on Git for Windows utilities such as `cygpath`.
 
 1. **Check prerequisites**:
diff --git a/README_zh.md b/README_zh.md
index 6e4a618c7..d5317082e 100644
--- a/README_zh.md
+++ b/README_zh.md
@@ -194,7 +194,7 @@ make down   # 停止并移除容器
 
 如果你更希望直接在本地启动各个服务：
 
-前提：先完成上面的“配置”步骤（`make config` 和模型 API key 配置）。`make dev` 需要有效配置文件，默认读取项目根目录下的 `config.yaml`，也可以通过 `DEER_FLOW_CONFIG_PATH` 覆盖。
+前提：先完成上面的“配置”步骤（`make config` 和模型 API key 配置）。`make dev` 需要有效配置文件，默认读取项目根目录下的 `config.yaml`。可以用 `DEER_FLOW_PROJECT_ROOT` 显式指定项目根目录，也可以用 `DEER_FLOW_CONFIG_PATH` 指向某个具体配置文件。运行期状态默认写到项目根目录下的 `.deer-flow`，可用 `DEER_FLOW_HOME` 覆盖；skills 默认读取项目根目录下的 `skills/`，可用 `DEER_FLOW_SKILLS_PATH` 覆盖。
 在 Windows 上，请使用 Git Bash 运行本地开发流程。基于 bash 的服务脚本不支持直接在原生 `cmd.exe` 或 PowerShell 中执行，且 WSL 也不保证可用，因为部分脚本依赖 Git for Windows 的 `cygpath` 等工具。
 
 1. **检查依赖环境**：
diff --git a/backend/app/channels/manager.py b/backend/app/channels/manager.py
index 3bd674596..f200a7145 100644
--- a/backend/app/channels/manager.py
+++ b/backend/app/channels/manager.py
@@ -420,7 +420,13 @@ async def _ingest_inbound_files(thread_id: str, msg: InboundMessage) -> list[dic
     if not msg.files:
         return []
 
-    from deerflow.uploads.manager import claim_unique_filename, ensure_uploads_dir, normalize_filename
+    from deerflow.uploads.manager import (
+        UnsafeUploadPathError,
+        claim_unique_filename,
+        ensure_uploads_dir,
+        normalize_filename,
+        write_upload_file_no_symlink,
+    )
 
     uploads_dir = ensure_uploads_dir(thread_id)
     seen_names = {entry.name for entry in uploads_dir.iterdir() if entry.is_file()}
@@ -471,7 +477,10 @@ async def _ingest_inbound_files(thread_id: str, msg: InboundMessage) -> list[dic
 
             dest = uploads_dir / safe_name
             try:
-                dest.write_bytes(data)
+                dest = write_upload_file_no_symlink(uploads_dir, safe_name, data)
+            except UnsafeUploadPathError:
+                logger.warning("[Manager] skipping inbound file with unsafe destination: %s", safe_name)
+                continue
             except Exception:
                 logger.exception("[Manager] failed to write inbound file: %s", dest)
                 continue
diff --git a/backend/app/gateway/routers/threads.py b/backend/app/gateway/routers/threads.py
index 484582839..cb048152e 100644
--- a/backend/app/gateway/routers/threads.py
+++ b/backend/app/gateway/routers/threads.py
@@ -13,11 +13,11 @@ matching the LangGraph Platform wire format expected by the
 from __future__ import annotations
 
 import logging
-import time
 import uuid
 from typing import Any
 
 from fastapi import APIRouter, HTTPException, Request
+from langgraph.checkpoint.base import empty_checkpoint
 from pydantic import BaseModel, Field, field_validator
 
 from app.gateway.authz import require_permission
@@ -26,6 +26,7 @@ from app.gateway.utils import sanitize_log_param
 from deerflow.config.paths import Paths, get_paths
 from deerflow.runtime import serialize_channel_values
 from deerflow.runtime.user_context import get_effective_user_id
+from deerflow.utils.time import coerce_iso, now_iso
 
 logger = logging.getLogger(__name__)
 router = APIRouter(prefix="/api/threads", tags=["threads"])
@@ -233,7 +234,7 @@ async def create_thread(body: ThreadCreateRequest, request: Request) -> ThreadRe
     checkpointer = get_checkpointer(request)
     thread_store = get_thread_store(request)
     thread_id = body.thread_id or str(uuid.uuid4())
-    now = time.time()
+    now = now_iso()
     # ``body.metadata`` is already stripped of server-reserved keys by
     # ``ThreadCreateRequest._strip_reserved`` — see the model definition.
 
@@ -243,8 +244,8 @@ async def create_thread(body: ThreadCreateRequest, request: Request) -> ThreadRe
         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", "")),
+            created_at=coerce_iso(existing_record.get("created_at", "")),
+            updated_at=coerce_iso(existing_record.get("updated_at", "")),
             metadata=existing_record.get("metadata", {}),
         )
 
@@ -262,8 +263,6 @@ async def create_thread(body: ThreadCreateRequest, request: Request) -> ThreadRe
     # Write an empty checkpoint so state endpoints work immediately
     config = {"configurable": {"thread_id": thread_id, "checkpoint_ns": ""}}
     try:
-        from langgraph.checkpoint.base import empty_checkpoint
-
         ckpt_metadata = {
             "step": -1,
             "source": "input",
@@ -281,8 +280,8 @@ async def create_thread(body: ThreadCreateRequest, request: Request) -> ThreadRe
     return ThreadResponse(
         thread_id=thread_id,
         status="idle",
-        created_at=str(now),
-        updated_at=str(now),
+        created_at=now,
+        updated_at=now,
         metadata=body.metadata,
     )
 
@@ -307,8 +306,11 @@ async def search_threads(body: ThreadSearchRequest, request: Request) -> list[Th
         ThreadResponse(
             thread_id=r["thread_id"],
             status=r.get("status", "idle"),
-            created_at=r.get("created_at", ""),
-            updated_at=r.get("updated_at", ""),
+            # ``coerce_iso`` heals legacy unix-second values that
+            # ``MemoryThreadMetaStore`` historically wrote with ``time.time()``;
+            # SQL-backed rows already arrive as ISO strings and pass through.
+            created_at=coerce_iso(r.get("created_at", "")),
+            updated_at=coerce_iso(r.get("updated_at", "")),
             metadata=r.get("metadata", {}),
             values={"title": r["display_name"]} if r.get("display_name") else {},
             interrupts={},
@@ -340,8 +342,8 @@ async def patch_thread(thread_id: str, body: ThreadPatchRequest, request: Reques
     return ThreadResponse(
         thread_id=thread_id,
         status=record.get("status", "idle"),
-        created_at=str(record.get("created_at", "")),
-        updated_at=str(record.get("updated_at", "")),
+        created_at=coerce_iso(record.get("created_at", "")),
+        updated_at=coerce_iso(record.get("updated_at", "")),
         metadata=record.get("metadata", {}),
     )
 
@@ -381,8 +383,8 @@ async def get_thread(thread_id: str, request: Request) -> ThreadResponse:
         record = {
             "thread_id": thread_id,
             "status": "idle",
-            "created_at": ckpt_meta.get("created_at", ""),
-            "updated_at": ckpt_meta.get("updated_at", ckpt_meta.get("created_at", "")),
+            "created_at": coerce_iso(ckpt_meta.get("created_at", "")),
+            "updated_at": coerce_iso(ckpt_meta.get("updated_at", ckpt_meta.get("created_at", ""))),
             "metadata": {k: v for k, v in ckpt_meta.items() if k not in ("created_at", "updated_at", "step", "source", "writes", "parents")},
         }
 
@@ -396,8 +398,8 @@ async def get_thread(thread_id: str, request: Request) -> ThreadResponse:
     return ThreadResponse(
         thread_id=thread_id,
         status=status,
-        created_at=str(record.get("created_at", "")),
-        updated_at=str(record.get("updated_at", "")),
+        created_at=coerce_iso(record.get("created_at", "")),
+        updated_at=coerce_iso(record.get("updated_at", "")),
         metadata=record.get("metadata", {}),
         values=serialize_channel_values(channel_values),
     )
@@ -448,10 +450,10 @@ async def get_thread_state(thread_id: str, request: Request) -> ThreadStateRespo
         values=values,
         next=next_tasks,
         metadata=metadata,
-        checkpoint={"id": checkpoint_id, "ts": str(metadata.get("created_at", ""))},
+        checkpoint={"id": checkpoint_id, "ts": coerce_iso(metadata.get("created_at", ""))},
         checkpoint_id=checkpoint_id,
         parent_checkpoint_id=parent_checkpoint_id,
-        created_at=str(metadata.get("created_at", "")),
+        created_at=coerce_iso(metadata.get("created_at", "")),
         tasks=tasks,
     )
 
@@ -501,7 +503,7 @@ async def update_thread_state(thread_id: str, body: ThreadStateUpdateRequest, re
         channel_values.update(body.values)
 
     checkpoint["channel_values"] = channel_values
-    metadata["updated_at"] = time.time()
+    metadata["updated_at"] = now_iso()
 
     if body.as_node:
         metadata["source"] = "update"
@@ -542,7 +544,7 @@ async def update_thread_state(thread_id: str, body: ThreadStateUpdateRequest, re
         next=[],
         metadata=metadata,
         checkpoint_id=new_checkpoint_id,
-        created_at=str(metadata.get("created_at", "")),
+        created_at=coerce_iso(metadata.get("created_at", "")),
     )
 
 
@@ -609,7 +611,7 @@ async def get_thread_history(thread_id: str, body: ThreadHistoryRequest, request
                     parent_checkpoint_id=parent_id,
                     metadata=user_meta,
                     values=values,
-                    created_at=str(metadata.get("created_at", "")),
+                    created_at=coerce_iso(metadata.get("created_at", "")),
                     next=next_tasks,
                 )
             )
diff --git a/backend/app/gateway/routers/uploads.py b/backend/app/gateway/routers/uploads.py
index 0ecc2266a..a4267f728 100644
--- a/backend/app/gateway/routers/uploads.py
+++ b/backend/app/gateway/routers/uploads.py
@@ -5,7 +5,7 @@ import os
 import stat
 
 from fastapi import APIRouter, Depends, File, HTTPException, Request, UploadFile
-from pydantic import BaseModel
+from pydantic import BaseModel, Field
 
 from app.gateway.authz import require_permission
 from app.gateway.deps import get_config
@@ -15,12 +15,14 @@ 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,
+    UnsafeUploadPathError,
     delete_file_safe,
     enrich_file_listing,
     ensure_uploads_dir,
     get_uploads_dir,
     list_files_in_dir,
     normalize_filename,
+    open_upload_file_no_symlink,
     upload_artifact_url,
     upload_virtual_path,
 )
@@ -30,6 +32,11 @@ logger = logging.getLogger(__name__)
 
 router = APIRouter(prefix="/api/threads/{thread_id}/uploads", tags=["uploads"])
 
+UPLOAD_CHUNK_SIZE = 8192
+DEFAULT_MAX_FILES = 10
+DEFAULT_MAX_FILE_SIZE = 50 * 1024 * 1024
+DEFAULT_MAX_TOTAL_SIZE = 100 * 1024 * 1024
+
 
 class UploadResponse(BaseModel):
     """Response model for file upload."""
@@ -37,6 +44,15 @@ class UploadResponse(BaseModel):
     success: bool
     files: list[dict[str, str]]
     message: str
+    skipped_files: list[str] = Field(default_factory=list)
+
+
+class UploadLimits(BaseModel):
+    """Application-level upload limits exposed to clients."""
+
+    max_files: int
+    max_file_size: int
+    max_total_size: int
 
 
 def _make_file_sandbox_writable(file_path: os.PathLike[str] | str) -> None:
@@ -69,6 +85,72 @@ def _get_uploads_config_value(app_config: AppConfig, key: str, default: object)
     return getattr(uploads_cfg, key, default)
 
 
+def _get_upload_limit(app_config: AppConfig, key: str, default: int, *, legacy_key: str | None = None) -> int:
+    try:
+        value = _get_uploads_config_value(app_config, key, None)
+        if value is None and legacy_key is not None:
+            value = _get_uploads_config_value(app_config, legacy_key, None)
+        if value is None:
+            value = default
+        limit = int(value)
+        if limit <= 0:
+            raise ValueError
+        return limit
+    except Exception:
+        logger.warning("Invalid uploads.%s value; falling back to %d", key, default)
+        return default
+
+
+def _get_upload_limits(app_config: AppConfig) -> UploadLimits:
+    return UploadLimits(
+        max_files=_get_upload_limit(app_config, "max_files", DEFAULT_MAX_FILES, legacy_key="max_file_count"),
+        max_file_size=_get_upload_limit(app_config, "max_file_size", DEFAULT_MAX_FILE_SIZE, legacy_key="max_single_file_size"),
+        max_total_size=_get_upload_limit(app_config, "max_total_size", DEFAULT_MAX_TOTAL_SIZE),
+    )
+
+
+def _cleanup_uploaded_paths(paths: list[os.PathLike[str] | str]) -> None:
+    for path in reversed(paths):
+        try:
+            os.unlink(path)
+        except FileNotFoundError:
+            pass
+        except Exception:
+            logger.warning("Failed to clean up upload path after rejected request: %s", path, exc_info=True)
+
+
+async def _write_upload_file_with_limits(
+    file: UploadFile,
+    *,
+    uploads_dir: os.PathLike[str] | str,
+    display_filename: str,
+    max_single_file_size: int,
+    max_total_size: int,
+    total_size: int,
+) -> tuple[os.PathLike[str] | str, int, int]:
+    file_size = 0
+    file_path, fh = open_upload_file_no_symlink(uploads_dir, display_filename)
+    try:
+        while chunk := await file.read(UPLOAD_CHUNK_SIZE):
+            file_size += len(chunk)
+            total_size += len(chunk)
+            if file_size > max_single_file_size:
+                raise HTTPException(status_code=413, detail=f"File too large: {display_filename}")
+            if total_size > max_total_size:
+                raise HTTPException(status_code=413, detail="Total upload size too large")
+            fh.write(chunk)
+    except Exception:
+        fh.close()
+        try:
+            os.unlink(file_path)
+        except FileNotFoundError:
+            pass
+        raise
+    else:
+        fh.close()
+    return file_path, file_size, total_size
+
+
 def _auto_convert_documents_enabled(app_config: AppConfig) -> bool:
     """Return whether automatic host-side document conversion is enabled.
 
@@ -96,12 +178,20 @@ async def upload_files(
     if not files:
         raise HTTPException(status_code=400, detail="No files provided")
 
+    limits = _get_upload_limits(config)
+    if len(files) > limits.max_files:
+        raise HTTPException(status_code=413, detail=f"Too many files: maximum is {limits.max_files}")
+
     try:
         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, user_id=get_effective_user_id())
     uploaded_files = []
+    written_paths = []
+    sandbox_sync_targets = []
+    skipped_files = []
+    total_size = 0
 
     sandbox_provider = get_sandbox_provider()
     sync_to_sandbox = not _uses_thread_data_mounts(sandbox_provider)
@@ -109,6 +199,8 @@ async def upload_files(
     if sync_to_sandbox:
         sandbox_id = sandbox_provider.acquire(thread_id)
         sandbox = sandbox_provider.get(sandbox_id)
+        if sandbox is None:
+            raise HTTPException(status_code=500, detail="Failed to acquire sandbox")
     auto_convert_documents = _auto_convert_documents_enabled(config)
 
     for file in files:
@@ -122,35 +214,40 @@ async def upload_files(
             continue
 
         try:
-            content = await file.read()
-            file_path = uploads_dir / safe_filename
-            file_path.write_bytes(content)
+            file_path, file_size, total_size = await _write_upload_file_with_limits(
+                file,
+                uploads_dir=uploads_dir,
+                display_filename=safe_filename,
+                max_single_file_size=limits.max_file_size,
+                max_total_size=limits.max_total_size,
+                total_size=total_size,
+            )
+            written_paths.append(file_path)
 
             virtual_path = upload_virtual_path(safe_filename)
 
-            if sync_to_sandbox and sandbox is not None:
-                _make_file_sandbox_writable(file_path)
-                sandbox.update_file(virtual_path, content)
+            if sync_to_sandbox:
+                sandbox_sync_targets.append((file_path, virtual_path))
 
             file_info = {
                 "filename": safe_filename,
-                "size": str(len(content)),
+                "size": str(file_size),
                 "path": str(sandbox_uploads / safe_filename),
                 "virtual_path": virtual_path,
                 "artifact_url": upload_artifact_url(thread_id, safe_filename),
             }
 
-            logger.info(f"Saved file: {safe_filename} ({len(content)} bytes) to {file_info['path']}")
+            logger.info(f"Saved file: {safe_filename} ({file_size} bytes) to {file_info['path']}")
 
             file_ext = file_path.suffix.lower()
             if auto_convert_documents and file_ext in CONVERTIBLE_EXTENSIONS:
                 md_path = await convert_file_to_markdown(file_path)
                 if md_path:
+                    written_paths.append(md_path)
                     md_virtual_path = upload_virtual_path(md_path.name)
 
-                    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())
+                    if sync_to_sandbox:
+                        sandbox_sync_targets.append((md_path, md_virtual_path))
 
                     file_info["markdown_file"] = md_path.name
                     file_info["markdown_path"] = str(sandbox_uploads / md_path.name)
@@ -159,17 +256,46 @@ async def upload_files(
 
             uploaded_files.append(file_info)
 
+        except HTTPException as e:
+            _cleanup_uploaded_paths(written_paths)
+            raise e
+        except UnsafeUploadPathError as e:
+            logger.warning("Skipping upload with unsafe destination %s: %s", file.filename, e)
+            skipped_files.append(safe_filename)
+            continue
         except Exception as e:
             logger.error(f"Failed to upload {file.filename}: {e}")
+            _cleanup_uploaded_paths(written_paths)
             raise HTTPException(status_code=500, detail=f"Failed to upload {file.filename}: {str(e)}")
 
+    if sync_to_sandbox:
+        for file_path, virtual_path in sandbox_sync_targets:
+            _make_file_sandbox_writable(file_path)
+            sandbox.update_file(virtual_path, file_path.read_bytes())
+
+    message = f"Successfully uploaded {len(uploaded_files)} file(s)"
+    if skipped_files:
+        message += f"; skipped {len(skipped_files)} unsafe file(s)"
+
     return UploadResponse(
-        success=True,
+        success=not skipped_files,
         files=uploaded_files,
-        message=f"Successfully uploaded {len(uploaded_files)} file(s)",
+        message=message,
+        skipped_files=skipped_files,
     )
 
 
+@router.get("/limits", response_model=UploadLimits)
+@require_permission("threads", "read", owner_check=True)
+async def get_upload_limits(
+    thread_id: str,
+    request: Request,
+    config: AppConfig = Depends(get_config),
+) -> UploadLimits:
+    """Return upload limits used by the gateway for this thread."""
+    return _get_upload_limits(config)
+
+
 @router.get("/list", response_model=dict)
 @require_permission("threads", "read", owner_check=True)
 async def list_uploaded_files(thread_id: str, request: Request) -> dict:
diff --git a/backend/docs/CONFIGURATION.md b/backend/docs/CONFIGURATION.md
index f87fdd236..26137951f 100644
--- a/backend/docs/CONFIGURATION.md
+++ b/backend/docs/CONFIGURATION.md
@@ -321,12 +321,16 @@ models:
 - `DEEPSEEK_API_KEY` - DeepSeek API key
 - `NOVITA_API_KEY` - Novita API key (OpenAI-compatible endpoint)
 - `TAVILY_API_KEY` - Tavily search API key
+- `DEER_FLOW_PROJECT_ROOT` - Project root for relative runtime paths
 - `DEER_FLOW_CONFIG_PATH` - Custom config file path
+- `DEER_FLOW_EXTENSIONS_CONFIG_PATH` - Custom extensions config file path
+- `DEER_FLOW_HOME` - Runtime state directory (defaults to `.deer-flow` under the project root)
+- `DEER_FLOW_SKILLS_PATH` - Skills directory when `skills.path` is omitted
 - `GATEWAY_ENABLE_DOCS` - Set to `false` to disable Swagger UI (`/docs`), ReDoc (`/redoc`), and OpenAPI schema (`/openapi.json`) endpoints (default: `true`)
 
 ## Configuration Location
 
-The configuration file should be placed in the **project root directory** (`deer-flow/config.yaml`), not in the backend directory.
+The configuration file should be placed in the **project root directory** (`deer-flow/config.yaml`). Set `DEER_FLOW_PROJECT_ROOT` when the process may start from another working directory, or set `DEER_FLOW_CONFIG_PATH` to point at a specific file.
 
 ## Configuration Priority
 
@@ -334,12 +338,12 @@ DeerFlow searches for configuration in this order:
 
 1. Path specified in code via `config_path` argument
 2. Path from `DEER_FLOW_CONFIG_PATH` environment variable
-3. `config.yaml` in current working directory (typically `backend/` when running)
-4. `config.yaml` in parent directory (project root: `deer-flow/`)
+3. `config.yaml` under `DEER_FLOW_PROJECT_ROOT`, or under the current working directory when `DEER_FLOW_PROJECT_ROOT` is unset
+4. Legacy backend/repository-root locations for monorepo compatibility
 
 ## Best Practices
 
-1. **Place `config.yaml` in project root** - Not in `backend/` directory
+1. **Place `config.yaml` in project root** - Set `DEER_FLOW_PROJECT_ROOT` if the runtime starts elsewhere
 2. **Never commit `config.yaml`** - It's already in `.gitignore`
 3. **Use environment variables for secrets** - Don't hardcode API keys
 4. **Keep `config.example.yaml` updated** - Document all new options
@@ -350,7 +354,7 @@ DeerFlow searches for configuration in this order:
 
 ### "Config file not found"
 - Ensure `config.yaml` exists in the **project root** directory (`deer-flow/config.yaml`)
-- The backend searches parent directory by default, so root location is preferred
+- If the runtime starts outside the project root, set `DEER_FLOW_PROJECT_ROOT`
 - Alternatively, set `DEER_FLOW_CONFIG_PATH` environment variable to custom location
 
 ### "Invalid API key"
@@ -360,7 +364,7 @@ DeerFlow searches for configuration in this order:
 ### "Skills not loading"
 - Check that `deer-flow/skills/` directory exists
 - Verify skills have valid `SKILL.md` files
-- Check `skills.path` configuration if using custom path
+- Check `skills.path` or `DEER_FLOW_SKILLS_PATH` if using a custom path
 
 ### "Docker sandbox fails to start"
 - Ensure Docker is running
diff --git a/backend/docs/FILE_UPLOAD.md b/backend/docs/FILE_UPLOAD.md
index bf6962e4f..2b15b27e7 100644
--- a/backend/docs/FILE_UPLOAD.md
+++ b/backend/docs/FILE_UPLOAD.md
@@ -22,6 +22,8 @@ POST /api/threads/{thread_id}/uploads
 **请求体：** `multipart/form-data`
 - `files`: 一个或多个文件
 
+网关会在应用层限制上传规模，默认最多 10 个文件、单文件 50 MiB、单次请求总计 100 MiB。可通过 `config.yaml` 的 `uploads.max_files`、`uploads.max_file_size`、`uploads.max_total_size` 调整；前端会读取同一组限制并在选择文件时提示，超过限制时后端返回 `413 Payload Too Large`。
+
 **响应：**
 ```json
 {
@@ -48,7 +50,23 @@ POST /api/threads/{thread_id}/uploads
 - `virtual_path`: Agent 在沙箱中使用的虚拟路径
 - `artifact_url`: 前端通过 HTTP 访问文件的 URL
 
-### 2. 列出已上传文件
+### 2. 查询上传限制
+```
+GET /api/threads/{thread_id}/uploads/limits
+```
+
+返回网关当前生效的上传限制，供前端在用户选择文件前提示和拦截。
+
+**响应：**
+```json
+{
+  "max_files": 10,
+  "max_file_size": 52428800,
+  "max_total_size": 104857600
+}
+```
+
+### 3. 列出已上传文件
 ```
 GET /api/threads/{thread_id}/uploads/list
 ```
@@ -71,7 +89,7 @@ GET /api/threads/{thread_id}/uploads/list
 }
 ```
 
-### 3. 删除文件
+### 4. 删除文件
 ```
 DELETE /api/threads/{thread_id}/uploads/{filename}
 ```
diff --git a/backend/docs/SETUP.md b/backend/docs/SETUP.md
index 50885eb3f..aff0e287f 100644
--- a/backend/docs/SETUP.md
+++ b/backend/docs/SETUP.md
@@ -23,6 +23,9 @@ DeerFlow uses a YAML configuration file that should be placed in the **project r
    # Option A: Set environment variables (recommended)
    export OPENAI_API_KEY="your-key-here"
 
+   # Optional: pin the project root when running from another directory
+   export DEER_FLOW_PROJECT_ROOT="/path/to/deer-flow"
+
    # Option B: Edit config.yaml directly
    vim config.yaml  # or your preferred editor
    ```
@@ -35,17 +38,20 @@ DeerFlow uses a YAML configuration file that should be placed in the **project r
 
 ## Important Notes
 
-- **Location**: `config.yaml` should be in `deer-flow/` (project root), not `deer-flow/backend/`
+- **Location**: `config.yaml` should be in `deer-flow/` (project root)
 - **Git**: `config.yaml` is automatically ignored by git (contains secrets)
-- **Priority**: If both `backend/config.yaml` and `../config.yaml` exist, backend version takes precedence
+- **Runtime root**: Set `DEER_FLOW_PROJECT_ROOT` if DeerFlow may start from outside the project root
+- **Runtime data**: State defaults to `.deer-flow` under the project root; set `DEER_FLOW_HOME` to move it
+- **Skills**: Skills default to `skills/` under the project root; set `DEER_FLOW_SKILLS_PATH` or `skills.path` to move them
 
 ## Configuration File Locations
 
 The backend searches for `config.yaml` in this order:
 
-1. `DEER_FLOW_CONFIG_PATH` environment variable (if set)
-2. `backend/config.yaml` (current directory when running from backend/)
-3. `deer-flow/config.yaml` (parent directory - **recommended location**)
+1. Explicit `config_path` argument from code
+2. `DEER_FLOW_CONFIG_PATH` environment variable (if set)
+3. `config.yaml` under `DEER_FLOW_PROJECT_ROOT`, or the current working directory when `DEER_FLOW_PROJECT_ROOT` is unset
+4. Legacy backend/repository-root locations for monorepo compatibility
 
 **Recommended**: Place `config.yaml` in project root (`deer-flow/config.yaml`).
 
@@ -77,8 +83,8 @@ python -c "from deerflow.config.app_config import AppConfig; print(AppConfig.res
 
 If it can't find the config:
 1. Ensure you've copied `config.example.yaml` to `config.yaml`
-2. Verify you're in the correct directory
-3. Check the file exists: `ls -la ../config.yaml`
+2. Verify you're in the project root, or set `DEER_FLOW_PROJECT_ROOT`
+3. Check the file exists: `ls -la config.yaml`
 
 ### Permission denied
 
@@ -89,4 +95,4 @@ chmod 600 ../config.yaml  # Protect sensitive configuration
 ## See Also
 
 - [Configuration Guide](CONFIGURATION.md) - Detailed configuration options
-- [Architecture Overview](../CLAUDE.md) - System architecture
\ No newline at end of file
+- [Architecture Overview](../CLAUDE.md) - System architecture
diff --git a/backend/packages/harness/deerflow/agents/lead_agent/agent.py b/backend/packages/harness/deerflow/agents/lead_agent/agent.py
index 12fedd5b2..a908e9f96 100644
--- a/backend/packages/harness/deerflow/agents/lead_agent/agent.py
+++ b/backend/packages/harness/deerflow/agents/lead_agent/agent.py
@@ -19,8 +19,6 @@ from deerflow.agents.middlewares.view_image_middleware import ViewImageMiddlewar
 from deerflow.agents.thread_state import ThreadState
 from deerflow.config.agents_config import load_agent_config, validate_agent_name
 from deerflow.config.app_config import AppConfig, get_app_config
-from deerflow.config.memory_config import get_memory_config
-from deerflow.config.summarization_config import get_summarization_config
 from deerflow.models import create_chat_model
 
 logger = logging.getLogger(__name__)
@@ -52,7 +50,8 @@ def _resolve_model_name(requested_model_name: str | None = None, *, app_config:
 
 def _create_summarization_middleware(*, app_config: AppConfig | None = None) -> DeerFlowSummarizationMiddleware | None:
     """Create and configure the summarization middleware from config."""
-    config = get_summarization_config()
+    resolved_app_config = app_config or get_app_config()
+    config = resolved_app_config.summarization
 
     if not config.enabled:
         return None
@@ -73,9 +72,9 @@ def _create_summarization_middleware(*, app_config: AppConfig | None = None) ->
     # 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, app_config=app_config)
+        model = create_chat_model(name=config.model_name, thinking_enabled=False, app_config=resolved_app_config)
     else:
-        model = create_chat_model(thinking_enabled=False, app_config=app_config)
+        model = create_chat_model(thinking_enabled=False, app_config=resolved_app_config)
     model = model.with_config(tags=["middleware:summarize"])
 
     # Prepare kwargs
@@ -92,18 +91,13 @@ def _create_summarization_middleware(*, app_config: AppConfig | None = None) ->
         kwargs["summary_prompt"] = config.summary_prompt
 
     hooks: list[BeforeSummarizationHook] = []
-    if get_memory_config().enabled:
+    if resolved_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:
-        resolved_app_config = app_config or get_app_config()
-        skills_container_path = resolved_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"
+    skills_container_path = resolved_app_config.skills.container_path or "/mnt/skills"
 
     return DeerFlowSummarizationMiddleware(
         **kwargs,
@@ -279,10 +273,10 @@ def _build_middlewares(
         middlewares.append(TokenUsageMiddleware())
 
     # Add TitleMiddleware
-    middlewares.append(TitleMiddleware())
+    middlewares.append(TitleMiddleware(app_config=resolved_app_config))
 
     # Add MemoryMiddleware (after TitleMiddleware)
-    middlewares.append(MemoryMiddleware(agent_name=agent_name))
+    middlewares.append(MemoryMiddleware(agent_name=agent_name, memory_config=resolved_app_config.memory))
 
     # Add ViewImageMiddleware only if the current model supports vision.
     # Use the resolved runtime model_name from make_lead_agent to avoid stale config values.
@@ -316,7 +310,9 @@ def _build_middlewares(
 
 def make_lead_agent(config: RunnableConfig):
     """LangGraph graph factory; keep the signature compatible with LangGraph Server."""
-    return _make_lead_agent(config, app_config=get_app_config())
+    runtime_config = _get_runtime_config(config)
+    runtime_app_config = runtime_config.get("app_config")
+    return _make_lead_agent(config, app_config=runtime_app_config or get_app_config())
 
 
 def _make_lead_agent(config: RunnableConfig, *, app_config: AppConfig):
diff --git a/backend/packages/harness/deerflow/agents/lead_agent/prompt.py b/backend/packages/harness/deerflow/agents/lead_agent/prompt.py
index 9b6fd9cd4..b02c86344 100644
--- a/backend/packages/harness/deerflow/agents/lead_agent/prompt.py
+++ b/backend/packages/harness/deerflow/agents/lead_agent/prompt.py
@@ -158,7 +158,7 @@ Skip simple one-off tasks.
 """
 
 
-def _build_available_subagents_description(available_names: list[str], bash_available: bool) -> str:
+def _build_available_subagents_description(available_names: list[str], bash_available: bool, *, app_config: AppConfig | None = None) -> str:
     """Dynamically build subagent type descriptions from registry.
 
     Mirrors Codex's pattern where agent_type_description is dynamically generated
@@ -180,7 +180,7 @@ def _build_available_subagents_description(available_names: list[str], bash_avai
         if name in builtin_descriptions:
             lines.append(f"- **{name}**: {builtin_descriptions[name]}")
         else:
-            config = get_subagent_config(name)
+            config = get_subagent_config(name, app_config=app_config)
             if config is not None:
                 desc = config.description.split("\n")[0].strip()  # First line only for brevity
                 lines.append(f"- **{name}**: {desc}")
@@ -188,7 +188,7 @@ def _build_available_subagents_description(available_names: list[str], bash_avai
     return "\n".join(lines)
 
 
-def _build_subagent_section(max_concurrent: int) -> str:
+def _build_subagent_section(max_concurrent: int, *, app_config: AppConfig | None = None) -> str:
     """Build the subagent system prompt section with dynamic concurrency limit.
 
     Args:
@@ -198,12 +198,12 @@ def _build_subagent_section(max_concurrent: int) -> str:
         Formatted subagent section string.
     """
     n = max_concurrent
-    available_names = get_available_subagent_names()
+    available_names = get_available_subagent_names(app_config=app_config) if app_config is not None else get_available_subagent_names()
     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)
+    available_subagents = _build_available_subagents_description(available_names, bash_available, app_config=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()'
@@ -530,21 +530,28 @@ 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(agent_name: str | None = None, *, app_config: AppConfig | 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.
+        app_config: Explicit application config. When provided, memory options
+            are read from this value instead of the global config singleton.
 
     Returns:
         Formatted memory context string wrapped in XML tags, or empty string if disabled.
     """
     try:
         from deerflow.agents.memory import format_memory_for_injection, get_memory_data
-        from deerflow.config.memory_config import get_memory_config
         from deerflow.runtime.user_context import get_effective_user_id
 
-        config = get_memory_config()
+        if app_config is None:
+            from deerflow.config.memory_config import get_memory_config
+
+            config = get_memory_config()
+        else:
+            config = app_config.memory
+
         if not config.enabled or not config.injection_enabled:
             return ""
 
@@ -558,8 +565,8 @@ def _get_memory_context(agent_name: str | None = None) -> str:
 {memory_content}
 </memory>
 """
-    except Exception as e:
-        logger.error("Failed to load memory context: %s", e)
+    except Exception:
+        logger.exception("Failed to load memory context")
         return ""
 
 
@@ -599,15 +606,20 @@ def get_skills_prompt_section(available_skills: set[str] | None = None, *, app_c
     """Generate the skills prompt section with available skills list."""
     skills = _get_enabled_skills_for_config(app_config)
 
-    try:
-        from deerflow.config import get_app_config
+    if app_config is None:
+        try:
+            from deerflow.config import get_app_config
 
-        config = app_config or 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
+    else:
+        config = 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
 
     if not skills and not skill_evolution_enabled:
         return ""
@@ -640,13 +652,17 @@ def get_deferred_tools_prompt_section(*, app_config: AppConfig | None = None) ->
     """
     from deerflow.tools.builtins.tool_search import get_deferred_registry
 
-    try:
-        from deerflow.config import get_app_config
+    if app_config is None:
+        try:
+            from deerflow.config import get_app_config
 
-        config = app_config or get_app_config()
-        if not config.tool_search.enabled:
+            config = get_app_config()
+        except Exception:
             return ""
-    except Exception:
+    else:
+        config = app_config
+
+    if not config.tool_search.enabled:
         return ""
 
     registry = get_deferred_registry()
@@ -657,15 +673,19 @@ def get_deferred_tools_prompt_section(*, app_config: AppConfig | None = None) ->
     return f"<available-deferred-tools>\n{names}\n</available-deferred-tools>"
 
 
-def _build_acp_section() -> str:
+def _build_acp_section(*, app_config: AppConfig | None = None) -> str:
     """Build the ACP agent prompt section, only if ACP agents are configured."""
-    try:
-        from deerflow.config.acp_config import get_acp_agents
+    if app_config is None:
+        try:
+            from deerflow.config.acp_config import get_acp_agents
 
-        agents = get_acp_agents()
-        if not agents:
+            agents = get_acp_agents()
+        except Exception:
             return ""
-    except Exception:
+    else:
+        agents = getattr(app_config, "acp_agents", {}) or {}
+
+    if not agents:
         return ""
 
     return (
@@ -679,14 +699,18 @@ def _build_acp_section() -> str:
 
 def _build_custom_mounts_section(*, app_config: AppConfig | None = None) -> str:
     """Build a prompt section for explicitly configured sandbox mounts."""
-    try:
-        from deerflow.config import get_app_config
+    if app_config is None:
+        try:
+            from deerflow.config import get_app_config
 
-        config = app_config or get_app_config()
-        mounts = config.sandbox.mounts or []
-    except Exception:
-        logger.exception("Failed to load configured sandbox mounts for the lead-agent prompt")
-        return ""
+            config = get_app_config()
+        except Exception:
+            logger.exception("Failed to load configured sandbox mounts for the lead-agent prompt")
+            return ""
+    else:
+        config = app_config
+
+    mounts = config.sandbox.mounts or []
 
     if not mounts:
         return ""
@@ -709,11 +733,11 @@ def apply_prompt_template(
     app_config: AppConfig | None = None,
 ) -> str:
     # Get memory context
-    memory_context = _get_memory_context(agent_name)
+    memory_context = _get_memory_context(agent_name, app_config=app_config)
 
     # 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=app_config) if subagent_enabled else ""
 
     # Add subagent reminder to critical_reminders if enabled
     subagent_reminder = (
@@ -740,7 +764,7 @@ def apply_prompt_template(
     deferred_tools_section = get_deferred_tools_prompt_section(app_config=app_config)
 
     # Build ACP agent section only if ACP agents are configured
-    acp_section = _build_acp_section()
+    acp_section = _build_acp_section(app_config=app_config)
     custom_mounts_section = _build_custom_mounts_section(app_config=app_config)
     acp_and_mounts_section = "\n".join(section for section in (acp_section, custom_mounts_section) if section)
 
diff --git a/backend/packages/harness/deerflow/agents/middlewares/memory_middleware.py b/backend/packages/harness/deerflow/agents/middlewares/memory_middleware.py
index 059f8ffc2..ae5f9cfbb 100644
--- a/backend/packages/harness/deerflow/agents/middlewares/memory_middleware.py
+++ b/backend/packages/harness/deerflow/agents/middlewares/memory_middleware.py
@@ -1,7 +1,7 @@
 """Middleware for memory mechanism."""
 
 import logging
-from typing import override
+from typing import TYPE_CHECKING, override
 
 from langchain.agents import AgentState
 from langchain.agents.middleware import AgentMiddleware
@@ -13,6 +13,9 @@ from deerflow.agents.memory.queue import get_memory_queue
 from deerflow.config.memory_config import get_memory_config
 from deerflow.runtime.user_context import get_effective_user_id
 
+if TYPE_CHECKING:
+    from deerflow.config.memory_config import MemoryConfig
+
 logger = logging.getLogger(__name__)
 
 
@@ -34,14 +37,17 @@ class MemoryMiddleware(AgentMiddleware[MemoryMiddlewareState]):
 
     state_schema = MemoryMiddlewareState
 
-    def __init__(self, agent_name: str | None = None):
+    def __init__(self, agent_name: str | None = None, *, memory_config: "MemoryConfig | None" = None):
         """Initialize the MemoryMiddleware.
 
         Args:
             agent_name: If provided, memory is stored per-agent. If None, uses global memory.
+            memory_config: Explicit memory config. When omitted, legacy global
+                config fallback is used.
         """
         super().__init__()
         self._agent_name = agent_name
+        self._memory_config = memory_config
 
     @override
     def after_agent(self, state: MemoryMiddlewareState, runtime: Runtime) -> dict | None:
@@ -54,7 +60,7 @@ class MemoryMiddleware(AgentMiddleware[MemoryMiddlewareState]):
         Returns:
             None (no state changes needed from this middleware).
         """
-        config = get_memory_config()
+        config = self._memory_config or get_memory_config()
         if not config.enabled:
             return None
 
diff --git a/backend/packages/harness/deerflow/agents/middlewares/title_middleware.py b/backend/packages/harness/deerflow/agents/middlewares/title_middleware.py
index 5cd5bb46c..01080be14 100644
--- a/backend/packages/harness/deerflow/agents/middlewares/title_middleware.py
+++ b/backend/packages/harness/deerflow/agents/middlewares/title_middleware.py
@@ -2,7 +2,7 @@
 
 import logging
 import re
-from typing import Any, NotRequired, override
+from typing import TYPE_CHECKING, Any, NotRequired, override
 
 from langchain.agents import AgentState
 from langchain.agents.middleware import AgentMiddleware
@@ -12,6 +12,10 @@ from langgraph.runtime import Runtime
 from deerflow.config.title_config import get_title_config
 from deerflow.models import create_chat_model
 
+if TYPE_CHECKING:
+    from deerflow.config.app_config import AppConfig
+    from deerflow.config.title_config import TitleConfig
+
 logger = logging.getLogger(__name__)
 
 
@@ -26,6 +30,18 @@ class TitleMiddleware(AgentMiddleware[TitleMiddlewareState]):
 
     state_schema = TitleMiddlewareState
 
+    def __init__(self, *, app_config: "AppConfig | None" = None, title_config: "TitleConfig | None" = None):
+        super().__init__()
+        self._app_config = app_config
+        self._title_config = title_config
+
+    def _get_title_config(self):
+        if self._title_config is not None:
+            return self._title_config
+        if self._app_config is not None:
+            return self._app_config.title
+        return get_title_config()
+
     def _normalize_content(self, content: object) -> str:
         if isinstance(content, str):
             return content
@@ -47,7 +63,7 @@ class TitleMiddleware(AgentMiddleware[TitleMiddlewareState]):
 
     def _should_generate_title(self, state: TitleMiddlewareState) -> bool:
         """Check if we should generate a title for this thread."""
-        config = get_title_config()
+        config = self._get_title_config()
         if not config.enabled:
             return False
 
@@ -72,7 +88,7 @@ class TitleMiddleware(AgentMiddleware[TitleMiddlewareState]):
 
         Returns (prompt_string, user_msg) so callers can use user_msg as fallback.
         """
-        config = get_title_config()
+        config = self._get_title_config()
         messages = state.get("messages", [])
 
         user_msg_content = next((m.content for m in messages if m.type == "human"), "")
@@ -94,14 +110,14 @@ class TitleMiddleware(AgentMiddleware[TitleMiddlewareState]):
 
     def _parse_title(self, content: object) -> str:
         """Normalize model output into a clean title string."""
-        config = get_title_config()
+        config = self._get_title_config()
         title_content = self._normalize_content(content)
         title_content = self._strip_think_tags(title_content)
         title = title_content.strip().strip('"').strip("'")
         return title[: config.max_chars] if len(title) > config.max_chars else title
 
     def _fallback_title(self, user_msg: str) -> str:
-        config = get_title_config()
+        config = self._get_title_config()
         fallback_chars = min(config.max_chars, 50)
         if len(user_msg) > fallback_chars:
             return user_msg[:fallback_chars].rstrip() + "..."
@@ -135,14 +151,17 @@ class TitleMiddleware(AgentMiddleware[TitleMiddlewareState]):
         if not self._should_generate_title(state):
             return None
 
-        config = get_title_config()
+        config = self._get_title_config()
         prompt, user_msg = self._build_title_prompt(state)
 
         try:
+            model_kwargs = {"thinking_enabled": False}
+            if self._app_config is not None:
+                model_kwargs["app_config"] = self._app_config
             if config.model_name:
-                model = create_chat_model(name=config.model_name, thinking_enabled=False)
+                model = create_chat_model(name=config.model_name, **model_kwargs)
             else:
-                model = create_chat_model(thinking_enabled=False)
+                model = create_chat_model(**model_kwargs)
             response = await model.ainvoke(prompt, config=self._get_runnable_config())
             title = self._parse_title(response.content)
             if title:
diff --git a/backend/packages/harness/deerflow/agents/middlewares/tool_error_handling_middleware.py b/backend/packages/harness/deerflow/agents/middlewares/tool_error_handling_middleware.py
index db0230cf9..4393bd360 100644
--- a/backend/packages/harness/deerflow/agents/middlewares/tool_error_handling_middleware.py
+++ b/backend/packages/harness/deerflow/agents/middlewares/tool_error_handling_middleware.py
@@ -136,11 +136,32 @@ def build_lead_runtime_middlewares(*, app_config: AppConfig, lazy_init: bool = T
     )
 
 
-def build_subagent_runtime_middlewares(*, app_config: AppConfig, lazy_init: bool = True) -> list[AgentMiddleware]:
+def build_subagent_runtime_middlewares(
+    *,
+    app_config: AppConfig | None = None,
+    model_name: str | None = None,
+    lazy_init: bool = True,
+) -> list[AgentMiddleware]:
     """Middlewares shared by subagent runtime before subagent-only middlewares."""
-    return _build_runtime_middlewares(
+    if app_config is None:
+        from deerflow.config import get_app_config
+
+        app_config = get_app_config()
+
+    middlewares = _build_runtime_middlewares(
         app_config=app_config,
         include_uploads=False,
         include_dangling_tool_call_patch=True,
         lazy_init=lazy_init,
     )
+
+    if model_name is None and app_config.models:
+        model_name = app_config.models[0].name
+
+    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:
+        from deerflow.agents.middlewares.view_image_middleware import ViewImageMiddleware
+
+        middlewares.append(ViewImageMiddleware())
+
+    return middlewares
diff --git a/backend/packages/harness/deerflow/community/aio_sandbox/aio_sandbox.py b/backend/packages/harness/deerflow/community/aio_sandbox/aio_sandbox.py
index b6041f7ed..97da4144d 100644
--- a/backend/packages/harness/deerflow/community/aio_sandbox/aio_sandbox.py
+++ b/backend/packages/harness/deerflow/community/aio_sandbox/aio_sandbox.py
@@ -48,6 +48,12 @@ class AioSandbox(Sandbox):
             self._home_dir = context.home_dir
         return self._home_dir
 
+    # Default no_change_timeout for exec_command (seconds).  Matches the
+    # client-level timeout so that long-running commands which produce no
+    # output are not prematurely terminated by the sandbox's built-in 120 s
+    # default.
+    _DEFAULT_NO_CHANGE_TIMEOUT = 600
+
     def execute_command(self, command: str) -> str:
         """Execute a shell command in the sandbox.
 
@@ -66,13 +72,13 @@ class AioSandbox(Sandbox):
         """
         with self._lock:
             try:
-                result = self._client.shell.exec_command(command=command)
+                result = self._client.shell.exec_command(command=command, no_change_timeout=self._DEFAULT_NO_CHANGE_TIMEOUT)
                 output = result.data.output if result.data else ""
 
                 if output and _ERROR_OBSERVATION_SIGNATURE in output:
                     logger.warning("ErrorObservation detected in sandbox output, retrying with a fresh session")
                     fresh_id = str(uuid.uuid4())
-                    result = self._client.shell.exec_command(command=command, id=fresh_id)
+                    result = self._client.shell.exec_command(command=command, id=fresh_id, no_change_timeout=self._DEFAULT_NO_CHANGE_TIMEOUT)
                     output = result.data.output if result.data else ""
 
                 return output if output else "(no output)"
@@ -108,7 +114,7 @@ class AioSandbox(Sandbox):
         """
         with self._lock:
             try:
-                result = self._client.shell.exec_command(command=f"find {shlex.quote(path)} -maxdepth {max_depth} -type f -o -type d 2>/dev/null | head -500")
+                result = self._client.shell.exec_command(command=f"find {shlex.quote(path)} -maxdepth {max_depth} -type f -o -type d 2>/dev/null | head -500", no_change_timeout=self._DEFAULT_NO_CHANGE_TIMEOUT)
                 output = result.data.output if result.data else ""
                 if output:
                     return [line.strip() for line in output.strip().split("\n") if line.strip()]
diff --git a/backend/packages/harness/deerflow/community/serper/__init__.py b/backend/packages/harness/deerflow/community/serper/__init__.py
new file mode 100644
index 000000000..876167859
--- /dev/null
+++ b/backend/packages/harness/deerflow/community/serper/__init__.py
@@ -0,0 +1,3 @@
+from .tools import web_search_tool
+
+__all__ = ["web_search_tool"]
diff --git a/backend/packages/harness/deerflow/community/serper/tools.py b/backend/packages/harness/deerflow/community/serper/tools.py
new file mode 100644
index 000000000..1cad11fb8
--- /dev/null
+++ b/backend/packages/harness/deerflow/community/serper/tools.py
@@ -0,0 +1,95 @@
+"""
+Web Search Tool - Search the web using Serper (Google Search API).
+
+Serper provides real-time Google Search results via a JSON API.
+An API key is required. Sign up at https://serper.dev to get one.
+"""
+
+import json
+import logging
+import os
+
+import httpx
+from langchain.tools import tool
+
+from deerflow.config import get_app_config
+
+logger = logging.getLogger(__name__)
+
+_SERPER_ENDPOINT = "https://google.serper.dev/search"
+_api_key_warned = False
+
+
+def _get_api_key() -> str | None:
+    config = get_app_config().get_tool_config("web_search")
+    if config is not None:
+        api_key = config.model_extra.get("api_key")
+        if isinstance(api_key, str) and api_key.strip():
+            return api_key
+    return os.getenv("SERPER_API_KEY")
+
+
+@tool("web_search", parse_docstring=True)
+def web_search_tool(query: str, max_results: int = 5) -> str:
+    """Search the web for information using Google Search via Serper.
+
+    Args:
+        query: Search keywords describing what you want to find. Be specific for better results.
+        max_results: Maximum number of search results to return. Default is 5.
+    """
+    global _api_key_warned
+
+    config = get_app_config().get_tool_config("web_search")
+    if config is not None and "max_results" in config.model_extra:
+        max_results = config.model_extra.get("max_results", max_results)
+
+    api_key = _get_api_key()
+    if not api_key:
+        if not _api_key_warned:
+            _api_key_warned = True
+            logger.warning("Serper API key is not set. Set SERPER_API_KEY in your environment or provide api_key in config.yaml. Sign up at https://serper.dev")
+        return json.dumps(
+            {"error": "SERPER_API_KEY is not configured", "query": query},
+            ensure_ascii=False,
+        )
+
+    headers = {
+        "X-API-KEY": api_key,
+        "Content-Type": "application/json",
+    }
+    payload = {"q": query, "num": max_results}
+
+    try:
+        with httpx.Client(timeout=30) as client:
+            response = client.post(_SERPER_ENDPOINT, headers=headers, json=payload)
+        response.raise_for_status()
+        data = response.json()
+    except httpx.HTTPStatusError as e:
+        logger.error(f"Serper API returned HTTP {e.response.status_code}: {e.response.text}")
+        return json.dumps(
+            {"error": f"Serper API error: HTTP {e.response.status_code}", "query": query},
+            ensure_ascii=False,
+        )
+    except Exception as e:
+        logger.error(f"Serper search failed: {type(e).__name__}: {e}")
+        return json.dumps({"error": str(e), "query": query}, ensure_ascii=False)
+
+    organic = data.get("organic", [])
+    if not organic:
+        return json.dumps({"error": "No results found", "query": query}, ensure_ascii=False)
+
+    normalized_results = [
+        {
+            "title": r.get("title", ""),
+            "url": r.get("link", ""),
+            "content": r.get("snippet", ""),
+        }
+        for r in organic[:max_results]
+    ]
+
+    output = {
+        "query": query,
+        "total_results": len(normalized_results),
+        "results": normalized_results,
+    }
+    return json.dumps(output, indent=2, ensure_ascii=False)
diff --git a/backend/packages/harness/deerflow/config/app_config.py b/backend/packages/harness/deerflow/config/app_config.py
index b31d396a5..dae41b14d 100644
--- a/backend/packages/harness/deerflow/config/app_config.py
+++ b/backend/packages/harness/deerflow/config/app_config.py
@@ -8,7 +8,7 @@ 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.acp_config import ACPAgentConfig, load_acp_config_from_dict
 from deerflow.config.agents_api_config import AgentsApiConfig, load_agents_api_config_from_dict
 from deerflow.config.checkpointer_config import CheckpointerConfig, load_checkpointer_config_from_dict
 from deerflow.config.database_config import DatabaseConfig
@@ -17,6 +17,7 @@ from deerflow.config.guardrails_config import GuardrailsConfig, load_guardrails_
 from deerflow.config.memory_config import MemoryConfig, load_memory_config_from_dict
 from deerflow.config.model_config import ModelConfig
 from deerflow.config.run_events_config import RunEventsConfig
+from deerflow.config.runtime_paths import existing_project_file
 from deerflow.config.sandbox_config import SandboxConfig
 from deerflow.config.skill_evolution_config import SkillEvolutionConfig
 from deerflow.config.skills_config import SkillsConfig
@@ -46,8 +47,8 @@ class CircuitBreakerConfig(BaseModel):
     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."""
+def _legacy_config_candidates() -> tuple[Path, ...]:
+    """Return source-tree config.yaml locations for monorepo compatibility."""
     backend_dir = Path(__file__).resolve().parents[4]
     repo_root = backend_dir.parent
     return (backend_dir / "config.yaml", repo_root / "config.yaml")
@@ -94,6 +95,7 @@ class AppConfig(BaseModel):
     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")
+    acp_agents: dict[str, ACPAgentConfig] = Field(default_factory=dict, description="ACP-compatible agent configuration")
     subagents: SubagentsAppConfig = Field(default_factory=SubagentsAppConfig, description="Subagent runtime configuration")
     guardrails: GuardrailsConfig = Field(default_factory=GuardrailsConfig, description="Guardrail middleware configuration")
     circuit_breaker: CircuitBreakerConfig = Field(default_factory=CircuitBreakerConfig, description="LLM circuit breaker configuration")
@@ -110,7 +112,8 @@ class AppConfig(BaseModel):
         Priority:
         1. If provided `config_path` argument, use it.
         2. If provided `DEER_FLOW_CONFIG_PATH` environment variable, use it.
-        3. Otherwise, search deterministic backend/repository-root defaults from `_default_config_candidates()`.
+        3. Otherwise, search the caller project root.
+        4. Finally, search legacy backend/repository-root defaults for monorepo compatibility.
         """
         if config_path:
             path = Path(config_path)
@@ -123,10 +126,14 @@ class AppConfig(BaseModel):
                 raise FileNotFoundError(f"Config file specified by environment variable `DEER_FLOW_CONFIG_PATH` not found at {path}")
             return path
         else:
-            for path in _default_config_candidates():
+            project_config = existing_project_file(("config.yaml",))
+            if project_config is not None:
+                return project_config
+
+            for path in _legacy_config_candidates():
                 if path.exists():
                     return path
-            raise FileNotFoundError("`config.yaml` file not found at the default backend or repository root locations")
+            raise FileNotFoundError("`config.yaml` file not found in the project root or legacy backend/repository root locations")
 
     @classmethod
     def from_file(cls, config_path: str | None = None) -> Self:
diff --git a/backend/packages/harness/deerflow/config/extensions_config.py b/backend/packages/harness/deerflow/config/extensions_config.py
index e7a48d166..a2daa71f4 100644
--- a/backend/packages/harness/deerflow/config/extensions_config.py
+++ b/backend/packages/harness/deerflow/config/extensions_config.py
@@ -7,6 +7,8 @@ from typing import Any, Literal
 
 from pydantic import BaseModel, ConfigDict, Field
 
+from deerflow.config.runtime_paths import existing_project_file
+
 
 class McpOAuthConfig(BaseModel):
     """OAuth configuration for an MCP server (HTTP/SSE transports)."""
@@ -73,8 +75,8 @@ class ExtensionsConfig(BaseModel):
         Priority:
         1. If provided `config_path` argument, use it.
         2. If provided `DEER_FLOW_EXTENSIONS_CONFIG_PATH` environment variable, use it.
-        3. Otherwise, check for `extensions_config.json` in the current directory, then in the parent directory.
-        4. For backward compatibility, also check for `mcp_config.json` if `extensions_config.json` is not found.
+        3. Otherwise, search the caller project root for `extensions_config.json`, then `mcp_config.json`.
+        4. For backward compatibility, also search legacy backend/repository-root defaults.
         5. If not found, return None (extensions are optional).
 
         Args:
@@ -83,8 +85,9 @@ class ExtensionsConfig(BaseModel):
         Resolution order:
             1. If provided `config_path` argument, use it.
             2. If provided `DEER_FLOW_EXTENSIONS_CONFIG_PATH` environment variable, use it.
-            3. Otherwise, search backend/repository-root defaults for
+            3. Otherwise, search the caller project root for
                `extensions_config.json`, then legacy `mcp_config.json`.
+            4. Finally, search backend/repository-root defaults for monorepo compatibility.
 
         Returns:
             Path to the extensions config file if found, otherwise None.
@@ -100,6 +103,10 @@ class ExtensionsConfig(BaseModel):
                 raise FileNotFoundError(f"Extensions config file specified by environment variable `DEER_FLOW_EXTENSIONS_CONFIG_PATH` not found at {path}")
             return path
         else:
+            project_config = existing_project_file(("extensions_config.json", "mcp_config.json"))
+            if project_config is not None:
+                return project_config
+
             backend_dir = Path(__file__).resolve().parents[4]
             repo_root = backend_dir.parent
             for path in (
diff --git a/backend/packages/harness/deerflow/config/paths.py b/backend/packages/harness/deerflow/config/paths.py
index f1ce7eae1..9fa633f54 100644
--- a/backend/packages/harness/deerflow/config/paths.py
+++ b/backend/packages/harness/deerflow/config/paths.py
@@ -3,6 +3,8 @@ import re
 import shutil
 from pathlib import Path, PureWindowsPath
 
+from deerflow.config.runtime_paths import runtime_home
+
 # Virtual path prefix seen by agents inside the sandbox
 VIRTUAL_PATH_PREFIX = "/mnt/user-data"
 
@@ -11,9 +13,8 @@ _SAFE_USER_ID_RE = re.compile(r"^[A-Za-z0-9_\-]+$")
 
 
 def _default_local_base_dir() -> Path:
-    """Return the repo-local DeerFlow state directory without relying on cwd."""
-    backend_dir = Path(__file__).resolve().parents[4]
-    return backend_dir / ".deer-flow"
+    """Return the caller project's writable DeerFlow state directory."""
+    return runtime_home()
 
 
 def _validate_thread_id(thread_id: str) -> str:
@@ -81,7 +82,7 @@ class Paths:
     BaseDir resolution (in priority order):
         1. Constructor argument `base_dir`
         2. DEER_FLOW_HOME environment variable
-        3. Repo-local fallback derived from this module path: `{backend_dir}/.deer-flow`
+        3. Caller project fallback: `{project_root}/.deer-flow`
     """
 
     def __init__(self, base_dir: str | Path | None = None) -> None:
diff --git a/backend/packages/harness/deerflow/config/runtime_paths.py b/backend/packages/harness/deerflow/config/runtime_paths.py
new file mode 100644
index 000000000..25157106f
--- /dev/null
+++ b/backend/packages/harness/deerflow/config/runtime_paths.py
@@ -0,0 +1,41 @@
+"""Runtime path resolution for standalone harness usage."""
+
+import os
+from pathlib import Path
+
+
+def project_root() -> Path:
+    """Return the caller project root for runtime-owned files."""
+    if env_root := os.getenv("DEER_FLOW_PROJECT_ROOT"):
+        root = Path(env_root).resolve()
+        if not root.exists():
+            raise ValueError(f"DEER_FLOW_PROJECT_ROOT is set to '{env_root}', but the resolved path '{root}' does not exist.")
+        if not root.is_dir():
+            raise ValueError(f"DEER_FLOW_PROJECT_ROOT is set to '{env_root}', but the resolved path '{root}' is not a directory.")
+        return root
+    return Path.cwd().resolve()
+
+
+def runtime_home() -> Path:
+    """Return the writable DeerFlow state directory."""
+    if env_home := os.getenv("DEER_FLOW_HOME"):
+        return Path(env_home).resolve()
+    return project_root() / ".deer-flow"
+
+
+def resolve_path(value: str | os.PathLike[str], *, base: Path | None = None) -> Path:
+    """Resolve absolute paths as-is and relative paths against the project root."""
+    path = Path(value)
+    if not path.is_absolute():
+        path = (base or project_root()) / path
+    return path.resolve()
+
+
+def existing_project_file(names: tuple[str, ...]) -> Path | None:
+    """Return the first existing named file under the project root."""
+    root = project_root()
+    for name in names:
+        candidate = root / name
+        if candidate.is_file():
+            return candidate
+    return None
diff --git a/backend/packages/harness/deerflow/config/skills_config.py b/backend/packages/harness/deerflow/config/skills_config.py
index 266a98b91..671b48fde 100644
--- a/backend/packages/harness/deerflow/config/skills_config.py
+++ b/backend/packages/harness/deerflow/config/skills_config.py
@@ -1,11 +1,9 @@
+import os
 from pathlib import Path
 
 from pydantic import BaseModel, Field
 
-
-def _default_repo_root() -> Path:
-    """Resolve the repo root without relying on the current working directory."""
-    return Path(__file__).resolve().parents[5]
+from deerflow.config.runtime_paths import project_root, resolve_path
 
 
 class SkillsConfig(BaseModel):
@@ -17,7 +15,7 @@ class SkillsConfig(BaseModel):
     )
     path: str | None = Field(
         default=None,
-        description="Path to skills directory. If not specified, defaults to ../skills relative to backend directory",
+        description="Path to skills directory. If not specified, defaults to skills under the caller project root.",
     )
     container_path: str = Field(
         default="/mnt/skills",
@@ -32,15 +30,11 @@ class SkillsConfig(BaseModel):
             Path to the skills directory
         """
         if self.path:
-            # Use configured path (can be absolute or relative)
-            path = Path(self.path)
-            if not path.is_absolute():
-                # If relative, resolve from the repo root for deterministic behavior.
-                path = _default_repo_root() / path
-            return path.resolve()
-        else:
-            # Default: <repo_root>/skills
-            return _default_repo_root() / "skills"
+            # Use configured path (can be absolute or relative to project root)
+            return resolve_path(self.path)
+        if env_path := os.getenv("DEER_FLOW_SKILLS_PATH"):
+            return resolve_path(env_path)
+        return project_root() / "skills"
 
     def get_skill_container_path(self, skill_name: str, category: str = "public") -> str:
         """
diff --git a/backend/packages/harness/deerflow/models/openai_codex_provider.py b/backend/packages/harness/deerflow/models/openai_codex_provider.py
index 86dee0fc6..95cf12b09 100644
--- a/backend/packages/harness/deerflow/models/openai_codex_provider.py
+++ b/backend/packages/harness/deerflow/models/openai_codex_provider.py
@@ -27,6 +27,34 @@ from deerflow.models.credential_loader import CodexCliCredential, load_codex_cli
 logger = logging.getLogger(__name__)
 
 CODEX_BASE_URL = "https://chatgpt.com/backend-api/codex"
+
+
+def _build_usage_metadata(oai_usage: dict) -> dict:
+    """Convert Codex/Responses API usage dict to LangChain usage_metadata format.
+
+    Maps OpenAI Responses API token usage fields to the dict structure that
+    LangChain AIMessage.usage_metadata expects. This avoids depending on
+    langchain_openai private helpers like ``_create_usage_metadata_responses``.
+    """
+    input_tokens = oai_usage.get("input_tokens", 0)
+    output_tokens = oai_usage.get("output_tokens", 0)
+    total_tokens = oai_usage.get("total_tokens", input_tokens + output_tokens)
+    metadata: dict = {
+        "input_tokens": input_tokens,
+        "output_tokens": output_tokens,
+        "total_tokens": total_tokens,
+    }
+    input_details = oai_usage.get("input_tokens_details") or {}
+    output_details = oai_usage.get("output_tokens_details") or {}
+    cache_read = input_details.get("cached_tokens")
+    if cache_read is not None:
+        metadata["input_token_details"] = {"cache_read": cache_read}
+    reasoning = output_details.get("reasoning_tokens")
+    if reasoning is not None:
+        metadata["output_token_details"] = {"reasoning": reasoning}
+    return metadata
+
+
 MAX_RETRIES = 3
 
 
@@ -346,6 +374,7 @@ class CodexChatModel(BaseChatModel):
                 )
 
         usage = response.get("usage", {})
+        usage_metadata = _build_usage_metadata(usage) if usage else None
         additional_kwargs = {}
         if reasoning_content:
             additional_kwargs["reasoning_content"] = reasoning_content
@@ -355,6 +384,7 @@ class CodexChatModel(BaseChatModel):
             tool_calls=tool_calls if tool_calls else [],
             invalid_tool_calls=invalid_tool_calls,
             additional_kwargs=additional_kwargs,
+            usage_metadata=usage_metadata,
             response_metadata={
                 "model": response.get("model", self.model),
                 "usage": usage,
diff --git a/backend/packages/harness/deerflow/persistence/thread_meta/memory.py b/backend/packages/harness/deerflow/persistence/thread_meta/memory.py
index ccf59ad42..fbe66fdaf 100644
--- a/backend/packages/harness/deerflow/persistence/thread_meta/memory.py
+++ b/backend/packages/harness/deerflow/persistence/thread_meta/memory.py
@@ -7,13 +7,13 @@ router for thread records.
 
 from __future__ import annotations
 
-import time
 from typing import Any
 
 from langgraph.store.base import BaseStore
 
 from deerflow.persistence.thread_meta.base import ThreadMetaStore
 from deerflow.runtime.user_context import AUTO, _AutoSentinel, resolve_user_id
+from deerflow.utils.time import coerce_iso, now_iso
 
 THREADS_NS: tuple[str, ...] = ("threads",)
 
@@ -48,7 +48,7 @@ class MemoryThreadMetaStore(ThreadMetaStore):
         metadata: dict | None = None,
     ) -> dict:
         resolved_user_id = resolve_user_id(user_id, method_name="MemoryThreadMetaStore.create")
-        now = time.time()
+        now = now_iso()
         record: dict[str, Any] = {
             "thread_id": thread_id,
             "assistant_id": assistant_id,
@@ -106,7 +106,7 @@ class MemoryThreadMetaStore(ThreadMetaStore):
         if record is None:
             return
         record["display_name"] = display_name
-        record["updated_at"] = time.time()
+        record["updated_at"] = now_iso()
         await self._store.aput(THREADS_NS, thread_id, record)
 
     async def update_status(self, thread_id: str, status: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
@@ -114,7 +114,7 @@ class MemoryThreadMetaStore(ThreadMetaStore):
         if record is None:
             return
         record["status"] = status
-        record["updated_at"] = time.time()
+        record["updated_at"] = now_iso()
         await self._store.aput(THREADS_NS, thread_id, record)
 
     async def update_metadata(self, thread_id: str, metadata: dict, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
@@ -124,7 +124,7 @@ class MemoryThreadMetaStore(ThreadMetaStore):
         merged = dict(record.get("metadata") or {})
         merged.update(metadata)
         record["metadata"] = merged
-        record["updated_at"] = time.time()
+        record["updated_at"] = now_iso()
         await self._store.aput(THREADS_NS, thread_id, record)
 
     async def delete(self, thread_id: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
@@ -144,6 +144,8 @@ class MemoryThreadMetaStore(ThreadMetaStore):
             "display_name": val.get("display_name"),
             "status": val.get("status", "idle"),
             "metadata": val.get("metadata", {}),
-            "created_at": str(val.get("created_at", "")),
-            "updated_at": str(val.get("updated_at", "")),
+            # ``coerce_iso`` heals legacy unix-second values written by
+            # earlier Gateway versions that called ``str(time.time())``.
+            "created_at": coerce_iso(val.get("created_at", "")),
+            "updated_at": coerce_iso(val.get("updated_at", "")),
         }
diff --git a/backend/packages/harness/deerflow/runtime/runs/manager.py b/backend/packages/harness/deerflow/runtime/runs/manager.py
index a54a408b8..533342c87 100644
--- a/backend/packages/harness/deerflow/runtime/runs/manager.py
+++ b/backend/packages/harness/deerflow/runtime/runs/manager.py
@@ -6,9 +6,10 @@ import asyncio
 import logging
 import uuid
 from dataclasses import dataclass, field
-from datetime import UTC, datetime
 from typing import TYPE_CHECKING
 
+from deerflow.utils.time import now_iso as _now_iso
+
 from .schemas import DisconnectMode, RunStatus
 
 if TYPE_CHECKING:
@@ -17,10 +18,6 @@ if TYPE_CHECKING:
 logger = logging.getLogger(__name__)
 
 
-def _now_iso() -> str:
-    return datetime.now(UTC).isoformat()
-
-
 @dataclass
 class RunRecord:
     """Mutable record for a single run."""
diff --git a/backend/packages/harness/deerflow/runtime/runs/worker.py b/backend/packages/harness/deerflow/runtime/runs/worker.py
index 1223c2127..2aecb9a1b 100644
--- a/backend/packages/harness/deerflow/runtime/runs/worker.py
+++ b/backend/packages/harness/deerflow/runtime/runs/worker.py
@@ -21,7 +21,9 @@ import inspect
 import logging
 from dataclasses import dataclass, field
 from functools import lru_cache
-from typing import TYPE_CHECKING, Any, Literal
+from typing import TYPE_CHECKING, Any, Literal, cast
+
+from langgraph.checkpoint.base import empty_checkpoint
 
 if TYPE_CHECKING:
     from langchain_core.messages import HumanMessage
@@ -39,12 +41,19 @@ logger = logging.getLogger(__name__)
 _VALID_LG_MODES = {"values", "updates", "checkpoints", "tasks", "debug", "messages", "custom"}
 
 
-def _build_runtime_context(thread_id: str, run_id: str, caller_context: Any | None) -> dict[str, Any]:
+def _build_runtime_context(
+    thread_id: str,
+    run_id: str,
+    caller_context: Any | None,
+    app_config: AppConfig | None = None,
+) -> dict[str, Any]:
     """Build the dict that becomes ``ToolRuntime.context`` for the run.
 
     Always includes ``thread_id`` and ``run_id``. Additional keys from the caller's
     ``config['context']`` (e.g. ``agent_name`` for the bootstrap flow — issue #2677)
-    are merged in but never override ``thread_id``/``run_id``.
+    are merged in but never override ``thread_id``/``run_id``. The resolved
+    ``AppConfig`` is added by the worker so tools can consume it without ambient
+    global lookups.
 
     langgraph 1.1+ surfaces this as ``runtime.context`` via the parent runtime stored
     under ``config['configurable']['__pregel_runtime']`` — see
@@ -54,6 +63,8 @@ def _build_runtime_context(thread_id: str, run_id: str, caller_context: Any | No
     if isinstance(caller_context, dict):
         for key, value in caller_context.items():
             runtime_ctx.setdefault(key, value)
+    if app_config is not None:
+        runtime_ctx["app_config"] = app_config
     return runtime_ctx
 
 
@@ -74,6 +85,18 @@ class RunContext:
     app_config: AppConfig | None = field(default=None)
 
 
+def _install_runtime_context(config: dict, runtime_context: dict[str, Any]) -> None:
+    existing_context = config.get("context")
+    if isinstance(existing_context, dict):
+        existing_context.setdefault("thread_id", runtime_context["thread_id"])
+        existing_context.setdefault("run_id", runtime_context["run_id"])
+        if "app_config" in runtime_context:
+            existing_context["app_config"] = runtime_context["app_config"]
+        return
+
+    config["context"] = dict(runtime_context)
+
+
 def _compute_agent_factory_supports_app_config(agent_factory: Any) -> bool:
     try:
         return "app_config" in inspect.signature(agent_factory).parameters
@@ -191,11 +214,9 @@ async def run_agent(
         # access thread-level data. langgraph-cli does this automatically; we must do it
         # manually here because we drive the graph through ``agent.astream(config=...)``
         # without passing the official ``context=`` parameter.
-        runtime_ctx = _build_runtime_context(thread_id, run_id, config.get("context"))
-        if "context" in config and isinstance(config["context"], dict):
-            config["context"].setdefault("thread_id", thread_id)
-            config["context"].setdefault("run_id", run_id)
-        runtime = Runtime(context=runtime_ctx, store=store)
+        runtime_ctx = _build_runtime_context(thread_id, run_id, config.get("context"), ctx.app_config)
+        _install_runtime_context(config, runtime_ctx)
+        runtime = Runtime(context=cast(Any, runtime_ctx), store=store)
         config.setdefault("configurable", {})["__pregel_runtime"] = runtime
 
         # Inject RunJournal as a LangChain callback handler.
@@ -423,6 +444,12 @@ async def _rollback_to_pre_run_checkpoint(
     if checkpoint_to_restore.get("id") is None:
         logger.warning("Run %s rollback skipped: pre-run checkpoint has no checkpoint id", run_id)
         return
+    restore_marker = _new_checkpoint_marker()
+    checkpoint_to_restore = {
+        **checkpoint_to_restore,
+        "id": restore_marker["id"],
+        "ts": restore_marker["ts"],
+    }
     metadata = pre_run_snapshot.get("metadata", {})
     metadata_to_restore = metadata if isinstance(metadata, dict) else {}
     raw_checkpoint_ns = pre_run_snapshot.get("checkpoint_ns")
@@ -474,6 +501,11 @@ async def _rollback_to_pre_run_checkpoint(
         )
 
 
+def _new_checkpoint_marker() -> dict[str, str]:
+    marker = empty_checkpoint()
+    return {"id": marker["id"], "ts": marker["ts"]}
+
+
 def _lg_mode_to_sse_event(mode: str) -> str:
     """Map LangGraph internal stream_mode name to SSE event name.
 
diff --git a/backend/packages/harness/deerflow/skills/storage/local_skill_storage.py b/backend/packages/harness/deerflow/skills/storage/local_skill_storage.py
index 047cd6163..4b7dffde4 100644
--- a/backend/packages/harness/deerflow/skills/storage/local_skill_storage.py
+++ b/backend/packages/harness/deerflow/skills/storage/local_skill_storage.py
@@ -12,7 +12,7 @@ from collections.abc import Iterable
 from datetime import UTC, datetime
 from pathlib import Path
 
-from deerflow.config.skills_config import _default_repo_root
+from deerflow.config.runtime_paths import resolve_path
 from deerflow.skills.storage.skill_storage import SKILL_MD_FILE, SkillStorage
 from deerflow.skills.types import SkillCategory
 
@@ -44,10 +44,7 @@ class LocalSkillStorage(SkillStorage):
             config = app_config or get_app_config()
             self._host_root: Path = config.skills.get_skills_path()
         else:
-            path = Path(host_path)
-            if not path.is_absolute():
-                path = _default_repo_root() / path
-            self._host_root = path.resolve()
+            self._host_root = resolve_path(host_path)
 
     # ------------------------------------------------------------------
     # Abstract operation implementations
diff --git a/backend/packages/harness/deerflow/subagents/config.py b/backend/packages/harness/deerflow/subagents/config.py
index a2c961b9d..b0b094e28 100644
--- a/backend/packages/harness/deerflow/subagents/config.py
+++ b/backend/packages/harness/deerflow/subagents/config.py
@@ -1,6 +1,10 @@
 """Subagent configuration definitions."""
 
 from dataclasses import dataclass, field
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from deerflow.config.app_config import AppConfig
 
 
 @dataclass
@@ -29,3 +33,24 @@ class SubagentConfig:
     model: str = "inherit"
     max_turns: int = 50
     timeout_seconds: int = 900
+
+
+def _default_model_name(app_config: "AppConfig") -> str:
+    if not app_config.models:
+        raise ValueError("No chat models are configured. Please configure at least one model in config.yaml.")
+    return app_config.models[0].name
+
+
+def resolve_subagent_model_name(config: SubagentConfig, parent_model: str | None, *, app_config: "AppConfig | None" = None) -> str:
+    """Resolve the effective model name a subagent should use."""
+    if config.model != "inherit":
+        return config.model
+
+    if parent_model is not None:
+        return parent_model
+
+    if app_config is None:
+        from deerflow.config import get_app_config
+
+        app_config = get_app_config()
+    return _default_model_name(app_config)
diff --git a/backend/packages/harness/deerflow/subagents/executor.py b/backend/packages/harness/deerflow/subagents/executor.py
index 539244af8..2fe5c05dc 100644
--- a/backend/packages/harness/deerflow/subagents/executor.py
+++ b/backend/packages/harness/deerflow/subagents/executor.py
@@ -20,9 +20,10 @@ from langchain_core.messages import AIMessage, HumanMessage, SystemMessage
 from langchain_core.runnables import RunnableConfig
 
 from deerflow.agents.thread_state import SandboxState, ThreadDataState, ThreadState
+from deerflow.config import get_app_config
 from deerflow.config.app_config import AppConfig
 from deerflow.models import create_chat_model
-from deerflow.subagents.config import SubagentConfig
+from deerflow.subagents.config import SubagentConfig, resolve_subagent_model_name
 
 logger = logging.getLogger(__name__)
 
@@ -167,6 +168,8 @@ def _get_isolated_subagent_loop() -> asyncio.AbstractEventLoop:
             _isolated_subagent_loop_thread = thread
             _isolated_subagent_loop_started = started_event
 
+        if _isolated_subagent_loop is None:
+            raise RuntimeError("Isolated subagent event loop is not initialized")
         return _isolated_subagent_loop
 
 
@@ -213,21 +216,6 @@ def _filter_tools(
     return filtered
 
 
-def _get_model_name(config: SubagentConfig, parent_model: str | None) -> str | None:
-    """Resolve the model name for a subagent.
-
-    Args:
-        config: Subagent configuration.
-        parent_model: The parent agent's model name.
-
-    Returns:
-        Model name to use, or None to use default.
-    """
-    if config.model == "inherit":
-        return parent_model
-    return config.model
-
-
 class SubagentExecutor:
     """Executor for running subagents."""
 
@@ -247,9 +235,9 @@ class SubagentExecutor:
         Args:
             config: Subagent configuration.
             tools: List of all available tools (will be filtered).
-            app_config: Resolved AppConfig; threaded into middleware factories
-                at agent-build time. When None, ``_create_agent`` falls back to
-                ``get_app_config()`` (matches the lead-agent factory's pattern).
+            app_config: Resolved AppConfig. When None, ``_create_agent`` falls
+                back to ``get_app_config()`` (matches the lead-agent factory's
+                pattern).
             parent_model: The parent agent's model name for inheritance.
             sandbox_state: Sandbox state from parent agent.
             thread_data: Thread data from parent agent.
@@ -259,6 +247,13 @@ class SubagentExecutor:
         self.config = config
         self.app_config = app_config
         self.parent_model = parent_model
+        # Resolve eagerly only when it does not require loading config.yaml; otherwise defer
+        # to _create_agent (which already loads app_config) so unit tests can construct
+        # executors without a config file present.
+        if config.model != "inherit" or parent_model is not None or app_config is not None:
+            self.model_name: str | None = resolve_subagent_model_name(config, parent_model, app_config=app_config)
+        else:
+            self.model_name = None
         self.sandbox_state = sandbox_state
         self.thread_data = thread_data
         self.thread_id = thread_id
@@ -276,17 +271,15 @@ class SubagentExecutor:
 
     def _create_agent(self):
         """Create the agent instance."""
-        # Mirror lead-agent factory pattern: prefer explicit app_config,
-        # fall back to ambient lookup at agent-build time.
-        from deerflow.config import get_app_config
-
-        resolved_app_config = self.app_config or get_app_config()
-        model_name = _get_model_name(self.config, self.parent_model)
-        model = create_chat_model(name=model_name, thinking_enabled=False, app_config=resolved_app_config)
+        app_config = self.app_config or get_app_config()
+        if self.model_name is None:
+            self.model_name = resolve_subagent_model_name(self.config, self.parent_model, app_config=app_config)
+        model = create_chat_model(name=self.model_name, thinking_enabled=False, app_config=app_config)
 
         from deerflow.agents.middlewares.tool_error_handling_middleware import build_subagent_runtime_middlewares
 
-        middlewares = build_subagent_runtime_middlewares(app_config=resolved_app_config, lazy_init=True)
+        # Reuse shared middleware composition with lead agent.
+        middlewares = build_subagent_runtime_middlewares(app_config=app_config, model_name=self.model_name, lazy_init=True)
 
         return create_agent(
             model=model,
@@ -317,8 +310,10 @@ class SubagentExecutor:
         try:
             from deerflow.skills.storage import get_or_new_skill_storage
 
+            storage_kwargs = {"app_config": self.app_config} if self.app_config is not None else {}
+            storage = await asyncio.to_thread(get_or_new_skill_storage, **storage_kwargs)
             # Use asyncio.to_thread to avoid blocking the event loop (LangGraph ASGI requirement)
-            all_skills = await asyncio.to_thread(get_or_new_skill_storage().load_skills, enabled_only=True)
+            all_skills = await asyncio.to_thread(storage.load_skills, enabled_only=True)
             logger.info(f"[trace={self.trace_id}] Subagent {self.config.name} loaded {len(all_skills)} enabled skills from disk")
         except Exception:
             logger.warning(f"[trace={self.trace_id}] Failed to load skills for subagent {self.config.name}", exc_info=True)
@@ -404,6 +399,10 @@ class SubagentExecutor:
                 status=SubagentStatus.RUNNING,
                 started_at=datetime.now(),
             )
+        ai_messages = result.ai_messages
+        if ai_messages is None:
+            ai_messages = []
+            result.ai_messages = ai_messages
 
         try:
             agent = self._create_agent()
@@ -413,10 +412,12 @@ class SubagentExecutor:
             run_config: RunnableConfig = {
                 "recursion_limit": self.config.max_turns,
             }
-            context = {}
+            context: dict[str, Any] = {}
             if self.thread_id:
                 run_config["configurable"] = {"thread_id": self.thread_id}
                 context["thread_id"] = self.thread_id
+            if self.app_config is not None:
+                context["app_config"] = self.app_config
 
             logger.info(f"[trace={self.trace_id}] Subagent {self.config.name} starting async execution with max_turns={self.config.max_turns}")
 
@@ -463,13 +464,13 @@ class SubagentExecutor:
                         message_id = message_dict.get("id")
                         is_duplicate = False
                         if message_id:
-                            is_duplicate = any(msg.get("id") == message_id for msg in result.ai_messages)
+                            is_duplicate = any(msg.get("id") == message_id for msg in ai_messages)
                         else:
-                            is_duplicate = message_dict in result.ai_messages
+                            is_duplicate = message_dict in ai_messages
 
                         if not is_duplicate:
-                            result.ai_messages.append(message_dict)
-                            logger.info(f"[trace={self.trace_id}] Subagent {self.config.name} captured AI message #{len(result.ai_messages)}")
+                            ai_messages.append(message_dict)
+                            logger.info(f"[trace={self.trace_id}] Subagent {self.config.name} captured AI message #{len(ai_messages)}")
 
             logger.info(f"[trace={self.trace_id}] Subagent {self.config.name} completed async execution")
 
diff --git a/backend/packages/harness/deerflow/subagents/registry.py b/backend/packages/harness/deerflow/subagents/registry.py
index b34d7e9bd..4c4f3f183 100644
--- a/backend/packages/harness/deerflow/subagents/registry.py
+++ b/backend/packages/harness/deerflow/subagents/registry.py
@@ -2,6 +2,7 @@
 
 import logging
 from dataclasses import replace
+from typing import Any
 
 from deerflow.sandbox.security import is_host_bash_allowed
 from deerflow.subagents.builtins import BUILTIN_SUBAGENTS
@@ -10,19 +11,26 @@ from deerflow.subagents.config import SubagentConfig
 logger = logging.getLogger(__name__)
 
 
-def _build_custom_subagent_config(name: str) -> SubagentConfig | None:
+def _resolve_subagents_app_config(app_config: Any | None = None):
+    if app_config is None:
+        from deerflow.config.subagents_config import get_subagents_app_config
+
+        return get_subagents_app_config()
+    return getattr(app_config, "subagents", app_config)
+
+
+def _build_custom_subagent_config(name: str, *, app_config: Any | None = None) -> SubagentConfig | None:
     """Build a SubagentConfig from config.yaml custom_agents section.
 
     Args:
         name: The name of the custom subagent.
+        app_config: Optional AppConfig or SubagentsAppConfig to resolve from.
 
     Returns:
         SubagentConfig if found in custom_agents, None otherwise.
     """
-    from deerflow.config.subagents_config import get_subagents_app_config
-
-    app_config = get_subagents_app_config()
-    custom = app_config.custom_agents.get(name)
+    subagents_config = _resolve_subagents_app_config(app_config)
+    custom = subagents_config.custom_agents.get(name)
     if custom is None:
         return None
 
@@ -39,7 +47,7 @@ def _build_custom_subagent_config(name: str) -> SubagentConfig | None:
     )
 
 
-def get_subagent_config(name: str) -> SubagentConfig | None:
+def get_subagent_config(name: str, *, app_config: Any | None = None) -> SubagentConfig | None:
     """Get a subagent configuration by name, with config.yaml overrides applied.
 
     Resolution order (mirrors Codex's config layering):
@@ -49,6 +57,7 @@ def get_subagent_config(name: str) -> SubagentConfig | None:
 
     Args:
         name: The name of the subagent.
+        app_config: Optional AppConfig or SubagentsAppConfig to resolve overrides from.
 
     Returns:
         SubagentConfig if found (with any config.yaml overrides applied), None otherwise.
@@ -56,7 +65,7 @@ def get_subagent_config(name: str) -> SubagentConfig | None:
     # Step 1: Look up built-in, then fall back to custom_agents
     config = BUILTIN_SUBAGENTS.get(name)
     if config is None:
-        config = _build_custom_subagent_config(name)
+        config = _build_custom_subagent_config(name, app_config=app_config)
     if config is None:
         return None
 
@@ -65,12 +74,9 @@ def get_subagent_config(name: str) -> SubagentConfig | None:
     # (timeout_seconds, max_turns at the top level) apply to built-in agents
     # but must NOT override custom agents' own values — custom agents define
     # their own defaults in the custom_agents section.
-    # Lazy import to avoid circular deps.
-    from deerflow.config.subagents_config import get_subagents_app_config
-
-    app_config = get_subagents_app_config()
+    subagents_config = _resolve_subagents_app_config(app_config)
     is_builtin = name in BUILTIN_SUBAGENTS
-    agent_override = app_config.agents.get(name)
+    agent_override = subagents_config.agents.get(name)
 
     overrides = {}
 
@@ -79,27 +85,27 @@ def get_subagent_config(name: str) -> SubagentConfig | None:
         if agent_override.timeout_seconds != config.timeout_seconds:
             logger.debug("Subagent '%s': timeout overridden (%ss -> %ss)", name, config.timeout_seconds, agent_override.timeout_seconds)
             overrides["timeout_seconds"] = agent_override.timeout_seconds
-    elif is_builtin and app_config.timeout_seconds != config.timeout_seconds:
-        logger.debug("Subagent '%s': timeout from global default (%ss -> %ss)", name, config.timeout_seconds, app_config.timeout_seconds)
-        overrides["timeout_seconds"] = app_config.timeout_seconds
+    elif is_builtin and subagents_config.timeout_seconds != config.timeout_seconds:
+        logger.debug("Subagent '%s': timeout from global default (%ss -> %ss)", name, config.timeout_seconds, subagents_config.timeout_seconds)
+        overrides["timeout_seconds"] = subagents_config.timeout_seconds
 
     # Max turns: per-agent override > global default (builtins only) > config's own value
     if agent_override is not None and agent_override.max_turns is not None:
         if agent_override.max_turns != config.max_turns:
             logger.debug("Subagent '%s': max_turns overridden (%s -> %s)", name, config.max_turns, agent_override.max_turns)
             overrides["max_turns"] = agent_override.max_turns
-    elif is_builtin and app_config.max_turns is not None and app_config.max_turns != config.max_turns:
-        logger.debug("Subagent '%s': max_turns from global default (%s -> %s)", name, config.max_turns, app_config.max_turns)
-        overrides["max_turns"] = app_config.max_turns
+    elif is_builtin and subagents_config.max_turns is not None and subagents_config.max_turns != config.max_turns:
+        logger.debug("Subagent '%s': max_turns from global default (%s -> %s)", name, config.max_turns, subagents_config.max_turns)
+        overrides["max_turns"] = subagents_config.max_turns
 
     # Model: per-agent override only (no global default for model)
-    effective_model = app_config.get_model_for(name)
+    effective_model = subagents_config.get_model_for(name)
     if effective_model is not None and effective_model != config.model:
         logger.debug("Subagent '%s': model overridden (%s -> %s)", name, config.model, effective_model)
         overrides["model"] = effective_model
 
     # Skills: per-agent override only (no global default for skills)
-    effective_skills = app_config.get_skills_for(name)
+    effective_skills = subagents_config.get_skills_for(name)
     if effective_skills is not None and effective_skills != config.skills:
         logger.debug("Subagent '%s': skills overridden (%s -> %s)", name, config.skills, effective_skills)
         overrides["skills"] = effective_skills
@@ -110,21 +116,21 @@ def get_subagent_config(name: str) -> SubagentConfig | None:
     return config
 
 
-def list_subagents() -> list[SubagentConfig]:
+def list_subagents(*, app_config: Any | None = None) -> list[SubagentConfig]:
     """List all available subagent configurations (with config.yaml overrides applied).
 
     Returns:
         List of all registered SubagentConfig instances (built-in + custom).
     """
     configs = []
-    for name in get_subagent_names():
-        config = get_subagent_config(name)
+    for name in get_subagent_names(app_config=app_config):
+        config = get_subagent_config(name, app_config=app_config)
         if config is not None:
             configs.append(config)
     return configs
 
 
-def get_subagent_names() -> list[str]:
+def get_subagent_names(*, app_config: Any | None = None) -> list[str]:
     """Get all available subagent names (built-in + custom).
 
     Returns:
@@ -133,25 +139,23 @@ def get_subagent_names() -> list[str]:
     names = list(BUILTIN_SUBAGENTS.keys())
 
     # Merge custom_agents from config.yaml
-    from deerflow.config.subagents_config import get_subagents_app_config
-
-    app_config = get_subagents_app_config()
-    for custom_name in app_config.custom_agents:
+    subagents_config = _resolve_subagents_app_config(app_config)
+    for custom_name in subagents_config.custom_agents:
         if custom_name not in names:
             names.append(custom_name)
 
     return names
 
 
-def get_available_subagent_names() -> list[str]:
+def get_available_subagent_names(*, app_config: Any | None = None) -> list[str]:
     """Get subagent names that should be exposed to the active runtime.
 
     Returns:
         List of subagent names visible to the current sandbox configuration.
     """
-    names = get_subagent_names()
+    names = get_subagent_names(app_config=app_config)
     try:
-        host_bash_allowed = is_host_bash_allowed()
+        host_bash_allowed = is_host_bash_allowed(app_config) if hasattr(app_config, "sandbox") else is_host_bash_allowed()
     except Exception:
         logger.debug("Could not determine host bash availability; exposing all subagents")
         return names
diff --git a/backend/packages/harness/deerflow/tools/builtins/task_tool.py b/backend/packages/harness/deerflow/tools/builtins/task_tool.py
index 59613272c..1328507b2 100644
--- a/backend/packages/harness/deerflow/tools/builtins/task_tool.py
+++ b/backend/packages/harness/deerflow/tools/builtins/task_tool.py
@@ -4,20 +4,39 @@ import asyncio
 import logging
 import uuid
 from dataclasses import replace
-from typing import Annotated
+from typing import TYPE_CHECKING, Annotated, Any, cast
 
 from langchain.tools import InjectedToolCallId, ToolRuntime, tool
 from langgraph.config import get_stream_writer
 from langgraph.typing import ContextT
 
 from deerflow.agents.thread_state import ThreadState
+from deerflow.config import get_app_config
 from deerflow.sandbox.security import LOCAL_BASH_SUBAGENT_DISABLED_MESSAGE, is_host_bash_allowed
 from deerflow.subagents import SubagentExecutor, get_available_subagent_names, get_subagent_config
-from deerflow.subagents.executor import SubagentStatus, cleanup_background_task, get_background_task_result, request_cancel_background_task
+from deerflow.subagents.config import resolve_subagent_model_name
+from deerflow.subagents.executor import (
+    SubagentStatus,
+    cleanup_background_task,
+    get_background_task_result,
+    request_cancel_background_task,
+)
+
+if TYPE_CHECKING:
+    from deerflow.config.app_config import AppConfig
 
 logger = logging.getLogger(__name__)
 
 
+def _get_runtime_app_config(runtime: Any) -> "AppConfig | None":
+    context = getattr(runtime, "context", None)
+    if isinstance(context, dict):
+        app_config = context.get("app_config")
+        if app_config is not None:
+            return cast("AppConfig", app_config)
+    return None
+
+
 def _merge_skill_allowlists(parent: list[str] | None, child: list[str] | None) -> list[str] | None:
     """Return the effective subagent skill allowlist under the parent policy."""
     if parent is None:
@@ -74,15 +93,18 @@ async def task_tool(
         subagent_type: The type of subagent to use. ALWAYS PROVIDE THIS PARAMETER THIRD.
         max_turns: Optional maximum number of agent turns. Defaults to subagent's configured max.
     """
-    available_subagent_names = get_available_subagent_names()
+    runtime_app_config = _get_runtime_app_config(runtime)
+    available_subagent_names = get_available_subagent_names(app_config=runtime_app_config) if runtime_app_config is not None else get_available_subagent_names()
 
     # Get subagent configuration
-    config = get_subagent_config(subagent_type)
+    config = get_subagent_config(subagent_type, app_config=runtime_app_config) if runtime_app_config is not None else get_subagent_config(subagent_type)
     if config is None:
         available = ", ".join(available_subagent_names)
         return f"Error: Unknown subagent type '{subagent_type}'. Available: {available}"
-    if subagent_type == "bash" and not is_host_bash_allowed():
-        return f"Error: {LOCAL_BASH_SUBAGENT_DISABLED_MESSAGE}"
+    if subagent_type == "bash":
+        host_bash_allowed = is_host_bash_allowed(runtime_app_config) if runtime_app_config is not None else is_host_bash_allowed()
+        if not host_bash_allowed:
+            return f"Error: {LOCAL_BASH_SUBAGENT_DISABLED_MESSAGE}"
 
     # Build config overrides
     overrides: dict = {}
@@ -129,20 +151,34 @@ async def task_tool(
 
     # Inherit parent agent's tool_groups so subagents respect the same restrictions
     parent_tool_groups = metadata.get("tool_groups")
+    resolved_app_config = runtime_app_config
+    if config.model == "inherit" and parent_model is None and resolved_app_config is None:
+        resolved_app_config = get_app_config()
+    effective_model = resolve_subagent_model_name(config, parent_model, app_config=resolved_app_config)
 
     # Subagents should not have subagent tools enabled (prevent recursive nesting)
-    tools = get_available_tools(model_name=parent_model, groups=parent_tool_groups, subagent_enabled=False)
+    available_tools_kwargs = {
+        "model_name": effective_model,
+        "groups": parent_tool_groups,
+        "subagent_enabled": False,
+    }
+    if resolved_app_config is not None:
+        available_tools_kwargs["app_config"] = resolved_app_config
+    tools = get_available_tools(**available_tools_kwargs)
 
     # Create executor
-    executor = SubagentExecutor(
-        config=config,
-        tools=tools,
-        parent_model=parent_model,
-        sandbox_state=sandbox_state,
-        thread_data=thread_data,
-        thread_id=thread_id,
-        trace_id=trace_id,
-    )
+    executor_kwargs = {
+        "config": config,
+        "tools": tools,
+        "parent_model": parent_model,
+        "sandbox_state": sandbox_state,
+        "thread_data": thread_data,
+        "thread_id": thread_id,
+        "trace_id": trace_id,
+    }
+    if resolved_app_config is not None:
+        executor_kwargs["app_config"] = resolved_app_config
+    executor = SubagentExecutor(**executor_kwargs)
 
     # Start background execution (always async to prevent blocking)
     # Use tool_call_id as task_id for better traceability
@@ -177,11 +213,12 @@ async def task_tool(
                 last_status = result.status
 
             # Check for new AI messages and send task_running events
-            current_message_count = len(result.ai_messages)
+            ai_messages = result.ai_messages or []
+            current_message_count = len(ai_messages)
             if current_message_count > last_message_count:
                 # Send task_running event for each new message
                 for i in range(last_message_count, current_message_count):
-                    message = result.ai_messages[i]
+                    message = ai_messages[i]
                     writer(
                         {
                             "type": "task_running",
diff --git a/backend/packages/harness/deerflow/tools/tools.py b/backend/packages/harness/deerflow/tools/tools.py
index 2ba6eb6b4..14d93e65f 100644
--- a/backend/packages/harness/deerflow/tools/tools.py
+++ b/backend/packages/harness/deerflow/tools/tools.py
@@ -141,10 +141,14 @@ def get_available_tools(
     # Add invoke_acp_agent tool if any ACP agents are configured
     acp_tools: list[BaseTool] = []
     try:
-        from deerflow.config.acp_config import get_acp_agents
         from deerflow.tools.builtins.invoke_acp_agent_tool import build_invoke_acp_agent_tool
 
-        acp_agents = get_acp_agents()
+        if app_config is None:
+            from deerflow.config.acp_config import get_acp_agents
+
+            acp_agents = get_acp_agents()
+        else:
+            acp_agents = getattr(config, "acp_agents", {}) or {}
         if acp_agents:
             acp_tools.append(build_invoke_acp_agent_tool(acp_agents))
             logger.info(f"Including invoke_acp_agent tool ({len(acp_agents)} agent(s): {list(acp_agents.keys())})")
diff --git a/backend/packages/harness/deerflow/uploads/manager.py b/backend/packages/harness/deerflow/uploads/manager.py
index c36151b38..1a1b63f09 100644
--- a/backend/packages/harness/deerflow/uploads/manager.py
+++ b/backend/packages/harness/deerflow/uploads/manager.py
@@ -4,8 +4,10 @@ Pure business logic — no FastAPI/HTTP dependencies.
 Both Gateway and Client delegate to these functions.
 """
 
+import errno
 import os
 import re
+import stat
 from pathlib import Path
 from urllib.parse import quote
 
@@ -17,6 +19,10 @@ class PathTraversalError(ValueError):
     """Raised when a path escapes its allowed base directory."""
 
 
+class UnsafeUploadPathError(ValueError):
+    """Raised when an upload destination is not a safe regular file path."""
+
+
 # thread_id must be alphanumeric, hyphens, underscores, or dots only.
 _SAFE_THREAD_ID = re.compile(r"^[a-zA-Z0-9._-]+$")
 
@@ -109,6 +115,64 @@ def validate_path_traversal(path: Path, base: Path) -> None:
         raise PathTraversalError("Path traversal detected") from None
 
 
+def open_upload_file_no_symlink(base_dir: Path, filename: str) -> tuple[Path, object]:
+    """Open an upload destination for safe streaming writes.
+
+    Upload directories may be mounted into local sandboxes. A sandbox process can
+    therefore leave a symlink at a future upload filename. Normal ``Path.write_bytes``
+    follows that link and can overwrite files outside the uploads directory with
+    gateway privileges. This helper rejects symlink destinations and uses
+    ``O_NOFOLLOW`` where available so the final path component cannot be raced into
+    a symlink between validation and open.
+    """
+    safe_name = normalize_filename(filename)
+    dest = base_dir / safe_name
+
+    try:
+        st = os.lstat(dest)
+    except FileNotFoundError:
+        st = None
+
+    if st is not None and not stat.S_ISREG(st.st_mode):
+        raise UnsafeUploadPathError(f"Upload destination is not a regular file: {safe_name}")
+
+    validate_path_traversal(dest, base_dir)
+
+    if not hasattr(os, "O_NOFOLLOW"):
+        raise UnsafeUploadPathError("Upload writes require O_NOFOLLOW support")
+
+    flags = os.O_WRONLY | os.O_CREAT | os.O_NOFOLLOW
+    if hasattr(os, "O_NONBLOCK"):
+        flags |= os.O_NONBLOCK
+
+    try:
+        fd = os.open(dest, flags, 0o600)
+    except OSError as exc:
+        if exc.errno in {errno.ELOOP, errno.EISDIR, errno.ENOTDIR, errno.ENXIO, errno.EAGAIN}:
+            raise UnsafeUploadPathError(f"Unsafe upload destination: {safe_name}") from exc
+        raise
+
+    try:
+        opened_stat = os.fstat(fd)
+        if not stat.S_ISREG(opened_stat.st_mode) or opened_stat.st_nlink != 1:
+            raise UnsafeUploadPathError(f"Upload destination is not an exclusive regular file: {safe_name}")
+        os.ftruncate(fd, 0)
+        fh = os.fdopen(fd, "wb")
+        fd = -1
+    finally:
+        if fd >= 0:
+            os.close(fd)
+    return dest, fh
+
+
+def write_upload_file_no_symlink(base_dir: Path, filename: str, data: bytes) -> Path:
+    """Write upload bytes without following a pre-existing destination symlink."""
+    dest, fh = open_upload_file_no_symlink(base_dir, filename)
+    with fh:
+        fh.write(data)
+    return dest
+
+
 def list_files_in_dir(directory: Path) -> dict:
     """List files (not directories) in *directory*.
 
diff --git a/backend/packages/harness/deerflow/utils/time.py b/backend/packages/harness/deerflow/utils/time.py
new file mode 100644
index 000000000..307a4b6b0
--- /dev/null
+++ b/backend/packages/harness/deerflow/utils/time.py
@@ -0,0 +1,75 @@
+"""ISO 8601 timestamp helpers for the Gateway and embedded runtime.
+
+DeerFlow stores and serializes thread/run timestamps as ISO 8601 UTC
+strings to match the LangGraph Platform schema (see
+``langgraph_sdk.schema.Thread``, where ``created_at`` / ``updated_at``
+are ``datetime`` and JSON-encode to ISO 8601). All timestamp generation
+should funnel through :func:`now_iso` so the wire format stays
+consistent across endpoints, the embedded ``RunManager``, and the
+checkpoint metadata written by the Gateway.
+
+:func:`coerce_iso` provides a forward-compatible read path for legacy
+records that historically stored ``str(time.time())`` floats.
+"""
+
+from __future__ import annotations
+
+import re
+from datetime import UTC, datetime
+
+__all__ = ["coerce_iso", "now_iso"]
+
+_UNIX_TIMESTAMP_PATTERN = re.compile(r"^\d{10}(?:\.\d+)?$")
+"""Matches the unix-timestamp string shape historically written by
+``str(time.time())`` (10-digit seconds with optional fractional part).
+The 10-digit anchor avoids accidentally rewriting ISO years like
+``"2026"`` and stays valid until the year 2286.
+"""
+
+
+def now_iso() -> str:
+    """Return the current UTC time as an ISO 8601 string.
+
+    Example: ``"2026-04-27T03:19:46.511479+00:00"``.
+    """
+    return datetime.now(UTC).isoformat()
+
+
+def coerce_iso(value: object) -> str:
+    """Best-effort coerce a stored timestamp to an ISO 8601 string.
+
+    Translates legacy unix-timestamp floats / strings written by older
+    DeerFlow versions into ISO without a one-shot migration. ISO strings
+    pass through unchanged; ``datetime`` instances are normalised to UTC
+    (tz-naive values are assumed to be UTC) and emitted via
+    ``isoformat()`` so the wire format always uses the ``T`` separator;
+    empty values become ``""``; unrecognised values are stringified as a
+    last resort.
+    """
+    if value is None or value == "":
+        return ""
+    if isinstance(value, bool):
+        # ``bool`` is a subclass of ``int`` — treat as garbage, not 0/1.
+        return str(value)
+    if isinstance(value, datetime):
+        # ``datetime`` must be handled before the ``int``/``float`` check;
+        # str(datetime) would produce ``"YYYY-MM-DD HH:MM:SS+00:00"``
+        # (space separator), which breaks strict ISO 8601 consumers.
+        if value.tzinfo is None:
+            value = value.replace(tzinfo=UTC)
+        else:
+            value = value.astimezone(UTC)
+        return value.isoformat()
+    if isinstance(value, (int, float)):
+        try:
+            return datetime.fromtimestamp(float(value), UTC).isoformat()
+        except (ValueError, OverflowError, OSError):
+            return str(value)
+    if isinstance(value, str):
+        if _UNIX_TIMESTAMP_PATTERN.match(value):
+            try:
+                return datetime.fromtimestamp(float(value), UTC).isoformat()
+            except (ValueError, OverflowError, OSError):
+                return value
+        return value
+    return str(value)
diff --git a/backend/pyproject.toml b/backend/pyproject.toml
index 64c6e74c3..1b74a77c4 100644
--- a/backend/pyproject.toml
+++ b/backend/pyproject.toml
@@ -47,4 +47,3 @@ members = ["packages/harness"]
 
 [tool.uv.sources]
 deerflow-harness = { workspace = true }
-
diff --git a/backend/tests/test_aio_sandbox.py b/backend/tests/test_aio_sandbox.py
index 789fbde20..c6acb46eb 100644
--- a/backend/tests/test_aio_sandbox.py
+++ b/backend/tests/test_aio_sandbox.py
@@ -133,6 +133,58 @@ class TestListDirSerialization:
         assert lock_was_held == [True], "list_dir must hold the lock during exec_command"
 
 
+class TestNoChangeTimeout:
+    """Verify that no_change_timeout is forwarded to every exec_command call."""
+
+    def test_execute_command_passes_no_change_timeout(self, sandbox):
+        """execute_command should pass no_change_timeout to exec_command."""
+        calls = []
+
+        def mock_exec(command, **kwargs):
+            calls.append(kwargs)
+            return SimpleNamespace(data=SimpleNamespace(output="ok"))
+
+        sandbox._client.shell.exec_command = mock_exec
+
+        sandbox.execute_command("echo hello")
+
+        assert len(calls) == 1
+        assert calls[0].get("no_change_timeout") == sandbox._DEFAULT_NO_CHANGE_TIMEOUT
+
+    def test_retry_passes_no_change_timeout(self, sandbox):
+        """The ErrorObservation retry path should also pass no_change_timeout."""
+        calls = []
+
+        def mock_exec(command, **kwargs):
+            calls.append(kwargs)
+            if len(calls) == 1:
+                return SimpleNamespace(data=SimpleNamespace(output="'ErrorObservation' object has no attribute 'exit_code'"))
+            return SimpleNamespace(data=SimpleNamespace(output="ok"))
+
+        sandbox._client.shell.exec_command = mock_exec
+
+        sandbox.execute_command("echo hello")
+
+        assert len(calls) == 2
+        assert calls[0].get("no_change_timeout") == sandbox._DEFAULT_NO_CHANGE_TIMEOUT
+        assert calls[1].get("no_change_timeout") == sandbox._DEFAULT_NO_CHANGE_TIMEOUT
+
+    def test_list_dir_passes_no_change_timeout(self, sandbox):
+        """list_dir should pass no_change_timeout to exec_command."""
+        calls = []
+
+        def mock_exec(command, **kwargs):
+            calls.append(kwargs)
+            return SimpleNamespace(data=SimpleNamespace(output="/a\n/b"))
+
+        sandbox._client.shell.exec_command = mock_exec
+
+        sandbox.list_dir("/test")
+
+        assert len(calls) == 1
+        assert calls[0].get("no_change_timeout") == sandbox._DEFAULT_NO_CHANGE_TIMEOUT
+
+
 class TestConcurrentFileWrites:
     """Verify file write paths do not lose concurrent updates."""
 
diff --git a/backend/tests/test_channel_file_attachments.py b/backend/tests/test_channel_file_attachments.py
index 7273b1c82..aa2e9b004 100644
--- a/backend/tests/test_channel_file_attachments.py
+++ b/backend/tests/test_channel_file_attachments.py
@@ -3,11 +3,12 @@
 from __future__ import annotations
 
 import asyncio
+import os
 from pathlib import Path
 from unittest.mock import MagicMock, patch
 
 from app.channels.base import Channel
-from app.channels.message_bus import MessageBus, OutboundMessage, ResolvedAttachment
+from app.channels.message_bus import InboundMessage, MessageBus, OutboundMessage, ResolvedAttachment
 
 
 def _run(coro):
@@ -248,6 +249,109 @@ class TestResolveAttachments:
         assert result[0].filename == "data.csv"
 
 
+# ---------------------------------------------------------------------------
+# Inbound file ingestion tests
+# ---------------------------------------------------------------------------
+
+
+class TestInboundFileIngestion:
+    def test_rejects_preexisting_symlink_destination(self, tmp_path):
+        from app.channels import manager
+
+        uploads_dir = tmp_path / "uploads"
+        uploads_dir.mkdir()
+        outside_file = tmp_path / "outside-created.txt"
+        (uploads_dir / "victim.txt").symlink_to(outside_file)
+
+        msg = InboundMessage(
+            channel_name="test-channel",
+            chat_id="chat-1",
+            user_id="user-1",
+            text="see attachment",
+            files=[{"filename": "victim.txt", "url": "https://example.invalid/victim.txt"}],
+        )
+
+        async def fake_reader(file_info, client):
+            return b"attacker data"
+
+        with (
+            patch("deerflow.uploads.manager.ensure_uploads_dir", return_value=uploads_dir),
+            patch.dict(manager.INBOUND_FILE_READERS, {"test-channel": fake_reader}, clear=False),
+        ):
+            result = _run(manager._ingest_inbound_files("thread-1", msg))
+
+        assert result == []
+        assert not outside_file.exists()
+        assert (uploads_dir / "victim.txt").is_symlink()
+
+    def test_rejects_dangling_symlink_destination(self, tmp_path):
+        from app.channels import manager
+
+        uploads_dir = tmp_path / "uploads"
+        uploads_dir.mkdir()
+        missing_target = tmp_path / "missing-created.txt"
+        (uploads_dir / "victim.txt").symlink_to(missing_target)
+
+        msg = InboundMessage(
+            channel_name="test-channel",
+            chat_id="chat-1",
+            user_id="user-1",
+            text="see attachment",
+            files=[{"filename": "victim.txt", "url": "https://example.invalid/victim.txt"}],
+        )
+
+        async def fake_reader(file_info, client):
+            return b"attacker data"
+
+        with (
+            patch("deerflow.uploads.manager.ensure_uploads_dir", return_value=uploads_dir),
+            patch.dict(manager.INBOUND_FILE_READERS, {"test-channel": fake_reader}, clear=False),
+        ):
+            result = _run(manager._ingest_inbound_files("thread-1", msg))
+
+        assert result == []
+        assert not missing_target.exists()
+        assert (uploads_dir / "victim.txt").is_symlink()
+
+    def test_hardlinked_existing_file_is_not_overwritten(self, tmp_path):
+        from app.channels import manager
+
+        uploads_dir = tmp_path / "uploads"
+        uploads_dir.mkdir()
+        outside_file = tmp_path / "outside-created.txt"
+        outside_file.write_text("protected", encoding="utf-8")
+        os.link(outside_file, uploads_dir / "victim.txt")
+
+        msg = InboundMessage(
+            channel_name="test-channel",
+            chat_id="chat-1",
+            user_id="user-1",
+            text="see attachment",
+            files=[{"filename": "victim.txt", "url": "https://example.invalid/victim.txt"}],
+        )
+
+        async def fake_reader(file_info, client):
+            return b"new attachment data"
+
+        with (
+            patch("deerflow.uploads.manager.ensure_uploads_dir", return_value=uploads_dir),
+            patch.dict(manager.INBOUND_FILE_READERS, {"test-channel": fake_reader}, clear=False),
+        ):
+            result = _run(manager._ingest_inbound_files("thread-1", msg))
+
+        assert result == [
+            {
+                "filename": "victim_1.txt",
+                "size": len(b"new attachment data"),
+                "path": "/mnt/user-data/uploads/victim_1.txt",
+                "is_image": False,
+            }
+        ]
+        assert outside_file.read_text(encoding="utf-8") == "protected"
+        assert (uploads_dir / "victim.txt").read_text(encoding="utf-8") == "protected"
+        assert (uploads_dir / "victim_1.txt").read_bytes() == b"new attachment data"
+
+
 # ---------------------------------------------------------------------------
 # Channel base class _on_outbound with attachments
 # ---------------------------------------------------------------------------
diff --git a/backend/tests/test_client_e2e.py b/backend/tests/test_client_e2e.py
index 0c3872e41..4b6a62ea9 100644
--- a/backend/tests/test_client_e2e.py
+++ b/backend/tests/test_client_e2e.py
@@ -17,6 +17,7 @@ import json
 import os
 import uuid
 import zipfile
+from pathlib import Path
 
 import pytest
 from dotenv import load_dotenv
@@ -94,12 +95,18 @@ def e2e_env(tmp_path, monkeypatch):
     """Isolated filesystem environment for E2E tests.
 
     - DEER_FLOW_HOME → tmp_path (all thread data lands in a temp dir)
+    - DEER_FLOW_PROJECT_ROOT → repository root (shared skills/config assets
+      still resolve correctly when tests run from backend/)
     - Singletons reset so they pick up the new env
     - Title/memory/summarization disabled to avoid extra LLM calls
     - AppConfig built programmatically (avoids config.yaml param-name issues)
     """
     # 1. Filesystem isolation
     monkeypatch.setenv("DEER_FLOW_HOME", str(tmp_path))
+    monkeypatch.setenv(
+        "DEER_FLOW_PROJECT_ROOT",
+        str(Path(__file__).resolve().parents[2]),
+    )
     monkeypatch.setattr("deerflow.config.paths._paths", None)
     monkeypatch.setattr("deerflow.sandbox.sandbox_provider._default_sandbox_provider", None)
 
diff --git a/backend/tests/test_codex_provider.py b/backend/tests/test_codex_provider.py
index 65e53a21d..1b9136b85 100644
--- a/backend/tests/test_codex_provider.py
+++ b/backend/tests/test_codex_provider.py
@@ -82,6 +82,36 @@ def test_parse_response_text_content():
     assert result.generations[0].message.content == "Hello world"
 
 
+def test_parse_response_populates_usage_metadata():
+    model = _make_model()
+    response = {
+        "output": [
+            {
+                "type": "message",
+                "content": [{"type": "output_text", "text": "Hello world"}],
+            }
+        ],
+        "usage": {
+            "input_tokens": 10,
+            "output_tokens": 5,
+            "total_tokens": 15,
+            "input_tokens_details": {"cached_tokens": 3},
+            "output_tokens_details": {"reasoning_tokens": 2},
+        },
+        "model": "gpt-5.4",
+    }
+
+    result = model._parse_response(response)
+
+    meta = result.generations[0].message.usage_metadata
+    assert meta is not None
+    assert meta["input_tokens"] == 10
+    assert meta["output_tokens"] == 5
+    assert meta["total_tokens"] == 15
+    assert meta["input_token_details"]["cache_read"] == 3
+    assert meta["output_token_details"]["reasoning"] == 2
+
+
 def test_parse_response_reasoning_content():
     model = _make_model()
     response = {
diff --git a/backend/tests/test_invoke_acp_agent_tool.py b/backend/tests/test_invoke_acp_agent_tool.py
index 3c5f6f0ff..8c44403b8 100644
--- a/backend/tests/test_invoke_acp_agent_tool.py
+++ b/backend/tests/test_invoke_acp_agent_tool.py
@@ -697,3 +697,33 @@ def test_get_available_tools_includes_invoke_acp_agent_when_agents_configured(mo
     assert "invoke_acp_agent" in [tool.name for tool in tools]
 
     load_acp_config_from_dict({})
+
+
+def test_get_available_tools_uses_explicit_app_config_for_acp_agents(monkeypatch):
+    explicit_agents = {"codex": ACPAgentConfig(command="codex-acp", description="Codex CLI")}
+    explicit_config = SimpleNamespace(
+        tools=[],
+        models=[],
+        tool_search=SimpleNamespace(enabled=False),
+        skill_evolution=SimpleNamespace(enabled=False),
+        get_model_config=lambda name: None,
+        acp_agents=explicit_agents,
+    )
+    sentinel_tool = SimpleNamespace(name="invoke_acp_agent")
+    captured: dict[str, object] = {}
+
+    def fail_get_acp_agents():
+        raise AssertionError("ambient get_acp_agents() must not be used when app_config is explicit")
+
+    def fake_build_invoke_acp_agent_tool(agents):
+        captured["agents"] = agents
+        return sentinel_tool
+
+    monkeypatch.setattr("deerflow.tools.tools.is_host_bash_allowed", lambda config=None: True)
+    monkeypatch.setattr("deerflow.config.acp_config.get_acp_agents", fail_get_acp_agents)
+    monkeypatch.setattr("deerflow.tools.builtins.invoke_acp_agent_tool.build_invoke_acp_agent_tool", fake_build_invoke_acp_agent_tool)
+
+    tools = get_available_tools(include_mcp=False, subagent_enabled=False, app_config=explicit_config)
+
+    assert captured["agents"] is explicit_agents
+    assert "invoke_acp_agent" in [tool.name for tool in tools]
diff --git a/backend/tests/test_lead_agent_model_resolution.py b/backend/tests/test_lead_agent_model_resolution.py
index c22377b88..b240116cd 100644
--- a/backend/tests/test_lead_agent_model_resolution.py
+++ b/backend/tests/test_lead_agent_model_resolution.py
@@ -72,6 +72,44 @@ def test_internal_make_lead_agent_uses_explicit_app_config(monkeypatch):
     assert result["model"] is not None
 
 
+def test_make_lead_agent_uses_runtime_app_config_from_context_without_global_read(monkeypatch):
+    app_config = _make_app_config([_make_model("context-model", supports_thinking=False)])
+
+    import deerflow.tools as tools_module
+
+    def _raise_get_app_config():
+        raise AssertionError("ambient get_app_config() must not be used when runtime context already carries app_config")
+
+    monkeypatch.setattr(lead_agent_module, "get_app_config", _raise_get_app_config)
+    monkeypatch.setattr(tools_module, "get_available_tools", lambda **kwargs: [])
+    monkeypatch.setattr(lead_agent_module, "_build_middlewares", lambda config, model_name, agent_name=None, **kwargs: [])
+
+    captured: dict[str, object] = {}
+
+    def _fake_create_chat_model(*, name, thinking_enabled, reasoning_effort=None, app_config=None):
+        captured["name"] = name
+        captured["app_config"] = app_config
+        return object()
+
+    monkeypatch.setattr(lead_agent_module, "create_chat_model", _fake_create_chat_model)
+    monkeypatch.setattr(lead_agent_module, "create_agent", lambda **kwargs: kwargs)
+
+    result = lead_agent_module.make_lead_agent(
+        {
+            "context": {
+                "model_name": "context-model",
+                "app_config": app_config,
+            }
+        }
+    )
+
+    assert captured == {
+        "name": "context-model",
+        "app_config": app_config,
+    }
+    assert result["model"] is not None
+
+
 def test_resolve_model_name_falls_back_to_default(monkeypatch, caplog):
     app_config = _make_app_config(
         [
@@ -276,6 +314,16 @@ def test_build_middlewares_passes_explicit_app_config_to_shared_factory(monkeypa
     )
     monkeypatch.setattr(lead_agent_module, "_create_summarization_middleware", lambda **kwargs: None)
     monkeypatch.setattr(lead_agent_module, "_create_todo_list_middleware", lambda is_plan_mode: None)
+    monkeypatch.setattr(
+        lead_agent_module,
+        "TitleMiddleware",
+        lambda *, app_config: captured.setdefault("title_app_config", app_config) or "title-middleware",
+    )
+    monkeypatch.setattr(
+        lead_agent_module,
+        "MemoryMiddleware",
+        lambda agent_name=None, *, memory_config: captured.setdefault("memory_config", memory_config) or "memory-middleware",
+    )
 
     middlewares = lead_agent_module._build_middlewares(
         {"configurable": {"is_plan_mode": False, "subagent_enabled": False}},
@@ -286,17 +334,16 @@ def test_build_middlewares_passes_explicit_app_config_to_shared_factory(monkeypa
     assert captured == {
         "app_config": app_config,
         "lazy_init": True,
+        "title_app_config": app_config,
+        "memory_config": app_config.memory,
     }
     assert middlewares[0] == "base-middleware"
 
 
 def test_create_summarization_middleware_uses_configured_model_alias(monkeypatch):
-    monkeypatch.setattr(
-        lead_agent_module,
-        "get_summarization_config",
-        lambda: SummarizationConfig(enabled=True, model_name="model-masswork"),
-    )
-    monkeypatch.setattr(lead_agent_module, "get_memory_config", lambda: MemoryConfig(enabled=False))
+    app_config = _make_app_config([_make_model("model-masswork", supports_thinking=False)])
+    app_config.summarization = SummarizationConfig(enabled=True, model_name="model-masswork")
+    app_config.memory = MemoryConfig(enabled=False)
 
     from unittest.mock import MagicMock
 
@@ -311,13 +358,55 @@ def test_create_summarization_middleware_uses_configured_model_alias(monkeypatch
         captured["app_config"] = app_config
         return fake_model
 
+    def _raise_get_app_config():
+        raise AssertionError("ambient get_app_config() must not be used when app_config is explicit")
+
+    monkeypatch.setattr(lead_agent_module, "get_app_config", _raise_get_app_config)
     monkeypatch.setattr(lead_agent_module, "create_chat_model", _fake_create_chat_model)
     monkeypatch.setattr(lead_agent_module, "DeerFlowSummarizationMiddleware", lambda **kwargs: kwargs)
 
-    middleware = lead_agent_module._create_summarization_middleware(app_config=_make_app_config([_make_model("model-masswork", supports_thinking=False)]))
+    middleware = lead_agent_module._create_summarization_middleware(app_config=app_config)
 
     assert captured["name"] == "model-masswork"
     assert captured["thinking_enabled"] is False
-    assert captured["app_config"] is not None
+    assert captured["app_config"] is app_config
     assert middleware["model"] is fake_model
     fake_model.with_config.assert_called_once_with(tags=["middleware:summarize"])
+
+
+def test_create_summarization_middleware_threads_resolved_app_config_to_model(monkeypatch):
+    fallback_app_config = _make_app_config([_make_model("fallback-model", supports_thinking=False)])
+    fallback_app_config.summarization = SummarizationConfig(enabled=True, model_name="fallback-model")
+    fallback_app_config.memory = MemoryConfig(enabled=False)
+
+    from unittest.mock import MagicMock
+
+    captured: dict[str, object] = {}
+    fake_model = MagicMock()
+    fake_model.with_config.return_value = fake_model
+
+    def _fake_create_chat_model(*, name=None, thinking_enabled, reasoning_effort=None, app_config=None):
+        captured["app_config"] = app_config
+        return fake_model
+
+    monkeypatch.setattr(lead_agent_module, "get_app_config", lambda: fallback_app_config)
+    monkeypatch.setattr(lead_agent_module, "create_chat_model", _fake_create_chat_model)
+    monkeypatch.setattr(lead_agent_module, "DeerFlowSummarizationMiddleware", lambda **kwargs: kwargs)
+
+    lead_agent_module._create_summarization_middleware()
+
+    assert captured["app_config"] is fallback_app_config
+
+
+def test_memory_middleware_uses_explicit_memory_config_without_global_read(monkeypatch):
+    from deerflow.agents.middlewares import memory_middleware as memory_middleware_module
+    from deerflow.agents.middlewares.memory_middleware import MemoryMiddleware
+
+    def _raise_get_memory_config():
+        raise AssertionError("ambient get_memory_config() must not be used when memory_config is explicit")
+
+    monkeypatch.setattr(memory_middleware_module, "get_memory_config", _raise_get_memory_config)
+
+    middleware = MemoryMiddleware(memory_config=MemoryConfig(enabled=False))
+
+    assert middleware.after_agent({"messages": []}, runtime=MagicMock(context={"thread_id": "thread-1"})) is None
diff --git a/backend/tests/test_lead_agent_prompt.py b/backend/tests/test_lead_agent_prompt.py
index edbcd5193..ecaca314a 100644
--- a/backend/tests/test_lead_agent_prompt.py
+++ b/backend/tests/test_lead_agent_prompt.py
@@ -4,6 +4,7 @@ from types import SimpleNamespace
 import anyio
 
 from deerflow.agents.lead_agent import prompt as prompt_module
+from deerflow.config.subagents_config import CustomSubagentConfig, SubagentsAppConfig
 from deerflow.skills.types import Skill
 
 
@@ -40,6 +41,21 @@ def test_build_custom_mounts_section_lists_configured_mounts(monkeypatch):
     assert "read-only" in section
 
 
+def test_build_custom_mounts_section_uses_explicit_app_config_without_global_read(monkeypatch):
+    mounts = [SimpleNamespace(container_path="/home/user/shared", read_only=False)]
+    config = SimpleNamespace(sandbox=SimpleNamespace(mounts=mounts))
+
+    def fail_get_app_config():
+        raise AssertionError("ambient get_app_config() must not be used when app_config is explicit")
+
+    monkeypatch.setattr("deerflow.config.get_app_config", fail_get_app_config)
+
+    section = prompt_module._build_custom_mounts_section(app_config=config)
+
+    assert "`/home/user/shared`" in section
+    assert "read-write" in section
+
+
 def test_apply_prompt_template_includes_custom_mounts(monkeypatch):
     mounts = [SimpleNamespace(container_path="/home/user/shared", read_only=False)]
     config = SimpleNamespace(
@@ -49,8 +65,8 @@ def test_apply_prompt_template_includes_custom_mounts(monkeypatch):
     monkeypatch.setattr("deerflow.config.get_app_config", lambda: config)
     monkeypatch.setattr(prompt_module, "_get_enabled_skills", lambda: [])
     monkeypatch.setattr(prompt_module, "get_deferred_tools_prompt_section", lambda **kwargs: "")
-    monkeypatch.setattr(prompt_module, "_build_acp_section", lambda: "")
-    monkeypatch.setattr(prompt_module, "_get_memory_context", lambda agent_name=None: "")
+    monkeypatch.setattr(prompt_module, "_build_acp_section", lambda **kwargs: "")
+    monkeypatch.setattr(prompt_module, "_get_memory_context", lambda agent_name=None, **kwargs: "")
     monkeypatch.setattr(prompt_module, "get_agent_soul", lambda agent_name=None: "")
 
     prompt = prompt_module.apply_prompt_template()
@@ -67,8 +83,8 @@ def test_apply_prompt_template_includes_relative_path_guidance(monkeypatch):
     monkeypatch.setattr("deerflow.config.get_app_config", lambda: config)
     monkeypatch.setattr(prompt_module, "_get_enabled_skills", lambda: [])
     monkeypatch.setattr(prompt_module, "get_deferred_tools_prompt_section", lambda **kwargs: "")
-    monkeypatch.setattr(prompt_module, "_build_acp_section", lambda: "")
-    monkeypatch.setattr(prompt_module, "_get_memory_context", lambda agent_name=None: "")
+    monkeypatch.setattr(prompt_module, "_build_acp_section", lambda **kwargs: "")
+    monkeypatch.setattr(prompt_module, "_get_memory_context", lambda agent_name=None, **kwargs: "")
     monkeypatch.setattr(prompt_module, "get_agent_soul", lambda agent_name=None: "")
 
     prompt = prompt_module.apply_prompt_template()
@@ -77,6 +93,123 @@ def test_apply_prompt_template_includes_relative_path_guidance(monkeypatch):
     assert "`hello.txt`, `../uploads/data.csv`, and `../outputs/report.md`" in prompt
 
 
+def test_apply_prompt_template_threads_explicit_app_config_without_global_config(monkeypatch):
+    mounts = [SimpleNamespace(container_path="/home/user/shared", read_only=False)]
+    explicit_config = SimpleNamespace(
+        sandbox=SimpleNamespace(mounts=mounts),
+        skills=SimpleNamespace(container_path="/mnt/explicit-skills"),
+        skill_evolution=SimpleNamespace(enabled=False),
+        tool_search=SimpleNamespace(enabled=False),
+        memory=SimpleNamespace(enabled=False, injection_enabled=True, max_injection_tokens=2000),
+        acp_agents={},
+    )
+
+    def fail_get_app_config():
+        raise AssertionError("ambient get_app_config() must not be used when app_config is explicit")
+
+    def fail_get_memory_config():
+        raise AssertionError("ambient get_memory_config() must not be used when app_config is explicit")
+
+    monkeypatch.setattr("deerflow.config.get_app_config", fail_get_app_config)
+    monkeypatch.setattr("deerflow.config.memory_config.get_memory_config", fail_get_memory_config)
+    monkeypatch.setattr(prompt_module, "get_or_new_skill_storage", lambda app_config=None: SimpleNamespace(load_skills=lambda enabled_only=True: []))
+    monkeypatch.setattr(prompt_module, "get_agent_soul", lambda agent_name=None: "")
+
+    prompt = prompt_module.apply_prompt_template(app_config=explicit_config)
+
+    assert "`/home/user/shared`" in prompt
+    assert "Custom Mounted Directories" in prompt
+
+
+def test_apply_prompt_template_threads_explicit_app_config_to_subagents_without_global_config(monkeypatch):
+    explicit_config = SimpleNamespace(
+        sandbox=SimpleNamespace(
+            use="deerflow.sandbox.local:LocalSandboxProvider",
+            allow_host_bash=False,
+            mounts=[],
+        ),
+        subagents=SubagentsAppConfig(
+            custom_agents={
+                "researcher": CustomSubagentConfig(
+                    description="Research agent\nwith details",
+                    system_prompt="You research.",
+                )
+            }
+        ),
+        skills=SimpleNamespace(container_path="/mnt/skills"),
+        skill_evolution=SimpleNamespace(enabled=False),
+        tool_search=SimpleNamespace(enabled=False),
+        memory=SimpleNamespace(enabled=False, injection_enabled=True, max_injection_tokens=2000),
+        acp_agents={},
+    )
+
+    def fail_get_app_config():
+        raise AssertionError("ambient get_app_config() must not be used when app_config is explicit")
+
+    def fail_get_subagents_app_config():
+        raise AssertionError("ambient get_subagents_app_config() must not be used when app_config is explicit")
+
+    monkeypatch.setattr("deerflow.config.get_app_config", fail_get_app_config)
+    monkeypatch.setattr("deerflow.config.subagents_config.get_subagents_app_config", fail_get_subagents_app_config)
+    monkeypatch.setattr(prompt_module, "get_or_new_skill_storage", lambda app_config=None: SimpleNamespace(load_skills=lambda enabled_only=True: []))
+    monkeypatch.setattr(prompt_module, "get_agent_soul", lambda agent_name=None: "")
+
+    prompt = prompt_module.apply_prompt_template(subagent_enabled=True, app_config=explicit_config)
+
+    assert "**researcher**: Research agent" in prompt
+    assert "**bash**" not in prompt
+
+
+def test_build_acp_section_uses_explicit_app_config_without_global_config(monkeypatch):
+    explicit_config = SimpleNamespace(acp_agents={"codex": object()})
+
+    def fail_get_acp_agents():
+        raise AssertionError("ambient get_acp_agents() must not be used when app_config is explicit")
+
+    monkeypatch.setattr("deerflow.config.acp_config.get_acp_agents", fail_get_acp_agents)
+
+    section = prompt_module._build_acp_section(app_config=explicit_config)
+
+    assert "ACP Agent Tasks" in section
+    assert "/mnt/acp-workspace/" in section
+
+
+def test_get_memory_context_uses_explicit_app_config_without_global_config(monkeypatch):
+    explicit_config = SimpleNamespace(
+        memory=SimpleNamespace(enabled=True, injection_enabled=True, max_injection_tokens=1234),
+    )
+    captured: dict[str, object] = {}
+
+    def fail_get_memory_config():
+        raise AssertionError("ambient get_memory_config() must not be used when app_config is explicit")
+
+    def fake_get_memory_data(agent_name=None, *, user_id=None):
+        captured["agent_name"] = agent_name
+        captured["user_id"] = user_id
+        return {"facts": []}
+
+    def fake_format_memory_for_injection(memory_data, *, max_tokens):
+        captured["memory_data"] = memory_data
+        captured["max_tokens"] = max_tokens
+        return "remember this"
+
+    monkeypatch.setattr("deerflow.config.memory_config.get_memory_config", fail_get_memory_config)
+    monkeypatch.setattr("deerflow.runtime.user_context.get_effective_user_id", lambda: "user-1")
+    monkeypatch.setattr("deerflow.agents.memory.get_memory_data", fake_get_memory_data)
+    monkeypatch.setattr("deerflow.agents.memory.format_memory_for_injection", fake_format_memory_for_injection)
+
+    context = prompt_module._get_memory_context("agent-a", app_config=explicit_config)
+
+    assert "<memory>" in context
+    assert "remember this" in context
+    assert captured == {
+        "agent_name": "agent-a",
+        "user_id": "user-1",
+        "memory_data": {"facts": []},
+        "max_tokens": 1234,
+    }
+
+
 def test_refresh_skills_system_prompt_cache_async_reloads_immediately(monkeypatch, tmp_path):
     def make_skill(name: str) -> Skill:
         skill_dir = tmp_path / name
diff --git a/backend/tests/test_lead_agent_skills.py b/backend/tests/test_lead_agent_skills.py
index fe983d916..576f6bd19 100644
--- a/backend/tests/test_lead_agent_skills.py
+++ b/backend/tests/test_lead_agent_skills.py
@@ -106,7 +106,11 @@ def test_get_skills_prompt_section_uses_explicit_config_for_enabled_skills(monke
         skill_evolution=SimpleNamespace(enabled=False),
     )
 
+    def fail_get_app_config():
+        raise AssertionError("ambient get_app_config() must not be used when app_config is explicit")
+
     monkeypatch.setattr("deerflow.agents.lead_agent.prompt._get_enabled_skills", lambda: [_make_skill("global-skill")])
+    monkeypatch.setattr("deerflow.config.get_app_config", fail_get_app_config)
     monkeypatch.setattr(
         "deerflow.agents.lead_agent.prompt.get_or_new_skill_storage",
         lambda app_config=None, **kwargs: __import__("types").SimpleNamespace(load_skills=lambda *, enabled_only: [_make_skill("explicit-skill")] if app_config is explicit_config else []),
diff --git a/backend/tests/test_run_worker_rollback.py b/backend/tests/test_run_worker_rollback.py
index b2b8da77f..0a4421e2f 100644
--- a/backend/tests/test_run_worker_rollback.py
+++ b/backend/tests/test_run_worker_rollback.py
@@ -1,8 +1,14 @@
+import asyncio
+from types import SimpleNamespace
 from unittest.mock import AsyncMock, call
 
 import pytest
+from langgraph.checkpoint.base import empty_checkpoint
+from langgraph.checkpoint.memory import InMemorySaver
 
-from deerflow.runtime.runs.worker import _agent_factory_supports_app_config, _build_runtime_context, _rollback_to_pre_run_checkpoint
+from deerflow.runtime.runs.manager import RunManager
+from deerflow.runtime.runs.schemas import RunStatus
+from deerflow.runtime.runs.worker import RunContext, _agent_factory_supports_app_config, _build_runtime_context, _install_runtime_context, _rollback_to_pre_run_checkpoint, run_agent
 
 
 class FakeCheckpointer:
@@ -12,6 +18,81 @@ class FakeCheckpointer:
         self.aput_writes = AsyncMock()
 
 
+def _make_checkpoint(checkpoint_id: str, messages: list[str], version: int):
+    checkpoint = empty_checkpoint()
+    checkpoint["id"] = checkpoint_id
+    checkpoint["channel_values"] = {"messages": messages}
+    checkpoint["channel_versions"] = {"messages": version}
+    return checkpoint
+
+
+def test_build_runtime_context_includes_app_config_when_present():
+    app_config = object()
+
+    context = _build_runtime_context("thread-1", "run-1", None, app_config)
+
+    assert context["thread_id"] == "thread-1"
+    assert context["run_id"] == "run-1"
+    assert context["app_config"] is app_config
+
+
+def test_install_runtime_context_preserves_existing_thread_id_and_threads_app_config():
+    app_config = object()
+    config = {"context": {"thread_id": "caller-thread"}}
+
+    _install_runtime_context(
+        config,
+        {
+            "thread_id": "record-thread",
+            "run_id": "run-1",
+            "app_config": app_config,
+        },
+    )
+
+    assert config["context"]["thread_id"] == "caller-thread"
+    assert config["context"]["run_id"] == "run-1"
+    assert config["context"]["app_config"] is app_config
+
+
+@pytest.mark.anyio
+async def test_run_agent_threads_explicit_app_config_into_config_only_factory():
+    run_manager = RunManager()
+    record = await run_manager.create("thread-1")
+    bridge = SimpleNamespace(
+        publish=AsyncMock(),
+        publish_end=AsyncMock(),
+        cleanup=AsyncMock(),
+    )
+    app_config = object()
+    captured: dict[str, object] = {}
+
+    class DummyAgent:
+        async def astream(self, graph_input, config=None, stream_mode=None, subgraphs=False):
+            captured["astream_context"] = config["context"]
+            yield {"messages": []}
+
+    def factory(*, config):
+        captured["factory_context"] = config["context"]
+        return DummyAgent()
+
+    await run_agent(
+        bridge,
+        run_manager,
+        record,
+        ctx=RunContext(checkpointer=None, app_config=app_config),
+        agent_factory=factory,
+        graph_input={},
+        config={},
+    )
+    await asyncio.sleep(0)
+
+    assert captured["factory_context"]["app_config"] is app_config
+    assert captured["astream_context"]["app_config"] is app_config
+    assert run_manager.get(record.run_id).status == RunStatus.success
+    bridge.publish_end.assert_awaited_once_with(record.run_id)
+    bridge.cleanup.assert_awaited_once_with(record.run_id, delay=60)
+
+
 @pytest.mark.anyio
 async def test_rollback_restores_snapshot_without_deleting_thread():
     checkpointer = FakeCheckpointer(put_result={"configurable": {"thread_id": "thread-1", "checkpoint_ns": "", "checkpoint_id": "restored-1"}})
@@ -39,16 +120,16 @@ async def test_rollback_restores_snapshot_without_deleting_thread():
     )
 
     checkpointer.adelete_thread.assert_not_awaited()
-    checkpointer.aput.assert_awaited_once_with(
-        {"configurable": {"thread_id": "thread-1", "checkpoint_ns": ""}},
-        {
-            "id": "ckpt-1",
-            "channel_versions": {"messages": 3},
-            "channel_values": {"messages": ["before"]},
-        },
-        {"source": "input"},
-        {"messages": 3},
-    )
+    checkpointer.aput.assert_awaited_once()
+    restore_config, restored_checkpoint, restored_metadata, new_versions = checkpointer.aput.await_args.args
+    assert restore_config == {"configurable": {"thread_id": "thread-1", "checkpoint_ns": ""}}
+    assert restored_checkpoint["id"] != "ckpt-1"
+    assert "channel_versions" in restored_checkpoint
+    assert "channel_values" in restored_checkpoint
+    assert restored_checkpoint["channel_versions"] == {"messages": 3}
+    assert restored_checkpoint["channel_values"] == {"messages": ["before"]}
+    assert restored_metadata == {"source": "input"}
+    assert new_versions == {"messages": 3}
     assert checkpointer.aput_writes.await_args_list == [
         call(
             {"configurable": {"thread_id": "thread-1", "checkpoint_ns": "", "checkpoint_id": "restored-1"}},
@@ -63,6 +144,40 @@ async def test_rollback_restores_snapshot_without_deleting_thread():
     ]
 
 
+@pytest.mark.anyio
+async def test_rollback_restored_checkpoint_becomes_latest_with_real_checkpointer():
+    checkpointer = InMemorySaver()
+    thread_config = {"configurable": {"thread_id": "thread-1", "checkpoint_ns": ""}}
+    before_checkpoint = _make_checkpoint("0001", ["before"], 1)
+    before_config = checkpointer.put(thread_config, before_checkpoint, {"step": 1}, {"messages": 1})
+    after_checkpoint = _make_checkpoint("0002", ["after"], 2)
+    after_config = checkpointer.put(before_config, after_checkpoint, {"step": 2}, {"messages": 2})
+    checkpointer.put_writes(after_config, [("messages", "pending-after")], task_id="task-after")
+
+    await _rollback_to_pre_run_checkpoint(
+        checkpointer=checkpointer,
+        thread_id="thread-1",
+        run_id="run-1",
+        pre_run_checkpoint_id="0001",
+        pre_run_snapshot={
+            "checkpoint_ns": "",
+            "checkpoint": before_checkpoint,
+            "metadata": {"step": 1},
+            "pending_writes": [("task-before", "messages", "pending-before")],
+        },
+        snapshot_capture_failed=False,
+    )
+
+    latest = checkpointer.get_tuple(thread_config)
+
+    assert latest is not None
+    assert latest.config["configurable"]["checkpoint_id"] != "0001"
+    assert latest.config["configurable"]["checkpoint_id"] != "0002"
+    assert latest.checkpoint["channel_values"] == {"messages": ["before"]}
+    assert latest.pending_writes == [("task-before", "messages", "pending-before")]
+    assert ("task-after", "messages", "pending-after") not in latest.pending_writes
+
+
 @pytest.mark.anyio
 async def test_rollback_deletes_thread_when_no_snapshot_exists():
     checkpointer = FakeCheckpointer(put_result=None)
@@ -123,12 +238,13 @@ async def test_rollback_normalizes_none_checkpoint_ns_to_root_namespace():
         snapshot_capture_failed=False,
     )
 
-    checkpointer.aput.assert_awaited_once_with(
-        {"configurable": {"thread_id": "thread-1", "checkpoint_ns": ""}},
-        {"id": "ckpt-1", "channel_versions": {}},
-        {},
-        {},
-    )
+    checkpointer.aput.assert_awaited_once()
+    restore_config, restored_checkpoint, restored_metadata, new_versions = checkpointer.aput.await_args.args
+    assert restore_config == {"configurable": {"thread_id": "thread-1", "checkpoint_ns": ""}}
+    assert restored_checkpoint["id"] != "ckpt-1"
+    assert restored_checkpoint["channel_versions"] == {}
+    assert restored_metadata == {}
+    assert new_versions == {}
 
 
 @pytest.mark.anyio
diff --git a/backend/tests/test_runtime_paths.py b/backend/tests/test_runtime_paths.py
new file mode 100644
index 000000000..aa9e94641
--- /dev/null
+++ b/backend/tests/test_runtime_paths.py
@@ -0,0 +1,145 @@
+"""Runtime path policy tests for standalone harness usage."""
+
+from pathlib import Path
+
+import pytest
+import yaml
+
+from deerflow.config import app_config as app_config_module
+from deerflow.config import extensions_config as extensions_config_module
+from deerflow.config.app_config import AppConfig
+from deerflow.config.extensions_config import ExtensionsConfig
+from deerflow.config.paths import Paths
+from deerflow.config.runtime_paths import project_root
+from deerflow.config.skills_config import SkillsConfig
+from deerflow.skills.storage import get_or_new_skill_storage
+
+
+def _clear_path_env(monkeypatch):
+    for name in (
+        "DEER_FLOW_CONFIG_PATH",
+        "DEER_FLOW_EXTENSIONS_CONFIG_PATH",
+        "DEER_FLOW_HOME",
+        "DEER_FLOW_PROJECT_ROOT",
+        "DEER_FLOW_SKILLS_PATH",
+    ):
+        monkeypatch.delenv(name, raising=False)
+
+
+def test_default_runtime_paths_resolve_from_current_project(tmp_path: Path, monkeypatch):
+    _clear_path_env(monkeypatch)
+    monkeypatch.chdir(tmp_path)
+
+    (tmp_path / "config.yaml").write_text(
+        yaml.safe_dump({"sandbox": {"use": "deerflow.sandbox.local:LocalSandboxProvider"}}),
+        encoding="utf-8",
+    )
+    (tmp_path / "extensions_config.json").write_text('{"mcpServers": {}, "skills": {}}', encoding="utf-8")
+
+    assert AppConfig.resolve_config_path() == tmp_path / "config.yaml"
+    assert ExtensionsConfig.resolve_config_path() == tmp_path / "extensions_config.json"
+    assert Paths().base_dir == tmp_path / ".deer-flow"
+    assert SkillsConfig().get_skills_path() == tmp_path / "skills"
+    assert get_or_new_skill_storage(skills_path=SkillsConfig().get_skills_path()).get_skills_root_path() == tmp_path / "skills"
+
+
+def test_deer_flow_project_root_overrides_current_directory(tmp_path: Path, monkeypatch):
+    _clear_path_env(monkeypatch)
+    project_root = tmp_path / "project"
+    other_cwd = tmp_path / "other"
+    project_root.mkdir()
+    other_cwd.mkdir()
+    monkeypatch.chdir(other_cwd)
+    monkeypatch.setenv("DEER_FLOW_PROJECT_ROOT", str(project_root))
+
+    (project_root / "config.yaml").write_text(
+        yaml.safe_dump({"sandbox": {"use": "deerflow.sandbox.local:LocalSandboxProvider"}}),
+        encoding="utf-8",
+    )
+    (project_root / "mcp_config.json").write_text('{"mcpServers": {}, "skills": {}}', encoding="utf-8")
+
+    assert AppConfig.resolve_config_path() == project_root / "config.yaml"
+    assert ExtensionsConfig.resolve_config_path() == project_root / "mcp_config.json"
+    assert Paths().base_dir == project_root / ".deer-flow"
+    assert SkillsConfig(path="custom-skills").get_skills_path() == project_root / "custom-skills"
+
+
+def test_deer_flow_skills_path_overrides_project_default(tmp_path: Path, monkeypatch):
+    _clear_path_env(monkeypatch)
+    monkeypatch.chdir(tmp_path)
+    monkeypatch.setenv("DEER_FLOW_SKILLS_PATH", "team-skills")
+
+    assert SkillsConfig().get_skills_path() == tmp_path / "team-skills"
+    assert get_or_new_skill_storage(skills_path=SkillsConfig().get_skills_path()).get_skills_root_path() == tmp_path / "team-skills"
+
+
+def test_deer_flow_project_root_must_exist(tmp_path: Path, monkeypatch):
+    _clear_path_env(monkeypatch)
+    missing_root = tmp_path / "missing"
+    monkeypatch.setenv("DEER_FLOW_PROJECT_ROOT", str(missing_root))
+
+    with pytest.raises(ValueError, match="does not exist"):
+        project_root()
+
+
+def test_deer_flow_project_root_must_be_directory(tmp_path: Path, monkeypatch):
+    _clear_path_env(monkeypatch)
+    project_root_file = tmp_path / "project-root"
+    project_root_file.write_text("", encoding="utf-8")
+    monkeypatch.setenv("DEER_FLOW_PROJECT_ROOT", str(project_root_file))
+
+    with pytest.raises(ValueError, match="not a directory"):
+        project_root()
+
+
+def test_app_config_falls_back_to_legacy_when_project_root_lacks_config(tmp_path: Path, monkeypatch):
+    """When DEER_FLOW_PROJECT_ROOT is unset and cwd has no config.yaml, the
+    legacy backend/repo-root candidates must be used for monorepo compatibility."""
+    _clear_path_env(monkeypatch)
+    cwd = tmp_path / "cwd"
+    cwd.mkdir()
+    monkeypatch.chdir(cwd)
+
+    legacy_backend = tmp_path / "legacy-backend"
+    legacy_repo = tmp_path / "legacy-repo"
+    legacy_backend.mkdir()
+    legacy_repo.mkdir()
+    legacy_backend_config = legacy_backend / "config.yaml"
+    legacy_backend_config.write_text(
+        yaml.safe_dump({"sandbox": {"use": "deerflow.sandbox.local:LocalSandboxProvider"}}),
+        encoding="utf-8",
+    )
+    repo_root_config = legacy_repo / "config.yaml"
+    repo_root_config.write_text("", encoding="utf-8")
+
+    monkeypatch.setattr(
+        app_config_module,
+        "_legacy_config_candidates",
+        lambda: (legacy_backend_config, repo_root_config),
+    )
+
+    assert AppConfig.resolve_config_path() == legacy_backend_config
+
+
+def test_extensions_config_falls_back_to_legacy_when_project_root_lacks_file(tmp_path: Path, monkeypatch):
+    """ExtensionsConfig should hit the legacy backend/repo-root locations when
+    the caller project root has no extensions_config.json/mcp_config.json."""
+    _clear_path_env(monkeypatch)
+    cwd = tmp_path / "cwd"
+    cwd.mkdir()
+    monkeypatch.chdir(cwd)
+
+    fake_backend = tmp_path / "fake-backend"
+    fake_repo = tmp_path / "fake-repo"
+    fake_backend.mkdir()
+    fake_repo.mkdir()
+    legacy_extensions = fake_backend / "extensions_config.json"
+    legacy_extensions.write_text('{"mcpServers": {}, "skills": {}}', encoding="utf-8")
+
+    fake_paths_module_file = fake_backend / "packages" / "harness" / "deerflow" / "config" / "extensions_config.py"
+    fake_paths_module_file.parent.mkdir(parents=True)
+    fake_paths_module_file.write_text("", encoding="utf-8")
+
+    monkeypatch.setattr(extensions_config_module, "__file__", str(fake_paths_module_file))
+
+    assert ExtensionsConfig.resolve_config_path() == legacy_extensions
diff --git a/backend/tests/test_serper_tools.py b/backend/tests/test_serper_tools.py
new file mode 100644
index 000000000..2e53b0351
--- /dev/null
+++ b/backend/tests/test_serper_tools.py
@@ -0,0 +1,308 @@
+"""Unit tests for the Serper community web search tool."""
+
+import json
+from unittest.mock import MagicMock, patch
+
+import httpx
+import pytest
+
+
+@pytest.fixture(autouse=True)
+def reset_api_key_warned():
+    """Reset the module-level warning flag before each test."""
+    import deerflow.community.serper.tools as serper_mod
+
+    serper_mod._api_key_warned = False
+    yield
+    serper_mod._api_key_warned = False
+
+
+@pytest.fixture
+def mock_config_with_key():
+    with patch("deerflow.community.serper.tools.get_app_config") as mock:
+        tool_config = MagicMock()
+        tool_config.model_extra = {"api_key": "test-serper-key", "max_results": 5}
+        mock.return_value.get_tool_config.return_value = tool_config
+        yield mock
+
+
+@pytest.fixture
+def mock_config_no_key():
+    with patch("deerflow.community.serper.tools.get_app_config") as mock:
+        tool_config = MagicMock()
+        tool_config.model_extra = {}
+        mock.return_value.get_tool_config.return_value = tool_config
+        yield mock
+
+
+def _make_serper_response(organic: list) -> MagicMock:
+    mock_resp = MagicMock()
+    mock_resp.json.return_value = {"organic": organic}
+    mock_resp.raise_for_status = MagicMock()
+    return mock_resp
+
+
+class TestGetApiKey:
+    def test_returns_config_key_when_present(self):
+        with patch("deerflow.community.serper.tools.get_app_config") as mock:
+            tool_config = MagicMock()
+            tool_config.model_extra = {"api_key": "from-config"}
+            mock.return_value.get_tool_config.return_value = tool_config
+
+            from deerflow.community.serper.tools import _get_api_key
+
+            assert _get_api_key() == "from-config"
+
+    def test_falls_back_to_env_when_config_key_empty(self):
+        with patch("deerflow.community.serper.tools.get_app_config") as mock:
+            tool_config = MagicMock()
+            tool_config.model_extra = {"api_key": ""}
+            mock.return_value.get_tool_config.return_value = tool_config
+            with patch.dict("os.environ", {"SERPER_API_KEY": "env-key"}):
+                from deerflow.community.serper.tools import _get_api_key
+
+                assert _get_api_key() == "env-key"
+
+    def test_falls_back_to_env_when_config_key_whitespace(self):
+        with patch("deerflow.community.serper.tools.get_app_config") as mock:
+            tool_config = MagicMock()
+            tool_config.model_extra = {"api_key": "   "}
+            mock.return_value.get_tool_config.return_value = tool_config
+            with patch.dict("os.environ", {"SERPER_API_KEY": "env-key"}):
+                from deerflow.community.serper.tools import _get_api_key
+
+                assert _get_api_key() == "env-key"
+
+    def test_falls_back_to_env_when_config_key_null(self):
+        with patch("deerflow.community.serper.tools.get_app_config") as mock:
+            tool_config = MagicMock()
+            tool_config.model_extra = {"api_key": None}
+            mock.return_value.get_tool_config.return_value = tool_config
+            with patch.dict("os.environ", {"SERPER_API_KEY": "env-key"}):
+                from deerflow.community.serper.tools import _get_api_key
+
+                assert _get_api_key() == "env-key"
+
+    def test_falls_back_to_env_when_no_config(self):
+        with patch("deerflow.community.serper.tools.get_app_config") as mock:
+            mock.return_value.get_tool_config.return_value = None
+            with patch.dict("os.environ", {"SERPER_API_KEY": "env-only"}):
+                from deerflow.community.serper.tools import _get_api_key
+
+                assert _get_api_key() == "env-only"
+
+    def test_returns_none_when_no_key_anywhere(self):
+        with patch("deerflow.community.serper.tools.get_app_config") as mock:
+            mock.return_value.get_tool_config.return_value = None
+            with patch.dict("os.environ", {}, clear=True):
+                import os
+
+                os.environ.pop("SERPER_API_KEY", None)
+                from deerflow.community.serper.tools import _get_api_key
+
+                assert _get_api_key() is None
+
+
+class TestWebSearchTool:
+    def test_basic_search_returns_normalized_results(self, mock_config_with_key):
+        organic = [
+            {"title": "Result 1", "link": "https://example.com/1", "snippet": "Snippet 1"},
+            {"title": "Result 2", "link": "https://example.com/2", "snippet": "Snippet 2"},
+        ]
+        mock_resp = _make_serper_response(organic)
+
+        with patch("deerflow.community.serper.tools.httpx.Client") as mock_client_cls:
+            mock_client_cls.return_value.__enter__.return_value.post.return_value = mock_resp
+
+            from deerflow.community.serper.tools import web_search_tool
+
+            result = web_search_tool.invoke({"query": "python tutorial"})
+            parsed = json.loads(result)
+
+        assert parsed["query"] == "python tutorial"
+        assert parsed["total_results"] == 2
+        assert parsed["results"][0]["title"] == "Result 1"
+        assert parsed["results"][0]["url"] == "https://example.com/1"
+        assert parsed["results"][0]["content"] == "Snippet 1"
+
+    def test_respects_max_results_from_config(self, mock_config_with_key):
+        mock_config_with_key.return_value.get_tool_config.return_value.model_extra = {
+            "api_key": "test-key",
+            "max_results": 3,
+        }
+        organic = [{"title": f"R{i}", "link": f"https://x.com/{i}", "snippet": f"S{i}"} for i in range(10)]
+        mock_resp = _make_serper_response(organic)
+
+        with patch("deerflow.community.serper.tools.httpx.Client") as mock_client_cls:
+            mock_client_cls.return_value.__enter__.return_value.post.return_value = mock_resp
+
+            from deerflow.community.serper.tools import web_search_tool
+
+            result = web_search_tool.invoke({"query": "test"})
+            parsed = json.loads(result)
+
+        assert parsed["total_results"] == 3
+        assert len(parsed["results"]) == 3
+
+    def test_max_results_parameter_accepted(self, mock_config_no_key):
+        """Tool accepts max_results as a call parameter when config does not override it."""
+        organic = [{"title": f"R{i}", "link": f"https://x.com/{i}", "snippet": f"S{i}"} for i in range(10)]
+        mock_resp = _make_serper_response(organic)
+
+        with patch.dict("os.environ", {"SERPER_API_KEY": "env-key"}):
+            with patch("deerflow.community.serper.tools.httpx.Client") as mock_client_cls:
+                mock_client_cls.return_value.__enter__.return_value.post.return_value = mock_resp
+
+                from deerflow.community.serper.tools import web_search_tool
+
+                result = web_search_tool.invoke({"query": "test", "max_results": 2})
+                parsed = json.loads(result)
+
+        assert parsed["total_results"] == 2
+
+    def test_config_max_results_overrides_parameter(self):
+        """Config max_results overrides the parameter passed at call time, matching ddg_search behaviour."""
+        with patch("deerflow.community.serper.tools.get_app_config") as mock:
+            tool_config = MagicMock()
+            tool_config.model_extra = {"api_key": "test-key", "max_results": 3}
+            mock.return_value.get_tool_config.return_value = tool_config
+
+            organic = [{"title": f"R{i}", "link": f"https://x.com/{i}", "snippet": f"S{i}"} for i in range(10)]
+            mock_resp = _make_serper_response(organic)
+
+            with patch("deerflow.community.serper.tools.httpx.Client") as mock_client_cls:
+                mock_client_cls.return_value.__enter__.return_value.post.return_value = mock_resp
+
+                from deerflow.community.serper.tools import web_search_tool
+
+                result = web_search_tool.invoke({"query": "test", "max_results": 8})
+                parsed = json.loads(result)
+
+        assert parsed["total_results"] == 3
+
+    def test_empty_organic_returns_error_json(self, mock_config_with_key):
+        """Empty organic list returns structured error, matching ddg_search convention."""
+        mock_resp = _make_serper_response([])
+
+        with patch("deerflow.community.serper.tools.httpx.Client") as mock_client_cls:
+            mock_client_cls.return_value.__enter__.return_value.post.return_value = mock_resp
+
+            from deerflow.community.serper.tools import web_search_tool
+
+            result = web_search_tool.invoke({"query": "no results"})
+            parsed = json.loads(result)
+
+        assert "error" in parsed
+        assert parsed["error"] == "No results found"
+        assert parsed["query"] == "no results"
+
+    def test_missing_api_key_returns_error_json(self, mock_config_no_key):
+        with patch.dict("os.environ", {}, clear=True):
+            import os
+
+            os.environ.pop("SERPER_API_KEY", None)
+
+            from deerflow.community.serper.tools import web_search_tool
+
+            result = web_search_tool.invoke({"query": "test"})
+            parsed = json.loads(result)
+
+        assert "error" in parsed
+        assert "SERPER_API_KEY" in parsed["error"]
+
+    def test_missing_api_key_logs_warning_once(self, mock_config_no_key, caplog):
+        import logging
+
+        with patch.dict("os.environ", {}, clear=True):
+            import os
+
+            os.environ.pop("SERPER_API_KEY", None)
+
+            from deerflow.community.serper.tools import web_search_tool
+
+            with caplog.at_level(logging.WARNING, logger="deerflow.community.serper.tools"):
+                web_search_tool.invoke({"query": "q1"})
+                web_search_tool.invoke({"query": "q2"})
+
+        warnings = [r for r in caplog.records if r.levelno == logging.WARNING]
+        assert len(warnings) == 1
+
+    def test_http_error_returns_structured_error(self, mock_config_with_key):
+        mock_error_response = MagicMock()
+        mock_error_response.status_code = 403
+        mock_error_response.text = "Forbidden"
+
+        with patch("deerflow.community.serper.tools.httpx.Client") as mock_client_cls:
+            mock_client_cls.return_value.__enter__.return_value.post.side_effect = httpx.HTTPStatusError("403", request=MagicMock(), response=mock_error_response)
+
+            from deerflow.community.serper.tools import web_search_tool
+
+            result = web_search_tool.invoke({"query": "test"})
+            parsed = json.loads(result)
+
+        assert "error" in parsed
+        assert "403" in parsed["error"]
+
+    def test_network_exception_returns_error_json(self, mock_config_with_key):
+        with patch("deerflow.community.serper.tools.httpx.Client") as mock_client_cls:
+            mock_client_cls.return_value.__enter__.return_value.post.side_effect = Exception("timeout")
+
+            from deerflow.community.serper.tools import web_search_tool
+
+            result = web_search_tool.invoke({"query": "test"})
+            parsed = json.loads(result)
+
+        assert "error" in parsed
+
+    def test_sends_correct_headers_and_payload(self, mock_config_with_key):
+        organic = [{"title": "T", "link": "https://x.com", "snippet": "S"}]
+        mock_resp = _make_serper_response(organic)
+
+        with patch("deerflow.community.serper.tools.httpx.Client") as mock_client_cls:
+            mock_post = mock_client_cls.return_value.__enter__.return_value.post
+            mock_post.return_value = mock_resp
+
+            from deerflow.community.serper.tools import web_search_tool
+
+            web_search_tool.invoke({"query": "hello world"})
+
+            call_kwargs = mock_post.call_args
+            headers = call_kwargs.kwargs["headers"]
+            payload = call_kwargs.kwargs["json"]
+
+        assert headers["X-API-KEY"] == "test-serper-key"
+        assert payload["q"] == "hello world"
+        assert payload["num"] == 5
+
+    def test_uses_env_key_when_config_absent(self):
+        with patch("deerflow.community.serper.tools.get_app_config") as mock:
+            mock.return_value.get_tool_config.return_value = None
+            with patch.dict("os.environ", {"SERPER_API_KEY": "env-only-key"}):
+                organic = [{"title": "T", "link": "https://x.com", "snippet": "S"}]
+                mock_resp = _make_serper_response(organic)
+
+                with patch("deerflow.community.serper.tools.httpx.Client") as mock_client_cls:
+                    mock_post = mock_client_cls.return_value.__enter__.return_value.post
+                    mock_post.return_value = mock_resp
+
+                    from deerflow.community.serper.tools import web_search_tool
+
+                    web_search_tool.invoke({"query": "env key test"})
+                    headers = mock_post.call_args.kwargs["headers"]
+
+                assert headers["X-API-KEY"] == "env-only-key"
+
+    def test_partial_fields_in_organic_result(self, mock_config_with_key):
+        """Missing title/link/snippet should default to empty string."""
+        organic = [{}]
+        mock_resp = _make_serper_response(organic)
+
+        with patch("deerflow.community.serper.tools.httpx.Client") as mock_client_cls:
+            mock_client_cls.return_value.__enter__.return_value.post.return_value = mock_resp
+
+            from deerflow.community.serper.tools import web_search_tool
+
+            result = web_search_tool.invoke({"query": "test"})
+            parsed = json.loads(result)
+
+        assert parsed["results"][0] == {"title": "", "url": "", "content": ""}
diff --git a/backend/tests/test_skills_loader.py b/backend/tests/test_skills_loader.py
index 5a03532c6..886090f71 100644
--- a/backend/tests/test_skills_loader.py
+++ b/backend/tests/test_skills_loader.py
@@ -14,12 +14,25 @@ def _write_skill(skill_dir: Path, name: str, description: str) -> None:
     (skill_dir / "SKILL.md").write_text(content, encoding="utf-8")
 
 
-def test_get_skills_root_path_points_to_project_root_skills():
-    """get_skills_root_path() should point to deer-flow/skills (sibling of backend/), not backend/packages/skills."""
+def test_get_skills_root_path_points_to_current_project_skills(tmp_path: Path, monkeypatch):
+    """get_skills_root_path() should point to the caller project skills directory."""
+    monkeypatch.delenv("DEER_FLOW_SKILLS_PATH", raising=False)
+    monkeypatch.delenv("DEER_FLOW_PROJECT_ROOT", raising=False)
+    monkeypatch.chdir(tmp_path)
+
     app_config = SimpleNamespace(skills=SkillsConfig())
     path = get_or_new_skill_storage(app_config=app_config).get_skills_root_path()
-    assert path.name == "skills", f"Expected 'skills', got '{path.name}'"
-    assert (path.parent / "backend").is_dir(), f"Expected skills path's parent to be project root containing 'backend/', but got {path}"
+    assert path == tmp_path / "skills"
+
+
+def test_get_skills_root_path_honors_env_override(tmp_path: Path, monkeypatch):
+    """DEER_FLOW_SKILLS_PATH should override the caller project skills directory."""
+    skills_root = tmp_path / "team-skills"
+    monkeypatch.setenv("DEER_FLOW_SKILLS_PATH", str(skills_root))
+
+    app_config = SimpleNamespace(skills=SkillsConfig())
+    path = get_or_new_skill_storage(app_config=app_config).get_skills_root_path()
+    assert path == skills_root
 
 
 def test_load_skills_discovers_nested_skills_and_sets_container_paths(tmp_path: Path):
diff --git a/backend/tests/test_subagent_executor.py b/backend/tests/test_subagent_executor.py
index 774bd2dd9..102ac091a 100644
--- a/backend/tests/test_subagent_executor.py
+++ b/backend/tests/test_subagent_executor.py
@@ -204,7 +204,7 @@ class TestAgentConstruction:
 
         SubagentExecutor = classes["SubagentExecutor"]
 
-        app_config = object()
+        app_config = SimpleNamespace(models=[SimpleNamespace(name="default-model")])
         model = object()
         middlewares = [object()]
         agent = object()
@@ -258,6 +258,7 @@ class TestAgentConstruction:
         }
         assert captured["middlewares"] == {
             "app_config": app_config,
+            "model_name": "parent-model",
             "lazy_init": True,
         }
         assert captured["agent"]["model"] is model
@@ -265,6 +266,43 @@ class TestAgentConstruction:
         assert captured["agent"]["tools"] == []
         assert captured["agent"]["system_prompt"] == base_config.system_prompt
 
+    @pytest.mark.anyio
+    async def test_load_skill_messages_uses_explicit_app_config_for_skill_storage(
+        self,
+        classes,
+        base_config,
+        monkeypatch: pytest.MonkeyPatch,
+        tmp_path,
+    ):
+        """Explicit app_config must be threaded into subagent skill storage lookup."""
+        SubagentExecutor = classes["SubagentExecutor"]
+
+        app_config = SimpleNamespace(models=[SimpleNamespace(name="default-model")])
+        skill_dir = tmp_path / "demo-skill"
+        skill_dir.mkdir()
+        skill_file = skill_dir / "SKILL.md"
+        skill_file.write_text("Use demo skill", encoding="utf-8")
+        captured: dict[str, object] = {}
+
+        def fake_get_or_new_skill_storage(*, app_config=None):
+            captured["app_config"] = app_config
+            return SimpleNamespace(load_skills=lambda *, enabled_only: [SimpleNamespace(name="demo-skill", skill_file=skill_file)])
+
+        monkeypatch.setattr("deerflow.skills.storage.get_or_new_skill_storage", fake_get_or_new_skill_storage)
+
+        executor = SubagentExecutor(
+            config=base_config,
+            tools=[],
+            app_config=app_config,
+            thread_id="test-thread",
+        )
+
+        messages = await executor._load_skill_messages()
+
+        assert captured["app_config"] is app_config
+        assert len(messages) == 1
+        assert "Use demo skill" in messages[0].content
+
 
 # -----------------------------------------------------------------------------
 # Async Execution Path Tests
diff --git a/backend/tests/test_subagent_skills_config.py b/backend/tests/test_subagent_skills_config.py
index f121ccf25..b1ca0c24d 100644
--- a/backend/tests/test_subagent_skills_config.py
+++ b/backend/tests/test_subagent_skills_config.py
@@ -9,6 +9,8 @@ Covers:
 - Skills filter passthrough in task_tool config assembly
 """
 
+from types import SimpleNamespace
+
 import pytest
 
 from deerflow.config.subagents_config import (
@@ -343,12 +345,54 @@ class TestRegistryCustomAgentLookup:
         assert config.timeout_seconds == 600
         assert config.model == "inherit"
 
+    def test_custom_agent_found_from_explicit_app_config_without_global_config(self, monkeypatch):
+        from deerflow.subagents.registry import get_subagent_config
+
+        def fail_get_subagents_app_config():
+            raise AssertionError("ambient get_subagents_app_config() must not be used when app_config is explicit")
+
+        monkeypatch.setattr("deerflow.config.subagents_config.get_subagents_app_config", fail_get_subagents_app_config)
+
+        app_config = SimpleNamespace(
+            subagents=SubagentsAppConfig(
+                custom_agents={
+                    "analysis": CustomSubagentConfig(
+                        description="Data analysis specialist",
+                        system_prompt="You are a data analysis subagent.",
+                        skills=["data-analysis"],
+                    )
+                }
+            )
+        )
+
+        config = get_subagent_config("analysis", app_config=app_config)
+
+        assert config is not None
+        assert config.name == "analysis"
+        assert config.skills == ["data-analysis"]
+
     def test_custom_agent_not_found(self):
         from deerflow.subagents.registry import get_subagent_config
 
         _reset_subagents_config()
         assert get_subagent_config("nonexistent") is None
 
+    def test_get_available_subagent_names_falls_back_when_subagents_app_config_lacks_sandbox(self, monkeypatch):
+        from deerflow.subagents import registry as registry_module
+        from deerflow.subagents.registry import get_available_subagent_names
+
+        captured: dict[str, tuple] = {}
+
+        def fake_is_host_bash_allowed(*args, **kwargs):
+            captured["args"] = args
+            return True
+
+        monkeypatch.setattr(registry_module, "is_host_bash_allowed", fake_is_host_bash_allowed)
+
+        get_available_subagent_names(app_config=SubagentsAppConfig())
+
+        assert captured["args"] == ()
+
     def test_builtin_takes_priority_over_custom(self):
         """If a custom agent has the same name as a builtin, builtin wins."""
         from deerflow.subagents.builtins import BUILTIN_SUBAGENTS
diff --git a/backend/tests/test_task_tool_core_logic.py b/backend/tests/test_task_tool_core_logic.py
index 1ae008df2..428b7a066 100644
--- a/backend/tests/test_task_tool_core_logic.py
+++ b/backend/tests/test_task_tool_core_logic.py
@@ -24,8 +24,11 @@ class FakeSubagentStatus(Enum):
     TIMED_OUT = "timed_out"
 
 
-def _make_runtime() -> SimpleNamespace:
+def _make_runtime(*, app_config=None) -> SimpleNamespace:
     # Minimal ToolRuntime-like object; task_tool only reads these three attributes.
+    context = {"thread_id": "thread-1"}
+    if app_config is not None:
+        context["app_config"] = app_config
     return SimpleNamespace(
         state={
             "sandbox": {"sandbox_id": "local"},
@@ -35,14 +38,14 @@ def _make_runtime() -> SimpleNamespace:
                 "outputs_path": "/tmp/outputs",
             },
         },
-        context={"thread_id": "thread-1"},
+        context=context,
         config={"metadata": {"model_name": "ark-model", "trace_id": "trace-1"}},
     )
 
 
-def _make_subagent_config() -> SubagentConfig:
+def _make_subagent_config(name: str = "general-purpose") -> SubagentConfig:
     return SubagentConfig(
-        name="general-purpose",
+        name=name,
         description="General helper",
         system_prompt="Base system prompt",
         max_turns=50,
@@ -112,6 +115,68 @@ def test_task_tool_rejects_bash_subagent_when_host_bash_disabled(monkeypatch):
     assert result.startswith("Error: Bash subagent is disabled")
 
 
+def test_task_tool_threads_runtime_app_config_to_subagent_dependencies(monkeypatch):
+    app_config = object()
+    config = _make_subagent_config(name="bash")
+    runtime = _make_runtime(app_config=app_config)
+    events = []
+    captured = {}
+
+    class DummyExecutor:
+        def __init__(self, **kwargs):
+            captured["executor_kwargs"] = kwargs
+
+        def execute_async(self, prompt, task_id=None):
+            captured["prompt"] = prompt
+            return task_id or "generated-task-id"
+
+    def fake_get_available_subagent_names(*, app_config):
+        captured["names_app_config"] = app_config
+        return ["bash"]
+
+    def fake_get_subagent_config(name, *, app_config):
+        captured["config_lookup"] = (name, app_config)
+        return config
+
+    def fake_is_host_bash_allowed(config):
+        captured["bash_gate_app_config"] = config
+        return True
+
+    def fake_get_available_tools(**kwargs):
+        captured["tools_kwargs"] = kwargs
+        return ["tool-a"]
+
+    monkeypatch.setattr(task_tool_module, "SubagentStatus", FakeSubagentStatus)
+    monkeypatch.setattr(task_tool_module, "SubagentExecutor", DummyExecutor)
+    monkeypatch.setattr(task_tool_module, "get_available_subagent_names", fake_get_available_subagent_names)
+    monkeypatch.setattr(task_tool_module, "get_subagent_config", fake_get_subagent_config)
+    monkeypatch.setattr(task_tool_module, "is_host_bash_allowed", fake_is_host_bash_allowed)
+    monkeypatch.setattr(
+        task_tool_module,
+        "get_background_task_result",
+        lambda _: _make_result(FakeSubagentStatus.COMPLETED, result="done"),
+    )
+    monkeypatch.setattr(task_tool_module, "get_stream_writer", lambda: events.append)
+    monkeypatch.setattr(task_tool_module.asyncio, "sleep", _no_sleep)
+    monkeypatch.setattr("deerflow.tools.get_available_tools", fake_get_available_tools)
+
+    output = _run_task_tool(
+        runtime=runtime,
+        description="运行命令",
+        prompt="inspect files",
+        subagent_type="bash",
+        tool_call_id="tc-explicit-config",
+    )
+
+    assert output == "Task Succeeded. Result: done"
+    assert captured["names_app_config"] is app_config
+    assert captured["config_lookup"] == ("bash", app_config)
+    assert captured["bash_gate_app_config"] is app_config
+    assert captured["tools_kwargs"]["app_config"] is app_config
+    assert captured["executor_kwargs"]["app_config"] is app_config
+    assert captured["executor_kwargs"]["tools"] == ["tool-a"]
+
+
 def test_task_tool_emits_running_and_completed_events(monkeypatch):
     config = _make_subagent_config()
     runtime = _make_runtime()
@@ -223,6 +288,56 @@ def test_task_tool_propagates_tool_groups_to_subagent(monkeypatch):
     get_available_tools.assert_called_once_with(model_name="ark-model", groups=parent_tool_groups, subagent_enabled=False)
 
 
+def test_task_tool_uses_subagent_model_override_for_tool_loading(monkeypatch):
+    """Subagent model overrides should drive model-gated tool loading."""
+    config = SubagentConfig(
+        name="general-purpose",
+        description="General helper",
+        system_prompt="Base system prompt",
+        model="vision-subagent-model",
+        max_turns=50,
+        timeout_seconds=10,
+    )
+    runtime = _make_runtime()
+    runtime.config["metadata"]["model_name"] = "parent-text-model"
+    events = []
+    get_available_tools = MagicMock(return_value=[])
+
+    class DummyExecutor:
+        def __init__(self, **kwargs):
+            pass
+
+        def execute_async(self, prompt, task_id=None):
+            return task_id or "generated-task-id"
+
+    monkeypatch.setattr(task_tool_module, "SubagentStatus", FakeSubagentStatus)
+    monkeypatch.setattr(task_tool_module, "SubagentExecutor", DummyExecutor)
+    monkeypatch.setattr(task_tool_module, "get_subagent_config", lambda _: config)
+    monkeypatch.setattr(
+        task_tool_module,
+        "get_background_task_result",
+        lambda _: _make_result(FakeSubagentStatus.COMPLETED, result="done"),
+    )
+    monkeypatch.setattr(task_tool_module, "get_stream_writer", lambda: events.append)
+    monkeypatch.setattr(task_tool_module.asyncio, "sleep", _no_sleep)
+    monkeypatch.setattr("deerflow.tools.get_available_tools", get_available_tools)
+
+    output = _run_task_tool(
+        runtime=runtime,
+        description="inspect image",
+        prompt="inspect the uploaded image",
+        subagent_type="general-purpose",
+        tool_call_id="tc-issue-2543",
+    )
+
+    assert output == "Task Succeeded. Result: done"
+    get_available_tools.assert_called_once_with(
+        model_name="vision-subagent-model",
+        groups=None,
+        subagent_enabled=False,
+    )
+
+
 def test_task_tool_inherits_parent_skill_allowlist_for_default_subagent(monkeypatch):
     config = _make_subagent_config()
     runtime = _make_runtime()
@@ -371,6 +486,8 @@ def test_task_tool_runtime_none_passes_groups_none(monkeypatch):
     monkeypatch.setattr(task_tool_module, "get_stream_writer", lambda: events.append)
     monkeypatch.setattr(task_tool_module.asyncio, "sleep", _no_sleep)
     monkeypatch.setattr("deerflow.tools.get_available_tools", get_available_tools)
+    fallback_app_config = SimpleNamespace(models=[SimpleNamespace(name="default-model")])
+    monkeypatch.setattr(task_tool_module, "get_app_config", lambda: fallback_app_config)
 
     output = _run_task_tool(
         runtime=None,
@@ -381,8 +498,13 @@ def test_task_tool_runtime_none_passes_groups_none(monkeypatch):
     )
 
     assert output == "Task Succeeded. Result: ok"
-    # runtime is None → metadata is empty dict → groups=None
-    get_available_tools.assert_called_once_with(model_name=None, groups=None, subagent_enabled=False)
+    # runtime is None -> metadata is empty dict -> groups=None, model falls back to app default.
+    get_available_tools.assert_called_once_with(
+        model_name="default-model",
+        groups=None,
+        subagent_enabled=False,
+        app_config=fallback_app_config,
+    )
 
     config = _make_subagent_config()
     events = []
diff --git a/backend/tests/test_threads_router.py b/backend/tests/test_threads_router.py
index 4ffa28a8c..daf0c0b13 100644
--- a/backend/tests/test_threads_router.py
+++ b/backend/tests/test_threads_router.py
@@ -1,12 +1,66 @@
+import re
 from unittest.mock import patch
 
 import pytest
 from _router_auth_helpers import make_authed_test_app
-from fastapi import HTTPException
+from fastapi import FastAPI, HTTPException
 from fastapi.testclient import TestClient
+from langgraph.checkpoint.memory import InMemorySaver
+from langgraph.store.memory import InMemoryStore
 
 from app.gateway.routers import threads
 from deerflow.config.paths import Paths
+from deerflow.persistence.thread_meta.memory import THREADS_NS, MemoryThreadMetaStore
+
+_ISO_TIMESTAMP_RE = re.compile(r"^\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}")
+
+
+class _PermissiveThreadMetaStore(MemoryThreadMetaStore):
+    """Memory store that skips user-id filtering for router tests.
+
+    Owner isolation is exercised separately in
+    ``test_memory_thread_meta_isolation.py``. Router tests need to drive
+    the FastAPI surface end-to-end with a single fixed app user, but the
+    stub auth middleware in ``_router_auth_helpers`` stamps a fresh UUID
+    on every request, so the production filtering would reject every
+    pre-seeded record. Bypass that filter so the test can focus on the
+    timestamp wire format.
+    """
+
+    async def _get_owned_record(self, thread_id, user_id, method_name):  # type: ignore[override]
+        item = await self._store.aget(THREADS_NS, thread_id)
+        return dict(item.value) if item is not None else None
+
+    async def check_access(self, thread_id, user_id, *, require_existing=False):  # type: ignore[override]
+        item = await self._store.aget(THREADS_NS, thread_id)
+        if item is None:
+            return not require_existing
+        return True
+
+    async def create(self, thread_id, *, assistant_id=None, user_id=None, display_name=None, metadata=None):  # type: ignore[override]
+        return await super().create(thread_id, assistant_id=assistant_id, user_id=None, display_name=display_name, metadata=metadata)
+
+    async def search(self, *, metadata=None, status=None, limit=100, offset=0, user_id=None):  # type: ignore[override]
+        return await super().search(metadata=metadata, status=status, limit=limit, offset=offset, user_id=None)
+
+
+def _build_thread_app() -> tuple[FastAPI, InMemoryStore, InMemorySaver]:
+    """Build a stub-authed FastAPI app wired with an in-memory ThreadMetaStore.
+
+    The thread_store on ``app.state`` is a permissive subclass of
+    ``MemoryThreadMetaStore`` so tests can drive ``/api/threads``
+    end-to-end and pre-seed legacy records via the underlying BaseStore.
+
+    Returns ``(app, store, checkpointer)`` for direct seeding/inspection.
+    """
+    app = make_authed_test_app()
+    store = InMemoryStore()
+    checkpointer = InMemorySaver()
+    app.state.store = store
+    app.state.checkpointer = checkpointer
+    app.state.thread_store = _PermissiveThreadMetaStore(store)
+    app.include_router(threads.router)
+    return app, store, checkpointer
 
 
 def test_delete_thread_data_removes_thread_directory(tmp_path):
@@ -136,3 +190,244 @@ def test_strip_reserved_metadata_empty_input():
 def test_strip_reserved_metadata_strips_all_reserved_keys():
     out = threads._strip_reserved_metadata({"user_id": "x", "keep": "me"})
     assert out == {"keep": "me"}
+
+
+# ---------------------------------------------------------------------------
+# ISO 8601 timestamp contract (issue #2594)
+# ---------------------------------------------------------------------------
+#
+# Threads endpoints document ``created_at`` / ``updated_at`` as ISO
+# timestamps and that is the format LangGraph Platform uses
+# (``langgraph_sdk.schema.Thread.created_at: datetime`` JSON-encodes to
+# ISO 8601). The tests below pin that contract end-to-end and also
+# exercise the ``coerce_iso`` healing path for legacy unix-timestamp
+# records written by older Gateway versions.
+
+
+def test_create_thread_returns_iso_timestamps() -> None:
+    app, _store, _checkpointer = _build_thread_app()
+
+    with TestClient(app) as client:
+        response = client.post("/api/threads", json={"metadata": {}})
+
+    assert response.status_code == 200, response.text
+    body = response.json()
+    assert _ISO_TIMESTAMP_RE.match(body["created_at"]), body["created_at"]
+    assert _ISO_TIMESTAMP_RE.match(body["updated_at"]), body["updated_at"]
+    assert body["created_at"] == body["updated_at"]
+
+
+def test_get_thread_returns_iso_for_legacy_unix_record() -> None:
+    """A thread record written by older versions stores ``time.time()``
+    floats. ``get_thread`` must transparently surface them as ISO so the
+    frontend's ``new Date(...)`` parser does not break.
+    """
+    app, store, checkpointer = _build_thread_app()
+
+    legacy_thread_id = "legacy-thread"
+    legacy_ts = "1777252410.411327"
+
+    async def _seed() -> None:
+        await store.aput(
+            THREADS_NS,
+            legacy_thread_id,
+            {
+                "thread_id": legacy_thread_id,
+                "status": "idle",
+                "created_at": legacy_ts,
+                "updated_at": legacy_ts,
+                "metadata": {},
+            },
+        )
+        from langgraph.checkpoint.base import empty_checkpoint
+
+        await checkpointer.aput(
+            {"configurable": {"thread_id": legacy_thread_id, "checkpoint_ns": ""}},
+            empty_checkpoint(),
+            {"step": -1, "source": "input", "writes": None, "parents": {}},
+            {},
+        )
+
+    import asyncio
+
+    asyncio.run(_seed())
+
+    with TestClient(app) as client:
+        response = client.get(f"/api/threads/{legacy_thread_id}")
+
+    assert response.status_code == 200, response.text
+    body = response.json()
+    assert _ISO_TIMESTAMP_RE.match(body["created_at"]), body["created_at"]
+    assert _ISO_TIMESTAMP_RE.match(body["updated_at"]), body["updated_at"]
+
+
+def test_patch_thread_returns_iso_and_advances_updated_at() -> None:
+    app, store, _checkpointer = _build_thread_app()
+    thread_id = "patch-target"
+
+    legacy_created = "1777000000.000000"
+    legacy_updated = "1777000000.000000"
+
+    async def _seed() -> None:
+        await store.aput(
+            THREADS_NS,
+            thread_id,
+            {
+                "thread_id": thread_id,
+                "status": "idle",
+                "created_at": legacy_created,
+                "updated_at": legacy_updated,
+                "metadata": {"k": "v0"},
+            },
+        )
+
+    import asyncio
+
+    asyncio.run(_seed())
+
+    with TestClient(app) as client:
+        response = client.patch(f"/api/threads/{thread_id}", json={"metadata": {"k": "v1"}})
+
+    assert response.status_code == 200, response.text
+    body = response.json()
+    assert _ISO_TIMESTAMP_RE.match(body["created_at"]), body["created_at"]
+    assert _ISO_TIMESTAMP_RE.match(body["updated_at"]), body["updated_at"]
+    # Patch issues a fresh ``updated_at`` via ``MemoryThreadMetaStore.update_metadata``,
+    # so it must be > the migrated legacy ``created_at`` (both ISO strings
+    # sort lexicographically by time when the format is consistent).
+    assert body["updated_at"] > body["created_at"]
+    assert body["metadata"] == {"k": "v1"}
+
+
+def test_search_threads_normalizes_legacy_unix_seconds_to_iso() -> None:
+    """``MemoryThreadMetaStore`` may hold legacy ``time.time()`` floats
+    written by older Gateway versions. ``/search`` must surface them as
+    ISO via ``coerce_iso`` so the frontend's ``new Date(...)`` parser
+    does not break.
+    """
+    app, store, _checkpointer = _build_thread_app()
+
+    async def _seed() -> None:
+        # Legacy unix-second float (the literal value from issue #2594).
+        await store.aput(
+            THREADS_NS,
+            "legacy",
+            {
+                "thread_id": "legacy",
+                "status": "idle",
+                "created_at": 1777000000.0,
+                "updated_at": 1777000000.0,
+                "metadata": {},
+            },
+        )
+        # Modern ISO string, slightly later.
+        await store.aput(
+            THREADS_NS,
+            "modern",
+            {
+                "thread_id": "modern",
+                "status": "idle",
+                "created_at": "2026-04-27T00:00:00+00:00",
+                "updated_at": "2026-04-27T00:00:00+00:00",
+                "metadata": {},
+            },
+        )
+
+    import asyncio
+
+    asyncio.run(_seed())
+
+    with TestClient(app) as client:
+        response = client.post("/api/threads/search", json={"limit": 10})
+
+    assert response.status_code == 200, response.text
+    items = response.json()
+    assert {item["thread_id"] for item in items} == {"legacy", "modern"}
+    for item in items:
+        assert _ISO_TIMESTAMP_RE.match(item["created_at"]), item
+        assert _ISO_TIMESTAMP_RE.match(item["updated_at"]), item
+
+
+def test_memory_thread_meta_store_writes_iso_on_create() -> None:
+    """``MemoryThreadMetaStore.create`` must emit ISO so newly created
+    threads serialize correctly without depending on the router's
+    ``coerce_iso`` heal path.
+    """
+    import asyncio
+
+    store = InMemoryStore()
+    repo = MemoryThreadMetaStore(store)
+
+    async def _scenario() -> dict:
+        await repo.create("fresh", user_id=None, metadata={"a": 1})
+        record = (await store.aget(THREADS_NS, "fresh")).value
+        return record
+
+    record = asyncio.run(_scenario())
+    assert _ISO_TIMESTAMP_RE.match(record["created_at"]), record
+    assert _ISO_TIMESTAMP_RE.match(record["updated_at"]), record
+
+
+def test_get_thread_state_returns_iso_for_legacy_checkpoint_metadata() -> None:
+    """Checkpoints written by older Gateway versions stored
+    ``created_at`` as a unix-second float in their metadata. The
+    ``/state`` endpoint must surface that value as ISO so the frontend's
+    ``new Date(...)`` parser does not break — same root cause as the
+    thread-record bug fixed in #2594, but on the checkpoint side.
+    """
+    app, _store, checkpointer = _build_thread_app()
+    thread_id = "legacy-state"
+
+    async def _seed() -> None:
+        from langgraph.checkpoint.base import empty_checkpoint
+
+        await checkpointer.aput(
+            {"configurable": {"thread_id": thread_id, "checkpoint_ns": ""}},
+            empty_checkpoint(),
+            {"step": -1, "source": "input", "writes": None, "parents": {}, "created_at": 1777252410.411327},
+            {},
+        )
+
+    import asyncio
+
+    asyncio.run(_seed())
+
+    with TestClient(app) as client:
+        response = client.get(f"/api/threads/{thread_id}/state")
+
+    assert response.status_code == 200, response.text
+    body = response.json()
+    assert _ISO_TIMESTAMP_RE.match(body["created_at"]), body["created_at"]
+    assert _ISO_TIMESTAMP_RE.match(body["checkpoint"]["ts"]), body["checkpoint"]
+
+
+def test_get_thread_history_returns_iso_for_legacy_checkpoint_metadata() -> None:
+    """``/history`` walks ``checkpointer.alist`` and emits one entry per
+    checkpoint. Each entry's ``created_at`` must come out as ISO even if
+    older checkpoints stored a unix-second float in their metadata.
+    """
+    app, _store, checkpointer = _build_thread_app()
+    thread_id = "legacy-history"
+
+    async def _seed() -> None:
+        from langgraph.checkpoint.base import empty_checkpoint
+
+        await checkpointer.aput(
+            {"configurable": {"thread_id": thread_id, "checkpoint_ns": ""}},
+            empty_checkpoint(),
+            {"step": -1, "source": "input", "writes": None, "parents": {}, "created_at": 1777252410.411327},
+            {},
+        )
+
+    import asyncio
+
+    asyncio.run(_seed())
+
+    with TestClient(app) as client:
+        response = client.post(f"/api/threads/{thread_id}/history", json={"limit": 10})
+
+    assert response.status_code == 200, response.text
+    entries = response.json()
+    assert entries, "expected at least one history entry"
+    for entry in entries:
+        assert _ISO_TIMESTAMP_RE.match(entry["created_at"]), entry
diff --git a/backend/tests/test_title_middleware_core_logic.py b/backend/tests/test_title_middleware_core_logic.py
index afd10f2b3..ede4dc0a4 100644
--- a/backend/tests/test_title_middleware_core_logic.py
+++ b/backend/tests/test_title_middleware_core_logic.py
@@ -1,6 +1,7 @@
 """Core behavior tests for TitleMiddleware."""
 
 import asyncio
+from types import SimpleNamespace
 from unittest.mock import AsyncMock, MagicMock
 
 from langchain_core.messages import AIMessage, HumanMessage
@@ -98,6 +99,34 @@ class TestTitleMiddlewareCoreLogic:
             "tags": ["middleware:title"],
         }
 
+    def test_generate_title_uses_explicit_app_config_without_global_config(self, monkeypatch):
+        title_config = TitleConfig(enabled=True, model_name="title-model", max_chars=20)
+        app_config = SimpleNamespace(title=title_config)
+        middleware = TitleMiddleware(app_config=app_config)
+        model = MagicMock()
+        model.ainvoke = AsyncMock(return_value=AIMessage(content="显式标题"))
+
+        def fail_get_title_config():
+            raise AssertionError("ambient get_title_config() must not be used when app_config is explicit")
+
+        monkeypatch.setattr(title_middleware_module, "get_title_config", fail_get_title_config)
+        monkeypatch.setattr(title_middleware_module, "create_chat_model", MagicMock(return_value=model))
+
+        state = {
+            "messages": [
+                HumanMessage(content="请帮我写一个标题"),
+                AIMessage(content="好的"),
+            ]
+        }
+        result = asyncio.run(middleware._agenerate_title_result(state))
+
+        assert result == {"title": "显式标题"}
+        title_middleware_module.create_chat_model.assert_called_once_with(
+            name="title-model",
+            thinking_enabled=False,
+            app_config=app_config,
+        )
+
     def test_generate_title_normalizes_structured_message_content(self, monkeypatch):
         _set_test_title_config(max_chars=20)
         middleware = TitleMiddleware()
diff --git a/backend/tests/test_token_usage_middleware.py b/backend/tests/test_token_usage_middleware.py
new file mode 100644
index 000000000..66a1f2229
--- /dev/null
+++ b/backend/tests/test_token_usage_middleware.py
@@ -0,0 +1,32 @@
+from unittest.mock import MagicMock, patch
+
+from langchain_core.messages import AIMessage
+
+from deerflow.agents.middlewares.token_usage_middleware import TokenUsageMiddleware
+
+
+def test_after_model_logs_usage_metadata_counts():
+    middleware = TokenUsageMiddleware()
+    state = {
+        "messages": [
+            AIMessage(
+                content="done",
+                usage_metadata={
+                    "input_tokens": 10,
+                    "output_tokens": 5,
+                    "total_tokens": 15,
+                },
+            )
+        ]
+    }
+
+    with patch("deerflow.agents.middlewares.token_usage_middleware.logger.info") as info_mock:
+        result = middleware.after_model(state=state, runtime=MagicMock())
+
+    assert result is None
+    info_mock.assert_called_once_with(
+        "LLM token usage: input=%s output=%s total=%s",
+        10,
+        5,
+        15,
+    )
diff --git a/backend/tests/test_tool_error_handling_middleware.py b/backend/tests/test_tool_error_handling_middleware.py
index 4add370f0..2c28dac35 100644
--- a/backend/tests/test_tool_error_handling_middleware.py
+++ b/backend/tests/test_tool_error_handling_middleware.py
@@ -9,11 +9,20 @@ from deerflow.agents.middlewares.tool_error_handling_middleware import (
     ToolErrorHandlingMiddleware,
     build_subagent_runtime_middlewares,
 )
+from deerflow.agents.middlewares.view_image_middleware import ViewImageMiddleware
 from deerflow.config.app_config import AppConfig, CircuitBreakerConfig
 from deerflow.config.guardrails_config import GuardrailsConfig
+from deerflow.config.model_config import ModelConfig
 from deerflow.config.sandbox_config import SandboxConfig
 
 
+def _request(name: str = "web_search", tool_call_id: str | None = "tc-1"):
+    tool_call = {"name": name}
+    if tool_call_id is not None:
+        tool_call["id"] = tool_call_id
+    return SimpleNamespace(tool_call=tool_call)
+
+
 def _module(name: str, **attrs):
     module = ModuleType(name)
     for key, value in attrs.items():
@@ -21,19 +30,62 @@ def _module(name: str, **attrs):
     return module
 
 
-def _make_app_config() -> AppConfig:
+def _make_app_config(*, supports_vision: bool = False) -> AppConfig:
     return AppConfig(
+        models=[
+            ModelConfig(
+                name="test-model",
+                display_name="test-model",
+                description=None,
+                use="langchain_openai:ChatOpenAI",
+                model="test-model",
+                supports_vision=supports_vision,
+            )
+        ],
         sandbox=SandboxConfig(use="test"),
         guardrails=GuardrailsConfig(enabled=False),
         circuit_breaker=CircuitBreakerConfig(failure_threshold=7, recovery_timeout_sec=11),
     )
 
 
-def _request(name: str = "web_search", tool_call_id: str | None = "tc-1"):
-    tool_call = {"name": name}
-    if tool_call_id is not None:
-        tool_call["id"] = tool_call_id
-    return SimpleNamespace(tool_call=tool_call)
+def _stub_runtime_middleware_imports(monkeypatch: pytest.MonkeyPatch) -> None:
+    class FakeMiddleware:
+        def __init__(self, *args, **kwargs):
+            self.args = args
+            self.kwargs = kwargs
+
+    class FakeLLMErrorHandlingMiddleware:
+        def __init__(self, *, app_config):
+            self.app_config = app_config
+
+    monkeypatch.setitem(
+        sys.modules,
+        "deerflow.agents.middlewares.llm_error_handling_middleware",
+        _module(
+            "deerflow.agents.middlewares.llm_error_handling_middleware",
+            LLMErrorHandlingMiddleware=FakeLLMErrorHandlingMiddleware,
+        ),
+    )
+    monkeypatch.setitem(
+        sys.modules,
+        "deerflow.agents.middlewares.thread_data_middleware",
+        _module("deerflow.agents.middlewares.thread_data_middleware", ThreadDataMiddleware=FakeMiddleware),
+    )
+    monkeypatch.setitem(
+        sys.modules,
+        "deerflow.sandbox.middleware",
+        _module("deerflow.sandbox.middleware", SandboxMiddleware=FakeMiddleware),
+    )
+    monkeypatch.setitem(
+        sys.modules,
+        "deerflow.agents.middlewares.dangling_tool_call_middleware",
+        _module("deerflow.agents.middlewares.dangling_tool_call_middleware", DanglingToolCallMiddleware=FakeMiddleware),
+    )
+    monkeypatch.setitem(
+        sys.modules,
+        "deerflow.agents.middlewares.sandbox_audit_middleware",
+        _module("deerflow.agents.middlewares.sandbox_audit_middleware", SandboxAuditMiddleware=FakeMiddleware),
+    )
 
 
 def test_build_subagent_runtime_middlewares_threads_app_config_to_llm_middleware(monkeypatch: pytest.MonkeyPatch):
@@ -166,3 +218,30 @@ async def test_awrap_tool_call_reraises_graph_interrupt():
 
     with pytest.raises(GraphInterrupt):
         await middleware.awrap_tool_call(req, _interrupt)
+
+
+def test_subagent_runtime_middlewares_include_view_image_for_vision_model(monkeypatch):
+    app_config = _make_app_config(supports_vision=True)
+    _stub_runtime_middleware_imports(monkeypatch)
+
+    middlewares = build_subagent_runtime_middlewares(app_config=app_config, model_name="test-model")
+
+    assert any(isinstance(middleware, ViewImageMiddleware) for middleware in middlewares)
+
+
+def test_subagent_runtime_middlewares_include_view_image_for_default_vision_model(monkeypatch):
+    app_config = _make_app_config(supports_vision=True)
+    _stub_runtime_middleware_imports(monkeypatch)
+
+    middlewares = build_subagent_runtime_middlewares(app_config=app_config, model_name=None)
+
+    assert any(isinstance(middleware, ViewImageMiddleware) for middleware in middlewares)
+
+
+def test_subagent_runtime_middlewares_skip_view_image_for_text_model(monkeypatch):
+    app_config = _make_app_config(supports_vision=False)
+    _stub_runtime_middleware_imports(monkeypatch)
+
+    middlewares = build_subagent_runtime_middlewares(app_config=app_config, model_name="test-model")
+
+    assert not any(isinstance(middleware, ViewImageMiddleware) for middleware in middlewares)
diff --git a/backend/tests/test_uploads_manager.py b/backend/tests/test_uploads_manager.py
index 64964c0b0..2cf1ae7fb 100644
--- a/backend/tests/test_uploads_manager.py
+++ b/backend/tests/test_uploads_manager.py
@@ -1,14 +1,20 @@
 """Tests for deerflow.uploads.manager — shared upload management logic."""
 
+import errno
+import os
+from unittest.mock import patch
+
 import pytest
 
 from deerflow.uploads.manager import (
     PathTraversalError,
+    UnsafeUploadPathError,
     claim_unique_filename,
     delete_file_safe,
     list_files_in_dir,
     normalize_filename,
     validate_path_traversal,
+    write_upload_file_no_symlink,
 )
 
 # ---------------------------------------------------------------------------
@@ -97,6 +103,54 @@ class TestValidatePathTraversal:
             validate_path_traversal(link, tmp_path)
 
 
+# ---------------------------------------------------------------------------
+# write_upload_file_no_symlink
+# ---------------------------------------------------------------------------
+
+
+class TestWriteUploadFileNoSymlink:
+    def test_writes_new_file(self, tmp_path):
+        dest = write_upload_file_no_symlink(tmp_path, "notes.txt", b"hello")
+
+        assert dest == tmp_path / "notes.txt"
+        assert dest.read_bytes() == b"hello"
+
+    def test_overwrites_existing_regular_file_with_single_link(self, tmp_path):
+        dest = tmp_path / "notes.txt"
+        dest.write_bytes(b"old contents")
+        assert os.stat(dest).st_nlink == 1
+
+        result = write_upload_file_no_symlink(tmp_path, "notes.txt", b"new contents")
+
+        assert result == dest
+        assert dest.read_bytes() == b"new contents"
+        assert os.stat(dest).st_nlink == 1
+
+    def test_fails_closed_without_no_follow_support(self, tmp_path, monkeypatch):
+        monkeypatch.delattr(os, "O_NOFOLLOW", raising=False)
+
+        with pytest.raises(UnsafeUploadPathError, match="O_NOFOLLOW"):
+            write_upload_file_no_symlink(tmp_path, "notes.txt", b"hello")
+
+        assert not (tmp_path / "notes.txt").exists()
+
+    def test_open_uses_nonblocking_flag_when_available(self, tmp_path):
+        with patch("deerflow.uploads.manager.os.open", side_effect=OSError(errno.ENXIO, "no reader")) as open_mock:
+            with pytest.raises(UnsafeUploadPathError, match="Unsafe upload destination"):
+                write_upload_file_no_symlink(tmp_path, "pipe.txt", b"hello")
+
+        flags = open_mock.call_args.args[1]
+        assert flags & os.O_NONBLOCK
+
+    @pytest.mark.parametrize("open_errno", [errno.ENXIO, errno.EAGAIN])
+    def test_nonblocking_special_file_open_errors_are_unsafe(self, tmp_path, open_errno):
+        with patch("deerflow.uploads.manager.os.open", side_effect=OSError(open_errno, "would block")):
+            with pytest.raises(UnsafeUploadPathError, match="Unsafe upload destination"):
+                write_upload_file_no_symlink(tmp_path, "pipe.txt", b"hello")
+
+        assert not (tmp_path / "pipe.txt").exists()
+
+
 # ---------------------------------------------------------------------------
 # list_files_in_dir
 # ---------------------------------------------------------------------------
diff --git a/backend/tests/test_uploads_router.py b/backend/tests/test_uploads_router.py
index 7f9b442d0..4a778345f 100644
--- a/backend/tests/test_uploads_router.py
+++ b/backend/tests/test_uploads_router.py
@@ -1,16 +1,40 @@
 import asyncio
+import os
 import stat
 from io import BytesIO
 from pathlib import Path
 from types import SimpleNamespace
 from unittest.mock import AsyncMock, MagicMock, patch
 
-from _router_auth_helpers import call_unwrapped
-from fastapi import UploadFile
+import pytest
+from _router_auth_helpers import call_unwrapped, make_authed_test_app
+from fastapi import HTTPException, UploadFile
+from fastapi.testclient import TestClient
 
 from app.gateway.routers import uploads
 
 
+class ChunkedUpload:
+    def __init__(self, filename: str, chunks: list[bytes]):
+        self.filename = filename
+        self._chunks = list(chunks)
+        self.read_calls: list[int | None] = []
+
+    async def read(self, size: int | None = None) -> bytes:
+        self.read_calls.append(size)
+        if size is None:
+            raise AssertionError("upload must be read with an explicit chunk size")
+        if not self._chunks:
+            return b""
+        return self._chunks.pop(0)
+
+
+def _mounted_provider() -> MagicMock:
+    provider = MagicMock()
+    provider.uses_thread_data_mounts = True
+    return provider
+
+
 def test_upload_files_writes_thread_storage_and_skips_local_sandbox_sync(tmp_path):
     thread_uploads_dir = tmp_path / "uploads"
     thread_uploads_dir.mkdir(parents=True)
@@ -178,6 +202,173 @@ def test_upload_files_does_not_adjust_permissions_for_local_sandbox(tmp_path):
     make_writable.assert_not_called()
 
 
+def test_upload_files_acquires_non_local_sandbox_before_writing(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+
+    provider = MagicMock()
+    provider.uses_thread_data_mounts = False
+    sandbox = MagicMock()
+    provider.get.return_value = sandbox
+
+    def acquire_before_writes(thread_id: str) -> str:
+        assert list(thread_uploads_dir.iterdir()) == []
+        return "aio-1"
+
+    provider.acquire.side_effect = acquire_before_writes
+
+    with (
+        patch.object(uploads, "ensure_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=provider),
+    ):
+        file = UploadFile(filename="notes.txt", file=BytesIO(b"hello uploads"))
+        result = asyncio.run(call_unwrapped(uploads.upload_files, "thread-aio", request=MagicMock(), files=[file], config=SimpleNamespace()))
+
+    assert result.success is True
+    provider.acquire.assert_called_once_with("thread-aio")
+    sandbox.update_file.assert_called_once_with("/mnt/user-data/uploads/notes.txt", b"hello uploads")
+
+
+def test_upload_files_fails_before_writing_when_non_local_sandbox_unavailable(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+
+    provider = MagicMock()
+    provider.uses_thread_data_mounts = False
+    provider.acquire.side_effect = RuntimeError("sandbox unavailable")
+    file = ChunkedUpload("notes.txt", [b"hello uploads"])
+
+    with (
+        patch.object(uploads, "ensure_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=provider),
+    ):
+        with pytest.raises(RuntimeError, match="sandbox unavailable"):
+            asyncio.run(call_unwrapped(uploads.upload_files, "thread-aio", request=MagicMock(), files=[file], config=SimpleNamespace()))
+
+    assert list(thread_uploads_dir.iterdir()) == []
+    assert file.read_calls == []
+    provider.get.assert_not_called()
+
+
+def test_upload_files_rejects_too_many_files_before_writing(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+
+    with (
+        patch.object(uploads, "ensure_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=_mounted_provider()),
+        patch.object(uploads, "_get_upload_limits", return_value=uploads.UploadLimits(max_files=1, max_file_size=10, max_total_size=20)),
+    ):
+        files = [
+            ChunkedUpload("one.txt", [b"one"]),
+            ChunkedUpload("two.txt", [b"two"]),
+        ]
+        with pytest.raises(HTTPException) as exc_info:
+            asyncio.run(call_unwrapped(uploads.upload_files, "thread-local", request=MagicMock(), files=files, config=SimpleNamespace()))
+
+    assert exc_info.value.status_code == 413
+    assert list(thread_uploads_dir.iterdir()) == []
+    assert files[0].read_calls == []
+    assert files[1].read_calls == []
+
+
+def test_upload_files_rejects_oversized_single_file_and_removes_partial_file(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+
+    provider = _mounted_provider()
+    file = ChunkedUpload("big.txt", [b"123456"])
+
+    with (
+        patch.object(uploads, "ensure_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=provider),
+        patch.object(uploads, "_get_upload_limits", return_value=uploads.UploadLimits(max_files=10, max_file_size=5, max_total_size=20)),
+    ):
+        with pytest.raises(HTTPException) as exc_info:
+            asyncio.run(call_unwrapped(uploads.upload_files, "thread-local", request=MagicMock(), files=[file], config=SimpleNamespace()))
+
+    assert exc_info.value.status_code == 413
+    assert not (thread_uploads_dir / "big.txt").exists()
+    assert file.read_calls == [8192]
+    provider.acquire.assert_not_called()
+
+
+def test_upload_files_rejects_total_size_over_limit_and_cleans_request_files(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+
+    with (
+        patch.object(uploads, "ensure_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=_mounted_provider()),
+        patch.object(uploads, "_get_upload_limits", return_value=uploads.UploadLimits(max_files=10, max_file_size=10, max_total_size=5)),
+    ):
+        files = [
+            ChunkedUpload("first.txt", [b"123"]),
+            ChunkedUpload("second.txt", [b"456"]),
+        ]
+        with pytest.raises(HTTPException) as exc_info:
+            asyncio.run(call_unwrapped(uploads.upload_files, "thread-local", request=MagicMock(), files=files, config=SimpleNamespace()))
+
+    assert exc_info.value.status_code == 413
+    assert not (thread_uploads_dir / "first.txt").exists()
+    assert not (thread_uploads_dir / "second.txt").exists()
+
+
+def test_upload_files_does_not_sync_non_local_sandbox_when_total_size_exceeds_limit(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+
+    provider = MagicMock()
+    provider.uses_thread_data_mounts = False
+    provider.acquire.return_value = "aio-1"
+    sandbox = MagicMock()
+    provider.get.return_value = sandbox
+
+    with (
+        patch.object(uploads, "ensure_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=provider),
+        patch.object(uploads, "_get_upload_limits", return_value=uploads.UploadLimits(max_files=10, max_file_size=10, max_total_size=5)),
+    ):
+        files = [
+            ChunkedUpload("first.txt", [b"123"]),
+            ChunkedUpload("second.txt", [b"456"]),
+        ]
+        with pytest.raises(HTTPException) as exc_info:
+            asyncio.run(call_unwrapped(uploads.upload_files, "thread-aio", request=MagicMock(), files=files, config=SimpleNamespace()))
+
+    assert exc_info.value.status_code == 413
+    provider.acquire.assert_called_once_with("thread-aio")
+    provider.get.assert_called_once_with("aio-1")
+    sandbox.update_file.assert_not_called()
+
+
+def test_upload_files_does_not_sync_non_local_sandbox_when_conversion_fails(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+
+    provider = MagicMock()
+    provider.uses_thread_data_mounts = False
+    provider.acquire.return_value = "aio-1"
+    sandbox = MagicMock()
+    provider.get.return_value = sandbox
+
+    with (
+        patch.object(uploads, "ensure_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=provider),
+        patch.object(uploads, "_auto_convert_documents_enabled", return_value=True),
+        patch.object(uploads, "convert_file_to_markdown", AsyncMock(side_effect=RuntimeError("conversion failed"))),
+    ):
+        file = UploadFile(filename="report.pdf", file=BytesIO(b"pdf-bytes"))
+        with pytest.raises(HTTPException) as exc_info:
+            asyncio.run(call_unwrapped(uploads.upload_files, "thread-aio", request=MagicMock(), files=[file], config=SimpleNamespace()))
+
+    assert exc_info.value.status_code == 500
+    provider.acquire.assert_called_once_with("thread-aio")
+    provider.get.assert_called_once_with("aio-1")
+    sandbox.update_file.assert_not_called()
+    assert not (thread_uploads_dir / "report.pdf").exists()
+
+
 def test_make_file_sandbox_writable_adds_write_bits_for_regular_files(tmp_path):
     file_path = tmp_path / "report.pdf"
     file_path.write_bytes(b"pdf-bytes")
@@ -238,6 +429,105 @@ def test_upload_files_rejects_dotdot_and_dot_filenames(tmp_path):
     assert [f.name for f in thread_uploads_dir.iterdir()] == ["passwd"]
 
 
+def test_upload_files_rejects_preexisting_symlink_destination(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+    outside_file = tmp_path / "outside.txt"
+    outside_file.write_text("protected", encoding="utf-8")
+    (thread_uploads_dir / "victim.txt").symlink_to(outside_file)
+
+    provider = MagicMock()
+    provider.uses_thread_data_mounts = True
+
+    with (
+        patch.object(uploads, "get_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "ensure_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=provider),
+    ):
+        file = UploadFile(filename="victim.txt", file=BytesIO(b"attacker upload"))
+        result = asyncio.run(uploads.upload_files("thread-local", files=[file]))
+
+    assert result.success is False
+    assert result.files == []
+    assert result.skipped_files == ["victim.txt"]
+    assert "skipped 1 unsafe file" in result.message
+    assert outside_file.read_text(encoding="utf-8") == "protected"
+    assert (thread_uploads_dir / "victim.txt").is_symlink()
+
+
+def test_upload_files_rejects_dangling_symlink_destination(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+    missing_target = tmp_path / "missing-target.txt"
+    (thread_uploads_dir / "victim.txt").symlink_to(missing_target)
+
+    provider = MagicMock()
+    provider.uses_thread_data_mounts = True
+
+    with (
+        patch.object(uploads, "get_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "ensure_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=provider),
+    ):
+        file = UploadFile(filename="victim.txt", file=BytesIO(b"attacker upload"))
+        result = asyncio.run(uploads.upload_files("thread-local", files=[file]))
+
+    assert result.success is False
+    assert result.files == []
+    assert result.skipped_files == ["victim.txt"]
+    assert not missing_target.exists()
+    assert (thread_uploads_dir / "victim.txt").is_symlink()
+
+
+def test_upload_files_rejects_hardlinked_destination_without_truncating(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+    outside_file = tmp_path / "outside.txt"
+    outside_file.write_text("protected", encoding="utf-8")
+    os.link(outside_file, thread_uploads_dir / "victim.txt")
+
+    provider = MagicMock()
+    provider.uses_thread_data_mounts = True
+
+    with (
+        patch.object(uploads, "get_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "ensure_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=provider),
+    ):
+        file = UploadFile(filename="victim.txt", file=BytesIO(b"attacker upload"))
+        result = asyncio.run(uploads.upload_files("thread-local", files=[file]))
+
+    assert result.success is False
+    assert result.files == []
+    assert result.skipped_files == ["victim.txt"]
+    assert outside_file.read_text(encoding="utf-8") == "protected"
+    assert (thread_uploads_dir / "victim.txt").read_text(encoding="utf-8") == "protected"
+
+
+def test_upload_files_overwrites_existing_regular_file(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+    existing_file = thread_uploads_dir / "notes.txt"
+    existing_file.write_bytes(b"old upload")
+    assert existing_file.stat().st_nlink == 1
+
+    provider = MagicMock()
+    provider.uses_thread_data_mounts = True
+
+    with (
+        patch.object(uploads, "get_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "ensure_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=provider),
+    ):
+        file = UploadFile(filename="notes.txt", file=BytesIO(b"new upload"))
+        result = asyncio.run(uploads.upload_files("thread-local", files=[file]))
+
+    assert result.success is True
+    assert [file_info["filename"] for file_info in result.files] == ["notes.txt"]
+    assert existing_file.read_bytes() == b"new upload"
+    assert existing_file.stat().st_nlink == 1
+
+
 def test_delete_uploaded_file_removes_generated_markdown_companion(tmp_path):
     thread_uploads_dir = tmp_path / "uploads"
     thread_uploads_dir.mkdir(parents=True)
@@ -286,3 +576,65 @@ def test_auto_convert_documents_enabled_accepts_boolean_and_string_truthy_values
     assert uploads._auto_convert_documents_enabled(true_cfg) is True
     assert uploads._auto_convert_documents_enabled(string_true_cfg) is True
     assert uploads._auto_convert_documents_enabled(string_false_cfg) is False
+
+
+def test_upload_limits_endpoint_reads_uploads_config():
+    cfg = MagicMock()
+    cfg.uploads = {
+        "max_files": 15,
+        "max_file_size": "1048576",
+        "max_total_size": 2097152,
+    }
+
+    result = asyncio.run(call_unwrapped(uploads.get_upload_limits, "thread-local", request=MagicMock(), config=cfg))
+
+    assert result.max_files == 15
+    assert result.max_file_size == 1048576
+    assert result.max_total_size == 2097152
+
+
+def test_upload_limits_endpoint_requires_thread_access():
+    cfg = MagicMock()
+    cfg.uploads = {}
+    app = make_authed_test_app(owner_check_passes=False)
+    app.state.config = cfg
+    app.include_router(uploads.router)
+
+    with TestClient(app) as client:
+        response = client.get("/api/threads/thread-local/uploads/limits")
+
+    assert response.status_code == 404
+
+
+def test_upload_limits_accept_legacy_config_keys():
+    cfg = MagicMock()
+    cfg.uploads = {
+        "max_file_count": 7,
+        "max_single_file_size": 123,
+        "max_total_size": 456,
+    }
+
+    limits = uploads._get_upload_limits(cfg)
+
+    assert limits == uploads.UploadLimits(max_files=7, max_file_size=123, max_total_size=456)
+
+
+def test_upload_files_uses_configured_file_count_limit(tmp_path):
+    thread_uploads_dir = tmp_path / "uploads"
+    thread_uploads_dir.mkdir(parents=True)
+
+    cfg = MagicMock()
+    cfg.uploads = {"max_files": 1}
+
+    with (
+        patch.object(uploads, "ensure_uploads_dir", return_value=thread_uploads_dir),
+        patch.object(uploads, "get_sandbox_provider", return_value=_mounted_provider()),
+    ):
+        files = [
+            ChunkedUpload("one.txt", [b"one"]),
+            ChunkedUpload("two.txt", [b"two"]),
+        ]
+        with pytest.raises(HTTPException) as exc_info:
+            asyncio.run(call_unwrapped(uploads.upload_files, "thread-local", request=MagicMock(), files=files, config=cfg))
+
+    assert exc_info.value.status_code == 413
diff --git a/backend/tests/test_utils_time.py b/backend/tests/test_utils_time.py
new file mode 100644
index 000000000..d873876c2
--- /dev/null
+++ b/backend/tests/test_utils_time.py
@@ -0,0 +1,90 @@
+"""Tests for ``deerflow.utils.time``."""
+
+from __future__ import annotations
+
+import re
+from datetime import UTC, datetime, timedelta, timezone
+
+from deerflow.utils.time import coerce_iso, now_iso
+
+_ISO_RE = re.compile(r"^\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}")
+
+
+def test_now_iso_is_utc_iso8601() -> None:
+    value = now_iso()
+    assert _ISO_RE.match(value), value
+    parsed = datetime.fromisoformat(value)
+    assert parsed.tzinfo is not None
+    assert parsed.tzinfo.utcoffset(parsed) == UTC.utcoffset(parsed)
+
+
+def test_coerce_iso_passes_iso_through() -> None:
+    iso = "2026-04-27T01:13:30.411334+00:00"
+    assert coerce_iso(iso) == iso
+
+
+def test_coerce_iso_converts_unix_float_string() -> None:
+    legacy = "1777252410.411327"
+    out = coerce_iso(legacy)
+    assert _ISO_RE.match(out), out
+    # Round-trip: parsed timestamp matches the original epoch.
+    parsed = datetime.fromisoformat(out)
+    assert abs(parsed.timestamp() - 1777252410.411327) < 1e-3
+
+
+def test_coerce_iso_converts_unix_int_string() -> None:
+    out = coerce_iso("1700000000")
+    assert _ISO_RE.match(out), out
+
+
+def test_coerce_iso_converts_numeric_types() -> None:
+    out_float = coerce_iso(1777252410.411327)
+    out_int = coerce_iso(1700000000)
+    assert _ISO_RE.match(out_float)
+    assert _ISO_RE.match(out_int)
+
+
+def test_coerce_iso_handles_empty_and_none() -> None:
+    assert coerce_iso(None) == ""
+    assert coerce_iso("") == ""
+
+
+def test_coerce_iso_does_not_misinterpret_short_numeric() -> None:
+    # A 4-digit year should never be parsed as a unix timestamp; only
+    # 10-digit unix-second strings match the legacy pattern.
+    assert coerce_iso("2026") == "2026"
+
+
+def test_coerce_iso_handles_unparseable_string() -> None:
+    assert coerce_iso("not-a-timestamp") == "not-a-timestamp"
+
+
+def test_coerce_iso_rejects_bool() -> None:
+    # ``bool`` is a subclass of ``int`` — must not be treated as epoch 0/1.
+    assert coerce_iso(True) == "True"
+    assert coerce_iso(False) == "False"
+
+
+def test_coerce_iso_handles_tz_aware_datetime() -> None:
+    # str(datetime) would emit a space separator; coerce_iso must use ``T``.
+    dt = datetime(2026, 4, 27, 1, 13, 30, 411327, tzinfo=UTC)
+    out = coerce_iso(dt)
+    assert out == "2026-04-27T01:13:30.411327+00:00"
+    assert "T" in out and " " not in out
+
+
+def test_coerce_iso_handles_tz_naive_datetime_as_utc() -> None:
+    dt = datetime(2026, 4, 27, 1, 13, 30, 411327)
+    out = coerce_iso(dt)
+    assert out == "2026-04-27T01:13:30.411327+00:00"
+    parsed = datetime.fromisoformat(out)
+    assert parsed.tzinfo is not None
+    assert parsed.utcoffset() == timedelta(0)
+
+
+def test_coerce_iso_normalises_non_utc_datetime_to_utc() -> None:
+    # +08:00 wall-clock 09:13 == UTC 01:13.
+    plus_eight = timezone(timedelta(hours=8))
+    dt = datetime(2026, 4, 27, 9, 13, 30, 411327, tzinfo=plus_eight)
+    out = coerce_iso(dt)
+    assert out == "2026-04-27T01:13:30.411327+00:00"
diff --git a/config.example.yaml b/config.example.yaml
index a14ca5886..7e282e46e 100644
--- a/config.example.yaml
+++ b/config.example.yaml
@@ -2,8 +2,11 @@
 #
 # Guidelines:
 # - Copy this file to `config.yaml` and customize it for your environment
-# - The default path of this configuration file is `config.yaml` in the current working directory.
-#   However you can change it using the `DEER_FLOW_CONFIG_PATH` environment variable.
+# - The default path of this configuration file is `config.yaml` in the project root.
+#   You can set `DEER_FLOW_PROJECT_ROOT` to define that root explicitly, or use
+#   `DEER_FLOW_CONFIG_PATH` to point at a specific config file.
+# - Runtime state defaults to `.deer-flow` under the project root. Override it
+#   with `DEER_FLOW_HOME` when you need a different writable data directory.
 # - Environment variables are available for all field values. Example: `api_key: $OPENAI_API_KEY`
 # - The `use` path is a string that looks like "package_name.sub_package_name.module_name:class_name/variable_name".
 
@@ -370,6 +373,16 @@ tools:
     use: deerflow.community.ddg_search.tools:web_search_tool
     max_results: 5
 
+  # Web search tool (uses Serper - Google Search API, requires SERPER_API_KEY)
+  # Serper provides real-time Google Search results. Sign up at https://serper.dev
+  # Note: set SERPER_API_KEY in your environment before starting the app, or
+  # uncomment and fill in api_key below (the $VAR syntax is resolved at startup).
+  # - name: web_search
+  #   group: web
+  #   use: deerflow.community.serper.tools:web_search_tool
+  #   max_results: 5
+  #   # api_key: $SERPER_API_KEY  # Optional if SERPER_API_KEY env var is set
+
   # Web search tool (requires Tavily API key)
   # - name: web_search
   #   group: web
@@ -501,6 +514,11 @@ tool_search:
 # Option 1: Local Sandbox (Default)
 # Executes commands directly on the host machine
 uploads:
+  # Application-level upload limits enforced by the gateway and exposed to the
+  # frontend before file selection.
+  max_files: 10
+  max_file_size: 52428800    # 50 MiB
+  max_total_size: 104857600  # 100 MiB
   # Automatic Office/PDF conversion runs on the backend host before sandbox
   # isolation applies. Keep this disabled unless uploads come from a fully
   # trusted source and you intentionally accept host-side parser risk.
@@ -673,7 +691,8 @@ sandbox:
 
 skills:
   # Path to skills directory on the host (relative to project root or absolute)
-  # Default: ../skills (relative to backend directory)
+  # Default: skills under the project root
+  # Override with DEER_FLOW_SKILLS_PATH when this field is omitted.
   # Uncomment to customize:
   # path: /absolute/path/to/custom/skills
 
diff --git a/docker/docker-compose-dev.yaml b/docker/docker-compose-dev.yaml
index 8fb95124d..6d00d71ff 100644
--- a/docker/docker-compose-dev.yaml
+++ b/docker/docker-compose-dev.yaml
@@ -157,6 +157,7 @@ services:
     working_dir: /app
     environment:
       - CI=true
+      - DEER_FLOW_PROJECT_ROOT=/app
       - DEER_FLOW_HOME=/app/backend/.deer-flow
       - DEER_FLOW_CHANNELS_LANGGRAPH_URL=${DEER_FLOW_CHANNELS_LANGGRAPH_URL:-http://gateway:8001/api}
       - DEER_FLOW_CHANNELS_GATEWAY_URL=${DEER_FLOW_CHANNELS_GATEWAY_URL:-http://gateway:8001}
diff --git a/docker/docker-compose.yaml b/docker/docker-compose.yaml
index 82cb62425..8d82980d3 100644
--- a/docker/docker-compose.yaml
+++ b/docker/docker-compose.yaml
@@ -8,9 +8,11 @@
 #   - provisioner: (optional) Sandbox provisioner for Kubernetes mode
 #
 # Key environment variables (set via environment/.env or scripts/deploy.sh):
-#   DEER_FLOW_HOME                   — runtime data dir, default $REPO_ROOT/backend/.deer-flow
+#   DEER_FLOW_PROJECT_ROOT           — project root for relative runtime paths
+#   DEER_FLOW_HOME                   — runtime data dir, default .deer-flow under $DEER_FLOW_PROJECT_ROOT (or cwd)
 #   DEER_FLOW_CONFIG_PATH            — path to config.yaml
 #   DEER_FLOW_EXTENSIONS_CONFIG_PATH — path to extensions_config.json
+#   DEER_FLOW_SKILLS_PATH            — skills dir, default $DEER_FLOW_PROJECT_ROOT/skills
 #   DEER_FLOW_DOCKER_SOCKET          — Docker socket path, default /var/run/docker.sock
 #   DEER_FLOW_REPO_ROOT              — repo root (used for skills host path in DooD)
 #   BETTER_AUTH_SECRET               — required for frontend auth/session security
@@ -93,6 +95,7 @@ services:
     working_dir: /app
     environment:
       - CI=true
+      - DEER_FLOW_PROJECT_ROOT=/app
       - DEER_FLOW_HOME=/app/backend/.deer-flow
       - DEER_FLOW_CONFIG_PATH=/app/backend/config.yaml
       - DEER_FLOW_EXTENSIONS_CONFIG_PATH=/app/backend/extensions_config.json