refactor: split backend into harness (deerflow.*) and app (app.*) (#1131)

* refactor: extract shared utils to break harness→app cross-layer imports

Move _validate_skill_frontmatter to src/skills/validation.py and
CONVERTIBLE_EXTENSIONS + convert_file_to_markdown to src/utils/file_conversion.py.
This eliminates the two reverse dependencies from client.py (harness layer)
into gateway/routers/ (app layer), preparing for the harness/app package split.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* refactor: split backend/src into harness (deerflow.*) and app (app.*)

Physically split the monolithic backend/src/ package into two layers:

- **Harness** (`packages/harness/deerflow/`): publishable agent framework
  package with import prefix `deerflow.*`. Contains agents, sandbox, tools,
  models, MCP, skills, config, and all core infrastructure.

- **App** (`app/`): unpublished application code with import prefix `app.*`.
  Contains gateway (FastAPI REST API) and channels (IM integrations).

Key changes:
- Move 13 harness modules to packages/harness/deerflow/ via git mv
- Move gateway + channels to app/ via git mv
- Rename all imports: src.* → deerflow.* (harness) / app.* (app layer)
- Set up uv workspace with deerflow-harness as workspace member
- Update langgraph.json, config.example.yaml, all scripts, Docker files
- Add build-system (hatchling) to harness pyproject.toml
- Add PYTHONPATH=. to gateway startup commands for app.* resolution
- Update ruff.toml with known-first-party for import sorting
- Update all documentation to reflect new directory structure

Boundary rule enforced: harness code never imports from app.
All 429 tests pass. Lint clean.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* chore: add harness→app boundary check test and update docs

Add test_harness_boundary.py that scans all Python files in
packages/harness/deerflow/ and fails if any `from app.*` or
`import app.*` statement is found. This enforces the architectural
rule that the harness layer never depends on the app layer.

Update CLAUDE.md to document the harness/app split architecture,
import conventions, and the boundary enforcement test.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* feat: add config versioning with auto-upgrade on startup

When config.example.yaml schema changes, developers' local config.yaml
files can silently become outdated. This adds a config_version field and
auto-upgrade mechanism so breaking changes (like src.* → deerflow.*
renames) are applied automatically before services start.

- Add config_version: 1 to config.example.yaml
- Add startup version check warning in AppConfig.from_file()
- Add scripts/config-upgrade.sh with migration registry for value replacements
- Add `make config-upgrade` target
- Auto-run config-upgrade in serve.sh and start-daemon.sh before starting services
- Add config error hints in service failure messages

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix comments

* fix: update src.* import in test_sandbox_tools_security to deerflow.*

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix: handle empty config and search parent dirs for config.example.yaml

Address Copilot review comments on PR #1131:
- Guard against yaml.safe_load() returning None for empty config files
- Search parent directories for config.example.yaml instead of only
  looking next to config.yaml, fixing detection in common setups

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix: correct skills root path depth and config_version type coercion

- loader.py: fix get_skills_root_path() to use 5 parent levels (was 3)
  after harness split, file lives at packages/harness/deerflow/skills/
  so parent×3 resolved to backend/packages/harness/ instead of backend/
- app_config.py: coerce config_version to int() before comparison in
  _check_config_version() to prevent TypeError when YAML stores value
  as string (e.g. config_version: "1")
- tests: add regression tests for both fixes

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix: update test imports from src.* to deerflow.*/app.* after harness refactor

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

docs/CODE_CHANGE_SUMMARY_BY_FILE.md

@@ -23,7 +23,7 @@
 
 ---
 
-### 2. `backend/src/agents/lead_agent/prompt.py`
+### 2. `backend/packages/harness/deerflow/agents/lead_agent/prompt.py`
 
 ```diff
 @@ -240,34 +240,8 @@ You have access to skills that provide optimized workflows for specific tasks. E
@@ -76,7 +76,7 @@
 
 ---
 
-### 3. `backend/src/gateway/routers/artifacts.py`
+### 3. `backend/app/gateway/routers/artifacts.py`
 
 ```diff
 @@ -1,12 +1,10 @@
@@ -92,7 +92,7 @@
 +from fastapi import APIRouter, HTTPException, Request
 +from fastapi.responses import FileResponse, HTMLResponse, PlainTextResponse, Response
  
- from src.gateway.path_utils import resolve_thread_virtual_path
+ from app.gateway.path_utils import resolve_thread_virtual_path
 ```
 
 - **第 1 行**：删除 `import json`。
@@ -176,7 +176,7 @@
 
 ---
 
-### 4. `backend/src/subagents/builtins/general_purpose.py`
+### 4. `backend/packages/harness/deerflow/subagents/builtins/general_purpose.py`
 
 ```diff
 @@ -24,21 +24,10 @@ Do NOT use for simple, single-step operations.""",

docs/SKILL_NAME_CONFLICT_FIX.md

@@ -48,7 +48,7 @@
 
 ## 详细代码改动
 
-### 一、后端配置层 (`backend/src/config/extensions_config.py`)
+### 一、后端配置层 (`backend/packages/harness/deerflow/config/extensions_config.py`)
 
 #### 1.1 新增方法: `get_skill_key()`
 
@@ -138,7 +138,7 @@ def is_skill_enabled(self, skill_name: str, skill_category: str) -> bool:
 
 ---
 
-### 二、后端技能加载器 (`backend/src/skills/loader.py`)
+### 二、后端技能加载器 (`backend/packages/harness/deerflow/skills/loader.py`)
 
 #### 2.1 添加重复检查逻辑
 
@@ -200,7 +200,7 @@ for category in ["public", "custom"]:
 
 ---
 
-### 三、后端 API 路由 (`backend/src/gateway/routers/skills.py`)
+### 三、后端 API 路由 (`backend/app/gateway/routers/skills.py`)
 
 #### 3.1 新增辅助函数: `_find_skill_by_name()`
 
@@ -830,9 +830,9 @@ Body: { "enabled": false }
 ### 改动统计
 
 - **后端文件**: 3 个文件修改
-  - `backend/src/config/extensions_config.py`: +1 方法，修改 1 方法
-  - `backend/src/skills/loader.py`: +重复检查逻辑
-  - `backend/src/gateway/routers/skills.py`: +1 辅助函数，修改 3 个端点
+  - `backend/packages/harness/deerflow/config/extensions_config.py`: +1 方法，修改 1 方法
+  - `backend/packages/harness/deerflow/skills/loader.py`: +重复检查逻辑
+  - `backend/app/gateway/routers/skills.py`: +1 辅助函数，修改 3 个端点
 
 - **前端文件**: 3 个文件修改
   - `frontend/src/core/skills/api.ts`: 修改 1 个函数