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- **App** (`app/`): unpublished application code with import prefix `app.*`.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files can silently become outdated.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>

backend/CONTRIBUTING.md

@@ -227,7 +227,7 @@ Example test:
 
 ```python
 import pytest
-from src.models.factory import create_chat_model
+from deerflow.models.factory import create_chat_model
 
 def test_create_chat_model_with_valid_name():
     """Test that a valid model name creates a model instance."""
@@ -269,10 +269,10 @@ Include in your PR description:
 
 ### Adding New Tools
 
-1. Create tool in `src/tools/builtins/` or `src/community/`:
+1. Create tool in `packages/harness/deerflow/tools/builtins/` or `packages/harness/deerflow/community/`:
 
 ```python
-# src/tools/builtins/my_tool.py
+# packages/harness/deerflow/tools/builtins/my_tool.py
 from langchain_core.tools import tool
 
 @tool
@@ -294,15 +294,15 @@ def my_tool(param: str) -> str:
 tools:
   - name: my_tool
     group: my_group
-    use: src.tools.builtins.my_tool:my_tool
+    use: deerflow.tools.builtins.my_tool:my_tool
 ```
 
 ### Adding New Middleware
 
-1. Create middleware in `src/agents/middlewares/`:
+1. Create middleware in `packages/harness/deerflow/agents/middlewares/`:
 
 ```python
-# src/agents/middlewares/my_middleware.py
+# packages/harness/deerflow/agents/middlewares/my_middleware.py
 from langchain.agents.middleware import BaseMiddleware
 from langchain_core.runnables import RunnableConfig
 
@@ -315,7 +315,7 @@ class MyMiddleware(BaseMiddleware):
         return state
 ```
 
-2. Register in `src/agents/lead_agent/agent.py`:
+2. Register in `packages/harness/deerflow/agents/lead_agent/agent.py`:
 
 ```python
 middlewares = [
@@ -329,10 +329,10 @@ middlewares = [
 
 ### Adding New API Endpoints
 
-1. Create router in `src/gateway/routers/`:
+1. Create router in `app/gateway/routers/`:
 
 ```python
-# src/gateway/routers/my_router.py
+# app/gateway/routers/my_router.py
 from fastapi import APIRouter
 
 router = APIRouter(prefix="/my-endpoint", tags=["my-endpoint"])
@@ -348,10 +348,10 @@ async def create_item(data: dict):
     return {"created": data}
 ```
 
-2. Register in `src/gateway/app.py`:
+2. Register in `app/gateway/app.py`:
 
 ```python
-from src.gateway.routers import my_router
+from app.gateway.routers import my_router
 
 app.include_router(my_router.router)
 ```
@@ -360,7 +360,7 @@ app.include_router(my_router.router)
 
 When adding new configuration options:
 
-1. Update `src/config/app_config.py` with new fields
+1. Update `packages/harness/deerflow/config/app_config.py` with new fields
 2. Add default values in `config.example.yaml`
 3. Document in `docs/CONFIGURATION.md`