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- **App** (`app/`): unpublished application code with import prefix `app.*`.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files can silently become outdated.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

@@ -5,8 +5,8 @@ from unittest.mock import MagicMock, patch
 
 import pytest
 
-from src.agents.checkpointer import get_checkpointer, reset_checkpointer
-from src.config.checkpointer_config import (
+from deerflow.agents.checkpointer import get_checkpointer, reset_checkpointer
+from deerflow.config.checkpointer_config import (
     CheckpointerConfig,
     get_checkpointer_config,
     load_checkpointer_config_from_dict,
@@ -195,7 +195,7 @@ class TestClientCheckpointerFallback:
         """DeerFlowClient._ensure_agent falls back to get_checkpointer() when checkpointer=None."""
         from langgraph.checkpoint.memory import InMemorySaver
 
-        from src.client import DeerFlowClient
+        from deerflow.client import DeerFlowClient
 
         load_checkpointer_config_from_dict({"type": "memory"})
 
@@ -212,12 +212,12 @@ class TestClientCheckpointerFallback:
         config_mock.checkpointer = None
 
         with (
-            patch("src.client.get_app_config", return_value=config_mock),
-            patch("src.client.create_agent", side_effect=fake_create_agent),
-            patch("src.client.create_chat_model", return_value=MagicMock()),
-            patch("src.client._build_middlewares", return_value=[]),
-            patch("src.client.apply_prompt_template", return_value=""),
-            patch("src.client.DeerFlowClient._get_tools", return_value=[]),
+            patch("deerflow.client.get_app_config", return_value=config_mock),
+            patch("deerflow.client.create_agent", side_effect=fake_create_agent),
+            patch("deerflow.client.create_chat_model", return_value=MagicMock()),
+            patch("deerflow.client._build_middlewares", return_value=[]),
+            patch("deerflow.client.apply_prompt_template", return_value=""),
+            patch("deerflow.client.DeerFlowClient._get_tools", return_value=[]),
         ):
             client = DeerFlowClient(checkpointer=None)
             config = client._get_runnable_config("test-thread")
@@ -228,7 +228,7 @@ class TestClientCheckpointerFallback:
 
     def test_client_explicit_checkpointer_takes_precedence(self):
         """An explicitly provided checkpointer is used even when config checkpointer is set."""
-        from src.client import DeerFlowClient
+        from deerflow.client import DeerFlowClient
 
         load_checkpointer_config_from_dict({"type": "memory"})
 
@@ -246,12 +246,12 @@ class TestClientCheckpointerFallback:
         config_mock.checkpointer = None
 
         with (
-            patch("src.client.get_app_config", return_value=config_mock),
-            patch("src.client.create_agent", side_effect=fake_create_agent),
-            patch("src.client.create_chat_model", return_value=MagicMock()),
-            patch("src.client._build_middlewares", return_value=[]),
-            patch("src.client.apply_prompt_template", return_value=""),
-            patch("src.client.DeerFlowClient._get_tools", return_value=[]),
+            patch("deerflow.client.get_app_config", return_value=config_mock),
+            patch("deerflow.client.create_agent", side_effect=fake_create_agent),
+            patch("deerflow.client.create_chat_model", return_value=MagicMock()),
+            patch("deerflow.client._build_middlewares", return_value=[]),
+            patch("deerflow.client.apply_prompt_template", return_value=""),
+            patch("deerflow.client.DeerFlowClient._get_tools", return_value=[]),
         ):
             client = DeerFlowClient(checkpointer=explicit_cp)
             config = client._get_runnable_config("test-thread")