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- **App** (`app/`): unpublished application code with import prefix `app.*`.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files can silently become outdated.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

@@ -3,8 +3,8 @@
 import json
 from unittest.mock import MagicMock, patch
 
-from src.community.infoquest import tools
-from src.community.infoquest.infoquest_client import InfoQuestClient
+from deerflow.community.infoquest import tools
+from deerflow.community.infoquest.infoquest_client import InfoQuestClient
 
 
 class TestInfoQuestClient:
@@ -24,7 +24,7 @@ class TestInfoQuestClient:
         assert client.fetch_navigation_timeout == 60
         assert client.search_time_range == 24
 
-    @patch("src.community.infoquest.infoquest_client.requests.post")
+    @patch("deerflow.community.infoquest.infoquest_client.requests.post")
     def test_fetch_success(self, mock_post):
         """Test successful fetch operation."""
         mock_response = MagicMock()
@@ -42,7 +42,7 @@ class TestInfoQuestClient:
         assert kwargs["json"]["url"] == "https://example.com"
         assert kwargs["json"]["format"] == "HTML"
 
-    @patch("src.community.infoquest.infoquest_client.requests.post")
+    @patch("deerflow.community.infoquest.infoquest_client.requests.post")
     def test_fetch_non_200_status(self, mock_post):
         """Test fetch operation with non-200 status code."""
         mock_response = MagicMock()
@@ -55,7 +55,7 @@ class TestInfoQuestClient:
 
         assert result == "Error: fetch API returned status 404: Not Found"
 
-    @patch("src.community.infoquest.infoquest_client.requests.post")
+    @patch("deerflow.community.infoquest.infoquest_client.requests.post")
     def test_fetch_empty_response(self, mock_post):
         """Test fetch operation with empty response."""
         mock_response = MagicMock()
@@ -68,7 +68,7 @@ class TestInfoQuestClient:
 
         assert result == "Error: no result found"
 
-    @patch("src.community.infoquest.infoquest_client.requests.post")
+    @patch("deerflow.community.infoquest.infoquest_client.requests.post")
     def test_web_search_raw_results_success(self, mock_post):
         """Test successful web_search_raw_results operation."""
         mock_response = MagicMock()
@@ -85,7 +85,7 @@ class TestInfoQuestClient:
         assert args[0] == "https://search.infoquest.bytepluses.com"
         assert kwargs["json"]["query"] == "test query"
 
-    @patch("src.community.infoquest.infoquest_client.requests.post")
+    @patch("deerflow.community.infoquest.infoquest_client.requests.post")
     def test_web_search_success(self, mock_post):
         """Test successful web_search operation."""
         mock_response = MagicMock()
@@ -133,7 +133,7 @@ class TestInfoQuestClient:
         assert cleaned[0]["thumbnail_url"] == "https://example.com/thumb1.jpg"
         assert cleaned[0]["url"] == "https://example.com/page1"
 
-    @patch("src.community.infoquest.tools._get_infoquest_client")
+    @patch("deerflow.community.infoquest.tools._get_infoquest_client")
     def test_web_search_tool(self, mock_get_client):
         """Test web_search_tool function."""
         mock_client = MagicMock()
@@ -146,7 +146,7 @@ class TestInfoQuestClient:
         mock_get_client.assert_called_once()
         mock_client.web_search.assert_called_once_with("test query")
 
-    @patch("src.community.infoquest.tools._get_infoquest_client")
+    @patch("deerflow.community.infoquest.tools._get_infoquest_client")
     def test_web_fetch_tool(self, mock_get_client):
         """Test web_fetch_tool function."""
         mock_client = MagicMock()
@@ -159,7 +159,7 @@ class TestInfoQuestClient:
         mock_get_client.assert_called_once()
         mock_client.fetch.assert_called_once_with("https://example.com")
 
-    @patch("src.community.infoquest.tools.get_app_config")
+    @patch("deerflow.community.infoquest.tools.get_app_config")
     def test_get_infoquest_client(self, mock_get_app_config):
         """Test _get_infoquest_client function with config."""
         mock_config = MagicMock()
@@ -173,7 +173,7 @@ class TestInfoQuestClient:
         assert client.fetch_timeout == 30
         assert client.fetch_navigation_timeout == 60
 
-    @patch("src.community.infoquest.infoquest_client.requests.post")
+    @patch("deerflow.community.infoquest.infoquest_client.requests.post")
     def test_web_search_api_error(self, mock_post):
         """Test web_search operation with API error."""
         mock_post.side_effect = Exception("Connection error")