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- **App** (`app/`): unpublished application code with import prefix `app.*`.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files can silently become outdated.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

@@ -8,7 +8,7 @@ Covers:
 - Async tool support (MCP tools)
 
 Note: Due to circular import issues in the main codebase, conftest.py mocks
-src.subagents.executor. This test file uses delayed import via fixture to test
+deerflow.subagents.executor. This test file uses delayed import via fixture to test
 the real implementation in isolation.
 """
 
@@ -21,13 +21,13 @@ import pytest
 
 # Module names that need to be mocked to break circular imports
 _MOCKED_MODULE_NAMES = [
-    "src.agents",
-    "src.agents.thread_state",
-    "src.agents.middlewares",
-    "src.agents.middlewares.thread_data_middleware",
-    "src.sandbox",
-    "src.sandbox.middleware",
-    "src.models",
+    "deerflow.agents",
+    "deerflow.agents.thread_state",
+    "deerflow.agents.middlewares",
+    "deerflow.agents.middlewares.thread_data_middleware",
+    "deerflow.sandbox",
+    "deerflow.sandbox.middleware",
+    "deerflow.models",
 ]
 
 
@@ -40,11 +40,11 @@ def _setup_executor_classes():
     """
     # Save original modules
     original_modules = {name: sys.modules.get(name) for name in _MOCKED_MODULE_NAMES}
-    original_executor = sys.modules.get("src.subagents.executor")
+    original_executor = sys.modules.get("deerflow.subagents.executor")
 
     # Remove mocked executor if exists (from conftest.py)
-    if "src.subagents.executor" in sys.modules:
-        del sys.modules["src.subagents.executor"]
+    if "deerflow.subagents.executor" in sys.modules:
+        del sys.modules["deerflow.subagents.executor"]
 
     # Set up mocks
     for name in _MOCKED_MODULE_NAMES:
@@ -53,8 +53,8 @@ def _setup_executor_classes():
     # Import real classes inside fixture
     from langchain_core.messages import AIMessage, HumanMessage
 
-    from src.subagents.config import SubagentConfig
-    from src.subagents.executor import (
+    from deerflow.subagents.config import SubagentConfig
+    from deerflow.subagents.executor import (
         SubagentExecutor,
         SubagentResult,
         SubagentStatus,
@@ -81,9 +81,9 @@ def _setup_executor_classes():
 
     # Restore executor module (conftest.py mock)
     if original_executor is not None:
-        sys.modules["src.subagents.executor"] = original_executor
-    elif "src.subagents.executor" in sys.modules:
-        del sys.modules["src.subagents.executor"]
+        sys.modules["deerflow.subagents.executor"] = original_executor
+    elif "deerflow.subagents.executor" in sys.modules:
+        del sys.modules["deerflow.subagents.executor"]
 
 
 # Helper classes that wrap real classes for testing
@@ -641,7 +641,7 @@ class TestCleanupBackgroundTask:
         # Re-import to get the real module with cleanup_background_task
         import importlib
 
-        from src.subagents import executor
+        from deerflow.subagents import executor
 
         return importlib.reload(executor)
 
@@ -749,9 +749,7 @@ class TestCleanupBackgroundTask:
         # Should not raise
         executor_module.cleanup_background_task("nonexistent-task")
 
-    def test_cleanup_removes_task_with_completed_at_even_if_running(
-        self, executor_module, classes
-    ):
+    def test_cleanup_removes_task_with_completed_at_even_if_running(self, executor_module, classes):
         """Test that cleanup removes task if completed_at is set, even if status is RUNNING.
 
         This is a safety net: if completed_at is set, the task is considered done