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- **App** (`app/`): unpublished application code with import prefix `app.*`.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files can silently become outdated.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/packages/harness/deerflow/config/tracing_config.py

@@ -0,0 +1,94 @@
+import logging
+import os
+import threading
+
+from pydantic import BaseModel, Field
+
+logger = logging.getLogger(__name__)
+_config_lock = threading.Lock()
+
+
+class TracingConfig(BaseModel):
+    """Configuration for LangSmith tracing."""
+
+    enabled: bool = Field(...)
+    api_key: str | None = Field(...)
+    project: str = Field(...)
+    endpoint: str = Field(...)
+
+    @property
+    def is_configured(self) -> bool:
+        """Check if tracing is fully configured (enabled and has API key)."""
+        return self.enabled and bool(self.api_key)
+
+
+_tracing_config: TracingConfig | None = None
+
+
+_TRUTHY_VALUES = {"1", "true", "yes", "on"}
+
+
+def _env_flag_preferred(*names: str) -> bool:
+    """Return the boolean value of the first env var that is present and non-empty.
+
+    Accepted truthy values (case-insensitive): ``1``, ``true``, ``yes``, ``on``.
+    Any other non-empty value is treated as falsy.  If none of the named
+    variables is set, returns ``False``.
+    """
+    for name in names:
+        value = os.environ.get(name)
+        if value is not None and value.strip():
+            return value.strip().lower() in _TRUTHY_VALUES
+    return False
+
+
+def _first_env_value(*names: str) -> str | None:
+    """Return the first non-empty environment value from candidate names."""
+    for name in names:
+        value = os.environ.get(name)
+        if value and value.strip():
+            return value.strip()
+    return None
+
+
+def get_tracing_config() -> TracingConfig:
+    """Get the current tracing configuration from environment variables.
+
+    ``LANGSMITH_*`` variables take precedence over their legacy ``LANGCHAIN_*``
+    counterparts.  For boolean flags (``enabled``), the *first* variable that is
+    present and non-empty in the priority list is the sole authority – its value
+    is parsed and returned without consulting the remaining candidates.  Accepted
+    truthy values are ``1``, ``true``, ``yes``, and ``on`` (case-insensitive);
+    any other non-empty value is treated as falsy.
+
+    Priority order:
+        enabled  : LANGSMITH_TRACING > LANGCHAIN_TRACING_V2 > LANGCHAIN_TRACING
+        api_key  : LANGSMITH_API_KEY  > LANGCHAIN_API_KEY
+        project  : LANGSMITH_PROJECT  > LANGCHAIN_PROJECT   (default: "deer-flow")
+        endpoint : LANGSMITH_ENDPOINT > LANGCHAIN_ENDPOINT  (default: https://api.smith.langchain.com)
+
+    Returns:
+        TracingConfig with current settings.
+    """
+    global _tracing_config
+    if _tracing_config is not None:
+        return _tracing_config
+    with _config_lock:
+        if _tracing_config is not None:  # Double-check after acquiring lock
+            return _tracing_config
+        _tracing_config = TracingConfig(
+            # Keep compatibility with both legacy LANGCHAIN_* and newer LANGSMITH_* variables.
+            enabled=_env_flag_preferred("LANGSMITH_TRACING", "LANGCHAIN_TRACING_V2", "LANGCHAIN_TRACING"),
+            api_key=_first_env_value("LANGSMITH_API_KEY", "LANGCHAIN_API_KEY"),
+            project=_first_env_value("LANGSMITH_PROJECT", "LANGCHAIN_PROJECT") or "deer-flow",
+            endpoint=_first_env_value("LANGSMITH_ENDPOINT", "LANGCHAIN_ENDPOINT") or "https://api.smith.langchain.com",
+        )
+        return _tracing_config
+
+
+def is_tracing_enabled() -> bool:
+    """Check if LangSmith tracing is enabled and configured.
+    Returns:
+        True if tracing is enabled and has an API key.
+    """
+    return get_tracing_config().is_configured