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- **App** (`app/`): unpublished application code with import prefix `app.*`.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files can silently become outdated.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

@@ -0,0 +1,47 @@
+"""File conversion utilities.
+
+Converts document files (PDF, PPT, Excel, Word) to Markdown using markitdown.
+No FastAPI or HTTP dependencies — pure utility functions.
+"""
+
+import logging
+from pathlib import Path
+
+logger = logging.getLogger(__name__)
+
+# File extensions that should be converted to markdown
+CONVERTIBLE_EXTENSIONS = {
+    ".pdf",
+    ".ppt",
+    ".pptx",
+    ".xls",
+    ".xlsx",
+    ".doc",
+    ".docx",
+}
+
+
+async def convert_file_to_markdown(file_path: Path) -> Path | None:
+    """Convert a file to markdown using markitdown.
+
+    Args:
+        file_path: Path to the file to convert.
+
+    Returns:
+        Path to the markdown file if conversion was successful, None otherwise.
+    """
+    try:
+        from markitdown import MarkItDown
+
+        md = MarkItDown()
+        result = md.convert(str(file_path))
+
+        # Save as .md file with same name
+        md_path = file_path.with_suffix(".md")
+        md_path.write_text(result.text_content, encoding="utf-8")
+
+        logger.info(f"Converted {file_path.name} to markdown: {md_path.name}")
+        return md_path
+    except Exception as e:
+        logger.error(f"Failed to convert {file_path.name} to markdown: {e}")
+        return None

backend/packages/harness/deerflow/utils/network.py

@@ -0,0 +1,139 @@
+"""Thread-safe network utilities."""
+
+import socket
+import threading
+from contextlib import contextmanager
+
+
+class PortAllocator:
+    """Thread-safe port allocator that prevents port conflicts in concurrent environments.
+
+    This class maintains a set of reserved ports and uses a lock to ensure that
+    port allocation is atomic. Once a port is allocated, it remains reserved until
+    explicitly released.
+
+    Usage:
+        allocator = PortAllocator()
+
+        # Option 1: Manual allocation and release
+        port = allocator.allocate(start_port=8080)
+        try:
+            # Use the port...
+        finally:
+            allocator.release(port)
+
+        # Option 2: Context manager (recommended)
+        with allocator.allocate_context(start_port=8080) as port:
+            # Use the port...
+            # Port is automatically released when exiting the context
+    """
+
+    def __init__(self):
+        self._lock = threading.Lock()
+        self._reserved_ports: set[int] = set()
+
+    def _is_port_available(self, port: int) -> bool:
+        """Check if a port is available for binding.
+
+        Args:
+            port: The port number to check.
+
+        Returns:
+            True if the port is available, False otherwise.
+        """
+        if port in self._reserved_ports:
+            return False
+
+        # Bind to 0.0.0.0 (wildcard) rather than localhost so that the check
+        # mirrors exactly what Docker does.  Docker binds to 0.0.0.0:PORT;
+        # checking only 127.0.0.1 can falsely report a port as available even
+        # when Docker already occupies it on the wildcard address.
+        with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+            try:
+                s.bind(("0.0.0.0", port))
+                return True
+            except OSError:
+                return False
+
+    def allocate(self, start_port: int = 8080, max_range: int = 100) -> int:
+        """Allocate an available port in a thread-safe manner.
+
+        This method is thread-safe. It finds an available port, marks it as reserved,
+        and returns it. The port remains reserved until release() is called.
+
+        Args:
+            start_port: The port number to start searching from.
+            max_range: Maximum number of ports to search.
+
+        Returns:
+            An available port number.
+
+        Raises:
+            RuntimeError: If no available port is found in the specified range.
+        """
+        with self._lock:
+            for port in range(start_port, start_port + max_range):
+                if self._is_port_available(port):
+                    self._reserved_ports.add(port)
+                    return port
+
+            raise RuntimeError(f"No available port found in range {start_port}-{start_port + max_range}")
+
+    def release(self, port: int) -> None:
+        """Release a previously allocated port.
+
+        Args:
+            port: The port number to release.
+        """
+        with self._lock:
+            self._reserved_ports.discard(port)
+
+    @contextmanager
+    def allocate_context(self, start_port: int = 8080, max_range: int = 100):
+        """Context manager for port allocation with automatic release.
+
+        Args:
+            start_port: The port number to start searching from.
+            max_range: Maximum number of ports to search.
+
+        Yields:
+            An available port number.
+        """
+        port = self.allocate(start_port, max_range)
+        try:
+            yield port
+        finally:
+            self.release(port)
+
+
+# Global port allocator instance for shared use across the application
+_global_port_allocator = PortAllocator()
+
+
+def get_free_port(start_port: int = 8080, max_range: int = 100) -> int:
+    """Get a free port in a thread-safe manner.
+
+    This function uses a global port allocator to ensure that concurrent calls
+    don't return the same port. The port is marked as reserved until release_port()
+    is called.
+
+    Args:
+        start_port: The port number to start searching from.
+        max_range: Maximum number of ports to search.
+
+    Returns:
+        An available port number.
+
+    Raises:
+        RuntimeError: If no available port is found in the specified range.
+    """
+    return _global_port_allocator.allocate(start_port, max_range)
+
+
+def release_port(port: int) -> None:
+    """Release a previously allocated port.
+
+    Args:
+        port: The port number to release.
+    """
+    _global_port_allocator.release(port)

backend/packages/harness/deerflow/utils/readability.py

@@ -0,0 +1,83 @@
+import logging
+import re
+import subprocess
+from urllib.parse import urljoin
+
+from markdownify import markdownify as md
+from readabilipy import simple_json_from_html_string
+
+logger = logging.getLogger(__name__)
+
+
+class Article:
+    url: str
+
+    def __init__(self, title: str, html_content: str):
+        self.title = title
+        self.html_content = html_content
+
+    def to_markdown(self, including_title: bool = True) -> str:
+        markdown = ""
+        if including_title:
+            markdown += f"# {self.title}\n\n"
+
+        if self.html_content is None or not str(self.html_content).strip():
+            markdown += "*No content available*\n"
+        else:
+            markdown += md(self.html_content)
+
+        return markdown
+
+    def to_message(self) -> list[dict]:
+        image_pattern = r"!\[.*?\]\((.*?)\)"
+
+        content: list[dict[str, str]] = []
+        markdown = self.to_markdown()
+
+        if not markdown or not markdown.strip():
+            return [{"type": "text", "text": "No content available"}]
+
+        parts = re.split(image_pattern, markdown)
+
+        for i, part in enumerate(parts):
+            if i % 2 == 1:
+                image_url = urljoin(self.url, part.strip())
+                content.append({"type": "image_url", "image_url": {"url": image_url}})
+            else:
+                text_part = part.strip()
+                if text_part:
+                    content.append({"type": "text", "text": text_part})
+
+        # If after processing all parts, content is still empty, provide a fallback message.
+        if not content:
+            content = [{"type": "text", "text": "No content available"}]
+
+        return content
+
+
+class ReadabilityExtractor:
+    def extract_article(self, html: str) -> Article:
+        try:
+            article = simple_json_from_html_string(html, use_readability=True)
+        except (subprocess.CalledProcessError, FileNotFoundError) as exc:
+            stderr = getattr(exc, "stderr", None)
+            if isinstance(stderr, bytes):
+                stderr = stderr.decode(errors="replace")
+            stderr_info = f"; stderr={stderr.strip()}" if isinstance(stderr, str) and stderr.strip() else ""
+            logger.warning(
+                "Readability.js extraction failed with %s%s; falling back to pure-Python extraction",
+                type(exc).__name__,
+                stderr_info,
+                exc_info=True,
+            )
+            article = simple_json_from_html_string(html, use_readability=False)
+
+        html_content = article.get("content")
+        if not html_content or not str(html_content).strip():
+            html_content = "No content could be extracted from this page"
+
+        title = article.get("title")
+        if not title or not str(title).strip():
+            title = "Untitled"
+
+        return Article(title=title, html_content=html_content)