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- **App** (`app/`): unpublished application code with import prefix `app.*`.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files can silently become outdated.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

@@ -0,0 +1,212 @@
+import os
+import shutil
+import subprocess
+from pathlib import Path
+
+from deerflow.sandbox.local.list_dir import list_dir
+from deerflow.sandbox.sandbox import Sandbox
+
+
+class LocalSandbox(Sandbox):
+    def __init__(self, id: str, path_mappings: dict[str, str] | None = None):
+        """
+        Initialize local sandbox with optional path mappings.
+
+        Args:
+            id: Sandbox identifier
+            path_mappings: Dictionary mapping container paths to local paths
+                          Example: {"/mnt/skills": "/absolute/path/to/skills"}
+        """
+        super().__init__(id)
+        self.path_mappings = path_mappings or {}
+
+    def _resolve_path(self, path: str) -> str:
+        """
+        Resolve container path to actual local path using mappings.
+
+        Args:
+            path: Path that might be a container path
+
+        Returns:
+            Resolved local path
+        """
+        path_str = str(path)
+
+        # Try each mapping (longest prefix first for more specific matches)
+        for container_path, local_path in sorted(self.path_mappings.items(), key=lambda x: len(x[0]), reverse=True):
+            if path_str.startswith(container_path):
+                # Replace the container path prefix with local path
+                relative = path_str[len(container_path) :].lstrip("/")
+                resolved = str(Path(local_path) / relative) if relative else local_path
+                return resolved
+
+        # No mapping found, return original path
+        return path_str
+
+    def _reverse_resolve_path(self, path: str) -> str:
+        """
+        Reverse resolve local path back to container path using mappings.
+
+        Args:
+            path: Local path that might need to be mapped to container path
+
+        Returns:
+            Container path if mapping exists, otherwise original path
+        """
+        path_str = str(Path(path).resolve())
+
+        # Try each mapping (longest local path first for more specific matches)
+        for container_path, local_path in sorted(self.path_mappings.items(), key=lambda x: len(x[1]), reverse=True):
+            local_path_resolved = str(Path(local_path).resolve())
+            if path_str.startswith(local_path_resolved):
+                # Replace the local path prefix with container path
+                relative = path_str[len(local_path_resolved) :].lstrip("/")
+                resolved = f"{container_path}/{relative}" if relative else container_path
+                return resolved
+
+        # No mapping found, return original path
+        return path_str
+
+    def _reverse_resolve_paths_in_output(self, output: str) -> str:
+        """
+        Reverse resolve local paths back to container paths in output string.
+
+        Args:
+            output: Output string that may contain local paths
+
+        Returns:
+            Output with local paths resolved to container paths
+        """
+        import re
+
+        # Sort mappings by local path length (longest first) for correct prefix matching
+        sorted_mappings = sorted(self.path_mappings.items(), key=lambda x: len(x[1]), reverse=True)
+
+        if not sorted_mappings:
+            return output
+
+        # Create pattern that matches absolute paths
+        # Match paths like /Users/... or other absolute paths
+        result = output
+        for container_path, local_path in sorted_mappings:
+            local_path_resolved = str(Path(local_path).resolve())
+            # Escape the local path for use in regex
+            escaped_local = re.escape(local_path_resolved)
+            # Match the local path followed by optional path components
+            pattern = re.compile(escaped_local + r"(?:/[^\s\"';&|<>()]*)?")
+
+            def replace_match(match: re.Match) -> str:
+                matched_path = match.group(0)
+                return self._reverse_resolve_path(matched_path)
+
+            result = pattern.sub(replace_match, result)
+
+        return result
+
+    def _resolve_paths_in_command(self, command: str) -> str:
+        """
+        Resolve container paths to local paths in a command string.
+
+        Args:
+            command: Command string that may contain container paths
+
+        Returns:
+            Command with container paths resolved to local paths
+        """
+        import re
+
+        # Sort mappings by length (longest first) for correct prefix matching
+        sorted_mappings = sorted(self.path_mappings.items(), key=lambda x: len(x[0]), reverse=True)
+
+        # Build regex pattern to match all container paths
+        # Match container path followed by optional path components
+        if not sorted_mappings:
+            return command
+
+        # Create pattern that matches any of the container paths
+        patterns = [re.escape(container_path) + r"(?:/[^\s\"';&|<>()]*)??" for container_path, _ in sorted_mappings]
+        pattern = re.compile("|".join(f"({p})" for p in patterns))
+
+        def replace_match(match: re.Match) -> str:
+            matched_path = match.group(0)
+            return self._resolve_path(matched_path)
+
+        return pattern.sub(replace_match, command)
+
+    @staticmethod
+    def _get_shell() -> str:
+        """Detect available shell executable with fallback.
+
+        Returns the first available shell in order of preference:
+        /bin/zsh → /bin/bash → /bin/sh → first `sh` found on PATH.
+        Raises a RuntimeError if no suitable shell is found.
+        """
+        for shell in ("/bin/zsh", "/bin/bash", "/bin/sh"):
+            if os.path.isfile(shell) and os.access(shell, os.X_OK):
+                return shell
+        shell_from_path = shutil.which("sh")
+        if shell_from_path is not None:
+            return shell_from_path
+        raise RuntimeError("No suitable shell executable found. Tried /bin/zsh, /bin/bash, /bin/sh, and `sh` on PATH.")
+
+    def execute_command(self, command: str) -> str:
+        # Resolve container paths in command before execution
+        resolved_command = self._resolve_paths_in_command(command)
+
+        result = subprocess.run(
+            resolved_command,
+            executable=self._get_shell(),
+            shell=True,
+            capture_output=True,
+            text=True,
+            timeout=600,
+        )
+        output = result.stdout
+        if result.stderr:
+            output += f"\nStd Error:\n{result.stderr}" if output else result.stderr
+        if result.returncode != 0:
+            output += f"\nExit Code: {result.returncode}"
+
+        final_output = output if output else "(no output)"
+        # Reverse resolve local paths back to container paths in output
+        return self._reverse_resolve_paths_in_output(final_output)
+
+    def list_dir(self, path: str, max_depth=2) -> list[str]:
+        resolved_path = self._resolve_path(path)
+        entries = list_dir(resolved_path, max_depth)
+        # Reverse resolve local paths back to container paths in output
+        return [self._reverse_resolve_paths_in_output(entry) for entry in entries]
+
+    def read_file(self, path: str) -> str:
+        resolved_path = self._resolve_path(path)
+        try:
+            with open(resolved_path) as f:
+                return f.read()
+        except OSError as e:
+            # Re-raise with the original path for clearer error messages, hiding internal resolved paths
+            raise type(e)(e.errno, e.strerror, path) from None
+
+    def write_file(self, path: str, content: str, append: bool = False) -> None:
+        resolved_path = self._resolve_path(path)
+        try:
+            dir_path = os.path.dirname(resolved_path)
+            if dir_path:
+                os.makedirs(dir_path, exist_ok=True)
+            mode = "a" if append else "w"
+            with open(resolved_path, mode) as f:
+                f.write(content)
+        except OSError as e:
+            # Re-raise with the original path for clearer error messages, hiding internal resolved paths
+            raise type(e)(e.errno, e.strerror, path) from None
+
+    def update_file(self, path: str, content: bytes) -> None:
+        resolved_path = self._resolve_path(path)
+        try:
+            dir_path = os.path.dirname(resolved_path)
+            if dir_path:
+                os.makedirs(dir_path, exist_ok=True)
+            with open(resolved_path, "wb") as f:
+                f.write(content)
+        except OSError as e:
+            # Re-raise with the original path for clearer error messages, hiding internal resolved paths
+            raise type(e)(e.errno, e.strerror, path) from None