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- **App** (`app/`): unpublished application code with import prefix `app.*`.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files can silently become outdated.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

@@ -5,35 +5,12 @@ description = "LangGraph-based AI agent system with sandbox execution capabiliti
 readme = "README.md"
 requires-python = ">=3.12"
 dependencies = [
-    "agent-sandbox>=0.0.19",
-    "dotenv>=0.9.9",
+    "deerflow-harness",
     "fastapi>=0.115.0",
     "httpx>=0.28.0",
-    "kubernetes>=30.0.0",
-    "langchain>=1.2.3",
-    "langchain-anthropic>=1.3.4",
-    "langchain-deepseek>=1.0.1",
-    "langchain-mcp-adapters>=0.1.0",
-    "langchain-openai>=1.1.7",
-    "langgraph>=1.0.6",
-    "langgraph-api>=0.7.0,<0.8.0",
-    "langgraph-cli>=0.4.14",
-    "langgraph-runtime-inmem>=0.22.1",
-    "markdownify>=1.2.2",
-    "markitdown[all,xlsx]>=0.0.1a2",
-    "pydantic>=2.12.5",
     "python-multipart>=0.0.20",
-    "pyyaml>=6.0.3",
-    "readabilipy>=0.3.0",
     "sse-starlette>=2.1.0",
-    "tavily-python>=0.7.17",
-    "firecrawl-py>=1.15.0",
-    "tiktoken>=0.8.0",
     "uvicorn[standard]>=0.34.0",
-    "ddgs>=9.10.0",
-    "duckdb>=1.4.4",
-    "langchain-google-genai>=4.2.1",
-    "langgraph-checkpoint-sqlite>=3.0.3",
     "lark-oapi>=1.4.0",
     "slack-sdk>=3.33.0",
     "python-telegram-bot>=21.0",
@@ -43,3 +20,9 @@ dependencies = [
 
 [dependency-groups]
 dev = ["pytest>=8.0.0", "ruff>=0.14.11"]
+
+[tool.uv.workspace]
+members = ["packages/harness"]
+
+[tool.uv.sources]
+deerflow-harness = { workspace = true }