feat(harness): integration ACP agent tool (#1344)

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- **App** (`app/`): unpublished application code with import prefix `app.*`.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files can silently become outdated.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

* feat(harness): add tool-first ACP agent invocation (#37)

* feat(harness): add tool-first ACP agent invocation

* build(harness): make ACP dependency required

* fix(harness): address ACP review feedback

* feat(harness): decouple ACP agent workspace from thread data

ACP agents (codex, claude-code) previously used per-thread workspace
directories, causing path resolution complexity and coupling task
execution to DeerFlow's internal thread data layout. This change:

- Replace _resolve_cwd() with a fixed _get_work_dir() that always uses
  {base_dir}/acp-workspace/, eliminating virtual path translation and
  thread_id lookups
- Introduce /mnt/acp-workspace virtual path for lead agent read-only
  access to ACP agent output files (same pattern as /mnt/skills)
- Add security guards: read-only validation, path traversal prevention,
  command path allowlisting, and output masking for acp-workspace
- Update system prompt and tool description to guide LLM: send
  self-contained tasks to ACP agents, copy results via /mnt/acp-workspace
- Add 11 new security tests for ACP workspace path handling

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* refactor(prompt): inject ACP section only when ACP agents are configured

The ACP agent guidance in the system prompt is now conditionally built
by _build_acp_section(), which checks get_acp_agents() and returns an
empty string when no ACP agents are configured. This avoids polluting
the prompt with irrelevant instructions for users who don't use ACP.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix lint

* fix(harness): address Copilot review comments on sandbox path handling and ACP tool

- local_sandbox: fix path-segment boundary bug in _resolve_path (== or startswith +"/")
  and add lookahead in _resolve_paths_in_command regex to prevent /mnt/skills matching
  inside /mnt/skills-extra
- local_sandbox_provider: replace print() with logger.warning(..., exc_info=True)
- invoke_acp_agent_tool: guard getattr(option, "optionId") with None default + continue;
  move full prompt from INFO to DEBUG level (truncated to 200 chars)
- sandbox/tools: fix _get_acp_workspace_host_path docstring to match implementation;
  remove misleading "read-only" language from validate_local_bash_command_paths

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix(acp): thread-isolated workspaces, permission guardrail, and ContextVar registry

P1.1 – ACP workspace thread isolation
- Add `Paths.acp_workspace_dir(thread_id)` for per-thread paths
- `_get_work_dir(thread_id)` in invoke_acp_agent_tool now uses
  `{base_dir}/threads/{thread_id}/acp-workspace/`; falls back to
  global workspace when thread_id is absent or invalid
- `_invoke` extracts thread_id from `RunnableConfig` via
  `Annotated[RunnableConfig, InjectedToolArg]`
- `sandbox/tools.py`: `_get_acp_workspace_host_path(thread_id)`,
  `_resolve_acp_workspace_path(path, thread_id)`, and all callers
  (`replace_virtual_paths_in_command`, `mask_local_paths_in_output`,
  `ls_tool`, `read_file_tool`) now resolve ACP paths per-thread

P1.2 – ACP permission guardrail
- New `auto_approve_permissions: bool = False` field in `ACPAgentConfig`
- `_build_permission_response(options, *, auto_approve: bool)` now
  defaults to deny; only approves when `auto_approve=True`
- Document field in `config.example.yaml`

P2 – Deferred tool registry race condition
- Replace module-level `_registry` global with `contextvars.ContextVar`
- Each asyncio request context gets its own registry; worker threads
  inherit the context automatically via `loop.run_in_executor`
- Expose `get_deferred_registry` / `set_deferred_registry` /
  `reset_deferred_registry` helpers

Tests: 831 pass (57 for affected modules, 3 new tests)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix(sandbox): mount /mnt/acp-workspace in docker sandbox container

The AioSandboxProvider was not mounting the ACP workspace into the
sandbox container, so /mnt/acp-workspace was inaccessible when the lead
agent tried to read ACP results in docker mode.

Changes:
- `ensure_thread_dirs`: also create `acp-workspace/` (chmod 0o777) so
  the directory exists before the sandbox container starts — required
  for Docker volume mounts
- `_get_thread_mounts`: add read-only `/mnt/acp-workspace` mount using
  the per-thread host path (`host_paths.acp_workspace_dir(thread_id)`)
- Update stale CLAUDE.md description (was "fixed global workspace")

Tests: `test_aio_sandbox_provider.py` (4 new tests)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix(lint): remove unused imports in test_aio_sandbox_provider

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix config

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

backend/packages/harness/deerflow/agents/lead_agent/prompt.py

@@ -250,6 +250,7 @@ You: "Deploying to staging..." [proceed]
 - For PDF, PPT, Excel, and Word files, converted Markdown versions (*.md) are available alongside originals
 - All temporary work happens in `/mnt/user-data/workspace`
 - Final deliverables must be copied to `/mnt/user-data/outputs` and presented using `present_file` tool
+{acp_section}
 </working_directory>
 
 <response_style>
@@ -444,6 +445,26 @@ def get_deferred_tools_prompt_section() -> str:
     return f"<available-deferred-tools>\n{names}\n</available-deferred-tools>"
 
 
+def _build_acp_section() -> str:
+    """Build the ACP agent prompt section, only if ACP agents are configured."""
+    try:
+        from deerflow.config.acp_config import get_acp_agents
+
+        agents = get_acp_agents()
+        if not agents:
+            return ""
+    except Exception:
+        return ""
+
+    return (
+        "\n**ACP Agent Tasks (invoke_acp_agent):**\n"
+        "- ACP agents (e.g. codex, claude_code) run in their own independent workspace — NOT in `/mnt/user-data/`\n"
+        "- When writing prompts for ACP agents, describe the task only — do NOT reference `/mnt/user-data` paths\n"
+        "- ACP agent results are accessible at `/mnt/acp-workspace/` (read-only) — use `ls`, `read_file`, or `bash cp` to retrieve output files\n"
+        "- To deliver ACP output to the user: copy from `/mnt/acp-workspace/<file>` to `/mnt/user-data/outputs/<file>`, then use `present_file`"
+    )
+
+
 def apply_prompt_template(subagent_enabled: bool = False, max_concurrent_subagents: int = 3, *, agent_name: str | None = None, available_skills: set[str] | None = None) -> str:
     # Get memory context
     memory_context = _get_memory_context(agent_name)
@@ -476,6 +497,9 @@ def apply_prompt_template(subagent_enabled: bool = False, max_concurrent_subagen
     # Get deferred tools section (tool_search)
     deferred_tools_section = get_deferred_tools_prompt_section()
 
+    # Build ACP agent section only if ACP agents are configured
+    acp_section = _build_acp_section()
+
     # Format the prompt with dynamic skills and memory
     prompt = SYSTEM_PROMPT_TEMPLATE.format(
         agent_name=agent_name or "DeerFlow 2.0",
@@ -486,6 +510,7 @@ def apply_prompt_template(subagent_enabled: bool = False, max_concurrent_subagen
         subagent_section=subagent_section,
         subagent_reminder=subagent_reminder,
         subagent_thinking=subagent_thinking,
+        acp_section=acp_section,
     )
 
     return prompt + f"\n<current_date>{datetime.now().strftime('%Y-%m-%d, %A')}</current_date>"