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- **App** (`app/`): unpublished application code with import prefix `app.*`.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files can silently become outdated.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>
This commit is contained in:
DanielWalnut
2026-03-14 22:55:52 +08:00
committed by GitHub
parent 9b49a80dda
commit 76803b826f
198 changed files with 1786 additions and 941 deletions

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from .config import SubagentConfig
from .executor import SubagentExecutor, SubagentResult
from .registry import get_subagent_config, list_subagents
__all__ = [
"SubagentConfig",
"SubagentExecutor",
"SubagentResult",
"get_subagent_config",
"list_subagents",
]

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"""Built-in subagent configurations."""
from .bash_agent import BASH_AGENT_CONFIG
from .general_purpose import GENERAL_PURPOSE_CONFIG
__all__ = [
"GENERAL_PURPOSE_CONFIG",
"BASH_AGENT_CONFIG",
]
# Registry of built-in subagents
BUILTIN_SUBAGENTS = {
"general-purpose": GENERAL_PURPOSE_CONFIG,
"bash": BASH_AGENT_CONFIG,
}

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"""Bash command execution subagent configuration."""
from deerflow.subagents.config import SubagentConfig
BASH_AGENT_CONFIG = SubagentConfig(
name="bash",
description="""Command execution specialist for running bash commands in a separate context.
Use this subagent when:
- You need to run a series of related bash commands
- Terminal operations like git, npm, docker, etc.
- Command output is verbose and would clutter main context
- Build, test, or deployment operations
Do NOT use for simple single commands - use bash tool directly instead.""",
system_prompt="""You are a bash command execution specialist. Execute the requested commands carefully and report results clearly.
<guidelines>
- Execute commands one at a time when they depend on each other
- Use parallel execution when commands are independent
- Report both stdout and stderr when relevant
- Handle errors gracefully and explain what went wrong
- Use absolute paths for file operations
- Be cautious with destructive operations (rm, overwrite, etc.)
</guidelines>
<output_format>
For each command or group of commands:
1. What was executed
2. The result (success/failure)
3. Relevant output (summarized if verbose)
4. Any errors or warnings
</output_format>
<working_directory>
You have access to the sandbox environment:
- User uploads: `/mnt/user-data/uploads`
- User workspace: `/mnt/user-data/workspace`
- Output files: `/mnt/user-data/outputs`
</working_directory>
""",
tools=["bash", "ls", "read_file", "write_file", "str_replace"], # Sandbox tools only
disallowed_tools=["task", "ask_clarification", "present_files"],
model="inherit",
max_turns=30,
)

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"""General-purpose subagent configuration."""
from deerflow.subagents.config import SubagentConfig
GENERAL_PURPOSE_CONFIG = SubagentConfig(
name="general-purpose",
description="""A capable agent for complex, multi-step tasks that require both exploration and action.
Use this subagent when:
- The task requires both exploration and modification
- Complex reasoning is needed to interpret results
- Multiple dependent steps must be executed
- The task would benefit from isolated context management
Do NOT use for simple, single-step operations.""",
system_prompt="""You are a general-purpose subagent working on a delegated task. Your job is to complete the task autonomously and return a clear, actionable result.
<guidelines>
- Focus on completing the delegated task efficiently
- Use available tools as needed to accomplish the goal
- Think step by step but act decisively
- If you encounter issues, explain them clearly in your response
- Return a concise summary of what you accomplished
- Do NOT ask for clarification - work with the information provided
</guidelines>
<output_format>
When you complete the task, provide:
1. A brief summary of what was accomplished
2. Key findings or results
3. Any relevant file paths, data, or artifacts created
4. Issues encountered (if any)
5. Citations: Use `[citation:Title](URL)` format for external sources
</output_format>
<working_directory>
You have access to the same sandbox environment as the parent agent:
- User uploads: `/mnt/user-data/uploads`
- User workspace: `/mnt/user-data/workspace`
- Output files: `/mnt/user-data/outputs`
</working_directory>
""",
tools=None, # Inherit all tools from parent
disallowed_tools=["task", "ask_clarification", "present_files"], # Prevent nesting and clarification
model="inherit",
max_turns=50,
)

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"""Subagent configuration definitions."""
from dataclasses import dataclass, field
@dataclass
class SubagentConfig:
"""Configuration for a subagent.
Attributes:
name: Unique identifier for the subagent.
description: When Claude should delegate to this subagent.
system_prompt: The system prompt that guides the subagent's behavior.
tools: Optional list of tool names to allow. If None, inherits all tools.
disallowed_tools: Optional list of tool names to deny.
model: Model to use - 'inherit' uses parent's model.
max_turns: Maximum number of agent turns before stopping.
timeout_seconds: Maximum execution time in seconds (default: 900 = 15 minutes).
"""
name: str
description: str
system_prompt: str
tools: list[str] | None = None
disallowed_tools: list[str] | None = field(default_factory=lambda: ["task"])
model: str = "inherit"
max_turns: int = 50
timeout_seconds: int = 900

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"""Subagent execution engine."""
import asyncio
import logging
import threading
import uuid
from concurrent.futures import Future, ThreadPoolExecutor
from concurrent.futures import TimeoutError as FuturesTimeoutError
from dataclasses import dataclass
from datetime import datetime
from enum import Enum
from typing import Any
from langchain.agents import create_agent
from langchain.tools import BaseTool
from langchain_core.messages import AIMessage, HumanMessage
from langchain_core.runnables import RunnableConfig
from deerflow.agents.thread_state import SandboxState, ThreadDataState, ThreadState
from deerflow.models import create_chat_model
from deerflow.subagents.config import SubagentConfig
logger = logging.getLogger(__name__)
class SubagentStatus(Enum):
"""Status of a subagent execution."""
PENDING = "pending"
RUNNING = "running"
COMPLETED = "completed"
FAILED = "failed"
TIMED_OUT = "timed_out"
@dataclass
class SubagentResult:
"""Result of a subagent execution.
Attributes:
task_id: Unique identifier for this execution.
trace_id: Trace ID for distributed tracing (links parent and subagent logs).
status: Current status of the execution.
result: The final result message (if completed).
error: Error message (if failed).
started_at: When execution started.
completed_at: When execution completed.
ai_messages: List of complete AI messages (as dicts) generated during execution.
"""
task_id: str
trace_id: str
status: SubagentStatus
result: str | None = None
error: str | None = None
started_at: datetime | None = None
completed_at: datetime | None = None
ai_messages: list[dict[str, Any]] | None = None
def __post_init__(self):
"""Initialize mutable defaults."""
if self.ai_messages is None:
self.ai_messages = []
# Global storage for background task results
_background_tasks: dict[str, SubagentResult] = {}
_background_tasks_lock = threading.Lock()
# Thread pool for background task scheduling and orchestration
_scheduler_pool = ThreadPoolExecutor(max_workers=3, thread_name_prefix="subagent-scheduler-")
# Thread pool for actual subagent execution (with timeout support)
# Larger pool to avoid blocking when scheduler submits execution tasks
_execution_pool = ThreadPoolExecutor(max_workers=3, thread_name_prefix="subagent-exec-")
def _filter_tools(
all_tools: list[BaseTool],
allowed: list[str] | None,
disallowed: list[str] | None,
) -> list[BaseTool]:
"""Filter tools based on subagent configuration.
Args:
all_tools: List of all available tools.
allowed: Optional allowlist of tool names. If provided, only these tools are included.
disallowed: Optional denylist of tool names. These tools are always excluded.
Returns:
Filtered list of tools.
"""
filtered = all_tools
# Apply allowlist if specified
if allowed is not None:
allowed_set = set(allowed)
filtered = [t for t in filtered if t.name in allowed_set]
# Apply denylist
if disallowed is not None:
disallowed_set = set(disallowed)
filtered = [t for t in filtered if t.name not in disallowed_set]
return filtered
def _get_model_name(config: SubagentConfig, parent_model: str | None) -> str | None:
"""Resolve the model name for a subagent.
Args:
config: Subagent configuration.
parent_model: The parent agent's model name.
Returns:
Model name to use, or None to use default.
"""
if config.model == "inherit":
return parent_model
return config.model
class SubagentExecutor:
"""Executor for running subagents."""
def __init__(
self,
config: SubagentConfig,
tools: list[BaseTool],
parent_model: str | None = None,
sandbox_state: SandboxState | None = None,
thread_data: ThreadDataState | None = None,
thread_id: str | None = None,
trace_id: str | None = None,
):
"""Initialize the executor.
Args:
config: Subagent configuration.
tools: List of all available tools (will be filtered).
parent_model: The parent agent's model name for inheritance.
sandbox_state: Sandbox state from parent agent.
thread_data: Thread data from parent agent.
thread_id: Thread ID for sandbox operations.
trace_id: Trace ID from parent for distributed tracing.
"""
self.config = config
self.parent_model = parent_model
self.sandbox_state = sandbox_state
self.thread_data = thread_data
self.thread_id = thread_id
# Generate trace_id if not provided (for top-level calls)
self.trace_id = trace_id or str(uuid.uuid4())[:8]
# Filter tools based on config
self.tools = _filter_tools(
tools,
config.tools,
config.disallowed_tools,
)
logger.info(f"[trace={self.trace_id}] SubagentExecutor initialized: {config.name} with {len(self.tools)} tools")
def _create_agent(self):
"""Create the agent instance."""
model_name = _get_model_name(self.config, self.parent_model)
model = create_chat_model(name=model_name, thinking_enabled=False)
from deerflow.agents.middlewares.tool_error_handling_middleware import build_subagent_runtime_middlewares
# Reuse shared middleware composition with lead agent.
middlewares = build_subagent_runtime_middlewares(lazy_init=True)
return create_agent(
model=model,
tools=self.tools,
middleware=middlewares,
system_prompt=self.config.system_prompt,
state_schema=ThreadState,
)
def _build_initial_state(self, task: str) -> dict[str, Any]:
"""Build the initial state for agent execution.
Args:
task: The task description.
Returns:
Initial state dictionary.
"""
state: dict[str, Any] = {
"messages": [HumanMessage(content=task)],
}
# Pass through sandbox and thread data from parent
if self.sandbox_state is not None:
state["sandbox"] = self.sandbox_state
if self.thread_data is not None:
state["thread_data"] = self.thread_data
return state
async def _aexecute(self, task: str, result_holder: SubagentResult | None = None) -> SubagentResult:
"""Execute a task asynchronously.
Args:
task: The task description for the subagent.
result_holder: Optional pre-created result object to update during execution.
Returns:
SubagentResult with the execution result.
"""
if result_holder is not None:
# Use the provided result holder (for async execution with real-time updates)
result = result_holder
else:
# Create a new result for synchronous execution
task_id = str(uuid.uuid4())[:8]
result = SubagentResult(
task_id=task_id,
trace_id=self.trace_id,
status=SubagentStatus.RUNNING,
started_at=datetime.now(),
)
try:
agent = self._create_agent()
state = self._build_initial_state(task)
# Build config with thread_id for sandbox access and recursion limit
run_config: RunnableConfig = {
"recursion_limit": self.config.max_turns,
}
context = {}
if self.thread_id:
run_config["configurable"] = {"thread_id": self.thread_id}
context["thread_id"] = self.thread_id
logger.info(f"[trace={self.trace_id}] Subagent {self.config.name} starting async execution with max_turns={self.config.max_turns}")
# Use stream instead of invoke to get real-time updates
# This allows us to collect AI messages as they are generated
final_state = None
async for chunk in agent.astream(state, config=run_config, context=context, stream_mode="values"): # type: ignore[arg-type]
final_state = chunk
# Extract AI messages from the current state
messages = chunk.get("messages", [])
if messages:
last_message = messages[-1]
# Check if this is a new AI message
if isinstance(last_message, AIMessage):
# Convert message to dict for serialization
message_dict = last_message.model_dump()
# Only add if it's not already in the list (avoid duplicates)
# Check by comparing message IDs if available, otherwise compare full dict
message_id = message_dict.get("id")
is_duplicate = False
if message_id:
is_duplicate = any(msg.get("id") == message_id for msg in result.ai_messages)
else:
is_duplicate = message_dict in result.ai_messages
if not is_duplicate:
result.ai_messages.append(message_dict)
logger.info(f"[trace={self.trace_id}] Subagent {self.config.name} captured AI message #{len(result.ai_messages)}")
logger.info(f"[trace={self.trace_id}] Subagent {self.config.name} completed async execution")
if final_state is None:
logger.warning(f"[trace={self.trace_id}] Subagent {self.config.name} no final state")
result.result = "No response generated"
else:
# Extract the final message - find the last AIMessage
messages = final_state.get("messages", [])
logger.info(f"[trace={self.trace_id}] Subagent {self.config.name} final messages count: {len(messages)}")
# Find the last AIMessage in the conversation
last_ai_message = None
for msg in reversed(messages):
if isinstance(msg, AIMessage):
last_ai_message = msg
break
if last_ai_message is not None:
content = last_ai_message.content
# Handle both str and list content types for the final result
if isinstance(content, str):
result.result = content
elif isinstance(content, list):
# Extract text from list of content blocks for final result only
text_parts = []
for block in content:
if isinstance(block, str):
text_parts.append(block)
elif isinstance(block, dict) and "text" in block:
text_parts.append(block["text"])
result.result = "\n".join(text_parts) if text_parts else "No text content in response"
else:
result.result = str(content)
elif messages:
# Fallback: use the last message if no AIMessage found
last_message = messages[-1]
logger.warning(f"[trace={self.trace_id}] Subagent {self.config.name} no AIMessage found, using last message: {type(last_message)}")
result.result = str(last_message.content) if hasattr(last_message, "content") else str(last_message)
else:
logger.warning(f"[trace={self.trace_id}] Subagent {self.config.name} no messages in final state")
result.result = "No response generated"
result.status = SubagentStatus.COMPLETED
result.completed_at = datetime.now()
except Exception as e:
logger.exception(f"[trace={self.trace_id}] Subagent {self.config.name} async execution failed")
result.status = SubagentStatus.FAILED
result.error = str(e)
result.completed_at = datetime.now()
return result
def execute(self, task: str, result_holder: SubagentResult | None = None) -> SubagentResult:
"""Execute a task synchronously (wrapper around async execution).
This method runs the async execution in a new event loop, allowing
asynchronous tools (like MCP tools) to be used within the thread pool.
Args:
task: The task description for the subagent.
result_holder: Optional pre-created result object to update during execution.
Returns:
SubagentResult with the execution result.
"""
# Run the async execution in a new event loop
# This is necessary because:
# 1. We may have async-only tools (like MCP tools)
# 2. We're running inside a ThreadPoolExecutor which doesn't have an event loop
#
# Note: _aexecute() catches all exceptions internally, so this outer
# try-except only handles asyncio.run() failures (e.g., if called from
# an async context where an event loop already exists). Subagent execution
# errors are handled within _aexecute() and returned as FAILED status.
try:
return asyncio.run(self._aexecute(task, result_holder))
except Exception as e:
logger.exception(f"[trace={self.trace_id}] Subagent {self.config.name} execution failed")
# Create a result with error if we don't have one
if result_holder is not None:
result = result_holder
else:
result = SubagentResult(
task_id=str(uuid.uuid4())[:8],
trace_id=self.trace_id,
status=SubagentStatus.FAILED,
)
result.status = SubagentStatus.FAILED
result.error = str(e)
result.completed_at = datetime.now()
return result
def execute_async(self, task: str, task_id: str | None = None) -> str:
"""Start a task execution in the background.
Args:
task: The task description for the subagent.
task_id: Optional task ID to use. If not provided, a random UUID will be generated.
Returns:
Task ID that can be used to check status later.
"""
# Use provided task_id or generate a new one
if task_id is None:
task_id = str(uuid.uuid4())[:8]
# Create initial pending result
result = SubagentResult(
task_id=task_id,
trace_id=self.trace_id,
status=SubagentStatus.PENDING,
)
logger.info(f"[trace={self.trace_id}] Subagent {self.config.name} starting async execution, task_id={task_id}, timeout={self.config.timeout_seconds}s")
with _background_tasks_lock:
_background_tasks[task_id] = result
# Submit to scheduler pool
def run_task():
with _background_tasks_lock:
_background_tasks[task_id].status = SubagentStatus.RUNNING
_background_tasks[task_id].started_at = datetime.now()
result_holder = _background_tasks[task_id]
try:
# Submit execution to execution pool with timeout
# Pass result_holder so execute() can update it in real-time
execution_future: Future = _execution_pool.submit(self.execute, task, result_holder)
try:
# Wait for execution with timeout
exec_result = execution_future.result(timeout=self.config.timeout_seconds)
with _background_tasks_lock:
_background_tasks[task_id].status = exec_result.status
_background_tasks[task_id].result = exec_result.result
_background_tasks[task_id].error = exec_result.error
_background_tasks[task_id].completed_at = datetime.now()
_background_tasks[task_id].ai_messages = exec_result.ai_messages
except FuturesTimeoutError:
logger.error(f"[trace={self.trace_id}] Subagent {self.config.name} execution timed out after {self.config.timeout_seconds}s")
with _background_tasks_lock:
_background_tasks[task_id].status = SubagentStatus.TIMED_OUT
_background_tasks[task_id].error = f"Execution timed out after {self.config.timeout_seconds} seconds"
_background_tasks[task_id].completed_at = datetime.now()
# Cancel the future (best effort - may not stop the actual execution)
execution_future.cancel()
except Exception as e:
logger.exception(f"[trace={self.trace_id}] Subagent {self.config.name} async execution failed")
with _background_tasks_lock:
_background_tasks[task_id].status = SubagentStatus.FAILED
_background_tasks[task_id].error = str(e)
_background_tasks[task_id].completed_at = datetime.now()
_scheduler_pool.submit(run_task)
return task_id
MAX_CONCURRENT_SUBAGENTS = 3
def get_background_task_result(task_id: str) -> SubagentResult | None:
"""Get the result of a background task.
Args:
task_id: The task ID returned by execute_async.
Returns:
SubagentResult if found, None otherwise.
"""
with _background_tasks_lock:
return _background_tasks.get(task_id)
def list_background_tasks() -> list[SubagentResult]:
"""List all background tasks.
Returns:
List of all SubagentResult instances.
"""
with _background_tasks_lock:
return list(_background_tasks.values())
def cleanup_background_task(task_id: str) -> None:
"""Remove a completed task from background tasks.
Should be called by task_tool after it finishes polling and returns the result.
This prevents memory leaks from accumulated completed tasks.
Only removes tasks that are in a terminal state (COMPLETED/FAILED/TIMED_OUT)
to avoid race conditions with the background executor still updating the task entry.
Args:
task_id: The task ID to remove.
"""
with _background_tasks_lock:
result = _background_tasks.get(task_id)
if result is None:
# Nothing to clean up; may have been removed already.
logger.debug("Requested cleanup for unknown background task %s", task_id)
return
# Only clean up tasks that are in a terminal state to avoid races with
# the background executor still updating the task entry.
is_terminal_status = result.status in {
SubagentStatus.COMPLETED,
SubagentStatus.FAILED,
SubagentStatus.TIMED_OUT,
}
if is_terminal_status or result.completed_at is not None:
del _background_tasks[task_id]
logger.debug("Cleaned up background task: %s", task_id)
else:
logger.debug(
"Skipping cleanup for non-terminal background task %s (status=%s)",
task_id,
result.status.value if hasattr(result.status, "value") else result.status,
)

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"""Subagent registry for managing available subagents."""
import logging
from dataclasses import replace
from deerflow.subagents.builtins import BUILTIN_SUBAGENTS
from deerflow.subagents.config import SubagentConfig
logger = logging.getLogger(__name__)
def get_subagent_config(name: str) -> SubagentConfig | None:
"""Get a subagent configuration by name, with config.yaml overrides applied.
Args:
name: The name of the subagent.
Returns:
SubagentConfig if found (with any config.yaml overrides applied), None otherwise.
"""
config = BUILTIN_SUBAGENTS.get(name)
if config is None:
return None
# Apply timeout override from config.yaml (lazy import to avoid circular deps)
from deerflow.config.subagents_config import get_subagents_app_config
app_config = get_subagents_app_config()
effective_timeout = app_config.get_timeout_for(name)
if effective_timeout != config.timeout_seconds:
logger.debug(f"Subagent '{name}': timeout overridden by config.yaml ({config.timeout_seconds}s -> {effective_timeout}s)")
config = replace(config, timeout_seconds=effective_timeout)
return config
def list_subagents() -> list[SubagentConfig]:
"""List all available subagent configurations (with config.yaml overrides applied).
Returns:
List of all registered SubagentConfig instances.
"""
return [get_subagent_config(name) for name in BUILTIN_SUBAGENTS]
def get_subagent_names() -> list[str]:
"""Get all available subagent names.
Returns:
List of subagent names.
"""
return list(BUILTIN_SUBAGENTS.keys())