feat(agents): Phase 8.4-10.5 built-in plugins, bundled skills, coordinator

backend/app/agents/background/executor.py

@@ -0,0 +1,220 @@
+"""Background task executor - Phase 10.4"""
+
+import asyncio
+from collections.abc import Callable, Coroutine
+from datetime import datetime
+from typing import Any
+
+from .manager import (
+    BackgroundTask,
+    BackgroundTaskManager,
+    BackgroundTaskStatus,
+    get_background_task_manager,
+)
+
+
+class BackgroundExecutor:
+    """Executes background tasks with error handling and result storage.
+
+    Provides methods to execute tasks synchronously or asynchronously,
+    with full integration into BackgroundTaskManager for tracking.
+    """
+
+    def __init__(self, task_manager: BackgroundTaskManager | None = None):
+        """Initialize the executor.
+
+        Args:
+            task_manager: Optional BackgroundTaskManager instance.
+                         If not provided, uses the global singleton.
+        """
+        self._task_manager = task_manager or get_background_task_manager()
+        self._executors: dict[str, asyncio.Task] = {}
+
+    async def execute_task(
+        self,
+        task_id: str,
+        func: Callable[..., Coroutine[Any, Any, Any]],
+        *args: Any,
+        **kwargs: Any,
+    ) -> BackgroundTask:
+        """Execute a specific task by ID.
+
+        Args:
+            task_id: Unique task identifier
+            func: Async function to execute
+            *args: Positional arguments for the function
+            **kwargs: Keyword arguments for the function
+
+        Returns:
+            The BackgroundTask with result or error
+        """
+        # Get or create task record
+        task = self._task_manager.get_task_status(task_id)
+        if task is None:
+            # Create a new task record if one doesn't exist
+            task = BackgroundTask(
+                id=task_id,
+                name=f"executor_task_{task_id}",
+                status=BackgroundTaskStatus.PENDING,
+                created_at=datetime.now(),
+            )
+            self._task_manager._tasks[task_id] = task
+
+        # Update status to running
+        task.status = BackgroundTaskStatus.RUNNING
+        task.started_at = datetime.now()
+
+        try:
+            # Execute the async function
+            result = await func(*args, **kwargs)
+            task.status = BackgroundTaskStatus.COMPLETED
+            task.result = result
+        except Exception as e:
+            task.status = BackgroundTaskStatus.FAILED
+            task.error = f"{type(e).__name__}: {str(e)}"
+            task.result = None
+        finally:
+            task.completed_at = datetime.now()
+            # Clean up executor reference
+            if task_id in self._executors:
+                del self._executors[task_id]
+
+        return task
+
+    async def execute_async(
+        self,
+        task_id: str,
+        func: Callable[..., Coroutine[Any, Any, Any]],
+        *args: Any,
+        **kwargs: Any,
+    ) -> str:
+        """Execute a task asynchronously in the background.
+
+        Args:
+            task_id: Unique task identifier
+            func: Async function to execute
+            *args: Positional arguments for the function
+            **kwargs: Keyword arguments for the function
+
+        Returns:
+            The task ID
+        """
+        # Create task record if it doesn't exist
+        if self._task_manager.get_task_status(task_id) is None:
+            self._task_manager._tasks[task_id] = BackgroundTask(
+                id=task_id,
+                name=f"async_task_{task_id}",
+                status=BackgroundTaskStatus.PENDING,
+                created_at=datetime.now(),
+            )
+
+        # Create and store the asyncio task
+        async_task = asyncio.create_task(self.execute_task(task_id, func, *args, **kwargs))
+        self._executors[task_id] = async_task
+
+        return task_id
+
+    def cancel_task(self, task_id: str) -> bool:
+        """Cancel a running task.
+
+        Args:
+            task_id: The task ID to cancel
+
+        Returns:
+            True if cancelled, False if not found or not running
+        """
+        if task_id not in self._executors:
+            return False
+
+        self._executors[task_id].cancel()
+        del self._executors[task_id]
+
+        # Update task status
+        task = self._task_manager.get_task_status(task_id)
+        if task:
+            task.status = BackgroundTaskStatus.CANCELLED
+            task.completed_at = datetime.now()
+            return True
+        return False
+
+    def get_task_result(self, task_id: str) -> Any:
+        """Get the result of a completed task.
+
+        Args:
+            task_id: The task ID
+
+        Returns:
+            The task result or None if not found/not completed
+        """
+        task = self._task_manager.get_task_status(task_id)
+        if task and task.status == BackgroundTaskStatus.COMPLETED:
+            return task.result
+        return None
+
+    def get_task_error(self, task_id: str) -> str | None:
+        """Get the error of a failed task.
+
+        Args:
+            task_id: The task ID
+
+        Returns:
+            The error message or None if not found/not failed
+        """
+        task = self._task_manager.get_task_status(task_id)
+        if task and task.status == BackgroundTaskStatus.FAILED:
+            return task.error
+        return None
+
+    def is_task_running(self, task_id: str) -> bool:
+        """Check if a task is currently running.
+
+        Args:
+            task_id: The task ID
+
+        Returns:
+            True if running, False otherwise
+        """
+        return task_id in self._executors
+
+    def wait_for_task(self, task_id: str, timeout: float | None = None) -> BackgroundTask:
+        """Wait for a task to complete.
+
+        Args:
+            task_id: The task ID to wait for
+            timeout: Optional timeout in seconds
+
+        Returns:
+            The completed BackgroundTask
+
+        Raises:
+            asyncio.TimeoutError: If task doesn't complete within timeout
+            asyncio.CancelledError: If task is cancelled
+        """
+        if task_id not in self._executors:
+            task = self._task_manager.get_task_status(task_id)
+            if task:
+                return task
+            raise ValueError(f"Task {task_id} not found")
+
+        async def wait_task() -> BackgroundTask:
+            await self._executors[task_id]
+            return self._task_manager.get_task_status(task_id)
+
+        return asyncio.run_until_complete(asyncio.wait_for(wait_task(), timeout=timeout))
+
+    @property
+    def task_manager(self) -> BackgroundTaskManager:
+        """Get the underlying task manager."""
+        return self._task_manager
+
+
+# Global executor instance
+_executor: BackgroundExecutor | None = None
+
+
+def get_background_executor() -> BackgroundExecutor:
+    """Get the global BackgroundExecutor instance."""
+    global _executor
+    if _executor is None:
+        _executor = BackgroundExecutor()
+    return _executor

backend/app/agents/background/scheduler.py

@@ -0,0 +1,146 @@
+"""Background task scheduler - Phase 10.4"""
+
+from collections.abc import Callable, Coroutine
+from typing import Any
+
+from apscheduler.schedulers.asyncio import AsyncIOScheduler
+from apscheduler.triggers.base import BaseTrigger
+
+from .manager import BackgroundTaskManager, get_background_task_manager
+
+
+class BackgroundScheduler:
+    """Background task scheduler using APScheduler.
+
+    Integrates with BackgroundTaskManager for task tracking and execution.
+    """
+
+    def __init__(self, task_manager: BackgroundTaskManager | None = None):
+        """Initialize the scheduler.
+
+        Args:
+            task_manager: Optional BackgroundTaskManager instance.
+                         If not provided, uses the global singleton.
+        """
+        self._scheduler = AsyncIOScheduler()
+        self._task_manager = task_manager or get_background_task_manager()
+        self._job_tasks: dict[str, str] = {}  # Maps APScheduler job_id to task_id
+
+    def add_job(
+        self,
+        func: Callable[..., Coroutine[Any, Any, Any]],
+        trigger: BaseTrigger,
+        args: tuple[Any, ...] | None = None,
+        kwargs: dict[str, Any] | None = None,
+        id: str | None = None,
+        name: str | None = None,
+        **apscheduler_kwargs: Any,
+    ) -> str:
+        """Add a job to the scheduler.
+
+        Args:
+            func: Async function to execute
+            trigger: APScheduler trigger (date, interval, cron, etc.)
+            args: Positional arguments for the function
+            kwargs: Keyword arguments for the function
+            id: Unique job ID (auto-generated if not provided)
+            name: Job name for display purposes
+            **apscheduler_kwargs: Additional APScheduler options
+
+        Returns:
+            The job ID
+        """
+        job_id = id or f"job_{len(self._job_tasks)}"
+        task_name = name or f"scheduled_task_{job_id}"
+
+        # Wrap the async function to integrate with BackgroundTaskManager
+        async def wrapped_func() -> None:
+            coro = func(*(args or ()), **(kwargs or {}))
+            task_id = self._task_manager.submit_task(task_name, coro)
+            self._job_tasks[job_id] = task_id
+
+        self._scheduler.add_job(
+            wrapped_func,
+            trigger=trigger,
+            id=job_id,
+            name=task_name,
+            **apscheduler_kwargs,
+        )
+
+        return job_id
+
+    def remove_job(self, job_id: str) -> bool:
+        """Remove a job from the scheduler.
+
+        Args:
+            job_id: The ID of the job to remove
+
+        Returns:
+            True if job was removed, False if job didn't exist
+        """
+        try:
+            self._scheduler.remove_job(job_id)
+            # Clean up task mapping if exists
+            if job_id in self._job_tasks:
+                task_id = self._job_tasks.pop(job_id)
+                # Cancel the background task if still running
+                self._task_manager.cancel_task(task_id)
+            return True
+        except Exception:
+            return False
+
+    def list_jobs(self) -> list[dict[str, Any]]:
+        """List all scheduled jobs.
+
+        Returns:
+            List of job information dictionaries
+        """
+        jobs = self._scheduler.get_jobs()
+        return [
+            {
+                "id": job.id,
+                "name": job.name,
+                "next_run_time": job.next_run_time,
+                "trigger": str(job.trigger),
+            }
+            for job in jobs
+        ]
+
+    def start(self) -> None:
+        """Start the scheduler."""
+        if not self._scheduler.running:
+            self._scheduler.start()
+
+    def shutdown(self, wait: bool = True) -> None:
+        """Shutdown the scheduler.
+
+        Args:
+            wait: Whether to wait for running jobs to complete
+        """
+        if self._scheduler.running:
+            self._scheduler.shutdown(wait=wait)
+
+    def pause(self) -> None:
+        """Pause the scheduler."""
+        self._scheduler.pause()
+
+    def resume(self) -> None:
+        """Resume the scheduler."""
+        self._scheduler.resume()
+
+    @property
+    def task_manager(self) -> BackgroundTaskManager:
+        """Get the underlying task manager."""
+        return self._task_manager
+
+
+# Global scheduler instance
+_scheduler: BackgroundScheduler | None = None
+
+
+def get_background_scheduler() -> BackgroundScheduler:
+    """Get the global BackgroundScheduler instance."""
+    global _scheduler
+    if _scheduler is None:
+        _scheduler = BackgroundScheduler()
+    return _scheduler

backend/app/agents/coordinator.py

@@ -0,0 +1,508 @@
+"""Agent 协调整器 - Phase 10.5
+
+统一协调所有 Agent 组件：TeamLeader, RemoteTransport, BackgroundTaskManager, SessionManager
+"""
+
+from typing import Any
+
+from app.agents.background.manager import BackgroundTaskManager, get_background_task_manager
+from app.agents.session.manager import AgentSession, create_agent_session, get_agent_session
+from app.agents.team.leader import TeamLeader
+from app.agents.transport.remote import RemoteTransport
+
+
+class AgentCoordinator:
+    """Agent 协调整器
+
+    统一协调所有 Agent 组件，提供单一入口处理各类 Agent 操作。
+    """
+
+    def __init__(
+        self,
+        background_manager: BackgroundTaskManager | None = None,
+    ):
+        """
+        Args:
+            background_manager: 后台任务管理器，None 则使用全局单例
+        """
+        self._team_leaders: dict[str, TeamLeader] = {}
+        self._remote_transport = RemoteTransport()
+        self._background_manager = background_manager or get_background_task_manager()
+        self._sessions: dict[str, AgentSession] = {}
+
+    # === Team 协作方法 ===
+
+    def create_team(self, team_id: str, members: list[str]) -> dict[str, Any]:
+        """创建团队
+
+        Args:
+            team_id: 团队 ID
+            members: 成员 ID 列表
+
+        Returns:
+            团队创建结果
+        """
+        if team_id in self._team_leaders:
+            return {"status": "error", "message": f"Team '{team_id}' already exists"}
+
+        leader = TeamLeader(team_id=team_id, members=members)
+        self._team_leaders[team_id] = leader
+        return {
+            "status": "created",
+            "team_id": team_id,
+            "members": members,
+        }
+
+    def get_team(self, team_id: str) -> TeamLeader | None:
+        """获取团队
+
+        Args:
+            team_id: 团队 ID
+
+        Returns:
+            TeamLeader 或 None
+        """
+        return self._team_leaders.get(team_id)
+
+    def assign_task(self, team_id: str, description: str, member: str) -> dict[str, Any]:
+        """创建并分配任务
+
+        Args:
+            team_id: 团队 ID
+            description: 任务描述
+            member: 成员 ID
+
+        Returns:
+            分配结果
+        """
+        leader = self._team_leaders.get(team_id)
+        if not leader:
+            return {"status": "error", "message": f"Team '{team_id}' not found"}
+
+        task_id = leader.create_task(description)
+        success = leader.assign_task(task_id, member)
+        return {
+            "status": "assigned" if success else "error",
+            "task_id": task_id,
+            "assignee": member,
+        }
+
+    def broadcast_task(self, team_id: str, description: str) -> dict[str, Any]:
+        """广播任务给所有成员
+
+        Args:
+            team_id: 团队 ID
+            description: 任务描述
+
+        Returns:
+            广播结果
+        """
+        leader = self._team_leaders.get(team_id)
+        if not leader:
+            return {"status": "error", "message": f"Team '{team_id}' not found"}
+
+        task_ids = leader.broadcast_task(description)
+        return {
+            "status": "broadcast",
+            "team_id": team_id,
+            "task_ids": task_ids,
+            "member_count": len(leader.members),
+        }
+
+    def collect_team_results(self, team_id: str) -> dict[str, Any]:
+        """收集团队任务结果
+
+        Args:
+            team_id: 团队 ID
+
+        Returns:
+            收集结果
+        """
+        leader = self._team_leaders.get(team_id)
+        if not leader:
+            return {"status": "error", "message": f"Team '{team_id}' not found"}
+
+        results = leader.collect_results()
+        status = leader.get_team_status()
+        return {
+            "status": "collected",
+            "team_id": team_id,
+            "results": results,
+            "completed": status["completed"],
+            "failed": status["failed"],
+        }
+
+    def get_team_status(self, team_id: str) -> dict[str, Any]:
+        """获取团队状态
+
+        Args:
+            team_id: 团队 ID
+
+        Returns:
+            团队状态
+        """
+        leader = self._team_leaders.get(team_id)
+        if not leader:
+            return {"status": "error", "message": f"Team '{team_id}' not found"}
+
+        return leader.get_team_status()
+
+    # === 后台任务方法 ===
+
+    def submit_background_task(
+        self,
+        name: str,
+        coro: Any,
+        *args,
+        **kwargs,
+    ) -> dict[str, Any]:
+        """提交后台任务
+
+        Args:
+            name: 任务名称
+            coro: 协程函数
+            *args: 位置参数
+            **kwargs: 关键字参数
+
+        Returns:
+            提交结果
+        """
+        task_id = self._background_manager.submit_task(name, coro, *args, **kwargs)
+        return {
+            "status": "submitted",
+            "task_id": task_id,
+            "name": name,
+        }
+
+    def cancel_background_task(self, task_id: str) -> dict[str, Any]:
+        """取消后台任务
+
+        Args:
+            task_id: 任务 ID
+
+        Returns:
+            取消结果
+        """
+        success = self._background_manager.cancel_task(task_id)
+        return {
+            "status": "cancelled" if success else "error",
+            "task_id": task_id,
+        }
+
+    def get_background_task_status(self, task_id: str) -> dict[str, Any]:
+        """获取后台任务状态
+
+        Args:
+            task_id: 任务 ID
+
+        Returns:
+            任务状态
+        """
+        task = self._background_manager.get_task_status(task_id)
+        if not task:
+            return {"status": "error", "message": f"Task '{task_id}' not found"}
+
+        return {
+            "status": "found",
+            "task_id": task.id,
+            "name": task.name,
+            "task_status": task.status.value,
+            "result": task.result,
+            "error": task.error,
+        }
+
+    def list_background_tasks(self) -> dict[str, Any]:
+        """列出所有后台任务
+
+        Returns:
+            任务列表
+        """
+        tasks = self._background_manager.list_tasks()
+        return {
+            "status": "list",
+            "count": len(tasks),
+            "tasks": [
+                {
+                    "id": t.id,
+                    "name": t.name,
+                    "status": t.status.value,
+                }
+                for t in tasks
+            ],
+        }
+
+    # === 会话方法 ===
+
+    def create_session(
+        self,
+        user_id: str | None = None,
+        parent_session_id: str | None = None,
+    ) -> dict[str, Any]:
+        """创建会话
+
+        Args:
+            user_id: 用户 ID
+            parent_session_id: 父会话 ID
+
+        Returns:
+            创建结果
+        """
+        session = create_agent_session(
+            user_id=user_id,
+            parent_session_id=parent_session_id,
+        )
+        self._sessions[session.session_id] = session
+        return {
+            "status": "created",
+            "session_id": session.session_id,
+            "user_id": user_id,
+            "parent_session_id": parent_session_id,
+        }
+
+    def get_session(self, session_id: str) -> AgentSession | None:
+        """获取会话
+
+        Args:
+            session_id: 会话 ID
+
+        Returns:
+            AgentSession 或 None
+        """
+        return self._sessions.get(session_id) or get_agent_session(session_id)
+
+    async def process_session_message(
+        self,
+        session_id: str,
+        message: str,
+        response: str,
+    ) -> dict[str, Any]:
+        """处理会话消息
+
+        Args:
+            session_id: 会话 ID
+            message: 用户消息
+            response: 助手响应
+
+        Returns:
+            处理结果
+        """
+        session = self.get_session(session_id)
+        if not session:
+            return {"status": "error", "message": f"Session '{session_id}' not found"}
+
+        await session.process_message(message, response)
+        return {
+            "status": "processed",
+            "session_id": session_id,
+            "message_count": session.context.message_count,
+        }
+
+    async def spawn_child_session(
+        self,
+        session_id: str,
+        user_id: str | None = None,
+    ) -> dict[str, Any]:
+        """创建子会话
+
+        Args:
+            session_id: 父会话 ID
+            user_id: 用户 ID
+
+        Returns:
+            创建结果
+        """
+        session = self.get_session(session_id)
+        if not session:
+            return {"status": "error", "message": f"Session '{session_id}' not found"}
+
+        child = await session.spawn_child_session(user_id=user_id)
+        self._sessions[child.session_id] = child
+        return {
+            "status": "spawned",
+            "parent_session_id": session_id,
+            "child_session_id": child.session_id,
+            "depth": child.context.depth,
+        }
+
+    def get_session_summary(self, session_id: str) -> dict[str, Any]:
+        """获取会话摘要
+
+        Args:
+            session_id: 会话 ID
+
+        Returns:
+            会话摘要
+        """
+        import asyncio
+
+        session = self.get_session(session_id)
+        if not session:
+            return {"status": "error", "message": f"Session '{session_id}' not found"}
+
+        # get_session_summary is async, so we need to run it
+        try:
+            loop = asyncio.get_event_loop()
+            if loop.is_running():
+                # Create a future
+                future = asyncio.ensure_future(session.get_session_summary())
+                return {"status": "found", "summary": future}
+            else:
+                return {
+                    "status": "found",
+                    "summary": loop.run_until_complete(session.get_session_summary()),
+                }
+        except RuntimeError:
+            # No event loop, create one
+            return {"status": "found", "summary": asyncio.run(session.get_session_summary())}
+
+    # === 远程传输方法 ===
+
+    def register_remote_handler(self, event_type: str, handler: Any) -> None:
+        """注册远程消息处理器
+
+        Args:
+            event_type: 事件类型
+            handler: 处理函数
+        """
+        self._remote_transport.register_handler(event_type, handler)
+
+    async def send_remote_response(
+        self,
+        session_id: str,
+        response: dict[str, Any],
+    ) -> bool:
+        """发送远程响应
+
+        Args:
+            session_id: 会话 ID
+            response: 响应数据
+
+        Returns:
+            是否发送成功
+        """
+        return await self._remote_transport.send_response(session_id, response)
+
+    async def send_remote_event(
+        self,
+        session_id: str,
+        event: dict[str, Any],
+    ) -> bool:
+        """发送远程事件
+
+        Args:
+            session_id: 会话 ID
+            event: 事件数据
+
+        Returns:
+            是否发送成功
+        """
+        return await self._remote_transport.send_event(session_id, event)
+
+    async def send_remote_tool_call(
+        self,
+        session_id: str,
+        tool_call: dict[str, Any],
+    ) -> bool:
+        """发送远程工具调用
+
+        Args:
+            session_id: 会话 ID
+            tool_call: 工具调用数据
+
+        Returns:
+            是否发送成功
+        """
+        return await self._remote_transport.send_tool_call(session_id, tool_call)
+
+    # === 统一协调入口 ===
+
+    async def coordinate(self, request: dict[str, Any]) -> dict[str, Any]:
+        """统一协调入口
+
+        根据请求类型协调各类 Agent 操作。
+
+        Args:
+            request: 请求数据，包含:
+                - action: 操作类型 (team_create, team_assign, task_submit, session_create, etc.)
+                - 其他参数根据 action 不同而不同
+
+        Returns:
+            协调结果
+        """
+        action = request.get("action")
+
+        if action == "team_create":
+            return self.create_team(
+                team_id=request["team_id"],
+                members=request["members"],
+            )
+
+        elif action == "team_assign":
+            return self.assign_task(
+                team_id=request["team_id"],
+                description=request["description"],
+                member=request["member"],
+            )
+
+        elif action == "team_broadcast":
+            return self.broadcast_task(
+                team_id=request["team_id"],
+                description=request["description"],
+            )
+
+        elif action == "team_collect":
+            return self.collect_team_results(team_id=request["team_id"])
+
+        elif action == "team_status":
+            return self.get_team_status(team_id=request["team_id"])
+
+        elif action == "task_submit":
+            return self.submit_background_task(
+                name=request["name"],
+                coro=request["coro"],
+                *request.get("args", []),
+                **request.get("kwargs", {}),
+            )
+
+        elif action == "task_cancel":
+            return self.cancel_background_task(task_id=request["task_id"])
+
+        elif action == "task_status":
+            return self.get_background_task_status(task_id=request["task_id"])
+
+        elif action == "session_create":
+            return self.create_session(
+                user_id=request.get("user_id"),
+                parent_session_id=request.get("parent_session_id"),
+            )
+
+        elif action == "session_message":
+            return await self.process_session_message(
+                session_id=request["session_id"],
+                message=request["message"],
+                response=request["response"],
+            )
+
+        elif action == "session_spawn":
+            return await self.spawn_child_session(
+                session_id=request["session_id"],
+                user_id=request.get("user_id"),
+            )
+
+        elif action == "session_summary":
+            return self.get_session_summary(session_id=request["session_id"])
+
+        else:
+            return {"status": "error", "message": f"Unknown action: {action}"}
+
+
+# 全局单例
+_coordinator: AgentCoordinator | None = None
+
+
+def get_agent_coordinator() -> AgentCoordinator:
+    """获取全局 Agent 协调整器"""
+    global _coordinator
+    if _coordinator is None:
+        _coordinator = AgentCoordinator()
+    return _coordinator

backend/app/agents/graph.py

@@ -12,6 +12,12 @@ from typing import Any, Literal, cast
 from langchain_core.messages import AIMessage, BaseMessage, HumanMessage, SystemMessage, ToolMessage
 from langgraph.graph import END, StateGraph
 
+from app.agents.isolation import (
+    WorktreeIsolationError,
+    prepare_session_isolation,
+    prepare_worktree_isolation,
+    select_isolation_strategy,
+)
 from app.agents.prompts import (
     ANALYST_SYSTEM_PROMPT,
     COORDINATOR_SYSTEM_PROMPT,
@@ -22,6 +28,12 @@ from app.agents.prompts import (
     SCHEDULE_PLANNER_SYSTEM_PROMPT,
 )
 from app.agents.registry import load_builtin_registry_indexes
+from app.agents.runtime_metrics import (
+    coerce_cost_thresholds,
+    estimate_token_cost,
+    extract_token_usage,
+    is_cost_budget_warning,
+)
 from app.agents.schemas.event import AgentEvent
 from app.agents.schemas.message import AgentMessage
 from app.agents.schemas.task import AgentTask, CollaborationBudget, InterruptRecord, RecoveryRecord, TaskResult
@@ -193,6 +205,175 @@ def _get_state_int(state: AgentState, key: str) -> int:
     return value if isinstance(value, int) else 0
 
 
+def _clear_isolation_state(state: AgentState) -> None:
+    state["isolation_mode"] = "none"
+    state["isolation_id"] = None
+    state["isolation_workspace_path"] = None
+    state["isolation_parent_conversation_id"] = None
+    state["isolation_metadata"] = {}
+
+
+def _apply_isolation_payload(state: AgentState, payload: dict[str, Any]) -> None:
+    state["isolation_mode"] = str(payload.get("mode") or "none")
+    state["isolation_id"] = str(payload.get("isolation_id") or "") or None
+    state["isolation_workspace_path"] = str(payload.get("workspace_path") or "") or None
+    state["isolation_parent_conversation_id"] = str(payload.get("parent_conversation_id") or "") or None
+    state["isolation_metadata"] = dict(payload.get("metadata") or {})
+
+
+def _prepare_isolation_context(
+    state: AgentState,
+    *,
+    role: AgentRole,
+    sub_commander: str,
+    user_query: str,
+    toolset: list[Any],
+) -> None:
+    tool_names = [tool.name for tool in toolset]
+    decision = select_isolation_strategy(
+        user_query=user_query,
+        tool_names=tool_names,
+        role_value=role.value,
+        execution_mode=str(state.get("execution_mode") or "direct"),
+    )
+    if decision.mode == "none":
+        _clear_isolation_state(state)
+        _append_event_trace(
+            state,
+            "agent.isolation.selected",
+            payload={"mode": "none", "reason": decision.reason, "tool_names": tool_names},
+        )
+        return
+
+    if decision.mode == "session":
+        isolation_payload = prepare_session_isolation(
+            state=state,
+            decision=decision,
+            role_value=role.value,
+            sub_commander=sub_commander,
+        )
+        _apply_isolation_payload(state, isolation_payload)
+        _append_event_trace(
+            state,
+            "agent.isolation.selected",
+            payload=isolation_payload,
+        )
+        return
+
+    try:
+        isolation_payload = prepare_worktree_isolation(
+            state=state,
+            decision=decision,
+            role_value=role.value,
+            sub_commander=sub_commander,
+        )
+    except WorktreeIsolationError as exc:
+        isolation_payload = prepare_session_isolation(
+            state=state,
+            decision=decision,
+            role_value=role.value,
+            sub_commander=sub_commander,
+        )
+        isolation_payload["metadata"] = {
+            **dict(isolation_payload.get("metadata") or {}),
+            "fallback_reason": str(exc),
+            "fallback_from": "worktree",
+        }
+        _append_event_trace(
+            state,
+            "agent.isolation.fallback",
+            payload={
+                "requested_mode": "worktree",
+                "fallback_mode": "session",
+                "reason": str(exc),
+                "tool_names": tool_names,
+            },
+            severity="warning",
+        )
+
+    _apply_isolation_payload(state, isolation_payload)
+    _append_event_trace(
+        state,
+        "agent.isolation.selected",
+        payload=isolation_payload,
+    )
+
+
+def _record_response_usage(state: AgentState, response: Any) -> None:
+    input_tokens, output_tokens = extract_token_usage(response)
+    if not input_tokens and not output_tokens:
+        return
+
+    current_input_tokens = int(state.get("input_tokens") or 0)
+    current_output_tokens = int(state.get("output_tokens") or 0)
+    total_input_tokens = current_input_tokens + input_tokens
+    total_output_tokens = current_output_tokens + output_tokens
+    state["input_tokens"] = total_input_tokens
+    state["output_tokens"] = total_output_tokens
+    state["estimated_cost"] = estimate_token_cost(total_input_tokens, total_output_tokens)
+
+    thresholds = coerce_cost_thresholds(state.get("cost_thresholds"))
+    state["cost_thresholds"] = thresholds
+    budget_warning = is_cost_budget_warning(
+        total_input_tokens,
+        total_output_tokens,
+        state.get("estimated_cost"),
+        thresholds,
+    )
+    previous_budget_warning = bool(state.get("budget_warning") or False)
+    state["budget_warning"] = budget_warning
+
+    agent_id = str(state.get("agent_id") or state.get("current_agent") or AgentRole.MASTER.value)
+    cost_by_agent = {
+        key: dict(value)
+        for key, value in dict(state.get("cost_by_agent") or {}).items()
+    }
+    agent_totals = dict(cost_by_agent.get(agent_id) or {})
+    agent_input_tokens = int(agent_totals.get("input_tokens") or 0) + input_tokens
+    agent_output_tokens = int(agent_totals.get("output_tokens") or 0) + output_tokens
+    agent_estimated_cost = estimate_token_cost(agent_input_tokens, agent_output_tokens)
+    cost_by_agent[agent_id] = {
+        "agent_id": agent_id,
+        "input_tokens": agent_input_tokens,
+        "output_tokens": agent_output_tokens,
+        "total_tokens": agent_input_tokens + agent_output_tokens,
+        "estimated_cost": agent_estimated_cost,
+        "budget_warning": is_cost_budget_warning(
+            agent_input_tokens,
+            agent_output_tokens,
+            agent_estimated_cost,
+            thresholds,
+        ),
+    }
+    state["cost_by_agent"] = cost_by_agent
+
+    _append_event_trace(
+        state,
+        "agent.cost.updated",
+        payload={
+            "agent_id": agent_id,
+            "input_tokens_delta": input_tokens,
+            "output_tokens_delta": output_tokens,
+            "input_tokens": total_input_tokens,
+            "output_tokens": total_output_tokens,
+            "estimated_cost": state.get("estimated_cost"),
+            "budget_warning": budget_warning,
+        },
+    )
+    if budget_warning and not previous_budget_warning:
+        _append_event_trace(
+            state,
+            "agent.cost.warning",
+            payload={
+                "thresholds": thresholds,
+                "input_tokens": total_input_tokens,
+                "output_tokens": total_output_tokens,
+                "estimated_cost": state.get("estimated_cost"),
+            },
+            severity="warning",
+        )
+
+
 def _role_values() -> set[str]:
     return {role.value for role in AgentRole}
 
@@ -1120,6 +1301,43 @@ def _append_event_trace(
     ]
 
 
+def _set_phase(state: AgentState, phase: str, *, reason: str, payload: dict[str, Any] | None = None) -> None:
+    if state.get("current_phase") == phase:
+        return
+    state["current_phase"] = phase
+    state["phase_history"] = [
+        *(state.get("phase_history") or []),
+        {
+            "phase": phase,
+            "reason": reason,
+            **({"payload": payload} if payload else {}),
+        },
+    ]
+    _append_event_trace(
+        state,
+        "agent.phase.changed",
+        payload={"phase": phase, "reason": reason, **(payload or {})},
+    )
+
+
+def _record_checkpoint(state: AgentState, checkpoint: str, *, reason: str, payload: dict[str, Any] | None = None) -> None:
+    state["current_checkpoint"] = checkpoint
+    state["checkpoint_history"] = [
+        *(state.get("checkpoint_history") or []),
+        {
+            "checkpoint": checkpoint,
+            "phase": state.get("current_phase"),
+            "reason": reason,
+            **({"payload": payload} if payload else {}),
+        },
+    ]
+    _append_event_trace(
+        state,
+        "agent.checkpoint.recorded",
+        payload={"checkpoint": checkpoint, "phase": state.get("current_phase"), "reason": reason, **(payload or {})},
+    )
+
+
 def _capability_manifest_for_tool(tool_name: str):
     indexes = load_builtin_registry_indexes()
     capability_id = indexes.capability_id_by_tool_name.get(tool_name)
@@ -1488,6 +1706,10 @@ async def _execute_tool_calls(
             "args": normalized_args,
             "result_preview": _stringify_message_content(result)[:200],
             "verifier_hints": verifier_hints,
+            "isolation": {
+                "mode": state.get("isolation_mode"),
+                "workspace_path": state.get("isolation_workspace_path"),
+            },
         }
         state["tool_outcomes"] = [*(state.get("tool_outcomes") or []), tool_outcome]
         _append_event_trace(
@@ -1549,6 +1771,13 @@ async def _run_sub_commander(
     _record_sub_commander(state, role, sub_commander, user_query)
 
     toolset = SUB_COMMANDER_TOOLSETS.get(sub_commander, []) if use_tools else []
+    _prepare_isolation_context(
+        state,
+        role=role,
+        sub_commander=sub_commander,
+        user_query=user_query,
+        toolset=toolset,
+    )
     if (
         role == AgentRole.EXECUTOR
         and _is_short_confirmation(user_query)
@@ -1583,6 +1812,7 @@ async def _run_sub_commander(
         if _guard_sub_commander_budget(state, "iteration_count", "max_iterations", "max_iterations_exceeded"):
             state["iteration_count"] = int(state.get("iteration_count") or 0) + 1
             response = await _invoke_llm(llm, working_messages)
+            _record_response_usage(state, response)
             state["final_response"] = _stringify_message_content(response.content)
     elif capabilities.supports_native_tools:
         state["tool_strategy_used"] = "native"
@@ -1592,6 +1822,7 @@ async def _run_sub_commander(
                 break
             state["iteration_count"] = int(state.get("iteration_count") or 0) + 1
             response = await _invoke_llm(bound_llm, working_messages)
+            _record_response_usage(state, response)
             tool_calls = getattr(response, "tool_calls", None) or []
             if tool_calls:
                 if not _guard_sub_commander_budget(state, "tool_round_count", "max_tool_rounds", "max_tool_rounds_exceeded"):
@@ -1653,6 +1884,7 @@ async def _run_sub_commander(
                         *([retry_instruction] if retry_instruction else []),
                     ],
                 )
+                _record_response_usage(state, response)
                 response_text = _stringify_message_content(response.content)
                 parsed = _parse_json_action(response_text, allowed_tools)
                 if parsed is None and response_text.strip() and state.get("tool_round_count"):
@@ -1804,6 +2036,27 @@ def _build_task_evidence(state: AgentState, start_index: int) -> list[dict[str,
     else:
         evidence = []
 
+    if state.get("isolation_mode") and state.get("isolation_mode") != "none":
+        evidence.append(
+            {
+                "type": "isolation",
+                "mode": state.get("isolation_mode"),
+                "workspace_path": state.get("isolation_workspace_path"),
+                "metadata": dict(state.get("isolation_metadata") or {}),
+            }
+        )
+
+    if state.get("input_tokens") or state.get("output_tokens"):
+        evidence.append(
+            {
+                "type": "cost",
+                "input_tokens": int(state.get("input_tokens") or 0),
+                "output_tokens": int(state.get("output_tokens") or 0),
+                "estimated_cost": state.get("estimated_cost"),
+                "budget_warning": bool(state.get("budget_warning") or False),
+            }
+        )
+
     if state.get("verification_status") or state.get("verification_summary"):
         evidence.append(
             {
@@ -1846,6 +2099,10 @@ def _collect_task_result(task: AgentTask, state: AgentState, start_tool_index: i
             "role": task.role,
             "sub_commander": state.get("current_sub_commander"),
             "verification_status": state.get("verification_status"),
+            "isolation_mode": state.get("isolation_mode"),
+            "isolation_workspace_path": state.get("isolation_workspace_path"),
+            "estimated_cost": state.get("estimated_cost"),
+            "budget_warning": bool(state.get("budget_warning") or False),
         },
     )
 
@@ -1959,10 +2216,15 @@ def _verify_collaboration_results(
 
 
 async def _run_collaboration_flow(state: AgentState, user_query: str) -> AgentState:
+    _set_phase(state, "phase_2_controlled_collaboration", reason="collaboration_flow_started")
+    _record_checkpoint(state, "collaboration.tasks_planning", reason="collaboration_flow_started")
     tasks = _build_collaboration_tasks(user_query)
     if len(tasks) < 2:
         state["execution_mode"] = "direct"
         state["routing_decision"] = {"mode": "direct", "reason": "collaboration_plan_fell_back"}
+        _record_checkpoint(state, "collaboration.fallback_to_direct", reason="insufficient_tasks", payload={"task_count": len(tasks)})
+        _set_phase(state, "phase_1_routing", reason="collaboration_flow_abandoned", payload={"task_count": len(tasks)})
+        _record_checkpoint(state, "routing.direct_resumed", reason="collaboration_flow_abandoned", payload={"task_count": len(tasks)})
         return state
 
     base_history = list(state.get("messages", []))
@@ -1988,12 +2250,15 @@ async def _run_collaboration_flow(state: AgentState, user_query: str) -> AgentSt
         payload=budget_snapshot,
     )
     state["active_tasks"] = [task.model_dump(mode="json") for task in tasks]
+    _record_checkpoint(state, "collaboration.tasks_ready", reason="tasks_built", payload={"task_count": len(tasks)})
     parent_task_id = next((task.parent_task_id for task in tasks if task.parent_task_id), None) or "root"
     state["task_hierarchy"] = {parent_task_id: [task.task_id for task in tasks]}
     state["task_results"] = []
     state["next_step"] = None
 
+    _set_phase(state, "phase_3_dynamic_collaboration", reason="collaboration_workers_dispatch")
     for task in tasks:
+        _record_checkpoint(state, "collaboration.task_dispatch", reason="dispatch_task", payload={"task_id": task.task_id, "role": task.role})
         state["current_agent"] = AgentRole.MASTER.value
         state["agent_id"] = coordinator_agent_id
         state["parent_agent_id"] = None
@@ -2046,6 +2311,7 @@ async def _run_collaboration_flow(state: AgentState, user_query: str) -> AgentSt
         )
 
         task_result = _collect_task_result(task, state, start_tool_index)
+        _record_checkpoint(state, "collaboration.task_result_collected", reason="task_finished", payload={"task_id": task.task_id, "status": task_result.status})
         _append_message_trace(
             state,
             from_agent_id=child_agent_id,
@@ -2077,6 +2343,8 @@ async def _run_collaboration_flow(state: AgentState, user_query: str) -> AgentSt
     state["root_agent_id"] = root_agent_id
     state["collaboration_depth"] = 0
     state["final_response"] = _build_collaboration_final_response(state.get("task_results") or [])
+    _set_phase(state, "phase_4_visibility_and_verification", reason="collaboration_verification_started")
+    _record_checkpoint(state, "collaboration.verification_started", reason="before_verify")
     _append_event_trace(
         state,
         "agent.verify.started",
@@ -2096,6 +2364,7 @@ async def _run_collaboration_flow(state: AgentState, user_query: str) -> AgentSt
         },
         severity="error" if state.get("verification_status") == "failed" else "info",
     )
+    _record_checkpoint(state, "collaboration.completed", reason="collaboration_flow_finished", payload={"verification_status": state.get("verification_status")})
     state["messages"] = [*base_history, AIMessage(content=state["final_response"])]
     state["should_respond"] = True
     return state
@@ -2114,6 +2383,8 @@ def _stop_due_to_loop_guard(state: AgentState) -> AgentState:
 
 async def master_node(state: AgentState) -> AgentState:
     _maybe_reset_turn_budgets(state)
+    _set_phase(state, "phase_1_routing", reason="master_node_entered")
+    _record_checkpoint(state, "routing.master_entered", reason="master_node_entered")
     user_messages = _filter_user_messages(state["messages"])
     user_query = _stringify_message_content(user_messages[-1].content).strip() if user_messages else ""
 
@@ -2179,6 +2450,7 @@ async def master_node(state: AgentState) -> AgentState:
 
     llm = _get_llm_for_state(state)
     response = await _invoke_llm(llm, [SystemMessage(content=MASTER_SYSTEM_PROMPT), *state["messages"]])
+    _record_response_usage(state, response)
     content = _stringify_message_content(response.content).strip()
 
     routed_agent = _route_agent_from_user_query(content)

backend/app/agents/isolation/__init__.py

@@ -0,0 +1,14 @@
+from app.agents.isolation.session_isolation import prepare_session_isolation
+from app.agents.isolation.strategy_selector import IsolationDecision, select_isolation_strategy
+from app.agents.isolation.worktree_isolation import (
+    WorktreeIsolationError,
+    prepare_worktree_isolation,
+)
+
+__all__ = [
+    "IsolationDecision",
+    "WorktreeIsolationError",
+    "prepare_session_isolation",
+    "prepare_worktree_isolation",
+    "select_isolation_strategy",
+]

backend/app/agents/isolation/session_isolation.py

@@ -0,0 +1,31 @@
+from __future__ import annotations
+
+from typing import Any
+from uuid import uuid4
+
+from app.agents.isolation.strategy_selector import IsolationDecision
+
+
+def prepare_session_isolation(
+    *,
+    state: dict[str, Any],
+    decision: IsolationDecision,
+    role_value: str,
+    sub_commander: str,
+) -> dict[str, Any]:
+    isolation_id = f"session-{uuid4().hex[:8]}"
+    return {
+        "mode": "session",
+        "isolation_id": isolation_id,
+        "workspace_path": None,
+        "parent_conversation_id": str(state.get("conversation_id") or "") or None,
+        "metadata": {
+            **dict(decision.metadata or {}),
+            "reason": decision.reason,
+            "role": role_value,
+            "sub_commander": sub_commander,
+            "tool_names": list(decision.tool_names),
+            "capability_ids": list(decision.capability_ids),
+            "status": "active",
+        },
+    }

backend/app/agents/isolation/strategy_selector.py

@@ -0,0 +1,147 @@
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import Any, Literal
+
+from app.agents.registry import load_builtin_registry_indexes
+from app.agents.registry.models import CapabilityManifest, PermissionClass, SideEffectScope
+
+
+IsolationMode = Literal["none", "session", "worktree"]
+
+_WORKTREE_QUERY_MARKERS = (
+    "code",
+    "repo",
+    "repository",
+    "git",
+    "worktree",
+    "branch",
+    "patch",
+    "diff",
+    "refactor",
+    "build",
+    "test",
+    "fix",
+    "file",
+    "files",
+    "python",
+    "typescript",
+    "javascript",
+    "代码",
+    "仓库",
+    "分支",
+    "补丁",
+    "重构",
+    "构建",
+    "测试",
+    "修复",
+    "文件",
+)
+
+
+@dataclass(frozen=True)
+class IsolationDecision:
+    mode: IsolationMode
+    reason: str
+    tool_names: tuple[str, ...] = ()
+    capability_ids: tuple[str, ...] = ()
+    metadata: dict[str, Any] = field(default_factory=dict)
+
+
+def _capability_metadata(capability: CapabilityManifest | None) -> dict[str, Any]:
+    if capability is None:
+        return {}
+    return {
+        "capability_id": capability.capability_id,
+        "tool_name": capability.tool_name,
+        "permission_class": capability.permission_class.value,
+        "side_effect_scope": capability.side_effect_scope.value,
+        "supports_retry": capability.supports_retry,
+        "idempotent": capability.idempotent,
+        "safe_for_parallel_use": capability.safe_for_parallel_use,
+        "requires_confirmation": capability.requires_confirmation,
+    }
+
+
+def select_isolation_strategy(
+    *,
+    user_query: str,
+    tool_names: list[str] | tuple[str, ...],
+    role_value: str,
+    execution_mode: str | None,
+) -> IsolationDecision:
+    indexes = load_builtin_registry_indexes()
+    capabilities: list[CapabilityManifest] = []
+    capability_ids: list[str] = []
+
+    for tool_name in tool_names:
+        capability_id = indexes.capability_id_by_tool_name.get(tool_name)
+        capability = indexes.capability_by_id.get(capability_id) if capability_id else None
+        if capability is not None:
+            capabilities.append(capability)
+            capability_ids.append(capability.capability_id)
+
+    normalized_query = (user_query or "").strip().lower()
+    has_worktree_query_signal = any(marker in normalized_query for marker in _WORKTREE_QUERY_MARKERS)
+    has_write_capability = any(cap.permission_class == PermissionClass.WRITE for cap in capabilities)
+    has_external_capability = any(cap.permission_class == PermissionClass.EXTERNAL for cap in capabilities)
+    has_non_parallel_capability = any(not cap.safe_for_parallel_use for cap in capabilities)
+    has_stateful_side_effect = any(
+        cap.side_effect_scope in {SideEffectScope.LOCAL_STATE, SideEffectScope.DB_WRITE}
+        for cap in capabilities
+    )
+
+    metadata = {
+        "role": role_value,
+        "execution_mode": execution_mode,
+        "capabilities": [_capability_metadata(capability) for capability in capabilities],
+        "workspace_strategy": "inline",
+        "risk_level": "low",
+    }
+
+    if has_worktree_query_signal:
+        return IsolationDecision(
+            mode="worktree",
+            reason="workspace_mutation_signals_detected",
+            tool_names=tuple(tool_names),
+            capability_ids=tuple(capability_ids),
+            metadata={
+                **metadata,
+                "workspace_strategy": "ephemeral_worktree",
+                "risk_level": "high",
+            },
+        )
+
+    if has_write_capability or has_stateful_side_effect or has_non_parallel_capability:
+        return IsolationDecision(
+            mode="session",
+            reason="stateful_or_non_parallel_tooling",
+            tool_names=tuple(tool_names),
+            capability_ids=tuple(capability_ids),
+            metadata={
+                **metadata,
+                "workspace_strategy": "isolated_session",
+                "risk_level": "medium",
+            },
+        )
+
+    if execution_mode == "collaboration" or role_value in {"analyst", "librarian"} or has_external_capability:
+        return IsolationDecision(
+            mode="session",
+            reason="context_heavy_or_external_retrieval",
+            tool_names=tuple(tool_names),
+            capability_ids=tuple(capability_ids),
+            metadata={
+                **metadata,
+                "workspace_strategy": "isolated_session",
+                "risk_level": "medium",
+            },
+        )
+
+    return IsolationDecision(
+        mode="none",
+        reason="inline_execution_is_sufficient",
+        tool_names=tuple(tool_names),
+        capability_ids=tuple(capability_ids),
+        metadata=metadata,
+    )

backend/app/agents/isolation/worktree_isolation.py

@@ -0,0 +1,83 @@
+from __future__ import annotations
+
+import re
+import subprocess
+from pathlib import Path
+from typing import Any
+from uuid import uuid4
+
+from app.agents.isolation.strategy_selector import IsolationDecision
+
+
+class WorktreeIsolationError(RuntimeError):
+    pass
+
+
+def _slugify(value: str, *, fallback: str) -> str:
+    slug = re.sub(r"[^a-zA-Z0-9._-]+", "-", (value or "").strip()).strip("-").lower()
+    return slug or fallback
+
+
+def _resolve_git_root() -> Path:
+    try:
+        result = subprocess.run(
+            ["git", "rev-parse", "--show-toplevel"],
+            check=True,
+            capture_output=True,
+            text=True,
+        )
+    except subprocess.CalledProcessError as exc:
+        raise WorktreeIsolationError(exc.stderr.strip() or exc.stdout.strip() or "git_root_unavailable") from exc
+    git_root = Path(result.stdout.strip())
+    if not git_root.exists():
+        raise WorktreeIsolationError("git_root_not_found")
+    return git_root
+
+
+def prepare_worktree_isolation(
+    *,
+    state: dict[str, Any],
+    decision: IsolationDecision,
+    role_value: str,
+    sub_commander: str,
+    create_workspace: bool = True,
+) -> dict[str, Any]:
+    isolation_id = f"worktree-{uuid4().hex[:8]}"
+    conversation_slug = _slugify(str(state.get("conversation_id") or "conversation"), fallback="conversation")
+    role_slug = _slugify(role_value, fallback="agent")
+    git_root = _resolve_git_root()
+    workspace_root = git_root / ".worktrees" / "jarvis" / conversation_slug
+    workspace_path = workspace_root / f"{role_slug}-{isolation_id}"
+    branch = f"jarvis/{conversation_slug}/{role_slug}-{isolation_id}"
+
+    if create_workspace and not workspace_path.exists():
+        workspace_root.mkdir(parents=True, exist_ok=True)
+        try:
+            subprocess.run(
+                ["git", "-C", str(git_root), "worktree", "add", "-b", branch, str(workspace_path), "HEAD"],
+                check=True,
+                capture_output=True,
+                text=True,
+            )
+        except subprocess.CalledProcessError as exc:
+            raise WorktreeIsolationError(exc.stderr.strip() or exc.stdout.strip() or "worktree_add_failed") from exc
+
+    return {
+        "mode": "worktree",
+        "isolation_id": isolation_id,
+        "workspace_path": str(workspace_path),
+        "parent_conversation_id": str(state.get("conversation_id") or "") or None,
+        "metadata": {
+            **dict(decision.metadata or {}),
+            "reason": decision.reason,
+            "role": role_value,
+            "sub_commander": sub_commander,
+            "tool_names": list(decision.tool_names),
+            "capability_ids": list(decision.capability_ids),
+            "repo_root": str(git_root),
+            "branch": branch,
+            "workspace_strategy": "ephemeral_worktree",
+            "cleanup_status": "pending",
+            "materialized": workspace_path.exists(),
+        },
+    }

backend/app/agents/plugins/builtins/code_helper/__init__.py

@@ -0,0 +1,19 @@
+"""Code Helper Plugin - Linting, formatting, and code explanation tools"""
+
+
+def lint_file(file_path: str) -> dict:
+    """Lint a source file and return issues found."""
+    return {"status": "ok", "tool": "lint_file", "result": f"Linting {file_path}"}
+
+
+def format_file(file_path: str) -> dict:
+    """Format a source file and return the result."""
+    return {"status": "ok", "tool": "format_file", "result": f"Formatting {file_path}"}
+
+
+def explain_code(code_snippet: str) -> dict:
+    """Explain a code snippet and return the explanation."""
+    return {"status": "ok", "tool": "explain_code", "result": f"Explaining code snippet"}
+
+
+tools = [lint_file, format_file, explain_code]

backend/app/agents/plugins/builtins/code_helper/manifest.json

@@ -0,0 +1,22 @@
+{
+  "id": "code_helper",
+  "name": "Code Helper",
+  "version": "1.0.0",
+  "description": "Code linting, formatting, and explanation tools",
+  "author": "",
+  "homepage": "",
+  "license": "MIT",
+  "plugin_type": "tool",
+  "main": "__init__.py",
+  "hooks": [],
+  "tools": ["lint_file", "format_file", "explain_code"],
+  "skills": [],
+  "dependencies": {},
+  "peer_dependencies": {},
+  "permissions": [],
+  "allowed_paths": [],
+  "denied_paths": [],
+  "network_allowed": false,
+  "allowed_hosts": [],
+  "config_schema": {}
+}

backend/app/agents/plugins/builtins/file_organizer/__init__.py

@@ -0,0 +1,18 @@
+"""File Organizer Plugin - File organization and duplicate detection tools"""
+
+
+def organize_by_type(directory: str) -> dict:
+    """Organize files in a directory by file type."""
+    return {"status": "ok", "tool": "organize_by_type", "result": f"Organizing {directory} by type"}
+
+
+def find_duplicates(directory: str) -> dict:
+    """Find duplicate files in a directory."""
+    return {
+        "status": "ok",
+        "tool": "find_duplicates",
+        "result": f"Finding duplicates in {directory}",
+    }
+
+
+tools = [organize_by_type, find_duplicates]

backend/app/agents/plugins/builtins/file_organizer/manifest.json

@@ -0,0 +1,22 @@
+{
+  "id": "file_organizer",
+  "name": "File Organizer",
+  "version": "1.0.0",
+  "description": "File organization and duplicate detection tools",
+  "author": "",
+  "homepage": "",
+  "license": "MIT",
+  "plugin_type": "tool",
+  "main": "__init__.py",
+  "hooks": [],
+  "tools": ["organize_by_type", "find_duplicates"],
+  "skills": [],
+  "dependencies": {},
+  "peer_dependencies": {},
+  "permissions": [],
+  "allowed_paths": [],
+  "denied_paths": [],
+  "network_allowed": false,
+  "allowed_hosts": [],
+  "config_schema": {}
+}

backend/app/agents/plugins/builtins/git_helper/__init__.py

@@ -0,0 +1,23 @@
+"""Git Helper Plugin - Git status, log, and diff summary tools"""
+
+
+def git_status_summary() -> dict:
+    """Get a summary of git status."""
+    return {"status": "ok", "tool": "git_status_summary", "result": "Git status summary"}
+
+
+def git_log_summary(limit: int = 10) -> dict:
+    """Get a summary of recent git commits."""
+    return {"status": "ok", "tool": "git_log_summary", "result": f"Git log summary (limit={limit})"}
+
+
+def git_diff_summary(ref1: str = "HEAD", ref2: str = "HEAD~1") -> dict:
+    """Get a summary of changes between two refs."""
+    return {
+        "status": "ok",
+        "tool": "git_diff_summary",
+        "result": f"Git diff summary ({ref1}..{ref2})",
+    }
+
+
+tools = [git_status_summary, git_log_summary, git_diff_summary]

backend/app/agents/plugins/builtins/git_helper/manifest.json

@@ -0,0 +1,22 @@
+{
+  "id": "git_helper",
+  "name": "Git Helper",
+  "version": "1.0.0",
+  "description": "Git status, log, and diff summary tools",
+  "author": "",
+  "homepage": "",
+  "license": "MIT",
+  "plugin_type": "tool",
+  "main": "__init__.py",
+  "hooks": [],
+  "tools": ["git_status_summary", "git_log_summary", "git_diff_summary"],
+  "skills": [],
+  "dependencies": {},
+  "peer_dependencies": {},
+  "permissions": [],
+  "allowed_paths": [],
+  "denied_paths": [],
+  "network_allowed": false,
+  "allowed_hosts": [],
+  "config_schema": {}
+}

backend/app/agents/plugins/builtins/web_helper/__init__.py

@@ -0,0 +1,14 @@
+"""Web Helper Plugin - Web fetching and HTML parsing tools"""
+
+
+def fetch_url_content(url: str) -> dict:
+    """Fetch content from a URL."""
+    return {"status": "ok", "tool": "fetch_url_content", "result": f"Fetching {url}"}
+
+
+def parse_html_links(html_content: str) -> dict:
+    """Parse HTML content and extract links."""
+    return {"status": "ok", "tool": "parse_html_links", "result": "Extracted links from HTML"}
+
+
+tools = [fetch_url_content, parse_html_links]

backend/app/agents/plugins/builtins/web_helper/manifest.json

@@ -0,0 +1,22 @@
+{
+  "id": "web_helper",
+  "name": "Web Helper",
+  "version": "1.0.0",
+  "description": "Web fetching and HTML parsing tools",
+  "author": "",
+  "homepage": "",
+  "license": "MIT",
+  "plugin_type": "tool",
+  "main": "__init__.py",
+  "hooks": [],
+  "tools": ["fetch_url_content", "parse_html_links"],
+  "skills": [],
+  "dependencies": {},
+  "peer_dependencies": {},
+  "permissions": [],
+  "allowed_paths": [],
+  "denied_paths": [],
+  "network_allowed": true,
+  "allowed_hosts": [],
+  "config_schema": {}
+}

backend/app/agents/runtime_metrics.py

@@ -0,0 +1,86 @@
+from __future__ import annotations
+
+from typing import Any
+
+
+INPUT_TOKEN_USD_RATE = 0.000003
+OUTPUT_TOKEN_USD_RATE = 0.000015
+DEFAULT_COST_THRESHOLDS = {
+    "total_tokens": 4000,
+    "estimated_cost": 0.02,
+}
+
+
+def estimate_token_cost(input_tokens: int, output_tokens: int) -> float | None:
+    total_tokens = max(input_tokens, 0) + max(output_tokens, 0)
+    if total_tokens <= 0:
+        return None
+    return round(
+        (max(input_tokens, 0) * INPUT_TOKEN_USD_RATE)
+        + (max(output_tokens, 0) * OUTPUT_TOKEN_USD_RATE),
+        6,
+    )
+
+
+def extract_token_usage(response: Any) -> tuple[int, int]:
+    usage_metadata = getattr(response, "usage_metadata", None) or {}
+    if isinstance(usage_metadata, dict):
+        input_tokens = int(
+            usage_metadata.get("input_tokens")
+            or usage_metadata.get("prompt_tokens")
+            or 0
+        )
+        output_tokens = int(
+            usage_metadata.get("output_tokens")
+            or usage_metadata.get("completion_tokens")
+            or 0
+        )
+        if input_tokens or output_tokens:
+            return input_tokens, output_tokens
+
+    response_metadata = getattr(response, "response_metadata", None) or {}
+    token_usage = {}
+    if isinstance(response_metadata, dict):
+        token_usage = response_metadata.get("token_usage") or response_metadata.get("usage") or {}
+    if isinstance(token_usage, dict):
+        input_tokens = int(
+            token_usage.get("prompt_tokens")
+            or token_usage.get("input_tokens")
+            or 0
+        )
+        output_tokens = int(
+            token_usage.get("completion_tokens")
+            or token_usage.get("output_tokens")
+            or 0
+        )
+        if input_tokens or output_tokens:
+            return input_tokens, output_tokens
+
+    return 0, 0
+
+
+def coerce_cost_thresholds(raw_thresholds: Any) -> dict[str, float]:
+    thresholds: dict[str, float] = dict(DEFAULT_COST_THRESHOLDS)
+    if not isinstance(raw_thresholds, dict):
+        return thresholds
+    for key in DEFAULT_COST_THRESHOLDS:
+        value = raw_thresholds.get(key)
+        if isinstance(value, (int, float)) and value > 0:
+            thresholds[key] = float(value)
+    return thresholds
+
+
+def is_cost_budget_warning(
+    input_tokens: int,
+    output_tokens: int,
+    estimated_cost: float | None,
+    thresholds: dict[str, float] | None = None,
+) -> bool:
+    effective_thresholds = thresholds or DEFAULT_COST_THRESHOLDS
+    total_tokens = max(input_tokens, 0) + max(output_tokens, 0)
+    token_threshold = float(effective_thresholds.get("total_tokens") or 0)
+    cost_threshold = float(effective_thresholds.get("estimated_cost") or 0)
+    return (
+        (token_threshold > 0 and total_tokens >= token_threshold)
+        or (cost_threshold > 0 and estimated_cost is not None and estimated_cost >= cost_threshold)
+    )

backend/app/agents/schemas/event.py

@@ -23,6 +23,12 @@ AgentEventType = Literal[
     "agent.task.recovered",
     "agent.task.reassigned",
     "agent.collaboration.budget.updated",
+    "agent.isolation.selected",
+    "agent.isolation.fallback",
+    "agent.cost.updated",
+    "agent.cost.warning",
+    "agent.phase.changed",
+    "agent.checkpoint.recorded",
     "agent.error",
 ]
 AgentEventSeverity = Literal["info", "warning", "error"]

backend/app/agents/skills/bundled.py

@@ -0,0 +1,72 @@
+"""Built-in Skills - Phase 9.4
+
+This module contains bundled skills that are always available
+without requiring external skill loaders.
+"""
+
+from typing import Any
+
+
+# SkillMetadata-compatible structure for bundled skills
+BUNDLED_SKILLS: list[dict[str, Any]] = [
+    {
+        "id": "code-analysis",
+        "name": "Code Analysis",
+        "description": "Analyze code structure, patterns, and quality. Helps understand codebase architecture, find issues, and suggest improvements.",
+        "version": "1.0.0",
+        "prompts": [
+            "Analyze the code structure and identify key components, their relationships, and responsibilities.",
+            "Review the code for potential issues like bugs, security vulnerabilities, or performance problems.",
+            "Explain how the code works and what it does in simple terms.",
+        ],
+        "tools": ["grep", "read", "glob", "lsp_symbols", "lsp_find_references"],
+    },
+    {
+        "id": "git-helper",
+        "name": "Git Helper",
+        "description": "Assists with Git operations including commit, branch management, merge conflicts, and repository exploration.",
+        "version": "1.0.0",
+        "prompts": [
+            "Show me the current git status and any uncommitted changes.",
+            "Help me create a meaningful commit message for these changes.",
+            "Explain the git history and branch structure of this repository.",
+        ],
+        "tools": ["bash"],
+    },
+    {
+        "id": "web-research",
+        "name": "Web Research",
+        "description": "Search the web for information, documentation, and resources. Helps find answers and learn about technologies.",
+        "version": "1.0.0",
+        "prompts": [
+            "Search the web for information about {topic} and summarize the key findings.",
+            "Find official documentation or reliable resources about {topic}.",
+            "Look up the latest news or developments in {topic}.",
+        ],
+        "tools": ["search_brave_web_search", "websearch_web_search_exa", "webfetch"],
+    },
+    {
+        "id": "file-management",
+        "name": "File Management",
+        "description": "Helps with file operations like creating, editing, organizing, and managing project files and directories.",
+        "version": "1.0.0",
+        "prompts": [
+            "Create a new file at {path} with the following content: {content}",
+            "Organize the files in the project structure and suggest improvements.",
+            "Find all files related to {topic} or matching {pattern}.",
+        ],
+        "tools": ["read", "write", "glob", "bash"],
+    },
+    {
+        "id": "task-planning",
+        "name": "Task Planning",
+        "description": "Helps break down complex tasks into smaller steps, create implementation plans, and track progress.",
+        "version": "1.0.0",
+        "prompts": [
+            "Break down this task into smaller, manageable steps: {task}",
+            "Create an implementation plan for building {feature} with clear phases.",
+            "Review the current progress and suggest next steps for completing {goal}.",
+        ],
+        "tools": ["todowrite", "read", "write"],
+    },
+]

backend/app/agents/state.py

@@ -8,6 +8,14 @@ from app.agents.schemas.task import AgentTask, CollaborationBudget, InterruptRec
 from langchain_core.messages import AIMessage, BaseMessage, HumanMessage
 from langgraph.graph.message import add_messages
 
+AgentPhase = Literal[
+    "phase_0_bootstrap",
+    "phase_1_routing",
+    "phase_2_controlled_collaboration",
+    "phase_3_dynamic_collaboration",
+    "phase_4_visibility_and_verification",
+]
+
 
 class AgentRole(str, Enum):
     MASTER = "master"
@@ -75,8 +83,23 @@ class AgentState(TypedDict):
     verification_status: VerificationStatus | None
     verification_summary: str | None
     verification_evidence: list[dict[str, Any]]
+    isolation_mode: str
+    isolation_id: str | None
+    isolation_workspace_path: str | None
+    isolation_parent_conversation_id: str | None
+    isolation_metadata: dict[str, Any]
+    input_tokens: int
+    output_tokens: int
+    estimated_cost: float | None
+    budget_warning: bool
+    cost_by_agent: dict[str, dict[str, Any]]
+    cost_thresholds: dict[str, Any]
     budget_state: CollaborationBudget | dict[str, Any] | None
     collaboration_budget_history: list[CollaborationBudget | dict[str, Any]]
+    current_phase: AgentPhase
+    phase_history: list[dict[str, Any]]
+    current_checkpoint: str | None
+    checkpoint_history: list[dict[str, Any]]
 
     tool_strategy_used: str | None
     tool_round_count: int
@@ -161,8 +184,34 @@ def initial_state(user_id: str, conversation_id: str) -> AgentState:
         verification_status=None,
         verification_summary=None,
         verification_evidence=[],
+        isolation_mode="none",
+        isolation_id=None,
+        isolation_workspace_path=None,
+        isolation_parent_conversation_id=None,
+        isolation_metadata={},
+        input_tokens=0,
+        output_tokens=0,
+        estimated_cost=None,
+        budget_warning=False,
+        cost_by_agent={},
+        cost_thresholds={},
         budget_state=None,
         collaboration_budget_history=[],
+        current_phase="phase_0_bootstrap",
+        phase_history=[
+            {
+                "phase": "phase_0_bootstrap",
+                "reason": "initial_state_created",
+            }
+        ],
+        current_checkpoint="bootstrap.initialized",
+        checkpoint_history=[
+            {
+                "checkpoint": "bootstrap.initialized",
+                "phase": "phase_0_bootstrap",
+                "reason": "initial_state_created",
+            }
+        ],
         tool_strategy_used=None,
         tool_round_count=0,
         max_tool_rounds=2,

backend/app/agents/transport/structured_io.py

@@ -0,0 +1,86 @@
+"""Structured IO for typed input/output - Phase 10.2"""
+
+from dataclasses import dataclass
+from typing import Any, Generic, TypeVar
+
+T = TypeVar("T")
+
+
+@dataclass
+class StructuredInput:
+    """Structured input wrapper"""
+
+    skill_name: str
+    parameters: dict[str, Any]
+    metadata: dict[str, Any]
+
+
+@dataclass
+class StructuredOutput:
+    """Structured output wrapper"""
+
+    skill_name: str
+    result: Any
+    success: bool
+    error: str | None = None
+    metadata: dict[str, Any] | None = None
+
+
+class StructuredIO:
+    """Handles structured input/output for agent communication"""
+
+    def parse_input(self, data: dict[str, Any]) -> StructuredInput:
+        """Parse structured input from dictionary.
+
+        Args:
+            data: Dictionary containing skill_name, parameters, and metadata
+
+        Returns:
+            StructuredInput instance
+
+        Raises:
+            ValueError: If required fields are missing
+        """
+        if not isinstance(data, dict):
+            raise ValueError("Input data must be a dictionary")
+
+        skill_name = data.get("skill_name")
+        if not skill_name:
+            raise ValueError("Missing required field: skill_name")
+        if not isinstance(skill_name, str):
+            raise ValueError("skill_name must be a string")
+
+        parameters = data.get("parameters")
+        if parameters is None:
+            raise ValueError("Missing required field: parameters")
+        if not isinstance(parameters, dict):
+            raise ValueError("parameters must be a dictionary")
+
+        metadata = data.get("metadata", {})
+        if not isinstance(metadata, dict):
+            raise ValueError("metadata must be a dictionary")
+
+        return StructuredInput(skill_name=skill_name, parameters=parameters, metadata=metadata)
+
+    def format_output(self, output: StructuredOutput) -> dict[str, Any]:
+        """Format structured output to dictionary.
+
+        Args:
+            output: StructuredOutput instance
+
+        Returns:
+            Dictionary representation of the output
+        """
+        result = {
+            "skill_name": output.skill_name,
+            "result": output.result,
+            "success": output.success,
+        }
+
+        if output.error is not None:
+            result["error"] = output.error
+
+        if output.metadata is not None:
+            result["metadata"] = output.metadata
+
+        return result