Fix all critical issues flagged in code review

- checkpoint.py: remove debug log file (strix_checkpoint_debug.log)
  that was writing to every user's home directory on each save
- checkpoint.py: acquire _agents_lock before iterating _agent_instances
  to prevent RuntimeError on concurrent sub-agent creation/removal
- checkpoint_restore.py: register restored sub-agents in _agent_graph,
  _agent_instances, and _agent_states so send_message_to_agent can
  route to them — previously they were unreachable after resume
- tracer.py: revert Path.home() back to Path.cwd() to avoid silent
  breaking change for all users; checkpoint logic in main.py already
  uses Path.home() directly so tracer change was not needed
- cli.py / tui.py: move checkpoint_restore imports to top of file
  per PEP 8, remove noqa: E402 suppressions

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

strix/interface/checkpoint_restore.py

@@ -7,6 +7,7 @@ from __future__ import annotations
 
 import asyncio
 import threading
+from datetime import UTC, datetime
 from typing import Any
 
 
@@ -91,6 +92,15 @@ def restore_sub_agents(checkpoint_data: Any, llm_config: Any) -> list[str]:
             t.start()
             with agents_graph_actions._agents_lock:
                 agents_graph_actions._running_agents[agent_id] = t
+                agents_graph_actions._agent_instances[agent_id] = agent
+                agents_graph_actions._agent_states[agent_id] = state
+            agents_graph_actions._agent_graph["nodes"][agent_id] = {
+                "status": "running",
+                "name": state.agent_name,
+                "task": state.task,
+                "parent_id": state.parent_id,
+                "started_at": datetime.now(UTC).isoformat(),
+            }
             restored_ids.append(agent_id)
 
         except Exception:  # noqa: BLE001

strix/interface/cli.py

@@ -11,6 +11,8 @@ from rich.panel import Panel
 from rich.text import Text
 
 from strix.agents.StrixAgent import StrixAgent
+from strix.interface.checkpoint_restore import build_root_resume_message as _build_resume_context_message
+from strix.interface.checkpoint_restore import restore_sub_agents as _restore_sub_agents
 from strix.llm.config import LLMConfig
 from strix.telemetry.tracer import Tracer, set_global_tracer
 
@@ -97,8 +99,6 @@ def _replay_previous_output(
             console.print()
 
 
-from strix.interface.checkpoint_restore import build_root_resume_message as _build_resume_context_message  # noqa: E402
-from strix.interface.checkpoint_restore import restore_sub_agents as _restore_sub_agents  # noqa: E402
 
 
 async def run_cli(args: Any) -> None:  # noqa: PLR0915

strix/interface/tui.py

@@ -29,6 +29,8 @@ from textual.widgets import Button, Label, Static, TextArea, Tree
 from textual.widgets.tree import TreeNode
 
 from strix.agents.StrixAgent import StrixAgent
+from strix.interface.checkpoint_restore import build_root_resume_message as _build_root_resume_message
+from strix.interface.checkpoint_restore import restore_sub_agents as _restore_sub_agents_tui
 from strix.interface.streaming_parser import parse_streaming_content
 from strix.interface.tool_components.agent_message_renderer import AgentMessageRenderer
 from strix.interface.tool_components.registry import get_tool_renderer
@@ -39,10 +41,6 @@ from strix.telemetry.tracer import Tracer, set_global_tracer
 
 
 logger = logging.getLogger(__name__)
-
-
-from strix.interface.checkpoint_restore import build_root_resume_message as _build_root_resume_message  # noqa: E402
-from strix.interface.checkpoint_restore import restore_sub_agents as _restore_sub_agents_tui  # noqa: E402
 def get_package_version() -> str:
     try:
         return pkg_version("strix-agent")

strix/telemetry/checkpoint.py

@@ -144,7 +144,9 @@ class CheckpointManager:
             try:
                 from strix.tools.agents_graph import agents_graph_actions
 
-                for sid, inst in list(agents_graph_actions._agent_instances.items()):
+                with agents_graph_actions._agents_lock:
+                    snapshot = list(agents_graph_actions._agent_instances.items())
+                for sid, inst in snapshot:
                     s = getattr(inst, "state", None)
                     if s is not None and s.parent_id is not None:
                         sub_agent_states[sid] = (
@@ -176,19 +178,9 @@ class CheckpointManager:
             )
             self._tmp_path.write_text(json_str, encoding="utf-8")
             os.rename(self._tmp_path, self.checkpoint_path)
-
-            with open(Path.home() / "strix_checkpoint_debug.log", "a") as _dbg:
-                _dbg.write(f"SAVED iter={agent_state.iteration} path={self.checkpoint_path}\n")
+            logger.debug("[Resume] Checkpoint saved iter=%s path=%s", agent_state.iteration, self.checkpoint_path)
 
         except Exception as e:  # noqa: BLE001
-            try:
-                with open(Path.home() / "strix_checkpoint_debug.log", "a") as _dbg:
-                    _dbg.write(
-                        f"FAILED iter={getattr(agent_state, 'iteration', '?')} "
-                        f"path={self.checkpoint_path} err={e}\n"
-                    )
-            except Exception:
-                pass
             logger.warning("[Resume] Checkpoint save failed (non-fatal): %s", e)
 
     def load(self) -> "CheckpointModel | None":

strix/telemetry/tracer.py

@@ -294,7 +294,7 @@ class Tracer:
 
     def get_run_dir(self) -> Path:
         if self._run_dir is None:
-            runs_dir = Path.home() / "strix_runs"
+            runs_dir = Path.cwd() / "strix_runs"
             runs_dir.mkdir(exist_ok=True)
 
             run_dir_name = self.run_name if self.run_name else self.run_id