refactor: break up shell.py::run() into helpers

Extract _build_run_env() and _exec_subprocess() from the 89-line run()
method, reducing it to ~30 lines that validate and delegate.

Fixes #539

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

src/infrastructure/hands/shell.py

@@ -144,6 +144,60 @@ class ShellHand:
 
         return None
 
+    @staticmethod
+    def _build_run_env(env: dict | None) -> dict:
+        """Merge *env* overrides into the current process environment."""
+        import os
+
+        run_env = os.environ.copy()
+        if env:
+            run_env.update(env)
+        return run_env
+
+    async def _exec_subprocess(
+        self,
+        command: str,
+        effective_timeout: int,
+        cwd: str | None,
+        run_env: dict,
+        start: float,
+    ) -> ShellResult:
+        """Launch *command*, enforce timeout, and return the result."""
+        proc = await asyncio.create_subprocess_shell(
+            command,
+            stdout=asyncio.subprocess.PIPE,
+            stderr=asyncio.subprocess.PIPE,
+            cwd=cwd,
+            env=run_env,
+        )
+
+        try:
+            stdout_bytes, stderr_bytes = await asyncio.wait_for(
+                proc.communicate(), timeout=effective_timeout
+            )
+        except TimeoutError:
+            proc.kill()
+            await proc.wait()
+            logger.warning("Shell command timed out after %ds: %s", effective_timeout, command)
+            return ShellResult(
+                command=command,
+                success=False,
+                exit_code=-1,
+                error=f"Command timed out after {effective_timeout}s",
+                latency_ms=(time.time() - start) * 1000,
+                timed_out=True,
+            )
+
+        exit_code = proc.returncode if proc.returncode is not None else -1
+        return ShellResult(
+            command=command,
+            success=exit_code == 0,
+            exit_code=exit_code,
+            stdout=stdout_bytes.decode("utf-8", errors="replace").strip(),
+            stderr=stderr_bytes.decode("utf-8", errors="replace").strip(),
+            latency_ms=(time.time() - start) * 1000,
+        )
+
     async def run(
         self,
         command: str,
@@ -164,7 +218,6 @@ class ShellHand:
         """
         start = time.time()
 
-        # Validate
         validation_error = self._validate_command(command)
         if validation_error:
             return ShellResult(
@@ -174,64 +227,21 @@ class ShellHand:
                 latency_ms=(time.time() - start) * 1000,
             )
 
-        effective_timeout = timeout or self._default_timeout
-        cwd = working_dir or self._working_dir
-
         try:
-            import os
-
-            run_env = os.environ.copy()
-            if env:
-                run_env.update(env)
-
-            proc = await asyncio.create_subprocess_shell(
+            return await self._exec_subprocess(
                 command,
-                stdout=asyncio.subprocess.PIPE,
-                stderr=asyncio.subprocess.PIPE,
-                cwd=cwd,
-                env=run_env,
+                effective_timeout=timeout or self._default_timeout,
+                cwd=working_dir or self._working_dir,
+                run_env=self._build_run_env(env),
+                start=start,
             )
-
-            try:
-                stdout_bytes, stderr_bytes = await asyncio.wait_for(
-                    proc.communicate(), timeout=effective_timeout
-                )
-            except TimeoutError:
-                proc.kill()
-                await proc.wait()
-                latency = (time.time() - start) * 1000
-                logger.warning("Shell command timed out after %ds: %s", effective_timeout, command)
-                return ShellResult(
-                    command=command,
-                    success=False,
-                    exit_code=-1,
-                    error=f"Command timed out after {effective_timeout}s",
-                    latency_ms=latency,
-                    timed_out=True,
-                )
-
-            latency = (time.time() - start) * 1000
-            exit_code = proc.returncode if proc.returncode is not None else -1
-            stdout = stdout_bytes.decode("utf-8", errors="replace").strip()
-            stderr = stderr_bytes.decode("utf-8", errors="replace").strip()
-
-            return ShellResult(
-                command=command,
-                success=exit_code == 0,
-                exit_code=exit_code,
-                stdout=stdout,
-                stderr=stderr,
-                latency_ms=latency,
-            )
-
         except Exception as exc:
-            latency = (time.time() - start) * 1000
             logger.warning("Shell command failed: %s — %s", command, exc)
             return ShellResult(
                 command=command,
                 success=False,
                 error=str(exc),
-                latency_ms=latency,
+                latency_ms=(time.time() - start) * 1000,
             )
 
     def status(self) -> dict:

src/timmy/thinking.py

@@ -772,23 +772,10 @@ class ThinkingEngine:
         except Exception as exc:
             logger.debug("Thought issue filing skipped: %s", exc)
 
-    def _gather_system_snapshot(self) -> str:
-        """Gather lightweight real system state for grounding thoughts in reality.
+    # ── System snapshot helpers ────────────────────────────────────────────
 
-        Returns a short multi-line string with current time, thought count,
-        recent chat activity, and task queue status. Never crashes — every
-        section is independently try/excepted.
-        """
-        parts: list[str] = []
-
-        # Current local time
-        now = datetime.now().astimezone()
-        tz = now.strftime("%Z") or "UTC"
-        parts.append(
-            f"Local time: {now.strftime('%I:%M %p').lstrip('0')} {tz}, {now.strftime('%A %B %d')}"
-        )
-
-        # Thought count today (cheap DB query)
+    def _snap_thought_count(self, now: datetime) -> str | None:
+        """Return today's thought count, or *None* on failure."""
         try:
             today_start = now.replace(hour=0, minute=0, second=0, microsecond=0)
             with _get_conn(self._db_path) as conn:
@@ -796,66 +783,94 @@ class ThinkingEngine:
                     "SELECT COUNT(*) as c FROM thoughts WHERE created_at >= ?",
                     (today_start.isoformat(),),
                 ).fetchone()["c"]
-            parts.append(f"Thoughts today: {count}")
+            return f"Thoughts today: {count}"
         except Exception as exc:
             logger.debug("Thought count query failed: %s", exc)
-            pass
+            return None
 
-        # Recent chat activity (in-memory, no I/O)
+    def _snap_chat_activity(self) -> list[str]:
+        """Return chat-activity lines (in-memory, no I/O)."""
         try:
             from infrastructure.chat_store import message_log
 
             messages = message_log.all()
             if messages:
-                parts.append(f"Chat messages this session: {len(messages)}")
                 last = messages[-1]
-                parts.append(f'Last chat ({last.role}): "{last.content[:80]}"')
-            else:
-                parts.append("No chat messages this session")
+                return [
+                    f"Chat messages this session: {len(messages)}",
+                    f'Last chat ({last.role}): "{last.content[:80]}"',
+                ]
+            return ["No chat messages this session"]
         except Exception as exc:
             logger.debug("Chat activity query failed: %s", exc)
-            pass
+            return []
 
-        # Task queue (lightweight DB query)
+    def _snap_task_queue(self) -> str | None:
+        """Return a one-line task queue summary, or *None*."""
         try:
             from swarm.task_queue.models import get_task_summary_for_briefing
 
-            summary = get_task_summary_for_briefing()
-            running = summary.get("running", 0)
-            pending = summary.get("pending_approval", 0)
-            done = summary.get("completed", 0)
-            failed = summary.get("failed", 0)
+            s = get_task_summary_for_briefing()
+            running, pending = s.get("running", 0), s.get("pending_approval", 0)
+            done, failed = s.get("completed", 0), s.get("failed", 0)
             if running or pending or done or failed:
-                parts.append(
+                return (
                     f"Tasks: {running} running, {pending} pending, "
                     f"{done} completed, {failed} failed"
                 )
         except Exception as exc:
             logger.debug("Task queue query failed: %s", exc)
-            pass
+        return None
 
-        # Workspace updates (file-based communication with Hermes)
+    def _snap_workspace(self) -> list[str]:
+        """Return workspace-update lines (file-based Hermes comms)."""
         try:
             from timmy.workspace import workspace_monitor
 
             updates = workspace_monitor.get_pending_updates()
+            lines: list[str] = []
             new_corr = updates.get("new_correspondence")
-            new_inbox = updates.get("new_inbox_files", [])
-
             if new_corr:
-                # Count entries (assuming each entry starts with a timestamp or header)
-                line_count = len([line for line in new_corr.splitlines() if line.strip()])
-                parts.append(
+                line_count = len([ln for ln in new_corr.splitlines() if ln.strip()])
+                lines.append(
                     f"Workspace: {line_count} new correspondence entries (latest from: Hermes)"
                 )
+            new_inbox = updates.get("new_inbox_files", [])
             if new_inbox:
                 files_str = ", ".join(new_inbox[:5])
                 if len(new_inbox) > 5:
                     files_str += f", ... (+{len(new_inbox) - 5} more)"
-                parts.append(f"Workspace: {len(new_inbox)} new inbox files: {files_str}")
+                lines.append(f"Workspace: {len(new_inbox)} new inbox files: {files_str}")
+            return lines
         except Exception as exc:
             logger.debug("Workspace check failed: %s", exc)
-            pass
+            return []
+
+    def _gather_system_snapshot(self) -> str:
+        """Gather lightweight real system state for grounding thoughts in reality.
+
+        Returns a short multi-line string with current time, thought count,
+        recent chat activity, and task queue status. Never crashes — every
+        section is independently try/excepted.
+        """
+        now = datetime.now().astimezone()
+        tz = now.strftime("%Z") or "UTC"
+
+        parts: list[str] = [
+            f"Local time: {now.strftime('%I:%M %p').lstrip('0')} {tz}, {now.strftime('%A %B %d')}"
+        ]
+
+        thought_line = self._snap_thought_count(now)
+        if thought_line:
+            parts.append(thought_line)
+
+        parts.extend(self._snap_chat_activity())
+
+        task_line = self._snap_task_queue()
+        if task_line:
+            parts.append(task_line)
+
+        parts.extend(self._snap_workspace())
 
         return "\n".join(parts) if parts else ""