fix: wait for killed process after shell timeout to prevent fd leaks

When a shell command times out, process.kill() is called but the
process object was never awaited after that. This leaves subprocess
pipes undrained and file descriptors open. If many commands time out,
fd leaks accumulate.

Add a bounded wait (5s) after kill to let the process fully terminate
and release its resources.

nanobot/agent/tools/shell.py

@@ -81,6 +81,12 @@ class ExecTool(Tool):
                 )
             except asyncio.TimeoutError:
                 process.kill()
+                # Wait for the process to fully terminate so pipes are
+                # drained and file descriptors are released.
+                try:
+                    await asyncio.wait_for(process.wait(), timeout=5.0)
+                except asyncio.TimeoutError:
+                    pass
                 return f"Error: Command timed out after {self.timeout} seconds"
             
             output_parts = []