Explicitely state which chunk is faulty when a timeout occurs

Instead of "silently" failing:

```
ERROR stdout:

stderr:

exit code:-1
```

It would be preferable if the tool would show on the output that the reason est due to a timeout occuring while the command was executing.

Start at the command-execution and error-reporting entry points, locating where timeout failures produce the shown stdout, stderr, and exit-code output. Trace how markdown chunks are identified during execution. Done means a timeout clearly states which chunk timed out and why, rather than only showing exit code -1.

Written by the indexing model from the issue text.