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Agents have time limits which are configurable. the agent backend code should take care of terminating the agent.
If you are running into issues like this, this usually is an indication of a different root cause. Mostly it is a matter of designing the application in the right way.
"hanging shell commands" is a good indication of a badly implemented solution.
If a thread in an application invokes a "shell" (a different program or system call in general) it gives up contol until this call has ended. There is nothing Domino could do. Or an application in general could do.
The only way around would be to start it detached and control the execution. In case of a detected hang you would kill the process.
Another way would be to have a separate thread that performs the call. But then what would you do in case of an detected hang? You can't kill this hanging thread if it is part of your application...
If you invoke another application (in general not just with Domino) you are giving up control (e.g. system(), popen() and other calls).
External call-outs are not always to avoid. In case you can't it is your responsibility that the called application returns and does not hang!
This is also an issue on hanging shell commands called via a web agent!