From the command line you can run the following to delete an Agent instance with comp_id of AGENT_COMP_ID
echo '{"comp_id": "AGENT_COMP_ID"}' | /opt/intwine/app/send delete_agent
What this does is tells the Gateway agent to delete the agent with the specified comp_id. The /opt/intwine/app/send script uses the Application Framework to send a direct message to a specific agent. The first parameter is the message type (in this case delete_agent). The second parameter is the comp_id of the agent to send the message to. If not specified, it will default to the Gateway agent.
The result of the direct message is a JSON object. The value of the "success" parameter will say if the command was executed successfully.