As far as I can tell, SimFactory 2 currently cleans up all simulations every time it is run. This is not scalable - if you are running with a slow production filesystem, just statting all the simulations could take a very long time. Similarly, if you do a sim sync, it currently cleans up all the simulations on your local machine, as well as the remote machine. Running sim --help even cleans up all your simulations!
This behaviour is very counter-intuitive (certainly not what a user would expect) and not suitable for production systems. I propose that simfactory should only clean up the simulation which is being referred to in the current command.