Currently simfactory stores the checkpoints for each restart in their own directory. This means that the Cactus mechanism for deleting all but the most recent N checkpoints does not see the previous checkpoints. This means that you can easily run out of quota space when doing very long simulations.
One solution to this would be for SimFactory to store the checkpoints in a directory above the output-NNNN directories and make the current checkpoints directories under output-NNNN symbolic links to the common directory. This way, all restarts would see the same directory for checkpoint files, and Cactus could clean up the old checkpoints. The current hardlinking mechanism would not be required any more. This solution might be undesirable because it means that each restart is no longer independent.
Another solution would be to give simfactory an option to delete old checkpoint files from previous restarts when a job starts. This would duplicate the functionality already available in Cactus.