checkpointing: consider allowing users to specify save frequency

[markmc]

In #222 we added a data checkpointing feature which has a "save frequency" parameter which tunes how often a checkpoint is saved.

Wed did not initially expose this to users because we felt the side effects of save_freq=1 - lots of files, some extra I/O - is not worth the extra user complexity of another command line parameter.

This issue tracks the need to consider this based on feedback and to decide whether we want to remove the parameter or expose it to users.