Fix the run_log directory structure so that it doesn't include dates

[drewoldag]

Initially I thought it would be great to include a date in the run log directory structure, but it's become a huge pain, and makes it very difficult to use checkpointing.

Remove the date component of the directory structure, and determine what the correct structure should be in order to use checkpointing correctly across multiple sets of staged files.

I.e. staged files in dir A should have checkpoints that don't interfere with staged files in dir B checkpoints.