Reduce number of files generated from optimization workflow

@rcarson3 is already working on this.

Since Sep 14, 2022.

The new optimization framework can potentially generate a ton of files due to all the symbolic links to common files for each run conducted.

As part of the post-processing step on a successful run, we should delete all of the symbolic link files and leave only the bare minimum files such as the as the toml file, properties file, and simulation log and error fileS. The average stress and auto dt file are saved off in the checkpoint files. The optimized parameter sets are also saved in the checkpoint file, so if we really need to we could eliminate the property file as well. So, we can recover that data later on if need be. Overall, this would bring us down from something like 10-20 files to only needing 4 files. A drastic reduction in file count if you have a ton of genes being used in the optimization routine.