Add `--keep_tmp option` as default so to not output many of the intermediate files

[madeline-scyphers]

Description of feature

Many intermediate files don't need to be outputted to the user

[madeline-scyphers]

Needs to be done with #452 since the intermediate files burden is linked to the cache burden. As in, if people think they aren't getting the tmp files, but they are just storing them in the workDir for caching, then we still have a problem.