executor: Write scripts into workspace instead of another temporary directory

Created by: efritz

I think this is why auto-indexing has been failing since lAsT yEaR (lol). If this doesn't fix it then at least we have a cleaner execution model: more things are now in the workspace directory so we have a minimal context area on disk for each run.

The other things we import are docker image gzip files, which we aren't currently copying into the workspace as we have a single shared directory in hopes that multiple organizations can benefit from using the same base images. We can likely do a quick on-host copy step to make things more uniform.