Avoid using temporary directory if the outdir is local

[nbren12]

It can be costly to copy every file from the temporary directory to the output directory, so this behavior shouldn't be required for all uses of run_native. After talking to @mcgibbon, any changes here should allow the following uses:

• want to work in scratch, copy to a persistent or remote location, and delete workdir
• work in the output location and not delete when done
• work in a temporary directory and copy to a local or remote location when done

[nbren12]

TBH, I think this issue is happening because run_native is doing a lot right now. It makes

1. temporary directories
2. downloads rundirectories,
3. runs the fv3model.
4. uploads/copies the data out of the temporary directory sometimes
5. capturing logging information.

I think the API is convenient for a certain set of uses, but it makes a lot of assumptions.