simplify output project

Currently we use the organize project command to add directories and files underneath a results directory:

https://github.com/Duke-GCB/lando-util/blob/604a26174ac1c03711545a2a0a0c4d9136c1af08/lando_util/organize_project/organizer.py#L4-L16

The results directory already contains the output files/directories created by the bioinformatics workflow. By adding the `docs` directory underneath `results` we complicate testing reproducibility.
These files and folders will need to be excluded in this process. There is also a possibility that a workflow might create an output directory named `docs`. This could cause that data to be lost.

Suggested new structure:
```
README.md
README.html
results/
...output files from workflow
scripts/
.cwl
job--input.json
logs/
bespin-workflow-output.json #stdout from cwl-runner - json job results
bespin-workflow-output.log #stderr from cwl-runner
```