simplify output project

[johnbradley]

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

lando-util/lando_util/organize_project/organizer.py

Lines 4 to 16 in 604a261

	Directory structure:
	results/ # this directory is uploaded in the store output stage (destination_dir in config)
	...output files from workflow
	docs/
	README.md
	README.html
	scripts/
	<workflow name>.cwl
	job-<jobid>-input.json
	logs/
	bespin-workflow-output.json #stdout from cwl-runner - json job results
	bespin-workflow-output.log #stderr from cwl-runner
	job-data.json # non-cwl job data used to create Bespin-Report.txt

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/ 
    <workflow name>.cwl 
    job-<jobid>-input.json 
logs/ 
    bespin-workflow-output.json   #stdout from cwl-runner - json job results 
    bespin-workflow-output.log    #stderr from cwl-runner