Now that #241 is merged, we should add parameters.settings.json to the template and update the linting to check for this file and validate the JSON.

Note that whilst adding this it would be great to see if we can use the JSON file in nextflow code to reduce duplication:

• In the --help output
• In the summary log output at the start
• In nextflow.config

It would be great if we could end up with the basic parameters being just set in parameters.settings.json

As a bonus, linting could also check the markdown documentation to ensure that all options are documented. We could also argue that usage documentation for the command line options is no longer required now that we have this metadata.