Alter command line interface for all cdds tools

Migrated Jira Issue CDDSO-330
Jira creation date 01/08/2023 11:43
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Tools such as rose and cylc have a useful interface pattern;

cylc []

I think it would make working with cdds a lot simpler if all our tools followed this pattern (Note I do not include MIP Convert here)
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The issue names no files, tests, or entry points; start by inventorying the CDDS command-line tools and their current invocation patterns. Define the command and argument structure for each tool, excluding MIP Convert, then verify that all included tools follow the agreed pattern.

Written by the indexing model from the issue text.