Review moving to using a CLI package for option parsing after tooling plugin updates

[cdcabrera]

Description

The number of options available for the CLI and programmatic use are set to expand again after the tool plugin implementation, see #22 . Review activating CLI tooling to help option parsing filtering/parsing.

Acceptance criteria

• A CLI option parser is activated or at min reviewed after the tooling plugin implementation options are added in.
• We can leverage base CLI option parsing work already in progress from tooling plugins, MCP tools should be expandable via tool-plugins #22

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Jira Issue: PF-3151