Add a --chaoss flag to generate a report using CHAOSS only metrics (the current report)

Following #111 what we want is to add a `--chaoss` flag which will allow the user to generate a report using CHAOSS metrics only i.e the current report that is being generated.

This will be the default behaviour of Manuscripts and this will allow us to add different flags (`--gmd`, `--risk` and so on) which will be responsible for generating reports using different metrics.

Start by tracing the current report-generation path and the CLI argument entry point, then review issue #111 for the intended flag structure. Confirm how the current report selects CHAOSS metrics. Done means --chaoss generates that report and remains the default behavior, without preventing future metric-specific flags.

Written by the indexing model from the issue text.