Move secondary_opts to opts.R

[jamesmbaazam]

Description

This PR closes #493.

The secondary_opts() function was previously defined in the estimate_secondary.R script. It has now been moved to the opts.R script where all other _opts*() related functions live. This will make it easier to find.

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[sbfnk]

Thanks! Can we move the function down e.g. to after generation_time_opts() as the estimate_infections model is the "primary" one so should come first?

[jamesmbaazam]

Thanks! Can we move the function down e.g. to after generation_time_opts() as the estimate_infections model is the "primary" one so should come first?

Done!