fix: Avoid duplicate downloads in nested subworkflows

[jvfe]

• Addresses Make the solution work with nested subworkflows #3

Modules.json test failures related to duplicate entries happens because meta.yml declares modules that are not imported in the actual subworkflow code, since they're only used in the nested subworkflow.

This way the module gets downloaded twice, hence the longer "installed_by" in modules.json.

This PR makes it so the new installation procedure checks if a module/subwf declared in meta.yml is actually imported in main.nf, and only proceeds with installation in that case.

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated