pipelines download not working as expected?

[fellen31]

Description of the bug

After looking at #3430 and this Slack thread, I thought the offline usage documentation needed an update, but found some issues and questions:

• With the current behaviour of the template, should --download-configuration be yes by default?
• Currently, nextflow.config is only updated when --container-system singularity and --container-cache-utilisation is set to copy but not amend, is this expected?
• Currently, with --container-system singularity and --container-cache-utilisation copy, nextflow.config is updated with the wrong paths if you've defined a shared Singularity image download folder.
• Should pipelines download really update the nextflow.config of the pipeline, or is there a better way to do this?

Command used and terminal output

System information

No response