Handle empty or missing manifests in `payu setup --repro`

[Qian-HuiChen]

When running payu setup --repro, payu raises an error when restart manifests are empty, e.g. ACCESS-OM2:

 Failed: Failed to run payu setup with --reproduce. Error: Restart manifest must exist and be populated if reproduce is configured to True

It should not error here and only error if there was no pre-existing manifest and a new restart manifest was generated.
Related to this payu setup check issue.