Genome Annotation in MAGs workflows: Change default values for some Bakta parameters

In the Genome Annotation in MAGs workflows, the default value for `Keep original contig header` is `No`.
It would be better to change it to `Yes`, so original names are kept and it simplified downstream analyses (e.g. extraction of subsequences).

@SantaMcCloud could you address this issue? Thanks a lot

Start by locating the Genome Annotation in MAGs workflows and inspect the Bakta parameter for `Keep original contig header`. Change its default from `No` to `Yes`, then verify that the workflow configuration consistently preserves original contig names and that no related workflow variant still uses the old default.

Written by the indexing model from the issue text.