Fix adding annotations with missing mRNAs

We noticed that the current tutorial dataset (the five chloroplasts) adds some weird proteins. I found out that this is because of a wrong interpretation of the provided gff3 files where no mRNA features are present. Instead, the CDS and exon features have the gene feature as direct parent. In the current develop branch, it is assumed that each CDS belongs to a separate gene. However, in the case of chloroplasts these multiple CDS features belong to one transcript. Therefore, this merge request makes that latter the default behaviour but it also adds a new option for add_annotations: --assume-one-mrna-per-cds which gives the original interpretation.

TODO:

• Update documentation with the new option and behaviour