Refactoring model so we could avoid shortcoming of linkml model

[yarikoptic]

Shortcoming in question:

• https://github.com/orgs/linkml/discussions/2154

AFAIK this should result in no changes necessary to metadata records since none of those "features" was used. So even though we break the model, I think we could just go with "patch" level progress forward.

Individual commits have more information.

TODOs also

• [ ] do something about genotype "Identifier" being abused to encapsulate records describing the genotype, hence better be parsed etc ??? file a separate issue.

[yarikoptic]

@candleindark please review test fails and what needs to be done to make it green