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December schema refactoring super issue - suggested updates

another example of biosample being overloaded is [img_identifiers](https://microbiomedata.github.io/nmdc-schema/img_identifiers/), this is an analysis identifier, which should be associated w/[MetagenomeAnnotationActivity](https://microbiomedata.github.io/nmdc-schema/MetagenomeAnnotationActivity/), [MetatranscriptomeAnnotationActivity](https://microbiomedata.github.io/nmdc-schema/MetatranscriptomeAnnotationActivity/), [MagsAnalysisActivity](https://microbiomedata.github.io/nmdc-schema/MagsAnalysisActivity/). Currently Sujay populates these values so the ingest process would...

December schema refactoring super issue - suggested updates

Alicia's list - [x] #1123 - [x] #1048 (overlap w/#1030 and #1027) - [ ] #1257 - [ ] #1000 - [x] #984 - [x] #1144

check if classes associated with `alternative_identifiers` can use ANY `alternative_identifiers`

Is this a linkml bug? If it is allowed why doesn't it show up in the documentation as an inherited slot?

do we intend to use `insdc_biosample_identifiers` or `insdc_secondary_sample_identifiers`

for biosample_set {'insdc_biosample_identifiers':{$exists:true}} returns 1354 records

berkeley-schema-fy24 must migrate string "type" to object types consisting of the instances' class' `class_uri`

@turbomam can this be closed? I believe in berkeley all classes now have type required with a range of a curie.

add referential integrity checks on external id used by nmdc-schema instances

Still needed in linkml but we can do this w/sparql queries now.

add referential integrity checks on external id used by nmdc-schema instances

Do we still need this now that we have refscan?

Explain the impact of the deriving `STUDY_IDS` from `local/gold-study-ids.yaml` in `project.Makefile`

Is this still relevant after re-iding?