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Fix Doctrine "Unable to find entity identifier"

John Flatness requested to merge zerocrates/Omeka-S-module-Reference:fix-identifier-issue into master

A fix for https://github.com/Daniel-KM/Omeka-S-module-Reference/issues/19

Doctrine tracks in the EM/UoW even the references you create, so references that are going to be persisted need to come from the EM that's going to do the persisting.

This fix changes CurrentReferenceMetadata to optionally take the entity manager as an argument, so it can use the "private" EM used by the job.

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