Review usage of `EntityManager.merge`

[amvanbaren]

As @hoangphamEclipse points out in EclipseFdn/open-vsx.org#2062 (comment), EntityManager.merge updates a JPA entity.

Review the code to determine where merge is used intentionally to update the entity and where it isn't.
Use EntityManager.find or another read operation without side effects to replace the calls to EntityManager.merge where it is used only to get a managed entity.