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The conformance check should be performed at operation boundaries only and not within operations. However, for custom migrations, the conformance check is performed after migrateAfter, but before the metamodel adaptations. This point in the migration is however not an operation boundary.
Since a custom migration is also a change and the conformance check is performed in the beforeChange method, it is not performed after the custom migration. In order to avoid this, the conformance check is now performed after the change for all kinds of changes.