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java CDK: clean up dependencies, refactor modules (#34745)
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airbyte-cdk/java/airbyte-cdk/acceptance-test-harness/build.gradle
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...ness/src/main/java/io/airbyte/workers/internal/VersionedAirbyteMessageBufferedWriter.java
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...c/main/java/io/airbyte/workers/internal/VersionedAirbyteMessageBufferedWriterFactory.java
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airbyte-cdk/java/airbyte-cdk/airbyte-commons-cli/build.gradle
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airbyte-cdk/java/airbyte-cdk/airbyte-commons-protocol/build.gradle
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...te-commons-protocol/src/main/java/io/airbyte/commons/protocol/AirbyteMessageMigrator.java
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...mmons-protocol/src/main/java/io/airbyte/commons/protocol/AirbyteMessageSerDeProvider.java
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...s-protocol/src/main/java/io/airbyte/commons/protocol/AirbyteMessageVersionedMigrator.java
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