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Please keep the discussion on the mailing list rather than commenting on the wiki (wiki discussions get unwieldy fast).
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Kafka Streams will automatically migrate offsets found in an existing .checkpoint file, and/or an existing .position file, to store those offsets directly in the StateStore, if managesOffsets returns true. Users of the in-built store types will not need to make any changes. See Upgrading.
Because checkpointed offsets are now stored inside the state stores, the state stores must be opened during KafkaStreams#start() to read the offsets, what implies that #start() might fail with new types of errors. This change is not a backward incompatible change because #start() already declares that StreamsException might be thrown, and thus existing code which is prepared for error handling would not be impacted.
flush deprecation
All internal usage of the StateStore#flush method has been removed/replaced. Therefore, the main concern is with end-users calling StateStore#flush directly from custom Processors. Obviously, users cannot safely call StateStore#commit, because they do not know the changelog offsets that correspond to the locally written state. Forcibly flushing/fsyncing recently written records to disk may also violate any transactional guarantees that StateStores are providing. Therefore, the default implementation of flush has been updated to a no-op. Users are now advised (via JavaDoc) that should instead request an early commit via. ProcessingContext#commit().
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