Ordinary database engine is deprecated but there is no simple mean to change database engine to Atomic for existing databases.

Possible options:
- ALTER DATABASE MODIFY ENGINE query.
- Flag that triggers migration at ClickHouse startup.

The latter should be easier to implement. 

#include <Storages/MergeTree/DataPartStorageOnDisk.h>
#include <Disks/ObjectStorages/IMetadataStorage.h>
#include <base/sort.h>
#include <Storages/AlterCommands.h>
#include <Storages/PartitionCommands.h>
#include <Storages/ColumnsDescription.h>
#include <Storages/StorageReplicatedMergeTree.h>
#include <Storages/MergeTree/IMergeTreeDataPart.h>
#include <Storages/MergeTree/MergeList.h>
#include <Storages/MergeTree/MergeTreeBackgroundExecutor.h>
#include <Storages/MergeTree/MergedBlockOutputStream.h>
#include <Storages/MergeTree/PinnedPartUUIDs.h>
#include <Storages/MergeTree/ReplicatedMergeTreeTableMetadata.h>
#include <Storages/MergeTree/ReplicatedMergeTreeSink.h>
#include <Storages/MergeTree/ReplicatedMergeTreeQuorumEntry.h>
#include <Storages/MergeTree/ReplicatedMergeTreeMutationEntry.h>
#include <Storages/MergeTree/ReplicatedMergeTreeAddress.h>
#include <Storages/MergeTree/ReplicatedMergeTreeQuorumAddedParts.h>
#include <Storages/MergeTree/ReplicatedMergeTreePartHeader.h>
#include <Storages/MergeTree/MergeFromLogEntryTask.h>
#include <Storages/MergeTree/MutateFromLogEntryTask.h>
#include <Storages/VirtualColumnUtils.h>
#include <Storages/MergeTree/MergeTreeReaderCompact.h>
#include <Storages/MergeTree/LeaderElection.h>
#include <Storages/MergeTree/ZeroCopyLock.h>
#include <Storages/MergeTree/extractZkPathFromCreateQuery.h>
#include <Storages/Freeze.h>
#include <Databases/DatabaseOnDisk.h>
#include <Databases/DatabaseReplicated.h>
#include <Parsers/formatAST.h>