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 <Interpreters/JIT/CompiledExpressionCache.h>
#include <Access/AccessControl.h>
#include <Storages/StorageReplicatedMergeTree.h>
#include <Storages/System/attachSystemTables.h>
#include <Storages/System/attachInformationSchemaTables.h>
#include <Storages/Cache/ExternalDataSourceCache.h>
#include <Storages/Cache/registerRemoteFileMetadatas.h>
#include <AggregateFunctions/registerAggregateFunctions.h>
#include <Functions/registerFunctions.h>
#include <TableFunctions/registerTableFunctions.h>
#include <Formats/registerFormats.h>
#include <Storages/registerStorages.h>
#include <QueryPipeline/ConnectionCollector.h>
#include <Dictionaries/registerDictionaries.h>
#include <Disks/registerDisks.h>
#include <Common/Config/ConfigReloader.h>
#include <Server/HTTPHandlerFactory.h>
#include "MetricsTransmitter.h"
#include <Common/StatusFile.h>
#include <Server/TCPHandlerFactory.h>
#include <Server/TCPServer.h>
#include <Common/SensitiveDataMasker.h>
#include <Common/ThreadFuzzer.h>
#include <Common/getHashOfLoadedBinary.h>
#include <Common/filesystemHelpers.h>
#include <Common/Elf.h>
#include <Compression/CompressionCodecEncrypted.h>
#include <Server/MySQLHandlerFactory.h>
#include <Server/PostgreSQLHandlerFactory.h>
#include <Server/CertificateReloader.h>