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. 

{
        server.context()->addWarningMessage("The setting 'allow_remote_fs_zero_copy_replication' is enabled for MergeTree tables."
            " But the feature of 'zero-copy replication' is under development and is not ready for production."
            " The usage of this feature can lead to data corruption and loss. The setting should be disabled in production.");
    }
}
int Server::main(const std::vector<std::string> & )
{
    Poco::Logger * log = &logger();
    UseSSL use_ssl;
    MainThreadStatus::getInstance();
    StackTrace::setShowAddresses(config().getBool("show_addresses_in_stack_traces", true));
    registerFunctions();
    registerAggregateFunctions();
    registerTableFunctions();
    registerStorages();
    registerDictionaries();
    registerDisks();
    registerFormats();
    registerRemoteFileMetadatas();
    CurrentMetrics::set(CurrentMetrics::Revision, ClickHouseRevision::getVersionRevision());
    CurrentMetrics::set(CurrentMetrics::VersionInteger, ClickHouseRevision::getVersionInteger());
    /** Context contains all that query execution is dependent:
      *  settings, available functions, data types, aggregate functions, databases, ...
      */
    auto shared_context = Context::createShared();
    global_context = Context::createGlobal(shared_context.get());
    global_context->makeGlobalContext();
    global_context->setApplicationType(Context::ApplicationType::SERVER);
#if !defined(NDEBUG) || !defined(__OPTIMIZE__)