Fix flaky test_version_update_after_mutation/test.py::test_upgrade_while_mutation

[kssenii]

Changelog category (leave one):

• Not for changelog (changelog entry is not required)

Closes #48377.

the test test_version_update_after_mutation/test.py::test_upgrade_while_mutation does
node3.restart_with_latest_version(signal=9, fix_metadata=True)
then on server startup it sees that data/system is not empty
actually there are only some leftovers

data/system
└── part_log
    ├── detached
    └── format_version.txt

because right before server was shutdown, it managed to create only part_log.sql.tmp, but did not manage to rename to part_log.sql

<Debug> SystemLog (system.part_log): Creating new table system.part_log for PartLog

then on server restart it removed part_log.sql.tmp :
<Information> DatabaseOrdinary (system): Removing file /var/lib/clickhouse/metadata/system/part_log.sql.tmp
and then started to move system table from ordinary to atomic db
but did not delete data/system/part_log/detached and data/system/part_log/format_version.txt because it transferred to atomic db only data of tables which were successfully loaded.
Therefore there was an exception on server startup

Cannot drop: filesystem error: in remove: Directory not empty ["/var/lib/clickhouse/data/system/"]. 

[kssenii]

ClickHouse special build check — 7/8 artifact groups are OK

Apr 14 15:29:46 [10005/11759] Building CXX object src/CMakeFiles/dbms.dir/Processors/Formats/IOutputFormat.cpp.o
Apr 14 15:29:49 [10006/11759] Building CXX object src/CMakeFiles/dbms.dir/Processors/Formats/PullingOutputFormat.cpp.o
Apr 14 15:29:51 [10007/11759] Building CXX object src/CMakeFiles/dbms.dir/Processors/Executors/PipelineExecutor.cpp.o
time="2023-04-14T15:29:56Z" level=error msg="error waiting for container: unexpected EOF"
Traceback (most recent call last):
  File "/home/ubuntu/actions-runner/_work/_temp/build_check/ClickHouse/docker/packager/./packager", line 495, in <module>
    main()
  File "/home/ubuntu/actions-runner/_work/_temp/build_check/ClickHouse/docker/packager/./packager", line 483, in main
    run_docker_image_with_env(
  File "/home/ubuntu/actions-runner/_work/_temp/build_check/ClickHouse/docker/packager/./packager", line 112, in run_docker_image_with_env
    subprocess.check_call(cmd, shell=True)
  File "/usr/lib/python3.10/subprocess.py", line 369, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'docker run --network=host --user=1000:1000 --rm --volume=/home/ubuntu/actions-runner/_work/_temp/build_check/binary_tidy:/output --volume=/home/ubuntu/actions-runner/_work/_temp/build_check/ClickHouse:/build  -e OUTPUT_DIR=/output -e DEB_ARCH=amd64 -e CC=clang-15 -e CXX=clang++-15 -e BUILD_TYPE=Debug -e SCCACHE_BUCKET=clickhouse-builds -e SCCACHE_S3_KEY_PREFIX=ccache/sccache -e CTCACHE_S3_BUCKET=clickhouse-builds -e CTCACHE_S3_FOLDER=ccache/clang-tidy-cache -e NINJA_FLAGS=-k0 -e VERSION_STRING='23.4.1.1' -e CMAKE_FLAGS="$CMAKE_FLAGS -DCMAKE_C_COMPILER=clang-15 -DCMAKE_CXX_COMPILER=clang++-15 -DCOMPILER_CACHE=sccache -DENABLE_CLANG_TIDY=1 -DENABLE_TESTS=1 -DENABLE_EXAMPLES=1 -DENABLE_UTILS=1" -e BUILD_TARGET='all'  clickhouse/binary-builder:latest' returned non-zero exit status 125.

:/