regression of cwltool performance by 5-7 minutes around 1st of june

Our PGAPX tool (ncbi/pgap on GitHub) uses cwltool as a CWL runner. We noticed that around 1st of June this year or TeamCity builds are running 5-7 minutes longer.

We tracked the issue to slow down in transition between calling a workflow and command line tool. For example:
```
[2023-09-29 01:38:51] DEBUG [job cluster_blastp_wnode_3] initial work dir {}
[2023-09-29 01:40:22] INFO [job cluster_blastp_wnode_3] /pgap/output/debug/tmp-outdir/kf1wjucm$ cluster_blastp_wnode \
```

See 1.5 min delay that used to be significantly smaller. The cwltool versions of "slow" and "fast" runs are correspondingly:
```
$ docker run -it ncbi/pgap-dev:2023-05-15.build4593 cwltool --version
/root/venv/bin/cwltool 3.1.20230513155734
$ docker run -it ncbi/pgap-dev:2023-06-06.build4641 cwltool --version
/root/venv/bin/cwltool 3.1.20230601100705
```

We directly tested that reversion of cwltool version to May value fixes the performance degradation issue.