The fact is that I use docker for running clearml server both on Linux and Windows.

My question was on running the agent, is it running with --docker flag, i.e. docker mode

Also, just forgot to note, that I'm running clearml-agent and clearml processes in virtual environment - conda environment on Windows and venv on Linux.

Yep that answers my question above 🙂

Does it make any sense to chdnge 

system_site_packages

 to 

true

 if I run in clearml using Docker?

No need, it does that automatically, and inherits the docker python system packages 🙂

I've previously included those tfrecord files into git repository. Now I've deleted the files, and set .gitignore to ignore files in work/tfrecord folder. Additionally, deleted cached repositories in system folder 'C:\Users\Super.clearml\vcs-cache' - but the issue remains. Can you help me with this?

I'm assuming you have some binary uncommited changes (tfrecord for example) which makes sense they could break git diff

Binary files a/work/tfrecord/train.record and b/work/tfrecord/train.record differ

Makes sure you remove the tfrecords from git (always a good practice), then commit the removal, then you will not have them in the uncommitted changes (the .gitignore you already took care of)

BTW, is there any way to automatically clean cached files?

What do you mean by cache files? clearml will manage it's own cache (and clean it up)