util/run: ensure env variable PWD is always correct

Some scripts may rely on $PWD to get current working directory. Since some commands are called after directory is changed by os.chdir(), this variable needs to be manually updated to reflect that change.

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• The other option would be to call subprocess.Popen(cwd=X) instead, but I saw you use the with cd(...): construct for other stuff as well, so I just did a minimal fix.
• This fixes Debian 9 packaging for knot-resolver (which relies on $PWD)
• It'd be great to get a pip release, since this blocks knot/knot-resolver!1178 (merged)
• integration test pipeline: https://gitlab.nic.cz/packaging/apkg/-/pipelines/83296